An internal thioester in a pathogen surface protein mediates covalent host binding

PubMed Central

Walden, Miriam; Edwards, John M; Dziewulska, Aleksandra M; Bergmann, Rene; Saalbach, Gerhard; Kan, Su-Yin; Miller, Ona K; Weckener, Miriam; Jackson, Rosemary J; Shirran, Sally L; Botting, Catherine H; Florence, Gordon J; Rohde, Manfred; Banfield, Mark J; Schwarz-Linek, Ulrich

2015-01-01

To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a ‘chemical harpoon’. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions. DOI: http://dx.doi.org/10.7554/eLife.06638.001 PMID:26032562

Role of intestinal microbiota and metabolites on gut homeostasis and human diseases.

PubMed

Lin, Lan; Zhang, Jianqiong

2017-01-06

A vast diversity of microbes colonizes in the human gastrointestinal tract, referred to intestinal microbiota. Microbiota and products thereof are indispensable for shaping the development and function of host innate immune system, thereby exerting multifaceted impacts in gut health. This paper reviews the effects on immunity of gut microbe-derived nucleic acids, and gut microbial metabolites, as well as the involvement of commensals in the gut homeostasis. We focus on the recent findings with an intention to illuminate the mechanisms by which the microbiota and products thereof are interacting with host immunity, as well as to scrutinize imbalanced gut microbiota (dysbiosis) which lead to autoimmune disorders including inflammatory bowel disease (IBD), Type 1 diabetes (T1D) and systemic immune syndromes such as rheumatoid arthritis (RA). In addition to their well-recognized benefits in the gut such as occupation of ecological niches and competition with pathogens, commensal bacteria have been shown to strengthen the gut barrier and to exert immunomodulatory actions within the gut and beyond. It has been realized that impaired intestinal microbiota not only contribute to gut diseases but also are inextricably linked to metabolic disorders and even brain dysfunction. A better understanding of the mutual interactions of the microbiota and host immune system, would shed light on our endeavors of disease prevention and broaden the path to our discovery of immune intervention targets for disease treatment.

Insights into the Roles of Gut Microbes in Obesity

PubMed Central

Sanz, Yolanda; Santacruz, Arlette; De Palma, Giada

2008-01-01

Obesity is a major public health issue as it enhances the risk of suffering several chronic diseases of increasing prevalence. Obesity results from an imbalance between energy intake and expenditure, associated with a chronic low-grade inflammation. Gut microbes are considered to contribute to body weight regulation and related disorders by influencing metabolic and immune host functions. The gut microbiota as a whole improves the host's ability to extract and store energy from the diet leading to body weight gain, while specific commensal microbes seem to exert beneficial effects on bile salt, lipoprotein, and cholesterol metabolism. The gut microbiota and some probiotics also regulate immune functions, protecting the host form infections and chronic inflammation. In contrast, dysbiosis and endotoxaemia may be inflammatory factors responsible for developing insulin resistance and body weight gain. In the light of the link between the gut microbiota, metabolism, and immunity, the use of dietary strategies to modulate microbiota composition is likely to be effective in controlling metabolic disorders. Although so far only a few preclinical and clinical trials have demonstrated the effects of specific gut microbes and prebiotics on biological markers of these disorders, the findings indicate that advances in this field could be of value in the struggle against obesity and its associated-metabolic disorders. PMID:19259329

A Hydroponic Co-cultivation System for Simultaneous and Systematic Analysis of Plant/Microbe Molecular Interactions and Signaling.

PubMed

Nathoo, Naeem; Bernards, Mark A; MacDonald, Jacqueline; Yuan, Ze-Chun

2017-07-22

An experimental design mimicking natural plant-microbe interactions is very important to delineate the complex plant-microbe signaling processes. Arabidopsis thaliana-Agrobacterium tumefaciens provides an excellent model system to study bacterial pathogenesis and plant interactions. Previous studies of plant-Agrobacterium interactions have largely relied on plant cell suspension cultures, the artificial wounding of plants, or the artificial induction of microbial virulence factors or plant defenses by synthetic chemicals. However, these methods are distinct from the natural signaling in planta, where plants and microbes recognize and respond in spatial and temporal manners. This work presents a hydroponic cocultivation system where intact plants are supported by metal mesh screens and cocultivated with Agrobacterium. In this cocultivation system, no synthetic phytohormone or chemical that induces microbial virulence or plant defense is supplemented. The hydroponic cocultivation system closely resembles natural plant-microbe interactions and signaling homeostasis in planta. Plant roots can be separated from the medium containing Agrobacterium, and the signaling and responses of both the plant hosts and the interacting microbes can be investigated simultaneously and systematically. At any given timepoint/interval, plant tissues or bacteria can be harvested separately for various "omics" analyses, demonstrating the power and efficacy of this system. The hydroponic cocultivation system can be easily adapted to study: 1) the reciprocal signaling of diverse plant-microbe systems, 2) signaling between a plant host and multiple microbial species (i.e. microbial consortia or microbiomes), 3) how nutrients and chemicals are implicated in plant-microbe signaling, and 4) how microbes interact with plant hosts and contribute to plant tolerance to biotic or abiotic stresses.

Understanding complex host-microbe interactions in Hydra

PubMed Central

Bosch, Thomas C.G.

2012-01-01

Any multicellular organism may be considered a metaorganism or holobiont—comprised of the macroscopic host and synergistic interdependence with bacteria, archaea, fungi, viruses, and numerous other microbial and eukaryotic species including algal symbionts. Defining the individual microbe-host conversations in these consortia is a challenging but necessary step on the path to understanding the function of the associations as a whole. Dissecting the fundamental principles that underlie all host-microbe interactions requires simple animal models with only a few specific bacterial species. Here I present Hydra as such a model with one of the simplest epithelia in the animal kingdom, with the availability of a fully sequenced genome and numerous genomic tools, and with few associated bacterial species. PMID:22688725

A Microbial Perspective on the Grand Challenges in Comparative Animal Physiology

PubMed Central

2018-01-01

ABSTRACT Interactions with microbial communities can have profound influences on animal physiology, thereby impacting animal performance and fitness. Therefore, it is important to understand the diversity and nature of host-microbe interactions in various animal groups (invertebrates, fish, amphibians, reptiles, birds, and mammals). In this perspective, I discuss how the field of host-microbe interactions can be used to address topics that have been identified as grand challenges in comparative animal physiology: (i) horizontal integration of physiological processes across organisms, (ii) vertical integration of physiological processes across organizational levels within organisms, and (iii) temporal integration of physiological processes during evolutionary change. Addressing these challenges will require the use of a variety of animal models and the development of systems approaches that can integrate large, multiomic data sets from both microbial communities and animal hosts. Integrating host-microbe interactions into the established field of comparative physiology represents an exciting frontier for both fields. PMID:29556549

With a Little Help from My Friends: Microbial Partners in Integrative and Comparative Biology-An Introduction to the Symposium.

PubMed

Kohl, Kevin D; Dearing, M Denise

2017-10-01

The role that host-associated microbes play in animal biology is gaining attention in comparative biology. Numerous research groups study the roles that microbes play in human health and nutrition, or in enhancing the production of agricultural animals. However, inclusion of host-associated microbes into research questions of integrative and comparative biology has lagged behind. We hosted a symposium to bring together top researchers in the field of host-associated microbes who also incorporate aspects of integrative and comparative biology. In this introduction, we highlight recent research demonstrating the profound roles that host-associated microbes play in many aspects of animal biology, such as immune function, endocrinology, and even behavior. It is our hope that integrative and comparative biologists will begin to include aspects of host-associated microbes into their research programs, enhancing both the fields of comparative biology and host-microbe interactions. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle.

PubMed

Jupe, Julietta; Stam, Remco; Howden, Andrew J M; Morris, Jenny A; Zhang, Runxuan; Hedley, Pete E; Huitema, Edgar

2013-06-25

Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome sequences of both hosts and microbes, little is known about the signal interplay between them during infection. In particular, accurate descriptions of coordinate relationships between host and microbe transcriptional programs are lacking. Here, we explore the molecular interaction between the hemi-biotrophic broad host range pathogen Phytophthora capsici and tomato. Infection assays and use of a composite microarray allowed us to unveil distinct changes in both P. capsici and tomato transcriptomes, associated with biotrophy and the subsequent switch to necrotrophy. These included two distinct transcriptional changes associated with early infection and the biotrophy to necrotrophy transition that may contribute to infection and completion of the P. capsici lifecycle Our results suggest dynamic but highly regulated transcriptional programming in both host and pathogen that underpin P. capsici disease and hemi-biotrophy. Dynamic expression changes of both effector-coding genes and host factors involved in immunity, suggests modulation of host immune signaling by both host and pathogen. With new unprecedented detail on transcriptional reprogramming, we can now explore the coordinate relationships that drive host-microbe interactions and the basic processes that underpin pathogen lifestyles. Deliberate alteration of lifestyle-associated transcriptional changes may allow prevention or perhaps disruption of hemi-biotrophic disease cycles and limit damage caused by epidemics.

Impact of the gut microbiota on inflammation, obesity, and metabolic disease.

PubMed

Boulangé, Claire L; Neves, Ana Luisa; Chilloux, Julien; Nicholson, Jeremy K; Dumas, Marc-Emmanuel

2016-04-20

The human gut harbors more than 100 trillion microbial cells, which have an essential role in human metabolic regulation via their symbiotic interactions with the host. Altered gut microbial ecosystems have been associated with increased metabolic and immune disorders in animals and humans. Molecular interactions linking the gut microbiota with host energy metabolism, lipid accumulation, and immunity have also been identified. However, the exact mechanisms that link specific variations in the composition of the gut microbiota with the development of obesity and metabolic diseases in humans remain obscure owing to the complex etiology of these pathologies. In this review, we discuss current knowledge about the mechanistic interactions between the gut microbiota, host energy metabolism, and the host immune system in the context of obesity and metabolic disease, with a focus on the importance of the axis that links gut microbes and host metabolic inflammation. Finally, we discuss therapeutic approaches aimed at reshaping the gut microbial ecosystem to regulate obesity and related pathologies, as well as the challenges that remain in this area.

A review of metabolic potential of human gut microbiome in human nutrition.

PubMed

Yadav, Monika; Verma, Manoj Kumar; Chauhan, Nar Singh

2018-03-01

The human gut contains a plethora of microbes, providing a platform for metabolic interaction between the host and microbiota. Metabolites produced by the gut microbiota act as a link between gut microbiota and its host. These metabolites act as messengers having the capacity to alter the gut microbiota. Recent advances in the characterization of the gut microbiota and its symbiotic relationship with the host have provided a platform to decode metabolic interactions. The human gut microbiota, a crucial component for dietary metabolism, is shaped by the genetic, epigenetic and dietary factors. The metabolic potential of gut microbiota explains its significance in host health and diseases. The knowledge of interactions between microbiota and host metabolism, as well as modification of microbial ecology, is really beneficial to have effective therapeutic treatments for many diet-related diseases in near future. This review cumulates the information to map the role of human gut microbiota in dietary component metabolism, the role of gut microbes derived metabolites in human health and host-microbe metabolic interactions in health and diseases.

Nutritional modulation of gut microbiota - the impact on metabolic disease pathophysiology.

PubMed

Ojeda, Patricia; Bobe, Alexandria; Dolan, Kyle; Leone, Vanessa; Martinez, Kristina

2016-02-01

The obesity epidemic afflicts over one third of the United States population. With few therapies available to combat obesity, a greater understanding of the systemic causes of this and other metabolic disorders is needed to develop new, effective treatments. The mammalian intestinal microbiota contributes to metabolic processes in the host. This review summarizes the research demonstrating the interplay of diet, intestinal microbiota and host metabolism. We detail the effects of diet-induced modifications in microbial activity and resultant impact on (1) sensory perception of macronutrients and total energy intake; (2) nutrient absorption, transport and storage; (3) liver and biliary function; (4) immune-mediated signaling related to adipose inflammation; and (5) circadian rhythm. We also discuss therapeutic strategies aimed to modify host-microbe interactions, including prebiotics, probiotics and postbiotics, as well as fecal microbiota transplantation. Elucidating the role of gut microbes in shaping metabolic homeostasis or dysregulation provides greater insight into disease development and a promising avenue for improved treatment of metabolic dysfunction. Copyright © 2015 Elsevier Inc. All rights reserved.

Novel Insights into Insect-Microbe Interactions—Role of Epigenomics and Small RNAs

PubMed Central

Kim, Dohyup; Thairu, Margaret W.; Hansen, Allison K.

2016-01-01

It has become increasingly clear that microbes form close associations with the vast majority of animal species, especially insects. In fact, an array of diverse microbes is known to form shared metabolic pathways with their insect hosts. A growing area of research in insect-microbe interactions, notably for hemipteran insects and their mutualistic symbionts, is to elucidate the regulation of this inter-domain metabolism. This review examines two new emerging mechanisms of gene regulation and their importance in host-microbe interactions. Specifically, we highlight how the incipient areas of research on regulatory “dark matter” such as epigenomics and small RNAs, can play a pivotal role in the evolution of both insect and microbe gene regulation. We then propose specific models of how these dynamic forms of gene regulation can influence insect-symbiont-plant interactions. Future studies in this area of research will give us a systematic understanding of how these symbiotic microbes and animals reciprocally respond to and regulate their shared metabolic processes. PMID:27540386

The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy.

PubMed

Magalhães, Andreia P; Azevedo, Nuno F; Pereira, Maria O; Lopes, Susana P

2016-02-01

The recent focus on the cystic fibrosis (CF) complex microbiome has led to the recognition that the microbes can interact between them and with the host immune system, affecting the disease progression and treatment routes. Although the main focus remains on the interactions between traditional pathogens, growing evidence supports the contribution and the role of emergent species. Understanding the mechanisms and the biological effects involved in polymicrobial interactions may be the key to improve effective therapies and also to define new strategies for disease control. This review focuses on the interactions between microbe-microbe and host-microbe, from an ecological point of view, discussing their impact on CF disease progression. There are increasing indications that these interactions impact the success of antimicrobial therapy. Consequently, a new approach where therapy is personalized to patients by taking into account their individual CF microbiome is suggested.

Plants and pathogens: putting infection strategies and defence mechanisms on the map.

PubMed

Faulkner, Christine; Robatzek, Silke

2012-12-01

All plant organs are vulnerable to colonisation and molecular manipulation by microbes. When this interaction allows proliferation of the microbe at the expense of the host, the microbe can be described as a pathogen. In our attempts to understand the full nature of the interactions that occur between a potential pathogen and its host, various aspects of the molecular mechanisms of infection and defence have begun to be characterised. There is significant variation in these mechanisms. While previous research has examined plant-pathogen interactions with whole plant/organ resolution, the specificity of infection strategies and changes in both gene expression and protein localisation of immune receptors upon infection suggest there is much to be gained from examination of plant-microbe interactions at the cellular level. Copyright © 2012 Elsevier Ltd. All rights reserved.

Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe.

PubMed

Lamichhane, Santosh; Sen, Partho; Dickens, Alex M; Orešič, Matej; Bertram, Hanne Christine

2018-04-30

It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding of the microbial functions. Finally, the emerging approaches of genome-scale metabolic modelling to study microbial co-metabolism and host-microbe interactions are highlighted. Copyright © 2018 Elsevier Inc. All rights reserved.

The Microbe-Free Plant: Fact or Artifact?

PubMed Central

Partida-Martínez, Laila P.; Heil, Martin

2011-01-01

Plant–microbe interactions are ubiquitous. Plants are threatened by pathogens, but they are even more commonly engaged in neutral or mutualistic interactions with microbes: belowground microbial plant associates are mycorrhizal fungi, Rhizobia, and plant-growth promoting rhizosphere bacteria, aboveground plant parts are colonized by internally living bacteria and fungi (endophytes) and by microbes in the phyllosphere (epiphytes). We emphasize here that a completely microbe-free plant is an exotic exception rather than the biologically relevant rule. The complex interplay of such microbial communities with the host–plant affects multiple vital parameters such as plant nutrition, growth rate, resistance to biotic and abiotic stressors, and plant survival and distribution. The mechanisms involved reach from direct ones such as nutrient acquisition, the production of plant hormones, or direct antibiosis, to indirect ones that are mediated by effects on host resistance genes or via interactions at higher trophic levels. Plant-associated microbes are heterotrophic and cause costs to their host plant, whereas the benefits depend on the current environment. Thus, the outcome of the interaction for the plant host is highly context dependent. We argue that considering the microbe-free plant as the “normal” or control stage significantly impairs research into important phenomena such as (1) phenotypic and epigenetic plasticity, (2) the “normal” ecological outcome of a given interaction, and (3) the evolution of plants. For the future, we suggest cultivation-independent screening methods using direct PCR from plant tissue of more than one fungal and bacterial gene to collect data on the true microbial diversity in wild plants. The patterns found could be correlated to host species and environmental conditions, in order to formulate testable hypotheses on the biological roles of plant endophytes in nature. Experimental approaches should compare different host–endophyte combinations under various relevant environmental conditions and study at the genetic, epigenetic, transcriptional, and physiological level the parameters that cause the interaction to shift along the mutualism–parasitism continuum. PMID:22639622

Resource conflict and cooperation between human host and gut microbiota: implications for nutrition and health.

PubMed

Wasielewski, Helen; Alcock, Joe; Aktipis, Athena

2016-05-01

Diet has been known to play an important role in human health since at least the time period of the ancient Greek physician Hippocrates. In the last decade, research has revealed that microorganisms inhabiting the digestive tract, known as the gut microbiota, are critical factors in human health. This paper draws on concepts of cooperation and conflict from ecology and evolutionary biology to make predictions about host-microbiota interactions involving nutrients. To optimally extract energy from some resources (e.g., fiber), hosts require cooperation from microbes. Other nutrients can be utilized by both hosts and microbes (e.g., simple sugars, iron) in their ingested form, which may lead to greater conflict over these resources. This framework predicts that some negative health effects of foods are driven by the direct effects of these foods on human physiology and by indirect effects resulting from microbiome-host competition and conflict (e.g., increased invasiveness and inflammation). Similarly, beneficial effects of some foods on host health may be enhanced by resource sharing and other cooperative behaviors between host and microbes that may downregulate inflammation and virulence. Given that some foods cultivate cooperation between hosts and microbes while others agitate conflict, host-microbe interactions may be novel targets for interventions aimed at improving nutrition and human health. © 2016 The Authors. Annals of the New York Academy of Sciences published by Wiley Periodicals, Inc. on behalf of New York Academy of Sciences.

Pathological and therapeutic interactions between bacteriophages, microbes and the host in inflammatory bowel disease.

PubMed

Babickova, Janka; Gardlik, Roman

2015-10-28

The intestinal microbiome is a dynamic system of interactions between the host and its microbes. Under physiological conditions, a fine balance and mutually beneficial relationship is present. Disruption of this balance is a hallmark of inflammatory bowel disease (IBD). Whether an altered microbiome is the consequence or the cause of IBD is currently not fully understood. The pathogenesis of IBD is believed to be a complex interaction between genetic predisposition, the immune system and environmental factors. In the recent years, metagenomic studies of the human microbiome have provided useful data that are helping to assemble the IBD puzzle. In this review, we summarize and discuss current knowledge on the composition of the intestinal microbiota in IBD, host-microbe interactions and therapeutic possibilities using bacteria in IBD. Moreover, an outlook on the possible contribution of bacteriophages in the pathogenesis and therapy of IBD is provided.

Microbe-Induced Inflammatory Signals Triggering Acquired Bone Marrow Failure Syndromes.

PubMed

Espinoza, J Luis; Kotecha, Ritesh; Nakao, Shinji

2017-01-01

Acquired bone marrow failure syndromes encompass a unique set of disorders characterized by a reduction in the effective production of mature cells by the bone marrow (BM). In the majority of cases, these syndromes are the result of the immune-mediated destruction of hematopoietic stem cells or their progenitors at various stages of differentiation. Microbial infection has also been associated with hematopoietic stem cell injury and may lead to associated transient or persistent BM failure, and recent evidence has highlighted the potential impact of commensal microbes and their metabolites on hematopoiesis. We summarize the interactions between microorganisms and the host immune system and emphasize how they may impact the development of acquired BM failure.

Microbe-Induced Inflammatory Signals Triggering Acquired Bone Marrow Failure Syndromes

PubMed Central

Espinoza, J. Luis; Kotecha, Ritesh; Nakao, Shinji

2017-01-01

Acquired bone marrow failure syndromes encompass a unique set of disorders characterized by a reduction in the effective production of mature cells by the bone marrow (BM). In the majority of cases, these syndromes are the result of the immune-mediated destruction of hematopoietic stem cells or their progenitors at various stages of differentiation. Microbial infection has also been associated with hematopoietic stem cell injury and may lead to associated transient or persistent BM failure, and recent evidence has highlighted the potential impact of commensal microbes and their metabolites on hematopoiesis. We summarize the interactions between microorganisms and the host immune system and emphasize how they may impact the development of acquired BM failure. PMID:28286502

The Control of Auxin Transport in Parasitic and Symbiotic Root–Microbe Interactions

PubMed Central

Ng, Jason Liang Pin; Perrine-Walker, Francine; Wasson, Anton P.; Mathesius, Ulrike

2015-01-01

Most field-grown plants are surrounded by microbes, especially from the soil. Some of these, including bacteria, fungi and nematodes, specifically manipulate the growth and development of their plant hosts, primarily for the formation of structures housing the microbes in roots. These developmental processes require the correct localization of the phytohormone auxin, which is involved in the control of cell division, cell enlargement, organ development and defense, and is thus a likely target for microbes that infect and invade plants. Some microbes have the ability to directly synthesize auxin. Others produce specific signals that indirectly alter the accumulation of auxin in the plant by altering auxin transport. This review highlights root–microbe interactions in which auxin transport is known to be targeted by symbionts and parasites to manipulate the development of their host root system. We include case studies for parasitic root–nematode interactions, mycorrhizal symbioses as well as nitrogen fixing symbioses in actinorhizal and legume hosts. The mechanisms to achieve auxin transport control that have been studied in model organisms include the induction of plant flavonoids that indirectly alter auxin transport and the direct targeting of auxin transporters by nematode effectors. In most cases, detailed mechanisms of auxin transport control remain unknown. PMID:27135343

Lessons from Digestive-Tract Symbioses Between Bacteria and Invertebrates.

PubMed

Graf, Joerg

2016-09-08

In most animals, digestive tracts harbor the greatest number of bacteria in the animal that contribute to its health: by aiding in the digestion of nutrients, provisioning essential nutrients and protecting against colonization by pathogens. Invertebrates have been used to enhance our understanding of metabolic processes and microbe-host interactions owing to experimental advantages. This review describes how advances in DNA sequencing technologies have dramatically altered how researchers investigate microbe-host interactions, including 16S rRNA gene surveys, metagenome experiments, and metatranscriptome studies. Advantages and challenges of each of these approaches are described herein. Hypotheses generated through omics studies can be directly tested using site-directed mutagenesis, and findings from transposon studies and site-directed experiments are presented. Finally, unique structural aspects of invertebrate digestive tracts that contribute to symbiont specificity are presented. The combination of omics approaches with genetics and microscopy allows researchers to move beyond correlations to identify conserved mechanisms of microbe-host interactions.

Host-to-host variation of ecological interactions in polymicrobial infections

NASA Astrophysics Data System (ADS)

Mukherjee, Sayak; Weimer, Kristin E.; Seok, Sang-Cheol; Ray, Will C.; Jayaprakash, C.; Vieland, Veronica J.; Swords, W. Edward; Das, Jayajit

2015-02-01

Host-to-host variability with respect to interactions between microorganisms and multicellular hosts are commonly observed in infection and in homeostasis. However, the majority of mechanistic models used to analyze host-microorganism relationships, as well as most of the ecological theories proposed to explain coevolution of hosts and microbes, are based on averages across a host population. By assuming that observed variations are random and independent, these models overlook the role of differences between hosts. Here, we analyze mechanisms underlying host-to-host variations of bacterial infection kinetics, using the well characterized experimental infection model of polymicrobial otitis media (OM) in chinchillas, in combination with population dynamic models and a maximum entropy (MaxEnt) based inference scheme. We find that the nature of the interactions between bacterial species critically regulates host-to-host variations in these interactions. Surprisingly, seemingly unrelated phenomena, such as the efficiency of individual bacterial species in utilizing nutrients for growth, and the microbe-specific host immune response, can become interdependent in a host population. The latter finding suggests a potential mechanism that could lead to selection of specific strains of bacterial species during the coevolution of the host immune response and the bacterial species.

Extracellular nanovesicles released from the commensal yeast Malassezia sympodialis are enriched in allergens and interact with cells in human skin.

PubMed

Johansson, Henrik J; Vallhov, Helen; Holm, Tina; Gehrmann, Ulf; Andersson, Anna; Johansson, Catharina; Blom, Hans; Carroni, Marta; Lehtiö, Janne; Scheynius, Annika

2018-06-15

Malassezia sympodialis is a dominant commensal fungi in the human skin mycobiome but is also associated with common skin disorders including atopic eczema (AE). M. sympodialis releases extracellular vesicles, designated MalaEx, which are carriers of small RNAs and allergens, and they can induce inflammatory cytokine responses. Here we explored how MalaEx are involved in host-microbe interactions by comparing protein content of MalaEx with that of the parental yeast cells, and by investigating interactions of MalaEx with cells in the skin. Cryo-electron tomography revealed a heterogeneous population of MalaEx. iTRAQ based quantitative proteomics identified in total 2439 proteins in all replicates of which 110 were enriched in MalaEx compared to the yeast cells. Among the MalaEx enriched proteins were two of the M. sympodialis allergens, Mala s 1 and s 7. Functional experiments indicated an active binding and internalization of MalaEx into human keratinocytes and monocytes, and MalaEx were found in close proximity of the nuclei using super-resolution fluorescence 3D-SIM imaging. Our results provides new insights into host-microbe interactions, supporting that MalaEx may have a role in the sensitization and maintenance of inflammation in AE by containing enriched amounts of allergens and with their ability to interact with skin cells.

Building the interaction interfaces: host responses upon infection with microorganisms.

PubMed

Yamazaki, Akihiro; Hayashi, Makoto

2015-02-01

Research fields of plant symbiosis and plant immunity were relatively ignorant with each other until a little while ago. Recently, however, increasing intercommunications between those two fields have begun to provide novel aspects and knowledge for understanding relationships between plants and microorganisms. Here, we review recent reports on plant-microbe interactions, focusing on the infection processes, in order to elucidate plant cellular responses that are triggered by both symbionts and pathogens. Highlighting the core elements of host responses over biotic interactions will provide insights into general mechanisms of plant-microbe interactions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Emergence of increased frequency and severity of multiple infections by viruses due to spatial clustering of hosts

NASA Astrophysics Data System (ADS)

Taylor, Bradford P.; Penington, Catherine J.; Weitz, Joshua S.

2016-12-01

Multiple virus particles can infect a target host cell. Such multiple infections (MIs) have significant and varied ecological and evolutionary consequences for both virus and host populations. Yet, the in situ rates and drivers of MIs in virus-microbe systems remain largely unknown. Here, we develop an individual-based model (IBM) of virus-microbe dynamics to probe how spatial interactions drive the frequency and nature of MIs. In our IBMs, we identify increasingly spatially correlated clusters of viruses given sufficient decreases in viral movement. We also identify increasingly spatially correlated clusters of viruses and clusters of hosts given sufficient increases in viral infectivity. The emergence of clusters is associated with an increase in multiply infected hosts as compared to expectations from an analogous mean field model. We also observe long-tails in the distribution of the multiplicity of infection in contrast to mean field expectations that such events are exponentially rare. We show that increases in both the frequency and severity of MIs occur when viruses invade a cluster of uninfected microbes. We contend that population-scale enhancement of MI arises from an aggregate of invasion dynamics over a distribution of microbe cluster sizes. Our work highlights the need to consider spatially explicit interactions as a potentially key driver underlying the ecology and evolution of virus-microbe communities.

A System Biology Perspective on Environment-Host-Microbe Interactions.

PubMed

Chen, Lianmin; Garmaeva, Sanzhima; Zherankova, Alexandra; Fu, Jingyuan; Wijmenga, Cisca

2018-04-16

A vast, complex and dynamic consortium of microorganisms known as the gut microbiome colonizes the human gut. Over the past few decades we have developed an increased awareness of its important role in human health. In this review we discuss the role of the gut microbiome in complex diseases and the possible causal scenarios behind its interactions with the host genome and environmental factors. We then propose a new analysis framework that combines a systems biology approach, cross-kingdom integration of multiple levels of omics data, and innovative in vitro models to yield an integrated picture of human host-microbe interactions. This new framework will lay the foundation for the development of the next phase in personalized medicine.

Microbial endocrinology: the interplay between the microbiota and the endocrine system.

PubMed

Neuman, Hadar; Debelius, Justine W; Knight, Rob; Koren, Omry

2015-07-01

The new field of microbiome research studies the microbes within multicellular hosts and the many effects of these microbes on the host's health and well-being. We now know that microbes influence metabolism, immunity and even behavior. Essential questions, which are just starting to be answered, are what are the mechanisms by which these bacteria affect specific host characteristics. One important but understudied mechanism appears to involve hormones. Although the precise pathways of microbiota-hormonal signaling have not yet been deciphered, specific changes in hormone levels correlate with the presence of the gut microbiota. The microbiota produces and secretes hormones, responds to host hormones and regulates expression levels of host hormones. Here, we summarize the links between the endocrine system and the gut microbiota. We categorize these interactions by the different functions of the hormones, including those affecting behavior, sexual attraction, appetite and metabolism, gender and immunity. Future research in this area will reveal additional connections, and elucidate the pathways and consequences of bacterial interactions with the host endocrine system. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Canine and Human Atopic Dermatitis: Two Faces of the Same Host-Microbe Interaction.

PubMed

Santoro, Domenico; Rodrigues Hoffmann, Aline

2016-06-01

Host-microbe interaction has been suggested to play a critical role in the pathogenesis of atopic dermatitis. The dog has been shown to be the best model to study both pathogenesis and microbiome modifications in atopic dermatitis. Bradley et al. show a significant correlation between microbiome diversity, clinical signs, and skin barrier function in atopic dogs before, during, and after antimicrobial therapy. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases.

PubMed

Leone, Vanessa; Chang, Eugene B; Devkota, Suzanne

2013-03-01

The incidence of inflammatory bowel diseases (IBD), as well as other inflammatory conditions, has dramatically increased over the past half century. While many studies have shown that IBD exhibits a genetic component via genome-wide association studies, genetic drift alone cannot account for this increase, and other factors, such as those found in the environment must play a role, suggesting a "multiple hit" phenomenon that precipitates disease. One major environmental factor, dietary intake, has shifted to a high fat, high carbohydrate Western-type diet in developing nations, nearly in direct correlation with the increasing incidence of IBD. Recent evidence suggests that specific changes in dietary intake have led to a shift in the composite human gut microbiota, resulting in the emergence of pathobionts that can thrive under specific conditions. In the genetically susceptible host, the emerging pathobionts can lead to increasing incidence and severity of IBD and other inflammatory disorders. Since the gut microbiota is plastic and responds to dietary modulations, the use of probiotics, prebiotics, and/or dietary alterations are all intriguing complementary therapeutic approaches to alleviate IBD symptoms. However, the interactions are complex and it is unlikely that a one-size-fits all approach can be utilized across all populations affected by IBD. Exploration into and thoroughly understanding the interactions between host and microbes, primarily in the genetically susceptible host, will help define strategies that can be tailored to an individual as we move towards an era of personalized medicine to treat IBD.

Eavesdropping on plant-insect-microbe chemical communications in agricultural ecology: a virtual issue on semiochemicals

USDA-ARS?s Scientific Manuscript database

Studies of plant-insect interactions, and more recently the interactions among plants, insects, and microbes, have revealed that volatiles often facilitate insect movement, aggregation, and host location by herbivores, predators and parasitoids, all of which could be used to help protect agriculture...

Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health.

PubMed

Ha, Connie W Y; Lam, Yan Y; Holmes, Andrew J

2014-11-28

Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging.

Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

PubMed Central

Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

2014-01-01

Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice.

PubMed

Stilling, Roman M; Moloney, Gerard M; Ryan, Feargal J; Hoban, Alan E; Bastiaanssen, Thomaz Fs; Shanahan, Fergus; Clarke, Gerard; Claesson, Marcus J; Dinan, Timothy G; Cryan, John F

2018-05-29

Social behaviour is regulated by activity of host-associated microbiota across multiple species. However, the molecular mechanisms mediating this relationship remain elusive. We therefore determined the dynamic, stimulus-dependent transcriptional regulation of germ-free (GF) and GF mice colonised post weaning (exGF) in the amygdala, a brain region critically involved in regulating social interaction. In GF mice the dynamic response seen in controls was attenuated and replaced by a marked increase in expression of splicing factors and alternative exon usage in GF mice upon stimulation, which was even more pronounced in exGF mice. In conclusion, we demonstrate a molecular basis for how the host microbiome is crucial for a normal behavioural response during social interaction. Our data further suggest that social behaviour is correlated with the gene-expression response in the amygdala, established during neurodevelopment as a result of host-microbe interactions. Our findings may help toward understanding neurodevelopmental events leading to social behaviour dysregulation, such as those found in autism spectrum disorders (ASDs). © 2018, Stilling et al.

Friend, foe or food? Recognition and the role of antimicrobial peptides in gut immunity and Drosophila-microbe interactions.

PubMed

Broderick, Nichole A

2016-05-26

Drosophila melanogaster lives, breeds and feeds on fermenting fruit, an environment that supports a high density, and often a diversity, of microorganisms. This association with such dense microbe-rich environments has been proposed as a reason that D. melanogaster evolved a diverse and potent antimicrobial peptide (AMP) response to microorganisms, especially to combat potential pathogens that might occupy this niche. Yet, like most animals, D. melanogaster also lives in close association with the beneficial microbes that comprise its microbiota, or microbiome, and recent studies have shown that antimicrobial peptides (AMPs) of the epithelial immune response play an important role in dictating these interactions and controlling the host response to gut microbiota. Moreover, D. melanogaster also eats microbes for food, consuming fermentative microbes of decaying plant material and their by-products as both larvae and adults. The processes of nutrient acquisition and host defence are remarkably similar and use shared functions for microbe detection and response, an observation that has led to the proposal that the digestive and immune systems have a common evolutionary origin. In this manner, D. melanogaster provides a powerful model to understand how, and whether, hosts differentiate between the microbes they encounter across this spectrum of associations.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'. © 2016 The Author(s).

Friend, foe or food? Recognition and the role of antimicrobial peptides in gut immunity and Drosophila–microbe interactions

PubMed Central

2016-01-01

Drosophila melanogaster lives, breeds and feeds on fermenting fruit, an environment that supports a high density, and often a diversity, of microorganisms. This association with such dense microbe-rich environments has been proposed as a reason that D. melanogaster evolved a diverse and potent antimicrobial peptide (AMP) response to microorganisms, especially to combat potential pathogens that might occupy this niche. Yet, like most animals, D. melanogaster also lives in close association with the beneficial microbes that comprise its microbiota, or microbiome, and recent studies have shown that antimicrobial peptides (AMPs) of the epithelial immune response play an important role in dictating these interactions and controlling the host response to gut microbiota. Moreover, D. melanogaster also eats microbes for food, consuming fermentative microbes of decaying plant material and their by-products as both larvae and adults. The processes of nutrient acquisition and host defence are remarkably similar and use shared functions for microbe detection and response, an observation that has led to the proposal that the digestive and immune systems have a common evolutionary origin. In this manner, D. melanogaster provides a powerful model to understand how, and whether, hosts differentiate between the microbes they encounter across this spectrum of associations. This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’. PMID:27160597

A comprehensive review of the nasal microbiome in chronic rhinosinusitis (CRS)

PubMed Central

Mahdavinia, Mahboobeh; Keshavarzian, Ali; Tobin, Mary C; Landay, Alan; Schleimer, Robert P.

2015-01-01

Chronic rhinosinusitis (CRS) has been known as a disease with strong infectious and inflammatory components for decades. The recent advancement in methods identifying microbes has helped implicate the airway microbiome in inflammatory respiratory diseases such as asthma and COPD. Such studies support a role of resident microbes in both health and disease of host tissue, especially in the case of inflammatory mucosal diseases. Identifying interactive events between microbes and elements of the immune system can help us to uncover the pathogenic mechanisms underlying chronic rhinosinusitis. Here we provide a review of the findings on the complex upper respiratory microbiome in CRS in comparison to healthy controls. Furthermore, we have reviewed the defects and alterations of the host immune system that interact with microbes and could be associated with dysbiosis in CRS. PMID:26510171

Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota.

PubMed

Wu, Richard Y; Määttänen, Pekka; Napper, Scott; Scruten, Erin; Li, Bo; Koike, Yuhki; Johnson-Henry, Kathene C; Pierro, Agostino; Rossi, Laura; Botts, Steven R; Surette, Michael G; Sherman, Philip M

2017-10-10

Prebiotics are non-digestible food ingredients that enhance the growth of certain microbes within the gut microbiota. Prebiotic consumption generates immune-modulatory effects that are traditionally thought to reflect microbial interactions within the gut. However, recent evidence suggests they may also impart direct microbe-independent effects on the host, though the mechanisms of which are currently unclear. Kinome arrays were used to profile the host intestinal signaling responses to prebiotic exposures in the absence of microbes. Identified pathways were functionally validated in Caco-2Bbe1 intestinal cell line and in vivo model of murine endotoxemia. We found that prebiotics directly regulate host mucosal signaling to alter response to bacterial infection. Intestinal epithelial cells (IECs) exposed to prebiotics are hyporesponsive to pathogen-induced mitogen-activated protein kinase (MAPK) and nuclear factor kappa B (NF-κB) activations, and have a kinome profile distinct from non-treated cells pertaining to multiple innate immune signaling pathways. Consistent with this finding, mice orally gavaged with prebiotics showed dampened inflammatory response to lipopolysaccharide (LPS) without alterations in the gut microbiota. These findings provide molecular mechanisms of direct host-prebiotic interactions to support prebiotics as potent modulators of host inflammation.

The interaction of gut microbes with host ABC transporters

PubMed Central

Mercado-Lubo, Regino

2010-01-01

ATP binding cassette (ABC) transporters are increasingly recognized for their ability to modulate the absorption, distribution, metabolism, secretion and toxicity of xenobiotics. In addition to their essential function in drug resistance, there is also emerging evidence documenting the important role ABC transporters play in tissue defense. In this respect, the gastrointestinal tract represents a critical vanguard of defense against oral exposure of drugs while at the same time functions as a physical barrier between the lumenal contents (including bacteria) and the intestinal epithelium. Given emerging evidence suggesting that multidrug resistance protein (MDR) plays an important role in host-bacterial interactions in the gastrointestinal tract, this review will discuss the interplay between MDR of the intestinal epithelial cell barrier and gut microbes in health and disease. In particular, we will explore host-microbe interactions involving three apically restricted ABC transporters of the intestinal epithelium; P-glycoprotein (P-gp), multidrug resistance-associated protein 2 (MRP2) and cystic fibrosis transmembrane regulator (CFTR). PMID:21327038

Detection of and Response to Signals Involved in Host-Microbe Interactions by Plant-Associated Bacteria

PubMed Central

Brencic, Anja; Winans, Stephen C.

2005-01-01

Diverse interactions between hosts and microbes are initiated by the detection of host-released chemical signals. Detection of these signals leads to altered patterns of gene expression that culminate in specific and adaptive changes in bacterial physiology that are required for these associations. This concept was first demonstrated for the members of the family Rhizobiaceae and was later found to apply to many other plant-associated bacteria as well as to microbes that colonize human and animal hosts. The family Rhizobiaceae includes various genera of rhizobia as well as species of Agrobacterium. Rhizobia are symbionts of legumes, which fix nitrogen within root nodules, while Agrobacterium tumefaciens is a pathogen that causes crown gall tumors on a wide variety of plants. The plant-released signals that are recognized by these bacteria are low-molecular-weight, diffusible molecules and are detected by the bacteria through specific receptor proteins. Similar phenomena are observed with other plant pathogens, including Pseudomonas syringae, Ralstonia solanacearum, and Erwinia spp., although here the signals and signal receptors are not as well defined. In some cases, nutritional conditions such as iron limitation or the lack of nitrogen sources seem to provide a significant cue. While much has been learned about the process of host detection over the past 20 years, our knowledge is far from being complete. The complex nature of the plant-microbe interactions makes it extremely challenging to gain a comprehensive picture of host detection in natural environments, and thus many signals and signal recognition systems remain to be described. PMID:15755957

Bivalve immunity and response to infections: Are we looking at the right place?

PubMed

Allam, Bassem; Pales Espinosa, Emmanuelle

2016-06-01

Significant progress has been made in the understanding of cellular and molecular mediators of immunity in invertebrates in general and bivalve mollusks in particular. Despite this information, there is a lack of understanding of factors affecting animal resistance and specific responses to infections. This in part results from limited consideration of the spatial (and to some extent temporal) heterogeneity of immune responses and very limited information on host-pathogen (and microbes in general) interactions at initial encounter/colonization sites. Of great concern is the fact that most studies on molluscan immunity focus on the circulating hemocytes and the humoral defense factors in the plasma while most relevant host-microbe interactions occur at mucosal interfaces. This paper summarizes information available on the contrasting value of information available on focal and systemic immune responses in infected bivalves, and highlights the role of mucosal immune factors in host-pathogen interactions. Available information underlines the diversity of immune effectors at molluscan mucosal interfaces and highlights the tailored immune response to pathogen stimuli. This context raises fascinating basic research questions around host-microbe crosstalk and feedback controls of these interactions and may lead to novel disease mitigation strategies and improve the assessment of resistant crops or the screening of probiotic candidates. Copyright © 2016 Elsevier Ltd. All rights reserved.

The role of gut microbiota in health and disease: In vitro modeling of host-microbe interactions at the aerobe-anaerobe interphase of the human gut.

PubMed

von Martels, Julius Z H; Sadaghian Sadabad, Mehdi; Bourgonje, Arno R; Blokzijl, Tjasso; Dijkstra, Gerard; Faber, Klaas Nico; Harmsen, Hermie J M

2017-04-01

The microbiota of the gut has many crucial functions in human health. Dysbiosis of the microbiota has been correlated to a large and still increasing number of diseases. Recent studies have mostly focused on analyzing the associations between disease and an aberrant microbiota composition. Functional studies using (in vitro) gut models are required to investigate the precise interactions that occur between specific bacteria (or bacterial mixtures) and gut epithelial cells. As most gut bacteria are obligate or facultative anaerobes, studying their effect on oxygen-requiring human gut epithelial cells is technically challenging. Still, several (anaerobic) bacterial-epithelial co-culture systems have recently been developed that mimic host-microbe interactions occurring in the human gut, including 1) the Transwell "apical anaerobic model of the intestinal epithelial barrier", 2) the Host-Microbiota Interaction (HMI) module, 3) the "Human oxygen-Bacteria anaerobic" (HoxBan) system, 4) the human gut-on-a-chip and 5) the HuMiX model. This review discusses the role of gut microbiota in health and disease and gives an overview of the characteristics and applications of these novel host-microbe co-culture systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Master manipulators: an update on Legionella pneumophila Icm/Dot translocated substrates and their host targets

PubMed Central

Isaac, Dervla T; Isberg, Ralph

2014-01-01

Macrophages are the front line of immune defense against invading microbes. Microbes, however, have evolved numerous and diverse mechanisms to thwart these host immune defenses and thrive intracellularly. Legionella pneumophila, a Gram-negative pathogen of amoebal and mammalian phagocytes, is one such microbe. In humans, it causes a potentially fatal pneumonia referred to as Legionnaires' disease. Armed with the Icm/Dot type IV secretion system, which is required for virulence, and approximately 300 translocated proteins, Legionella is able to enter host cells, direct the biogenesis of its own vacuolar compartment, and establish a replicative niche, where it grows to high levels before lysing the host cell. Efforts to understand the pathogenesis of this bacterium have focused on characterizing the molecular activities of its many effectors. In this article, we highlight recent strides that have been made in understanding how Legionella effectors mediate host-pathogen interactions. PMID:24762308

Friends with social benefits: host-microbe interactions as a driver of brain evolution and development?

PubMed Central

Stilling, Roman M.; Bordenstein, Seth R.; Dinan, Timothy G.; Cryan, John F.

2014-01-01

The tight association of the human body with trillions of colonizing microbes that we observe today is the result of a long evolutionary history. Only very recently have we started to understand how this symbiosis also affects brain function and behavior. In this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. In particular, we explore the integration of human brain development with evolution, symbiosis, and RNA biology, which together represent a “social triangle” that drives human social behavior and cognition. We argue that, in order to understand how inter-kingdom communication can affect brain adaptation and plasticity, it is inevitable to consider epigenetic mechanisms as important mediators of genome-microbiome interactions on an individual as well as a transgenerational time scale. Finally, we unite these interpretations with the hologenome theory of evolution. Taken together, we propose a tighter integration of neuroscience fields with host-associated microbiology by taking an evolutionary perspective. PMID:25401092

How effectors promote beneficial interactions.

PubMed

Miwa, Hiroki; Okazaki, Shin

2017-08-01

Beneficial microbes such as rhizobia possess effector proteins that are secreted into the host cytoplasm where they modulate host-signaling pathways. Among these effectors, type 3 secreted effectors (T3Es) of rhizobia play roles in promoting nitrogen-fixing nodule symbiosis, suppressing host defenses and directly activating symbiosis-related processes. Rhizobia use the same strategy as pathogenic bacteria to suppress host defenses such as targeting the MAPK cascade. In addition, rhizobial T3E can promote root nodule symbiosis by directly activating Nod factor signaling, which bypasses Nod factor perception. The various strategies employed by beneficial microbes to promote infection and maintain viability in the host are therefore crucial for plant endosymbiosis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nicotiana benthamiana as a nonhost of Zymoseptoria tritici

USDA-ARS?s Scientific Manuscript database

In nature, plants are continually being bombarded by microbes. However, actual host-pathogen interactions that negatively affect (result in disease) any given plant species are by far the exception, rather than the rule. The plant protection mechanism effective against this plethora of microbes that...

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions

PubMed Central

Kwong, Waldan K.; McFrederick, Quinn; Anderson, Kirk E.; Barribeau, Seth Michael; Chandler, James Angus; Cornman, R. Scott; Dainat, Jacques; Doublet, Vincent; Emery, Olivier; Evans, Jay D.; Farinelli, Laurent; Flenniken, Michelle L.; Granberg, Fredrik; Grasis, Juris A.; Gauthier, Laurent; Hayer, Juliette; Koch, Hauke; Kocher, Sarah; Martinson, Vincent G.; Moran, Nancy; Munoz-Torres, Monica; Newton, Irene; Paxton, Robert J.; Powell, Eli; Sadd, Ben M.; Schmid-Hempel, Paul; Schmid-Hempel, Regula; Schwarz, Ryan S.; vanEngelsdorp, Dennis

2016-01-01

ABSTRACT As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health. PMID:27118586

The bee microbiome: Impact on bee health and model for evolution and ecology of host-microbe interactions

USGS Publications Warehouse

Engel, Philipp; Kwong, Waldan K.; McFrederick, Quinn; Anderson, Kirk E.; Barribeau, Seth Michael; Chandler, James Angus; Cornman, Robert S.; Dainat, Jacques; de Miranda, Joachim R.; Doublet, Vincent; Emery, Olivier; Evans, Jay D.; Farinelli, Laurent; Flenniken, Michelle L.; Granberg, Fredrik; Grasis, Juris A.; Gauthier, Laurent; Hayer, Juliette; Koch, Hauke; Kocher, Sarah; Martinson, Vincent G.; Moran, Nancy; Munoz-Torres, Monica; Newton, Irene; Paxton, Robert J.; Powell, Eli; Sadd, Ben M.; Schmid-Hempel, Paul; Schmid-Hempel, Regula; Song, Se Jin; Schwarz, Ryan S.; vanEngelsdorp, Dennis; Dainat, Benjamin

2016-01-01

As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.

PubMed

Engel, Philipp; Kwong, Waldan K; McFrederick, Quinn; Anderson, Kirk E; Barribeau, Seth Michael; Chandler, James Angus; Cornman, R Scott; Dainat, Jacques; de Miranda, Joachim R; Doublet, Vincent; Emery, Olivier; Evans, Jay D; Farinelli, Laurent; Flenniken, Michelle L; Granberg, Fredrik; Grasis, Juris A; Gauthier, Laurent; Hayer, Juliette; Koch, Hauke; Kocher, Sarah; Martinson, Vincent G; Moran, Nancy; Munoz-Torres, Monica; Newton, Irene; Paxton, Robert J; Powell, Eli; Sadd, Ben M; Schmid-Hempel, Paul; Schmid-Hempel, Regula; Song, Se Jin; Schwarz, Ryan S; vanEngelsdorp, Dennis; Dainat, Benjamin

2016-04-26

As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health. Copyright © 2016 Engel et al.

What Is a Host? Incorporating the Microbiota into the Damage-Response Framework

PubMed Central

Pirofski, Liise-anne

2014-01-01

Since proof of the germ theory of disease in the late 19th century, a major focus of the fields of microbiology and infectious diseases has been to seek differences between pathogenic and nonpathogenic microbes and the role that the host plays in microbial pathogenesis. Remarkably, despite the increasing recognition that host immunity plays a role in microbial pathogenesis, there has been little discussion about what constitutes a host. Historically, hosts have been viewed in the context of their fitness or immunological status and characterized by adjectives such as immune, immunocompetent, immunosuppressed, immunocompromised, or immunologically impaired. However, in recent years it has become apparent that the microbiota has profound effects on host homeostasis and susceptibility to microbial diseases in addition to its effects on host immunity. This raises the question of how to incorporate the microbiota into defining a host. This definitional problem is further complicated because neither host nor microbial properties are adequate to predict the outcome of host-microbe interaction because this outcome exhibits emergent properties. In this essay, we revisit the damage-response framework (DRF) of microbial pathogenesis and demonstrate how it can incorporate the rapidly accumulating information being generated by the microbiome revolution. We use the tenets of the DRF to put forth the following definition of a host: a host is an entity that houses an associated microbiome/microbiota and interacts with microbes such that the outcome results in damage, benefit, or indifference, thus resulting in the states of symbiosis, colonization, commensalism, latency, and disease. PMID:25385796

Cnidarian-microbe interactions and the origin of innate immunity in metazoans.

PubMed

Bosch, Thomas C G

2013-01-01

Most epithelia in animals are colonized by microbial communities. These resident microbes influence fitness and thus ecologically important traits of their hosts, ultimately forming a metaorganism consisting of a multicellular host and a community of associated microorganisms. Recent discoveries in the cnidarian Hydra show that components of the innate immune system as well as transcriptional regulators of stem cells are involved in maintaining homeostasis between animals and their resident microbiota. Here I argue that components of the innate immune system with its host-specific antimicrobial peptides and a rich repertoire of pattern recognition receptors evolved in early-branching metazoans because of the need to control the resident beneficial microbes, not because of invasive pathogens. I also propose a mutual intertwinement between the stem cell regulatory machinery of the host and the resident microbiota composition, such that disturbances in one trigger a restructuring and resetting of the other.

Host gene-microbiome interactions: molecular mechanisms in inflammatory bowel disease.

PubMed

Chu, Hiutung

2017-07-24

Recent studies have identified links between host genetic variants and microbial recognition of the microbiome. Defects in host-microbiome interactions in individuals harboring inflammatory bowel disease risk alleles may result in imbalances of the microbial community, impaired pathogen clearance, and failure to sense beneficial commensal microbes. These findings highlight the importance of maintaining bi-directional communication at the mucosal interface during intestinal homeostasis.

Polymicrobial infection and bacterium-mediated epigenetic modification of DNA tumor viruses contribute to pathogenesis.

PubMed

Doolittle, J M; Webster-Cyriaque, J

2014-04-29

ABSTRACT The human body plays host to a wide variety of microbes, commensal and pathogenic. In addition to interacting with their host, different microbes, such as bacteria and viruses, interact with each other, sometimes in ways that exacerbate disease. In particular, gene expression of a number of viruses, including Kaposi's sarcoma-associated herpesvirus (KSHV), Epstein-Barr virus (EBV), and human immunodeficiency virus (HIV), is known to be regulated by epigenetic modifications induced by bacteria. These viruses establish latent infection in their host cells and can be reactivated by bacterial products. Viral reactivation has been suggested to contribute to periodontal disease and AIDS. In addition, bacterium-virus interactions may play a role in cancers, such as Kaposi's sarcoma, gastric cancer, and head and neck cancer. It is important to consider the effects of coexisting bacterial infections when studying viral diseases in vivo.

In vitro cell and tissue models for studying host-microbe interactions: a review.

PubMed

Bermudez-Brito, Miriam; Plaza-Díaz, Julio; Fontana, Luis; Muñoz-Quezada, Sergio; Gil, Angel

2013-01-01

Ideally, cell models should resemble the in vivo conditions; however, in most in vitro experimental models, epithelial cells are cultivated as monolayers, in which the establishment of functional epithelial features is not achieved. To overcome this problem, co-culture experiments with probiotics, dendritic cells and intestinal epithelial cells and three-dimensional models attempt to reconcile the complex and dynamic interactions that exist in vivo between the intestinal epithelium and bacteria on the luminal side and between the epithelium and the underlying immune system on the basolateral side. Additional models include tissue explants, bioreactors and organoids. The present review details the in vitro models used to study host-microbe interactions and explores the new tools that may help in understanding the molecular mechanisms of these interactions.

The Metronome of Symbiosis: Interactions Between Microbes and the Host Circadian Clock.

PubMed

Heath-Heckman, Elizabeth A C

2016-11-01

The entrainment of circadian rhythms, physiological cycles with a period of about 24 h, is regulated by a variety of mechanisms, including nonvisual photoreception. While circadian rhythms have been shown to be integral to many processes in multicellular organisms, including immune regulation, the effect of circadian rhythms on symbiosis, or host-microbe interactions, has only recently begun to be studied. This review summarizes recent work in the interactions of both pathogenic and mutualistic associations with host and symbiont circadian rhythms, focusing specifically on three mutualistic systems in which this phenomenon has been best studied. One important theme taken from these studies is the fact that mutualisms are profoundly affected by the circadian rhythms of the host, but that the microbial symbionts in these associations can, in turn, manipulate host rhythms. The interplay between circadian rhythms and symbiosis is a promising new field with effects that should be kept in mind when designing future studies across biology. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Chemotaxis and flow disorder shape microbial dispersion in porous media

NASA Astrophysics Data System (ADS)

De Anna, Pietro; Yawata, Yutaka; Stocker, Roman; Juanes, Ruben

2017-04-01

Bacteria drive a plethora of natural processes in the subsurface, consuming organic matter and catalysing chemical reactions that are key to global elemental cycles. These macro-scale consequences result from the collective action of individual bacteria at the micro-scale, which are modulated by the highly heterogeneous subsurface environment, dominated by flow disorder and strong chemical gradients. Yet, despite the generally recognized importance of these microscale processes, microbe-host medium interaction at the pore scale remain poorly characterized and understood. Here, we introduce a microfluidic model system to directly image and quantify the role of cell motility on bacterial dispersion and residence time in confined, porous, media. Using the soil-dwelling bacterium Bacillus subtilis and the common amino acid serine as a resource, we observe that chemotaxis in highly disordered and confined physico-chemical environment affords bacteria an increase in their ability to persistently occupy the host medium. Our findings illustrate that the interplay between bacterial behaviour and pore-scale disorder in fluid velocity and nutrient concentration directly impacts the residence time, transport and bio-geo-chemical transformation rates of biota in the subsurface, and thus likely the processes they mediate.

Evolutionary and ecological forces that shape the bacterial communities of the human gut

PubMed Central

Messer, Jeannette S.; Liechty, Emma R; Vogel, Olivia A.; Chang, Eugene B.

2017-01-01

Since microbes were first described in the mid-1600's, we have come to appreciate that they live all around and within us with both beneficial and detrimental effects on nearly every aspect of our lives. The human gastrointestinal tract is inhabited by a dynamic community of trillions of bacteria that constantly interact with each other and their human host. The acquisition of these bacteria is not stochastic, but determined by circumstance (environment), host rules (genetics, immune state, mucus, etc), and dynamic self-selection among microbes to form stable, resilient communities that are in balance with the host. In this review, we will discuss how these factors lead to formation of the gut bacterial community and influence its interactions with the host. We will also address how gut bacteria contribute to disease and how they could potentially be targeted to prevent and treat a variety of human ailments. PMID:28145439

Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

PubMed Central

Bhatnagar, Srijak; Eisen, Jonathan A.; Kopp, Artyom

2011-01-01

Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in wild Drosophila populations, while the most abundant associates of natural Drosophila populations are rare in the lab. PMID:21966276

Skin microbes on frogs prevent morbidity and mortality caused by a lethal skin fungus.

PubMed

Harris, Reid N; Brucker, Robert M; Walke, Jenifer B; Becker, Matthew H; Schwantes, Christian R; Flaherty, Devon C; Lam, Brianna A; Woodhams, Douglas C; Briggs, Cheryl J; Vredenburg, Vance T; Minbiole, Kevin P C

2009-07-01

Emerging infectious diseases threaten human and wildlife populations. Altered ecological interactions between mutualistic microbes and hosts can result in disease, but an understanding of interactions between host, microbes and disease-causing organisms may lead to management strategies to affect disease outcomes. Many amphibian species in relatively pristine habitats are experiencing dramatic population declines and extinctions due to the skin disease chytridiomycosis, which is caused by the chytrid fungus Batrachochytrium dendrobatidis. Using a randomized, replicated experiment, we show that adding an antifungal bacterial species, Janthinobacterium lividum, found on several species of amphibians to the skins of the frog Rana muscosa prevented morbidity and mortality caused by the pathogen. The bacterial species produces the anti-chytrid metabolite violacein, which was found in much higher concentrations on frog skins in the treatments where J. lividum was added. Our results show that cutaneous microbes are a part of amphibians' innate immune system, the microbial community structure on frog skins is a determinant of disease outcome and altering microbial interactions on frog skins can prevent a lethal disease outcome. A bioaugmentation strategy may be an effective management tool to control chytridiomycosis in amphibian survival assurance colonies and in nature.

Regulation of DUOX by the Galphaq-phospholipase Cbeta-Ca2+ pathway in Drosophila gut immunity.

PubMed

Ha, Eun-Mi; Lee, Kyung-Ah; Park, Seon Hwa; Kim, Sung-Hee; Nam, Hyuck-Jin; Lee, Hyo-Young; Kang, Dongmin; Lee, Won-Jae

2009-03-01

All metazoan guts are in constant contact with diverse food-borne microorganisms. The signaling mechanisms by which the host regulates gut-microbe interactions, however, are not yet clear. Here, we show that phospholipase C-beta (PLCbeta) signaling modulates dual oxidase (DUOX) activity to produce microbicidal reactive oxygen species (ROS) essential for normal host survival. Gut-microbe contact rapidly activates PLCbeta through Galphaq, which in turn mobilizes intracellular Ca(2+) through inositol 1,4,5-trisphosphate generation for DUOX-dependent ROS production. PLCbeta mutant flies had a short life span due to the uncontrolled propagation of an essential nutritional microbe, Saccharomyces cerevisiae, in the gut. Gut-specific reintroduction of the PLCbeta restored efficient DUOX-dependent microbe-eliminating capacity and normal host survival. These results demonstrate that the Galphaq-PLCbeta-Ca(2+)-DUOX-ROS signaling pathway acts as a bona fide first line of defense that enables gut epithelia to dynamically control yeast during the Drosophila life cycle.

Gut immune system: a new frontier for nutritional modulation of gut health

USDA-ARS?s Scientific Manuscript database

The gut represents a continuously evolving ecosystem consisting of trillions of commensal bacteria living in symbiosis with the host. The host-microbe interplay plays a crucial role in physiological development and health of the host. There is increasing evidence that shows a dynamic interaction be...

Intrinsic disorder in pathogen effectors: protein flexibility as an evolutionary hallmark in a molecular arms race.

PubMed

Marín, Macarena; Uversky, Vladimir N; Ott, Thomas

2013-09-01

Effector proteins represent a refined mechanism of bacterial pathogens to overcome plants' innate immune systems. These modular proteins often manipulate host physiology by directly interfering with immune signaling of plant cells. Even if host cells have developed efficient strategies to perceive the presence of pathogenic microbes and to recognize intracellular effector activity, it remains an open question why only few effectors are recognized directly by plant resistance proteins. Based on in-silico genome-wide surveys and a reevaluation of published structural data, we estimated that bacterial effectors of phytopathogens are highly enriched in long-disordered regions (>50 residues). These structurally flexible segments have no secondary structure under physiological conditions but can fold in a stimulus-dependent manner (e.g., during protein-protein interactions). The high abundance of intrinsic disorder in effectors strongly suggests positive evolutionary selection of this structural feature and highlights the dynamic nature of these proteins. We postulate that such structural flexibility may be essential for (1) effector translocation, (2) evasion of the innate immune system, and (3) host function mimicry. The study of these dynamical regions will greatly complement current structural approaches to understand the molecular mechanisms of these proteins and may help in the prediction of new effectors.

From evolutionary advantage to disease agents: forensic re-evaluation of host-microbe interactions and pathogenicity

PubMed Central

Rivera-Pérez, Jessica I.; González, Alfredo A.; Toranzos, Gary A.

2016-01-01

As the “human microbiome era” continues, there is an increasing awareness of our resident microbiota and its indispensable role in our increased fitness as holobionts. However, the host-microbe relationship is not so clearly defined for some human symbionts. Here we discuss examples of “accidental pathogens”, meaning previously non-pathogenic and/or environmental microbes thought to have inadvertently experienced an evolutionary shift towards pathogenicity. For instance, symbionts such as Helicobacter pylori and JC Polyomavirus have been shown to accompany humans since prehistoric times and are still abundant in extant populations as part of the microbiome. And yet, the relationship between a subgroup of these microbes and their human hosts seems to have changed with time, and they have recently gained notoriety as gastrointestinal and neuropathogens, respectively. On the other hand, environmental microbes such as Legionella spp. have recently experienced a shift in host range and are now a major problem in industrialized countries as a result of artificial ecosystems. Other variables involved in this accidental phenomenon could be the apparent change or reduction in the diversity of human-associated microbiota because of modern medicine and lifestyles. All of this could result in an increased prevalence of “accidental pathogens” in the form of emerging pathogens. PMID:28155809

Impact of Microbes on the Pathogenesis of Primary Biliary Cirrhosis (PBC) and Primary Sclerosing Cholangitis (PSC)

PubMed Central

Mattner, Jochen

2016-01-01

Primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC) represent the major clinical entities of chronic cholestatic liver diseases. Both disorders are characterized by portal inflammation and slowly progress to obliterative fibrosis and eventually liver cirrhosis. Although immune-pathogenic mechanisms have been implicated in the pathogenesis of PBC and PSC, neither disorder is considered to be a classical autoimmune disease, as PSC and PBC patients do not respond to immune-suppressants. Furthermore, the decreased bile flow resulting from the immune-mediated tissue assault and the subsequent accumulation of toxic bile products in PBC and PSC not only perpetuates biliary epithelial damage, but also alters the composition of the intestinal and biliary microbiota and its mutual interactions with the host. Consistent with the close association of PSC and inflammatory bowel disease (IBD), the polyclonal hyper IgM response in PBC and (auto-)antibodies which cross-react to microbial antigens in both diseases, an expansion of individual microbes leads to shifts in the composition of the intestinal or biliary microbiota and a subsequent altered integrity of epithelial layers, promoting microbial translocation. These changes have been implicated in the pathogenesis of both devastating disorders. Thus, we will discuss here these recent findings in the context of novel and alternative therapeutic options. PMID:27834858

Contentious host-microbiota relationship in inflammatory bowel disease--can foes become friends again?

PubMed

Satokari, Reetta

2015-01-01

Inflammatory bowel diseases (IBDs) are chronic debilitating disorders of unknown etiology, consisting of two main conditions, ulcerative colitis and Crohn's disease. Major advances have recently taken place in human genetic studies of IBD and over 160 risk loci for these two diseases have been uncovered. These genetic data highlight a key role for genes that code for immunological and epithelial barrier functions. Environmental factors also make substantial contributions to the pathogenesis of IBD and account for the growing incidence of the diseases around the world. Intestinal microbiota creates resistance to infection, provides nutrients, and educates the immune system and in many ways has a significant impact on human health. Aberrant microbiota composition and decreased diversity (dysbiotic microbiota) are key etiopathological events in IBD. Dysbiotic microbiota can lead to loss of normal, regulatory immune effects in the gut mucosa. This may play a central role in the development and perpetuation of chronic inflammation. Further, the expression of specific innate immune receptors that recognize microbes is altered in the IBD epithelium. Therefore, the combination of host side epithelial barrier functions and the presence of dysbiotic microbiota in the gut together promote inflammation. New therapeutic options targeting microbiota are currently considered for IBD and they may, in the future, provide means to reverse the pathogenic host-microbiota relationship into a symbiotic one. In this review, the focus is on the intestinal microbiota and host-microbe interactions in IBD.

Microbial contributions to chronic inflammation and metabolic disease.

PubMed

Shanahan, Fergus; Sheehan, Donal

2016-07-01

It is long known that immune and metabolic cascades intersect at various cross-points. More recently, the regulatory influence of the microbiota on both of these cascades has emerged. Advances with therapeutic implications for chronic immunologic and metabolic disorders are examined. Disturbances of the microbiota, particularly in early life, may be the proximate environmental risk factor in socioeconomically developed societies for development of chronic immune-allergic and metabolic disorders, including obesity. Antibiotics and dietary factors contribute to this risk. Multiple microbial signalling molecules mediate host-microbe interactions including bacterial metabolites such as short-chain fatty acids, bile salts and others. New strategies for manipulating the composition and metabolic activity of the gut microbiota have emerged and offer a realistic prospect of personalized therapeutic options in immune and metabolic diseases.

The primate vaginal microbiome: comparative context and implications for human health and disease.

PubMed

Stumpf, Rebecca M; Wilson, Brenda A; Rivera, Angel; Yildirim, Suleyman; Yeoman, Carl J; Polk, John D; White, Bryan A; Leigh, Steven R

2013-12-01

The primate body hosts trillions of microbes. Interactions between primate hosts and these microbes profoundly affect primate physiology, reproduction, health, survival, and ultimately, evolution. It is increasingly clear that primate health cannot be understood fully without knowledge of host-microbial interactions. Our goals here are to review what is known about microbiomes of the female reproductive tract and to explore several factors that influence variation within individuals, as well as within and between primate species. Much of our knowledge of microbial variation derives from studies of humans, and from microbes located in nonreproductive regions (e.g., the gut). We review work suggesting that the vaginal microbiota affects female health, fecundity, and pregnancy outcomes, demonstrating the selective potential for these agents. We explore the factors that correlate with microbial variation within species. Initial colonization by microbes depends on the manner of birth; most microbial variation is structured by estrogen levels that change with age (i.e., at puberty and menopause) and through the menstrual cycle. Microbial communities vary by location within the vagina and can depend on the sampling methods used (e.g., swab, lavage, or pap smear). Interindividual differences also exist, and while this variation is not completely understood, evidence points more to differences in estrogen levels, rather than differences in external physical environment. When comparing across species, reproductive-age humans show distinct microbial communities, generally dominated by Lactobacillus, unlike other primates. We develop evolutionary hypotheses to explain the marked differences in microbial communities. While much remains to be done to test these hypotheses, we argue that the ample variation in primate mating and reproductive behavior offers excellent opportunities to evaluate host-microbe coevolution and adaptation. Copyright © 2013 Wiley Periodicals, Inc.

Host-Pathogen Interactions and Chronic Lung Allograft Dysfunction.

PubMed

Belperio, John; Palmer, Scott M; Weigt, S Sam

2017-09-01

Lung transplantation is now considered to be a therapeutic option for patients with advanced-stage lung diseases. Unfortunately, due to post-transplant complications, both infectious and noninfectious, it is only a treatment and not a cure. Infections (e.g., bacterial, viral, and fungal) in the immunosuppressed lung transplant recipient are a common cause of mortality post transplant. Infections have more recently been explored as factors contributing to the risk of chronic lung allograft dysfunction (CLAD). Each major class of infection-(1) bacterial (Staphylococcus aureus and Pseudomonas aeruginosa); (2) viral (cytomegalovirus and community-acquired respiratory viruses); and (3) fungal (Aspergillus)-has been associated with the development of CLAD. Mechanistically, the microbe seems to be interacting with the allograft cells, stimulating the induction of chemokines, which recruit recipient leukocytes to the graft. The recipient leukocyte interactions with the microbe further up-regulate chemokines, amplifying the influx of allograft-infiltrating mononuclear cells. These events can promote recipient leukocytes to interact with the allograft, triggering an alloresponse and graft dysfunction. Overall, interactions between the microbe-allograft-host immune system alters chemokine production, which, in part, plays a role in the pathobiology of CLAD and mortality due to CLAD.

Various antibiotic alternative strategies to reduce pathogen-induced inflammation and to maintain gut homeostasis in broiler chickens

USDA-ARS?s Scientific Manuscript database

The gut represents a continuously evolving ecosystem consisting of trillions of commensal bacteria living in symbiosis with the host. This host-microbe interplay plays a crucial role in physiological development and health of the host. There is increasing evidence that shows a dynamic interaction b...

Modulation of host cell biology by plant pathogenic microbes.

PubMed

Le Fevre, Ruth; Evangelisti, Edouard; Rey, Thomas; Schornack, Sebastian

2015-01-01

Plant-pathogen interactions can result in dramatic visual changes in the host, such as galls, phyllody, pseudoflowers, and altered root-system architecture, indicating that the invading microbe has perturbed normal plant growth and development. These effects occur on a cellular level but range up to the organ scale, and they commonly involve attenuation of hormone homeostasis and deployment of effector proteins with varying activities to modify host cell processes. This review focuses on the cellular-reprogramming mechanisms of filamentous and bacterial plant pathogens that exhibit a biotrophic lifestyle for part, if not all, of their lifecycle in association with the host. We also highlight strategies for exploiting our growing knowledge of microbial host reprogramming to study plant processes other than immunity and to explore alternative strategies for durable plant resistance.

Cross-regulatory circuit between AHR and microbiota.

PubMed

Ji, Jian; Qu, Hao

2018-01-29

The gut microbes have a close symbiotic relationship with their host. Interactions between host and the microbiota affect the nutritional, immunological, and physiological status of the host. The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that mediates the toxicity of xenobiotics. Recently, the relationship between the gut microbiota and AHR has attracted the attention of many researchers. The AHR influences the intestinal microbiota population and mediates host-microbe homeostasis. Interestingly, the gut microbiota also produces ligands of AHR from bacterial metabolism and thereby activates the AHR signaling pathway. This review presents current knowledge of the cross-regulatory circuit between the AHR and intestinal microbiota. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Incorporating the gut microbiota into models of human and non-human primate ecology and evolution.

PubMed

Amato, Katherine R

2016-01-01

The mammalian gut is home to a diverse community of microbes. Advances in technology over the past two decades have allowed us to examine this community, the gut microbiota, in more detail, revealing a wide range of influences on host nutrition, health, and behavior. These host-gut microbe interactions appear to shape host plasticity and fitness in a variety of contexts, and therefore represent a key factor missing from existing models of human and non-human primate ecology and evolution. However, current studies of the gut microbiota tend to include limited contextual data or are clinical, making it difficult to directly test broad anthropological hypotheses. Here, I review what is known about the animal gut microbiota and provide examples of how gut microbiota research can be integrated into the study of human and non-human primate ecology and evolution with targeted data collection. Specifically, I examine how the gut microbiota may impact primate diet, energetics, disease resistance, and cognition. While gut microbiota research is proliferating rapidly, especially in the context of humans, there remain important gaps in our understanding of host-gut microbe interactions that will require an anthropological perspective to fill. Likewise, gut microbiota research will be an important tool for filling remaining gaps in anthropological research. © 2016 Wiley Periodicals, Inc.

Teleosts as Model Organisms To Understand Host-Microbe Interactions.

PubMed

Lescak, Emily A; Milligan-Myhre, Kathryn C

2017-08-01

Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis. Copyright © 2017 Lescak and Milligan-Myhre.

Teleosts as Model Organisms To Understand Host-Microbe Interactions

PubMed Central

2017-01-01

ABSTRACT Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis. PMID:28439034

AMP: Assembly Matching Pursuit.

PubMed

Biswas, S; Jojic, V

2013-01-01

Metagenomics, the study of the total genetic material isolated from a biological host, promises to reveal host-microbe or microbe-microbe interactions that may help to personalize medicine or improve agronomic practice. We introduce a method that discovers metagenomic units (MGUs) relevant for phenotype prediction through sequence-based dictionary learning. The method aggregates patient-specific dictionaries and estimates MGU abundances in order to summarize a whole population and yield universally predictive biomarkers. We analyze the impact of Gaussian, Poisson, and Negative Binomial read count models in guiding dictionary construction by examining classification efficiency on a number of synthetic datasets and a real dataset from Ref. 1. Each outperforms standard methods of dictionary composition, such as random projection and orthogonal matching pursuit. Additionally, the predictive MGUs they recover are biologically relevant.

Modulating airway defenses against microbes.

PubMed

Reynolds, Herbert Y

2002-05-01

Prevention and treatment of respiratory infections remain an important health care challenge as the US population ages, contains more susceptible or high-risk people, and encounters new pathogens or antibiotic resistant bacteria. Reasonably protective vaccines against very common microbes are available for childhood and adult immunization, but, generally, these are underutilized. A broader definition of higher risk individuals is evolving, which will include more for immunization. Different approaches to vaccine development through design of new component vaccines are necessary. This review has updated host defense mechanisms at three levels in the human respiratory tract: naso-oropharynx (upper airways), conducting airways, and alveolar space. Examples of representative pathogenic microbes have been inserted at the respective airway segment where they may colonize or create infection (influenza, measles virus, Porphyromonas gingivalis causing periodontitis, Bordetella pertussis, Chlamydia pneumoniae, Streptococcus pneumoniae, and Bacillus anthracis ). Hopefully, microbe-host interactions will suggest new approaches for preventing these kinds of infections.

Pattern Recognition Receptors in Innate Immunity, Host Defense, and Immunopathology

ERIC Educational Resources Information Center

Suresh, Rahul; Mosser, David M.

2013-01-01

Infection by pathogenic microbes initiates a set of complex interactions between the pathogen and the host mediated by pattern recognition receptors. Innate immune responses play direct roles in host defense during the early stages of infection, and they also exert a profound influence on the generation of the adaptive immune responses that ensue.…

Pseudomonas sax genes overcome aliphatic isothiocyanate-mediated non-host resistance in Arabidopsis

Treesearch

Jun Fan; Casey Crooks; Gary Creissen; Lionel Hill; Shirley Fairhurst; Peter Doerner; Chris Lamb

2011-01-01

Most plant-microbe interactions do not result in disease; natural products restrict non-host pathogens. We found that sulforaphane (4-methylsulfinylbutyl isothiocyanate), a natural product derived from aliphatic glucosinolates, inhibits growth in Arabidopsis of non-host Pseudomonas bacteria in planta. Multiple sax genes (saxCAB/F/D/G) were identified in Pseudomonas...

Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium

PubMed Central

Hill, David R; Huang, Sha; Nagy, Melinda S; Yadagiri, Veda K; Fields, Courtney; Mukherjee, Dishari; Bons, Brooke; Dedhia, Priya H; Chin, Alana M; Tsai, Yu-Hwai; Thodla, Shrikar; Schmidt, Thomas M; Walk, Seth

2017-01-01

The human gastrointestinal tract is immature at birth, yet must adapt to dramatic changes such as oral nutrition and microbial colonization. The confluence of these factors can lead to severe inflammatory disease in premature infants; however, investigating complex environment-host interactions is difficult due to limited access to immature human tissue. Here, we demonstrate that the epithelium of human pluripotent stem-cell-derived human intestinal organoids is globally similar to the immature human epithelium and we utilize HIOs to investigate complex host-microbe interactions in this naive epithelium. Our findings demonstrate that the immature epithelium is intrinsically capable of establishing a stable host-microbe symbiosis. Microbial colonization leads to complex contact and hypoxia driven responses resulting in increased antimicrobial peptide production, maturation of the mucus layer, and improved barrier function. These studies lay the groundwork for an improved mechanistic understanding of how colonization influences development of the immature human intestine. PMID:29110754

Models of microbiome evolution incorporating host and microbial selection.

PubMed

Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

2017-09-25

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong parental contribution, when host-mediated selection acts on microbes concomitantly. We present a computational framework that integrates different selective processes acting on the evolution of microbiomes. Our framework demonstrates that selection acting on microbes can have a strong effect on microbial diversities and fitnesses, whereas selection on hosts can have weaker outcomes.

Where simplicity meets complexity: hydra, a model for host-microbe interactions.

PubMed

Augustin, René; Fraune, Sebastian; Franzenburg, Sören; Bosch, Thomas C G

2012-01-01

For a long time, the main purpose of microbiology and immunology was to study pathogenic bacteria and infectious disease; the potential benefit of commensal bacteria remained unrecognised. Discovering that individuals from Hydra to man are not solitary, homogenous entities but consist of complex communities of many species that likely evolved during a billion years of coexistence (Fraune and Bosch 2010) led to the hologenome theory of evolution (Zilber-Rosenberg and Rosenberg 2008) which considers the holobiont with its hologenome as the unit of selection in evolution. Defining the individual microbe-host conversations in these consortia is a challenging but necessary step on the path to understanding the function of the associations as a whole. Untangling the complex interactions requires simple animal models with only a few specific bacterial species. Such models can function as living test tubes and may be key to dissecting the fundamental principles that underlie all host-microbe interactions. Here we introduce Hydra (Bosch et al. 2009) as such a model with one of the simplest epithelia in the animal kingdom (only two cell layers), with few cell types derived from only three distinct stem cell lineages, and with the availability of a fully sequenced genome and numerous genomic tools including transgenesis. Recognizing the entire system with its inputs, outputs and the interconnections (Fraune and Bosch 2010; Bosch et al. 2009; Fraune and Bosch 2007; Fraune et al. 2009a) we here present observations which may have profound impact on understanding a strictly microbe-dependent life style and its evolutionary consequences.

Evolution of microbial markets.

PubMed

Werner, Gijsbert D A; Strassmann, Joan E; Ivens, Aniek B F; Engelmoer, Daniel J P; Verbruggen, Erik; Queller, David C; Noë, Ronald; Johnson, Nancy Collins; Hammerstein, Peter; Kiers, E Toby

2014-01-28

Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions.

Evolution of microbial markets

PubMed Central

Werner, Gijsbert D. A.; Strassmann, Joan E.; Ivens, Aniek B. F.; Engelmoer, Daniel J. P.; Verbruggen, Erik; Queller, David C.; Noë, Ronald; Johnson, Nancy Collins; Hammerstein, Peter; Kiers, E. Toby

2014-01-01

Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions. PMID:24474743

Three-dimensional visualization and a deep-learning model reveal complex fungal parasite networks in behaviorally manipulated ants

PubMed Central

Fredericksen, Maridel A.; Zhang, Yizhe; Hazen, Missy L.; Loreto, Raquel G.; Mangold, Colleen A.; Chen, Danny Z.; Hughes, David P.

2017-01-01

Some microbes possess the ability to adaptively manipulate host behavior. To better understand how such microbial parasites control animal behavior, we examine the cell-level interactions between the species-specific fungal parasite Ophiocordyceps unilateralis sensu lato and its carpenter ant host (Camponotus castaneus) at a crucial moment in the parasite’s lifecycle: when the manipulated host fixes itself permanently to a substrate by its mandibles. The fungus is known to secrete tissue-specific metabolites and cause changes in host gene expression as well as atrophy in the mandible muscles of its ant host, but it is unknown how the fungus coordinates these effects to manipulate its host’s behavior. In this study, we combine techniques in serial block-face scanning-electron microscopy and deep-learning–based image segmentation algorithms to visualize the distribution, abundance, and interactions of this fungus inside the body of its manipulated host. Fungal cells were found throughout the host body but not in the brain, implying that behavioral control of the animal body by this microbe occurs peripherally. Additionally, fungal cells invaded host muscle fibers and joined together to form networks that encircled the muscles. These networks may represent a collective foraging behavior of this parasite, which may in turn facilitate host manipulation. PMID:29114054

Talking microbes: When gut bacteria interact with diet and host organs

PubMed Central

Everard, Amandine

2016-01-01

Obesity and diabetes have reached epidemic proportions. Evidence suggests that besides dietary habits and physical activity, other environmental factors, such as gut microbes, are recognized as additional partners implicated in the control of energy homeostasis. Studies on the human gut microbiota have shown that the general population can be stratified on the sole basis of three dominant bacteria (i.e., the concept of enterotypes), while some others have suggested categorizing the population according to their microbiome gene richness. Both aspects have been strengthened by recent studies investigating the impact of nutrients (e.g., dietary fibers, fat feeding) and dietary habits (i.e., vegans versus omnivores) of different populations. Using preclinical models, quite a few novel mechanisms have been proposed in these gut microbiota–host interactions, including the role of novel bacteria, the regulation of antimicrobial peptide production, the maintenance of the gut barrier function and intestinal innate immunity. In this review, we discuss several of the aforementioned aspects. Nonetheless, determining the overall mechanisms by which microbes dialogue with host cells will require further investigations before anticipating the development of next‐generation nutritional interventions using prebiotics, probiotics, synbiotics, or even specific nutrients for promoting health benefits. PMID:26178924

Cell-autonomous defense, re-organization and trafficking of membranes in plant-microbe interactions.

PubMed

Dörmann, Peter; Kim, Hyeran; Ott, Thomas; Schulze-Lefert, Paul; Trujillo, Marco; Wewer, Vera; Hückelhoven, Ralph

2014-12-01

Plant cells dynamically change their architecture and molecular composition following encounters with beneficial or parasitic microbes, a process referred to as host cell reprogramming. Cell-autonomous defense reactions are typically polarized to the plant cell periphery underneath microbial contact sites, including de novo cell wall biosynthesis. Alternatively, host cell reprogramming converges in the biogenesis of membrane-enveloped compartments for accommodation of beneficial bacteria or invasive infection structures of filamentous microbes. Recent advances have revealed that, in response to microbial encounters, plasma membrane symmetry is broken, membrane tethering and SNARE complexes are recruited, lipid composition changes and plasma membrane-to-cytoskeleton signaling is activated, either for pre-invasive defense or for microbial entry. We provide a critical appraisal on recent studies with a focus on how plant cells re-structure membranes and the associated cytoskeleton in interactions with microbial pathogens, nitrogen-fixing rhizobia and mycorrhiza fungi. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

The plastid genome as a platform for the expression of microbial resistance genes

USDA-ARS?s Scientific Manuscript database

In recent years, our fundamental understanding of host-microbe interaction has developed considerably. We have begun to tease out the genetic components that influence host resistance to microbial colonization. The use of advancing molecular technologies such as microarray expression profiling and...

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

DOE PAGES

Lin, Kuei -Han; Liao, Ben -Yang; Chang, Hao -Wei; ...

2015-12-03

Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted othermore » carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. In conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.« less

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Kuei -Han; Liao, Ben -Yang; Chang, Hao -Wei

Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted othermore » carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. In conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.« less

Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer.

PubMed

Yuan, Ce; Burns, Michael B; Subramanian, Subbaya; Blekhman, Ran

2018-01-01

Although variation in gut microbiome composition has been linked with colorectal cancer (CRC), the factors that mediate the interactions between CRC tumors and the microbiome are poorly understood. MicroRNAs (miRNAs) are known to regulate CRC progression and are associated with patient survival outcomes. In addition, recent studies suggested that host miRNAs can also regulate bacterial growth and influence the composition of the gut microbiome. Here, we investigated the association between miRNA expression and microbiome composition in human CRC tumor and normal tissues. We identified 76 miRNAs as differentially expressed (DE) in tissue from CRC tumors and normal tissue, including the known oncogenic miRNAs miR-182, miR-503, and mir-17~92 cluster. These DE miRNAs were correlated with the relative abundances of several bacterial taxa, including Firmicutes , Bacteroidetes , and Proteobacteria . Bacteria correlated with DE miRNAs were enriched with distinct predicted metabolic categories. Additionally, we found that miRNAs that correlated with CRC-associated bacteria are predicted to regulate targets that are relevant for host-microbiome interactions and highlight a possible role for miRNA-driven glycan production in the recruitment of pathogenic microbial taxa. Our work characterized a global relationship between microbial community composition and miRNA expression in human CRC tissues. IMPORTANCE Recent studies have found an association between colorectal cancer (CRC) and the gut microbiota. One potential mechanism by which the microbiota can influence host physiology is through affecting gene expression in host cells. MicroRNAs (miRNAs) are small noncoding RNA molecules that can regulate gene expression and have important roles in cancer development. Here, we investigated the link between the gut microbiota and the expression of miRNA in CRC. We found that dozens of miRNAs are differentially regulated in CRC tumors and adjacent normal colon and that these miRNAs are correlated with the abundance of microbes in the tumor microenvironment. Moreover, we found that microbes that have been previously associated with CRC are correlated with miRNAs that regulate genes related to interactions with microbes. Notably, these miRNAs likely regulate glycan production, which is important for the recruitment of pathogenic microbial taxa to the tumor. This work provides a first systems-level map of the association between microbes and host miRNAs in the context of CRC and provides targets for further experimental validation and potential interventions.

Parasite-Microbiota Interactions With the Vertebrate Gut: Synthesis Through an Ecological Lens

PubMed Central

Leung, Jacqueline M.; Graham, Andrea L.; Knowles, Sarah C. L.

2018-01-01

The vertebrate gut teems with a large, diverse, and dynamic bacterial community that has pervasive effects on gut physiology, metabolism, and immunity. Under natural conditions, these microbes share their habitat with a similarly dynamic community of eukaryotes (helminths, protozoa, and fungi), many of which are well-known parasites. Both parasites and the prokaryotic microbiota can dramatically alter the physical and immune landscape of the gut, creating ample opportunities for them to interact. Such interactions may critically alter infection outcomes and affect overall host health and disease. For instance, parasite infection can change how a host interacts with its bacterial flora, either driving or protecting against dysbiosis and inflammatory disease. Conversely, the microbiota can alter a parasite's colonization success, replication, and virulence, shifting it along the parasitism-mutualism spectrum. The mechanisms and consequences of these interactions are just starting to be elucidated in an emergent transdisciplinary area at the boundary of microbiology and parasitology. However, heterogeneity in experimental designs, host and parasite species, and a largely phenomenological and taxonomic approach to synthesizing the literature have meant that common themes across studies remain elusive. Here, we use an ecological perspective to review the literature on interactions between the prokaryotic microbiota and eukaryotic parasites in the vertebrate gut. Using knowledge about parasite biology and ecology, we discuss mechanisms by which they may interact with gut microbes, the consequences of such interactions for host health, and how understanding parasite-microbiota interactions may lead to novel approaches in disease control. PMID:29867790

Parasite-Microbiota Interactions With the Vertebrate Gut: Synthesis Through an Ecological Lens.

PubMed

Leung, Jacqueline M; Graham, Andrea L; Knowles, Sarah C L

2018-01-01

The vertebrate gut teems with a large, diverse, and dynamic bacterial community that has pervasive effects on gut physiology, metabolism, and immunity. Under natural conditions, these microbes share their habitat with a similarly dynamic community of eukaryotes (helminths, protozoa, and fungi), many of which are well-known parasites. Both parasites and the prokaryotic microbiota can dramatically alter the physical and immune landscape of the gut, creating ample opportunities for them to interact. Such interactions may critically alter infection outcomes and affect overall host health and disease. For instance, parasite infection can change how a host interacts with its bacterial flora, either driving or protecting against dysbiosis and inflammatory disease. Conversely, the microbiota can alter a parasite's colonization success, replication, and virulence, shifting it along the parasitism-mutualism spectrum. The mechanisms and consequences of these interactions are just starting to be elucidated in an emergent transdisciplinary area at the boundary of microbiology and parasitology. However, heterogeneity in experimental designs, host and parasite species, and a largely phenomenological and taxonomic approach to synthesizing the literature have meant that common themes across studies remain elusive. Here, we use an ecological perspective to review the literature on interactions between the prokaryotic microbiota and eukaryotic parasites in the vertebrate gut. Using knowledge about parasite biology and ecology, we discuss mechanisms by which they may interact with gut microbes, the consequences of such interactions for host health, and how understanding parasite-microbiota interactions may lead to novel approaches in disease control.

Genomics and Health Impact Update

MedlinePlus

... Antimicrobial Resistance Detection/ Diagnosis Epidemiology/ Outbreaks/ Transmission Antimicrobials/ Vaccines/ Interventions Host-Microbe Interactions Updates on Specific Diseases Alzheimer’s Disease Autism Blood Diseases Breast Cancer Cancer Cardiomyopathy Colorectal Cancer ...

An Aphid Effector Targets Trafficking Protein VPS52 in a Host-Specific Manner to Promote Virulence1[OPEN

PubMed Central

2017-01-01

Plant- and animal-feeding insects secrete saliva inside their hosts, containing effectors, which may promote nutrient release and suppress immunity. Although for plant pathogenic microbes it is well established that effectors target host proteins to modulate host cell processes and promote disease, the host cell targets of herbivorous insects remain elusive. Here, we show that the existing plant pathogenic microbe effector paradigm can be extended to herbivorous insects in that effector-target interactions inside host cells modify critical host processes to promote plant susceptibility. We showed that the effector Mp1 from Myzus persicae associates with the host Vacuolar Protein Sorting Associated Protein52 (VPS52). Using natural variants, we provide a strong link between effector virulence activity and association with VPS52, and show that the association is highly specific to M. persicae-host interactions. Also, coexpression of Mp1, but not Mp1-like variants, specifically with host VPS52s resulted in effector relocalization to vesicle-like structures that associate with prevacuolar compartments. We show that high VPS52 levels negatively impact virulence, and that aphids are able to reduce VPS52 levels during infestation, indicating that VPS52 is an important virulence target. Our work is an important step forward in understanding, at the molecular level, how a major agricultural pest promotes susceptibility during infestation of crop plants. We give evidence that an herbivorous insect employs effectors that interact with host proteins as part of an effective virulence strategy, and that these effectors likely function in a species-specific manner. PMID:28100451

Protein interaction networks at the host-microbe interface in Diaphorina citri, the insect vector of the citrus greening pathogen.

PubMed

Ramsey, J S; Chavez, J D; Johnson, R; Hosseinzadeh, S; Mahoney, J E; Mohr, J P; Robison, F; Zhong, X; Hall, D G; MacCoss, M; Bruce, J; Cilia, M

2017-02-01

The Asian citrus psyllid ( Diaphorina citri) is the insect vector responsible for the worldwide spread of ' Candidatus Liberibacter asiaticus' (CLas), the bacterial pathogen associated with citrus greening disease. Developmental changes in the insect vector impact pathogen transmission, such that D. citri transmission of CLas is more efficient when bacteria are acquired by nymphs when compared with adults. We hypothesize that expression changes in the D. citri immune system and commensal microbiota occur during development and regulate vector competency. In support of this hypothesis, more proteins, with greater fold changes, were differentially expressed in response to CLas in adults when compared with nymphs, including insect proteins involved in bacterial adhesion and immunity. Compared with nymphs, adult insects had a higher titre of CLas and the bacterial endosymbionts Wolbachia, Profftella and Carsonella. All Wolbachia and Profftella proteins differentially expressed between nymphs and adults are upregulated in adults, while most differentially expressed Carsonella proteins are upregulated in nymphs. Discovery of protein interaction networks has broad applicability to the study of host-microbe relationships. Using protein interaction reporter technology, a D. citri haemocyanin protein highly upregulated in response to CLas was found to physically interact with the CLas coenzyme A (CoA) biosynthesis enzyme phosphopantothenoylcysteine synthetase/decarboxylase. CLas pantothenate kinase, which catalyses the rate-limiting step of CoA biosynthesis, was found to interact with a D. citri myosin protein. Two Carsonella enzymes involved in histidine and tryptophan biosynthesis were found to physically interact with D. citri proteins. These co-evolved protein interaction networks at the host-microbe interface are highly specific targets for controlling the insect vector responsible for the spread of citrus greening.

Interactions between Drosophila and its natural yeast symbionts-Is Saccharomyces cerevisiae a good model for studying the fly-yeast relationship?

PubMed

Hoang, Don; Kopp, Artyom; Chandler, James Angus

2015-01-01

Yeasts play an important role in the biology of the fruit fly, Drosophila melanogaster. In addition to being a valuable source of nutrition, yeasts affect D. melanogaster behavior and interact with the host immune system. Most experiments investigating the role of yeasts in D. melanogaster biology use the baker's yeast, Saccharomyces cerevisiae. However, S. cerevisiae is rarely found with natural populations of D. melanogaster or other Drosophila species. Moreover, the strain of S. cerevisiae used most often in D. melanogaster experiments is a commercially and industrially important strain that, to the best of our knowledge, was not isolated from flies. Since disrupting natural host-microbe interactions can have profound effects on host biology, the results from D. melanogaster-S. cerevisiae laboratory experiments may not be fully representative of host-microbe interactions in nature. In this study, we explore the D. melanogaster-yeast relationship using five different strains of yeast that were isolated from wild Drosophila populations. Ingested live yeasts have variable persistence in the D. melanogaster gastrointestinal tract. For example, Hanseniaspora occidentalis persists relative to S. cerevisiae, while Brettanomyces naardenensis is removed. Despite these differences in persistence relative to S. cerevisiae, we find that all yeasts decrease in total abundance over time. Reactive oxygen species (ROS) are an important component of the D. melanogaster anti-microbial response and can inhibit S. cerevisiae growth in the intestine. To determine if sensitivity to ROS explains the differences in yeast persistence, we measured yeast growth in the presence and absence of hydrogen peroxide. We find that B. naardenesis is completely inhibited by hydrogen peroxide, while H. occidentalis is not, which is consistent with yeast sensitivity to ROS affecting persistence within the D. melanogaster gastrointestinal tract. We also compared the feeding preference of D. melanogaster when given the choice between a naturally associated yeast and S. cerevisiae. We do not find a correlation between preferred yeasts and those that persist in the intestine. Notably, in no instances is S. cerevisiae preferred over the naturally associated strains. Overall, our results show that D. melanogaster-yeast interactions are more complex than might be revealed in experiments that use only S. cerevisiae. We propose that future research utilize other yeasts, and especially those that are naturally associated with Drosophila, to more fully understand the role of yeasts in Drosophila biology. Since the genetic basis of host-microbe interactions is shared across taxa and since many of these genes are initially discovered in D. melanogaster, a more realistic fly-yeast model system will benefit our understanding of host-microbe interactions throughout the animal kingdom.

Microbiota transplantation: concept, methodology and strategy for its modernization.

PubMed

Zhang, Faming; Cui, Bota; He, Xingxiang; Nie, Yuqiang; Wu, Kaichun; Fan, Daiming

2018-05-01

Fecal microbiota transplantation (FMT) has become a research focus of biomedicine and clinical medicine in recent years. The clinical response from FMT for different diseases provided evidence for microbiota-host interactions associated with various disorders, including Clostridium difficile infection, inflammatory bowel disease, diabetes mellitus, cancer, liver cirrhosis, gut-brain disease and others. To discuss the experiences of using microbes to treat human diseases from ancient China to current era should be important in moving standardized FMT forward and achieving a better future. Here, we review the changing concept of microbiota transplantation from FMT to selective microbiota transplantation, methodology development of FMT and step-up FMT strategy based on literature and state experts' perspectives.

Modulation of host immunity by beneficial microbes.

PubMed

Zamioudis, Christos; Pieterse, Corné M J

2012-02-01

In nature, plants abundantly form beneficial associations with soilborne microbes that are important for plant survival and, as such, affect plant biodiversity and ecosystem functioning. Classical examples of symbiotic microbes are mycorrhizal fungi that aid in the uptake of water and minerals, and Rhizobium bacteria that fix atmospheric nitrogen for the plant. Several other types of beneficial soilborne microbes, such as plant-growth-promoting rhizobacteria and fungi with biological control activity, can stimulate plant growth by directly suppressing deleterious soilborne pathogens or by priming aboveground plant parts for enhanced defense against foliar pathogens or insect herbivores. The establishment of beneficial associations requires mutual recognition and substantial coordination of plant and microbial responses. A growing body of evidence suggests that beneficial microbes are initially recognized as potential invaders, after which an immune response is triggered, whereas, at later stages of the interaction, mutualists are able to short-circuit plant defense responses to enable successful colonization of host roots. Here, we review our current understanding of how symbiotic and nonsymbiotic beneficial soil microbes modulate the plant immune system and discuss the role of local and systemic defense responses in establishing the delicate balance between the two partners.

Skin microbiome: genomics-based insights into the diversity and role of skin microbes

PubMed Central

Kong, Heidi H.

2011-01-01

Recent advances in DNA sequencing methodology have enabled studies of human skin microbes that circumvent difficulties in isolating and characterizing fastidious microbes. Sequence-based approaches have identified greater diversity of cutaneous bacteria than studies using traditional cultivation techniques. However, improved sequencing technologies and analytical methods are needed to study all skin microbes, including bacteria, archaea, fungi, viruses, and mites, and how they interact with each other and their human hosts. This review discusses current skin microbiome research, with a primary focus on bacteria, and the challenges facing investigators striving to understand how skin micro-organisms contribute to health and disease. PMID:21376666

Antivirulence Activity of the Human Gut Metabolome

PubMed Central

Antunes, L. Caetano M.; McDonald, Julie A. K.; Schroeter, Kathleen; Carlucci, Christian; Ferreira, Rosana B. R.; Wang, Melody; Yurist-Doutsch, Sophie; Hira, Gill; Jacobson, Kevan; Davies, Julian; Allen-Vercoe, Emma

2014-01-01

ABSTRACT The mammalian gut contains a complex assembly of commensal microbes termed microbiota. Although much has been learned about the role of these microbes in health, the mechanisms underlying these functions are ill defined. We have recently shown that the mammalian gut contains thousands of small molecules, most of which are currently unidentified. Therefore, we hypothesized that these molecules function as chemical cues used by hosts and microbes during their interactions in health and disease. Thus, a search was initiated to identify molecules produced by the microbiota that are sensed by pathogens. We found that a secreted molecule produced by clostridia acts as a strong repressor of Salmonella virulence, obliterating expression of the Salmonella pathogenicity island 1 as well as host cell invasion. It has been known for decades that the microbiota protects its hosts from invading pathogens, and these data suggest that chemical sensing may be involved in this phenomenon. Further investigations should reveal the exact biological role of this molecule as well as its therapeutic potential. PMID:25073640

Quantitative Imaging of Gut Microbiota Spatial Organization

PubMed Central

Earle, Kristen A.; Billings, Gabriel; Sigal, Michael; Lichtman, Joshua S.; Hansson, Gunnar C.; Elias, Joshua E.; Amieva, Manuel R.; Huang, Kerwyn Casey; Sonnenburg, Justin L.

2015-01-01

Summary Genomic technologies have significantly advanced our understanding of the composition and diversity of host-associated microbial populations. However, their spatial organization and functional interactions relative to the host have been more challenging to study. Here we present a pipeline for the assessment of intestinal microbiota localization within immunofluorescence images of fixed gut cross-sections that includes a flexible software package, BacSpace, for high-throughput quantification of microbial organization. Applying this pipeline to gnotobiotic and human microbiota-colonized mice, we demonstrate that elimination of microbiota accessible carbohydrates (MACs) from the diet results in thinner mucus in the distal colon, increased proximity of microbes to the epithelium, and heightened expression of the inflammatory marker REG3β. Measurements of microbe-microbe proximity reveal that a MAC-deficient diet alters monophyletic spatial clustering. Furthermore, we quantify the invasion of Helicobacter pylori into the glands of the mouse stomach relative to host mitotic progenitor cells, illustrating the generalizability of this approach. PMID:26439864

Lipopolysaccharides in diazotrophic bacteria.

PubMed

Serrato, Rodrigo V

2014-01-01

Biological nitrogen fixation (BNF) is a process in which the atmospheric nitrogen (N2) is transformed into ammonia (NH3) by a select group of nitrogen-fixing organisms, or diazotrophic bacteria. In order to furnish the biologically useful nitrogen to plants, these bacteria must be in constant molecular communication with their host plants. Some of these molecular plant-microbe interactions are very specific, resulting in a symbiotic relationship between the diazotroph and the host. Others are found between associative diazotrophs and plants, resulting in plant infection and colonization of internal tissues. Independent of the type of ecological interaction, glycans, and glycoconjugates produced by these bacteria play an important role in the molecular communication prior and during colonization. Even though exopolysaccharides (EPS) and lipochitooligosaccharides (LCO) produced by diazotrophic bacteria and released onto the environment have their importance in the microbe-plant interaction, it is the lipopolysaccharides (LPS), anchored on the external membrane of these bacteria, that mediates the direct contact of the diazotroph with the host cells. These molecules are extremely variable among the several species of nitrogen fixing-bacteria, and there are evidences of the mechanisms of infection being closely related to their structure.

Microbial Interactions in Plants: Perspectives and Applications of Proteomics.

PubMed

Imam, Jahangir; Shukla, Pratyoosh; Mandal, Nimai Prasad; Variar, Mukund

2017-01-01

The structure and function of proteins involved in plant-microbe interactions is investigated through large-scale proteomics technology in a complex biological sample. Since the whole genome sequences are now available for several plant species and microbes, proteomics study has become easier, accurate and huge amount of data can be generated and analyzed during plant-microbe interactions. Proteomics approaches are highly important and relevant in many studies and showed that only genomics approaches are not sufficient enough as much significant information are lost as the proteins and not the genes coding them are final product that is responsible for the observed phenotype. Novel approaches in proteomics are developing continuously enabling the study of the various aspects in arrangements and configuration of proteins and its functions. Its application is becoming more common and frequently used in plant-microbe interactions with the advancement in new technologies. They are more used for the portrayal of cell and extracellular destructiveness and pathogenicity variables delivered by pathogens. This distinguishes the protein level adjustments in host plants when infected with pathogens and advantageous partners. This review provides a brief overview of different proteomics technology which is currently available followed by their exploitation to study the plant-microbe interaction. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Host-rumen microbe interactions may be leveraged to improve the productivity of dairy cows

USDA-ARS?s Scientific Manuscript database

The cattle rumen serves as a digestive bioreactor for the dairy cow, yet our knowledge of the microbial contents, ecology, and host selection within the rumen is only precursory. This is despite the knowledge that the volatile fatty acids (VFA) and microbial crude protein (MCP) produced by rumen mic...

The role of lipids in host microbe interactions.

PubMed

Lang, Roland; Mattner, Jochen

2017-06-01

Lipids are one of the major subcellular constituents and serve as signal molecules, energy sources, metabolic precursors and structural membrane components in various organisms. The function of lipids can be modified by multiple biochemical processes such as (de-)phosphorylation or (de-)glycosylation, and the organization of fatty acids into distinct cellular pools and subcellular compartments plays a pivotal role for the morphology and function of various cell populations. Thus, lipids regulate, for example, phagosome formation and maturation within host cells and thus, are critical for the elimination of microbial pathogens. Vice versa, microbial pathogens can manipulate the lipid composition of phagosomal membranes in host cells, and thus avoid their delivery to phagolysosomes. Lipids of microbial origin belong also to the strongest and most versatile inducers of mammalian immune responses upon engagement of distinct receptors on myeloid and lymphoid cells. Furthermore, microbial lipid toxins can induce membrane injuries and cell death. Thus, we will review here selected examples for mutual host-microbe interactions within the broad and divergent universe of lipids in microbial defense, tissue injury and immune evasion.

Cross Talk: The Microbiota and Neurodevelopmental Disorders

PubMed Central

Kelly, John R.; Minuto, Chiara; Cryan, John F.; Clarke, Gerard; Dinan, Timothy G.

2017-01-01

Humans evolved within a microbial ecosystem resulting in an interlinked physiology. The gut microbiota can signal to the brain via the immune system, the vagus nerve or other host-microbe interactions facilitated by gut hormones, regulation of tryptophan metabolism and microbial metabolites such as short chain fatty acids (SCFA), to influence brain development, function and behavior. Emerging evidence suggests that the gut microbiota may play a role in shaping cognitive networks encompassing emotional and social domains in neurodevelopmental disorders. Drawing upon pre-clinical and clinical evidence, we review the potential role of the gut microbiota in the origins and development of social and emotional domains related to Autism spectrum disorders (ASD) and schizophrenia. Small preliminary clinical studies have demonstrated gut microbiota alterations in both ASD and schizophrenia compared to healthy controls. However, we await the further development of mechanistic insights, together with large scale longitudinal clinical trials, that encompass a systems level dimensional approach, to investigate whether promising pre-clinical and initial clinical findings lead to clinical relevance. PMID:28966571

Volatile affairs in microbial interactions

PubMed Central

Schmidt, Ruth; Cordovez, Viviane; de Boer, Wietse; Raaijmakers, Jos; Garbeva, Paolina

2015-01-01

Microorganisms are important factors in shaping our environment. One key characteristic that has been neglected for a long time is the ability of microorganisms to release chemically diverse volatile compounds. At present, it is clear that the blend of volatiles released by microorganisms can be very complex and often includes many unknown compounds for which the chemical structures remain to be elucidated. The biggest challenge now is to unravel the biological and ecological functions of these microbial volatiles. There is increasing evidence that microbial volatiles can act as infochemicals in interactions among microbes and between microbes and their eukaryotic hosts. Here, we review and discuss recent advances in understanding the natural roles of volatiles in microbe–microbe interactions. Specific emphasis will be given to the antimicrobial activities of microbial volatiles and their effects on bacterial quorum sensing, motility, gene expression and antibiotic resistance. PMID:26023873

Noisy neighbourhoods: quorum sensing in fungal–polymicrobial infections

PubMed Central

Dixon, Emily F.

2015-01-01

Summary Quorum sensing was once considered a way in which a species was able to sense its cell density and regulate gene expression accordingly. However, it is now becoming apparent that multiple microbes can sense particular quorum‐sensing molecules, enabling them to sense and respond to other microbes in their neighbourhood. Such interactions are significant within the context of polymicrobial disease, in which the competition or cooperation of microbes can alter disease progression. Fungi comprise a small but important component of the human microbiome and are in constant contact with bacteria and viruses. The discovery of quorum‐sensing pathways in fungi has led to the characterization of a number of interkingdom quorum‐sensing interactions. Here, we review the recent developments in quorum sensing in medically important fungi, and the implications these interactions have on the host's innate immune response. PMID:26243526

An Aphid Effector Targets Trafficking Protein VPS52 in a Host-Specific Manner to Promote Virulence.

PubMed

Rodriguez, Patricia A; Escudero-Martinez, Carmen; Bos, Jorunn I B

2017-03-01

Plant- and animal-feeding insects secrete saliva inside their hosts, containing effectors, which may promote nutrient release and suppress immunity. Although for plant pathogenic microbes it is well established that effectors target host proteins to modulate host cell processes and promote disease, the host cell targets of herbivorous insects remain elusive. Here, we show that the existing plant pathogenic microbe effector paradigm can be extended to herbivorous insects in that effector-target interactions inside host cells modify critical host processes to promote plant susceptibility. We showed that the effector Mp1 from Myzus persicae associates with the host Vacuolar Protein Sorting Associated Protein52 (VPS52). Using natural variants, we provide a strong link between effector virulence activity and association with VPS52, and show that the association is highly specific to M persicae -host interactions. Also, coexpression of Mp1, but not Mp1-like variants, specifically with host VPS52s resulted in effector relocalization to vesicle-like structures that associate with prevacuolar compartments. We show that high VPS52 levels negatively impact virulence, and that aphids are able to reduce VPS52 levels during infestation, indicating that VPS52 is an important virulence target. Our work is an important step forward in understanding, at the molecular level, how a major agricultural pest promotes susceptibility during infestation of crop plants. We give evidence that an herbivorous insect employs effectors that interact with host proteins as part of an effective virulence strategy, and that these effectors likely function in a species-specific manner. © 2017 American Society of Plant Biologists. All Rights Reserved.

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

PubMed Central

Henderson, Gemma; Cox, Faith; Ganesh, Siva; Jonker, Arjan; Young, Wayne; Abecia, Leticia; Angarita, Erika; Aravena, Paula; Nora Arenas, Graciela; Ariza, Claudia; Attwood, Graeme T.; Mauricio Avila, Jose; Avila-Stagno, Jorge; Bannink, André; Barahona, Rolando; Batistotti, Mariano; Bertelsen, Mads F.; Brown-Kav, Aya; Carvajal, Andres M.; Cersosimo, Laura; Vieira Chaves, Alexandre; Church, John; Clipson, Nicholas; Cobos-Peralta, Mario A.; Cookson, Adrian L.; Cravero, Silvio; Cristobal Carballo, Omar; Crosley, Katie; Cruz, Gustavo; Cerón Cucchi, María; de la Barra, Rodrigo; De Menezes, Alexandre B.; Detmann, Edenio; Dieho, Kasper; Dijkstra, Jan; dos Reis, William L. S.; Dugan, Mike E. R.; Hadi Ebrahimi, Seyed; Eythórsdóttir, Emma; Nde Fon, Fabian; Fraga, Martín; Franco, Francisco; Friedeman, Chris; Fukuma, Naoki; Gagić, Dragana; Gangnat, Isabelle; Javier Grilli, Diego; Guan, Le Luo; Heidarian Miri, Vahideh; Hernandez-Sanabria, Emma; Gomez, Alma Ximena Ibarra; Isah, Olubukola A.; Ishaq, Suzanne; Jami, Elie; Jelincic, Juan; Kantanen, Juha; Kelly, William J.; Kim, Seon-Ho; Klieve, Athol; Kobayashi, Yasuo; Koike, Satoshi; Kopecny, Jan; Nygaard Kristensen, Torsten; Julie Krizsan, Sophie; LaChance, Hannah; Lachman, Medora; Lamberson, William R.; Lambie, Suzanne; Lassen, Jan; Leahy, Sinead C.; Lee, Sang-Suk; Leiber, Florian; Lewis, Eva; Lin, Bo; Lira, Raúl; Lund, Peter; Macipe, Edgar; Mamuad, Lovelia L.; Cuquetto Mantovani, Hilário; Marcoppido, Gisela Ariana; Márquez, Cristian; Martin, Cécile; Martinez, Gonzalo; Eugenia Martinez, Maria; Lucía Mayorga, Olga; McAllister, Tim A.; McSweeney, Chris; Mestre, Lorena; Minnee, Elena; Mitsumori, Makoto; Mizrahi, Itzhak; Molina, Isabel; Muenger, Andreas; Munoz, Camila; Murovec, Bostjan; Newbold, John; Nsereko, Victor; O’Donovan, Michael; Okunade, Sunday; O’Neill, Brendan; Ospina, Sonia; Ouwerkerk, Diane; Parra, Diana; Pereira, Luiz Gustavo Ribeiro; Pinares-Patino, Cesar; Pope, Phil B.; Poulsen, Morten; Rodehutscord, Markus; Rodriguez, Tatiana; Saito, Kunihiko; Sales, Francisco; Sauer, Catherine; Shingfield, Kevin; Shoji, Noriaki; Simunek, Jiri; Stojanović-Radić, Zorica; Stres, Blaz; Sun, Xuezhao; Swartz, Jeffery; Liang Tan, Zhi; Tapio, Ilma; Taxis, Tasia M.; Tomkins, Nigel; Ungerfeld, Emilio; Valizadeh, Reza; van Adrichem, Peter; Van Hamme, Jonathan; Van Hoven, Woulter; Waghorn, Garry; John Wallace, R.; Wang, Min; Waters, Sinéad M.; Keogh, Kate; Witzig, Maren; Wright, Andre-Denis G.; Yamano, Hidehisa; Yan, Tianhai; Yanez-Ruiz, David R.; Yeoman, Carl J.; Zambrano, Ricardo; Zeitz, Johanna; Zhou, Mi; Wei Zhou, Hua; Xia Zou, Cai; Zunino, Pablo; Janssen, Peter H.

2015-01-01

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific. PMID:26449758

Decoding molecular interactions in microbial communities

PubMed Central

Abreu, Nicole A.; Taga, Michiko E.

2016-01-01

Microbial communities govern numerous fundamental processes on earth. Discovering and tracking molecular interactions among microbes is critical for understanding how single species and complex communities impact their associated host or natural environment. While recent technological developments in DNA sequencing and functional imaging have led to new and deeper levels of understanding, we are limited now by our inability to predict and interpret the intricate relationships and interspecies dependencies within these communities. In this review, we highlight the multifaceted approaches investigators have taken within their areas of research to decode interspecies molecular interactions that occur between microbes. Understanding these principles can give us greater insight into ecological interactions in natural environments and within synthetic consortia. PMID:27417261

Ankyrin-repeat containing proteins of microbes: a conserved structure with functional diversity

PubMed Central

Al-Khodor, Souhaila; Price, Christopher T.; Kalia, Awdhesh; Kwaik, Yousef Abu

2009-01-01

Summary The ankyrin repeat (ANK) is the most common protein-protein interaction motif in nature and predominantly found in eukaryotic proteins. The genome sequencing of various pathogenic or symbiotic bacteria and eukaryotic viruses identified numerous genes encoding ANK-containing proteins that were proposed to have been acquired from eukaryotes by horizontal gene transfer. However, the recent discovery of additional ANK-containing proteins encoded in the genomes of archaea and free-living bacteria suggests either a more ancient origin of the ANK motif or multiple convergent evolution events. Many bacterial pathogens employ various types of secretion systems to deliver ANK-containing proteins into eukaryotic cells where they mimic or manipulate various host functions. Understanding the molecular and biochemical functions of this family of proteins will enhance our understanding of important host-microbe interactions. PMID:19962898

Homeostatic Immunity and the Microbiota.

PubMed

Belkaid, Yasmine; Harrison, Oliver J

2017-04-18

The microbiota plays a fundamental role in the induction, education, and function of the host immune system. In return, the host immune system has evolved multiple means by which to maintain its symbiotic relationship with the microbiota. The maintenance of this dialogue allows the induction of protective responses to pathogens and the utilization of regulatory pathways involved in the sustained tolerance to innocuous antigens. The ability of microbes to set the immunological tone of tissues, both locally and systemically, requires tonic sensing of microbes and complex feedback loops between innate and adaptive components of the immune system. Here we review the dominant cellular mediators of these interactions and discuss emerging themes associated with our current understanding of the homeostatic immunological dialogue between the host and its microbiota. Published by Elsevier Inc.

Homeostatic immunity and the microbiota

PubMed Central

Belkaid, Yasmine; Harrison, Oliver J.

2017-01-01

The microbiota plays a fundamental role in the induction, education and function of the host immune system. In return, the host immune system has evolved multiple means by which to maintain its symbiotic relationship with the microbiota. The maintenance of this dialogue allows the induction of protective responses to pathogens and the utilization of regulatory pathways involved in the sustained tolerance to innocuous antigens. The ability of microbes to set the immunological tone of tissues, both locally and systemically, requires tonic sensing of microbes and complex feedback loops between innate and adaptive components of the immune system. In this review, we will highlight the dominant cellular mediators of these interactions and discuss emerging themes associated with our current understanding of the homeostatic immunological dialogue between the host and its microbiota. PMID:28423337

Representing virus-host interactions and other multi-organism processes in the Gene Ontology.

PubMed

Foulger, R E; Osumi-Sutherland, D; McIntosh, B K; Hulo, C; Masson, P; Poux, S; Le Mercier, P; Lomax, J

2015-07-28

The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. The Gene Ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms. To address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology. Describing microbial and viral gene products brings with it the additional challenge of capturing both the host and the microbe. Recognising this, we have worked closely with annotation groups to test and optimize the GO classes, and we describe here a set of annotation guidelines that allow the controlled description of two interacting organisms. Building on the microbial resources already in existence such as ViralZone, UniProtKB keywords and MeGO, this project provides an integrated ontology to describe interactions between microbial species and their hosts, with mappings to the external resources above. Housing this information within the freely-accessible Gene Ontology project allows the classes and annotation structure to be utilized by a large community of biologists and users.

Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars.

PubMed

Chaturvedi, Samridhi; Rego, Alexandre; Lucas, Lauren K; Gompert, Zachariah

2017-09-12

Microbes can mediate insect-plant interactions and have been implicated in major evolutionary transitions to herbivory. Whether microbes also play a role in more modest host shifts or expansions in herbivorous insects is less clear. Here we evaluate the potential for gut microbial communities to constrain or facilitate host plant use in the Melissa blue butterfly (Lycaeides melissa). We conducted a larval rearing experiment where caterpillars from two populations were fed plant tissue from two hosts. We used 16S rRNA sequencing to quantify the relative effects of sample type (frass versus whole caterpillar), diet (plant species), butterfly population and development (caterpillar age) on the composition and diversity of the caterpillar gut microbial communities, and secondly, to test for a relationship between microbial community and larval performance. Gut microbial communities varied over time (that is, with caterpillar age) and differed between frass and whole caterpillar samples. Diet (host plant) and butterfly population had much more limited effects on microbial communities. We found no evidence that gut microbe community composition was associated with caterpillar weight, and thus, our results provide no support for the hypothesis that variation in microbial community affects performance in L. melissa.

Biotrophy at Its Best: Novel Findings and Unsolved Mysteries of the Arabidopsis-Powdery Mildew Pathosystem.

PubMed

Kuhn, Hannah; Kwaaitaal, Mark; Kusch, Stefan; Acevedo-Garcia, Johanna; Wu, Hongpo; Panstruga, Ralph

2016-01-01

It is generally accepted in plant-microbe interactions research that disease is the exception rather than a common outcome of pathogen attack. However, in nature, plants with symptoms that signify colonization by obligate biotrophic powdery mildew fungi are omnipresent. The pervasiveness of the disease and the fact that many economically important plants are prone to infection by powdery mildew fungi drives research on this interaction. The competence of powdery mildew fungi to establish and maintain true biotrophic relationships renders the interaction a paramount example of a pathogenic plant-microbe biotrophy. However, molecular details underlying the interaction are in many respects still a mystery. Since its introduction in 1990, the Arabidopsis-powdery mildew pathosystem has become a popular model to study molecular processes governing powdery mildew infection. Due to the many advantages that the host Arabidopsis offers in terms of molecular and genetic tools this pathosystem has great capacity to answer some of the questions of how biotrophic pathogens overcome plant defense and establish a persistent interaction that nourishes the invader while in parallel maintaining viability of the plant host.

Biotrophy at Its Best: Novel Findings and Unsolved Mysteries of the Arabidopsis-Powdery Mildew Pathosystem

PubMed Central

Kuhn, Hannah; Kwaaitaal, Mark; Kusch, Stefan; Acevedo-Garcia, Johanna; Wu, Hongpo; Panstruga, Ralph

2016-01-01

It is generally accepted in plant-microbe interactions research that disease is the exception rather than a common outcome of pathogen attack. However, in nature, plants with symptoms that signify colonization by obligate biotrophic powdery mildew fungi are omnipresent. The pervasiveness of the disease and the fact that many economically important plants are prone to infection by powdery mildew fungi drives research on this interaction. The competence of powdery mildew fungi to establish and maintain true biotrophic relationships renders the interaction a paramount example of a pathogenic plant-microbe biotrophy. However, molecular details underlying the interaction are in many respects still a mystery. Since its introduction in 1990, the Arabidopsis-powdery mildew pathosystem has become a popular model to study molecular processes governing powdery mildew infection. Due to the many advantages that the host Arabidopsis offers in terms of molecular and genetic tools this pathosystem has great capacity to answer some of the questions of how biotrophic pathogens overcome plant defense and establish a persistent interaction that nourishes the invader while in parallel maintaining viability of the plant host. PMID:27489521

Harnessing Host-Vector Microbiome for Sustainable Plant Disease Management of Phloem-Limited Bacteria.

PubMed

Trivedi, Pankaj; Trivedi, Chanda; Grinyer, Jasmine; Anderson, Ian C; Singh, Brajesh K

2016-01-01

Plant health and productivity is strongly influenced by their intimate interaction with deleterious and beneficial organisms, including microbes, and insects. Of the various plant diseases, insect-vectored diseases are of particular interest, including those caused by obligate parasites affecting plant phloem such as Candidatus ( Ca .) Phytoplasma species and several species of Ca. Liberibacter. Recent studies on plant-microbe and plant-insect interactions of these pathogens have demonstrated that plant-microbe-insect interactions have far reaching consequences for the functioning and evolution of the organisms involved. These interactions take place within complex pathosystems and are shaped by a myriad of biotic and abiotic factors. However, our current understanding of these processes and their implications for the establishment and spread of insect-borne diseases remains limited. This article highlights the molecular, ecological, and evolutionary aspects of interactions among insects, plants, and their associated microbial communities with a focus on insect vectored and phloem-limited pathogens belonging to Ca. Phytoplasma and Ca. Liberibacter species. We propose that innovative and interdisciplinary research aimed at linking scales from the cellular to the community level will be vital for increasing our understanding of the mechanisms underpinning plant-insect-microbe interactions. Examination of such interactions could lead us to applied solutions for sustainable disease and pest management.

Role of Osmolytes in Regulating Immune System.

PubMed

Kumar, Tarun; Yadav, Manisha; Singh, Laishram Rajendrakumar

2016-01-01

The immune system has evolved to protect the host organism from diverse range of pathogenic microbes that are themselves constantly evolving. It is a complex network of cells, humoral factors, chemokines and cytokines. Dysregulation of immune system results in various kinds of immunological disorders. There are several external agents which govern the regulation of immune system. Recent studies have indicated the role of osmolytes in regulation of various immunological processes such as Ag-Ab interaction, Ig assembly, Ag presentation etc. In this present review, we have systematically discussed the role of osmolytes involved in regulation of several key immunological processes. Osmolytes are involved in the regulation of several key immunological processes such as immunoglobulin assembly and folding, immune cells proliferation, regulation of immune cells function, Ag-Ab interaction, antigen presentation, inflammatory response and protection against photo-immunosuppression. Hence, osmolytes and their transporters might be used as potential drug and drug targets respectively. This review is therefore designed to help clinicians in development of osmolyte based therapeutic strategies in the treatment of various immunological disorders. Appropriate future perspectives have also been included.

Real-Time Sensing of Enteropathogenic E. coli-Induced Effects on Epithelial Host Cell Height, Cell-Substrate Interactions, and Endocytic Processes by Infrared Surface Plasmon Spectroscopy

PubMed Central

Zlotkin-Rivkin, Efrat; Rund, David; Melamed-Book, Naomi; Zahavi, Eitan Erez; Perlson, Eran; Mercone, Silvana; Golosovsky, Michael; Davidov, Dan; Aroeti, Benjamin

2013-01-01

Enteropathogenic Escherichia coli (EPEC) is an important, generally non-invasive, bacterial pathogen that causes diarrhea in humans. The microbe infects mainly the enterocytes of the small intestine. Here we have applied our newly developed infrared surface plasmon resonance (IR-SPR) spectroscopy approach to study how EPEC infection affects epithelial host cells. The IR-SPR experiments showed that EPEC infection results in a robust reduction in the refractive index of the infected cells. Assisted by confocal and total internal reflection microscopy, we discovered that the microbe dilates the intercellular gaps and induces the appearance of fluid-phase-filled pinocytic vesicles in the lower basolateral regions of the host epithelial cells. Partial cell detachment from the underlying substratum was also observed. Finally, the waveguide mode observed by our IR-SPR analyses showed that EPEC infection decreases the host cell's height to some extent. Together, these observations reveal novel impacts of the pathogen on the host cell architecture and endocytic functions. We suggest that these changes may induce the infiltration of a watery environment into the host cell, and potentially lead to failure of the epithelium barrier functions. Our findings also indicate the great potential of the label-free IR-SPR approach to study the dynamics of host-pathogen interactions with high spatiotemporal sensitivity. PMID:24194932

Carbohydrates and the human gut microbiota.

PubMed

Chassard, Christophe; Lacroix, Christophe

2013-07-01

Due to its scale and its important role in maintaining health, the gut microbiota can be considered as a 'new organ' inside the human body. Many complex carbohydrates are degraded and fermented by the human gut microbiota in the large intestine to both yield basic energy salvage and impact gut health through produced metabolites. This review will focus on the gut microbes and microbial mechanisms responsible for polysaccharides degradation and fermentation in the large intestine. Gut microbes and bacterial metabolites impact the host at many levels, including modulation of inflammation, and glucose and lipid metabolisms. A complex relationship occurs in the intestine between the human gut microbiota, diet and the host. Research on carbohydrates and gut microbiota composition and functionality is fast developing and will open opportunities for prevention and treatment of obesity, diabetes and other related metabolic disorders through manipulation of the gut ecosystem.

Lipopolysaccharides in diazotrophic bacteria

PubMed Central

Serrato, Rodrigo V.

2014-01-01

Biological nitrogen fixation (BNF) is a process in which the atmospheric nitrogen (N2) is transformed into ammonia (NH3) by a select group of nitrogen-fixing organisms, or diazotrophic bacteria. In order to furnish the biologically useful nitrogen to plants, these bacteria must be in constant molecular communication with their host plants. Some of these molecular plant-microbe interactions are very specific, resulting in a symbiotic relationship between the diazotroph and the host. Others are found between associative diazotrophs and plants, resulting in plant infection and colonization of internal tissues. Independent of the type of ecological interaction, glycans, and glycoconjugates produced by these bacteria play an important role in the molecular communication prior and during colonization. Even though exopolysaccharides (EPS) and lipochitooligosaccharides (LCO) produced by diazotrophic bacteria and released onto the environment have their importance in the microbe-plant interaction, it is the lipopolysaccharides (LPS), anchored on the external membrane of these bacteria, that mediates the direct contact of the diazotroph with the host cells. These molecules are extremely variable among the several species of nitrogen fixing-bacteria, and there are evidences of the mechanisms of infection being closely related to their structure. PMID:25232535

Rhizobium–legume symbiosis shares an exocytotic pathway required for arbuscule formation

PubMed Central

Ivanov, Sergey; Fedorova, Elena E.; Limpens, Erik; De Mita, Stephane; Genre, Andrea; Bonfante, Paola; Bisseling, Ton

2012-01-01

Endosymbiotic interactions are characterized by the formation of specialized membrane compartments, by the host in which the microbes are hosted, in an intracellular manner. Two well-studied examples, which are of major agricultural and ecological importance, are the widespread arbuscular mycorrhizal symbiosis and the Rhizobium–legume symbiosis. In both symbioses, the specialized host membrane that surrounds the microbes forms a symbiotic interface, which facilitates the exchange of, for example, nutrients in a controlled manner and, therefore, forms the heart of endosymbiosis. Despite their key importance, the molecular and cellular mechanisms underlying the formation of these membrane interfaces are largely unknown. Recent studies strongly suggest that the Rhizobium–legume symbiosis coopted a signaling pathway, including receptor, from the more ancient arbuscular mycorrhizal symbiosis to form a symbiotic interface. Here, we show that two highly homologous exocytotic vesicle-associated membrane proteins (VAMPs) are required for formation of the symbiotic membrane interface in both interactions. Silencing of these Medicago VAMP72 genes has a minor effect on nonsymbiotic plant development and nodule formation. However, it blocks symbiosome as well as arbuscule formation, whereas root colonization by the microbes is not affected. Identification of these VAMP72s as common symbiotic regulators in exocytotic vesicle trafficking suggests that the ancient exocytotic pathway forming the periarbuscular membrane compartment has also been coopted in the Rhizobium–legume symbiosis. PMID:22566631

Host Responses to Malassezia spp. in the Mammalian Skin

PubMed Central

Sparber, Florian; LeibundGut-Landmann, Salomé

2017-01-01

The skin of mammalian organisms is home for a myriad of microbes. Many of these commensals are thought to have beneficial effects on the host by critically contributing to immune homeostasis. Consequently, dysbiosis can have detrimental effects for the host that may manifest with inflammatory diseases at the barrier tissue. Besides bacteria, fungi make an important contribution to the microbiota and among these, the yeast Malassezia widely dominates in most areas of the skin in healthy individuals. There is accumulating evidence that Malassezia spp. are involved in a variety of skin disorders in humans ranging from non- or mildly inflammatory conditions such as dandruff and pityriasis versicolor to more severe inflammatory skin diseases like seborrheic eczema and atopic dermatitis. In addition, Malassezia is strongly linked to the development of dermatitis and otitis externa in dogs. However, the association of Malassezia spp. with such diseases remains poorly characterized. Until now, studies on the fungus–host interaction remain sparse and they are mostly limited to experiments with isolated host cells in vitro. They suggest a multifaceted crosstalk of Malassezia spp. with the skin by direct activation of the host via conserved pattern recognition receptors and indirectly via the release of fungus-derived metabolites that can modulate the function of hematopoietic and/or non-hematopoietic cells in the barrier tissue. In this review, we discuss our current understanding of the host response to Malassezia spp. in the mammalian skin. PMID:29213272

Host Responses to Malassezia spp. in the Mammalian Skin.

PubMed

Sparber, Florian; LeibundGut-Landmann, Salomé

2017-01-01

The skin of mammalian organisms is home for a myriad of microbes. Many of these commensals are thought to have beneficial effects on the host by critically contributing to immune homeostasis. Consequently, dysbiosis can have detrimental effects for the host that may manifest with inflammatory diseases at the barrier tissue. Besides bacteria, fungi make an important contribution to the microbiota and among these, the yeast Malassezia widely dominates in most areas of the skin in healthy individuals. There is accumulating evidence that Malassezia spp. are involved in a variety of skin disorders in humans ranging from non- or mildly inflammatory conditions such as dandruff and pityriasis versicolor to more severe inflammatory skin diseases like seborrheic eczema and atopic dermatitis. In addition, Malassezia is strongly linked to the development of dermatitis and otitis externa in dogs. However, the association of Malassezia spp. with such diseases remains poorly characterized. Until now, studies on the fungus-host interaction remain sparse and they are mostly limited to experiments with isolated host cells in vitro . They suggest a multifaceted crosstalk of Malassezia spp. with the skin by direct activation of the host via conserved pattern recognition receptors and indirectly via the release of fungus-derived metabolites that can modulate the function of hematopoietic and/or non-hematopoietic cells in the barrier tissue. In this review, we discuss our current understanding of the host response to Malassezia spp. in the mammalian skin.

Root and bacterial secretions regulate the interaction between plants and PGPR leading to distinct plant growth promotion effects

USDA-ARS?s Scientific Manuscript database

Plant growth-promoting rhizobacteria (PGPR) have garnered interest in agriculture due to their ability to influence the growth and production of host plants. ATP-binding cassette (ABC) transporters play important roles in plant-microbe interactions by modulating plant root exudation. The present stu...

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs

USDA-ARS?s Scientific Manuscript database

Legumes and many nonleguminous plants enter symbiotic interactions with microbes, and it is poorly understood how host plants respond to promote beneficial, symbiotic microbial interactions while suppressing those that are deleterious or pathogenic. Trans-acting siRNAs (tasiRNAs) negatively regulate...

Transition metals at the host–pathogen interface: How Neisseria exploit human metalloproteins for acquiring iron and zinc

PubMed Central

Neumann, Wilma; Hadley, Rose C.; Nolan, Elizabeth M.

2017-01-01

Transition metals are essential nutrients for all organisms and important players in the host-microbe interaction. During bacterial infection, a tug-of-war between the host and microbe for nutrient metals occurs: the host innate immune system responds to the pathogen by reducing metal availability and the pathogen tries to outmaneuver this response. The outcome of this competition, which involves metal-sequestering host-defense proteins and microbial metal acquisition machinery, is an important variable for whether infection occurs. One strategy bacterial pathogens employ to overcome metal restriction involves hijacking abundant host metalloproteins. The obligate human pathogens Neisseria spp. express TonB-dependent transport systems that capture human metalloproteins, extract the bound metal ions, and deliver these nutrients into the bacterial cell. This Essay highlights structural and mechanistic investigations that provide insights into how Neisseria acquire iron from the Fe(III)-transport protein transferrin, the Fe(III)-chelating host-defense protein lactoferrin, and the oxygen-transport protein hemoglobin, and obtain zinc from the metal-sequestering antimicrobial protein calprotectin. PMID:28487398

Microbiota as Therapeutic Targets.

PubMed

Xavier, Ramnik J

Inflammatory bowel disease (IBD) represents a family of diseases including Crohn's disease and ulcerative colitis. IBD has garnered significant attention in recent years due to successes in 2 areas of basic science: complex human genetics and host-microbe interactions. Advances in understanding the genetics of IBD, mainly driven by genome-wide association studies, have identified more than 160 genetic loci that modulate the risk of disease. Notably, several of these genes have pointed to alterations in host-microbe interactions as being critical factors in pathogenesis. Investigations into the microbial communities of the gastrointestinal tract (or the 'gut microbiome') in IBD have yielded important insights into several aspects of interactions between microbiota and the host immune system, including how alterations to microbial community composition and function have important consequences for immune homeostasis. The anatomy of the gastrointestinal tract plays a role in defining not only intestinal function, but also the microbial ecosystem that lives within the gut. Careful investigations into the composition and function of these microbial communities have suggested that patients with IBD have an imbalance in their gut microbiota, termed dysbiosis. These studies, as well as studies using samples from healthy individuals, have begun to uncover mechanisms of crosstalk between particular microbes (and microbial products) and immunomodulatory pathways, alterations which may drive immune diseases such as IBD. Investigations into the role of the microbiome in IBD have provided important clues to potential pathogenic mechanisms. Harnessing this knowledge to develop therapeutics and identify biomarkers is currently a major translational goal, holding great promise for clinically meaningful progress. © 2016 S. Karger AG, Basel.

Parasitic plants of the genus Cuscuta and their interaction with susceptible and resistant host plants

PubMed Central

Kaiser, Bettina; Vogg, Gerd; Fürst, Ursula B.; Albert, Markus

2015-01-01

By comparison with plant–microbe interaction, little is known about the interaction of parasitic plants with their hosts. Plants of the genus Cuscuta belong to the family of Cuscutaceae and comprise about 200 species, all of which live as stem holoparasites on other plants. Cuscuta spp. possess no roots nor fully expanded leaves and the vegetative portion appears to be a stem only. The parasite winds around plants and penetrates the host stems via haustoria, forming direct connections to the vascular bundles of their hosts to withdraw water, carbohydrates, and other solutes. Besides susceptible hosts, a few plants exist that exhibit an active resistance against infestation by Cuscuta spp. For example, cultivated tomato (Solanum lycopersicum) fends off Cuscuta reflexa by means of a hypersensitive-type response occurring in the early penetration phase. This report on the plant–plant dialog between Cuscuta spp. and its host plants focuses on the incompatible interaction of C. reflexa with tomato. PMID:25699071

Parasitic plants of the genus Cuscuta and their interaction with susceptible and resistant host plants.

PubMed

Kaiser, Bettina; Vogg, Gerd; Fürst, Ursula B; Albert, Markus

2015-01-01

By comparison with plant-microbe interaction, little is known about the interaction of parasitic plants with their hosts. Plants of the genus Cuscuta belong to the family of Cuscutaceae and comprise about 200 species, all of which live as stem holoparasites on other plants. Cuscuta spp. possess no roots nor fully expanded leaves and the vegetative portion appears to be a stem only. The parasite winds around plants and penetrates the host stems via haustoria, forming direct connections to the vascular bundles of their hosts to withdraw water, carbohydrates, and other solutes. Besides susceptible hosts, a few plants exist that exhibit an active resistance against infestation by Cuscuta spp. For example, cultivated tomato (Solanum lycopersicum) fends off Cuscuta reflexa by means of a hypersensitive-type response occurring in the early penetration phase. This report on the plant-plant dialog between Cuscuta spp. and its host plants focuses on the incompatible interaction of C. reflexa with tomato.

From perception to activation: the molecular-genetic and biochemical landscape of disease resistance signaling in plants.

PubMed

Knepper, Caleb; Day, Brad

2010-01-01

More than 60 years ago, H.H. Flor proposed the "Gene-for-Gene" hypothesis, which described the genetic relationship between host plants and pathogens. In the decades that followed Flor's seminal work, our understanding of the plant-pathogen interaction has evolved into a sophisticated model, detailing the molecular genetic and biochemical processes that control host-range, disease resistance signaling and susceptibility. The interaction between plants and microbes is an intimate exchange of signals that has evolved for millennia, resulting in the modification and adaptation of pathogen virulence strategies and host recognition elements. In total, plants have evolved mechanisms to combat the ever-changing landscape of biotic interactions bombarding their environment, while in parallel, plant pathogens have co-evolved mechanisms to sense and adapt to these changes. On average, the typical plant is susceptible to attack by dozens of microbial pathogens, yet in most cases, remains resistant to many of these challenges. The sum of research in our field has revealed that these interactions are regulated by multiple layers of intimately linked signaling networks. As an evolved model of Flor's initial observations, the current paradigm in host-pathogen interactions is that pathogen effector molecules, in large part, drive the recognition, activation and subsequent physiological responses in plants that give rise to resistance and susceptibility. In this Chapter, we will discuss our current understanding of the association between plants and microbial pathogens, detailing the pressures placed on both host and microbe to either maintain disease resistance, or induce susceptibility and disease. From recognition to transcriptional reprogramming, we will review current data and literature that has advanced the classical model of the Gene-for-Gene hypothesis to our current understanding of basal and effector triggered immunity.

Exploring the applications of invertebrate host-pathogen models for in vivo biofilm infections.

PubMed

Edwards, Sarah; Kjellerup, Birthe V

2012-07-01

In the natural environment, microorganisms exist together in self-produced polymeric matrix biofilms. Often, several species, which can belong to both bacterial and fungal kingdoms, coexist and interact in ways which are not completely understood. Biofilm infections have become prevalent largely in medical settings because of the increasing use of indwelling medical devices such as catheters or prosthetics. These infections are resistant to common antimicrobial therapies because of the inherent nature of their structure. In terms of infectious biofilms, it is important to understand the microbe-microbe interactions and how the host immune system reacts in order to discover therapeutic targets. Currently, single infection immune response studies are thriving with the use of invertebrate models. This review highlights the advances in single microbial-host immune response as well as the promising aspects of polymicrobial biofilm study in five invertebrate models: Lemna minor (duckweed), Arabidopsis thaliana (thale cress), Dictyostelium discoideum (slime mold), Drosophila melanogaster (common fruit fly), and Caenorhabditis elegans (roundworm). © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.

PubMed

Milani, Christian; Duranti, Sabrina; Bottacini, Francesca; Casey, Eoghan; Turroni, Francesca; Mahony, Jennifer; Belzer, Clara; Delgado Palacio, Susana; Arboleya Montes, Silvia; Mancabelli, Leonardo; Lugli, Gabriele Andrea; Rodriguez, Juan Miguel; Bode, Lars; de Vos, Willem; Gueimonde, Miguel; Margolles, Abelardo; van Sinderen, Douwe; Ventura, Marco

2017-12-01

The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease. Copyright © 2017 American Society for Microbiology.

Insect Resistance

USDA-ARS?s Scientific Manuscript database

Insect pests exhibit a diverse array of genetic-based responses when interacting with crop systems; these changes can be in response to pathogens, symbiotic microbes, host plants, chemicals, and the environment. Agricultural research has for decades focused on gathering crucial information on the bi...

Interspecies Interactions Determine the Impact of the Gut Microbiota on Nutrient Allocation in Drosophila melanogaster

PubMed Central

Douglas, Angela E.

2014-01-01

The animal gut is perpetually exposed to microorganisms, and this microbiota affects development, nutrient allocation, and immune homeostasis. A major challenge is to understand the contribution of individual microbial species and interactions among species in shaping these microbe-dependent traits. Using the Drosophila melanogaster gut microbiota, we tested whether microbe-dependent performance and nutritional traits of Drosophila are functionally modular, i.e., whether the impact of each microbial taxon on host traits is independent of the presence of other microbial taxa. Gnotobiotic flies were constructed with one or a set of five of the Acetobacter and Lactobacillus species which dominate the gut microbiota of conventional flies (Drosophila with untreated microbiota). Axenic (microbiota-free) flies exhibited prolonged development time and elevated glucose and triglyceride contents. The low glucose content of conventional flies was recapitulated in gnotobiotic Drosophila flies colonized with any of the 5 bacterial taxa tested. In contrast, the development rates and triglyceride levels in monocolonized flies varied depending on the taxon present: Acetobacter species supported the largest reductions, while most Lactobacillus species had no effect. Only flies with both Acetobacter and Lactobacillus had triglyceride contents restored to the level in conventional flies. This could be attributed to two processes: Lactobacillus-mediated promotion of Acetobacter abundance in the fly and a significant negative correlation between fly triglyceride content and Acetobacter abundance. We conclude that the microbial basis of host traits varies in both specificity and modularity; microbe-mediated reduction in glucose is relatively nonspecific and modular, while triglyceride content is influenced by interactions among microbes. PMID:24242251

Probiotics: Interaction with gut microbiome and antiobesity potential.

PubMed

Arora, Tulika; Singh, Satvinder; Sharma, Raj Kumar

2013-04-01

Obesity is a metabolic disorder afflicting people globally. There has been a pivotal advancement in the understanding of the intestinal microbiota composition and its implication in extraintestinal (metabolic) diseases. Therefore, any agent modulating gut microbiota may produce an influential effect in preventing the pathogenesis of disease. Probiotics are live microbes that, when administered in adequate amounts, have been shown to confer health benefits to the host. Over the years, probiotics have been a part of the human diet in the form of different fermented foods consumed around the world. Their influence on different physiologic functions in the host is increasingly being documented. The antiobesity potential of probiotics is also gaining wide attention because of increasing evidence of the role of gut microbiota in energy homeostasis and fat accumulation. Probiotics have also been shown to interact with the resident bacterial members already present in the gut by altering their properties, which may also affect the metabolic pathways involved in the regulation of fat metabolism. The underlying pathways governing the antiobesity effects of probiotics remain unclear. However, it is hoped that the evidence presented and discussed in this review will encourage and thus drive more extensive research in this field. Copyright © 2013 Elsevier Inc. All rights reserved.

Entomopathogenic Fungi: New Insights into Host-Pathogen Interactions.

PubMed

Butt, T M; Coates, C J; Dubovskiy, I M; Ratcliffe, N A

2016-01-01

Although many insects successfully live in dangerous environments exposed to diverse communities of microbes, they are often exploited and killed by specialist pathogens. Studies of host-pathogen interactions (HPI) provide valuable insights into the dynamics of the highly aggressive coevolutionary arms race between entomopathogenic fungi (EPF) and their arthropod hosts. The host defenses are designed to exclude the pathogen or mitigate the damage inflicted while the pathogen responds with immune evasion and utilization of host resources. EPF neutralize their immediate surroundings on the insect integument and benefit from the physiochemical properties of the cuticle and its compounds that exclude competing microbes. EPF also exhibit adaptations aimed at minimizing trauma that can be deleterious to both host and pathogen (eg, melanization of hemolymph), form narrow penetration pegs that alleviate host dehydration and produce blastospores that lack immunogenic sugars/enzymes but facilitate rapid assimilation of hemolymph nutrients. In response, insects deploy an extensive armory of hemocytes and macromolecules, such as lectins and phenoloxidase, that repel, immobilize, and kill EPF. New evidence suggests that immune bioactives work synergistically (eg, lysozyme with antimicrobial peptides) to combat infections. Some proteins, including transferrin and apolipophorin III, also demonstrate multifunctional properties, participating in metabolism, homeostasis, and pathogen recognition. This review discusses the molecular intricacies of these HPI, highlighting the interplay between immunity, stress management, and metabolism. Increased knowledge in this area could enhance the efficacy of EPF, ensuring their future in integrated pest management programs. Copyright © 2016 Elsevier Inc. All rights reserved.

Targeting gut microbiome: A novel and potential therapy for autism.

PubMed

Yang, Yongshou; Tian, Jinhu; Yang, Bo

2018-02-01

Autism spectrum disorder (ASD) is a severely neurodevelopmental disorder that impairs a child's ability to communicate and interact with others. Children with neurodevelopmental disorder, including ASD, are regularly affected by gastrointestinal problems and dysbiosis of gut microbiota. On the other hand, humans live in a co-evolutionary association with plenty of microorganisms that resident on the exposed and internal surfaces of our bodies. The microbiome, refers to the collection of microbes and their genetic material, confers a variety of physiologic benefits to the host in many key aspects of life as well as being responsible for some diseases. A large body of preclinical literature indicates that gut microbiome plays an important role in the bidirectional gut-brain axis that communicates between the gut and central nervous system. Moreover, accumulating evidences suggest that the gut microbiome is involved in the pathogenesis of ASD. The present review introduces the increasing evidence suggesting the reciprocal interaction network among microbiome, gut and brain. It also discusses the possible mechanisms by which gut microbiome influences the etiology of ASD via altering gut-brain axis. Most importantly, it highlights the new findings of targeting gut microbiome, including probiotic treatment and fecal microbiota transplant, as novel and potential therapeutics for ASD diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

Allometry of animal-microbe interactions and global census of animal-associated microbes.

PubMed

Kieft, Thomas L; Simmons, Karen A

2015-07-07

Animals live in close association with microorganisms, mostly prokaryotes, living in or on them as commensals, mutualists or parasites, and profoundly affecting host fitness. Most animal-microbe studies focus on microbial community structure; for this project, allometry (scaling of animal attributes with animal size) was applied to animal-microbe relationships across a range of species spanning 12 orders of magnitude in animal mass, from nematodes to whales. Microbial abundances per individual animal were gleaned from published literature and also microscopically counted in three species. Abundance of prokaryotes/individual versus animal mass scales as a nearly linear power function (exponent = 1.07, R(2) = 0.94). Combining this power function with allometry of animal abundance indicates that macrofauna have an outsized share of animal-associated microorganisms. The total number of animal-associated prokaryotes in Earth's land animals was calculated to be 1.3-1.4 × 10(25) cells and the total of marine animal-associated microbes was calculated to be 8.6-9.0 × 10(24) cells. Animal-associated microbes thus total 2.1-2.3 × 10(25) of the approximately 10(30) prokaryotes on the Earth. Microbes associated with humans comprise 3.3-3.5% of Earth's animal-associated microbes, and domestic animals harbour 14-20% of all animal-associated microbes, adding a new dimension to the scale of human impact on the biosphere. This novel allometric power function may reflect underlying mechanisms involving the transfer of energy and materials between microorganisms and their animal hosts. Microbial diversity indices of animal gut communities and gut microbial species richness for 60 mammals did not indicate significant scaling relationships with animal body mass; however, further research in this area is warranted. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

A systems biology perspective on plant-microbe interactions: biochemical and structural targets of pathogen effectors.

PubMed

Pritchard, Leighton; Birch, Paul

2011-04-01

Plants have biochemical defences against stresses from predators, parasites and pathogens. In this review we discuss the interaction of plant defences with microbial pathogens such as bacteria, fungi and oomycetes, and viruses. We examine principles of complex dynamic networks that allow identification of network components that are differentially and predictably sensitive to perturbation, thus making them likely effector targets. We relate these principles to recent developments in our understanding of known effector targets in plant-pathogen systems, and propose a systems-level framework for the interpretation and modelling of host-microbe interactions mediated by effectors. We describe this framework briefly, and conclude by discussing useful experimental approaches for populating this framework. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Physiological and molecular implications of plant polyamine metabolism during biotic interactions

PubMed Central

Jiménez-Bremont, Juan F.; Marina, María; Guerrero-González, María de la Luz; Rossi, Franco R.; Sánchez-Rangel, Diana; Rodríguez-Kessler, Margarita; Ruiz, Oscar A.; Gárriz, Andrés

2014-01-01

During ontogeny, plants interact with a wide variety of microorganisms. The association with mutualistic microbes results in benefits for the plant. By contrast, pathogens may cause a remarkable impairment of plant growth and development. Both types of plant–microbe interactions provoke notable changes in the polyamine (PA) metabolism of the host and/or the microbe, being each interaction a complex and dynamic process. It has been well documented that the levels of free and conjugated PAs undergo profound changes in plant tissues during the interaction with microorganisms. In general, this is correlated with a precise and coordinated regulation of PA biosynthetic and catabolic enzymes. Interestingly, some evidence suggests that the relative importance of these metabolic pathways may depend on the nature of the microorganism, a concept that stems from the fact that these amines mediate the activation of plant defense mechanisms. This effect is mediated mostly through PA oxidation, even though part of the response is activated by non-oxidized PAs. In the last years, a great deal of effort has been devoted to profile plant gene expression following microorganism recognition. In addition, the phenotypes of transgenic and mutant plants in PA metabolism genes have been assessed. In this review, we integrate the current knowledge on this field and analyze the possible roles of these amines during the interaction of plants with microbes. PMID:24672533

Candida albicans Pathogenesis: Fitting within the Host-Microbe Damage Response Framework

PubMed Central

Kong, Eric F.; Tsui, Christina; Nguyen, M. Hong; Clancy, Cornelius J.; Fidel, Paul L.; Noverr, Mairi

2016-01-01

Historically, the nature and extent of host damage by a microbe were considered highly dependent on virulence attributes of the microbe. However, it has become clear that disease is a complex outcome which can arise because of pathogen-mediated damage, host-mediated damage, or both, with active participation from the host microbiota. This awareness led to the formulation of the damage response framework (DRF), a revolutionary concept that defined microbial virulence as a function of host immunity. The DRF outlines six classifications of host damage outcomes based on the microbe and the strength of the immune response. In this review, we revisit this concept from the perspective of Candida albicans, a microbial pathogen uniquely adapted to its human host. This fungus commonly colonizes various anatomical sites without causing notable damage. However, depending on environmental conditions, a diverse array of diseases may occur, ranging from mucosal to invasive systemic infections resulting in microbe-mediated and/or host-mediated damage. Remarkably, C. albicans infections can fit into all six DRF classifications, depending on the anatomical site and associated host immune response. Here, we highlight some of these diverse and site-specific diseases and how they fit the DRF classifications, and we describe the animal models available to uncover pathogenic mechanisms and related host immune responses. PMID:27430274

Signal Integration by the IκB Protein Pickle Shapes Drosophila Innate Host Defense.

PubMed

Morris, Otto; Liu, Xi; Domingues, Celia; Runchel, Christopher; Chai, Andrea; Basith, Shaherin; Tenev, Tencho; Chen, Haiyang; Choi, Sangdun; Pennetta, Giuseppa; Buchon, Nicolas; Meier, Pascal

2016-09-14

Pattern recognition receptors are activated following infection and trigger transcriptional programs important for host defense. Tight regulation of NF-κB activation is critical to avoid detrimental and misbalanced responses. We describe Pickle, a Drosophila nuclear IκB that integrates signaling inputs from both the Imd and Toll pathways by skewing the transcriptional output of the NF-κB dimer repertoire. Pickle interacts with the NF-κB protein Relish and the histone deacetylase dHDAC1, selectively repressing Relish homodimers while leaving other NF-κB dimer combinations unscathed. Pickle's ability to selectively inhibit Relish homodimer activity contributes to proper host immunity and organismal health. Although loss of pickle results in hyper-induction of Relish target genes and improved host resistance to pathogenic bacteria in the short term, chronic inactivation of pickle causes loss of immune tolerance and shortened lifespan. Pickle therefore allows balanced immune responses that protect from pathogenic microbes while permitting the establishment of beneficial commensal host-microbe relationships. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Interplay Between Innate Immunity and the Plant Microbiota.

PubMed

Hacquard, Stéphane; Spaepen, Stijn; Garrido-Oter, Ruben; Schulze-Lefert, Paul

2017-08-04

The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.

Host and Symbiont Jointly Control Gut Microbiota during Complete Metamorphosis

PubMed Central

Johnston, Paul R.; Rolff, Jens

2015-01-01

Holometabolous insects undergo a radical anatomical re-organisation during metamorphosis. This poses a developmental challenge: the host must replace the larval gut but at the same time retain symbiotic gut microbes and avoid infection by opportunistic pathogens. By manipulating host immunity and bacterial competitive ability, we study how the host Galleria mellonella and the symbiotic bacterium Enterococcus mundtii interact to manage the composition of the microbiota during metamorphosis. Disenabling one or both symbiotic partners alters the composition of the gut microbiota, which incurs fitness costs: adult hosts with a gut microbiota dominated by pathogens such as Serratia and Staphylococcus die early. Our results reveal an interaction that guarantees the safe passage of the symbiont through metamorphosis and benefits the resulting adult host. Host-symbiont “conspiracies” as described here are almost certainly widespread in holometobolous insects including many disease vectors. PMID:26544881

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions.

PubMed

He, Tianliang; Li, Hongyun; Zhang, Xiaobo

2017-07-11

Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions. IMPORTANCE Viruses are the most abundant biological entities in the oceans and have very important roles in regulating microbial community structure and biogeochemical cycles. The relationship between virus and host microbes is broadly thought to be that of predator and prey. Viruses can lyse host cells to control microbial population sizes and affect community structures of hosts by killing specific microbes. However, viruses also influence their hosts through manipulation of bacterial metabolism. We found that viral genes not only participated in most microbial metabolic pathways but also formed branched pathways in microbial metabolisms. The metabolic compensation of hosts mediated by viruses may help hosts to adapt to extreme environments and may be essential for host survival. Copyright © 2017 He et al.

The Chemistry of Plant–Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance

PubMed Central

Mhlongo, Msizi I.; Piater, Lizelle A.; Madala, Ntakadzeni E.; Labuschagne, Nico; Dubery, Ian A.

2018-01-01

Plant roots communicate with microbes in a sophisticated manner through chemical communication within the rhizosphere, thereby leading to biofilm formation of beneficial microbes and, in the case of plant growth-promoting rhizomicrobes/-bacteria (PGPR), resulting in priming of defense, or induced resistance in the plant host. The knowledge of plant–plant and plant–microbe interactions have been greatly extended over recent years; however, the chemical communication leading to priming is far from being well understood. Furthermore, linkage between below- and above-ground plant physiological processes adds to the complexity. In metabolomics studies, the main aim is to profile and annotate all exo- and endo-metabolites in a biological system that drive and participate in physiological processes. Recent advances in this field has enabled researchers to analyze 100s of compounds in one sample over a short time period. Here, from a metabolomics viewpoint, we review the interactions within the rhizosphere and subsequent above-ground ‘signalomics’, and emphasize the contributions that mass spectrometric-based metabolomic approaches can bring to the study of plant-beneficial – and priming events. PMID:29479360

Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity.

PubMed

Troussellier, Marc; Escalas, Arthur; Bouvier, Thierry; Mouillot, David

2017-01-01

Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism-microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares , which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members.

Symbiosis-inspired approaches to antibiotic discovery.

PubMed

Adnani, Navid; Rajski, Scott R; Bugni, Tim S

2017-07-06

Covering: 2010 up to 2017Life on Earth is characterized by a remarkable abundance of symbiotic and highly refined relationships among life forms. Defined as any kind of close, long-term association between two organisms, symbioses can be mutualistic, commensalistic or parasitic. Historically speaking, selective pressures have shaped symbioses in which one organism (typically a bacterium or fungus) generates bioactive small molecules that impact the host (and possibly other symbionts); the symbiosis is driven fundamentally by the genetic machineries available to the small molecule producer. The human microbiome is now integral to the most recent chapter in animal-microbe symbiosis studies and plant-microbe symbioses have significantly advanced our understanding of natural products biosynthesis; this also is the case for studies of fungal-microbe symbioses. However, much less is known about microbe-microbe systems involving interspecies interactions. Microbe-derived small molecules (i.e. antibiotics and quorum sensing molecules, etc.) have been shown to regulate transcription in microbes within the same environmental niche, suggesting interspecies interactions whereas, intraspecies interactions, such as those that exploit autoinducing small molecules, also modulate gene expression based on environmental cues. We, and others, contend that symbioses provide almost unlimited opportunities for the discovery of new bioactive compounds whose activities and applications have been evolutionarily optimized. Particularly intriguing is the possibility that environmental effectors can guide laboratory expression of secondary metabolites from "orphan", or silent, biosynthetic gene clusters (BGCs). Notably, many of the studies summarized here result from advances in "omics" technologies and highlight how symbioses have given rise to new anti-bacterial and antifungal natural products now being discovered.

Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior

PubMed Central

Fischer, Caleb N; Trautman, Eric P; Crawford, Jason M; Stabb, Eric V; Handelsman, Jo; Broderick, Nichole A

2017-01-01

Animals host multi-species microbial communities (microbiomes) whose properties may result from inter-species interactions; however, current understanding of host-microbiome interactions derives mostly from studies in which elucidation of microbe-microbe interactions is difficult. In exploring how Drosophila melanogaster acquires its microbiome, we found that a microbial community influences Drosophila olfactory and egg-laying behaviors differently than individual members. Drosophila prefers a Saccharomyces-Acetobacter co-culture to the same microorganisms grown individually and then mixed, a response mainly due to the conserved olfactory receptor, Or42b. Acetobacter metabolism of Saccharomyces-derived ethanol was necessary, and acetate and its metabolic derivatives were sufficient, for co-culture preference. Preference correlated with three emergent co-culture properties: ethanol catabolism, a distinct volatile profile, and yeast population decline. Egg-laying preference provided a context-dependent fitness benefit to larvae. We describe a molecular mechanism by which a microbial community affects animal behavior. Our results support a model whereby emergent metabolites signal a beneficial multispecies microbiome. DOI: http://dx.doi.org/10.7554/eLife.18855.001 PMID:28068220

Nanovesicles from Malassezia sympodialis and Host Exosomes Induce Cytokine Responses – Novel Mechanisms for Host-Microbe Interactions in Atopic Eczema

PubMed Central

Gehrmann, Ulf; Qazi, Khaleda Rahman; Johansson, Catharina; Hultenby, Kjell; Karlsson, Maria; Lundeberg, Lena

2011-01-01

Background Intercellular communication can occur via the release of membrane vesicles. Exosomes are nanovesicles released from the endosomal compartment of cells. Depending on their cell of origin and their cargo they can exert different immunoregulatory functions. Recently, fungi were found to produce extracellular vesicles that can influence host-microbe interactions. The yeast Malassezia sympodialis which belongs to our normal cutaneous microbial flora elicits specific IgE- and T-cell reactivity in approximately 50% of adult patients with atopic eczema (AE). Whether exosomes or other vesicles contribute to the inflammation has not yet been investigated. Objective To investigate if M. sympodialis can release nanovesicles and whether they or endogenous exosomes can activate PBMC from AE patients sensitized to M. sympodialis. Methods Extracellular nanovesicles isolated from M. sympodialis, co-cultures of M. sympodialis and dendritic cells, and from plasma of patients with AE and healthy controls (HC) were characterised using flow cytometry, sucrose gradient centrifugation, Western blot and electron microscopy. Their ability to stimulate IL-4 and TNF-alpha responses in autologous CD14, CD34 depleted PBMC was determined using ELISPOT and ELISA, respectively. Results We show for the first time that M. sympodialis releases extracellular vesicles carrying allergen. These vesicles can induce IL-4 and TNF-α responses with a significantly higher IL-4 production in patients compared to HC. Exosomes from dendritic cell and M. sympodialis co-cultures induced IL-4 and TNF-α responses in autologous CD14, CD34 depleted PBMC of AE patients and HC while plasma exosomes induced TNF-α but not IL-4 in undepleted PBMC. Conclusions Extracellular vesicles from M. sympodialis, dendritic cells and plasma can contribute to cytokine responses in CD14, CD34 depleted and undepleted PBMC of AE patients and HC. These novel observations have implications for understanding host-microbe interactions in the pathogenesis of AE. PMID:21799736

Microbial Metabolic Networks at the Mucus Layer Lead to Diet-Independent Butyrate and Vitamin B12 Production by Intestinal Symbionts.

PubMed

Belzer, Clara; Chia, Loo Wee; Aalvink, Steven; Chamlagain, Bhawani; Piironen, Vieno; Knol, Jan; de Vos, Willem M

2017-09-19

Akkermansia muciniphila has evolved to specialize in the degradation and utilization of host mucus, which it may use as the sole source of carbon and nitrogen. Mucus degradation and fermentation by A. muciniphila are known to result in the liberation of oligosaccharides and subsequent production of acetate, which becomes directly available to microorganisms in the vicinity of the intestinal mucosa. Coculturing experiments of A muciniphila with non-mucus-degrading butyrate-producing bacteria Anaerostipes caccae , Eubacterium hallii , and Faecalibacterium prausnitzii resulted in syntrophic growth and production of butyrate. In addition, we demonstrate that the production of pseudovitamin B 12 by E. hallii results in production of propionate by A. muciniphila , which suggests that this syntrophy is indeed bidirectional. These data are proof of concept for syntrophic and other symbiotic microbe-microbe interactions at the intestinal mucosal interface. The observed metabolic interactions between A muciniphila and butyrogenic bacterial taxa support the existence of colonic vitamin and butyrate production pathways that are dependent on host glycan production and independent of dietary carbohydrates. We infer that the intestinal symbiont A. muciniphila can indirectly stimulate intestinal butyrate levels in the vicinity of the intestinal epithelial cells with potential health benefits to the host. IMPORTANCE The intestinal microbiota is said to be a stable ecosystem where many networks between microorganisms are formed. Here we present a proof of principle study of microbial interaction at the intestinal mucus layer. We show that indigestible oligosaccharide chains within mucus become available for a broad range of intestinal microbes after degradation and liberation of sugars by the species Akkermansia muciniphila This leads to the microbial synthesis of vitamin B 12 , 1,2-propanediol, propionate, and butyrate, which are beneficial to the microbial ecosystem and host epithelial cells. Copyright © 2017 Belzer et al.

Alternatives to Antibiotics to Prevent Necrotic Enteritis in Broiler Chickens: A Microbiologist's Perspective

PubMed Central

Caly, Delphine L.; D'Inca, Romain; Auclair, Eric; Drider, Djamel

2015-01-01

Since the 2006 European ban on the use of antibiotics as growth promoters in animal feed, numerous studies have been published describing alternative strategies to prevent diseases in animals. A particular focus has been on prevention of necrotic enteritis in poultry caused by Clostridium perfringens by the use of microbes or microbe-derived products. Microbes produce a plethora of molecules with antimicrobial properties and they can also have beneficial effects through interactions with their host. Here we review recent developments in novel preventive treatments against C. perfringens-induced necrotic enteritis in broiler chickens that employ yeasts, bacteria and bacteriophages or secondary metabolites and other microbial products in disease control. PMID:26648920

Inflammasomes make the case for littermate-controlled experimental design in studying host-microbiota interactions.

PubMed

Mamantopoulos, Michail; Ronchi, Francesca; McCoy, Kathy D; Wullaert, Andy

2018-04-19

Several human diseases are thought to evolve due to a combination of host genetic mutations and environmental factors that include alterations in intestinal microbiota composition termed dysbiosis. Although in some cases, host genetics may shape the gut microbiota and enable it to provoke disease, experimentally disentangling cause and consequence in such host-microbe interactions requires strict control over non-genetic confounding factors. Mouse genetic studies previously proposed Nlrp6/ASC inflammasomes as innate immunity regulators of the intestinal ecosystem. In contrast, using littermate-controlled experimental setups, we recently showed that Nlrp6/ASC inflammasomes do not alter the gut microbiota composition. Our analyses indicated that maternal inheritance and long-term separate housing are non-genetic confounders that preclude the use of non-littermate mice when analyzing host genetic effects on intestinal ecology. Here, we summarize and discuss our gut microbiota analyses in inflammasome-deficient mice for illustrating the importance of littermate experimental design in studying host-microbiota interactions.

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis.

PubMed

Cross, Karissa L; Chirania, Payal; Xiong, Weili; Beall, Clifford J; Elkins, James G; Giannone, Richard J; Griffen, Ann L; Guss, Adam M; Hettich, Robert L; Joshi, Snehal S; Mokrzan, Elaine M; Martin, Roman K; Zhulin, Igor B; Leys, Eugene J; Podar, Mircea

2018-03-13

The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously uncultured Desulfobulbus oralis , the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives, D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities. The genes that enable free-living Desulfobulbus to synthesize the potent neurotoxin methylmercury were also lost by D. oralis , a notably positive outcome of host association. However, horizontal gene acquisitions from other members of the microbiota provided novel mechanisms of interaction with the human host, including toxins like leukotoxin and hemolysins. Proteomic and transcriptomic analysis revealed that most of those factors are actively expressed, including in the subgingival environment, and some are secreted. Similar to other known oral pathobionts, D. oralis can trigger a proinflammatory response in oral epithelial cells, suggesting a direct role in the development of periodontal disease. IMPORTANCE Animal-associated microbiota likely assembled as a result of numerous independent colonization events by free-living microbes followed by coevolution with their host and other microbes. Through specific adaptation to various body sites and physiological niches, microbes have a wide range of contributions, from beneficial to disease causing. Desulfobulbus oralis provides insights into genomic and physiological transformations associated with transition from an open environment to a host-dependent lifestyle and the emergence of pathogenicity. Through a multifaceted mechanism triggering a proinflammatory response, D. oralis is a novel periodontal pathobiont. Even though culture-independent approaches can provide insights into the potential role of the human microbiome "dark matter," cultivation and experimental characterization remain important to studying the roles of individual organisms in health and disease.

Generating Germ-Free Drosophila to Study Gut-Microbe Interactions: Protocol to Rear Drosophila Under Axenic Conditions.

PubMed

Kietz, Christa; Pollari, Vilma; Meinander, Annika

2018-06-22

As several diseases have been linked to dysbiosis of the human intestinal microflora, manipulation of the microbiota has emerged as an exciting new strategy for potentially treating and preventing diseases. However, the human microbiota consists of a plethora of different species, and distinguishing the impact of a specific bacterial species on human health is challenging. In tackling this challenge, the fruit fly Drosophila melanogaster, with its far simpler microbial composition, has emerged as a powerful model for unraveling host-microbe interactions. To study the interplay between the resident commensal microbiome and the host, flies can be made germ-free, or axenic. To elucidate the impact of specific bacteria, axenic flies can then be re-introduced to specific microbial species. In this unit, we provide a step-by-step protocol on how to rear Drosophila melanogaster under axenic conditions and confirm the axenity of flies. © 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

Understanding the plant-pathogen interactions in the context of proteomics-generated apoplastic proteins inventory.

PubMed

Gupta, Ravi; Lee, So Eui; Agrawal, Ganesh K; Rakwal, Randeep; Park, Sangryeol; Wang, Yiming; Kim, Sun T

2015-01-01

The extracellular space between cell wall and plasma membrane acts as the first battle field between plants and pathogens. Bacteria, fungi, and oomycetes that colonize the living plant tissues are encased in this narrow region in the initial step of infection. Therefore, the apoplastic region is believed to be an interface which mediates the first crosstalk between host and pathogen. The secreted proteins and other metabolites, derived from both host and pathogen, interact in this apoplastic region and govern the final relationship between them. Hence, investigation of protein secretion and apoplastic interaction could provide a better understanding of plant-microbe interaction. Here, we are briefly discussing the methods available for the isolation and normalization of the apoplastic proteins, as well as the current state of secretome studies focused on the in-planta interaction between the host and the pathogen.

Unraveling the environmental and genetic interactions in atherosclerosis: Central role of the gut microbiota

PubMed Central

Org, Elin; Mehrabian, Margarete; Lusis, Aldons J.

2015-01-01

Recent studies have convincingly linked gut microbiota to traits relevant to atherosclerosis, such as insulin resistance, dyslipidemia and inflammation, and have revealed novel disease pathways involving microbe-derived metabolites. These results have important implications for understanding how environmental and genetic factors act together to influence cardiovascular disease (CVD) risk. Thus, dietary constituents are not only absorbed and metabolized by the host but they also perturb the gut microbiota, which in turn influence host metabolism and inflammation. It also appears that host genetics helps to shape the gut microbiota community. Here, we discuss challenges in understanding these interactions and the role they play in CVD. PMID:26071662

Specialized metabolites from the microbiome in health and disease

PubMed Central

Sharon, Gil; Garg, Neha; Debelius, Justine; Knight, Rob; Dorrestein, Pieter C.; Mazmanian, Sarkis K.

2015-01-01

The microbiota, and the genes that comprise its microbiome, play key roles in human health. Host-microbe interactions affect immunity, metabolism, development, and behavior, and dysbiosis of gut bacteria contributes to disease. Despite advances in correlating changes in the microbiota with various conditions, specific mechanisms of host-microbiota signaling remain largely elusive. We discuss the synthesis of microbial metabolites, their absorption, and potential physiological effects on the host. We propose that the effects of specialized metabolites may explain present knowledge gaps linking the gut microbiota to biological host mechanisms during initial colonization, and in health and disease. PMID:25440054

Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy.

PubMed

Moen, Aina E F; Tannæs, Tone M; Vatn, Simen; Ricanek, Petr; Vatn, Morten Harald; Jahnsen, Jørgen

2016-06-28

Nucleic acid purification methods are of importance when performing microbiota studies and especially when analysing the intestinal microbiota as we here find a wide range of different microbes. Various considerations must be taken to lyse the microbial cell wall of each microbe. In the present article, we compare several tissue lysis steps and commercial purification kits, to achieve a joint RNA and DNA purification protocol for the purpose of investigating the microbiota and the microbiota-host interactions in a single colonic mucosal tissue sample. A further optimised tissue homogenisation and lysis protocol comprising mechanical bead beating, lysis buffer replacement and enzymatic treatment, in combination with the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) resulted in efficient and simultaneous purification of microbial and human RNA and DNA from a single mucosal colonic tissue sample. The present work provides a unique possibility to study RNA and DNA from the same mucosal biopsy sample, making a direct comparison between metabolically active microbes and total microbial DNA. The protocol also offers an opportunity to investigate other members of a microbiota such as viruses, fungi and micro-eukaryotes, and moreover the possibility to extract data on microbiota and host interactions from one single mucosal biopsy.

The Gut Microbiota: Ecology and Function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willing, B.P.; Jansson, J.K.

The gastrointestinal (GI) tract is teeming with an extremely abundant and diverse microbial community. The members of this community have coevolved along with their hosts over millennia. Until recently, the gut ecosystem was viewed as black box with little knowledge of who or what was there or their specific functions. Over the past decade, however, this ecosystem has become one of fastest growing research areas of focus in microbial ecology and human and animal physiology. This increased interest is largely in response to studies tying microbes in the gut to important diseases afflicting modern society, including obesity, allergies, inflammatory bowelmore » diseases, and diabetes. Although the importance of a resident community of microorganisms in health was first hypothesized by Pasteur over a century ago (Sears, 2005), the multiplicity of physiological changes induced by commensal bacteria has only recently been recognized (Hooper et al., 2001). The term 'ecological development' was recently coined to support the idea that development of the GI tract is a product of the genetics of the host and the host's interactions with resident microbes (Hooper, 2004). The search for new therapeutic targets and disease biomarkers has escalated the need to understand the identities and functions of the microorganisms inhabiting the gut. Recent studies have revealed new insights into the membership of the gut microbial community, interactions within that community, as well as mechanisms of interaction with the host. This chapter focuses on the microbial ecology of the gut, with an emphasis on information gleaned from recent molecular studies.« less

Gut microbial adaptation to dietary consumption of fructose, artificial sweeteners and sugar alcohols: implications for host-microbe interactions contributing to obesity.

PubMed

Payne, A N; Chassard, C; Lacroix, C

2012-09-01

The Western diet, comprised of highly refined carbohydrates and fat but reduced complex plant polysaccharides, has been attributed to the prevalence of obesity. A concomitant rise in the consumption of fructose and sugar substitutes such as sugar alcohols, artificial sweeteners, even rare sugars, has mirrored this trend, as both probable contributor and solution to the epidemic. Acknowledgement of the gut microbiota as a factor involved in obesity has sparked much controversy as to the cause and consequence of this relationship. Dietary intakes are a known modulator of gut microbial phylogeny and metabolic activity, frequently exploited to stimulate beneficial bacteria, promoting health benefits. Comparably little research exists on the impact of 'unconscious' dietary modulation on the resident commensal community mediated by increased fructose and sugar substitute consumption. This review highlights mechanisms of potential host and gut microbial fructose and sugar substitute metabolism. Evidence is presented suggesting these sugar compounds, particularly fructose, condition the microbiota, resulting in acquisition of a westernized microbiome with altered metabolic capacity. Disturbances in host-microbe interactions resulting from fructose consumption are also explored. © 2012 The Authors. obesity reviews © 2012 International Association for the Study of Obesity.

Human Skin Is the Largest Epithelial Surface for Interaction with Microbes.

PubMed

Gallo, Richard L

2017-06-01

Human skin contains an abundant and diverse population of microbial organisms. Many of these microbes inhabit follicular structures of the skin. Furthermore, numerous studies have shown that the interaction of some members of the skin microbiome with host cells will result in changes in cell function. However, estimates of the potential for the microbiome to influence human health through skin have ignored the inner follicular surface, and therefore vastly underestimated the potential of the skin microbiome to have a systemic effect on the human body. By calculating the surface area of follicular and the interfollicular epithelial surface it is shown that skin provides a vast interface for interactions with the microbiome. Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

Microbial ecology and host-microbiota interactions during early life stages

PubMed Central

Collado, Maria Carmen; Cernada, Maria; Baüerl, Christine; Vento, Máximo; Pérez-Martínez, Gaspar

2012-01-01

The role of human microbiota has been redefined during recent years and its physiological role is now much more important than earlier understood. Intestinal microbial colonization is essential for the maturation of immune system and for the developmental regulation of the intestinal physiology. Alterations in this process of colonization have been shown to predispose and increase the risk to disease later in life. The first contact of neonates with microbes is provided by the maternal microbiota. Moreover, mode of delivery, type of infant feeding and other perinatal factors can influence the establishment of the infant microbiota. Taken into consideration all the available information it could be concluded that the exposure to the adequate microbes early in gestation and neonatal period seems to have a relevant role in health. Maternal microbial environment affects maternal and fetal immune physiology and, of relevance, this interaction with microbes at the fetal-maternal interface could be modulated by specific microbes administered to the pregnant mother. Indeed, probiotic interventions aiming to reduce the risk of immune-mediated diseases may appear effective during early life. PMID:22743759

Q&A: What are strigolactones and why are they important to plants and soil microbes?

PubMed

Smith, Steven M

2014-03-31

What are strigolactones? Strigolactones are signaling compounds made by plants. They have two main functions: first, as endogenous hormones to control plant development, and second as components of root exudates to promote symbiotic interactions between plants and soil microbes. Some plants that are parasitic on other plants have established a third function, which is to stimulate germination of their seeds when in close proximity to the roots of a suitable host plant. It is this third function that led to the original discovery and naming of strigolactones.

PATHWAYS IN MICROBE-INDUCED OBESITY

PubMed Central

Cox, Laura M.; Blaser, Martin J.

2013-01-01

Diet, host gene composition, and alterations in the intestinal microbiota can contribute to obesity. In microbe-induced obesity, metabolic changes stem from primary perturbation of the microbiota, consequent to modern changes in human biology. Microbiota disruption during early development can result in syndromes of metabolic dysfunction. We focus on the pathways involved in these interactions, particularly related to energy extraction and the role of inflammation in the metabolic phenotypes. Model physiologic systems and perturbations including gastric bypass surgery, pregnancy, and hibernation provide insight into the respective roles of the critical participants. PMID:23747247

Norovirus Regulation by Host and Microbe

PubMed Central

Baldridge, Megan T.; Turula, Holly; Wobus, Christiane E.

2016-01-01

Norovirus (NoV) infection is the leading cause of epidemic gastroenteritis globally, and can lead to detrimental chronic infection in immunocompromised hosts. Despite its prevalence as a cause of diarrheal illness, the study of human NoVs (HNoVs) has historically been limited by a paucity of models. The use of murine NoV (MNoV) to interrogate mechanisms of host control of viral infection has facilitated the exploration of different genetic mouse models, revealing roles for both innate and adaptive immunity in viral regulation. MNoV studies have also recently identified important interactions between the commensal micro-biota and NoV with clear extensions to HNoVs. In this review, we discuss the most current understanding of how the host, the microbiome, and their interactions regulate NoV infections. PMID:27887808

Amphibian skin may select for rare environmental microbes

PubMed Central

Walke, Jenifer B; Becker, Matthew H; Loftus, Stephen C; House, Leanna L; Cormier, Guy; Jensen, Roderick V; Belden, Lisa K

2014-01-01

Host-microbe symbioses rely on the successful transmission or acquisition of symbionts in each new generation. Amphibians host a diverse cutaneous microbiota, and many of these symbionts appear to be mutualistic and may limit infection by the chytrid fungus, Batrachochytrium dendrobatidis, which has caused global amphibian population declines and extinctions in recent decades. Using bar-coded 454 pyrosequencing of the 16S rRNA gene, we addressed the question of symbiont transmission by examining variation in amphibian skin microbiota across species and sites and in direct relation to environmental microbes. Although acquisition of environmental microbes occurs in some host-symbiont systems, this has not been extensively examined in free-living vertebrate-microbe symbioses. Juvenile bullfrogs (Rana catesbeiana), adult red-spotted newts (Notophthalmus viridescens), pond water and pond substrate were sampled at a single pond to examine host-specificity and potential environmental transmission of microbiota. To assess population level variation in skin microbiota, adult newts from two additional sites were also sampled. Cohabiting bullfrogs and newts had distinct microbial communities, as did newts across the three sites. The microbial communities of amphibians and the environment were distinct; there was very little overlap in the amphibians' core microbes and the most abundant environmental microbes, and the relative abundances of OTUs that were shared by amphibians and the environment were inversely related. These results suggest that, in a host species-specific manner, amphibian skin may select for microbes that are generally in low abundance in the environment. PMID:24858782

Advances in understanding tree fruit-rhizosphere microbiome relationships for enhanced plant health

USDA-ARS?s Scientific Manuscript database

Host-microbe interactions in the rhizosphere influence numerous processes that determine plant productivity and health. The importance of the rhizo-microbiome for plant function is well known, influencing functions ranging from protection of the plant from pathogen attack to enhanced nutrient avail...

Inflammatory bowel disease: cause and immunobiology.

PubMed

Baumgart, Daniel C; Carding, Simon R

2007-05-12

Crohn's disease and ulcerative colitis are idiopathic inflammatory bowel disorders. In this paper, we discuss how environmental factors (eg, geography, cigarette smoking, sanitation and hygiene), infectious microbes, ethnic origin, genetic susceptibility, and a dysregulated immune system can result in mucosal inflammation. After describing the symbiotic interaction of the commensal microbiota with the host, oral tolerance, epithelial barrier function, antigen recognition, and immunoregulation by the innate and adaptive immune system, we examine the initiating and perpetuating events of mucosal inflammation. We pay special attention to pattern-recognition receptors, such as toll-like receptors and nucleotide-binding-oligomerisation-domains (NOD), NOD-like receptors and their mutual interaction on epithelial cells and antigen-presenting cells. We also discuss the important role of dendritic cells in directing tolerance and immunity by modulation of subpopulations of effector T cells, regulatory T cells, Th17 cells, natural killer T cells, natural killer cells, and monocyte-macrophages in mucosal inflammation. Implications for novel therapies, which are discussed in detail in the second paper in this Series, are covered briefly.

Ticks and Tick-Borne Infections: Complex Ecology, Agents, and Host Interactions.

PubMed

Wikel, Stephen K

2018-06-20

Ticks transmit the most diverse array of infectious agents of any arthropod vector. Both ticks and the microbes they transmit are recognized as significant threats to human and veterinary public health. This article examines the potential impacts of climate change on the distribution of ticks and the infections they transmit; the emergence of novel tick-borne pathogens, increasing geographic range and incidence of tick-borne infections; and advances in the characterization of tick saliva mediated modulation of host defenses and the implications of those interactions for transmission, establishment, and control of tick infestation and tick-borne infectious agents.

Harnessing Host-Vector Microbiome for Sustainable Plant Disease Management of Phloem-Limited Bacteria

PubMed Central

Trivedi, Pankaj; Trivedi, Chanda; Grinyer, Jasmine; Anderson, Ian C.; Singh, Brajesh K.

2016-01-01

Plant health and productivity is strongly influenced by their intimate interaction with deleterious and beneficial organisms, including microbes, and insects. Of the various plant diseases, insect-vectored diseases are of particular interest, including those caused by obligate parasites affecting plant phloem such as Candidatus (Ca.) Phytoplasma species and several species of Ca. Liberibacter. Recent studies on plant–microbe and plant–insect interactions of these pathogens have demonstrated that plant–microbe–insect interactions have far reaching consequences for the functioning and evolution of the organisms involved. These interactions take place within complex pathosystems and are shaped by a myriad of biotic and abiotic factors. However, our current understanding of these processes and their implications for the establishment and spread of insect-borne diseases remains limited. This article highlights the molecular, ecological, and evolutionary aspects of interactions among insects, plants, and their associated microbial communities with a focus on insect vectored and phloem-limited pathogens belonging to Ca. Phytoplasma and Ca. Liberibacter species. We propose that innovative and interdisciplinary research aimed at linking scales from the cellular to the community level will be vital for increasing our understanding of the mechanisms underpinning plant–insect–microbe interactions. Examination of such interactions could lead us to applied solutions for sustainable disease and pest management. PMID:27746788

Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress.

PubMed

Bharwani, Aadil; Mian, M Firoz; Surette, Michael G; Bienenstock, John; Forsythe, Paul

2017-01-11

Stress-related disorders involve systemic alterations, including disruption of the intestinal microbial community. Given the putative connections between the microbiota, immunity, neural function, and behaviour, we investigated the potential for microbe-induced gut-to-brain signalling to modulate the impact of stress on host behaviour and immunoregulation. Male C57BL/6 mice treated orally over 28 days with either Lactobacillus rhamnosus (JB-1) ™ or vehicle were subjected to chronic social defeat and assessed for alterations in behaviour and immune cell phenotype. 16S rRNA sequencing and mass spectrometry were employed to analyse the faecal microbial community and metabolite profile. Treatment with JB-1 decreased stress-induced anxiety-like behaviour and prevented deficits in social interaction with conspecifics. However, JB-1 did not alter development of aggressor avoidance following social defeat. Microbial treatment attenuated stress-related activation of dendritic cells while increasing IL-10+ regulatory T cells. Furthermore, JB-1 modulated the effect of stress on faecal metabolites with neuroactive and immunomodulatory properties. Exposure to social defeat altered faecal microbial community composition and reduced species richness and diversity, none of which was prevented by JB-1. Stress-related microbiota disruptions persisted in vehicle-treated mice for 3 weeks following stressor cessation. These data demonstrate that despite the complexity of the gut microbiota, exposure to a single microbial strain can protect against certain stress-induced behaviours and systemic immune alterations without preventing dysbiosis. This work supports microbe-based interventions for stress-related disorders.

Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes.

PubMed

Gerardo, Nicole; Hurst, Gregory

2017-12-27

Over the past decade, there has been a pronounced shift in the study of host-microbe associations, with recognition that many of these associations are beneficial, and often critical, for a diverse array of hosts. There may also be pronounced benefits for the microbes, though this is less well empirically understood. Significant progress has been made in understanding how ecology and evolution shape simple associations between hosts and one or a few microbial species, and this work can serve as a foundation to study the ecology and evolution of host associations with their often complex microbial communities (microbiomes).

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma.

PubMed

Pérez-Losada, Marcos; Castro-Nallar, Eduardo; Bendall, Matthew L; Freishtat, Robert J; Crandall, Keith A

2015-01-01

High-throughput sequencing (HTS) analysis of microbial communities from the respiratory airways has heavily relied on the 16S rRNA gene. Given the intrinsic limitations of this approach, airway microbiome research has focused on assessing bacterial composition during health and disease, and its variation in relation to clinical and environmental factors, or other microbiomes. Consequently, very little effort has been dedicated to describing the functional characteristics of the airway microbiota and even less to explore the microbe-host interactions. Here we present a simultaneous assessment of microbiome and host functional diversity and host-microbe interactions from the same RNA-seq experiment, while accounting for variation in clinical metadata. Transcriptomic (host) and metatranscriptomic (microbiota) sequences from the nasal epithelium of 8 asthmatics and 6 healthy controls were separated in silico and mapped to available human and NCBI-NR protein reference databases. Human genes differentially expressed in asthmatics and controls were then used to infer upstream regulators involved in immune and inflammatory responses. Concomitantly, microbial genes were mapped to metabolic databases (COG, SEED, and KEGG) to infer microbial functions differentially expressed in asthmatics and controls. Finally, multivariate analysis was applied to find associations between microbiome characteristics and host upstream regulators while accounting for clinical variation. Our study showed significant differences in the metabolism of microbiomes from asthmatic and non-asthmatic children for up to 25% of the functional properties tested. Enrichment analysis of 499 differentially expressed host genes for inflammatory and immune responses revealed 43 upstream regulators differentially activated in asthma. Microbial adhesion (virulence) and Proteobacteria abundance were significantly associated with variation in the expression of the upstream regulator IL1A; suggesting that microbiome characteristics modulate host inflammatory and immune systems during asthma.

Hidden state prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses.

PubMed

Zaneveld, Jesse R R; Thurber, Rebecca L V

2014-01-01

Complex symbioses between animal or plant hosts and their associated microbiotas can involve thousands of species and millions of genes. Because of the number of interacting partners, it is often impractical to study all organisms or genes in these host-microbe symbioses individually. Yet new phylogenetic predictive methods can use the wealth of accumulated data on diverse model organisms to make inferences into the properties of less well-studied species and gene families. Predictive functional profiling methods use evolutionary models based on the properties of studied relatives to put bounds on the likely characteristics of an organism or gene that has not yet been studied in detail. These techniques have been applied to predict diverse features of host-associated microbial communities ranging from the enzymatic function of uncharacterized genes to the gene content of uncultured microorganisms. We consider these phylogenetically informed predictive techniques from disparate fields as examples of a general class of algorithms for Hidden State Prediction (HSP), and argue that HSP methods have broad value in predicting organismal traits in a variety of contexts, including the study of complex host-microbe symbioses.

Skin microbiota and allergic symptoms associate with exposure to environmental microbes

PubMed Central

Sinkko, Hanna; Hielm-Björkman, Anna; Tiira, Katriina; Laatikainen, Tiina; Mäkeläinen, Sanna; Kaukonen, Maria; Uusitalo, Liisa; Hanski, Ilkka; Lohi, Hannes; Ruokolainen, Lasse

2018-01-01

A rural environment and farming lifestyle are known to provide protection against allergic diseases. This protective effect is expected to be mediated via exposure to environmental microbes that are needed to support a normal immune tolerance. However, the triangle of interactions between environmental microbes, host microbiota, and immune system remains poorly understood. Here, we have studied these interactions using a canine model (two breeds, n = 169), providing an intermediate approach between complex human studies and artificial mouse model studies. We show that the skin microbiota reflects both the living environment and the lifestyle of a dog. Remarkably, the prevalence of spontaneous allergies is also associated with residential environment and lifestyle, such that allergies are most common among urban dogs living in single-person families without other animal contacts, and least common among rural dogs having opposite lifestyle features. Thus, we show that living environment and lifestyle concurrently associate with skin microbiota and allergies, suggesting that these factors might be causally related. Moreover, microbes commonly found on human skin tend to dominate the urban canine skin microbiota, while environmental microbes are rich in the rural canine skin microbiota. This in turn suggests that skin microbiota is a feasible indicator of exposure to environmental microbes. As short-term exposure to environmental microbes via exercise is not associated with allergies, we conclude that prominent and sustained exposure to environmental microbiotas should be promoted by urban planning and lifestyle changes to support health of urban populations. PMID:29686089

Skin microbiota and allergic symptoms associate with exposure to environmental microbes.

PubMed

Lehtimäki, Jenni; Sinkko, Hanna; Hielm-Björkman, Anna; Salmela, Elina; Tiira, Katriina; Laatikainen, Tiina; Mäkeläinen, Sanna; Kaukonen, Maria; Uusitalo, Liisa; Hanski, Ilkka; Lohi, Hannes; Ruokolainen, Lasse

2018-05-08

A rural environment and farming lifestyle are known to provide protection against allergic diseases. This protective effect is expected to be mediated via exposure to environmental microbes that are needed to support a normal immune tolerance. However, the triangle of interactions between environmental microbes, host microbiota, and immune system remains poorly understood. Here, we have studied these interactions using a canine model (two breeds, n = 169), providing an intermediate approach between complex human studies and artificial mouse model studies. We show that the skin microbiota reflects both the living environment and the lifestyle of a dog. Remarkably, the prevalence of spontaneous allergies is also associated with residential environment and lifestyle, such that allergies are most common among urban dogs living in single-person families without other animal contacts, and least common among rural dogs having opposite lifestyle features. Thus, we show that living environment and lifestyle concurrently associate with skin microbiota and allergies, suggesting that these factors might be causally related. Moreover, microbes commonly found on human skin tend to dominate the urban canine skin microbiota, while environmental microbes are rich in the rural canine skin microbiota. This in turn suggests that skin microbiota is a feasible indicator of exposure to environmental microbes. As short-term exposure to environmental microbes via exercise is not associated with allergies, we conclude that prominent and sustained exposure to environmental microbiotas should be promoted by urban planning and lifestyle changes to support health of urban populations. Copyright © 2018 the Author(s). Published by PNAS.

A novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes.

PubMed

Nakjang, Sirintra; Ndeh, Didier A; Wipat, Anil; Bolam, David N; Hirt, Robert P

2012-01-01

The mucosal microbiota is recognised as an important factor for our health, with many disease states linked to imbalances in the normal community structure. Hence, there is considerable interest in identifying the molecular basis of human-microbe interactions. In this work we investigated the capacity of microbes to thrive on mucosal surfaces, either as mutualists, commensals or pathogens, using comparative genomics to identify co-occurring molecular traits. We identified a novel domain we named M60-like/PF13402 (new Pfam entry PF13402), which was detected mainly among proteins from animal host mucosa-associated prokaryotic and eukaryotic microbes ranging from mutualists to pathogens. Lateral gene transfers between distantly related microbes explained their shared M60-like/PF13402 domain. The novel domain is characterised by a zinc-metallopeptidase-like motif and is distantly related to known viral enhancin zinc-metallopeptidases. Signal peptides and/or cell surface anchoring features were detected in most microbial M60-like/PF13402 domain-containing proteins, indicating that these proteins target an extracellular substrate. A significant subset of these putative peptidases was further characterised by the presence of associated domains belonging to carbohydrate-binding module family 5/12, 32 and 51 and other glycan-binding domains, suggesting that these novel proteases are targeted to complex glycoproteins such as mucins. An in vitro mucinase assay demonstrated degradation of mammalian mucins by a recombinant form of an M60-like/PF13402-containing protein from the gut mutualist Bacteroides thetaiotaomicron. This study reveals that M60-like domains are peptidases targeting host glycoproteins. These peptidases likely play an important role in successful colonisation of both vertebrate mucosal surfaces and the invertebrate digestive tract by both mutualistic and pathogenic microbes. Moreover, 141 entries across various peptidase families described in the MEROPS database were also identified with carbohydrate-binding modules defining a new functional context for these glycan-binding domains and providing opportunities to engineer proteases targeting specific glycoproteins for both biomedical and industrial applications.

The HMI™ module: a new tool to study the Host-Microbiota Interaction in the human gastrointestinal tract in vitro.

PubMed

Marzorati, Massimo; Vanhoecke, Barbara; De Ryck, Tine; Sadaghian Sadabad, Mehdi; Pinheiro, Iris; Possemiers, Sam; Van den Abbeele, Pieter; Derycke, Lara; Bracke, Marc; Pieters, Jan; Hennebel, Tom; Harmsen, Hermie J; Verstraete, Willy; Van de Wiele, Tom

2014-05-22

Recent scientific developments have shed more light on the importance of the host-microbe interaction, particularly in the gut. However, the mechanistic study of the host-microbe interplay is complicated by the intrinsic limitations in reaching the different areas of the gastrointestinal tract (GIT) in vivo. In this paper, we present the technical validation of a new device--the Host-Microbiota Interaction (HMI) module--and the evidence that it can be used in combination with a gut dynamic simulator to evaluate the effect of a specific treatment at the level of the luminal microbial community and of the host surface colonization and signaling. The HMI module recreates conditions that are physiologically relevant for the GIT: i) a mucosal area to which bacteria can adhere under relevant shear stress (3 dynes cm(-2)); ii) the bilateral transport of low molecular weight metabolites (4 to 150 kDa) with permeation coefficients ranging from 2.4 × 10(-6) to 7.1 × 10(-9) cm sec(-1); and iii) microaerophilic conditions at the bottom of the growing biofilm (PmO2 = 2.5 × 10(-4) cm sec(-1)). In a long-term study, the host's cells in the HMI module were still viable after a 48-hour exposure to a complex microbial community. The dominant mucus-associated microbiota differed from the luminal one and its composition was influenced by the treatment with a dried product derived from yeast fermentation. The latter--with known anti-inflammatory properties--induced a decrease of pro-inflammatory IL-8 production between 24 and 48 h. The study of the in vivo functionality of adhering bacterial communities in the human GIT and of the localized effect on the host is frequently hindered by the complexity of reaching particular areas of the GIT. The HMI module offers the possibility of co-culturing a gut representative microbial community with enterocyte-like cells up to 48 h and may therefore contribute to the mechanistic understanding of host-microbiome interactions.

Gut-associated microbes of Drosophila melanogaster

PubMed Central

Broderick, Nichole; Lemaitre, Bruno

2012-01-01

There is growing interest in using Drosophila melanogaster to elucidate mechanisms that underlie the complex relationships between a host and its microbiota. In addition to the many genetic resources and tools Drosophila provides, its associated microbiota is relatively simple (1–30 taxa), in contrast to the complex diversity associated with vertebrates (> 500 taxa). These attributes highlight the potential of this system to dissect the complex cellular and molecular interactions that occur between a host and its microbiota. In this review, we summarize what is known regarding the composition of gut-associated microbes of Drosophila and their impact on host physiology. We also discuss these interactions in the context of their natural history and ecology and describe some recent insights into mechanisms by which Drosophila and its gut microbiota interact. “Workers with Drosophila have been considered fortunate in that they deal with the first multicellular invertebrate to be cultured monoxenically (Delcourt and Guyenot, 1910); the first to be handled axenically on a semisynthetic diet (Guyenot, 1917); and the first to be grown on a defined diet (Schultz et al., 1946). This list of advantages is somewhat embarrassing, since it implies an interest in nutrition that, in reality, was only secondary. The very first studies were concerned with the reduction of variability in genetic experiments (Delcourt and Guyenot, 1910) and standardization of the nutritional environment.” -James Sang, 1959 Ann NY Acad 1 PMID:22572876

A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aderem, Alan; Adkins, Joshua N.; Ansong, Charles

The 20th century was marked by extraordinary advances in our understanding of microbes and infectious disease, but pandemics remain, food and water borne illnesses are frequent, multi-drug resistant microbes are on the rise, and the needed drugs and vaccines have not been developed. The scientific approaches of the past—including the intense focus on individual genes and proteins typical of molecular biology—have not been sufficient to address these challenges. The first decade of the 21st century has seen remarkable innovations in technology and computational methods. These new tools provide nearly comprehensive views of complex biological systems and can provide a correspondinglymore » deeper understanding of pathogen-host interactions. To take full advantage of these innovations, the National Institute of Allergy and Infectious Diseases recently initiated the Systems Biology Program for Infectious Disease Research. As participants of the Systems Biology Program we think that the time is at hand to redefine the pathogen-host research paradigm.« less

A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm

PubMed Central

Aderem, Alan; Adkins, Joshua N.; Ansong, Charles; Galagan, James; Kaiser, Shari; Korth, Marcus J.; Law, G. Lynn; McDermott, Jason G.; Proll, Sean C.; Rosenberger, Carrie; Schoolnik, Gary; Katze, Michael G.

2011-01-01

The twentieth century was marked by extraordinary advances in our understanding of microbes and infectious disease, but pandemics remain, food and waterborne illnesses are frequent, multidrug-resistant microbes are on the rise, and the needed drugs and vaccines have not been developed. The scientific approaches of the past—including the intense focus on individual genes and proteins typical of molecular biology—have not been sufficient to address these challenges. The first decade of the twenty-first century has seen remarkable innovations in technology and computational methods. These new tools provide nearly comprehensive views of complex biological systems and can provide a correspondingly deeper understanding of pathogen-host interactions. To take full advantage of these innovations, the National Institute of Allergy and Infectious Diseases recently initiated the Systems Biology Program for Infectious Disease Research. As participants of the Systems Biology Program, we think that the time is at hand to redefine the pathogen-host research paradigm. PMID:21285433

Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity

PubMed Central

Troussellier, Marc; Escalas, Arthur; Bouvier, Thierry; Mouillot, David

2017-01-01

Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism–microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares, which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members. PMID:28611749

Biodiversity and Functional Genomics in the Human Microbiome

PubMed Central

Morgan, Xochitl C.; Segata, Nicola; Huttenhower, Curtis

2012-01-01

Over the course of our lives, humans are colonized by a tremendous diversity of commensal microbes, which comprise the human microbiome. The collective genetic potential (metagenome) of the human microbiome is orders of magnitude more than the human genome, and it profoundly affects human health and disease in ways we are only beginning to understand. Advances in computing and high-throughput sequencing have enabled population-level surveys such as MetaHIT and the recently-released Human Microbiome Project, detailed investigations of the microbiome in human disease, and mechanistic studies employing gnotobiotic model organisms. The resulting knowledge of human microbiome composition, function, and range of variation across multiple body sites has begun to assemble a rich picture of commensal host-microbe and microbe- microbe interactions as well as their roles in human health and disease and their potential as diagnostic and therapeutic tools. PMID:23140990

Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle

PubMed Central

Gutzwiller, Florence; Carmo, Catarina R.; Miller, Danny E.; Rice, Danny W.; Newton, Irene L. G.; Hawley, R. Scott; Teixeira, Luis; Bergman, Casey M.

2015-01-01

Symbiotic interactions between microbes and their multicellular hosts have manifold biological consequences. To better understand how bacteria maintain symbiotic associations with animal hosts, we analyzed genome-wide gene expression for the endosymbiotic α-proteobacteria Wolbachia pipientis across the entire life cycle of Drosophila melanogaster. We found that the majority of Wolbachia genes are expressed stably across the D. melanogaster life cycle, but that 7.8% of Wolbachia genes exhibit robust stage- or sex-specific expression differences when studied in the whole-organism context. Differentially-expressed Wolbachia genes are typically up-regulated after Drosophila embryogenesis and include many bacterial membrane, secretion system, and ankyrin repeat-containing proteins. Sex-biased genes are often organized as small operons of uncharacterized genes and are mainly up-regulated in adult Drosophila males in an age-dependent manner. We also systematically investigated expression levels of previously-reported candidate genes thought to be involved in host-microbe interaction, including those in the WO-A and WO-B prophages and in the Octomom region, which has been implicated in regulating bacterial titer and pathogenicity. Our work provides comprehensive insight into the developmental dynamics of gene expression for a widespread endosymbiont in its natural host context, and shows that public gene expression data harbor rich resources to probe the functional basis of the Wolbachia-Drosophila symbiosis and annotate the transcriptional outputs of the Wolbachia genome. PMID:26497146

Special issue Oceans and Humans Health: the ecology of marine opportunists.

PubMed

Burge, Colleen A; Kim, Catherine J S; Lyles, Jillian M; Harvell, C Drew

2013-05-01

Opportunistic marine pathogens, like opportunistic terrestrial pathogens, are ubiquitous in the environment (waters, sediments, and organisms) and only cause disease in immune-compromised or stressed hosts. In this review, we discuss four host-pathogen interactions within the marine environment that are typically considered opportunistic: sea fan coral-fungus, eelgrass-Labyrinthula zosterae, sea fan-Labyrinthulomycetes, and hard clam-Quahog Parasite Unknown with particular focus on disease ecology, parasite pathology, host response, and known associated environmental conditions. Disease is a natural part of all ecosystems; however, in some cases, a shift in the balance between the host, pathogen, and the environment may lead to epizootics in natural or cultured populations. In marine systems, host-microbe interactions are less understood than their terrestrial counterparts. The biological and physical changes to the world's oceans, coupled with other anthropogenic influences, will likely lead to more opportunistic diseases in the marine environment.

Role of antimicrobial peptides in controlling symbiotic bacterial populations.

PubMed

Mergaert, P

2018-04-25

Covering: up to 2018 Antimicrobial peptides (AMPs) have been known for well over three decades as crucial mediators of the innate immune response in animals and plants, where they are involved in the killing of infecting microbes. However, AMPs have now also been found to be produced by eukaryotic hosts during symbiotic interactions with bacteria. These symbiotic AMPs target the symbionts and therefore have a more subtle biological role: not eliminating the microbial symbiont population but rather keeping it in check. The arsenal of AMPs and the symbionts' adaptations to resist them are in a careful balance, which contributes to the establishment of the host-microbe homeostasis. Although in many cases the biological roles of symbiotic AMPs remain elusive, for a number of symbiotic interactions, precise functions have been assigned or proposed to the AMPs, which are discussed here. The microbiota living on epithelia in animals, from the most primitive ones to the mammals, are challenged by a cocktail of AMPs that determine the specific composition of the bacterial community as well as its spatial organization. In the symbiosis of legume plants with nitrogen-fixing rhizobium bacteria, the host deploys an extremely large panel of AMPs - called nodule-specific cysteine-rich (NCR) peptides - that drive the bacteria into a terminally differentiated state and manipulate the symbiont physiology to maximize the benefit for the host. The NCR peptides are used as tools to enslave the bacterial symbionts, limiting their reproduction but keeping them metabolically active for nitrogen fixation. In the nutritional symbiotic interactions of insects and protists that have vertically transmitted bacterial symbionts with reduced genomes, symbiotic AMPs could facilitate the integration of the endosymbiont and host metabolism by favouring the flow of metabolites across the symbiont membrane through membrane permeabilization.

Unraveling the environmental and genetic interactions in atherosclerosis: Central role of the gut microbiota.

PubMed

Org, Elin; Mehrabian, Margarete; Lusis, Aldons J

2015-08-01

Recent studies have convincingly linked gut microbiota to traits relevant to atherosclerosis, such as insulin resistance, dyslipidemia and inflammation, and have revealed novel disease pathways involving microbe-derived metabolites. These results have important implications for understanding how environmental and genetic factors act together to influence cardiovascular disease (CVD) risk. Thus, dietary constituents are not only absorbed and metabolized by the host but they also perturb the gut microbiota, which in turn influence host metabolism and inflammation. It also appears that host genetics helps to shape the gut microbiota community. Here, we discuss challenges in understanding these interactions and the role they play in CVD. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Sponge-Associated Microorganisms: Evolution, Ecology, and Biotechnological Potential†

PubMed Central

Taylor, Michael W.; Radax, Regina; Steger, Doris; Wagner, Michael

2007-01-01

Summary: Marine sponges often contain diverse and abundant microbial communities, including bacteria, archaea, microalgae, and fungi. In some cases, these microbial associates comprise as much as 40% of the sponge volume and can contribute significantly to host metabolism (e.g., via photosynthesis or nitrogen fixation). We review in detail the diversity of microbes associated with sponges, including extensive 16S rRNA-based phylogenetic analyses which support the previously suggested existence of a sponge-specific microbiota. These analyses provide a suitable vantage point from which to consider the potential evolutionary and ecological ramifications of these widespread, sponge-specific microorganisms. Subsequently, we examine the ecology of sponge-microbe associations, including the establishment and maintenance of these sometimes intimate partnerships, the varied nature of the interactions (ranging from mutualism to host-pathogen relationships), and the broad-scale patterns of symbiont distribution. The ecological and evolutionary importance of sponge-microbe associations is mirrored by their enormous biotechnological potential: marine sponges are among the animal kingdom's most prolific producers of bioactive metabolites, and in at least some cases, the compounds are of microbial rather than sponge origin. We review the status of this important field, outlining the various approaches (e.g., cultivation, cell separation, and metagenomics) which have been employed to access the chemical wealth of sponge-microbe associations. PMID:17554047

Standardised animal models of host microbial mutualism

PubMed Central

Macpherson, A J; McCoy, K D

2015-01-01

An appreciation of the importance of interactions between microbes and multicellular organisms is currently driving research in biology and biomedicine. Many human diseases involve interactions between the host and the microbiota, so investigating the mechanisms involved is important for human health. Although microbial ecology measurements capture considerable diversity of the communities between individuals, this diversity is highly problematic for reproducible experimental animal models that seek to establish the mechanistic basis for interactions within the overall host-microbial superorganism. Conflicting experimental results may be explained away through unknown differences in the microbiota composition between vivaria or between the microenvironment of different isolated cages. In this position paper, we propose standardised criteria for stabilised and defined experimental animal microbiotas to generate reproducible models of human disease that are suitable for systematic experimentation and are reproducible across different institutions. PMID:25492472

Impact of simulated microgravity on the normal developmental time line of an animal-bacteria symbiosis

PubMed Central

Foster, Jamie S.; Khodadad, Christina L. M.; Ahrendt, Steven R.; Parrish, Mirina L.

2013-01-01

The microgravity environment during space flight imposes numerous adverse effects on animal and microbial physiology. It is unclear, however, how microgravity impacts those cellular interactions between mutualistic microbes and their hosts. Here, we used the symbiosis between the host squid Euprymna scolopes and its luminescent bacterium Vibrio fischeri as a model system. We examined the impact of simulated microgravity on the timeline of bacteria-induced development in the host light organ, the site of the symbiosis. To simulate the microgravity environment, host squid and symbiosis-competent bacteria were incubated together in high-aspect ratio rotating wall vessel bioreactors and examined throughout the early stages of the bacteria-induced morphogenesis. The host innate immune response was suppressed under simulated microgravity; however, there was an acceleration of bacteria-induced apoptosis and regression in the host tissues. These results suggest that the space flight environment may alter the cellular interactions between animal hosts and their natural healthy microbiome. PMID:23439280

Kingdom-agnostic Metagenomics and the Importance of Complete Characterization of Enteric Microbial Communities

PubMed Central

Norman, Jason M.; Handley, Scott A.; Virgin, Herbert W.

2014-01-01

Advanced sequencing techniques have shown that bacteria are not the only complex and important microbes in the human intestine. Non-bacterial organisms, particularly the virome and the mycobiome, are important regulators of intestinal immunity and inflammation. The virome is mucosal and systemic; it can alter the host response to bacteria and interact with host genes and bacteria to contribute to disease pathogenesis. The human mycobiome is also complex and can contribute to intestinal inflammation. We review what has recently been learned about the non-bacterial and non-archaeal microbes in the gastrointestinal tract, discussing their potential effects on health and disease and analytical approaches for their study. Studies of associations between the microbiome and intestinal pathology should incorporate kingdom-agnostic approaches if we are to fully understand intestinal health and disease. PMID:24508599

Advances and perspectives in in vitro human gut fermentation modeling.

PubMed

Payne, Amanda N; Zihler, Annina; Chassard, Christophe; Lacroix, Christophe

2012-01-01

The gut microbiota is a highly specialized organ containing host-specific assemblages of microbes whereby metabolic activity directly impacts human health and disease. In vitro gut fermentation models present an unmatched opportunity of performing studies frequently challenged in humans and animals owing to ethical concerns. Multidisciplinary systems biology analyses supported by '-omics' platforms remain widely neglected in the field of in vitro gut fermentation modeling but are key to advancing the significance of these models. Model-driven experimentation using a combination of in vitro gut fermentation and in vitro human cell models represent an advanced approach in identifying complex host-microbe interactions and niches central to gut fermentation processes. The aim of this review is to highlight the advances and challenges exhibited by in vitro human gut fermentation modeling. Copyright © 2011 Elsevier Ltd. All rights reserved.

Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems: Variable phage-host infection interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holmfeldt, Karin; Solonenko, Natalie; Howard-Varona, Cristina

Microbes drive ecosystem functioning and their viruses modulate these impacts through mortality, gene transfer and metabolic reprogramming. Despite the importance of virus-host interactions and likely variable infection efficiencies of individual phages across hosts, such variability is seldom quantified. In this paper, we quantify infection efficiencies of 38 phages against 19 host strains in aquatic Cellulophaga (Bacteroidetes) phage-host model systems. Binary data revealed that some phages infected only one strain while others infected 17, whereas quantitative data revealed that efficiency of infection could vary 10 orders of magnitude, even among phages within one population. This provides a baseline for understanding andmore » modeling intrapopulation host range variation. Genera specific host ranges were also informative. For example, the Cellulophaga Microviridae, showed a markedly broader intra-species host range than previously observed in Escherichia coli systems. Further, one phage genus, Cba41, was examined to investigate nonheritable changes in plating efficiency and burst size that depended on which host strain it most recently infected. While consistent with host modification of phage DNA, no differences in nucleotide sequence or DNA modifications were detected, leaving the observation repeatable, but the mechanism unresolved. Overall, this study highlights the importance of quantitatively considering replication variations in studies of phage-host interactions.« less

Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems: Variable phage-host infection interactions

DOE PAGES

Holmfeldt, Karin; Solonenko, Natalie; Howard-Varona, Cristina; ...

2016-06-28

Microbes drive ecosystem functioning and their viruses modulate these impacts through mortality, gene transfer and metabolic reprogramming. Despite the importance of virus-host interactions and likely variable infection efficiencies of individual phages across hosts, such variability is seldom quantified. In this paper, we quantify infection efficiencies of 38 phages against 19 host strains in aquatic Cellulophaga (Bacteroidetes) phage-host model systems. Binary data revealed that some phages infected only one strain while others infected 17, whereas quantitative data revealed that efficiency of infection could vary 10 orders of magnitude, even among phages within one population. This provides a baseline for understanding andmore » modeling intrapopulation host range variation. Genera specific host ranges were also informative. For example, the Cellulophaga Microviridae, showed a markedly broader intra-species host range than previously observed in Escherichia coli systems. Further, one phage genus, Cba41, was examined to investigate nonheritable changes in plating efficiency and burst size that depended on which host strain it most recently infected. While consistent with host modification of phage DNA, no differences in nucleotide sequence or DNA modifications were detected, leaving the observation repeatable, but the mechanism unresolved. Overall, this study highlights the importance of quantitatively considering replication variations in studies of phage-host interactions.« less

First impressions in a glowing host-microbe partnership.

PubMed

Wernegreen, Jennifer J

2013-08-14

Despite the clear significance of beneficial animal-microbe associations, mechanisms underlying their initiation and establishment are rarely understood. In this issue of Cell Host & Microbe, Kremer et al. (2013) reveal that first contact within the squid-vibrio symbiosis triggers profound molecular and chemical changes that are crucial for bacterial colonization. Copyright © 2013 Elsevier Inc. All rights reserved.

Communication between Bacteria and Their Hosts

PubMed Central

2013-01-01

It is clear that a dialogue is occurring between microbes and their hosts and that chemical signals are the language of this interkingdom communication. Microbial endocrinology shows that, through their long coexistence with animals and plants, microorganisms have evolved sensors for detecting eukaryotic hormones, which the microbe uses to determine that they are within proximity of a suitable host and to optimally time the expression of genes needed for host colonisation. It has also been shown that some prokaryotic chemical communication signals are recognized by eukaryotes. Deciphering what is being said during the cross-talk between microbe and host is therefore important, as it could lead to new strategies for preventing or treating bacterial infections. PMID:24381789

Microbes in the coral holobiont: partners through evolution, development, and ecological interactions

PubMed Central

Thompson, Janelle R.; Rivera, Hanny E.; Closek, Collin J.; Medina, Mónica

2015-01-01

In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health—not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein, we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al. (2013) in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: (1) How do corals and their microbiome affect each other's genomes? (2) How does coral development depend on microbial partners? (3) How is homeostasis maintained between corals and their microbial symbionts? (4) How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions. PMID:25621279

Gut Microbiota Modulation and Its Relationship with Obesity Using Prebiotic Fibers and Probiotics: A Review.

PubMed

Dahiya, Dinesh K; Renuka; Puniya, Monica; Shandilya, Umesh K; Dhewa, Tejpal; Kumar, Nikhil; Kumar, Sanjeev; Puniya, Anil K; Shukla, Pratyoosh

2017-01-01

In the present world scenario, obesity has almost attained the level of a pandemic and is progressing at a rapid rate. This disease is the mother of all other metabolic disorders, which apart from placing an added financial burden on the concerned patient also has a negative impact on his/her well-being and health in the society. Among the various plausible factors for the development of obesity, the role of gut microbiota is very crucial. In general, the gut of an individual is inhabited by trillions of microbes that play a significant role in host energy homeostasis by their symbiotic interactions. Dysbiosis in gut microbiota causes disequilibrium in energy homeostasis that ultimately leads to obesity. Numerous mechanisms have been reported by which gut microbiota induces obesity in experimental models. However, which microbial community is directly linked to obesity is still unknown due to the complex nature of gut microbiota. Prebiotics and probiotics are the safer and effective dietary substances available, which can therapeutically alter the gut microbiota of the host. In this review, an effort was made to discuss the current mechanisms through which gut microbiota interacts with host energy metabolism in the context of obesity. Further, the therapeutic approaches (prebiotics/probiotics) that helped in positively altering the gut microbiota were discussed by taking experimental evidence from animal and human studies. In the closing statement, the challenges and future tasks within the field were discussed.

Gut Microbiota Modulation and Its Relationship with Obesity Using Prebiotic Fibers and Probiotics: A Review

PubMed Central

Dahiya, Dinesh K.; Renuka; Puniya, Monica; Shandilya, Umesh K.; Dhewa, Tejpal; Kumar, Nikhil; Kumar, Sanjeev; Puniya, Anil K.; Shukla, Pratyoosh

2017-01-01

In the present world scenario, obesity has almost attained the level of a pandemic and is progressing at a rapid rate. This disease is the mother of all other metabolic disorders, which apart from placing an added financial burden on the concerned patient also has a negative impact on his/her well-being and health in the society. Among the various plausible factors for the development of obesity, the role of gut microbiota is very crucial. In general, the gut of an individual is inhabited by trillions of microbes that play a significant role in host energy homeostasis by their symbiotic interactions. Dysbiosis in gut microbiota causes disequilibrium in energy homeostasis that ultimately leads to obesity. Numerous mechanisms have been reported by which gut microbiota induces obesity in experimental models. However, which microbial community is directly linked to obesity is still unknown due to the complex nature of gut microbiota. Prebiotics and probiotics are the safer and effective dietary substances available, which can therapeutically alter the gut microbiota of the host. In this review, an effort was made to discuss the current mechanisms through which gut microbiota interacts with host energy metabolism in the context of obesity. Further, the therapeutic approaches (prebiotics/probiotics) that helped in positively altering the gut microbiota were discussed by taking experimental evidence from animal and human studies. In the closing statement, the challenges and future tasks within the field were discussed. PMID:28421057

Multi-omics analysis of inflammatory bowel disease.

PubMed

Huang, Hu; Vangay, Pajau; McKinlay, Christopher E; Knights, Dan

2014-12-01

Crohn's disease and ulcerative colitis, known together as inflammatory bowel disease (IBD), are severe autoimmune disorders now causing gut inflammation and ulceration, among other symptoms, in up to 1 in 250 people worldwide. Incidence and prevalence of IBD have been increasing dramatically over the past several decades, although the causes for this increase are still unknown. IBD has both a complex genotype and a complex phenotype, and although it has received substantial attention from the medical research community over recent years, much of the etiology remains unexplained. Genome-wide association studies have identified a rich genetic signature of disease risk in patients with IBD, consisting of at least 163 genetic loci. Many of these loci contain genes directly involved in microbial handling, indicating that the genetic architecture of the disease has been driven by host-microbe interactions. In addition, systematic shifts in gut microbiome structure (enterotype) and function have been observed in patients with IBD. Furthermore, both the host genotype and enterotype are associated with aspects of the disease phenotype, including location of the disease. This provides strong evidence of interactions between host genotype and enterotype; however, there is a lack of published multi-omics data from IBD patients, and a lack of bioinformatics tools for modeling such systems. In this article we discuss, from a computational biologist's point of view, the potential benefits of and the challenges involved in designing and analyzing such multi-omics studies of IBD. Copyright © 2014 Elsevier B.V. All rights reserved.

Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions.

PubMed

Dheilly, Nolwenn M; Bolnick, Daniel; Bordenstein, Seth; Brindley, Paul J; Figuères, Cédric; Holmes, Edward C; Martínez Martínez, Joaquín; Phillips, Anna J; Poulin, Robert; Rosario, Karyna

2017-01-01

Understanding how microbiomes affect host resistance, parasite virulence, and parasite-associated diseases requires a collaborative effort between parasitologists, microbial ecologists, virologists, and immunologists. We hereby propose the Parasite Microbiome Project to bring together researchers with complementary expertise and to study the role of microbes in host-parasite interactions. Data from the Parasite Microbiome Project will help identify the mechanisms driving microbiome variation in parasites and infected hosts and how that variation is associated with the ecology and evolution of parasites and their disease outcomes. This is a call to arms to prevent fragmented research endeavors, encourage best practices in experimental approaches, and allow reliable comparative analyses across model systems. It is also an invitation to foundations and national funding agencies to propel the field of parasitology into the microbiome/metagenomic era.

Understanding and engineering beneficial plant–microbe interactions: plant growth promotion in energy crops

PubMed Central

Farrar, Kerrie; Bryant, David; Cope-Selby, Naomi

2014-01-01

Plant production systems globally must be optimized to produce stable high yields from limited land under changing and variable climates. Demands for food, animal feed, and feedstocks for bioenergy and biorefining applications, are increasing with population growth, urbanization and affluence. Low-input, sustainable, alternatives to petrochemical-derived fertilizers and pesticides are required to reduce input costs and maintain or increase yields, with potential biological solutions having an important role to play. In contrast to crops that have been bred for food, many bioenergy crops are largely undomesticated, and so there is an opportunity to harness beneficial plant–microbe relationships which may have been inadvertently lost through intensive crop breeding. Plant–microbe interactions span a wide range of relationships in which one or both of the organisms may have a beneficial, neutral or negative effect on the other partner. A relatively small number of beneficial plant–microbe interactions are well understood and already exploited; however, others remain understudied and represent an untapped reservoir for optimizing plant production. There may be near-term applications for bacterial strains as microbial biopesticides and biofertilizers to increase biomass yield from energy crops grown on land unsuitable for food production. Longer term aims involve the design of synthetic genetic circuits within and between the host and microbes to optimize plant production. A highly exciting prospect is that endosymbionts comprise a unique resource of reduced complexity microbial genomes with adaptive traits of great interest for a wide variety of applications. PMID:25431199

Yersinia vs. host Immunity: how a pathogen evades or triggers a protective response

PubMed Central

Chung, Lawton K.; Bliska, James B.

2015-01-01

The human pathogenic Yersinia species cause diseases that represent a significant source of morbidity and mortality. Despite this, specific mechanisms underlying Yersinia pathogenesis and protective host responses remain poorly understood. Recent studies have shown that Yersinia disrupt cell death pathways, perturb inflammatory processes and exploit immune cells to promote disease. The ensuing host responses following Yersinia infection include coordination of innate and adaptive immune responses in an attempt to control bacterial replication. Here, we highlight current advances in our understanding of the interactions between the pathogenic yersiniae and host cells, as well as the protective host responses mobilized to counteract these pathogens. Together, these studies enhance our understanding of Yersinia pathogenesis and highlight the ongoing battle between host and microbe. PMID:26638030

Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis.

PubMed

Sung, Jaeyun; Kim, Seunghyeon; Cabatbat, Josephine Jill T; Jang, Sungho; Jin, Yong-Su; Jung, Gyoo Yeol; Chia, Nicholas; Kim, Pan-Jun

2017-06-06

A system-level framework of complex microbe-microbe and host-microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a literature-curated interspecies network of the human gut microbiota, called NJS16. This is an extensive data resource composed of ∼570 microbial species and 3 human cell types metabolically interacting through >4,400 small-molecule transport and macromolecule degradation events. Based on the contents of our network, we develop a mathematical approach to elucidate representative microbial and metabolic features of the gut microbial community in a given population, such as a disease cohort. Applying this strategy to microbiome data from type 2 diabetes patients reveals a context-specific infrastructure of the gut microbial ecosystem, core microbial entities with large metabolic influence, and frequently produced metabolic compounds that might indicate relevant community metabolic processes. Our network presents a foundation towards integrative investigations of community-scale microbial activities within the human gut.

Review: Pathogenesis of canine atopic dermatitis: skin barrier and host-micro-organism interaction.

PubMed

Santoro, Domenico; Marsella, Rosanna; Pucheu-Haston, Cherie M; Eisenschenk, Melissa N C; Nuttall, Tim; Bizikova, Petra

2015-04-01

Canine atopic dermatitis (AD) is a common, genetically predisposed, inflammatory and pruritic skin disease. The pathogenesis of canine AD is incompletely understood. The aim of this review is to provide an in-depth update on the involvement of skin barrier and host-microbiome interaction in the pathogenesis of canine AD. Online citation databases and abstracts from international meetings were searched for publications related to skin barrier and host-microbiome interaction (e.g. bacteria, yeast, antimicrobial peptides). A total of 126 publications were identified. This review article focuses on epidermal barrier dysfunction and the interaction between cutaneous microbes (bacteria and yeasts) and the host (antimicrobial peptides). Epidemiological updates on the presence of pathogenic organisms and canine AD are also provided. Major advances have been made in the investigation of skin barrier dysfunction in canine AD, although many questions still remain. Skin barrier dysfunction and host-microbiome interactions are emerging as primary alterations in canine AD. Based on this review, it is clear that future studies focused on the development of drugs able to restore the skin barrier and increase the natural defences against pathogenic organisms are needed. © 2015 ESVD and ACVD.

Nutrient-Dependent Impact of Microbes on Drosophila suzukii Development.

PubMed

Bing, XiaoLi; Gerlach, Joseph; Loeb, Gregory; Buchon, Nicolas

2018-03-20

Drosophila suzukii Matsumura is an invasive species of vinegar fly that has become a prominent pest of berries and other soft-skinned fruits. Unlike most other Drosophila species, female D. suzukii flies lay their eggs in ripening and ripe fruits and larvae develop within the fruit. To understand how D. suzukii larvae utilize ripe and ripening fruits, which usually have low levels of protein, we investigated the microbiota of field-captured and laboratory-reared D. suzukii flies and further examined the combined influence of diet and microbes on host fitness. Field-captured flies were associated with diverse microbiota, which varied significantly with sampling location and season. In contrast, laboratory-reared flies possessed strikingly lower bacterial abundance and diversity. A comparison of conventionally reared (CR) and germ-free (GF) flies revealed that the microbiota of D. suzukii does not alter its development significantly but decreases its life span under conditions of a nutrient-sufficient diet. However, the microbiota is essential for D. suzukii development on strawberry-based or blueberry-based fruit diets. This developmental failure could be rescued by reassociation with single bacterial or fungal species or by the addition of a high quantity of heat-killed microbes. In addition, we found that proteins are limiting with respect to fly development on fruit-based diets and that GF flies show signs of protein starvation. Taken together, our study results demonstrate that the microbiota provides key proteins required for the development of D. suzukii reared on fresh fruit. Our work shows that the impact of microbes on fly fitness depends strongly on nutritional conditions. IMPORTANCE Animals are commonly associated with specific microbes, which play important roles in host development and fitness. However, little information about the function of microbes has been available for the important invasive pest Drosophila suzukii , also known as Spotted wing drosophila. Our study results demonstrate that the abundance and structure of microbiota in D. suzukii are strongly affected by the environment, where microbes have variable roles depending on the nutritional situation. For instance, we found that the presence of microbes is deleterious for flies growing on a protein-rich diet and yet is beneficial for flies growing on a diet of protein-poor fruits. Additionally, germ-free flies must feed on microbes to obtain the necessary protein for larval development on strawberries and blueberries. Our report validates the complexity seen in host-microbe interactions and may provide information useful for D. suzukii pest control. Copyright © 2018 Bing et al.

Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem1[C

PubMed Central

Lakshmanan, Venkatachalam; Selvaraj, Gopinath; Bais, Harsh P.

2014-01-01

There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security. PMID:25059708

The HMI™ module: a new tool to study the Host-Microbiota Interaction in the human gastrointestinal tract in vitro

PubMed Central

2014-01-01

Background Recent scientific developments have shed more light on the importance of the host-microbe interaction, particularly in the gut. However, the mechanistic study of the host-microbe interplay is complicated by the intrinsic limitations in reaching the different areas of the gastrointestinal tract (GIT) in vivo. In this paper, we present the technical validation of a new device - the Host-Microbiota Interaction (HMI) module - and the evidence that it can be used in combination with a gut dynamic simulator to evaluate the effect of a specific treatment at the level of the luminal microbial community and of the host surface colonization and signaling. Results The HMI module recreates conditions that are physiologically relevant for the GIT: i) a mucosal area to which bacteria can adhere under relevant shear stress (3 dynes cm−2); ii) the bilateral transport of low molecular weight metabolites (4 to 150 kDa) with permeation coefficients ranging from 2.4 × 10−6 to 7.1 × 10−9 cm sec−1; and iii) microaerophilic conditions at the bottom of the growing biofilm (PmO2 = 2.5 × 10−4 cm sec−1). In a long-term study, the host’s cells in the HMI module were still viable after a 48-hour exposure to a complex microbial community. The dominant mucus-associated microbiota differed from the luminal one and its composition was influenced by the treatment with a dried product derived from yeast fermentation. The latter - with known anti-inflammatory properties - induced a decrease of pro-inflammatory IL-8 production between 24 and 48 h. Conclusions The study of the in vivo functionality of adhering bacterial communities in the human GIT and of the localized effect on the host is frequently hindered by the complexity of reaching particular areas of the GIT. The HMI module offers the possibility of co-culturing a gut representative microbial community with enterocyte-like cells up to 48 h and may therefore contribute to the mechanistic understanding of host-microbiome interactions. PMID:24884540

Host-microbe interactions in distal airways: relevance to chronic airway diseases.

PubMed

Martin, Clémence; Burgel, Pierre-Régis; Lepage, Patricia; Andréjak, Claire; de Blic, Jacques; Bourdin, Arnaud; Brouard, Jacques; Chanez, Pascal; Dalphin, Jean-Charles; Deslée, Gaetan; Deschildre, Antoine; Gosset, Philippe; Touqui, Lhousseine; Dusser, Daniel

2015-03-01

This article is the summary of a workshop, which took place in November 2013, on the roles of microorganisms in chronic respiratory diseases. Until recently, it was assumed that lower airways were sterile in healthy individuals. However, it has long been acknowledged that microorganisms could be identified in distal airway secretions from patients with various respiratory diseases, including cystic fibrosis (CF) and non-CF bronchiectasis, chronic obstructive pulmonary disease, asthma and other chronic airway diseases (e.g. post-transplantation bronchiolitis obliterans). These microorganisms were sometimes considered as infectious agents that triggered host immune responses and contributed to disease onset and/or progression; alternatively, microorganisms were often considered as colonisers, which were considered unlikely to play roles in disease pathophysiology. These concepts were developed at a time when the identification of microorganisms relied on culture-based methods. Importantly, the majority of microorganisms cannot be cultured using conventional methods, and the use of novel culture-independent methods that rely on the identification of microorganism genomes has revealed that healthy distal airways display a complex flora called the airway microbiota. The present article reviews some aspects of current literature on host-microbe (mostly bacteria and viruses) interactions in healthy and diseased airways, with a special focus on distal airways. Copyright ©ERS 2015.

Microbial Metabolic Networks at the Mucus Layer Lead to Diet-Independent Butyrate and Vitamin B12 Production by Intestinal Symbionts

PubMed Central

Chia, Loo Wee; Aalvink, Steven; Chamlagain, Bhawani; Piironen, Vieno; Knol, Jan; de Vos, Willem M.

2017-01-01

ABSTRACT Akkermansia muciniphila has evolved to specialize in the degradation and utilization of host mucus, which it may use as the sole source of carbon and nitrogen. Mucus degradation and fermentation by A. muciniphila are known to result in the liberation of oligosaccharides and subsequent production of acetate, which becomes directly available to microorganisms in the vicinity of the intestinal mucosa. Coculturing experiments of A. muciniphila with non-mucus-degrading butyrate-producing bacteria Anaerostipes caccae, Eubacterium hallii, and Faecalibacterium prausnitzii resulted in syntrophic growth and production of butyrate. In addition, we demonstrate that the production of pseudovitamin B12 by E. hallii results in production of propionate by A. muciniphila, which suggests that this syntrophy is indeed bidirectional. These data are proof of concept for syntrophic and other symbiotic microbe-microbe interactions at the intestinal mucosal interface. The observed metabolic interactions between A. muciniphila and butyrogenic bacterial taxa support the existence of colonic vitamin and butyrate production pathways that are dependent on host glycan production and independent of dietary carbohydrates. We infer that the intestinal symbiont A. muciniphila can indirectly stimulate intestinal butyrate levels in the vicinity of the intestinal epithelial cells with potential health benefits to the host. PMID:28928206

Comparative analysis of Leishmania exoproteomes: implication for host-pathogen interactions.

PubMed

Peysselon, Franck; Launay, Guillaume; Lisacek, Frédérique; Duclos, Bertrand; Ricard-Blum, Sylvie

2013-12-01

Leishmaniasis is a vector-borne disease caused by the protozoa Leishmania. We have analyzed and compared the sequences of three experimental exoproteomes of Leishmania promastigotes from different species to determine their specific features and to identify new candidate proteins involved in interactions of Leishmania with the host. The exoproteomes differ from the proteomes by a decrease in the average molecular weight per protein, in disordered amino acid residues and in basic proteins. The exoproteome of the visceral species is significantly enriched in sites predicted to be phosphorylated as well as in features frequently associated with molecular interactions (intrinsic disorder, number of disordered binding regions per protein, interaction and/or trafficking motifs) compared to the other species. The visceral species might thus have a larger interaction repertoire with the host than the other species. Less than 10% of the exoproteomes contain heparin-binding and RGD sequences, and ~30% the host targeting signal RXLXE/D/Q. These latter proteins might thus be exported inside the host cell during the intracellular stage of the infection. Furthermore we have identified nine protein families conserved in the three exoproteomes with specific combinations of Pfam domains and selected eleven proteins containing at least three interaction and/or trafficking motifs including two splicing factors, phosphomannomutase, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, the paraflagellar rod protein-1D and a putative helicase. Their role in host-Leishmania interactions warrants further investigation but the putative ATP-dependent DEAD/H RNA helicase, which contains numerous interaction motifs, a host targeting signal and two disordered regions, is a very promising candidate. © 2013.

Protein interaction networks at the host-microbe interface in Diaphorina citri, the insect vector of the citrus greening pathogen

USDA-ARS?s Scientific Manuscript database

The Asian citrus psyllid (Diaphorina citri) is the insect vector responsible for the worldwide spread of Candidatus Liberibacter asiaticus, the bacterial pathogen associated with citrus greening disease. Developmental changes in the insect vector impact pathogen transmission, such that D. citri tra...

Pyrosequencing reveals the predominance of Pseudomonadaceae in gut microbiome of a Gall Midge

USDA-ARS?s Scientific Manuscript database

Gut microbes are known to play various roles in insects such as digestion of inaccessible nutrients, synthesis of deficient amino acids, and interaction with ecological environments, including host plants. Here, we analyzed the gut microbiome in Hessian fly, a serious pest of wheat. A total of 3,654...

The common mouse protozoa Tritrichomonas muris alters mucosal T cell homeostasis and colitis susceptibility.

PubMed

Escalante, Nichole K; Lemire, Paul; Cruz Tleugabulova, Mayra; Prescott, David; Mortha, Arthur; Streutker, Catherine J; Girardin, Stephen E; Philpott, Dana J; Mallevaey, Thierry

2016-12-12

The mammalian gastrointestinal tract hosts a diverse community of microbes including bacteria, fungi, protozoa, helminths, and viruses. Through coevolution, mammals and these microbes have developed a symbiosis that is sustained through the host's continuous sensing of microbial factors and the generation of a tolerant or pro-inflammatory response. While analyzing T cell-driven colitis in nonlittermate mouse strains, we serendipitously identified that a nongenetic transmissible factor dramatically increased disease susceptibility. We identified the protozoan Tritrichomonas muris as the disease-exacerbating element. Furthermore, experimental colonization with T. muris induced an elevated Th1 response in the cecum of naive wild-type mice and accelerated colitis in Rag1 -/- mice after T cell transfer. Overall, we describe a novel cross-kingdom interaction within the murine gut that alters immune cell homeostasis and disease susceptibility. This example of unpredicted microbial priming of the immune response highlights the importance of studying trans-kingdom interactions and serves as a stark reminder of the importance of using littermate controls in all mouse research. © 2016 Escalante et al.

Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential

PubMed Central

Haldar, Shyamalina; Sengupta, Sanghamitra

2015-01-01

Rhizosphere, the interface between soil and plant roots, is a chemically complex environment which supports the development and growth of diverse microbial communities. The composition of the rhizosphere microbiome is dynamic and controlled by multiple biotic and abiotic factors that include environmental parameters, physiochemical properties of the soil, biological activities of the plants and chemical signals from the plants and bacteria which inhabit the soil adherent to root-system. Recent advancement in molecular and microbiological techniques has unravelled the interactions among rhizosphere residents at different levels. In this review, we elaborate on various factors that determine plant-microbe and microbe-microbe interactions in the rhizosphere, with an emphasis on the impact of host genotype and developmental stages which together play pivotal role in shaping the nature and diversity of root exudations. We also discuss about the coherent functional groups of microorganisms that colonize rhizosphere and enhance plant growth and development by several direct and indirect mechanisms. Insights into the underlying structural principles of indigenous microbial population and the key determinants governing rhizosphere ecology will provide directions for developing techniques for profitable applicability of beneficial microorganisms in sustainable agriculture and nature restoration. PMID:25926899

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis

DOE PAGES

Cross, Karissa L.; Chirania, Payal; Xiong, Weili; ...

2018-03-13

The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously unculturedDesulfobulbus oralis , the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives,D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities. The genes that enable free-living Desulfobulbus to synthesize the potent neurotoxin methylmercury weremore » also lost byD. oralis, a notably positive outcome of host association. However, horizontal gene acquisitions from other members of the microbiota provided novel mechanisms of interaction with the human host, including toxins like leukotoxin and hemolysins. Proteomic and transcriptomic analysis revealed that most of those factors are actively expressed, including in the subgingival environment, and some are secreted. Similar to other known oral pathobionts, D. oralis can trigger a proinflammatory response in oral epithelial cells, suggesting a direct role in the development of periodontal disease. Animal-associated microbiota likely assembled as a result of numerous independent colonization events by free-living microbes followed by coevolution with their host and other microbes. Through specific adaptation to various body sites and physiological niches, microbes have a wide range of contributions, from beneficial to disease causing.Desulfobulbus oralis provides insights into genomic and physiological transformations associated with transition from an open environment to a host-dependent lifestyle and the emergence of pathogenicity. Through a multifaceted mechanism triggering a proinflammatory response, D. oralis is a novel periodontal pathobiont. Even though culture-independent approaches can provide insights into the potential role of the human microbiome “dark matter,” cultivation and experimental characterization remain important to studying the roles of individual organisms in health and disease.« less

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cross, Karissa L.; Chirania, Payal; Xiong, Weili

The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously unculturedDesulfobulbus oralis , the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives,D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities. The genes that enable free-living Desulfobulbus to synthesize the potent neurotoxin methylmercury weremore » also lost byD. oralis, a notably positive outcome of host association. However, horizontal gene acquisitions from other members of the microbiota provided novel mechanisms of interaction with the human host, including toxins like leukotoxin and hemolysins. Proteomic and transcriptomic analysis revealed that most of those factors are actively expressed, including in the subgingival environment, and some are secreted. Similar to other known oral pathobionts, D. oralis can trigger a proinflammatory response in oral epithelial cells, suggesting a direct role in the development of periodontal disease. Animal-associated microbiota likely assembled as a result of numerous independent colonization events by free-living microbes followed by coevolution with their host and other microbes. Through specific adaptation to various body sites and physiological niches, microbes have a wide range of contributions, from beneficial to disease causing.Desulfobulbus oralis provides insights into genomic and physiological transformations associated with transition from an open environment to a host-dependent lifestyle and the emergence of pathogenicity. Through a multifaceted mechanism triggering a proinflammatory response, D. oralis is a novel periodontal pathobiont. Even though culture-independent approaches can provide insights into the potential role of the human microbiome “dark matter,” cultivation and experimental characterization remain important to studying the roles of individual organisms in health and disease.« less

Inflammatory phenotypes in the intestine of poultry: Not all inflammation is created equally

USDA-ARS?s Scientific Manuscript database

The intestinal tract harbors a diverse community of microbes that have co-evolved with the host immune system. Although many of these microbes execute functions that are critical for host physiology, the host immune system must control the microbial community so that the dynamics of this interdepen...

Three-way interaction among plants, bacteria, and coleopteran insects.

PubMed

Wielkopolan, Beata; Obrępalska-Stęplowska, Aleksandra

2016-08-01

Coleoptera, the largest and the most diverse Insecta order, is characterized by multiple adaptations to plant feeding. Insect-associated microorganisms can be important mediators and modulators of interactions between insects and plants. Interactions between plants and insects are highly complex and involve multiple factors. There are various defense mechanisms initiated by plants upon attack by herbivorous insects, including the development of morphological structures and the synthesis of toxic secondary metabolites and volatiles. In turn, herbivores have adapted to feeding on plants and further sophisticated adaptations to overcome plant responses may continue to evolve. Herbivorous insects may detoxify toxic phytocompounds, sequester poisonous plant factors, and alter their own overall gene expression pattern. Moreover, insects are associated with microbes, which not only considerably affect insects, but can also modify plant defense responses to the benefit of their host. Plants are also frequently associated with endophytes, which may act as bioinsecticides. Therefore, it is very important to consider the factors influencing the interaction between plants and insects. Herbivorous insects cause considerable damage to global crop production. Coleoptera is the largest and the most diverse order in the class Insecta. In this review, various aspects of the interactions among insects, microbes, and plants are described with a focus on coleopteran species, their bacterial symbionts, and their plant hosts to demonstrate that many factors contribute to the success of coleopteran herbivory.

Searching for the gut microbial contributing factors to social behavior in rodent models of autism spectrum disorder.

PubMed

Needham, Brittany D; Tang, Weiyi; Wu, Wei-Li

2018-05-01

Social impairment is one of the major symptoms in multiple psychiatric disorders, including autism spectrum disorder (ASD). Accumulated studies indicate a crucial role for the gut microbiota in social development, but these mechanisms remain unclear. This review focuses on two strategies adopted to elucidate the complicated relationship between gut bacteria and host social behavior. In a top-down approach, researchers have attempted to correlate behavioral abnormalities with altered gut microbial profiles in rodent models of ASD, including BTBR mice, maternal immune activation (MIA), maternal valproic acid (VPA) and maternal high-fat diet (MHFD) offspring. In a bottom-up approach, researchers use germ-free (GF) animals, antibiotics, probiotics or pathogens to manipulate the intestinal environment and ascertain effects on social behavior. The combination of both approaches will hopefully pinpoint specific bacterial communities that control host social behavior. Further discussion of how brain development and circuitry is impacted by depletion of gut microbiota is also included. The converging evidence strongly suggests that gut microbes affect host social behavior through the alteration of brain neural circuits. Investigation of intestinal microbiota and host social behavior will unveil any bidirectional communication between the gut and brain and provide alternative therapeutic targets for ASD. © 2018 Wiley Periodicals, Inc. Develop Neurobiol 78: 474-499, 2018. © 2018 Wiley Periodicals, Inc.

What is a pathogen? Toward a process view of host-parasite interactions

PubMed Central

Méthot, Pierre-Olivier; Alizon, Samuel

2014-01-01

Until quite recently and since the late 19th century, medical microbiology has been based on the assumption that some micro-organisms are pathogens and others are not. This binary view is now strongly criticized and is even becoming untenable. We first provide a historical overview of the changing nature of host-parasite interactions, in which we argue that large-scale sequencing not only shows that identifying the roots of pathogenesis is much more complicated than previously thought, but also forces us to reconsider what a pathogen is. To address the challenge of defining a pathogen in post-genomic science, we present and discuss recent results that embrace the microbial genetic diversity (both within- and between-host) and underline the relevance of microbial ecology and evolution. By analyzing and extending earlier work on the concept of pathogen, we propose pathogenicity (or virulence) should be viewed as a dynamical feature of an interaction between a host and microbes. PMID:25483864

Interactome of E. piscicida and grouper liver proteins reveals strategies of bacterial infection and host immune response.

PubMed

Li, Hui; Zhu, Qing-Feng; Peng, Xuan-Xian; Peng, Bo

2017-01-03

The occurrence of infectious diseases is related to heterogeneous protein interactions between a host and a microbe. Therefore, elucidating the host-pathogen interplay is essential. We previously revealed the protein interactome between Edwardsiella piscicida and fish gill cells, and the present study identified the protein interactome between E. piscicida and E. drummondhayi liver cells. E. drummondhayi liver cells and bacterial pull-down approaches were used to identify E. piscicida outer membrane proteins that bind to liver cells and fish liver cell proteins that interact with bacterial cells, respectively. Eight bacterial proteins and 11 fish proteins were characterized. Heterogeneous protein-protein interactions between these bacterial cells and fish liver cells were investigated through far-Western blotting and co-immunoprecipitation. A network was constructed based on 42 heterogeneous protein-protein interactions between seven bacterial proteins and 10 fish proteins. A comparison of the new interactome with the previously reported interactome showed that four bacterial proteins overlapped, whereas all of the identified fish proteins were new, suggesting a difference between bacterial tricks for evading host immunity and the host strategy for combating bacterial infection. Furthermore, these bacterial proteins were found to regulate the expression of host innate immune-related proteins. These findings indicate that the interactome contributes to bacterial infection and host immunity.

Species-Specific Viromes in the Ancestral Holobiont Hydra

PubMed Central

Anton-Erxleben, Friederike; Lim, Yan Wei; Schmieder, Robert; Fraune, Sebastian; Franzenburg, Sören; Insua, Santiago; Machado, GloriaMay; Haynes, Matthew; Little, Mark; Kimble, Robert; Rosenstiel, Philip; Rohwer, Forest L.; Bosch, Thomas C. G.

2014-01-01

Recent evidence showing host specificity of colonizing bacteria supports the view that multicellular organisms are holobionts comprised of the macroscopic host in synergistic interdependence with a heterogeneous and host-specific microbial community. Whereas host-bacteria interactions have been extensively investigated, comparatively little is known about host-virus interactions and viral contribution to the holobiont. We sought to determine the viral communities associating with different Hydra species, whether these viral communities were altered with environmental stress, and whether these viruses affect the Hydra-associated holobiont. Here we show that each species of Hydra harbors a diverse host-associated virome. Primary viral families associated with Hydra are Myoviridae, Siphoviridae, Inoviridae, and Herpesviridae. Most Hydra-associated viruses are bacteriophages, a reflection of their involvement in the holobiont. Changes in environmental conditions alter the associated virome, increase viral diversity, and affect the metabolism of the holobiont. The specificity and dynamics of the virome point to potential viral involvement in regulating microbial associations in the Hydra holobiont. While viruses are generally regarded as pathogenic agents, our study suggests an evolutionary conserved ability of viruses to function as holobiont regulators and, therefore, constitutes an emerging paradigm shift in host-microbe interactions. PMID:25343582

Species-specific viromes in the ancestral holobiont Hydra.

PubMed

Grasis, Juris A; Lachnit, Tim; Anton-Erxleben, Friederike; Lim, Yan Wei; Schmieder, Robert; Fraune, Sebastian; Franzenburg, Sören; Insua, Santiago; Machado, GloriaMay; Haynes, Matthew; Little, Mark; Kimble, Robert; Rosenstiel, Philip; Rohwer, Forest L; Bosch, Thomas C G

2014-01-01

Recent evidence showing host specificity of colonizing bacteria supports the view that multicellular organisms are holobionts comprised of the macroscopic host in synergistic interdependence with a heterogeneous and host-specific microbial community. Whereas host-bacteria interactions have been extensively investigated, comparatively little is known about host-virus interactions and viral contribution to the holobiont. We sought to determine the viral communities associating with different Hydra species, whether these viral communities were altered with environmental stress, and whether these viruses affect the Hydra-associated holobiont. Here we show that each species of Hydra harbors a diverse host-associated virome. Primary viral families associated with Hydra are Myoviridae, Siphoviridae, Inoviridae, and Herpesviridae. Most Hydra-associated viruses are bacteriophages, a reflection of their involvement in the holobiont. Changes in environmental conditions alter the associated virome, increase viral diversity, and affect the metabolism of the holobiont. The specificity and dynamics of the virome point to potential viral involvement in regulating microbial associations in the Hydra holobiont. While viruses are generally regarded as pathogenic agents, our study suggests an evolutionary conserved ability of viruses to function as holobiont regulators and, therefore, constitutes an emerging paradigm shift in host-microbe interactions.

The changing microbial landscape of Western society: Diet, dwellings and discordance.

PubMed

Broussard, Josiane L; Devkota, Suzanne

2016-09-01

The last 50-100 years has been marked by a sharp rise in so-called "Western-diseases" in those countries that have experienced major industrial advances and shifts towards urbanized living. These diseases include obesity, type 2 diabetes, inflammatory bowel diseases, and food allergies in which chronic dysregulation of metabolic and/or immune processes appear to be involved, and are likely a byproduct of new environmental influences on our ancient genome. What we now appreciate is that this genome consists of both human and co-evolved microbial genes of the trillions of microbes residing in our body. Together, host-microbe interactions may be determined by the changing diets and behaviors of the Western lifestyle, influencing the etiopathogenesis of "new-age" diseases. This review takes an anthropological approach to the potential interplay of the host and its gut microbiome in the post-industrialization rise in chronic inflammatory and metabolic diseases. The discussion highlights both the changes in diet and the physical environment that have co-occurred with these diseases and the latest evidence demonstrating the role of host-microbe interactions in understanding biological responses to the changing environment. Technological advances that have led to changes in agriculture and engineering have altered our eating and living behaviors in ways never before possible in human history. These changes also have altered the bacterial communities within the human body in ways that are seemingly linked with the rise of many intestinal and systemic metabolic and inflammatory diseases. Insights into the mechanisms of this reciprocal exchange between the environment and the human gut microbiome may offer potential to attenuate the chronic health conditions that derail quality of life. This article is part of a special issue on microbiota.

Microbiological Lessons Learned from the Space Shuttle

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Bruce, Rebekah; Castro, Victoria A.; Mehta, Satish K.

2011-01-01

After 30 years of being the centerpiece of NASA s human spacecraft, the Space Shuttle will retire. This highly successful program provided many valuable lessons for the International Space Station (ISS) and future spacecraft. Major microbiological risks to crewmembers include food, water, air, surfaces, payloads, animals, other crewmembers, and ground support personnel. Adverse effects of microorganisms are varied and can jeopardize crew health and safety, spacecraft systems, and mission objectives. Engineering practices and operational procedures can minimize the negative effects of microorganisms. To minimize problems associated with microorganisms, appropriate steps must begin in the design phase of new spacecraft or space habitats. Spacecraft design must include requirements to control accumulation of water including humidity, leaks, and condensate on surfaces. Materials used in habitable volumes must not contribute to microbial growth. Use of appropriate materials and the implementation of robust housekeeping that utilizes periodic cleaning and disinfection will prevent high levels of microbial growth on surfaces. Air filtration can ensure low levels of bioaerosols and particulates in the breathing air. The use of physical and chemical steps to disinfect drinking water coupled with filtration can provide safe drinking water. Thorough preflight examination of flight crews, consumables, and the environment can greatly reduce pathogens in spacecraft. The advances in knowledge of living and working onboard the Space Shuttle formed the foundation for environmental microbiology requirements and operations for the International Space Station (ISS) and future spacecraft. Research conducted during the Space Shuttle Program resulted in an improved understanding of the effects of spaceflight on human physiology, microbial properties, and specifically the host-microbe interactions. Host-microbe interactions are substantially affected by spaceflight. Astronaut immune functions were found to be altered. Selected microorganisms were found to become more virulent during spaceflight. The increased knowledge gained on the Space Shuttle resulted in further studies of the host-microbe interactions on the ISS to determine if countermeasures were necessary. Lessons learned from the Space Shuttle Program were integrated into the ISS resulting in the safest space habitat to date.

Identification of the interactome between fish plasma proteins and Edwardsiella tarda reveals tissue-specific strategies against bacterial infection.

PubMed

Li, Hui; Huang, Xiaoyan; Zeng, Zaohai; Peng, Xuan-Xian; Peng, Bo

2016-09-01

Elucidating the complex pathogen-host interaction is essential for a comprehensive understanding of how these remarkable agents invade their hosts and how the hosts defend against these invaders. During the infection, pathogens interact intensively with host to enable their survival, which can be revealed through their interactome. Edwardsiella tarda is a Gram-negative bacterial pathogen causing huge economic loss in aquaculture and a spectrum of intestinal and extraintestinal diseases in humans. E. tarda is an ideal model for host-pathogen investigation as it infects fish in three distinct steps: entering the host, circulating through the blood and establishing infection. We adopted a previous established proteomic approach that inactivated E. tarda cells and covalent crosslink fish plasma proteins were used to capture plasma proteins and bacterial outer membrane proteins, respectively. By the combinatorial use of proteomic and biochemical approaches, six plasma proteins and seven outer membrane proteins (OMPs) were identified. Interactions among these proteins were validated with protein-array, far-Western blotting and co-immunoprecipitation. At last, seventeen plasma protein-bacteria protein-protein interaction were confirmed to be involved in the interaction network, forming a complex interactome. Compared to our previous results, different host proteins were detected, whereas some of the bacterial proteins were similar, which indicates that hosts adopt tissue-specific strategies to cope with the same pathogen during infection. Thus, our results provide a robust demonstration of both bacterial initiators and host receptors or interacting proteins to further explore infection and anti-infective mechanisms between hosts and microbes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Morphogenesis and maturation of the embryonic and postnatal intestine.

PubMed

Chin, Alana M; Hill, David R; Aurora, Megan; Spence, Jason R

2017-06-01

The intestine is a vital organ responsible for nutrient absorption, bile and waste excretion, and a major site of host immunity. In order to keep up with daily demands, the intestine has evolved a mechanism to expand the absorptive surface area by undergoing a morphogenetic process to generate finger-like units called villi. These villi house specialized cell types critical for both absorbing nutrients from food, and for protecting the host from commensal and pathogenic microbes present in the adult gut. In this review, we will discuss mechanisms that coordinate intestinal development, growth, and maturation of the small intestine, starting from the formation of the early gut tube, through villus morphogenesis and into early postnatal life when the intestine must adapt to the acquisition of nutrients through food intake, and to interactions with microbes. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Microbial ecology of the skin in the era of metagenomics and molecular microbiology.

PubMed

Hannigan, Geoffrey D; Grice, Elizabeth A

2013-12-01

The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease.

Pathogenomics: an updated European Research Agenda.

PubMed

Demuth, Andreas; Aharonowitz, Yair; Bachmann, Till T; Blum-Oehler, Gabriele; Buchrieser, Carmen; Covacci, Antonello; Dobrindt, Ulrich; Emödy, Levente; van der Ende, Arie; Ewbank, Jonathan; Fernández, Luis Angel; Frosch, Matthias; García-Del Portillo, Francisco; Gilmore, Michael S; Glaser, Philippe; Goebel, Werner; Hasnain, Seyed E; Heesemann, Jürgen; Islam, Khalid; Korhonen, Timo; Maiden, Martin; Meyer, Thomas F; Montecucco, Cesare; Oswald, Eric; Parkhill, Julian; Pucciarelli, M Graciela; Ron, Eliora; Svanborg, Catharina; Uhlin, Bernt Eric; Wai, Sun Nyunt; Wehland, Jürgen; Hacker, Jörg

2008-05-01

The emerging genomic technologies and bioinformatics provide novel opportunities for studying life-threatening human pathogens and to develop new applications for the improvement of human and animal health and the prevention, treatment, and diagnosis of infections. Based on the ecology and population biology of pathogens and related organisms and their connection to epidemiology, more accurate typing technologies and approaches will lead to better means of disease control. The analysis of the genome plasticity and gene pools of pathogenic bacteria including antigenic diversity and antigenic variation results in more effective vaccines and vaccine implementation programs. The study of newly identified and uncultivated microorganisms enables the identification of new threats. The scrutiny of the metabolism of the pathogen in the host allows the identification of new targets for anti-infectives and therapeutic approaches. The development of modulators of host responses and mediators of host damage will be facilitated by the research on interactions of microbes and hosts, including mechanisms of host damage, acute and chronic relationships as well as commensalisms. The study of multiple pathogenic and non-pathogenic microbes interacting in the host will improve the management of multiple infections and will allow probiotic and prebiotic interventions. Needless to iterate, the application of the results of improved prevention and treatment of infections into clinical tests will have a positive impact on the management of human and animal disease. The Pathogenomics Research Agenda draws on discussions with experts of the Network of Excellence "EuroPathoGenomics" at the management board meeting of the project held during 18-21 April 2007, in the Villa Vigoni, Menaggio, Italy. Based on a proposed European Research Agenda in the field of pathogenomics by the ERA-NET PathoGenoMics the meeting's participants updated the established list of topics as the research agenda for the future.

Hidden state prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses

PubMed Central

Zaneveld, Jesse R. R.; Thurber, Rebecca L. V.

2014-01-01

Complex symbioses between animal or plant hosts and their associated microbiotas can involve thousands of species and millions of genes. Because of the number of interacting partners, it is often impractical to study all organisms or genes in these host-microbe symbioses individually. Yet new phylogenetic predictive methods can use the wealth of accumulated data on diverse model organisms to make inferences into the properties of less well-studied species and gene families. Predictive functional profiling methods use evolutionary models based on the properties of studied relatives to put bounds on the likely characteristics of an organism or gene that has not yet been studied in detail. These techniques have been applied to predict diverse features of host-associated microbial communities ranging from the enzymatic function of uncharacterized genes to the gene content of uncultured microorganisms. We consider these phylogenetically informed predictive techniques from disparate fields as examples of a general class of algorithms for Hidden State Prediction (HSP), and argue that HSP methods have broad value in predicting organismal traits in a variety of contexts, including the study of complex host-microbe symbioses. PMID:25202302

Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases.

PubMed

Huang, Edmond Y; Inoue, Takuya; Leone, Vanessa A; Dalal, Sushila; Touw, Ketrija; Wang, Yunwei; Musch, Mark W; Theriault, Betty; Higuchi, Kazuhide; Donovan, Sharon; Gilbert, Jack; Chang, Eugene B

2015-05-01

Commensal gut microbiota play an important role in regulating metabolic and inflammatory conditions. Reshaping intestinal microbiota through pharmacologic means may be a viable treatment option. We sought to delineate the functional characteristics of glucocorticoid-mediated alterations on gut microbiota and their subsequent repercussions on host mucin regulation and colonic inflammation. Adult male C57Bl/6 mice, germ-free, Muc2-heterozygote (±), or Muc2-knockout (-/-) were injected with dexamethasone, a synthetic glucocorticoid, for 4 weeks. Fecal samples were collected for gut microbiota analysis through 16S rRNA terminal restriction fragment length polymorphism and amplicon sequencing. Intestinal mucosa was collected for mucin gene expression studies. Germ-free mice were conventionalized with gut microbes from treated and nontreated groups to determine their functional capacities in recipient hosts. Exposure to dexamethasone in wild-type mice led to substantial shifts in gut microbiota over a 4-week period. Furthermore, a significant downregulation of colonic Muc2 gene expression was observed after treatment. Muc2-knockout mice harbored a proinflammatory environment of gut microbes, characterized by the increase or decrease in prevalence of specific microbiota populations such as Clostridiales and Lactobacillaceae, respectively. This colitogenic phenotype was transmissible to IL10-knockout mice, a genetically susceptible model of colonic inflammatory disorders. Microbiota from donors pretreated with dexamethasone, however, ameliorated symptoms of inflammation. Commensal gut bacteria may be a key mediator of the anti-inflammatory effects observed in the large intestine after glucocorticoid exposure. These findings underscore the notion that intestinal microbes comprise a "microbial organ" essential for host physiology that can be targeted by therapeutic approaches to restore intestinal homeostasis.

The Plant Actin Cytoskeleton Responds to Signals from Microbe-Associated Molecular Patterns

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henty-Ridilla, Jessica L.; Shimono, Masaki; Li, Jiejie

2013-04-04

Plants are constantly exposed to a large and diverse array of microbes; however, most plants are immune to the majority of potential invaders and susceptible to only a small subset of pathogens. The cytoskeleton comprises a dynamic intracellular framework that responds rapidly to biotic stresses and supports numerous fundamental cellular processes including vesicle trafficking, endocytosis and the spatial distribution of organelles and protein complexes. For years, the actin cytoskeleton has been assumed to play a role in plant innate immunity against fungi and oomycetes, based largely on static images and pharmacological studies. To date, however, there is little evidence thatmore » the host-cell actin cytoskeleton participates in responses to phytopathogenic bacteria. Here, we quantified the spatiotemporal changes in host-cell cytoskeletal architecture during the immune response to pathogenic and non-pathogenic strains of Pseudomonas syringae pv. tomato DC3000. Two distinct changes to host cytoskeletal arrays were observed that correspond to distinct phases of plant-bacterial interactions i.e. the perception of microbe-associated molecular patterns (MAMPs) during pattern-triggered immunity (PTI) and perturbations by effector proteins during effector-triggered susceptibility (ETS). We demonstrate that an immediate increase in actin filament abundance is a conserved and novel component of PTI. Notably, treatment of leaves with a MAMP peptide mimic was sufficient to elicit a rapid change in actin organization in epidermal cells, and this actin response required the host-cell MAMP receptor kinase complex, including FLS2, BAK1 and BIK1. Finally, we found that actin polymerization is necessary for the increase in actin filament density and that blocking this increase with the actin-disrupting drug latrunculin B leads to enhanced susceptibility of host plants to pathogenic and non-pathogenic bacteria.« less

Yersinia versus host immunity: how a pathogen evades or triggers a protective response.

PubMed

Chung, Lawton K; Bliska, James B

2016-02-01

The human pathogenic Yersinia species cause diseases that represent a significant source of morbidity and mortality. Despite this, specific mechanisms underlying Yersinia pathogenesis and protective host responses remain poorly understood. Recent studies have shown that Yersinia disrupt cell death pathways, perturb inflammatory processes and exploit immune cells to promote disease. The ensuing host responses following Yersinia infection include coordination of innate and adaptive immune responses in an attempt to control bacterial replication. Here, we highlight current advances in our understanding of the interactions between the pathogenic yersiniae and host cells, as well as the protective host responses mobilized to counteract these pathogens. Together, these studies enhance our understanding of Yersinia pathogenesis and highlight the ongoing battle between host and microbe. Copyright © 2015 Elsevier Ltd. All rights reserved.

Investigating the chemical preferences of marine microbes in situ at organismal scales

NASA Astrophysics Data System (ADS)

Lambert, B.; Raina, J. B.; Seymour, J.; Rinke, C.; Tyson, G. W.; Hugenholtz, P.; Stocker, R.

2016-02-01

The chemical preferences of marine microbes underpin many fundamental microbial functions, from the quest for nutrients to the attraction of pathogens to hosts. Our understanding of these processes is currently based solely on experiments with laboratory isolates, due to the difficulty of assaying chemical preferences in situ. The ISCA (In Situ Chemotaxis Assay) is a custom-built chip designed to assess the ability of marine microbes to respond to chemical cues in their natural environment. It consists of 25 wells, each connected to the outside seawater by one inlet port. Upon deployment, each well produces a controlled microplume of a desired chemical, to which microbes can respond by swimming into the well. Flow-cytometric, molecular analysis, and high-speed video microscopy allow determination of the number and identity of the responding microbes, providing unique links between microbial identity and chemical preferences. Here we present highly resolved spatiotemporal accumulation profiles with a model bacterium and chemoattractants as well as initial data from field deployments. These initial results indicate that the ISCA will be a valuable new tool for understanding microbial interactions in the natural environment.

Associations between Ectomycorrhizal Fungi and Bacterial Needle Endophytes in Pinus radiata: Implications for Biotic Selection of Microbial Communities

PubMed Central

Rúa, Megan A.; Wilson, Emily C.; Steele, Sarah; Munters, Arielle R.; Hoeksema, Jason D.; Frank, Anna C.

2016-01-01

Studies of the ecological and evolutionary relationships between plants and their associated microbes have long been focused on single microbes, or single microbial guilds, but in reality, plants associate with a diverse array of microbes from a varied set of guilds. As such, multitrophic interactions among plant-associated microbes from multiple guilds represent an area of developing research, and can reveal how complex microbial communities are structured around plants. Interactions between coniferous plants and their associated microbes provide a good model system for such studies, as conifers host a suite of microorganisms including mutualistic ectomycorrhizal (ECM) fungi and foliar bacterial endophytes. To investigate the potential role ECM fungi play in structuring foliar bacterial endophyte communities, we sampled three isolated, native populations of Monterey pine (Pinus radiata), and used constrained analysis of principal coordinates to relate the community matrices of the ECM fungi and bacterial endophytes. Our results suggest that ECM fungi may be important factors for explaining variation in bacterial endophyte communities but this effect is influenced by population and environmental characteristics, emphasizing the potential importance of other factors — biotic or abiotic — in determining the composition of bacterial communities. We also classified ECM fungi into categories based on known fungal traits associated with substrate exploration and nutrient mobilization strategies since variation in these traits allows the fungi to acquire nutrients across a wide range of abiotic conditions and may influence the outcome of multi-species interactions. Across populations and environmental factors, none of the traits associated with fungal foraging strategy types significantly structured bacterial assemblages, suggesting these ECM fungal traits are not important for understanding endophyte-ECM interactions. Overall, our results suggest that both biotic species interactions and environmental filtering are important for structuring microbial communities but emphasize the need for more research into these interactions. PMID:27065966

Microbe-independent entry of oomycete RxLR effectors and fungal RxLR-like effectors into plant and animal cells is specific and reproducible.

PubMed

Tyler, Brett M; Kale, Shiv D; Wang, Qunqing; Tao, Kai; Clark, Helen R; Drews, Kelly; Antignani, Vincenzo; Rumore, Amanda; Hayes, Tristan; Plett, Jonathan M; Fudal, Isabelle; Gu, Biao; Chen, Qinghe; Affeldt, Katharyn J; Berthier, Erwin; Fischer, Gregory J; Dou, Daolong; Shan, Weixing; Keller, Nancy P; Martin, Francis; Rouxel, Thierry; Lawrence, Christopher B

2013-06-01

A wide diversity of pathogens and mutualists of plant and animal hosts, including oomycetes and fungi, produce effector proteins that enter the cytoplasm of host cells. A major question has been whether or not entry by these effectors can occur independently of the microbe or requires machinery provided by the microbe. Numerous publications have documented that oomycete RxLR effectors and fungal RxLR-like effectors can enter plant and animal cells independent of the microbe. A recent reexamination of whether the RxLR domain of oomycete RxLR effectors is sufficient for microbe-independent entry into host cells concluded that the RxLR domains of Phytophthora infestans Avr3a and of P. sojae Avr1b alone are NOT sufficient to enable microbe-independent entry of proteins into host and nonhost plant and animal cells. Here, we present new, more detailed data that unambiguously demonstrate that the RxLR domain of Avr1b does show efficient and specific entry into soybean root cells and also into wheat leaf cells, at levels well above background nonspecific entry. We also summarize host cell entry experiments with a wide diversity of oomycete and fungal effectors with RxLR or RxLR-like motifs that have been independently carried out by the seven different labs that coauthored this letter. Finally we discuss possible technical reasons why specific cell entry may have been not detected by Wawra et al. (2013).

Best practices for germ-free derivation and gnotobiotic zebrafish husbandry

PubMed Central

Melancon, E.; De La Torre Canny, S. Gomez; Sichel, S.; Kelly, M.; Wiles, T.J.; Rawls, J.F.; Eisen, J.S.; Guillemin, K.

2017-01-01

All animals are ecosystems with resident microbial communities, referred to as microbiota, which play profound roles in host development, physiology, and evolution. Enabled by new DNA sequencing technologies, there is a burgeoning interest in animal–microbiota interactions, but dissecting the specific impacts of microbes on their hosts is experimentally challenging. Gnotobiology, the study of biological systems in which all members are known, enables precise experimental analysis of the necessity and sufficiency of microbes in animal biology by deriving animals germ-free (GF) and inoculating them with defined microbial lineages. Mammalian host models have long dominated gnotobiology, but we have recently adapted gnotobiotic approaches to the zebrafish (Danio rerio), an important aquatic model. Zebrafish offer several experimental attributes that enable rapid, large-scale gnotobiotic experimentation with high replication rates and exquisite optical resolution. Here we describe detailed protocols for three procedures that form the foundation of zebrafish gnotobiology: derivation of GF embryos, microbial association of GF animals, and long-term, GF husbandry. Our aim is to provide sufficient guidance in zebrafish gnotobiotic methodology to expand and enrich this exciting field of research. PMID:28129860

Does plant immunity play a critical role during initiation of the legume-rhizobium symbiosis?

PubMed

Tóth, Katalin; Stacey, Gary

2015-01-01

Plants are exposed to many different microbes in their habitats. These microbes may be benign or pathogenic, but in some cases they are beneficial for the host. The rhizosphere provides an especially rich palette for colonization by beneficial (associative and symbiotic) microorganisms, which raises the question as to how roots can distinguish such 'friends' from possible 'foes' (i.e., pathogens). Plants possess an innate immune system that can recognize pathogens, through an arsenal of protein receptors, including receptor-like kinases (RLKs) and receptor-like proteins (RLPs) located at the plasma membrane. In addition, the plant host has intracellular receptors (so called NBS-LRR proteins or R proteins) that directly or indirectly recognize molecules released by microbes into the plant cell. A successful cooperation between legume plants and rhizobia leads to beneficial symbiotic interaction. The key rhizobial, symbiotic signaling molecules [lipo-chitooligosaccharide Nod factors (NF)] are perceived by the host legume plant using lysin motif-domain containing RLKs. Perception of the symbiotic NFs trigger signaling cascades leading to bacterial infection and accommodation of the symbiont in a newly formed root organ, the nodule, resulting in a nitrogen-fixing root nodule symbiosis. The net result of this symbiosis is the intracellular colonization of the plant with thousands of bacteria; a process that seems to occur in spite of the immune ability of plants to prevent pathogen infection. In this review, we discuss the potential of the invading rhizobial symbiont to actively avoid this innate immune response, as well as specific examples of where the plant immune response may modulate rhizobial infection and host range.

Functional metagenomics to decipher food-microbe-host crosstalk.

PubMed

Larraufie, Pierre; de Wouters, Tomas; Potocki-Veronese, Gabrielle; Blottière, Hervé M; Doré, Joël

2015-02-01

The recent developments of metagenomics permit an extremely high-resolution molecular scan of the intestinal microbiota giving new insights and opening perspectives for clinical applications. Beyond the unprecedented vision of the intestinal microbiota given by large-scale quantitative metagenomics studies, such as the EU MetaHIT project, functional metagenomics tools allow the exploration of fine interactions between food constituents, microbiota and host, leading to the identification of signals and intimate mechanisms of crosstalk, especially between bacteria and human cells. Cloning of large genome fragments, either from complex intestinal communities or from selected bacteria, allows the screening of these biological resources for bioactivity towards complex plant polymers or functional food such as prebiotics. This permitted identification of novel carbohydrate-active enzyme families involved in dietary fibre and host glycan breakdown, and highlighted unsuspected bacterial players at the top of the intestinal microbial food chain. Similarly, exposure of fractions from genomic and metagenomic clones onto human cells engineered with reporter systems to track modulation of immune response, cell proliferation or cell metabolism has allowed the identification of bioactive clones modulating key cell signalling pathways or the induction of specific genes. This opens the possibility to decipher mechanisms by which commensal bacteria or candidate probiotics can modulate the activity of cells in the intestinal epithelium or even in distal organs such as the liver, adipose tissue or the brain. Hence, in spite of our inability to culture many of the dominant microbes of the human intestine, functional metagenomics open a new window for the exploration of food-microbe-host crosstalk.

Microbiota-gut-brain axis: Interaction of gut microbes and their metabolites with host epithelial barriers.

PubMed

Bhattarai, Y

2018-06-01

The gastrointestinal barrier and the blood brain barrier represent an important line of defense to protect the underlying structures against harmful external stimuli. These host barriers are composed of epithelial and endothelial cells interconnected by tight junction proteins along with several other supporting structures. Disruption in host barrier structures has therefore been implicated in various diseases of the gastrointestinal tract and the central nervous system. While there are several factors that influence host barrier, recently there is an increasing appreciation of the role of gut microbiota and their metabolites in regulating barrier integrity. In the current issue of Neurogastroenterology and Motility, Marungruang et al. describe the effect of gastrointestinal barrier maturation on gut microbiota and the blood brain barrier adding to the growing evidence of microbiota-barrier interactions. In this mini-review I will discuss the effect of gut microbiota on host epithelial barriers and its implications for diseases associated with disrupted gut-brain axis. © 2018 John Wiley & Sons Ltd.

Xanthomonas TAL effectors hijack host basal transcription factor IIA α and γ subunits for invasion.

PubMed

Ma, Ling; Wang, Qiang; Yuan, Meng; Zou, Tingting; Yin, Ping; Wang, Shiping

2018-02-05

The Xanthomonas genus includes Gram-negative plant-pathogenic bacteria, which infect a broad range of crops and wild plant species, cause symptoms with leaf blights, streaks, spots, stripes, necrosis, wilt, cankers and gummosis on leaves, stems and fruits in a wide variety of plants via injecting their effector proteins into the host cell during infection. Among these virulent effectors, transcription activator-like effectors (TALEs) interact with the γ subunit of host transcription factor IIA (TFIIAγ) to activate the transcription of host disease susceptibility genes. Functional TFIIA is a ternary complex comprising α, β and γ subunits. However, whether TALEs recruit TFIIAα, TFIIAβ, or both remains unknown. The underlying molecular mechanisms by which TALEs mediate host susceptibility gene activation require full elucidation. Here, we show that TALEs interact with the α+γ binary subcomplex but not the α+β+γ ternary complex of rice TFIIA (holo-OsTFIIA). The transcription factor binding (TFB) regions of TALEs, which are highly conserved in Xanthomonas species, have a dominant role in these interactions. Furthermore, the interaction between TALEs and the α+γ complex exhibits robust DNA binding activity in vitro. These results collectively demonstrate that TALE-carrying pathogens hijack the host basal transcription factors TFIIAα and TFIIAγ, but not TFIIAβ, to enhance host susceptibility during pathogen infection. The uncovered mechanism widens new insights on host-microbe interaction and provide an applicable strategy to breed high-resistance crop varieties. Copyright © 2018 Elsevier Inc. All rights reserved.

Effect of microgravity & space radiation on microbes.

PubMed

Senatore, Giuliana; Mastroleo, Felice; Leys, Natalie; Mauriello, Gianluigi

2018-06-01

One of the new challenges facing humanity is to reach increasingly further distant space targets. It is therefore of upmost importance to understand the behavior of microorganisms that will unavoidably reach the space environment together with the human body and equipment. Indeed, microorganisms could activate their stress defense mechanisms, modifying properties related to human pathogenesis. The host-microbe interactions, in fact, could be substantially affected under spaceflight conditions and the study of microorganisms' growth and activity is necessary for predicting these behaviors and assessing precautionary measures during spaceflight. This review gives an overview of the effects of microgravity and space radiation on microorganisms both in real and simulated conditions.

Understanding the Effects of Host Evolution and Skin Bacteria Composition on Disease Vector Choices

DTIC Science & Technology

2016-04-14

attractiveness of hosts to microbes suggests that if we are to develop a probiotic that deters mosquitoes that its value will depend greatly on the genome of the...influence of a single human gene on the attractiveness of hosts to microbes suggests that if we are to develop a probiotic that deters mosquitoes that

Streptomyces scabies 87-22 contains a coronafacic acid-like biosynthetic cluster that contributes to plant-microbe interactions.

PubMed

Bignell, Dawn R D; Seipke, Ryan F; Huguet-Tapia, José C; Chambers, Alan H; Parry, Ronald J; Loria, Rosemary

2010-02-01

Plant-pathogenic Streptomyces spp. cause scab disease on economically important root and tuber crops, the most important of which is potato. Key virulence determinants produced by these species include the cellulose synthesis inhibitor, thaxtomin A, and the secreted Nec1 protein that is required for colonization of the plant host. Recently, the genome sequence of Streptomyces scabies 87-22 was completed, and a biosynthetic cluster was identified that is predicted to synthesize a novel compound similar to coronafacic acid (CFA), a component of the virulence-associated coronatine phytotoxin produced by the plant-pathogenic bacterium Pseudomonas syringae. Southern analysis indicated that the cfa-like cluster in S. scabies 87-22 is likely conserved in other strains of S. scabies but is absent from two other pathogenic streptomycetes, S. turgidiscabies and S. acidiscabies. Transcriptional analyses demonstrated that the cluster is expressed during plant-microbe interactions and that expression requires a transcriptional regulator embedded in the cluster as well as the bldA tRNA. A knockout strain of the biosynthetic cluster displayed a reduced virulence phenotype on tobacco seedlings compared with the wild-type strain. Thus, the cfa-like biosynthetic cluster is a newly discovered locus in S. scabies that contributes to host-pathogen interactions.

Coral-associated micro-organisms and their roles in promoting coral health and thwarting diseases

PubMed Central

Krediet, Cory J.; Ritchie, Kim B.; Paul, Valerie J.; Teplitski, Max

2013-01-01

Over the last decade, significant advances have been made in characterization of the coral microbiota. Shifts in its composition often correlate with the appearance of signs of diseases and/or bleaching, thus suggesting a link between microbes, coral health and stability of reef ecosystems. The understanding of interactions in coral-associated microbiota is informed by the on-going characterization of other microbiomes, which suggest that metabolic pathways and functional capabilities define the ‘core’ microbiota more accurately than the taxonomic diversity of its members. Consistent with this hypothesis, there does not appear to be a consensus on the specificity in the interactions of corals with microbial commensals, even though recent studies report potentially beneficial functions of the coral-associated bacteria. They cycle sulphur, fix nitrogen, produce antimicrobial compounds, inhibit cell-to-cell signalling and disrupt virulence in opportunistic pathogens. While their beneficial functions have been documented, it is not certain whether or how these microbes are selected by the hosts. Therefore, understanding the role of innate immunity, signal and nutrient exchange in the establishment of coral microbiota and in controlling its functions will probably reveal ancient, evolutionarily conserved mechanisms that dictate the outcomes of host–microbial interactions, and impact the resilience of the host. PMID:23363627

Fecal microbiome in the bovine animal

USDA-ARS?s Scientific Manuscript database

Bacteria in the gastrointestinal tract have often been an afterthought in regard to the mammalian host. In recent year for humans, the gastrointestinal microbes appear to be associated with host immune function, health, and well-being. In addition, microbes can competitively exclude other bacteria...

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease

PubMed Central

Jostins, Luke; Ripke, Stephan; Weersma, Rinse K; Duerr, Richard H; McGovern, Dermot P; Hui, Ken Y; Lee, James C; Schumm, L Philip; Sharma, Yashoda; Anderson, Carl A; Essers, Jonah; Mitrovic, Mitja; Ning, Kaida; Cleynen, Isabelle; Theatre, Emilie; Spain, Sarah L; Raychaudhuri, Soumya; Goyette, Philippe; Wei, Zhi; Abraham, Clara; Achkar, Jean-Paul; Ahmad, Tariq; Amininejad, Leila; Ananthakrishnan, Ashwin N; Andersen, Vibeke; Andrews, Jane M; Baidoo, Leonard; Balschun, Tobias; Bampton, Peter A; Bitton, Alain; Boucher, Gabrielle; Brand, Stephan; Büning, Carsten; Cohain, Ariella; Cichon, Sven; D’Amato, Mauro; De Jong, Dirk; Devaney, Kathy L; Dubinsky, Marla; Edwards, Cathryn; Ellinghaus, David; Ferguson, Lynnette R; Franchimont, Denis; Fransen, Karin; Gearry, Richard; Georges, Michel; Gieger, Christian; Glas, Jürgen; Haritunians, Talin; Hart, Ailsa; Hawkey, Chris; Hedl, Matija; Hu, Xinli; Karlsen, Tom H; Kupcinskas, Limas; Kugathasan, Subra; Latiano, Anna; Laukens, Debby; Lawrance, Ian C; Lees, Charlie W; Louis, Edouard; Mahy, Gillian; Mansfield, John; Morgan, Angharad R; Mowat, Craig; Newman, William; Palmieri, Orazio; Ponsioen, Cyriel Y; Potocnik, Uros; Prescott, Natalie J; Regueiro, Miguel; Rotter, Jerome I; Russell, Richard K; Sanderson, Jeremy D; Sans, Miquel; Satsangi, Jack; Schreiber, Stefan; Simms, Lisa A; Sventoraityte, Jurgita; Targan, Stephan R; Taylor, Kent D; Tremelling, Mark; Verspaget, Hein W; De Vos, Martine; Wijmenga, Cisca; Wilson, David C; Winkelmann, Juliane; Xavier, Ramnik J; Zeissig, Sebastian; Zhang, Bin; Zhang, Clarence K; Zhao, Hongyu; Silverberg, Mark S; Annese, Vito; Hakonarson, Hakon; Brant, Steven R; Radford-Smith, Graham; Mathew, Christopher G; Rioux, John D; Schadt, Eric E; Daly, Mark J; Franke, Andre; Parkes, Miles; Vermeire, Severine; Barrett, Jeffrey C; Cho, Judy H

2012-01-01

Crohn’s disease (CD) and ulcerative colitis (UC), the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry with rising prevalence in other populations1. Genome-wide association studies (GWAS) and subsequent meta-analyses of CD and UC2,3 as separate phenotypes implicated previously unsuspected mechanisms, such as autophagy4, in pathogenesis and showed that some IBD loci are shared with other inflammatory diseases5. Here we expand knowledge of relevant pathways by undertaking a meta-analysis of CD and UC genome-wide association scans, with validation of significant findings in more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional and balancing selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe striking overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD. PMID:23128233

Pharmacological Targeting of the Host-Pathogen Interaction: Alternatives to Classical Antibiotics to Combat Drug-Resistant Superbugs

PubMed Central

Munguia, Jason; Nizet, Victor

2017-01-01

The rise of multidrug-resistant pathogens and the dearth of new antibiotic development place an existential strain on successful infectious disease therapy. Breakthrough strategies that go beyond classical antibiotic mechanisms are needed to combat this looming public health catastrophe. Reconceptualizing antibiotic therapy in the richer context of the host-pathogen interaction is required for innovative solutions. By defining specific virulence factors, the essence of a pathogen, and pharmacologically neutralizing their activities, one can block disease progression and sensitize microbes to immune clearance. Likewise, host-directed strategies to boost phagocyte bactericidal activity, enhance leukocyte recruitment, or reverse pathogen-induced immunosuppression seek to replicate the success of cancer immunotherapy in the field of infectious diseases. The answer to the threat of multidrug-resistant pathogens lies “outside-the-box” of current antibiotic paradigms. PMID:28283200

The impact of microbiota on brain and behavior: mechanisms & therapeutic potential.

PubMed

Borre, Yuliya E; Moloney, Rachel D; Clarke, Gerard; Dinan, Timothy G; Cryan, John F

2014-01-01

There is increasing evidence that host-microbe interactions play a key role in maintaining homeostasis. Alterations in gut microbial composition is associated with marked changes in behaviors relevant to mood, pain and cognition, establishing the critical importance of the bi-directional pathway of communication between the microbiota and the brain in health and disease. Dysfunction of the microbiome-brain-gut axis has been implicated in stress-related disorders such as depression, anxiety and irritable bowel syndrome and neurodevelopmental disorders such as autism. Bacterial colonization of the gut is central to postnatal development and maturation of key systems that have the capacity to influence central nervous system (CNS) programming and signaling, including the immune and endocrine systems. Moreover, there is now expanding evidence for the view that enteric microbiota plays a role in early programming and later response to acute and chronic stress. This view is supported by studies in germ-free mice and in animals exposed to pathogenic bacterial infections, probiotic agents or antibiotics. Although communication between gut microbiota and the CNS are not fully elucidated, neural, hormonal, immune and metabolic pathways have been suggested. Thus, the concept of a microbiome-brain-gut axis is emerging, suggesting microbiota-modulating strategies may be a tractable therapeutic approach for developing novel treatments for CNS disorders.

The Infant Intestinal Microbiome: Friend or Foe?

PubMed Central

Mshvildadze, Maka; Neu, Josef

2013-01-01

During the course of mammalian evolution there has been a close relationship between microbes residing in the gastrointestinal (GI) tract and the mammalian host. Interactions of resident intestinal microbes with the luminal contents and the mucosal surface play important roles in normal intestinal development, nutrition and adaptive innate immunity. The GI tract of the premature infant has a large but fragile surface area covered by a thin monolayer of epithelial cells that overlies a highly immunoreactive submucosa. Interactions in the lumen between microbes, nutrients and the intestinal mucosa can range from a healthy homeostasis to an uncontrolled systemic inflammatory response syndrome (SIRS) that leads to multiple organ system failure and death. Recent advances in molecular microbiota analytic methodology that stem from advances in high throughput sequencing technology have provided us with the tools to determine the GI microbiota in great depth, including the nearly 80 % of microbes in the intestine that are very difficult if not impossible to culture by current methodology. Application of these techniques to derive a better understanding of the developing intestinal ecosystem in the premature neonate may hold the key to understand and eventually prevent several important diseases including necrotizing enterocolitis (NEC) and late onset neonatal sepsis that may be acquired via translocation through the GI tract. PMID:20116944

Active migration is associated with specific and consistent changes to gut microbiota in Calidris shorebirds.

PubMed

Risely, Alice; Waite, David W; Ujvari, Beata; Hoye, Bethany J; Klaassen, Marcel

2018-03-01

Gut microbes are increasingly recognised for their role in regulating an animal's metabolism and immunity. However, identifying repeatable associations between host physiological processes and their gut microbiota has proved challenging, in part because microbial communities often respond stochastically to host physiological stress (e.g. fasting, forced exercise or infection). Migratory birds provide a valuable system in which to test host-microbe interactions under physiological extremes because these hosts are adapted to predictable metabolic and immunological challenges as they undergo seasonal migrations, including temporary gut atrophy during long-distance flights. These physiological challenges may either temporarily disrupt gut microbial ecosystems, or, alternatively, promote predictable host-microbe associations during migration. To determine the relationship between migration and gut microbiota, we compared gut microbiota composition between migrating and non-migrating ("resident") conspecific shorebirds sharing a flock. We performed this across two sandpiper species, Calidris ferruginea and Calidris ruficollis, in north-western Australia, and an additional C. ruficollis population 3,000 km away in southern Australia. We found that migrants consistently had higher abundances of the bacterial genus Corynebacterium (average 28% abundance) compared to conspecific residents (average <1% abundance), with this effect holding across both species and sites. However, other than this specific association, community structure and diversity was almost identical between migrants and residents, with migration status accounting for only 1% of gut community variation when excluding Corynebacterium. Our findings suggest a consistent relationship between Corynebacterium and Calidris shorebirds during migration, with further research required to identify causal mechanisms behind the association, and to elucidate functionality to the host. However, outside this specific association, migrating shorebirds broadly maintained gut community structure, which may allow them to quickly recover gut function after a migratory flight. This study provides a rare example of a repeatable and specific response of the gut microbiota to a major physiological challenge across two species and two distant populations. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment.

PubMed

Burns, Michael B; Montassier, Emmanuel; Abrahante, Juan; Priya, Sambhawa; Niccum, David E; Khoruts, Alexander; Starr, Timothy K; Knights, Dan; Blekhman, Ran

2018-06-20

Variation in the gut microbiome has been linked to colorectal cancer (CRC), as well as to host genetic variation. However, we do not know whether, in addition to baseline host genetics, somatic mutational profiles in CRC tumors interact with the surrounding tumor microbiome, and if so, whether these changes can be used to understand microbe-host interactions with potential functional biological relevance. Here, we characterized the association between CRC microbial communities and tumor mutations using microbiome profiling and whole-exome sequencing in 44 pairs of tumors and matched normal tissues. We found statistically significant associations between loss-of-function mutations in tumor genes and shifts in the abundances of specific sets of bacterial taxa, suggestive of potential functional interaction. This correlation allows us to statistically predict interactions between loss-of-function tumor mutations in cancer-related genes and pathways, including MAPK and Wnt signaling, solely based on the composition of the microbiome. In conclusion, our study shows that CRC microbiomes are correlated with tumor mutational profiles, pointing towards possible mechanisms of molecular interaction.

Commensal bacteria modulate the tumor microenvironment.

PubMed

Poutahidis, Theofilos; Erdman, Susan E

2016-09-28

It has been recently shown that gut microbes modulate whole host immune and hormonal factors impacting the fate of distant preneoplastic lesions toward malignancy or regression. This raises the possibility that the tumor microenvironment interacts with broader systemic microbial-immune networks. These accumulated findings suggest novel therapeutic opportunities for holobiont engineering in emerging tumor microenvironments. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Host-microbiota interactions: Epigenomic regulation

PubMed Central

Woo, Vivienne; Alenghat, Theresa

2016-01-01

The coevolution of mammalian hosts and their commensal microbiota has led to the development of complex symbiotic relationships between resident microbes and mammalian cells. Epigenomic modifications enable host cells to alter gene expression without modifying the genetic code, and therefore represent potent mechanisms by which mammalian cells can transcriptionally respond, transiently or stably, to environmental cues. Advances in genome-wide approaches are accelerating our appreciation of microbial influences on host physiology, and increasing evidence highlights that epigenomics represent a level of regulation by which the host integrates and responds to microbial signals. In particular, bacterial-derived short chain fatty acids have emerged as one clear link between how the microbiota intersects with host epigenomic pathways. Here we review recent findings describing crosstalk between the microbiota and epigenomic pathways in multiple mammalian cell populations. Further, we discuss interesting links that suggest that the scope of our understanding of epigenomic regulation in the host-microbiota relationship is still in its infancy. PMID:28103497

Host Responses to the Pathogen Mycobacterium avium subsp. paratuberculosis and Beneficial Microbes Exhibit Host Sex Specificity

PubMed Central

McMahon, K. Wyatt; Chang, David; Brashears, Mindy M.

2014-01-01

Differences between microbial pathogenesis in male and female hosts are well characterized in disease conditions connected to sexual transmission. However, limited biological insight is available on variances attributed to sex specificity in host-microbe interactions, and it is most often a minimized variable outside these transmission events. In this work, we studied two gut microbes—a pathogen, Mycobacterium avium subsp. paratuberculosis, and a probiotic, Lactobacillus animalis NP-51—and the interaction between each agent and the male and female gastrointestinal systems. This trial was conducted in BALB/c mice (n = 5 per experimental group and per sex at a given time point), with analysis at four time points over 180 days. Host responses to M. avium subsp. paratuberculosis and L. animalis were sensitive to sex. Cytokines that were significantly different (P ≤ 0.05) between the sexes included interleukin-1α/β (IL-1α/β), IL-17, IL-6, IL-10, IL-12, and gamma interferon (IFN-γ) and were dependent on experimental conditions. However, granulocyte-macrophage colony-stimulating factor (GM-CSF), vascular endothelial growth factor (VEGF), and IL-13/23 showed no sex specificity. A metabolomics study indicated a 0.5- to 2.0-fold (log2 scale) increase in short-chain fatty acids (butyrate and acetate) in males and greater increases in o-phosphocholine or histidine from female colon tissues; variances distinct to each sex were observed with age or long-term probiotic consumption. Two genera, Staphylococcus and Roseburia, were consistently overrepresented in females compared to males; other species were specific to one sex but fluctuated depending on experimental conditions. The differences observed suggest that male and female gut tissues and microbiota respond to newly introduced microorganisms differently and that gut-associated microorganisms with host immune system responses and metabolic activity are supported by biology distinct to the host sex. PMID:24814797

Bacterial protection of beetle-fungus mutualism

Treesearch

Jarrod J. Scott; Dong-Chan Oh; M. Cetin Yuceer; Kier D. Klepzig; Jon Clardy; Cameron R. Currie

2008-01-01

The pervasiveness of beneficial associations between symbiotic microbes and plants and animals in every ecosystem illustrates how the acquisition of a microbe’s physiological capacity confers substantial fitness benefits to hosts (1). However, dependence on mutualistic microbes becomes a liability if antagonistic microbes attack or outcompete beneficial ones (2)....

Discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria

DOE PAGES

Seshadri, Rekha; Reeve, Wayne G.; Ardley, Julie K.; ...

2015-11-20

Root nodule bacteria (RNB) or “rhizobia” are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. In this study, we sequenced the genomes of 110 RNB from diverse hosts and biogeographical regions, and undertook a global exploration of all available RNB genera with the aim of identifying novel genetic determinants of symbiotic association and plant growth promotion. Specifically, we performed a subtractive comparative analysis with non-RNB genomes, employed relevant transcriptomic data, and leveraged phylogeneticmore » distribution patterns and sequence signatures based on known precepts of symbioticand host-microbe interactions. A total of 184 protein families were delineated, including known factors for nodulation and nitrogen fixation, and candidates with previously unexplored functions, for which a role in host-interaction, -regulation, biocontrol, and more, could be posited. Lastly, these analyses expand our knowledge of the RNB purview and provide novel targets for strain improvement in the ultimate quest to enhance plant productivity and agricultural sustainability.« less

Using Corticosteroids to Reshape the Gut Microbiome: Implications for Inflammatory Bowel Diseases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Edmond Y.; Inoue, Takuya; Leone, Vanessa A.

Introduction—Commensal gut microbiota play an important role in regulating metabolic and inflammatory conditions. Reshaping intestinal microbiota through pharmacologic means may be a viable treatment option. Here we sought to delineate the functional characteristics of glucocorticoid-mediated alterations on gut microbiota and their subsequent repercussions on host mucin regulation and colonic inflammation. Methods—Adult male C57Bl/6 mice, germ-free (GF), Muc2-heterozygote (±), or Muc2-knockout (-/-) were injected with dexamethasone, a synthetic glucocorticoid, for four weeks. Fecal samples were collected for gut microbiota analysis via 16S rRNA T-RFLP and amplicon sequencing. Intestinal mucosa was collected for mucin gene expression studies. GF mice were conventionalized withmore » gut microbes from treated- and non-treated groups to determine their functional capacities in recipient hosts. Results—Exposure to DEX in WT mice led to substantial shifts in gut microbiota over a four-week period. Furthermore, a significant down-regulation of colonic Muc2 gene expression was observed after treatment. Muc2-knockout mice harbored a pro-inflammatory environment of gut microbes, characterized by the increase or decrease in prevalence of specific microbiota populations such as Clostridiales and Lactobacillaceae, respectively. This colitogenic phenotype was transmissible to IL10-knockout (IL10-KO) mice, a genetically susceptible model of colonic inflammatory disorders. Microbiota from donors pre-treated with DEX, however, ameliorated symptoms of inflammation. We conclude that commensal gut bacteria may be a key mediator of the anti-inflammatory effects observed in the large intestine after GC exposure. These findings underscore the notion that intestinal microbes comprise a “microbial organ” essential for host physiology that can be targeted by therapeutic approaches to restore intestinal homeostasis.« less

Glucose metabolism: focus on gut microbiota, the endocannabinoid system and beyond.

PubMed

Cani, P D; Geurts, L; Matamoros, S; Plovier, H; Duparc, T

2014-09-01

The gut microbiota is now considered as a key factor in the regulation of numerous metabolic pathways. Growing evidence suggests that cross-talk between gut bacteria and host is achieved through specific metabolites (such as short-chain fatty acids) and molecular patterns of microbial membranes (lipopolysaccharides) that activate host cell receptors (such as toll-like receptors and G-protein-coupled receptors). The endocannabinoid (eCB) system is an important target in the context of obesity, type 2 diabetes (T2D) and inflammation. It has been demonstrated that eCB system activity is involved in the control of glucose and energy metabolism, and can be tuned up or down by specific gut microbes (for example, Akkermansia muciniphila). Numerous studies have also shown that the composition of the gut microbiota differs between obese and/or T2D individuals and those who are lean and non-diabetic. Although some shared taxa are often cited, there is still no clear consensus on the precise microbial composition that triggers metabolic disorders, and causality between specific microbes and the development of such diseases is yet to be proven in humans. Nevertheless, gastric bypass is most likely the most efficient procedure for reducing body weight and treating T2D. Interestingly, several reports have shown that the gut microbiota is profoundly affected by the procedure. It has been suggested that the consistent postoperative increase in certain bacterial groups such as Proteobacteria, Bacteroidetes and Verrucomicrobia (A. muciniphila) may explain its beneficial impact in gnotobiotic mice. Taken together, these data suggest that specific gut microbes modulate important host biological systems that contribute to the control of energy homoeostasis, glucose metabolism and inflammation in obesity and T2D. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Using Corticosteroids to Reshape the Gut Microbiome: Implications for Inflammatory Bowel Diseases

DOE PAGES

Huang, Edmond Y.; Inoue, Takuya; Leone, Vanessa A.; ...

2015-05-01

Introduction—Commensal gut microbiota play an important role in regulating metabolic and inflammatory conditions. Reshaping intestinal microbiota through pharmacologic means may be a viable treatment option. Here we sought to delineate the functional characteristics of glucocorticoid-mediated alterations on gut microbiota and their subsequent repercussions on host mucin regulation and colonic inflammation. Methods—Adult male C57Bl/6 mice, germ-free (GF), Muc2-heterozygote (±), or Muc2-knockout (-/-) were injected with dexamethasone, a synthetic glucocorticoid, for four weeks. Fecal samples were collected for gut microbiota analysis via 16S rRNA T-RFLP and amplicon sequencing. Intestinal mucosa was collected for mucin gene expression studies. GF mice were conventionalized withmore » gut microbes from treated- and non-treated groups to determine their functional capacities in recipient hosts. Results—Exposure to DEX in WT mice led to substantial shifts in gut microbiota over a four-week period. Furthermore, a significant down-regulation of colonic Muc2 gene expression was observed after treatment. Muc2-knockout mice harbored a pro-inflammatory environment of gut microbes, characterized by the increase or decrease in prevalence of specific microbiota populations such as Clostridiales and Lactobacillaceae, respectively. This colitogenic phenotype was transmissible to IL10-knockout (IL10-KO) mice, a genetically susceptible model of colonic inflammatory disorders. Microbiota from donors pre-treated with DEX, however, ameliorated symptoms of inflammation. We conclude that commensal gut bacteria may be a key mediator of the anti-inflammatory effects observed in the large intestine after GC exposure. These findings underscore the notion that intestinal microbes comprise a “microbial organ” essential for host physiology that can be targeted by therapeutic approaches to restore intestinal homeostasis.« less

The microbiota regulates neutrophil homeostasis and host resistance to Escherichia coli K1 sepsis in neonatal mice.

PubMed

Deshmukh, Hitesh S; Liu, Yuhong; Menkiti, Ogechukwu R; Mei, Junjie; Dai, Ning; O'Leary, Claire E; Oliver, Paula M; Kolls, Jay K; Weiser, Jeffrey N; Worthen, G Scott

2014-05-01

Neonatal colonization by microbes, which begins immediately after birth, is influenced by gestational age and the mother's microbiota and is modified by exposure to antibiotics. In neonates, prolonged duration of antibiotic therapy is associated with increased risk of late-onset sepsis (LOS), a disorder controlled by neutrophils. A role for the microbiota in regulating neutrophil development and susceptibility to sepsis in the neonate remains unclear. We exposed pregnant mouse dams to antibiotics in drinking water to limit transfer of maternal microbes to the neonates. Antibiotic exposure of dams decreased the total number and composition of microbes in the intestine of the neonates. This was associated with decreased numbers of circulating and bone marrow neutrophils and granulocyte/macrophage-restricted progenitor cells in the bone marrow of antibiotic-treated and germ-free neonates. Antibiotic exposure of dams reduced the number of interleukin-17 (IL-17)-producing cells in the intestine and production of granulocyte colony-stimulating factor (G-CSF). Granulocytopenia was associated with impaired host defense and increased susceptibility to Escherichia coli K1 and Klebsiella pneumoniae sepsis in antibiotic-treated neonates, which could be partially reversed by administration of G-CSF. Transfer of a normal microbiota into antibiotic-treated neonates induced IL-17 production by group 3 innate lymphoid cells (ILCs) in the intestine, increasing plasma G-CSF levels and neutrophil numbers in a Toll-like receptor 4 (TLR4)- and myeloid differentiation factor 88 (MyD88)-dependent manner and restored IL-17-dependent resistance to sepsis. Specific depletion of ILCs prevented IL-17- and G-CSF-dependent granulocytosis and resistance to sepsis. These data support a role for the intestinal microbiota in regulation of granulocytosis, neutrophil homeostasis and host resistance to sepsis in neonates.

Of genes and microbes: solving the intricacies in host genomes.

PubMed

Wang, Jun; Chen, Liang; Zhao, Na; Xu, Xizhan; Xu, Yakun; Zhu, Baoli

2018-05-01

Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.

Mutual reinforcement of pathophysiological host-microbe interactions in intestinal stasis models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Touw, Ketrija; Ringus, Daina L.; Hubert, Nathaniel

Chronic diseases arise when there is mutual reinforcement of pathophysiological processes that cause an aberrant steady state. Such a sequence of events may underlie chronic constipation, which has been associated with dysbiosis of the gut. In this study we hypothesized that assemblage of microbial communities, directed by slow gastrointestinal transit, affects host function in a way that reinforces constipation and further maintains selection on microbial communities. In our study, we used two models – an opioid-induced consti- pation model in mice, and a humanized mouse model where germ-free mice were colonized with stool from a patient with constipation-predominant irritable bowelmore » syndrome (IBS-C) in humans. We examined the impact of pharmacologically (loperamide)-induced constipation (PIC) and IBS-C on the structural and functional profile of the gut microbiota. Germ-free (GF) mice were colonized with microbiota from PIC donor mice and IBS-C patients to determine how the microbiota affects the host. PIC and IBS-C promoted changes in the gut microbiota, characterized by increased relative abundance of Bacteroides ovatus and Parabacteroides distasonis in both models. PIC mice exhibited decreased luminal concentrations of butyrate in the cecum and altered metabolic profiles of the gut microbiota. Colonization of GF mice with PIC-associated mice cecal or human IBS-C fecal microbiota significantly increased GI transit time when compared to control microbiota recipients. IBS-C-associated gut microbiota also impacted colonic contractile properties. Lastly, our findings support the concept that constipation is characterized by dis- ease-associated steady states caused by reinforcement of pathophysiological factors in host-microbe interactions.« less

Mutual reinforcement of pathophysiological host-microbe interactions in intestinal stasis models

DOE PAGES

Touw, Ketrija; Ringus, Daina L.; Hubert, Nathaniel; ...

2017-03-20

Chronic diseases arise when there is mutual reinforcement of pathophysiological processes that cause an aberrant steady state. Such a sequence of events may underlie chronic constipation, which has been associated with dysbiosis of the gut. In this study we hypothesized that assemblage of microbial communities, directed by slow gastrointestinal transit, affects host function in a way that reinforces constipation and further maintains selection on microbial communities. In our study, we used two models – an opioid-induced consti- pation model in mice, and a humanized mouse model where germ-free mice were colonized with stool from a patient with constipation-predominant irritable bowelmore » syndrome (IBS-C) in humans. We examined the impact of pharmacologically (loperamide)-induced constipation (PIC) and IBS-C on the structural and functional profile of the gut microbiota. Germ-free (GF) mice were colonized with microbiota from PIC donor mice and IBS-C patients to determine how the microbiota affects the host. PIC and IBS-C promoted changes in the gut microbiota, characterized by increased relative abundance of Bacteroides ovatus and Parabacteroides distasonis in both models. PIC mice exhibited decreased luminal concentrations of butyrate in the cecum and altered metabolic profiles of the gut microbiota. Colonization of GF mice with PIC-associated mice cecal or human IBS-C fecal microbiota significantly increased GI transit time when compared to control microbiota recipients. IBS-C-associated gut microbiota also impacted colonic contractile properties. Lastly, our findings support the concept that constipation is characterized by dis- ease-associated steady states caused by reinforcement of pathophysiological factors in host-microbe interactions.« less

Host-Microbe Interactions in the Neonatal Intestine: Role of Human Milk Oligosaccharides123

PubMed Central

Donovan, Sharon M.; Wang, Mei; Li, Min; Friedberg, Iddo; Schwartz, Scott L.; Chapkin, Robert S.

2012-01-01

The infant intestinal microbiota is shaped by genetics and environment, including the route of delivery and early dietary intake. Data from germ-free rodents and piglets support a critical role for the microbiota in regulating gastrointestinal and immune development. Human milk oligosaccharides (HMO) both directly and indirectly influence intestinal development by regulating cell proliferation, acting as prebiotics for beneficial bacteria and modulating immune development. We have shown that the gut microbiota, the microbial metatranscriptome, and metabolome differ between porcine milk–fed and formula-fed (FF) piglets. Our goal is to define how early nutrition, specifically HMO, shapes host-microbe interactions in breast-fed (BF) and FF human infants. We an established noninvasive method that uses stool samples containing intact sloughed epithelial cells to quantify intestinal gene expression profiles in human infants. We hypothesized that a systems biology approach, combining i) HMO composition of the mother’s milk with the infant’s gut gene expression and fecal bacterial composition, ii) gene expression, and iii short-chain fatty acid profiles would identify important mechanistic pathways affecting intestinal development of BF and FF infants in the first few months of life. HMO composition was analyzed by HLPC Chip/time-of-flight MS and 3 HMO clusters were identified using principle component analysis. Initial findings indicated that both host epithelial cell mRNA expression and the microbial phylogenetic profiles provided strong feature sets that distinctly classified the BF and FF infants. Ongoing analyses are designed to integrate the host transcriptome, bacterial phylogenetic profiles, and functional metagenomic data using multivariate statistical analyses. PMID:22585924

Neutrophil evasion strategies by Streptococcus pneumoniae and Staphylococcus aureus.

PubMed

Lewis, Megan L; Surewaard, Bas G J

2018-03-01

Humans are well equipped to defend themselves against bacteria. The innate immune system employs diverse mechanisms to recognize, control and initiate a response that can destroy millions of different microbes. Microbes that evade the sophisticated innate immune system are able to escape detection and could become pathogens. The pathogens Streptococcus pneumoniae and Staphylococcus aureus are particularly successful due to the development of a wide variety of virulence strategies for bacterial pathogenesis and they invest significant efforts towards mechanisms that allow for neutrophil evasion. Neutrophils are a primary cellular defense and can rapidly kill invading microbes, which is an indispensable function for maintaining host health. This review compares the key features of Streptococcus pneumoniae and Staphylococcus aureus in epidemiology, with a specific focus on virulence mechanisms utilized to evade neutrophils in bacterial pathogenesis. It is important to understand the complex interactions between pathogenic bacteria and neutrophils so that we can disrupt the ability of pathogens to cause disease.

Aspergillus fumigatus Copper Export Machinery and Reactive Oxygen Intermediate Defense Counter Host Copper-Mediated Oxidative Antimicrobial Offense.

PubMed

Wiemann, Philipp; Perevitsky, Adi; Lim, Fang Yun; Shadkchan, Yana; Knox, Benjamin P; Landero Figueora, Julio A; Choera, Tsokyi; Niu, Mengyao; Steinberger, Andrew J; Wüthrich, Marcel; Idol, Rachel A; Klein, Bruce S; Dinauer, Mary C; Huttenlocher, Anna; Osherov, Nir; Keller, Nancy P

2017-05-02

The Fenton-chemistry-generating properties of copper ions are considered a potent phagolysosome defense against pathogenic microbes, yet our understanding of underlying host/microbe dynamics remains unclear. We address this issue in invasive aspergillosis and demonstrate that host and fungal responses inextricably connect copper and reactive oxygen intermediate (ROI) mechanisms. Loss of the copper-binding transcription factor AceA yields an Aspergillus fumigatus strain displaying increased sensitivity to copper and ROI in vitro, increased intracellular copper concentrations, decreased survival in challenge with murine alveolar macrophages (AMΦs), and reduced virulence in a non-neutropenic murine model. ΔaceA survival is remediated by dampening of host ROI (chemically or genetically) or enhancement of copper-exporting activity (CrpA) in A. fumigatus. Our study exposes a complex host/microbe multifactorial interplay that highlights the importance of host immune status and reveals key targetable A. fumigatus counter-defenses. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Exploring Arabidopsis thaliana Root Endophytes via Single-Cell Genomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lundberg, Derek; Woyke, Tanja; Tringe, Susannah

2014-03-19

Land plants grow in association with microbial communities both on their surfaces and inside the plant (endophytes). The relationships between microbes and their host can vary from pathogenic to mutualistic. Colonization of the endophyte compartment occurs in the presence of a sophisticated plant immune system, implying finely tuned discrimination of pathogens from mutualists and commensals. Despite the importance of the microbiome to the plant, relatively little is known about the specific interactions between plants and microbes, especially in the case of endophytes. The vast majority of microbes have not been grown in the lab, and thus one of the fewmore » ways of studying them is by examining their DNA. Although metagenomics is a powerful tool for examining microbial communities, its application to endophyte samples is technically difficult due to the presence of large amounts of host plant DNA in the sample. One method to address these difficulties is single-cell genomics where a single microbial cell is isolated from a sample, lysed, and its genome amplified by multiple displacement amplification (MDA) to produce enough DNA for genome sequencing. This produces a single-cell amplified genome (SAG). We have applied this technology to study the endophytic microbes in Arabidopsis thaliana roots. Extensive 16S gene profiling of the microbial communities in the roots of multiple inbred A. thaliana strains has identified 164 OTUs as being significantly enriched in all the root endophyte samples compared to their presence in bulk soil.« less

The Pathogenic Potential of a Microbe

PubMed Central

2017-01-01

ABSTRACT Virulence is a microbial property that is realized only in susceptible hosts. There is no absolute measurement for virulence, and consequently it is always measured relative to a standard, usually another microbe or host. This article introduces the concept of pathogenic potential, which provides a new approach to measuring the capacity of microbes for virulence. The pathogenic potential is proportional to the fraction of individuals who become symptomatic after infection with a defined inoculum and can include such attributes as mortality, communicability, and the time from infection to disease. The calculation of the pathogenic potential has significant advantages over the use of the lethal dose that kills 50% of infected individuals (LD50) and allows direct comparisons between individual microbes. An analysis of the pathogenic potential of several microbes for mice reveals a continuum, which in turn supports the view that there is no dividing line between pathogenic and nonpathogenic microbes. PMID:28251180

Mining the Human Gut Microbiota for Immunomodulatory Organisms.

PubMed

Geva-Zatorsky, Naama; Sefik, Esen; Kua, Lindsay; Pasman, Lesley; Tan, Tze Guan; Ortiz-Lopez, Adriana; Yanortsang, Tsering Bakto; Yang, Liang; Jupp, Ray; Mathis, Diane; Benoist, Christophe; Kasper, Dennis L

2017-02-23

Within the human gut reside diverse microbes coexisting with the host in a mutually advantageous relationship. Evidence has revealed the pivotal role of the gut microbiota in shaping the immune system. To date, only a few of these microbes have been shown to modulate specific immune parameters. Herein, we broadly identify the immunomodulatory effects of phylogenetically diverse human gut microbes. We monocolonized mice with each of 53 individual bacterial species and systematically analyzed host immunologic adaptation to colonization. Most microbes exerted several specialized, complementary, and redundant transcriptional and immunomodulatory effects. Surprisingly, these were independent of microbial phylogeny. Microbial diversity in the gut ensures robustness of the microbiota's ability to generate a consistent immunomodulatory impact, serving as a highly important epigenetic system. This study provides a foundation for investigation of gut microbiota-host mutualism, highlighting key players that could identify important therapeutics. Copyright © 2017 Elsevier Inc. All rights reserved.

Interactions of dietary fiber with nutritional components on gut microbial composition, function, and health in monogastrics.

PubMed

Seidu, A; Dongsheng, Che; Guixin, Qin; Hailong, Jiang; Han, Rui; Tlotliso Sello, Cornelius

2018-05-07

The relation between dietary fiber and wellbeing of human and other monogastrics has recently became a hot topic as showed in an increasing number of publication of the related research. The aim of this review is to describe through a logical approach the scientific suggestion linking possible benefits of dietary fiber on nutritional components and their effect on the gastrointestinal composition in relation to disease conditions in humans or animals. Dietary fiber plays a key role in influencing blood glucose or insulin concentrations, stool bulkiness, reduce the pH within the digestive tract, synthesize volatile fatty acids (VFA), reduce intestinal transit time, stimulate growth of intestinal microbes, and constructively enhance various blood parameters. The available literature suggests that fiber influences the bioavailability of nutrients, and maintains the host wellbeing by controlling disorders and disease prevalent with a Western way of life such as constipation and diarrhea, diabetes, obesity, gastrointestinal inflammation, atherosclerosis, and colon cancer. Although there are some studies demonstrating that dietary fiber may be effective in prevention and treatment of this disorders, however, the mechanisms involved are yet to be understood. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

A Plethora of Virulence Strategies Hidden Behind Nuclear Targeting of Microbial Effectors

PubMed Central

Rivas, Susana; Genin, Stéphane

2011-01-01

Plant immune responses depend on the ability to couple rapid recognition of the invading microbe to an efficient response. During evolution, plant pathogens have acquired the ability to deliver effector molecules inside host cells in order to manipulate cellular and molecular processes and establish pathogenicity. Following translocation into plant cells, microbial effectors may be addressed to different subcellular compartments. Intriguingly, a significant number of effector proteins from different pathogenic microorganisms, including viruses, oomycetes, fungi, nematodes, and bacteria, is targeted to the nucleus of host cells. In agreement with this observation, increasing evidence highlights the crucial role played by nuclear dynamics, and nucleocytoplasmic protein trafficking during a great variety of analyzed plant–pathogen interactions. Once in the nucleus, effector proteins are able to manipulate host transcription or directly subvert essential host components to promote virulence. Along these lines, it has been suggested that some effectors may affect histone packing and, thereby, chromatin configuration. In addition, microbial effectors may either directly activate transcription or target host transcription factors to alter their regular molecular functions. Alternatively, nuclear translocation of effectors may affect subcellular localization of their cognate resistance proteins in a process that is essential for resistance protein-mediated plant immunity. Here, we review recent progress in our field on the identification of microbial effectors that are targeted to the nucleus of host plant cells. In addition, we discuss different virulence strategies deployed by microbes, which have been uncovered through examination of the mechanisms that guide nuclear localization of effector proteins. PMID:22639625

Host- and microbe determinants that may influence the success of S. aureus colonization

PubMed Central

Johannessen, Mona; Sollid, Johanna E.; Hanssen, Anne-Merethe

2012-01-01

Staphylococcus aureus may cause serious skin and soft tissue infections, deep abscesses, endocarditis, osteomyelitis, pneumonia, and sepsis. S. aureus persistently colonizes 25–30% of the adult human population, and S. aureus carriers have an increased risk for infections caused by the bacterium. The major site of colonization is the nose, i.e., the vestibulum nasi, which is covered with ordinary skin and hair follicles. Several host and microbe determinants are assumed to be associated with colonization. These include the presence and expression level of bacterial adhesins, which can adhere to various proteins in the extracellular matrix or on the cellular surface of human skin. The host expresses several antimicrobial peptides and lipids. The level of β-defensin 3, free sphingosine, and cis-6-hexadecenoic acid are found to be associated with nasal carriage of S. aureus. Other host factors are certain polymorphisms in Toll-like receptor 2, mannose-binding lectin, C-reactive protein, glucocorticoid-, and vitamin D receptor. Additional putative determinants for carriage include genetic variation and expression of microbial surface components recognizing adhesive matrix molecules and their interaction partners, as well as variation among humans in the ability of recognizing and responding appropriately to the bacteria. Moreover, the available microflora may influence the success of S. aureus colonization. In conclusion, colonization is a complex interplay between the bacteria and its host. Several bacterial and host factors are involved, and an increased molecular understanding of these are needed. PMID:22919647

Host- and microbe determinants that may influence the success of S. aureus colonization.

PubMed

Johannessen, Mona; Sollid, Johanna E; Hanssen, Anne-Merethe

2012-01-01

Staphylococcus aureus may cause serious skin and soft tissue infections, deep abscesses, endocarditis, osteomyelitis, pneumonia, and sepsis. S. aureus persistently colonizes 25-30% of the adult human population, and S. aureus carriers have an increased risk for infections caused by the bacterium. The major site of colonization is the nose, i.e., the vestibulum nasi, which is covered with ordinary skin and hair follicles. Several host and microbe determinants are assumed to be associated with colonization. These include the presence and expression level of bacterial adhesins, which can adhere to various proteins in the extracellular matrix or on the cellular surface of human skin. The host expresses several antimicrobial peptides and lipids. The level of β-defensin 3, free sphingosine, and cis-6-hexadecenoic acid are found to be associated with nasal carriage of S. aureus. Other host factors are certain polymorphisms in Toll-like receptor 2, mannose-binding lectin, C-reactive protein, glucocorticoid-, and vitamin D receptor. Additional putative determinants for carriage include genetic variation and expression of microbial surface components recognizing adhesive matrix molecules and their interaction partners, as well as variation among humans in the ability of recognizing and responding appropriately to the bacteria. Moreover, the available microflora may influence the success of S. aureus colonization. In conclusion, colonization is a complex interplay between the bacteria and its host. Several bacterial and host factors are involved, and an increased molecular understanding of these are needed.

Immune and genetic gardening of the intestinal microbiome

PubMed Central

Jacobs, Jonathan P.; Braun, Jonathan

2014-01-01

The mucosal immune system – consisting of adaptive and innate immune cells as well as the epithelium – is profoundly influenced by its microbial environment. There is now growing evidence that the converse is also true, that the immune system shapes the composition of the intestinal microbiome. During conditions of health, this bidirectional interaction achieves a homeostasis in which inappropriate immune responses to nonpathogenic microbes are averted and immune activity suppresses blooms of potentially pathogenic microbes (pathobionts). Genetic alteration in immune/epithelial function can affect host gardening of the intestinal microbiome, contributing to the diversity of intestinal microbiota within a population and in some cases allowing for unfavorable microbial ecologies (dysbiosis) that confer disease susceptibility. PMID:24613921

Fixed points and limit cycles in the population dynamics of lysogenic viruses and their hosts

NASA Astrophysics Data System (ADS)

Wang, Zhenyu; Goldenfeld, Nigel

2010-07-01

Starting with stochastic rate equations for the fundamental interactions between microbes and their viruses, we derive a mean-field theory for the population dynamics of microbe-virus systems, including the effects of lysogeny. In the absence of lysogeny, our model is a generalization of that proposed phenomenologically by Weitz and Dushoff. In the presence of lysogeny, we analyze the possible states of the system, identifying a limit cycle, which we interpret physically. To test the robustness of our mean-field calculations to demographic fluctuations, we have compared our results with stochastic simulations using the Gillespie algorithm. Finally, we estimate the range of parameters that delineate the various steady states of our model.

Tick receptor for outer surface protein A from Ixodes ricinus — the first intrinsically disordered protein involved in vector-microbe recognition

NASA Astrophysics Data System (ADS)

Urbanowicz, Anna; Lewandowski, Dominik; Szpotkowski, Kamil; Figlerowicz, Marek

2016-04-01

The tick receptor for outer surface protein A (TROSPA) is the only identified factor involved in tick gut colonization by various Borrelia species. TROSPA is localized in the gut epithelium and can recognize and bind the outer surface bacterial protein OspA via an unknown mechanism. Based on earlier reports and our latest observations, we considered that TROSPA would be the first identified intrinsically disordered protein (IDP) involved in the interaction between a vector and a pathogenic microbe. To verify this hypothesis, we performed structural studies of a TROSPA mutant from Ixodes ricinus using both computational and experimental approaches. Irrespective of the method used, we observed that the secondary structure content of the TROSPA polypeptide chain is low. In addition, the collected SAXS data indicated that this protein is highly extended and exists in solution as a set of numerous conformers. These features are all commonly considered hallmarks of IDPs. Taking advantage of our SAXS data, we created structural models of TROSPA and proposed a putative mechanism for the TROSPA-OspA interaction. The disordered nature of TROSPA may explain the ability of a wide spectrum of Borrelia species to colonize the tick gut.

Investigating a holobiont: Microbiota perturbations and transkingdom networks.

PubMed

Greer, Renee; Dong, Xiaoxi; Morgun, Andrey; Shulzhenko, Natalia

2016-01-01

The scientific community has recently come to appreciate that, rather than existing as independent organisms, multicellular hosts and their microbiota comprise a complex evolving superorganism or metaorganism, termed a holobiont. This point of view leads to a re-evaluation of our understanding of different physiological processes and diseases. In this paper we focus on experimental and computational approaches which, when combined in one study, allowed us to dissect mechanisms (traditionally named host-microbiota interactions) regulating holobiont physiology. Specifically, we discuss several approaches for microbiota perturbation, such as use of antibiotics and germ-free animals, including advantages and potential caveats of their usage. We briefly review computational approaches to characterize the microbiota and, more importantly, methods to infer specific components of microbiota (such as microbes or their genes) affecting host functions. One such approach called transkingdom network analysis has been recently developed and applied in our study. (1) Finally, we also discuss common methods used to validate the computational predictions of host-microbiota interactions using in vitro and in vivo experimental systems.

Molecular basis of recognition between phytophthora pathogens and their hosts.

PubMed

Tyler, Brett M

2002-01-01

Recognition is the earliest step in any direct plant-microbe interaction. Recognition between Phytophthora pathogens, which are oomycetes, phylogenetically distinct from fungi, has been studied at two levels. Recognition of the host by the pathogen has focused on recognition of chemical, electrical, and physical features of plant roots by zoospores. Both host-specific factors such as isoflavones, and host-nonspecific factors such as amino acids, calcium, and electrical fields, influence zoospore taxis, encystment, cyst germination, and hyphal chemotropism in guiding the pathogen to potential infection sites. Recognition of the pathogen by the host defense machinery has been analyzed using biochemical and genetic approaches. Biochemical approaches have identified chemical elicitors of host defense responses, and in some cases, their cognate receptors from the host. Some elicitors, such as glucans and fatty acids, have broad host ranges, whereas others such as elicitins have narrow host ranges. Most elicitors identified appear to contribute primarily to basic or nonhost resistance. Genetic analysis has identified host resistance (R) genes and pathogen avirulence (Avr) genes that interact in a gene-for-gene manner. One Phytophthora Avr gene, Avr1b from P. sojae, has been cloned and characterized. It encodes a secreted elicitor that triggers a system-wide defense response in soybean plants carrying the cognate R gene, Rps1b.

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, Y. Anny; Sinsabaugh, Robert L.; Kuske, Cheryl Rae

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefitsmore » of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. In conclusion, the findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.« less

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

DOE PAGES

Chung, Y. Anny; Sinsabaugh, Robert L.; Kuske, Cheryl Rae; ...

2017-03-22

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefitsmore » of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. In conclusion, the findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.« less

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

USGS Publications Warehouse

Chung, Y. Anny; Sinsabaugh, Robert L; Kuske, Cheryl R.; Reed, Sasha C.; Rudgers, Jennifer A.

2017-01-01

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefits of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. The findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.

Individual diet has sex-dependent effects on vertebrate gut microbiota

PubMed Central

Bolnick, Daniel I.; Snowberg, Lisa K.; Hirsch, Philipp E.; Lauber, Christian L.; Org, Elin; Parks, Brian; Lusis, Aldons J.; Knight, Rob; Caporaso, J. Gregory; Svanbäck, Richard

2014-01-01

Vertebrates harbour diverse communities of symbiotic gut microbes. Host diet is known to alter microbiota composition, implying that dietary treatments might alleviate diseases arising from altered microbial composition (‘dysbiosis’). However, it remains unclear whether diet effects are general or depend on host genotype. Here we show that gut microbiota composition depends on interactions between host diet and sex within populations of wild and laboratory fish, laboratory mice and humans. Within each of two natural fish populations (threespine stickleback and Eurasian perch), among-individual diet variation is correlated with individual differences in gut microbiota. However, these diet–microbiota associations are sex dependent. We document similar sex-specific diet–microbiota correlations in humans. Experimental diet manipulations in laboratory stickleback and mice confirmed that diet affects microbiota differently in males versus females. The prevalence of such genotype by environment (sex by diet) interactions implies that therapies to treat dysbiosis might have sex-specific effects. PMID:25072318

Pharmacological Targeting of the Host-Pathogen Interaction: Alternatives to Classical Antibiotics to Combat Drug-Resistant Superbugs.

PubMed

Munguia, Jason; Nizet, Victor

2017-05-01

The rise of multidrug-resistant pathogens and the dearth of new antibiotic development place an existential strain on successful infectious disease therapy. Breakthrough strategies that go beyond classical antibiotic mechanisms are needed to combat this looming public health catastrophe. Reconceptualizing antibiotic therapy in the richer context of the host-pathogen interaction is required for innovative solutions. By defining specific virulence factors, the essence of a pathogen, and pharmacologically neutralizing their activities, one can block disease progression and sensitize microbes to immune clearance. Likewise, host-directed strategies to boost phagocyte bactericidal activity, enhance leukocyte recruitment, or reverse pathogen-induced immunosuppression seek to replicate the success of cancer immunotherapy in the field of infectious diseases. The answer to the threat of multidrug-resistant pathogens lies 'outside the box' of current antibiotic paradigms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Individual diet has sex-dependent effects on vertebrate gut microbiota.

PubMed

Bolnick, Daniel I; Snowberg, Lisa K; Hirsch, Philipp E; Lauber, Christian L; Org, Elin; Parks, Brian; Lusis, Aldons J; Knight, Rob; Caporaso, J Gregory; Svanbäck, Richard

2014-07-29

Vertebrates harbour diverse communities of symbiotic gut microbes. Host diet is known to alter microbiota composition, implying that dietary treatments might alleviate diseases arising from altered microbial composition ('dysbiosis'). However, it remains unclear whether diet effects are general or depend on host genotype. Here we show that gut microbiota composition depends on interactions between host diet and sex within populations of wild and laboratory fish, laboratory mice and humans. Within each of two natural fish populations (threespine stickleback and Eurasian perch), among-individual diet variation is correlated with individual differences in gut microbiota. However, these diet-microbiota associations are sex dependent. We document similar sex-specific diet-microbiota correlations in humans. Experimental diet manipulations in laboratory stickleback and mice confirmed that diet affects microbiota differently in males versus females. The prevalence of such genotype by environment (sex by diet) interactions implies that therapies to treat dysbiosis might have sex-specific effects.

Lessons from a cooperative, bacterial-animal association: the Vibrio fischeri-Euprymna scolopes light organ symbiosis.

PubMed

Ruby, E G

1996-01-01

Although the study of microbe-host interactions has been traditionally dominated by an interest in pathogenic associations, there is an increasing awareness of the importance of cooperative symbiotic interactions in the biology of many bacteria and their animal and plant hosts. This review examines a model system for the study of such symbioses, the light organ association between the bobtail squid Euprymna scolopes and the marine luminous bacterium Vibrio fischeri. Specifically, the initiation, establishment, and persistence of the benign bacterial infection of the juvenile host light organ are described, as are efforts to understand the mechanisms underlying this specific colonization program. Using molecular genetic techniques, mutant strains of V. fischeri have been constructed that are defective at specific stages of the development of the association. Some of the lessons that these mutants have begun to teach us about the complex and long-term nature of this cooperative venture are summarized.

The galvanizing of Mycobacterium tuberculosis: An antimicrobial mechanism

PubMed Central

Russell, David G

2011-01-01

Summary Evolving under constant threat from invading microbes, macrophages have acquired multiple means of killing bacteria. In this issue of Cell Host & Microbe, Botella and colleagues describe a novel anti-microbial mechanism based on elevated levels of intraphagosomal Zn2+ and the corresponding induction of bacterial genes to ameliorate this host-derived stress. PMID:21925106

Burstiness in Viral Bursts: How Stochasticity Affects Spatial Patterns in Virus-Microbe Dynamics

NASA Astrophysics Data System (ADS)

Lin, Yu-Hui; Taylor, Bradford P.; Weitz, Joshua S.

Spatial patterns emerge in living systems at the scale of microbes to metazoans. These patterns can be driven, in part, by the stochasticity inherent to the birth and death of individuals. For microbe-virus systems, infection and lysis of hosts by viruses results in both mortality of hosts and production of viral progeny. Here, we study how variation in the number of viral progeny per lysis event affects the spatial clustering of both viruses and microbes. Each viral ''burst'' is initially localized at a near-cellular scale. The number of progeny in a single lysis event can vary in magnitude between tens and thousands. These perturbations are not accounted for in mean-field models. Here we developed individual-based models to investigate how stochasticity affects spatial patterns in virus-microbe systems. We measured the spatial clustering of individuals using pair correlation functions. We found that increasing the burst size of viruses while maintaining the same production rate led to enhanced clustering. In this poster we also report on preliminary analysis on the evolution of the burstiness of viral bursts given a spatially distributed host community.

Pathogen-Mediated Inhibition of Anorexia Promotes Host Survival and Transmission.

PubMed

Rao, Sheila; Schieber, Alexandria M Palaferri; O'Connor, Carolyn P; Leblanc, Mathias; Michel, Daniela; Ayres, Janelle S

2017-01-26

Sickness-induced anorexia is a conserved behavior induced during infections. Here, we report that an intestinal pathogen, Salmonella Typhimurium, inhibits anorexia by manipulating the gut-brain axis. Inhibition of inflammasome activation by the S. Typhimurium effector, SlrP, prevented anorexia caused by IL-1β-mediated signaling to the hypothalamus via the vagus nerve. Rather than compromising host defenses, pathogen-mediated inhibition of anorexia increased host survival. SlrP-mediated inhibition of anorexia prevented invasion and systemic infection by wild-type S. Typhimurium, reducing virulence while increasing transmission to new hosts, suggesting that there are trade-offs between transmission and virulence. These results clarify the complex and contextual role of anorexia in host-pathogen interactions and suggest that microbes have evolved mechanisms to modulate sickness-induced behaviors to promote health of their host and their transmission at the expense of virulence. Copyright © 2017 Elsevier Inc. All rights reserved.

Spring Research Festival Theme Explores Host­–Microbe Interactions | Poster

Cancer.gov

By Andrea Frydl, Contributing Writer The 18th annual Spring Research Festival (SRF) will take place May 5–8 at the NCI Campus at Frederick and Fort Detrick.  This is the second year that the event is sponsored by the National Interagency Confederation for Biological Research (NICBR), an interagency committee made up of various research entities located within Fort Detrick. Theme

Microbiome-on-a-Chip: New Frontiers in Plant-Microbiota Research.

PubMed

Stanley, Claire E; van der Heijden, Marcel G A

2017-08-01

An enigmatic concoction of interactions between microbes and hosts takes place below ground, yet the function(s) of the individual components in this complex playground are far from understood. This Forum article highlights how microfluidic - or 'Microbiome-on-a-Chip' - technology could help to shed light on such relationships, opening new frontiers in plant-microbiota research. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spring Research Festival Theme Explores Host­–Microbe Interactions | Poster

Cancer.gov

By Andrea Frydl, Contributing Writer The 18th annual Spring Research Festival (SRF) will take place May 5–8 at the NCI Campus at Frederick and Fort Detrick.  This is the second year that the event is sponsored by the National Interagency Confederation for Biological Research (NICBR), an interagency committee made up of various research entities located within Fort Detrick.

A novel growth-promoting microbe, Methylobacterium funariae sp. nov., isolated from the leaf surface of a common moss.

PubMed

Schauer, S; Kutschera, U

2011-04-01

Land plants (embryophytes) evolved in the presence of prokaryotic microbes. As a result, numerous mutually beneficial associations (symbioses) developed that can be analyzed using a variety of methods. Here we describe the isolation and characterization of a new pink-pigmented facultatively methylotrophic symbiotic bacterium of the genus Methylobacterium (laboratory strain F3.2) that was isolated from the gametophytic phylloids of the common cord moss Funaria hygrometrica Hedw. Plantlets were collected in the field and analyzed in the laboratory. Colonies of methylobacteria were obtained by the agar-impression-method. Based on its unique phenotype (the bacterial cells are characterized by fimbriae-like appendages), a comparative 16S rRNA gene (DNA) sequence analysis, and an average DNA-DNA hybridization value of 8,4 %, compared with its most closely related sister taxon, this isolate is described as a new species, Methylobacterium funariae sp. nov. (type strain F3.2). This new epiphytic bacterium inhabits the leaf surface of "primitive" land plants such as mosses and interacts with its host organism via the secretion of phytohormones (cytokinines, auxins). These external signals are perceived by the plant cells that divide and grow more rapidly than in the absence of their prokaryotic phytosymbionts. We suggest that M. funariae sp. nov. uses methanol emitted from the stomatal pores as principal carbon source for cell metabolism. However, our novel data indicate that, in this unique symbiotic plant-microbe interaction, the uptake of amino acids leached from the surface of the epidermal cells of the green host organism may be of importance as microbial carbon- and nitrogen-source.

2013 Advanced Environmental Health/Advanced Food Technology Standing Review Panel Final Report

NASA Technical Reports Server (NTRS)

Steinberg, Susan

2014-01-01

The 2013 Advanced Environmental Health/Advanced Food Technology (AEH/AFT) Standing Review Panel (from here on referred to as the SRP) participated in a WebEx/teleconference with members of the Space Human Factors and Habitability (SHFH) Element, representatives from the Human Research Program (HRP), and NASA Headquarters on November 22, 2013 (list of participants is in Section IX of this report). The SRP reviewed the updated research plans for the Risk of Adverse Health Effects Due to Alterations in Host-Microorganism Interactions (Host Microbe Risk) and the Risk of Performance Decrement and Crew Illness Due to an Inadequate Food System (Food Risk). The SRP also received a status update on the Risk of Adverse Health Effects of Exposure to Dust and Volatiles during Exploration of Celestial Bodies (Dust Risk). Overall, the SRP was impressed with the strong research plans presented by the scientists and staff associated with the SHFH Element. The SRP also thought that the updated research plans were thorough, well organized, and presented in a comprehensive manner. The SRP agrees with the changes made to the Host Microbe Risk and Food Risk portfolios and thinks that the targets for Gap closure are appropriate.

The role of belowground plant-microbe interactions in climate change induced range shifts

NASA Astrophysics Data System (ADS)

Ramirez, Kelly; Snoek, Basten; van der Putten, Wim

2017-04-01

With climate change, plants have been able to shift their ranges into novel environments were conditions have been made suitable due to warming temperature and changes in precipitation. Much belowground range expansion research has focused on either positive plant-soil interactions, such as AMF symbiosis, or on negative plant-soil interactions, such as pathogens. Less focus has been given to the core microbiome of plant hosts. Many unknowns remain in how the soil microbiome may contribute to plant adaptation to climate change, and how this may feedback to plant-soil interactions and ecosystem functions. Using high-throughput Illumina sequencing we assessed soil and root microbial communities under native and range expanding plant species spanning a north-south latitudinal transect in central Europe. As expected, the soil and root microbiomes are both strongly influenced by the plant species under which they grow. Specifically, about 10% of the microbiome could be related to the host plant species. Interestingly, we found that microbiomes associated with range shifting species are less variable than those associated with native species. Further, the enrichment of microbes in roots (from the soil) is stronger with range expanding species than with native plant species. Our research indicates that the soil and root microbiomes can provide insight into plant range shifts and may be important for plant establishment. Our results are also important at a continental and global level, as ecosystems and plant communities worldwide are effected by climate change induced range-expansions.

Partitioning the effects of mating and nuptial feeding on the microbiome in gift-giving insects.

PubMed

Smith, Chad C; Srygley, Robert B; Dietrich, Emma I; Mueller, Ulrich G

2017-04-01

Mating is a ubiquitous social interaction with the potential to influence the microbiome by facilitating transmission, modifying host physiology, and in species where males donate nuptial gifts to females, altering diet. We manipulated mating and nuptial gift consumption in two insects that differ in nuptial gift size, the Mormon cricket Anabrus simplex and the decorated cricket Gryllodes sigillatus, with the expectation that larger gifts are more likely to affect the gut microbiome. Surprisingly, mating, but not nuptial gift consumption, affected the structure of bacterial communities in the gut, and only in Mormon crickets. The change in structure was due to a precipitous drop in the abundance of lactic-acid bacteria in unmated females, a taxon known for their beneficial effects on nutrition and immunity. Mating did not affect phenoloxidase or lysozyme-like antibacterial activity in either species, suggesting that any physiological response to mating on host-microbe interactions is decoupled from systemic immunity. Protein supplementation also did not affect the gut microbiome in decorated crickets, suggesting that insensitivity of gut microbes to dietary protein could contribute to the lack of an effect of nuptial gift consumption. Our study provides experimental evidence that sexual interactions can affect the microbiome and suggests mating can promote beneficial gut bacteria. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Intraspecific Competition Impacts Vibrio fischeri Strain Diversity during Initial Colonization of the Squid Light Organ

PubMed Central

Sun, Yan; LaSota, Elijah D.; Cecere, Andrew G.; LaPenna, Kyle B.; Larios-Valencia, Jessie; Wollenberg, Michael S.

2016-01-01

ABSTRACT Animal development and physiology depend on beneficial interactions with microbial symbionts. In many cases, the microbial symbionts are horizontally transmitted among hosts, thereby making the acquisition of these microbes from the environment an important event within the life history of each host. The light organ symbiosis established between the Hawaiian squid Euprymna scolopes and the bioluminescent bacterium Vibrio fischeri is a model system for examining how hosts acquire horizontally transmitted microbial symbionts. Recent studies have revealed that the light organ of wild-caught E. scolopes squid contains polyclonal populations of V. fischeri bacteria; however, the function and development of such strain diversity in the symbiosis are unknown. Here, we report our phenotypic and phylogenetic characterizations of FQ-A001, which is a V. fischeri strain isolated directly from the light organ of an E. scolopes individual. Relative to the type strain ES114, FQ-A001 exhibits similar growth in rich medium but displays increased bioluminescence and decreased motility in soft agar. FQ-A001 outcompetes ES114 in colonizing the crypt spaces of the light organs. Remarkably, we find that animals cocolonized with FQ-A001 and ES114 harbor singly colonized crypts, in contrast to the cocolonized crypts observed from competition experiments involving single genotypes. The results with our two-strain system suggest that strain diversity within the squid light organ is a consequence of diversity in the single-strain colonization of individual crypt spaces. IMPORTANCE The developmental programs and overall physiologies of most animals depend on diverse microbial symbionts that are acquired from the environment. However, the basic principles underlying how microbes colonize their hosts remain poorly understood. Here, we report our findings of bacterial strain competition within the coevolved animal-microbe symbiosis composed of the Hawaiian squid and bioluminescent bacterium Vibrio fischeri. Using fluorescent proteins to differentially label two distinct V. fischeri strains, we find that the strains are unable to coexist in the same niche within the host. Our results suggest that strain competition for distinct colonization sites dictates the strain diversity associated with the host. Our study provides a platform for studying how strain diversity develops within a host. PMID:27016564

Companion animals symposium: role of microbes in canine and feline health.

PubMed

Kil, D Y; Swanson, K S

2011-05-01

Whether in an ocean reef, a landfill, or a gastrointestinal tract (GIT), invisible communities of highly active and adaptable microbes prosper. Over time, mammals have developed a symbiosis with microbes that are important inhabitants not only in the GIT, but also in the mouth, skin, and urogenital tract. In the GIT, the number of commensal microbes exceeds the total number of host cells by at least 10 times. The GIT microbes play a critical role in nutritional, developmental, defensive, and physiologic processes in the host. Recent evidence also suggests a role of GIT microbes in metabolic phenotype and disease risk (e.g., obesity, metabolic syndrome) of the host. Proper balance is a key to maintaining GIT health. Balanced microbial colonization is also important for other body regions such as the oral cavity, the region with the greatest prevalence of disease in dogs and cats. A significant obstruction to studying microbial populations has been the lack of tools to identify and quantify microbial communities accurately and efficiently. Most of the current knowledge of microbial populations has been established by traditional cultivation methods that are not only laborious, time-consuming, and often inaccurate, but also greatly limited in scope. However, recent advances in molecular-based techniques have resulted in a dramatic improvement in studying microbial communities. These DNA-based high-throughput technologies have enabled us to more clearly characterize the identity and metabolic activity of microbes living in the host and their association with health and diseases. Despite this recent progress, however, published data pertaining to microbial communities of dogs and cats are still lacking in comparison with data in humans and other animals. More research is required to provide a more detailed description of the canine and feline microbiome and its role in health and disease.

Host-Pathogen interactions modulated by small RNAs.

PubMed

Islam, Waqar; Islam, Saif Ul; Qasim, Muhammad; Wang, Liande

2017-07-03

Biological processes such as defense mechanisms and microbial offense strategies are regulated through RNA induced interference in eukaryotes. Genetic mutations are modulated through biogenesis of small RNAs which directly impacts upon host development. Plant defense mechanisms are regulated and supported by a diversified group of small RNAs which are involved in streamlining several RNA interference pathways leading toward the initiation of pathogen gene silencing mechanisms. In the similar context, pathogens also utilize the support of small RNAs to launch their offensive attacks. Also there are strong evidences about the active involvement of these RNAs in symbiotic associations. Interestingly, small RNAs are not limited to the individuals in whom they are produced; they also show cross kingdom influences through variable interactions with other species thus leading toward the inter-organismic gene silencing. The phenomenon is understandable in the microbes which utilize these mechanisms to overcome host defense line. Understanding the mechanism of triggering host defense strategies can be a valuable step toward the generation of disease resistant host plants. We think that the cross kingdom trafficking of small RNA is an interesting insight that is needed to be explored for its vitality.

[Plant-microbe symbioses as an evolutionary continuum].

PubMed

Provorov, N A

2009-01-01

In spite of enormous taxonomic, structural and functional diversity of plant-microbe interactions, they are characterized by a historical succession which allows us to consider different forms of symbioses as the components of an evolutionary continuum. Their ancestral form is represented by arbuscular mycorrhiza (AM) which originated at the outset of terrestrial flora evolution and constituted a key factor for the land colonization by plants. In the course of AM evolution the plant acquired a basal set of genes for regulating the performance of microbes which colonize the root tissues. Later, these genes were repeatedly reorganized to meet the involvement of novel mutualistic symbionts (N2-fixing bacteria, ectomycorrhizal fungi, endophytes and epiphytes) and pathogens into the symbiotic interactions. Form the microbial side, the evolutionary succession of mutualism and antagonism is restricted to the defensive symbioses formed by plants with the ergot fungi, Clavibacter, Bacillus and Pseudomonas bacteria. Involvement of the similar systems for symbiotic interactions may be related to convergent evolution in the distant microorganisms (adaptation to the conservative host defense/regulatory factors), to molecular mimicry (imitation of the mechanisms of interaction used by the more ancient symbionts) or to the horizontal gene transfer. The hypotheses of the successive substitution of symbionts is suggested to address the relationships between AM and N2-fixing nodular symbioses in dicotyledons plants. AM formation is considered as a source of preadaptations responsible for the substitution of glomalean fungi which occupied the plant symbiotic compartments by the actinomycetes Frankia (in Rosid I plants) which were exchanged for the more competitive root nodule bacteria (in legumes). The development of nutritional symbioses with microbes is considered as an ancestral function of plant roots which were later supplemented or substituted with the function of assimilating the soil nutrients.

Microbial secondary metabolites and their impacts on insect symbioses.

PubMed

Klassen, Jonathan L

2014-10-01

All insects host communities of microbes that interact both with the insect and each other. Secondary metabolites are understood to mediate many of these interactions, although examples having robust genetic, chemical and/or ecological evidence are relatively rare. Here, I review secondary metabolites mediating community interactions in the beewolf, entomopathogenic nematode and fungus-growing ant symbioses, using the logic of Koch's postulates to emphasize well-validated symbiotic functions mediated by these metabolites. I especially highlight how these interaction networks are structured by both ecological and evolutionary processes, and how selection acting on secondary metabolite production can be multidimensional. Copyright © 2014 Elsevier Inc. All rights reserved.

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat

PubMed Central

Hyde, Embriette R.; Navas-Molina, Jose A.; Kueneman, Jordan G.; Ackermann, Gail; Cardona, Cesar; Humphrey, Gregory; Boyer, Don; Weaver, Tom; Mendelson, Joseph R.; McKenzie, Valerie J.; Gilbert, Jack A.

2016-01-01

ABSTRACT Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon (Varanus komodoensis) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon’s environment are similar to the Komodo dragon’s salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals’ environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions. PMID:27822543

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat.

PubMed

Hyde, Embriette R; Navas-Molina, Jose A; Song, Se Jin; Kueneman, Jordan G; Ackermann, Gail; Cardona, Cesar; Humphrey, Gregory; Boyer, Don; Weaver, Tom; Mendelson, Joseph R; McKenzie, Valerie J; Gilbert, Jack A; Knight, Rob

2016-01-01

Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon ( Varanus komodoensis ) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon's environment are similar to the Komodo dragon's salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals' environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions.

Soil pathogen-aphid interactions under differences in soil organic matter and mineral fertilizer.

PubMed

van Gils, Stijn; Tamburini, Giovanni; Marini, Lorenzo; Biere, Arjen; van Agtmaal, Maaike; Tyc, Olaf; Kos, Martine; Kleijn, David; van der Putten, Wim H

2017-01-01

There is increasing evidence showing that microbes can influence plant-insect interactions. In addition, various studies have shown that aboveground pathogens can alter the interactions between plants and insects. However, little is known about the role of soil-borne pathogens in plant-insect interactions. It is also not known how environmental conditions, that steer the performance of soil-borne pathogens, might influence these microbe-plant-insect interactions. Here, we studied effects of the soil-borne pathogen Rhizoctonia solani on aphids (Sitobion avenae) using wheat (Triticum aestivum) as a host. In a greenhouse experiment, we tested how different levels of soil organic matter (SOM) and fertilizer addition influence the interactions between plants and aphids. To examine the influence of the existing soil microbiome on the pathogen effects, we used both unsterilized field soil and sterilized field soil. In unsterilized soil with low SOM content, R. solani addition had a negative effect on aphid biomass, whereas it enhanced aphid biomass in soil with high SOM content. In sterilized soil, however, aphid biomass was enhanced by R. solani addition and by high SOM content. Plant biomass was enhanced by fertilizer addition, but only when SOM content was low, or in the absence of R. solani. We conclude that belowground pathogens influence aphid performance and that the effect of soil pathogens on aphids can be more positive in the absence of a soil microbiome. This implies that experiments studying the effect of pathogens under sterile conditions might not represent realistic interactions. Moreover, pathogen-plant-aphid interactions can be more positive for aphids under high SOM conditions. We recommend that soil conditions should be taken into account in the study of microbe-plant-insect interactions.

Butyrate-producing bacteria, including mucin degraders, from the swine intestinal tract

USDA-ARS?s Scientific Manuscript database

Butyrate-producing microbes promote gastrointestinal health in the human gut, and similar benefits are likely derived from butyrate-producing microbes in other animal hosts. Consequently, there is considerable potential for butyrate-producing microbes to be utilized in health-promoting application...

Symbiont interactions with non-native hosts limit the formation of new symbioses.

PubMed

Niepoth, Natalie; Ellers, Jacintha; Henry, Lee M

2018-03-12

Facultative symbionts are common in eukaryotes and can provide their hosts with significant fitness benefits. Despite the advantage of carrying these microbes, they are typically only found in a fraction of the individuals within a population and are often non-randomly distributed among host populations. It is currently unclear why facultative symbionts are only found in certain host individuals and populations. Here we provide evidence for a mechanism to help explain this phenomenon: that when symbionts interact with non-native host genotypes it can limit the horizontal transfer of symbionts to particular host lineages and populations of related hosts. Using reciprocal transfections of the facultative symbiont Hamiltonella defensa into different pea aphid clones, we demonstrate that particular symbiont strains can cause high host mortality and inhibit offspring production when injected into aphid clones other than their native host lineage. However, once established, the symbiont's ability to protect against parasitoids was not influenced by its origin. We then demonstrate that H. defensa is also more likely to establish a symbiotic relationship with aphid clones from a plant-adapted population (biotype) that typically carry H. defensa in nature, compared to clones from a biotype that does not normally carry this symbiont. These results provide evidence that certain aphid lineages and populations of related hosts are predisposed to establishing a symbiotic relationship with H. defensa. Our results demonstrate that host-symbiont genotype interactions represent a potential barrier to horizontal transmission that can limit the spread of symbionts, and adaptive traits they carry, to certain host lineages.

Drosophila melanogaster as a High-Throughput Model for Host-Microbiota Interactions.

PubMed

Trinder, Mark; Daisley, Brendan A; Dube, Josh S; Reid, Gregor

2017-01-01

Microbiota research often assumes that differences in abundance and identity of microorganisms have unique influences on host physiology. To test this concept mechanistically, germ-free mice are colonized with microbial communities to assess causation. Due to the cost, infrastructure challenges, and time-consuming nature of germ-free mouse models, an alternative approach is needed to investigate host-microbial interactions. Drosophila melanogaster (fruit flies) can be used as a high throughput in vivo screening model of host-microbiome interactions as they are affordable, convenient, and replicable. D. melanogaster were essential in discovering components of the innate immune response to pathogens. However, axenic D. melanogaster can easily be generated for microbiome studies without the need for ethical considerations. The simplified microbiota structure enables researchers to evaluate permutations of how each microbial species within the microbiota contribute to host phenotypes of interest. This enables the possibility of thorough strain-level analysis of host and microbial properties relevant to physiological outcomes. Moreover, a wide range of mutant D. melanogaster strains can be affordably obtained from public stock centers. Given this, D. melanogaster can be used to identify candidate mechanisms of host-microbe symbioses relevant to pathogen exclusion, innate immunity modulation, diet, xenobiotics, and probiotic/prebiotic properties in a high throughput manner. This perspective comments on the most promising areas of microbiota research that could immediately benefit from using the D. melanogaster model.

Understanding Luminal Microorganisms and their Potential Effectiveness in Treating Intestinal Inflammation

PubMed Central

Ince, M. Nedim; Blazar, Bruce R.; Edmond, Michael B.; Tricot, Guido; Wannemuehler, Michael J.

2015-01-01

The human intestine contains 1014 bacteria, which outnumber the mammalian cells 10-fold. Certain other commensal or infectious agents, like helminthic parasites become members of this microbial ecosystem, especially in populations living under less hygienic conditions. Intestinal microbes, also called the microbiome or microbiota, shape the host immune reactivity to self and nonself throughout life. Changes in microbiome composition may impair the maturation of immune regulatory pathways and predispose the host to develop various forms of inflammatory disorders, like Crohn's disease or ulcerative colitis. The microbiome is also critical to successful transplantation of organs or grafts. After allogeneic hematopoietic stem cell transplantation (HSCT), when the new donor cells, such as T lymphocytes learn to discriminate “the new-self from nonself” in the transplant recipient, they need healthy microbiota-derived signals to preserve the immune homeostasis. Restoring microbiota via intestinal delivery of bacterial strains, helminths, fecal microbiota transplantation or stool substitutes have the potential to improve and correct aberrant immune reactivity in various disorders. PMID:26457381

Microbiota and environmental stress: how pollution affects microbial communities in Manila clams.

PubMed

Milan, M; Carraro, L; Fariselli, P; Martino, M E; Cavalieri, D; Vitali, F; Boffo, L; Patarnello, T; Bargelloni, L; Cardazzo, B

2018-01-01

Given the crucial role of microbiota in host development, health, and environmental interactions, genomic analyses focusing on host-microbiota interactions should certainly be considered in the investigation of the adaptive mechanisms to environmental stress. Recently, several studies suggested that microbiota associated to digestive tract is a key, although still not fully understood, player that must be considered to assess the toxicity of environmental contaminants. Bacteria-dependent metabolism of xenobiotics may indeed modulate the host toxicity. Conversely, environmental variables (including pollution) may alter the microbial community and/or its metabolic activity leading to host physiological alterations that may contribute to their toxicity. Here, 16s rRNA gene amplicon sequencing has been applied to characterize the hepatopancreas microbiota composition of the Manila clam, Ruditapes philippinarum. The animals were collected in the Venice lagoon area, which is subject to different anthropogenic pressures, mainly represented by the industrial activities of Porto Marghera (PM). Seasonal and geographic differences in clam microbiotas were explored and linked to host response to chemical stress identified in a previous study at the transcriptome level, establishing potential interactions among hosts, microbes, and environmental parameters. The obtained results showed the recurrent presence of putatively detoxifying bacterial taxa in PM clams during winter and over-representation of several metabolic pathways involved in xenobiotic degradation, which suggested the potential for host-microbial synergistic detoxifying actions. Strong interaction between seasonal and chemically-induced responses was also observed, which partially obscured such potentially synergistic actions. Seasonal variables and exposure to toxicants were therefore shown to interact and substantially affect clam microbiota, which appeared to mirror host response to environmental variation. It is clear that understanding how animals respond to chemical stress cannot ignore a key component of such response, the microbiota. Copyright © 2017 Elsevier B.V. All rights reserved.

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics.

PubMed

Cardona, Cesar; Lax, Simon; Larsen, Peter; Stephens, Brent; Hampton-Marcell, Jarrad; Edwardson, Christian F; Henry, Chris; Van Bonn, Bill; Gilbert, Jack A

2018-01-01

Host-associated microbial dynamics are influenced by dietary and immune factors, but how exogenous microbial exposure shapes host-microbe dynamics remains poorly characterized. To investigate this phenomenon, we characterized the skin, rectum, and respiratory tract-associated microbiota in four aquarium-housed dolphins daily over a period of 6 weeks, including administration of a probiotic during weeks 4 to 6. The environmental bacterial sources were also characterized, including the animals' human handlers, the aquarium air and water, and the dolphins' food supply. Continuous microbial exposure occurred between all sites, yet each environment maintained a characteristic microbiota, suggesting that the majority of exposure events do not result in colonization. Small changes in water physicochemistry had a significant but weak correlation with change in dolphin-associated bacterial richness but had no influence on phylogenetic diversity. Food and air microbiota were the richest and had the largest conditional influence on other microbiota in the absence of probiotics, but during probiotic administration, food alone had the largest influence on the stability of the dolphin microbiota. Our results suggest that respiratory tract and gastrointestinal epithelium interactions with air- and food-associated microbes had the biggest influence on host-microbiota dynamics, while other interactions, such as skin transmission, played only a minor role. Finally, direct oral stimulation with a foreign exogenous microbial source can have a profound effect on microbial stability. IMPORTANCE These results provide valuable insights into the ecological influence of exogenous microbial exposure, as well as laying the foundation for improving aquarium management practices. By comparing data for dolphins from aquaria that use natural versus artificial seawater, we demonstrate the potential influence of aquarium water disinfection procedures on dolphin microbial dynamics.

Towards an Enhanced Understanding of Plant–Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism

PubMed Central

Thijs, Sofie; Sillen, Wouter; Rineau, Francois; Weyens, Nele; Vangronsveld, Jaco

2016-01-01

Phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. However, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant–microbe interactions is needed. A number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely understood. Moreover, current approaches that target the plant host, and environment separately to improve phytoremediation, potentially overlook microbial functions and properties that are part of the multiscale complexity of the plant-environment wherein biodegradation takes place. In contrast, in situ studies of phytoremediation research at the metaorganism level (host and microbiome together) are lacking. Here, we discuss a competition-driven model, based on recent evidence from the metagenomics level, and hypotheses generated by microbial community ecology, to explain the establishment of a catabolic rhizosphere microbiome in a contaminated soil. There is evidence to ground that if the host provides the right level and mix of resources (exudates) over which the microbes can compete, then a competitive catabolic and plant-growth promoting (PGP) microbiome can be selected for as long as it provides a competitive superiority in the niche. The competition-driven model indicates four strategies to interfere with the microbiome. Specifically, the rhizosphere microbiome community can be shifted using treatments that alter the host, resources, environment, and that take advantage of prioritization in inoculation. Our model and suggestions, considering the metaorganism in its natural context, would allow to gain further knowledge on the plant–microbial functions, and facilitate translation to more effective, and predictable phytotechnologies. PMID:27014254

Studying the Symbiotic Bacterium Xenorhabdus nematophila in Individual, Living Steinernema carpocapsae Nematodes Using Microfluidic Systems.

PubMed

Stilwell, Matthew D; Cao, Mengyi; Goodrich-Blair, Heidi; Weibel, Douglas B

2018-01-01

Animal-microbe symbioses are ubiquitous in nature and scientifically important in diverse areas, including ecology, medicine, and agriculture. Steinernema nematodes and Xenorhabdus bacteria compose an established, successful model system for investigating microbial pathogenesis and mutualism. The bacterium Xenorhabdus nematophila is a species-specific mutualist of insect-infecting Steinernema carpocapsae nematodes. The bacterium colonizes a specialized intestinal pocket within the infective stage of the nematode, which transports the bacteria between insects that are killed and consumed by the pair for reproduction. Current understanding of the interaction between the infective-stage nematode and its bacterial colonizers is based largely on population-level, snapshot time point studies on these organisms. This limitation arises because investigating temporal dynamics of the bacterium within the nematode is impeded by the difficulty of isolating and maintaining individual living nematodes and tracking colonizing bacterial cells over time. To overcome this challenge, we developed a microfluidic system that enables us to spatially isolate and microscopically observe individual, living Steinernema nematodes and monitor the growth and development of the associated X. nematophila bacterial communities-starting from a single cell or a few cells-over weeks. Our data demonstrate, to our knowledge, the first direct, temporal, in vivo visual analysis of a symbiosis system and the application of this system to reveal continuous dynamics of the symbiont population in the living host animal. IMPORTANCE This paper describes an experimental system for directly investigating population dynamics of a symbiotic bacterium, Xenorhabdus nematophila , in its host-the infective stage of the entomopathogenic nematode Steinernema carpocapsae . Tracking individual and groups of bacteria in individual host nematodes over days and weeks yielded insight into dynamic growth and topology changes of symbiotic bacterial populations within infective juvenile nematodes. Our approach for studying symbioses between bacteria and nematodes provides a system to investigate long-term host-microbe interactions in individual nematodes and extrapolate the lessons learned to other bacterium-animal interactions.

Mucosal barrier injury, fever and infection in neutropenic patients with cancer: introducing the paradigm febrile mucositis.

PubMed

van der Velden, Walter J F M; Herbers, Alexandra H E; Netea, Mihai G; Blijlevens, Nicole M A

2014-11-01

Infection remains one of the most prominent complications after cytotoxic treatment for cancer. The connection between neutropenia and both infections and fever has long been designated as 'febrile neutropenia', but treatment with antimicrobial agents and haematopoietic growth factors has failed to significantly reduce its incidence. Moreover, emerging antimicrobial resistance is becoming a concern that necessitates the judicious use of available antimicrobial agents. In addition to neutropenia, patients who receive cytotoxic therapy experience mucosal barrier injury (MBI) or 'mucositis'. MBI creates a port-de-entrée for resident micro-organisms to cause blood stream infections and contributes directly to the occurrence of fever by disrupting the highly regulated host-microbe interactions, which, even in the absence of an infection, can result in strong inflammatory reactions. Indeed, MBI has been shown to be a pivotal factor in the occurrence of inflammatory complications after cytotoxic therapy. Hence, the concept 'febrile neutropenia' alone may no longer suffice and a new concept 'febrile mucositis' should be recognized as the two are at least complementary. This review we summarizes the existing evidence for both paradigms and proposes new therapeutic approaches to tackle the perturbed host-microbe interactions arising from cytotoxic therapy-induced tissue damage in order to reduce fever in neutropenic patients with cancer. © 2014 John Wiley & Sons Ltd.

Intestinal commensal microbes as immune modulators

PubMed Central

Ivanov, Ivaylo I.; Honda, Kenya

2012-01-01

Commensal bacteria are necessary for the development and maintenance of a healthy immune system. Harnessing the ability of microbiota to affect host immunity is considered an important therapeutic strategy for many mucosal and non-mucosal immune-related conditions, such as inflammatory bowel diseases (IBD), celiac disease, metabolic syndrome, diabetes and microbial infections. In addition to well-established immunostimulatory effects of the microbiota, the presence of individual mutualistic commensal bacteria with immunomodulatory effects has been described. These organisms are permanent members of the commensal microbiota and affect host immune homeostasis in specific ways. Identification of individual examples of such immunomodulatory commensals and understanding their mechanisms of interaction with the host will be invaluable in designing therapeutic strategies to reverse intestinal dysbiosis and recover immunological homeostasis. PMID:23084918

Current understanding of dysbiosis in disease in human and animal models

PubMed Central

DeGruttola, Arianna K.; Low, Daren; Mizoguchi, Atsushi; Mizoguchi, Emiko

2016-01-01

Inflammatory bowel disease (IBD) is an intestinal inflammatory condition that affects over two million people in the United States. Although the etiology and pathogenesis of IBD are still largely unknown, dysregulated host/enteric microbial interactions are requisite for the development of IBD. So far, many researchers have tried to identify a precise relationship between IBD and an imbalance of the intestinal microbiota, termed “dysbiosis”. In spite of the extensive efforts, it is still largely unknown about the interplay among microbes, their hosts, and their environments, and whether dysbiosis is a causal factor or an effect of IBD. Recently, deep-sequencing analyses of the microbiota in IBD patients have been instrumental in characterizing the strong association between dysbiosis and IBD development, although it is still unable to identify specific-associated species level changes in most cases. Based on many recent reports, dysbiosis of the commensal microbiota is implicated in the pathogenesis of several diseases, including IBD, obesity, and allergic disorders, in both human and animal models. In this review article, we have focused on explaining the multiple types of dysbiosis, as well as dysbiosis-related diseases and potential treatments in order to apply this knowledge to understand a possible cause and potentially find therapeutic strategies for IBD as well as the other dysbiosis-related diseases. PMID:27070911

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.

PubMed

Jostins, Luke; Ripke, Stephan; Weersma, Rinse K; Duerr, Richard H; McGovern, Dermot P; Hui, Ken Y; Lee, James C; Schumm, L Philip; Sharma, Yashoda; Anderson, Carl A; Essers, Jonah; Mitrovic, Mitja; Ning, Kaida; Cleynen, Isabelle; Theatre, Emilie; Spain, Sarah L; Raychaudhuri, Soumya; Goyette, Philippe; Wei, Zhi; Abraham, Clara; Achkar, Jean-Paul; Ahmad, Tariq; Amininejad, Leila; Ananthakrishnan, Ashwin N; Andersen, Vibeke; Andrews, Jane M; Baidoo, Leonard; Balschun, Tobias; Bampton, Peter A; Bitton, Alain; Boucher, Gabrielle; Brand, Stephan; Büning, Carsten; Cohain, Ariella; Cichon, Sven; D'Amato, Mauro; De Jong, Dirk; Devaney, Kathy L; Dubinsky, Marla; Edwards, Cathryn; Ellinghaus, David; Ferguson, Lynnette R; Franchimont, Denis; Fransen, Karin; Gearry, Richard; Georges, Michel; Gieger, Christian; Glas, Jürgen; Haritunians, Talin; Hart, Ailsa; Hawkey, Chris; Hedl, Matija; Hu, Xinli; Karlsen, Tom H; Kupcinskas, Limas; Kugathasan, Subra; Latiano, Anna; Laukens, Debby; Lawrance, Ian C; Lees, Charlie W; Louis, Edouard; Mahy, Gillian; Mansfield, John; Morgan, Angharad R; Mowat, Craig; Newman, William; Palmieri, Orazio; Ponsioen, Cyriel Y; Potocnik, Uros; Prescott, Natalie J; Regueiro, Miguel; Rotter, Jerome I; Russell, Richard K; Sanderson, Jeremy D; Sans, Miquel; Satsangi, Jack; Schreiber, Stefan; Simms, Lisa A; Sventoraityte, Jurgita; Targan, Stephan R; Taylor, Kent D; Tremelling, Mark; Verspaget, Hein W; De Vos, Martine; Wijmenga, Cisca; Wilson, David C; Winkelmann, Juliane; Xavier, Ramnik J; Zeissig, Sebastian; Zhang, Bin; Zhang, Clarence K; Zhao, Hongyu; Silverberg, Mark S; Annese, Vito; Hakonarson, Hakon; Brant, Steven R; Radford-Smith, Graham; Mathew, Christopher G; Rioux, John D; Schadt, Eric E; Daly, Mark J; Franke, Andre; Parkes, Miles; Vermeire, Severine; Barrett, Jeffrey C; Cho, Judy H

2012-11-01

Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations. Genome-wide association studies and subsequent meta-analyses of these two diseases as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy, in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases. Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.

Graft-versus-host disease: regulation by microbe-associated molecules and innate immune receptors.

PubMed

Penack, Olaf; Holler, Ernst; van den Brink, Marcel R M

2010-03-11

Acute graft-versus-host disease (GVHD) remains the major obstacle to a more favorable therapeutic outcome of allogeneic hematopoietic stem cell transplantation (HSCT). GVHD is characterized by tissue damage in gut, liver, and skin, caused by donor T cells that are critical for antitumor and antimicrobial immunity after HSCT. One obstacle in combating GVHD used to be the lack of understanding the molecular mechanisms that are involved in the initiation phase of this syndrome. Recent research has demonstrated that interactions between microbial-associated molecules (pathogen-associated molecular patterns [PAMPs]) and innate immune receptors (pathogen recognition receptors [PRRs]), such as NOD-like receptors (NLRs) and Toll-like receptors (TLRs), control adaptive immune responses in inflammatory disorders. Polymorphisms of the genes encoding NOD2 and TLR4 are associated with a higher incidence of GVHD in HSC transplant recipients. Interestingly, NOD2 regulates GVHD through its inhibitory effect on antigen-presenting cell (APC) function. These insights identify important mechanisms regarding the induction of GVHD through the interplay of microbial molecules and innate immunity, thus opening a new area for future therapeutic approaches. This review covers current knowledge of the role of PAMPs and PRRs in the control of adaptive immune responses during inflammatory diseases, particularly GVHD.

Production of cross-kingdom oxylipins by pathogenic fungi: An update on their role in development and pathogenicity.

PubMed

Fischer, Gregory J; Keller, Nancy P

2016-03-01

Oxylipins are a class of molecules derived from the incorporation of oxygen into polyunsaturated fatty acid substrates through the action of oxygenases. While extensively investigated in the context of mammalian immune responses, over the last decade it has become apparent that oxylipins are a common means of communication among and between plants, animals, and fungi to control development and alter host-microbe interactions. In fungi, some oxylipins are derived nonenzymatically while others are produced by lipoxygenases, cyclooxygenases, and monooxygenases with homology to plant and human enzymes. Recent investigations of numerous plant and human fungal pathogens have revealed oxylipins to be involved in the establishment and progression of disease. This review highlights oxylipin production by pathogenic fungi and their role in fungal development and pathogen/host interactions.

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes.

PubMed

Theis, Kevin R; Dheilly, Nolwenn M; Klassen, Jonathan L; Brucker, Robert M; Baines, John F; Bosch, Thomas C G; Cryan, John F; Gilbert, Scott F; Goodnight, Charles J; Lloyd, Elisabeth A; Sapp, Jan; Vandenkoornhuyse, Philippe; Zilber-Rosenberg, Ilana; Rosenberg, Eugene; Bordenstein, Seth R

2016-01-01

Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization-what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.

Multiple Vibrio fischeri genes are involved in biofilm formation and host colonization

PubMed Central

Chavez-Dozal, Alba; Hogan, David; Gorman, Clayton; Quintanal-Villalonga, Alvaro; Nishiguchi, Michele K.

2012-01-01

Biofilms are increasingly recognized as the predominant form for survival in the environment for most bacteria. The successful colonization of Vibrio fischeri in its squid host Euprymna tasmanica, involves complex microbe-host interactions mediated by specific genes that are essential for biofilm formation and colonization. In the present investigation, structural and regulatory genes were selected to study their role in biofilm formation and host colonization. We have mutated several genes (pilT, pilU, flgF, motY, ibpA and mifB) by an insertional inactivation strategy. Results demonstrate that structural genes responsible for synthesis of type IV pili and flagella are crucial for biofilm formation and host infection. Moreover, regulatory genes affect colony aggregation by various mechanisms including alteration of synthesis of transcriptional factors and regulation of extracellular polysaccharide production. These results reflect the significance of how genetic alterations influence communal behavior, which is important in understanding symbiotic relationships. PMID:22486781

Biome engineering-2020.

PubMed

Brüssow, Harald

2016-09-01

The gut microbiome research is going from a descriptive into an intervention phase. To optimize beneficial microbe-host interaction, we need to understand how to steer the system by modulating the nutrient input with which the system is literally fed (e.g. diets, fibres, prebiotics, human milk oligosaccharides), and we must learn how to modulate the composition of the gut microbiota by adding beneficial microbes (e.g. probiotics, faecal transplants) and by eliminating disturbing microbial members using, for example, bacteriophages in this highly complex ecosystem. The current status of the field is reviewed together with an outlook what might be expected until 2020, highlighting obstacles to progress and possible solutions to these problems. © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Reciprocal Interactions of the Intestinal Microbiota and Immune System

PubMed Central

Maynard, Craig L.; Elson, Charles O.; Hatton, Robin D.; Weaver, Casey T.

2013-01-01

Preface Emergence of the adaptive immune system in vertebrates set the stage for evolution of an advanced symbiotic relationship with the intestinal microbiota. The defining features of specificity and memory that characterize adaptive immunity have afforded vertebrates mechanisms for efficiently tailoring immune responses to diverse types of microbes, whether to promote mutualism or host defense. These same attributes carry risk for immune-mediated diseases that are increasingly linked to the intestinal microbiota. Understanding how the adaptive immune system copes with the remarkable number and diversity of microbes that colonize the digestive tract, and how it integrates with more primitive innate immune mechanisms to maintain immune homeostasis, holds considerable promise for new approaches to modulate immune networks in order to treat and prevent disease. PMID:22972296

Modulating bacterial and gut mucosal interactions with engineered biofilm matrix proteins.

PubMed

Duraj-Thatte, Anna M; Praveschotinunt, Pichet; Nash, Trevor R; Ward, Frederick R; Joshi, Neel S

2018-02-22

Extracellular appendages play a significant role in mediating communication between bacteria and their host. Curli fibers are a class of bacterial fimbria that is highly amenable to engineering. We demonstrate the use of engineered curli fibers to rationally program interactions between bacteria and components of the mucosal epithelium. Commensal E. coli strains were engineered to produce recombinant curli fibers fused to the trefoil family of human cytokines. Biofilms formed from these strains bound more mucins than those producing wild-type curli fibers, and modulated mucin rheology as well. When treated with bacteria producing the curli-trefoil fusions mammalian cells behaved identically in terms of their migration behavior as when they were treated with the corresponding soluble trefoil factors. Overall, this demonstrates the potential utility of curli fibers as a scaffold for the display of bioactive domains and an untapped approach to rationally modulating host-microbe interactions using bacterial matrix proteins.

Diversity, structure and convergent evolution of the global sponge microbiome

PubMed Central

Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel; Björk, Johannes R.; Easson, Cole; Astudillo-García, Carmen; Olson, Julie B.; Erwin, Patrick M.; López-Legentil, Susanna; Luter, Heidi; Chaves-Fonnegra, Andia; Costa, Rodrigo; Schupp, Peter J.; Steindler, Laura; Erpenbeck, Dirk; Gilbert, Jack; Knight, Rob; Ackermann, Gail; Victor Lopez, Jose; Taylor, Michael W.; Thacker, Robert W.; Montoya, Jose M.; Hentschel, Ute; Webster, Nicole S.

2016-01-01

Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host–microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions. PMID:27306690

A Multifaceted Role of Tryptophan Metabolism and Indoleamine 2,3-Dioxygenase Activity in Aspergillus fumigatus-Host Interactions.

PubMed

Choera, Tsokyi; Zelante, Teresa; Romani, Luigina; Keller, Nancy P

2017-01-01

Aspergillus fumigatus is the most prevalent filamentous fungal pathogen of humans, causing either severe allergic bronchopulmonary aspergillosis or often fatal invasive pulmonary aspergillosis (IPA) in individuals with hyper- or hypo-immune deficiencies, respectively. Disease is primarily initiated upon the inhalation of the ubiquitous airborne conidia-the initial inoculum produced by A. fumigatus -which are complete developmental units with an ability to exploit diverse environments, ranging from agricultural composts to animal lungs. Upon infection, conidia initially rely on their own metabolic processes for survival in the host's lungs, a nutritionally limiting environment. One such nutritional limitation is the availability of aromatic amino acids (AAAs) as animals lack the enzymes to synthesize tryptophan (Trp) and phenylalanine and only produce tyrosine from dietary phenylalanine. However, A. fumigatus produces all three AAAs through the shikimate-chorismate pathway, where they play a critical role in fungal growth and development and in yielding many downstream metabolites. The downstream metabolites of Trp in A. fumigatus include the immunomodulatory kynurenine derived from indoleamine 2,3-dioxygenase (IDO) and toxins such as fumiquinazolines, gliotoxin, and fumitremorgins. Host IDO activity and/or host/microbe-derived kynurenines are increasingly correlated with many Aspergillus diseases including IPA and infections of chronic granulomatous disease patients. In this review, we will describe the potential metabolic cross talk between the host and the pathogen, specifically focusing on Trp metabolism, the implications for therapeutics, and the recent studies on the coevolution of host and microbe IDO activation in regulating inflammation, while controlling infection.

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish.

PubMed

Stagaman, Keaton; Burns, Adam R; Guillemin, Karen; Bohannan, Brendan Jm

2017-07-01

All animals live in intimate association with communities of microbes, collectively referred to as their microbiota. Certain host traits can influence which microbial taxa comprise the microbiota. One potentially important trait in vertebrate animals is the adaptive immune system, which has been hypothesized to act as an ecological filter, promoting the presence of some microbial taxa over others. Here we surveyed the intestinal microbiota of 68 wild-type zebrafish, with functional adaptive immunity, and 61 rag1 - zebrafish, lacking functional B- and T-cell receptors, to test the role of adaptive immunity as an ecological filter on the intestinal microbiota. In addition, we tested the robustness of adaptive immunity's filtering effects to host-host interaction by comparing the microbiota of fish populations segregated by genotype to those containing both genotypes. The presence of adaptive immunity individualized the gut microbiota and decreased the contributions of neutral processes to gut microbiota assembly. Although mixing genotypes led to increased phylogenetic diversity in each, there was no significant effect of adaptive immunity on gut microbiota composition in either housing condition. Interestingly, the most robust effect on microbiota composition was co-housing within a tank. In all, these results suggest that adaptive immunity has a role as an ecological filter of the zebrafish gut microbiota, but it can be overwhelmed by other factors, including transmission of microbes among hosts.

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome.

PubMed

Chassaing, Benoit; Koren, Omry; Goodrich, Julia K; Poole, Angela C; Srinivasan, Shanthi; Ley, Ruth E; Gewirtz, Andrew T

2015-03-05

The intestinal tract is inhabited by a large and diverse community of microbes collectively referred to as the gut microbiota. While the gut microbiota provides important benefits to its host, especially in metabolism and immune development, disturbance of the microbiota-host relationship is associated with numerous chronic inflammatory diseases, including inflammatory bowel disease and the group of obesity-associated diseases collectively referred to as metabolic syndrome. A primary means by which the intestine is protected from its microbiota is via multi-layered mucus structures that cover the intestinal surface, thereby allowing the vast majority of gut bacteria to be kept at a safe distance from epithelial cells that line the intestine. Thus, agents that disrupt mucus-bacterial interactions might have the potential to promote diseases associated with gut inflammation. Consequently, it has been hypothesized that emulsifiers, detergent-like molecules that are a ubiquitous component of processed foods and that can increase bacterial translocation across epithelia in vitro, might be promoting the increase in inflammatory bowel disease observed since the mid-twentieth century. Here we report that, in mice, relatively low concentrations of two commonly used emulsifiers, namely carboxymethylcellulose and polysorbate-80, induced low-grade inflammation and obesity/metabolic syndrome in wild-type hosts and promoted robust colitis in mice predisposed to this disorder. Emulsifier-induced metabolic syndrome was associated with microbiota encroachment, altered species composition and increased pro-inflammatory potential. Use of germ-free mice and faecal transplants indicated that such changes in microbiota were necessary and sufficient for both low-grade inflammation and metabolic syndrome. These results support the emerging concept that perturbed host-microbiota interactions resulting in low-grade inflammation can promote adiposity and its associated metabolic effects. Moreover, they suggest that the broad use of emulsifying agents might be contributing to an increased societal incidence of obesity/metabolic syndrome and other chronic inflammatory diseases.

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome

PubMed Central

Chassaing, Benoit; Koren, Omry; Goodrich, Julia; Poole, Angela; Srinivasan, Shanthi; Ley, Ruth E.; Gewirtz, Andrew T.

2015-01-01

Summary The intestinal tract is inhabited by a large diverse community of microbes collectively referred to as gut microbiota. While gut microbiota provide important benefits to its host, especially in metabolism and immune development, disturbance of the microbiota-host relationship is associated with numerous chronic inflammatory diseases, including inflammatory bowel disease (IBD) and the group of obesity-associated diseases collectively referred to as metabolic syndrome. A primary means by which the intestine is protected from its microbiota is via multilayered mucus structures that cover the intestinal surface thus allowing the vast majority of gut bacteria to be kept at a safe distance from epithelial cells that line the intestine 1. Thus, agents that disrupt mucus-bacterial interactions might have the potential to promote diseases associated with gut inflammation. Consequently, it has been hypothesized that emulsifiers, detergent-like molecules that are a ubiquitous component of processed foods and that can increase bacterial translocation across epithelia in vitro 2, might be promoting the post-mid 20th century increase in IBD 3. Herein, we observed that, in mice, relatively low concentrations of two commonly used emulsifiers, namely carboxymethylcellulose and polysorbate-80, induced low-grade inflammation and obesity/metabolic syndrome in WT hosts and promoted robust colitis in mice predisposed to this disorder. Emulsifier-induced metabolic syndrome was associated with microbiota encroachment, altered species composition, and increased pro-inflammatory potential. Use of germ-free mice and fecal transplants indicated that such changes in microbiota were necessary and sufficient for both low-grade inflammation and metabolic syndrome. These results support the emerging concept that perturbed host-microbiota interactions resulting in low-grade inflammation can promote adiposity and its associated metabolic effects. Moreover, they suggest that broad use of emulsifying agents might be contributing to increased societal incidence of obesity/metabolic syndrome and other chronic inflammatory diseases. PMID:25731162

Microbiome influences on insect host vector competence

PubMed Central

Weiss, Brian

2011-01-01

Insect symbioses lack the complexity and diversity of those associated with higher eukaryotic hosts. Symbiotic microbiomes are beneficial to their insect hosts in many ways, including dietary supplementation, tolerance to environmental perturbations and maintenance and/or enhancement of host immune system homeostasis. Recent studies have also highlighted the importance of the microbiome in the context of host pathogen transmission processes. Here we provide an overview of the relationship between insect disease vectors, such as tsetse flies and mosquitoes, and their associated microbiome. Several mechanisms are discussed through which symbiotic microbes may influence their host’s ability to transmit pathogens, as well as potential disease control strategies that harness symbiotic microbes to reduce pathogen transmission through an insect vector. PMID:21697014

Interactions between Drosophila and its natural yeast symbionts—Is Saccharomyces cerevisiae a good model for studying the fly-yeast relationship?

PubMed Central

Hoang, Don; Kopp, Artyom

2015-01-01

Yeasts play an important role in the biology of the fruit fly, Drosophila melanogaster. In addition to being a valuable source of nutrition, yeasts affect D. melanogaster behavior and interact with the host immune system. Most experiments investigating the role of yeasts in D. melanogaster biology use the baker’s yeast, Saccharomyces cerevisiae. However, S. cerevisiae is rarely found with natural populations of D. melanogaster or other Drosophila species. Moreover, the strain of S. cerevisiae used most often in D. melanogaster experiments is a commercially and industrially important strain that, to the best of our knowledge, was not isolated from flies. Since disrupting natural host–microbe interactions can have profound effects on host biology, the results from D. melanogaster–S. cerevisiae laboratory experiments may not be fully representative of host–microbe interactions in nature. In this study, we explore the D. melanogaster-yeast relationship using five different strains of yeast that were isolated from wild Drosophila populations. Ingested live yeasts have variable persistence in the D. melanogaster gastrointestinal tract. For example, Hanseniaspora occidentalis persists relative to S. cerevisiae, while Brettanomyces naardenensis is removed. Despite these differences in persistence relative to S. cerevisiae, we find that all yeasts decrease in total abundance over time. Reactive oxygen species (ROS) are an important component of the D. melanogaster anti-microbial response and can inhibit S. cerevisiae growth in the intestine. To determine if sensitivity to ROS explains the differences in yeast persistence, we measured yeast growth in the presence and absence of hydrogen peroxide. We find that B. naardenesis is completely inhibited by hydrogen peroxide, while H. occidentalis is not, which is consistent with yeast sensitivity to ROS affecting persistence within the D. melanogaster gastrointestinal tract. We also compared the feeding preference of D. melanogaster when given the choice between a naturally associated yeast and S. cerevisiae. We do not find a correlation between preferred yeasts and those that persist in the intestine. Notably, in no instances is S. cerevisiae preferred over the naturally associated strains. Overall, our results show that D. melanogaster-yeast interactions are more complex than might be revealed in experiments that use only S. cerevisiae. We propose that future research utilize other yeasts, and especially those that are naturally associated with Drosophila, to more fully understand the role of yeasts in Drosophila biology. Since the genetic basis of host–microbe interactions is shared across taxa and since many of these genes are initially discovered in D. melanogaster, a more realistic fly-yeast model system will benefit our understanding of host–microbe interactions throughout the animal kingdom. PMID:26336636

A novel growth-promoting microbe, Methylobacterium funariae sp. nov., isolated from the leaf surface of a common moss

PubMed Central

Schauer, S

2011-01-01

Land plants (embryophytes) evolved in the presence of prokaryotic microbes. As a result, numerous mutually beneficial associations (symbioses) developed that can be analyzed using a variety of methods. Here we describe the isolation and characterization of a new pink-pigmented facultatively methylotrophic symbiotic bacterium of the genus Methylobacterium (laboratory strain F3.2) that was isolated from the gametophytic phylloids of the common cord moss Funaria hygrometrica Hedw. Plantlets were collected in the field and analyzed in the laboratory. Colonies of methylobacteria were obtained by the agar-impression-method. Based on its unique phenotype (the bacterial cells are characterized by fimbriae-like appendages), a comparative 16S rRNA gene (DNA) sequence analysis and an average DNA-DNA hybridization value of 8.4%, compared with its most closely related sister taxon, this isolate is described as a new species, Methylobacterium funariae sp. nov. (type strain F3.2). This new epiphytic bacterium inhabits the leaf surface of “primitive” land plants such as mosses and interacts with its host organism via the secretion of phytohormones (cytokinines, auxins). These external signals are perceived by the plant cells that divide and grow more rapidly than in the absence of their prokaryotic phytosymbionts. We suggest that M. funariae sp. nov. uses methanol emitted from the stomatal pores as principal carbon source for cell metabolism. However, our novel data indicate that, in this unique symbiotic plant-microbe interaction, the uptake of amino acids leached from the surface of the epidermal cells of the green host organism may be of importance as microbial carbon- and nitrogen-source. PMID:21673511

Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity.

PubMed

Huang, Yolanda Y; Martínez-Del Campo, Ana; Balskus, Emily P

2018-02-06

The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ 1 -pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.

The Gut of Geographically Disparate Ciona intestinalis Harbors a Core Microbiota

DOE PAGES

Dishaw, Larry J.; Flores-Torres, Jaime; Lax, Simon; ...

2014-04-02

It is now widely understood that all animals engage in complex interactions with bacteria (or microbes) throughout their various life stages. This ancient exchange can involve cooperation and has resulted in a wide range of evolved host-microbial interdependencies, including those observed in the gut. Ciona intestinalis, a filter-feeding basal chordate and classic developmental model that can be experimentally manipulated, is being employed to help define these relationships. Ciona larvae are first exposed internally to microbes upon the initiation of feeding in metamorphosed individuals; however, whether or not these microbes subsequently colonize the gut and whether or not Ciona forms relationshipsmore » with specific bacteria in the gut remains unknown. Here in this report, we show that the Ciona gut not only is colonized by a complex community of bacteria, but also that samples from three geographically isolated populations reveal striking similarity in abundant operational taxonomic units (OTUs) consistent with the selection of a core community by the gut ecosystem.« less

Early Development of the Gut Microbiota and Immune Health

PubMed Central

Francino, M. Pilar

2014-01-01

In recent years, the increase in human microbiome research brought about by the rapidly evolving “omic” technologies has established that the balance among the microbial groups present in the human gut, and their multipronged interactions with the host, are crucial for health. On the other hand, epidemiological and experimental support has also grown for the ‘early programming hypothesis’, according to which factors that act in utero and early in life program the risks for adverse health outcomes later on. The microbiota of the gut develops during infancy, in close interaction with immune development, and with extensive variability across individuals. It follows that the specific process of gut colonization and the microbe-host interactions established in an individual during this period have the potential to represent main determinants of life-long propensity to immune disease. Although much remains to be learnt on the progression of events by which the gut microbiota becomes established and initiates its intimate relationships with the host, and on the long-term repercussions of this process, recent works have advanced significatively in this direction. PMID:25438024

The skin microbiome: current perspectives and future challenges

PubMed Central

Chen, Yiyin Erin; Tsao, Hensin

2013-01-01

Complex communities of bacteria, fungi, and viruses thrive on our skin. The composition of these communities depends on skin characteristics, such as sebaceous gland concentration, moisture content, and temperature, as well as on host genetics and exogenous environmental factors. Recent metagenomic studies have uncovered a surprising diversity within these ecosystems and have fostered a new view of commensal organisms as playing a much larger role in immune modulation and epithelial health than previously expected. Understanding microbe-host interactions and discovering the factors that drive microbial colonization will help us understand the pathogenesis of skin diseases and develop new promicrobial and antimicrobial therapeutics. PMID:23489584

A new synthesis for antibody-mediated immunity

PubMed Central

Casadevall, Arturo; Pirofski, Liise-anne

2013-01-01

The view that immunoglobulins function largely by potentiating neutralization, cytotoxicity or phagocytosis is being replaced by a new synthesis whereby antibodies participate in all aspects of the immune response, from protecting the host at the earliest time of encounter with a microbe to later challenges. Perhaps the most transformative concept is that immunoglobulins manifest emergent properties, from their structure and function as individual molecules to their interactions with microbial targets and the host immune system. Given that emergent properties are neither reducible to first principles nor predictable, there is a need for new conceptual approaches for understanding antibody function and mechanisms of antibody immunity. PMID:22179281

The galvanizing of Mycobacterium tuberculosis: an antimicrobial mechanism.

PubMed

Russell, David G

2011-09-15

Evolving under constant threat from invading microbes, macrophages have acquired multiple means of killing bacteria. In this issue of Cell Host & Microbe, Botella and colleagues (Botella et al., 2011) describe a novel antimicrobial mechanism based on elevated levels of intraphagosomal Zn(2+) and the corresponding induction of bacterial genes to ameliorate this host-derived stress. Copyright © 2011 Elsevier Inc. All rights reserved.

Principles of Chemical Biology: From Sexy Fatty Acids and EBV probes to Anti-Acid Antibiotic via Post-Biotics and Host-Microbe Metabolic Complementarity.

PubMed

2017-06-22

This month: The role of fatty acids in sex determination; a probe to monitor and inhibit EBNA1 at the same time; a biological role for post-biotics; what happens when you mix microbes, hosts, and drugs; and an antibiotic that cross-protects with acid. Copyright © 2017. Published by Elsevier Ltd.

A Plant-Associated Microbe Genome Initiative

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jan E. Leach; Scott Gold; Sue Tolin

2003-03-06

Plant-associated microorganisms are critical to agricultural and food security and are key components in maintaining the balance of our ecosystems. Some of these diverse microbes, which include viruses, bacteria, oomycetes, fungi, and nematodes, cause plant diseases, whereas others prevent diseases or enhance plant growth. Despite their importance, we know little about them on a genomic level. To intervene in disease and understand the basis of biological control or symbiotic relationships, a concerted and coordinated genomic analysis of these microbes is essential. Genome analysis, in this context, refers to the structural and functional analysis of the microbe DNA including the genes,more » the proteins encoded by those genes, as well as noncoding sequences involved in genome dynamics and function. The ultimate emphasis is on understanding genomic functions involved in plant associations. Members of The American Phytopathological Society (APS) developed a prioritized list of plant-associated microbes for genome analysis. With this list as a foundation for discussions, a Workshop on Genomic Analysis of Plant-Associated Microorganisms was held in Washington, D.C., on 9 to 11 April 2002. The workshop was organized by the Public Policy Board of APS, and was funded by the Department of Energy (DOE), the National Science Foundation (NSF), U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), and USDA-National Research Initiatives (USDA-NRI). The workshop included academic, industrial, and governmental experts from the genomics and microbial research communities and observers from the federal funding agencies. After reviewing current and near-term technologies, workshop participants proposed a comprehensive, international initiative to obtain the genomic information needed to understand these important microbes and their interactions with host plants and the environment. Specifically, the recommendations call for a 5-year, $500 million international public effort for genome analysis of plant-associated microbes. The goals are to (i) obtain genome sequence information for several representative groups of microbes; (ii) identify and determine function for the genes/proteins and other genomic elements involved in plant-microbe interactions; (iii) develop and implement standardized bioinformatic tools and a database system that is applicable across all microbes; and (iv) educate and train scientists with skills and knowledge of biological and computational sciences who will apply the information to the protection of our food sources and environment.« less

Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics.

PubMed

Moitinho-Silva, Lucas; Díez-Vives, Cristina; Batani, Giampiero; Esteves, Ana Is; Jahn, Martin T; Thomas, Torsten

2017-07-01

Despite an increased understanding of functions in sponge microbiomes, the interactions among the symbionts and between symbionts and host are not well characterized. Here we reconstructed the metabolic interactions within the sponge Cymbastela concentrica microbiome in the context of functional features of symbiotic diatoms and the host. Three genome bins (CcPhy, CcNi and CcThau) were recovered from metagenomic data of C. concentrica, belonging to the proteobacterial family Phyllobacteriaceae, the Nitrospira genus and the thaumarchaeal order Nitrosopumilales. Gene expression was estimated by mapping C. concentrica metatranscriptomic reads. Our analyses indicated that CcPhy is heterotrophic, while CcNi and CcThau are chemolithoautotrophs. CcPhy expressed many transporters for the acquisition of dissolved organic compounds, likely available through the sponge's filtration activity and symbiotic carbon fixation. Coupled nitrification by CcThau and CcNi was reconstructed, supported by the observed close proximity of the cells in fluorescence in situ hybridization. CcPhy facultative anaerobic respiration and assimilation by diatoms may consume the resulting nitrate. Transcriptional analysis of diatom and sponge functions indicated that these organisms are likely sources of organic compounds, for example, creatine/creatinine and dissolved organic carbon, for other members of the symbiosis. Our results suggest that organic nitrogen compounds, for example, creatine, creatinine, urea and cyanate, fuel the nitrogen cycle within the sponge. This study provides an unprecedented view of the metabolic interactions within sponge-microbe symbiosis, bridging the gap between cell- and community-level knowledge.

Bacteria-Phagocyte Interactions: Emerging Tactics in an Ancient Rivalry

DTIC Science & Technology

1990-01-01

afhitan. mechanisms by which microbes cvade the deposi- Mimicry of decay -accelerating factor aExample. T ’ruzi tion of immunogiobulin and complement on...their , Possible Isis of decay accelerating factor on host cell, surfaces have been well-studied (Table 2). For Example. Bacterial phospholipase example...activators of protein that mimics the action of decay accelerat- the alternate complement pathway 1171. ing factor (DAF) [261. This protein is part of a

Porphyromonas gingivalis sinks teeth into the oral microbiota and periodontal disease.

PubMed

Honda, Kenya

2011-11-17

Periodontitis is linked to polymicrobial interactions and the presence of Porphyromonas gingivalis. In this issue of Cell Host & Microbe, Hajishengallis et al. (2011) demonstrate that P. gingivalis colonization in the oral cavity changes the composition of the oral commensal microbiota and accelerates microbiota-mediated bone-destructive periodontitis, indicating that this single, low-abundance species is a keystone in periodontal disease. Copyright © 2011 Elsevier Inc. All rights reserved.

Microbial mitigation-exacerbation continuum: a novel framework for microbiome effects on hosts in the face of stress.

PubMed

David, Aaron S; Thapa-Magar, Khum B; Afkhami, Michelle E

2018-03-01

A key challenge to understanding microbiomes and their role in ecological processes is contextualizing their effects on host organisms, particularly when faced with environmental stress. One influential theory, the Stress Gradient Hypothesis, might predict that the frequency of positive interactions increases with stressful conditions such that microbial taxa would mitigate harmful effects on host performance. Yet, equally plausible is that microbial taxa could exacerbate these effects. Here, we introduce the Mitigation-Exacerbation Continuum as a novel framework to conceptualize microbial mediation of stress. We (1) use this continuum to quantify microbial mediation of stress for six plant species and (2) test the association between these continuum values and natural species' abundance. We factorially manipulated a common stress (allelopathy) and the presence of soil microbes to quantify microbial effects in benign and stressed environments for two critical early life-history metrics, seed germination and seedling biomass. Although we found evidence of both mitigation and exacerbation among the six species, exacerbation was more common. Across species, the degree of microbial-mediated effects on germination explained >80% of the variation of natural field abundances. Our results suggest a critical role of soil microbes in mediating plant stress responses, and a potential microbial mechanism underlying species abundance. © 2018 by the Ecological Society of America.

Gut microbiota in Drosophila melanogaster interacts with Wolbachia but does not contribute to Wolbachia-mediated antiviral protection.

PubMed

Ye, Yixin H; Seleznev, Andrei; Flores, Heather A; Woolfit, Megan; McGraw, Elizabeth A

2017-02-01

Animals experience near constant infection with microorganisms. A significant proportion of these microbiota reside in the alimentary tract. There is a growing appreciation for the roles gut microbiota play in host biology. The gut microbiota of insects, for example, have been shown to help the host overcome pathogen infection either through direct competition or indirectly by stimulating host immunity. These defenses may also be supplemented by coinfecting maternally inherited microbes such as Wolbachia. The presence of Wolbachia in a host can delay and/or reduce death caused by RNA viruses. Whether the gut microbiota of the host interacts with Wolbachia, or vice versa, the precise role of Wolbachia in antiviral protection is not known. In this study, we used 16S rDNA sequencing to characterise changes in gut microbiota composition in Drosophila melanogaster associated with Wolbachia infection and antibiotic treatment. We subsequently tested whether changes in gut composition via antibiotic treatment altered Wolbachia-mediated antiviral properties. We found that both antibiotics and Wolbachia significantly reduced the biodiversity of the gut microbiota without changing the total microbial load. We also showed that changing the gut microbiota composition with antibiotic treatment enhanced Wolbachia density but did not confer greater antiviral protection against Drosophila C virus to the host. We concluded there are significant interactions between Wolbachia and gut microbiota, but changing gut microbiota composition is not likely to be a means through which Wolbachia conveys antiviral protection to its host. Copyright © 2016. Published by Elsevier Inc.

Infection of zebrafish embryos with live fluorescent Streptococcus pneumoniae as a real-time pneumococcal meningitis model.

PubMed

Jim, Kin Ki; Engelen-Lee, JooYeon; van der Sar, Astrid M; Bitter, Wilbert; Brouwer, Matthijs C; van der Ende, Arie; Veening, Jan-Willem; van de Beek, Diederik; Vandenbroucke-Grauls, Christina M J E

2016-08-19

Streptococcus pneumoniae is one of the most important causes of bacterial meningitis, an infection where unfavourable outcome is driven by bacterial and host-derived toxins. In this study, we developed and characterized a pneumococcal meningitis model in zebrafish embryos that allows for real-time investigation of early host-microbe interaction. Zebrafish embryos were infected in the caudal vein or hindbrain ventricle with green fluorescent wild-type S. pneumoniae D39 or a pneumolysin-deficient mutant. The kdrl:mCherry transgenic zebrafish line was used to visualize the blood vessels, whereas phagocytic cells were visualized by staining with far red anti-L-plastin or in mpx:GFP/mpeg1:mCherry zebrafish, that have green fluorescent neutrophils and red fluorescent macrophages. Imaging was performed by fluorescence confocal and time-lapse microscopy. After infection by caudal vein, we saw focal clogging of the pneumococci in the blood vessels and migration of bacteria through the blood-brain barrier into the subarachnoid space and brain tissue. Infection with pneumolysin-deficient S. pneumoniae in the hindbrain ventricle showed attenuated growth and migration through the brain as compared to the wild-type strain. Time-lapse and confocal imaging revealed that the initial innate immune response to S. pneumoniae in the subarachnoid space mainly consisted of neutrophils and that pneumolysin-mediated cytolytic activity caused a marked reduction of phagocytes. This new meningitis model permits detailed analysis and visualization of host-microbe interaction in pneumococcal meningitis in real time and is a very promising tool to further our insights in the pathogenesis of pneumococcal meningitis.

Host-Pathogen interactions modulated by small RNAs

PubMed Central

Islam, Waqar; Islam, Saif ul; Qasim, Muhammad; Wang, Liande

2017-01-01

ABSTRACT Biological processes such as defense mechanisms and microbial offense strategies are regulated through RNA induced interference in eukaryotes. Genetic mutations are modulated through biogenesis of small RNAs which directly impacts upon host development. Plant defense mechanisms are regulated and supported by a diversified group of small RNAs which are involved in streamlining several RNA interference pathways leading toward the initiation of pathogen gene silencing mechanisms. In the similar context, pathogens also utilize the support of small RNAs to launch their offensive attacks. Also there are strong evidences about the active involvement of these RNAs in symbiotic associations. Interestingly, small RNAs are not limited to the individuals in whom they are produced; they also show cross kingdom influences through variable interactions with other species thus leading toward the inter-organismic gene silencing. The phenomenon is understandable in the microbes which utilize these mechanisms to overcome host defense line. Understanding the mechanism of triggering host defense strategies can be a valuable step toward the generation of disease resistant host plants. We think that the cross kingdom trafficking of small RNA is an interesting insight that is needed to be explored for its vitality. PMID:28430077

Genomic analysis of three Bifidobacterium species isolated from the calf gastrointestinal tract

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelly, William J.; Cookson, Adrian L.; Altermann, Eric

Ruminant animals contribute significantly to the global value of agriculture and rely on a complex microbial community for efficient digestion. However, little is known of how this microbial-host relationship develops and is maintained. To begin to address this, we have determined the ability of three Bifidobacterium species isolated from the faeces of newborn calves to grow on carbohydrates typical of a newborn ruminant diet. Genome sequences have been determined for these bacteria with analysis of the genomes providing insights into the host association and identification of several genes that may mediate interactions with the ruminant gastrointestinal tract. The present studymore » provides a starting point from which we can define the role of potential beneficial microbes in the nutrition of young ruminants and begin to influence the interactions between the microbiota and the host. The differences observed in genomic content hint at niche partitioning among the bifidobacterial species analysed and the different strategies they employ to successfully adapt to this habitat.« less

A host plant genome ( Zizania latifolia ) after a century-long endophyte infection

DOE PAGES

Guo, Longbiao; Qiu, Jie; Han, Zujing; ...

2015-06-13

In spite of the importance of host–microbe interactions in natural ecosystems, agriculture and medicine, the impact of long-term (especially decades or longer) microbial colonization on the dynamics of host genomes is not well understood. Moreover, the vegetable crop ‘Jiaobai’ with enlarged edible stems was domesticated from wild Zizania latifolia (Oryzeae) approximately 2000 years ago as a result of persistent infection by a fungal endophyte, Ustilago esculenta. Asexual propagation via infected rhizomes is the only means of Jiaobai production, and the Z. latifolia–endophyte complex has been maintained continuously for two centuries. Here, genomic analysis revealed that cultivated Z. latifolia has amore » significantly smaller repertoire of immune receptors compared with wild Z. latifolia. There are widespread gene losses/mutations and expression changes in the plant–pathogen interaction pathway in Jiaobai. Finally, these results show that continuous long-standing endophyte association can have a major effect on the evolution of the structural and transcriptomic components of the host genome.« less

Genomic analysis of three Bifidobacterium species isolated from the calf gastrointestinal tract

DOE PAGES

Kelly, William J.; Cookson, Adrian L.; Altermann, Eric; ...

2016-07-29

Ruminant animals contribute significantly to the global value of agriculture and rely on a complex microbial community for efficient digestion. However, little is known of how this microbial-host relationship develops and is maintained. To begin to address this, we have determined the ability of three Bifidobacterium species isolated from the faeces of newborn calves to grow on carbohydrates typical of a newborn ruminant diet. Genome sequences have been determined for these bacteria with analysis of the genomes providing insights into the host association and identification of several genes that may mediate interactions with the ruminant gastrointestinal tract. The present studymore » provides a starting point from which we can define the role of potential beneficial microbes in the nutrition of young ruminants and begin to influence the interactions between the microbiota and the host. The differences observed in genomic content hint at niche partitioning among the bifidobacterial species analysed and the different strategies they employ to successfully adapt to this habitat.« less

Mutualism in a Reduced Gravity Environment (MuRGE)

NASA Technical Reports Server (NTRS)

Patel, Karishma K.

2010-01-01

MuRGE (Mutualism in a Reduced Gravity Environment) is a NASA flight-research experiment to investigate the microgravity effects associated with cell-cell communication and beneficial microbe-host interactions using a plant-fungal model system. This investigation will use a clinostat, an instrument that slowly rotates the plants to negate the effects of gravitational pull on plant growth (gravitropism) and development, to simulate microgravity. I will be using the endophytic fungus Piriformospora indica (Pi) and the model plant species Arabidopsis thaliana (At). P. indica has been shown to colonize roots of various plant species, including A. thaliana, and to increase plant growth and resistance to stress. The fungus has the ability to grow from spores or in axenic cultures without the presence of a host. P. indica spores and P. indica extract will be used to inoculate Arabidopsis seeds germinated on a clinostat in order to determine if simulated microgravity affects the interaction between the fungus and its plant host.

Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose

PubMed Central

Gao, Guangliang; Zhao, Xianzhi; Li, Qin; He, Chuan; Zhao, Wenjing; Liu, Shuyun; Ding, Jinmei; Ye, Weixing; Wang, Jun; Chen, Ye; Wang, Haiwei; Li, Jing; Luo, Yi; Su, Jian; Huang, Yong; Liu, Zuohua; Dai, Ronghua; Shi, Yixiang; Meng, He; Wang, Qigui

2016-01-01

The goose is an economically important waterfowl that exhibits unique characteristics and abilities, such as liver fat deposition and fibre digestion. Here, we report de novo whole-genome assemblies for the goose and swan goose and describe the evolutionary relationships among 7 bird species, including domestic and wild geese, which diverged approximately 3.4~6.3 million years ago (Mya). In contrast to chickens as a proximal species, the expanded and rapidly evolving genes found in the goose genome are mainly involved in metabolism, including energy, amino acid and carbohydrate metabolism. Further integrated analysis of the host genome and gut metagenome indicated that the most widely shared functional enrichment of genes occurs for functions such as glycolysis/gluconeogenesis, starch and sucrose metabolism, propanoate metabolism and the citrate cycle. We speculate that the unique physiological abilities of geese benefit from the adaptive evolution of the host genome and symbiotic interactions with gut microbes. PMID:27608918

[Mutualism in a Reduced Gravity Environment (MuRGE)

NASA Technical Reports Server (NTRS)

Patel, Karishma

2010-01-01

MuRGE (Mutualism in a Reduced Gravity Environment) is a NASA flight-research experiment to investigate the microgravity effects associated with cell-cell communication and beneficial microbe-host interactions using a plant-fungal model system. This investigation will use a clinostat, an instrument that slowly rotates the plants to negate the effects of gravitational pull on plant growth (gravitropism) and development, to simulate microgravity. I will be using the endophytic fungus Piriformospora indica (Pi) and the model plant species Arabidopsis thaliana (At). P. indica has been shown to colonize roots of various plant species, including A. thaliana, and to increase plant growth and resistance to stress. The fungus has the ability to grow from spores or in axenic cultures without the presence of a host. P. indica spores and P. indica extract will be used to inoculate Arabidopsis seeds germinated on a clinostat in order to determine if simulated microgravity affects the interaction between the fungus and its plant host.

In vivo imaging and tracking of host-microbiota interactions via metabolic labeling of gut anaerobic bacteria

PubMed Central

Geva-Zatorsky, Naama; Alvarez, David; Hudak, Jason E.; Reading, Nicola C.; Erturk-Hasdemir, Deniz; Dasgupta, Suryasarathi; von Andrian, Ulrich H.; Kasper, Dennis L.

2015-01-01

The intestine is densely populated by anaerobic commensal bacteria. These microorganisms shape immune system development, but our understanding of host–commensal interactions is hampered by a lack of tools for studying the anaerobic intestinal environment. We applied metabolic oligosaccharide engineering and bioorthogonal click-chemistry to label various commensal anaerobes, including Bacteroides fragilis, a common and immunologically important commensal. We studied the dissemination of B. fragilis following acute peritonitis, and characterized the interactions of the intact microbe and its polysaccharide components in myeloid and B cell lineages. The distribution and colonization of labeled B. fragilis along the intestine can be assessed, as well as niche competition following coadministration of multiple species of the microbiota. Nine additional anaerobic commensals (both gram-negative and gram-positive) from three phyla common in the gut—Bacteroidetes, Firmicutes, and Proteobacteria—and five families and one aerobic pathogen (Staphylococcus aureus) were also fluorescently labeled. This strategy permits visualization of the anaerobic microbial niche by various methods, including intravital two-photon microscopy and non-invasive whole-body imaging, and an approach to study microbial colonization and host–microbe interactions in real-time. PMID:26280120

Intestinal commensal microbes as immune modulators.

PubMed

Ivanov, Ivaylo I; Honda, Kenya

2012-10-18

Commensal bacteria are necessary for the development and maintenance of a healthy immune system. Harnessing the ability of microbiota to affect host immunity is considered an important therapeutic strategy for many mucosal and nonmucosal immune-related conditions, such as inflammatory bowel diseases (IBDs), celiac disease, metabolic syndrome, diabetes, and microbial infections. In addition to well-established immunostimulatory effects of the microbiota, the presence of individual mutualistic commensal bacteria with immunomodulatory effects has been described. These organisms are permanent members of the commensal microbiota and affect host immune homeostasis in specific ways. Identification of individual examples of such immunomodulatory commensals and understanding their mechanisms of interaction with the host will be invaluable in designing therapeutic strategies to reverse intestinal dysbiosis and recover immunological homeostasis. Copyright © 2012 Elsevier Inc. All rights reserved.

Production of cross-kingdom oxylipins by pathogenic fungi: An update on their role in development and pathogenicity

PubMed Central

Fischer, Gregory J.; Keller, Nancy P.

2016-01-01

Oxylipins are a class of molecules derived from the incorporation of oxygen into polyunsaturated fatty acid substrates through the action of oxygenases. While extensively investigated in the context of mammalian immune responses, over the last decade it has become apparent that oxylipins are a common means of communication among and between plants, animals, and fungi to control development and alter host-microbe interactions. In fungi, some oxylipins are derived non-enzymatically while others are produced by lipoxygenases, cyclooxygenases, and monooxygenases with homology to plant and human enzymes. Recent investigations of numerous plant and human fungal pathogens have revealed oxylipins to be involved in the establishment and progression of disease This review highlights oxylipin production by pathogenic fungi and their role in fungal development and pathogen/host interactions. PMID:26920885

Regulatory T cells in the control of host-microorganism interactions (*).

PubMed

Belkaid, Yasmine; Tarbell, Kristin

2009-01-01

Each microenvironment requires a specific set of regulatory elements that are finely and constantly tuned to maintain local homeostasis. Various populations of regulatory T cells contribute to the maintenance of this equilibrium and establishment of controlled immune responses. In particular, regulatory T cells limit the magnitude of effector responses, which may result in failure to adequately control infection. However, regulatory T cells also help limit collateral tissue damage caused by vigorous antimicrobial immune responses against pathogenic microbes as well as commensals. In this review, we describe various situations in which the balance between regulatory T cells and effector immune functions influence the outcome of host-microorganism coexistence and discuss current hypotheses and points of polemic associated with the origin, target, and antigen specificity of both endogenous and induced regulatory T cells during these interactions.

Helicobacter pylori virulence factors in development of gastric carcinoma.

PubMed

Wang, Ming-Yi; Liu, Xiao-Fei; Gao, Xiao-Zhong

2015-01-01

Helicobacter pylori plays a vital role in the pathogenesis of gastric carcinoma. However, only a relatively small proportion of individuals infected with H. pylori develop gastric carcinoma. Differences in the incidence of gastric carcinoma among infected individuals can be explained, at least partly, by the different genotypes of H. pylori virulence factors. Thus far, many virulence factors of H. pylori, such as Cag PAI, VacA, OMPs and DupA, have been reported to be involved in the development of gastric cancer. The risk of developing gastric cancer during H. pylori infection is affected by specific host-microbe interactions that are independent of H. pylori virulence factors. In this review, we discuss virulence factors of H. pylori and their role in the development of gastric carcinoma that will provide further understanding of the biological interactions of H. pylori with the host.

Bacterial-modulated host immunity and stem cell activation for gut homeostasis.

PubMed

Lee, Won-Jae

2009-10-01

Although it is widely accepted that dynamic cross-talk between gut epithelia and microorganisms must occur to achieve gut homeostasis, the critical mechanisms by which gut-microbe interactions are regulated remain uncertain. In this issue of Genes & Development, Buchon and colleagues (pp. 2333-2344) revealed that the reaction of the gut to microorganisms is not restricted to activating immune systems, but extends to integrated responses essential for gut tissue homeostasis, including self-renewal and the differentiation of stem cells. Further investigation of the connection between immune response and stem cell regulation at the molecular level in the microbe-laden mucosal epithelia will accelerate our understanding of the regulatory mechanisms of gut homeostasis and of the pathogenesis of diseases such as chronic inflammatory diseases and colorectal cancers.

Is there a link between food and intestinal microbes and the occurrence of Crohn's disease and ulcerative colitis?

PubMed

Asakura, Hitoshi; Suzuki, Kenji; Kitahora, Tetsuji; Morizane, Toshio

2008-12-01

The pathogenesis of Crohn's disease (CD) and ulcerative colitis (UC) is not fully understood. The interaction between intestinal environmental factors of food and intestinal microbes and the immunological system of hosts seems to be an important aspect. We have reviewed the relationship of the daily consumption of dietary animal meat and fats, dairy products, sugar, and other factors that may be linked to the occurrence of CD and UC from the literature and Japanese epidemiological data. In the present study, we reviewed the association between food and intestinal microbes and other factors contributing to the occurence of inflammatory bowel disease (IBD) from epidemiological data and case-control studies of IBD in the literature that appeared on Medline, and assessed the reports of intestinal microbes involved in the occurrence of IBD. We found several papers describing the positive association of animal meat and sweets and sugar with the occurrence of CD and UC. An analysis of Japanese epidemiological data suggested that the registered number of patients with CD or UC started to increase more than 20 years after an increased daily consumption of dietary animal meat and fats, and milk and dairy products, and after a decreased consumption of rice. Many studies implied a positive role of intestinal microbes in the occurrence of IBD. Intestinal environmental factors, such as Westernized food and intestinal microbes, seem to be involved in the increased occurrence of IBD.

The Road to Infection: Host-Microbe Interactions Defining the Pathogenicity of Streptococcus bovis/Streptococcus equinus Complex Members

PubMed Central

Jans, Christoph; Boleij, Annemarie

2018-01-01

The Streptococcus bovis/Streptococcus equinus complex (SBSEC) comprises several species inhabiting the animal and human gastrointestinal tract (GIT). They match the pathobiont description, are potential zoonotic agents and technological organisms in fermented foods. SBSEC members are associated with multiple diseases in humans and animals including ruminal acidosis, infective endocarditis (IE) and colorectal cancer (CRC). Therefore, this review aims to re-evaluate adhesion and colonization abilities of SBSEC members of animal, human and food origin paired with genomic and functional host-microbe interaction data on their road from colonization to infection. SBSEC seem to be a marginal population during GIT symbiosis that can proliferate as opportunistic pathogens. Risk factors for human colonization are considered living in rural areas and animal-feces contact. Niche adaptation plays a pivotal role where Streptococcus gallolyticus subsp. gallolyticus (SGG) retained the ability to proliferate in various environments. Other SBSEC members have undergone genome reduction and niche-specific gene gain to yield important commensal, pathobiont and technological species. Selective colonization of CRC tissue is suggested for SGG, possibly related to increased adhesion to cancerous cell types featuring enhanced collagen IV accessibility. SGG can colonize, proliferate and may shape the tumor microenvironment to their benefit by tumor promotion upon initial neoplasia development. Bacteria cell surface structures including lipotheichoic acids, capsular polysaccharides and pilus loci (pil1, pil2, and pil3) govern adhesion. Only human blood-derived SGG contain complete pilus loci and other disease-associated surface proteins. Rumen or feces-derived SGG and other SBSEC members lack or harbor mutated pili. Pili also contribute to binding to fibrinogen upon invasion and translocation of cells from the GIT into the blood system, subsequent immune evasion, human contact system activation and collagen-I-binding on damaged heart valves. Only SGG carrying complete pilus loci seem to have highest IE potential in humans with significant links between SGG bacteremia/IE and underlying diseases including CRC. Other SBSEC host-microbe combinations might rely on currently unknown mechanisms. Comparative genome data of blood, commensal and food isolates are limited but required to elucidate the role of pili and other virulence factors, understand pathogenicity mechanisms, host specificity and estimate health risks for animals, humans and food alike. PMID:29692760

Are pathogenic bacteria just looking for food? Metabolism and microbial pathogenesis

PubMed Central

Rohmer, Laurence; Hocquet, Didier; Miller, Samuel I.

2011-01-01

It is interesting to speculate that the evolutionary drive of microbes to develop pathogenic characteristics was to access the nutrient resources that animals provided. Environments in animals that pathogens colonize have also driven the evolution of new bacterial characteristics to maximize these new nutritional opportunities. This review focuses on genomic and functional aspects of pathogen metabolism that allow efficient utilization of nutrient resources provided by animals. Similar to genes encoding specific virulence traits, some genes encoding metabolic functions have been horizontally acquired by pathogens to provide a selective advantage in host tissues. Selective advantage in host tissues can also be gained in some circumstances by loss of function due to mutations that alter metabolic capabilities. Greater understanding of bacterial metabolism within host tissues should be important for increased understanding of host-pathogen interactions and the development of future therapeutic strategies. PMID:21600774

Genome-wide association study of Arabidopsis thaliana leaf microbial community.

PubMed

Horton, Matthew W; Bodenhausen, Natacha; Beilsmith, Kathleen; Meng, Dazhe; Muegge, Brian D; Subramanian, Sathish; Vetter, M Madlen; Vilhjálmsson, Bjarni J; Nordborg, Magnus; Gordon, Jeffrey I; Bergelson, Joy

2014-11-10

Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.

[Microbiota and autoimmunity].

PubMed

Miyake, Sachiko

2014-01-01

The microbiota plays a fundamental role in the development and the maintenance of the host immune system. Since microbiota is important in the induction and the expansion of Th17 cells and regulatory T cells, growing evidence supports that microbiome affect the induction and the disease course of autoimmune disorders. In this review, we describe the recent studies on the involvement of microbes in animal models of autoimmune diseases such as rheumatoid arthritis (RA) and multiple sclerosis (MS) using germ-free conditions, antibiotics treatment and gnotobiotic mice. Furthermore, we introduce the studies on analysis of microbiota in human autoimmune diseases including RA and MS.

Inter-kingdom prediction certainty evaluation of protein subcellular localization tools: microbial pathogenesis approach for deciphering host microbe interaction.

PubMed

Khan, Abdul Arif; Khan, Zakir; Kalam, Mohd Abul; Khan, Azmat Ali

2018-01-01

Microbial pathogenesis involves several aspects of host-pathogen interactions, including microbial proteins targeting host subcellular compartments and subsequent effects on host physiology. Such studies are supported by experimental data, but recent detection of bacterial proteins localization through computational eukaryotic subcellular protein targeting prediction tools has also come into practice. We evaluated inter-kingdom prediction certainty of these tools. The bacterial proteins experimentally known to target host subcellular compartments were predicted with eukaryotic subcellular targeting prediction tools, and prediction certainty was assessed. The results indicate that these tools alone are not sufficient for inter-kingdom protein targeting prediction. The correct prediction of pathogen's protein subcellular targeting depends on several factors, including presence of localization signal, transmembrane domain and molecular weight, etc., in addition to approach for subcellular targeting prediction. The detection of protein targeting in endomembrane system is comparatively difficult, as the proteins in this location are channelized to different compartments. In addition, the high specificity of training data set also creates low inter-kingdom prediction accuracy. Current data can help to suggest strategy for correct prediction of bacterial protein's subcellular localization in host cell. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Gut microbiota and the development of obesity.

PubMed

Boroni Moreira, A P; Fiche Salles Teixeira, T; do C Gouveia Peluzio, M; de Cássia Gonçalves Alfenas, R

2012-01-01

Advances in tools for molecular investigations have allowed deeper understanding of how microbes can influence host physiology. A very interesting field of research that has gained attention recently is the possible role of gut microbiota in the development of obesity and metabolic disorders. The aim of this review is to discuss mechanisms that explain the influence of gut microbiota on host metabolism. The gut microbiota is important for normal physiology of the host. However, differences in their composition may have different impacts on host metabolism. It has been shown that obese and lean subjects present different microbiota composition profile. These differences in microbiota composition may contribute to weight imbalance and impaired metabolism. The evidences from animal models suggest that it is possible that the microbiota of obese subjects has higher capacity to harvest energy from the diet providing substrates that can activate lipogenic pathways. In addition, microorganisms can also influence the activity of lipoprotein lipase interfering in the accumulation of triglycerides in the adipose tissue. The interaction of gut microbiota with the endocannabinoid system provides a route through which intestinal permeability can be altered. Increased intestinal permeability allows the entrance of endotoxins to the circulation, which are related to the induction of inflammation and insulin resistance in mice. The impact of the proposed mechanisms for humans still needs further investigations. However, the fact that gut microbiota can be modulated through dietary components highlights the importance to study how fatty acids, carbohydrates, micronutrients, prebiotics, and probiotics can influence gut microbiota composition and the management of obesity. Gut microbiota seems to be an important and promising target in the prevention and treatment of obesity and its related metabolic disturbances in future studies and in clinical practice.

Coercion in the Evolution of Plant-Microbe Communication: A Perspective.

PubMed

Rowe, S L; Norman, J S; Friesen, M L

2018-06-06

Plants and microbes are dependent on chemical signals as a means of interkingdom communication. There are two predicted paths for the evolution of these signals. Ritualization is the oft-assumed pathway for the evolution of plant-microbe communication systems. In this process, chemical signals, which benefit both receiver and sender, evolve from chemical cues, which benefit only the receiver. However, plant-microbe signaling may evolve from coercive interactions as well, a process known as sensory manipulation. Here, we aim to highlight the prevalence of coercive interactions and discuss sensory manipulation in the context of plant-microbe interactions. We present two examples of stabilized coercion: microbial coercion of plants via the release of phytohormones and plant coercion of microbes via manipulation of quorum-sensing compounds. Furthermore, we provide an evolutionary framework for the emergence of signaling from coercive plant-microbe interactions through the process of sensory manipulation. We hope that researchers will recognize the relevance of coercive interactions in plant-microbe systems and consider sensory manipulation as a plausible evolutionary trajectory for the emergence of plant-microbe signaling.

Economic game theory for mutualism and cooperation.

PubMed

Archetti, Marco; Scheuring, István; Hoffman, Moshe; Frederickson, Megan E; Pierce, Naomi E; Yu, Douglas W

2011-12-01

We review recent work at the interface of economic game theory and evolutionary biology that provides new insights into the evolution of partner choice, host sanctions, partner fidelity feedback and public goods. (1) The theory of games with asymmetrical information shows that the right incentives allow hosts to screen-out parasites and screen-in mutualists, explaining successful partner choice in the absence of signalling. Applications range from ant-plants to microbiomes. (2) Contract theory distinguishes two longstanding but weakly differentiated explanations of host response to defectors: host sanctions and partner fidelity feedback. Host traits that selectively punish misbehaving symbionts are parsimoniously interpreted as pre-adaptations. Yucca-moth and legume-rhizobia mutualisms are argued to be examples of partner fidelity feedback. (3) The theory of public goods shows that cooperation in multi-player interactions can evolve in the absence of assortment, in one-shot social dilemmas among non-kin. Applications include alarm calls in vertebrates and exoenzymes in microbes. 2011 Blackwell Publishing Ltd/CNRS.

Polymers in the gut compress the colonic mucus hydrogel.

PubMed

Datta, Sujit S; Preska Steinberg, Asher; Ismagilov, Rustem F

2016-06-28

Colonic mucus is a key biological hydrogel that protects the gut from infection and physical damage and mediates host-microbe interactions and drug delivery. However, little is known about how its structure is influenced by materials it comes into contact with regularly. For example, the gut abounds in polymers such as dietary fibers or administered therapeutics, yet whether such polymers interact with the mucus hydrogel, and if so, how, remains unclear. Although several biological processes have been identified as potential regulators of mucus structure, the polymeric composition of the gut environment has been ignored. Here, we demonstrate that gut polymers do in fact regulate mucus hydrogel structure, and that polymer-mucus interactions can be described using a thermodynamic model based on Flory-Huggins solution theory. We found that both dietary and therapeutic polymers dramatically compressed murine colonic mucus ex vivo and in vivo. This behavior depended strongly on both polymer concentration and molecular weight, in agreement with the predictions of our thermodynamic model. Moreover, exposure to polymer-rich luminal fluid from germ-free mice strongly compressed the mucus hydrogel, whereas exposure to luminal fluid from specific-pathogen-free mice-whose microbiota degrade gut polymers-did not; this suggests that gut microbes modulate mucus structure by degrading polymers. These findings highlight the role of mucus as a responsive biomaterial, and reveal a mechanism of mucus restructuring that must be integrated into the design and interpretation of studies involving therapeutic polymers, dietary fibers, and fiber-degrading gut microbes.

Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts

PubMed Central

Eisen, Jonathan A.; Kopp, Artyom

2012-01-01

The combination of ecological diversity with genetic and experimental tractability makes Drosophila a powerful model for the study of animal-associated microbial communities. Despite the known importance of yeasts in Drosophila physiology, behavior, and fitness, most recent work has focused on Drosophila-bacterial interactions. In order to get a more complete understanding of the Drosophila microbiome, we characterized the yeast communities associated with different Drosophila species collected around the world. We focused on the phylum Ascomycota because it constitutes the vast majority of the Drosophila-associated yeasts. Our sampling strategy allowed us to compare the distribution and structure of the yeast and bacterial communities in the same host populations. We show that yeast communities are dominated by a small number of abundant taxa, that the same yeast lineages are associated with different host species and populations, and that host diet has a greater effect than host species on yeast community composition. These patterns closely parallel those observed in Drosophila bacterial communities. However, we do not detect a significant correlation between the yeast and bacterial communities of the same host populations. Comparative analysis of different symbiont groups provides a more comprehensive picture of host-microbe interactions. Future work on the role of symbiont communities in animal physiology, ecological adaptation, and evolution would benefit from a similarly holistic approach. PMID:22885750

Comparative Analysis of Drosophila melanogaster Gut Microbiota with Respect to Host Strain, Sex, and Age.

PubMed

Han, Gangsik; Lee, Hyo Jung; Jeong, Sang Eun; Jeon, Che Ok; Hyun, Seogang

2017-07-01

Microbiota has a significant impact on the health of the host individual. The complexity of the interactions between mammalian hosts and their microbiota highlights the value of using Drosophila melanogaster as a model organism, because of its relatively simple microbial community and ease of physiological and genetic manipulation. However, highly variable and sometimes inconsistent results regarding the microbiota of D. melanogaster have been reported for host samples collected from different geographical locations; discrepancies that may be because of the inherent physiological conditions of the D. melanogaster host. Here, we conducted a comparative analysis of the gut microbiota of two D. melanogaster laboratory strains, w 1118 and Canton S, with respect to the sex and age of the host, by pyrosequencing of the 16S rRNA gene. In addition to the widespread and abundant commensal bacterial genera Lactobacillus and Acetobacter, we identified Enterococcus and Leuconostoc as major host-strain-specific bacterial genera. The relative proportions of these bacterial genera, and those of the species within each, were found to differ markedly with respect to strain, sex, and age of the host, even though host individuals were reared under the same nutritional conditions. By using various bioinformatic tools, we uncovered several characteristic features of microbiota corresponding to specific categories of the flies: host-sex-bias association of specific bacteria, age-dependent alteration of microbiota across host species and sex, and uniqueness of the microbiota of female w 1118 flies. Our results, thus, help to further our understanding of host-microbe interactions in the D. melanogaster model.

Epigenetic Mechanisms: An Emerging Player in Plant-Microbe Interactions.

PubMed

Zhu, Qian-Hao; Shan, Wei-Xing; Ayliffe, Michael A; Wang, Ming-Bo

2016-03-01

Plants have developed diverse molecular and cellular mechanisms to cope with a lifetime of exposure to a variety of pathogens. Host transcriptional reprogramming is a central part of plant defense upon pathogen recognition. Recent studies link DNA methylation and demethylation as well as chromatin remodeling by posttranslational histone modifications, including acetylation, methylation, and ubiquitination, to changes in the expression levels of defense genes upon pathogen challenge. Remarkably these inducible defense mechanisms can be primed prior to pathogen attack by epigenetic modifications and this heightened resistance state can be transmitted to subsequent generations by inheritance of these modification patterns. Beside the plant host, epigenetic mechanisms have also been implicated in virulence development of pathogens. This review highlights recent findings and insights into epigenetic mechanisms associated with interactions between plants and pathogens, in particular bacterial and fungal pathogens, and demonstrates the positive role they can have in promoting plant defense.

Insights into the virulence of oral biofilms: discoveries from proteomics.

PubMed

Kuboniwa, Masae; Tribble, Gena D; Hendrickson, Erik L; Amano, Atsuo; Lamont, Richard J; Hackett, Murray

2012-06-01

This review covers developments in the study of polymicrobial communities, biofilms and selected areas of host response relevant to dental plaque and related areas of oral biology. The emphasis is on recent studies in which proteomic methods, particularly those using mass spectrometry as a readout, have played a major role in the investigation. The last 5-10 years have seen a transition of such methods from the periphery of oral biology to the mainstream, as in other areas of biomedical science. For reasons of focus and space, the authors do not discuss biomarker studies relevant to improved diagnostics for oral health, as this literature is rather substantial in its own right and deserves a separate treatment. Here, global gene regulation studies of plaque-component organisms, biofilm formation, multispecies interactions and host-microbe interactions are discussed. Several aspects of proteomics methodology that are relevant to the studies of multispecies systems are commented upon.

Microbial Invasion vs. Tick Immune Regulation.

PubMed

Sonenshine, Daniel E; Macaluso, Kevin R

2017-01-01

Ticks transmit a greater variety of pathogenic agents that cause disease in humans and animals than any other haematophagous arthropod, including Lyme disease, Rocky Mountain spotted fever, human granulocytic anaplasmosis, babesiosis, tick-borne encephalitis, Crimean Congo haemorhagic fever, and many others (Gulia-Nuss et al., 2016). Although diverse explanations have been proposed to explain their remarkable vectorial capacity, among the most important are their blood feeding habit, their long term off-host survival, the diverse array of bioactive molecules that disrupt the host's natural hemostatic mechanisms, facilitate blood flow, pain inhibitors, and minimize inflammation to prevent immune rejection (Hajdušek et al., 2013). Moreover, the tick's unique intracellular digestive processes allow the midgut to provide a relatively permissive microenvironment for survival of invading microbes. Although tick-host-pathogen interactions have evolved over more than 300 million years (Barker and Murrell, 2008), few microbes have been able to overcome the tick's innate immune system, comprising both humoral and cellular processes that reject them. Similar to most eukaryotes, the signaling pathways that regulate the innate immune response, i.e., the Toll, IMD (Immunodeficiency) and JAK-STAT (Janus Kinase/ Signal Transducers and Activators of Transcription) also occur in ticks (Gulia-Nuss et al., 2016). Recognition of pathogen-associated molecular patterns (PAMPs) on the microbial surface triggers one or the other of these pathways. Consequently, ticks are able to mount an impressive array of humoral and cellular responses to microbial challenge, including anti-microbial peptides (AMPs), e.g., defensins, lysozymes, microplusins, etc., that directly kill, entrap or inhibit the invaders. Equally important are cellular processes, primarily phagocytosis, that capture, ingest, or encapsulate invading microbes, regulated by a primordial system of thioester-containing proteins, fibrinogen-related lectins and convertase factors (Hajdušek et al., 2013). Ticks also express reactive oxygen species (ROS) as well as glutathione-S-transferase, superoxide dismutase, heat shock proteins and even protease inhibitors that kill or inhibit microbes. Nevertheless, many tick-borne microorganisms are able to evade the tick's innate immune system and survive within the tick's body. The examples that follow describe some of the many different strategies that have evolved to enable ticks to transmit the agents of human and/or animal disease.

Fungi on the Skin: Dermatophytes and Malassezia

PubMed Central

White, Theodore C.; Findley, Keisha; Dawson, Thomas L.; Scheynius, Annika; Boekhout, Teun; Cuomo, Christina A.; Xu, Jun; Saunders, Charles W.

2014-01-01

Several human skin diseases and disorders are associated with two groups of fungi, the dermatophytes and Malassezia. Although these skin-related problems are not generally life threatening, they are among the most common diseases and disorders of mankind. These fungi are phylogenetically divergent, with the dermatophytes within the Ascomycota and Malassezia within Basidiomycota. Genome analysis indicates that the adaptations to the skin environment are different in these two groups of fungi. Malassezia are dependent on host lipids and secrete lipases and phospholipases that likely release host fatty acids. The dermatophytes encode multiple enzymes with potential roles in modulating host interactions: polyketide synthases, nonribosomal peptide synthetases, LysM, proteases, kinases, and pseudokinases. These two fungal groups have maximized their interactions with the host using two very different mechanisms. PMID:25085959

Zika virus alters the microRNA expression profile and elicits an RNAi response in Aedes aegypti mosquitoes

PubMed Central

Hart, Charles E.; Widen, Steven G.; Wood, Thomas G.; Thangamani, Saravanan; Asgari, Sassan

2017-01-01

Zika virus (ZIKV), a flavivirus transmitted primarily by Aedes aegypti, has recently spread globally in an unprecedented fashion, yet we have a poor understanding of host-microbe interactions in this system. To gain insights into the interplay between ZIKV and the mosquito, we sequenced the small RNA profiles in ZIKV-infected and non-infected Ae. aegypti mosquitoes at 2, 7 and 14 days post-infection. ZIKA induced an RNAi response in the mosquito with virus-derived short interfering RNAs and PIWI-interacting RNAs dramatically increased in abundance post-infection. Further, we found 17 host microRNAs (miRNAs) that were modulated by ZIKV infection at all time points. Strikingly, many of these regulated miRNAs have been reported to have their expression altered by dengue and West Nile viruses, while the response was divergent from that induced by the alphavirus Chikungunya virus in mosquitoes. This suggests that conserved miRNA responses occur within mosquitoes in response to flavivirus infection. This study expands our understanding of ZIKV-vector interactions and provides potential avenues to be further investigated to target ZIKV in the mosquito host. PMID:28715413

Food-mediated modulation of immunity in a phytophagous insect: An effect of nutrition rather than parasitic contamination.

PubMed

Vogelweith, Fanny; Moreau, Jérôme; Thiéry, Denis; Moret, Yannick

2015-06-01

Inherent to the cost of immunity, the immune system itself can exhibit tradeoffs between its arms. Phytophagous insects face a wide range of microbial and eukaryotic parasites, each activating different immune pathways that could compromise the activity of the others. Feeding larvae are primarily exposed to microbes, which growth is controlled by antibiotic secondary metabolites produced by the host plant. The resulting variation in abundance of microbes on plants is expected to differentially stimulate the insect antimicrobial immune defenses. Under the above tradeoff hypothesis, stimulation of the insect antimicrobial defenses is expected to compromise immune activity against eukaryote parasites. In the European grape berry moth, Eupoecilia ambiguella, immune effectors directed towards microbes are negatively correlated to those directed towards eukaryotic parasites among host plants. Here, we hypothesize this relationship is caused by a variable control of the microbial community among host plants by their antibiotic metabolites. To test this hypothesis, we first quantified antimicrobial activity in berries of several grape varieties. We then measured immune defenses of E. ambiguella larvae raised on artificial diets in which we mimicked levels of antimicrobial activity of grape berries using tetracycline to control the abundance of growing microbes. Another group of larvae was raised on artificial diets made of berry extracts only to control for the effect of nutrition. We found that controlling microbe abundance with tetracycline in diets did not explain variation in the immune function whereas the presence of berry extracts did. This suggests that variation in immune defenses of E. ambiguella among grape varieties is caused by nutritional difference among host plants rather than microbe abundance. Further study of the effects of berry compounds on larval immune parameters will be needed to explain the observed tradeoff among immune system components. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbiota-induced changes in drosophila melanogaster host gene expression and gut morphology.

PubMed

Broderick, Nichole A; Buchon, Nicolas; Lemaitre, Bruno

2014-05-27

To elucidate mechanisms underlying the complex relationships between a host and its microbiota, we used the genetically tractable model Drosophila melanogaster. Consistent with previous studies, the microbiota was simple in composition and diversity. However, analysis of single flies revealed high interfly variability that correlated with differences in feeding. To understand the effects of this simple and variable consortium, we compared the transcriptome of guts from conventionally reared flies to that for their axenically reared counterparts. Our analysis of two wild-type fly lines identified 121 up- and 31 downregulated genes. The majority of these genes were associated with immune responses, tissue homeostasis, gut physiology, and metabolism. By comparing the transcriptomes of young and old flies, we identified temporally responsive genes and showed that the overall impact of microbiota was greater in older flies. In addition, comparison of wild-type gene expression with that of an immune-deficient line revealed that 53% of upregulated genes exerted their effects through the immune deficiency (Imd) pathway. The genes included not only classic immune response genes but also those involved in signaling, gene expression, and metabolism, unveiling new and unexpected connections between immunity and other systems. Given these findings, we further characterized the effects of gut-associated microbes on gut morphology and epithelial architecture. The results showed that the microbiota affected gut morphology through their impacts on epithelial renewal rate, cellular spacing, and the composition of different cell types in the epithelium. Thus, while bacteria in the gut are highly variable, the influence of the microbiota at large has far-reaching effects on host physiology. The guts of animals are in constant association with microbes, and these interactions are understood to have important roles in animal development and physiology. Yet we know little about the mechanisms underlying the establishment and function of these associations. Here, we used the fruit fly to understand how the microbiota affects host function. Importantly, we found that the microbiota has far-reaching effects on host physiology, ranging from immunity to gut structure. Our results validate the notion that important insights on complex host-microbe relationships can be obtained from the use of a well-established and genetically tractable invertebrate model. Copyright © 2014 Broderick et al.

Perception of pathogenic or beneficial bacteria and their evasion of host immunity: pattern recognition receptors in the frontline

PubMed Central

Trdá, Lucie; Boutrot, Freddy; Claverie, Justine; Brulé, Daphnée; Dorey, Stephan; Poinssot, Benoit

2015-01-01

Plants are continuously monitoring the presence of microorganisms to establish an adapted response. Plants commonly use pattern recognition receptors (PRRs) to perceive microbe- or pathogen-associated molecular patterns (MAMPs/PAMPs) which are microorganism molecular signatures. Located at the plant plasma membrane, the PRRs are generally receptor-like kinases (RLKs) or receptor-like proteins (RLPs). MAMP detection will lead to the establishment of a plant defense program called MAMP-triggered immunity (MTI). In this review, we overview the RLKs and RLPs that assure early recognition and control of pathogenic or beneficial bacteria. We also highlight the crucial function of PRRs during plant-microbe interactions, with a special emphasis on the receptors of the bacterial flagellin and peptidoglycan. In addition, we discuss the multiple strategies used by bacteria to evade PRR-mediated recognition. PMID:25904927

Listeria monocytogenes Induces a Virulence-Dependent microRNA Signature That Regulates the Immune Response in Galleria mellonella

PubMed Central

Mannala, Gopala K.; Izar, Benjamin; Rupp, Oliver; Schultze, Tilman; Goesmann, Alexander; Chakraborty, Trinad; Hain, Torsten

2017-01-01

microRNAs (miRNAs) coordinate several physiological and pathological processes by regulating the fate of mRNAs. Studies conducted in vitro indicate a role of microRNAs in the control of host-microbe interactions. However, there is limited understanding of miRNA functions in in vivo models of bacterial infections. In this study, we systematically explored changes in miRNA expression levels of Galleria mellonella larvae (greater-wax moth), a model system that recapitulates the vertebrate innate immunity, following infection with L. monocytogenes. Using an insect-specific miRNA microarray with more than 2000 probes, we found differential expression of 90 miRNAs (39 upregulated and 51 downregulated) in response to infection with L. monocytogenes. We validated the expression of a subset of miRNAs which have mammalian homologs of known or predicted function. In contrast, non-pathogenic L. innocua failed to induce these miRNAs, indicating a virulence-dependent miRNA deregulation. To predict miRNA targets using established algorithms, we generated a publically available G. mellonella transcriptome database. We identified miRNA targets involved in innate immunity, signal transduction and autophagy, including spätzle, MAP kinase, and optineurin, respectively, which exhibited a virulence-specific differential expression. Finally, in silico estimation of minimum free energy of miRNA-mRNA duplexes of validated microRNAs and target transcripts revealed a regulatory network of the host immune response to L. monocytogenes. In conclusion, this study provides evidence for a role of miRNAs in the regulation of the innate immune response following bacterial infection in a simple, rapid and scalable in vivo model that may predict host-microbe interactions in higher vertebrates. PMID:29312175

The influence of the microbiota on the immune response to transplantation

PubMed Central

Bartman, Caroline; Chong, Anita S.; Alegre, Maria-Luisa

2015-01-01

Purpose of review In the past decade, appreciation of the important effects of commensal microbes on immunity has grown exponentially. The effect of the microbiota on transplantation has only recently begun to be explored; however, our understanding of the mechanistic details of host-microbe interactions is still lacking. Recent findings It has become clear that transplantation is associated with changes in the microbiota in many different settings although what clinical events and therapeutic interventions contribute to these changes remains to be parsed out. Research groups have begun to identify associations between specific communities of organisms and transplant outcomes but it remains to be established whether microbial changes precede or follow transplant rejection episodes. Finally, results from continuing exploration of basic mechanisms by which microbial communities affect innate and adaptive immunity in various animal models of disease continues to inform research on the microbiota’s effects on immune responses against transplanted organs. Summary Commensal microbes may alter immune responses to organ transplantation, but direct experiments are only beginning in the field to identify species and immune pathways responsible for these putative effects. PMID:25563985

On Growth and Form of the Zebrafish Gut Microbiome

NASA Astrophysics Data System (ADS)

Jemielita, Matthew; Taormina, Michael; Rolig, Annah; Burns, Adam; Hampton, Jennifer; Guillemin, Karen; Parthasarathy, Raghuveer

2014-03-01

The vertebrate gut is home to a diverse microbial community whose composition has a strong influence on the development and health of the host organism. Researchers can identify the members of the microbiota, yet little is known about the spatial and temporal dynamics of these microbial communities, including the mechanisms guiding their nucleation, growth, and interactions. We address these issues using the larval zebrafish (Danio rerio) as a model organism, which are raised microbe-free and then inoculated with controlled compositions of fluorophore-expressing bacteria. Live imaging using light sheet fluorescence microscopy enables visualization of the gut's entire microbial population over the first 24 hours of colonization. Image analysis allows us to quantify microbial populations that range from a few individuals to tens of thousands of microbes, and analyze the structure and growth kinetics of gut bacterial communities. We find that genetically-identical microbes can show surprisingly different growth rates and colonization abilities depending on their order of arrival. This demonstrates that knowing only the constituents of the gut community is insufficient to determine their dynamics; rather, the history of colonization matters.

A perspective on inter-kingdom signaling in plant-beneficial microbe interactions.

PubMed

Rosier, Amanda; Bishnoi, Usha; Lakshmanan, Venkatachalam; Sherrier, D Janine; Bais, Harsh P

2016-04-01

Recent work has shown that the rhizospheric and phyllospheric microbiomes of plants are composed of highly diverse microbial species. Though the information pertaining to the diversity of the aboveground and belowground microbes associated with plants is known, an understanding of the mechanisms by which these diverse microbes function is still in its infancy. Plants are sessile organisms, that depend upon chemical signals to interact with the microbiota. Of late, the studies related to the impact of microbes on plants have gained much traction in the research literature, supporting diverse functional roles of microbes on plant health. However, how these microbes interact as a community to confer beneficial traits to plants is still poorly understood. Recent advances in the use of "biologicals" as bio-fertilizers and biocontrol agents for sustainable agricultural practices is promising, and a fundamental understanding of how microbes in community work on plants could help this approach be more successful. This review attempts to highlight the importance of different signaling events that mediate a beneficial plant microbe interaction. Fundamental research is needed to understand how plants react to different benign microbes and how these microbes are interacting with each other. This review highlights the importance of chemical signaling, and biochemical and genetic events which determine the efficacy of benign microbes to promote the development of beneficial traits in plants.

MAMPs and MIMPs: proposed classifications for inducers of innate immunity.

PubMed

Mackey, David; McFall, Aidan J

2006-09-01

Plants encode a sophisticated innate immune system. Resistance against potential pathogens often relies on active responses. Prerequisite to the induction of defences is recognition of the pathogenic threat. Significant advances have been made in our understanding of the non-self molecules that are recognized by plants and the means by which plants perceive them. Established terms describing these recognition events, including microbe-associated molecular pattern (MAMP), MAMP-receptor, effector, and resistance (R) protein, need clarification to represent our current knowledge adequately. In this review we propose criteria to classify inducers of plant defence as either MAMPs or microbe-induced molecular patterns (MIMPs). We refine the definition of MAMP to mean a molecular sequence or structure in ANY pathogen-derived molecule that is perceived via direct interaction with a host defence receptor. MIMPs are modifications of host-derived molecules that are induced by an intrinsic activity of a pathogen-derived effector and are perceived by a host defence receptor. MAMP-receptors have previously been classified separately from R-proteins as a discrete class of surveillance molecules. However, MAMP-receptors and R-proteins cannot be distinguished on the basis of their protein structures or their induced responses. We propose that MAMP-receptors and MIMP-receptors are each a subset of R-proteins. Although our review is based on examples from plant pathogens and plants, the principles discussed might prove applicable to other organisms.

Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults.

PubMed

Tap, Julien; Furet, Jean-Pierre; Bensaada, Martine; Philippe, Catherine; Roth, Hubert; Rabot, Sylvie; Lakhdari, Omar; Lombard, Vincent; Henrissat, Bernard; Corthier, Gérard; Fontaine, Eric; Doré, Joël; Leclerc, Marion

2015-12-01

Gut microbiota richness and stability are important parameters in host-microbe symbiosis. Diet modification, notably using dietary fibres, might be a way to restore a high richness and stability in the gut microbiota. In this work, during a 6-week nutritional trial, 19 healthy adults consumed a basal diet supplemented with 10 or 40 g dietary fibre per day for 5 days, followed by 15-day washout periods. Fecal samples were analysed by a combination of 16S rRNA gene pyrosequencing, intestinal cell genotoxicity assay, metatranscriptomics sequencing approach and short-chain fatty analysis. This short-term change in the dietary fibre level did not have the same impact for all individuals but remained significant within each individual gut microbiota at genus level. Higher microbiota richness was associated with higher microbiota stability upon increased dietary fibre intake. Increasing fibre modulated the expression of numerous microbiota metabolic pathways such as glycan metabolism, with genes encoding carbohydrate-active enzymes active on fibre or host glycans. High microbial richness was also associated with high proportions of Prevotella and Coprococcus species and high levels of caproate and valerate. This study provides new insights on the role of gut microbial richness in healthy adults upon dietary changes and host microbes' interaction. © 2015 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Reciprocal Interactions between Nematodes and Their Microbial Environments

PubMed Central

Midha, Ankur; Schlosser, Josephine; Hartmann, Susanne

2017-01-01

Parasitic nematode infections are widespread in nature, affecting humans as well as wild, companion, and livestock animals. Most parasitic nematodes inhabit the intestines of their hosts living in close contact with the intestinal microbiota. Many species also have tissue migratory life stages in the absence of severe systemic inflammation of the host. Despite the close coexistence of helminths with numerous microbes, little is known concerning these interactions. While the environmental niche is considerably different, the free-living nematode Caenorhabditis elegans (C. elegans) is also found amongst a diverse microbiota, albeit on decaying organic matter. As a very well characterized model organism that has been intensively studied for several decades, C. elegans interactions with bacteria are much more deeply understood than those of their parasitic counterparts. The enormous breadth of understanding achieved by the C. elegans research community continues to inform many aspects of nematode parasitology. Here, we summarize what is known regarding parasitic nematode-bacterial interactions while comparing and contrasting this with information from work in C. elegans. This review highlights findings concerning responses to bacterial stimuli, antimicrobial peptides, and the reciprocal influences between nematodes and their environmental bacteria. Furthermore, the microbiota of nematodes as well as alterations in the intestinal microbiota of mammalian hosts by helminth infections are discussed. PMID:28497029

Reciprocal Interactions between Nematodes and Their Microbial Environments.

PubMed

Midha, Ankur; Schlosser, Josephine; Hartmann, Susanne

2017-01-01

Parasitic nematode infections are widespread in nature, affecting humans as well as wild, companion, and livestock animals. Most parasitic nematodes inhabit the intestines of their hosts living in close contact with the intestinal microbiota. Many species also have tissue migratory life stages in the absence of severe systemic inflammation of the host. Despite the close coexistence of helminths with numerous microbes, little is known concerning these interactions. While the environmental niche is considerably different, the free-living nematode Caenorhabditis elegans ( C. elegans ) is also found amongst a diverse microbiota, albeit on decaying organic matter. As a very well characterized model organism that has been intensively studied for several decades, C. elegans interactions with bacteria are much more deeply understood than those of their parasitic counterparts. The enormous breadth of understanding achieved by the C. elegans research community continues to inform many aspects of nematode parasitology. Here, we summarize what is known regarding parasitic nematode-bacterial interactions while comparing and contrasting this with information from work in C. elegans . This review highlights findings concerning responses to bacterial stimuli, antimicrobial peptides, and the reciprocal influences between nematodes and their environmental bacteria. Furthermore, the microbiota of nematodes as well as alterations in the intestinal microbiota of mammalian hosts by helminth infections are discussed.

Imaging of bacterial multicellular behaviour in biofilms in liquid by atmospheric scanning electron microscopy

PubMed Central

Sugimoto, Shinya; Okuda, Ken-ichi; Miyakawa, Reina; Sato, Mari; Arita-Morioka, Ken-ichi; Chiba, Akio; Yamanaka, Kunitoshi; Ogura, Teru; Mizunoe, Yoshimitsu; Sato, Chikara

2016-01-01

Biofilms are complex communities of microbes that attach to biotic or abiotic surfaces causing chronic infectious diseases. Within a biofilm, microbes are embedded in a self-produced soft extracellular matrix (ECM), which protects them from the host immune system and antibiotics. The nanoscale visualisation of delicate biofilms in liquid is challenging. Here, we develop atmospheric scanning electron microscopy (ASEM) to visualise Gram-positive and -negative bacterial biofilms immersed in aqueous solution. Biofilms cultured on electron-transparent film were directly imaged from below using the inverted SEM, allowing the formation of the region near the substrate to be studied at high resolution. We visualised intercellular nanostructures and the exocytosis of membrane vesicles, and linked the latter to the trafficking of cargos, including cytoplasmic proteins and the toxins hemolysin and coagulase. A thick dendritic nanotube network was observed between microbes, suggesting multicellular communication in biofilms. A universal immuno-labelling system was developed for biofilms and tested on various examples, including S. aureus biofilms. In the ECM, fine DNA and protein networks were visualised and the precise distribution of protein complexes was determined (e.g., straight curli, flagella, and excreted cytoplasmic molecular chaperones). Our observations provide structural insights into bacteria-substratum interactions, biofilm development and the internal microbe community. PMID:27180609

The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders.

PubMed

Karlsen, C; Ottem, K F; Brevik, Øyvind Jakobsen; Davey, M; Sørum, H; Winther-Larsen, H C

2017-11-01

The Norwegian aquaculture of Atlantic salmon (Salmo salar L.) is hampered by ulcerative disorders associated with bacterial infections. Chronic ulceration may provide microenvironments that disturb the normal microbial biodiversity of external surfaces. Studying the composition of microbial communities in skin ulcers will enhance our understanding of ulcer aetiology. To achieve this, we tested marine farmed Atlantic salmon and sampled the base and edge of ulcers at the end of winter (April) and end of summer (September), in addition to skin mucus of healthy individuals. In order to assess microbiota associated with the host and obtain insight into the environmental ecology, we also sampled sea water, the sediment layer underneath the farm facility and the distal intestine of Atlantic salmon. The skin microbiota of Atlantic salmon was different from that of the surrounding water. Residential Tenacibaculum and Arcobacter species persistently dominated the cutaneous skin and ulcer mucus surfaces of Atlantic salmon during both winter and summer periods. The intestinal microbiota was dominated by Mycoplasma with an increase in Aliivibrio and Alcaligenes abundance in the intestine of fish with ulcerative disorder at the end of winter. These findings suggest the presence of resilient microbes in the mucus surfaces of Atlantic salmon. © 2017 John Wiley & Sons Ltd.

The Dynamic Interactions between Salmonella and the Microbiota, within the Challenging Niche of the Gastrointestinal Tract

PubMed Central

Khan, C. M. Anjam

2014-01-01

Understanding how Salmonella species establish successful infections remains a foremost research priority. This gastrointestinal pathogen not only faces the hostile defenses of the host's immune system, but also faces fierce competition from the large and diverse community of microbiota for space and nutrients. Salmonella have solved these challenges ingeniously. To jump-start growth, Salmonella steal hydrogen produced by the gastrointestinal microbiota. Type 3 effector proteins are subsequently secreted by Salmonella to trigger potent inflammatory responses, which generate the alternative terminal electron acceptors tetrathionate and nitrate. Salmonella exclusively utilize these electron acceptors for anaerobic respiration, permitting metabolic access to abundant substrates such as ethanolamine to power growth blooms. Chemotaxis and flagella-mediated motility enable the identification of nutritionally beneficial niches. The resulting growth blooms also promote horizontal gene transfer amongst the resident microbes. Within the gastrointestinal tract there are opportunities for chemical signaling between host cells, the microbiota, and Salmonella. Host produced catecholamines and bacterial autoinducers form components of this chemical dialogue leading to dynamic interactions. Thus, Salmonella have developed remarkable strategies to initially shield against host defenses and to transiently compete against the intestinal microbiota leading to successful infections. However, the immunocompetent host is subsequently able to reestablish control and clear the infection. PMID:27437481

The Dynamic Interactions between Salmonella and the Microbiota, within the Challenging Niche of the Gastrointestinal Tract.

PubMed

Khan, C M Anjam

2014-01-01

Understanding how Salmonella species establish successful infections remains a foremost research priority. This gastrointestinal pathogen not only faces the hostile defenses of the host's immune system, but also faces fierce competition from the large and diverse community of microbiota for space and nutrients. Salmonella have solved these challenges ingeniously. To jump-start growth, Salmonella steal hydrogen produced by the gastrointestinal microbiota. Type 3 effector proteins are subsequently secreted by Salmonella to trigger potent inflammatory responses, which generate the alternative terminal electron acceptors tetrathionate and nitrate. Salmonella exclusively utilize these electron acceptors for anaerobic respiration, permitting metabolic access to abundant substrates such as ethanolamine to power growth blooms. Chemotaxis and flagella-mediated motility enable the identification of nutritionally beneficial niches. The resulting growth blooms also promote horizontal gene transfer amongst the resident microbes. Within the gastrointestinal tract there are opportunities for chemical signaling between host cells, the microbiota, and Salmonella. Host produced catecholamines and bacterial autoinducers form components of this chemical dialogue leading to dynamic interactions. Thus, Salmonella have developed remarkable strategies to initially shield against host defenses and to transiently compete against the intestinal microbiota leading to successful infections. However, the immunocompetent host is subsequently able to reestablish control and clear the infection.

Adaptive immune education by gut microbiota antigens.

PubMed

Zhao, Qing; Elson, Charles O

2018-05-01

Host-microbiota mutualism has been established during long-term co-evolution. A diverse and rich gut microbiota plays an essential role in the development and maturation of the host immune system. Education of the adaptive immune compartment by gut microbiota antigens is important in establishing immune balance. In particular, a critical time frame immediately after birth provides a 'window of opportunity' for the development of lymphoid structures, differentiation and maturation of T and B cells and, most importantly, establishment of immune tolerance to gut commensals. Depending on the colonization niche, antigen type and metabolic property of different gut microbes, CD4 T-cell responses vary greatly, which results in differentiation into distinct subsets. As a consequence, certain bacteria elicit effector-like immune responses by promoting the production of pro-inflammatory cytokines such as interferon-γ and interleukin-17A, whereas other bacteria favour the generation of regulatory CD4 T cells and provide help with gut homeostasis. The microbiota have profound effects on B cells also. Gut microbial exposure leads to a continuous diversification of B-cell repertoire and the production of T-dependent and -independent antibodies, especially IgA. These combined effects of the gut microbes provide an elegant educational process to the adaptive immune network. Contrariwise, failure of this process results in a reduced homeostasis with the gut microbiota, and an increased susceptibility to various immune disorders, both inside and outside the gut. With more definitive microbial-immune relations waiting to be discovered, modulation of the host gut microbiota has a promising future for disease intervention. © 2018 John Wiley & Sons Ltd.

Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats.

PubMed

Schuelke, Taruna; Pereira, Tiago José; Hardy, Sarah M; Bik, Holly M

2018-04-01

Studies of host-associated microbes are critical for advancing our understanding of ecology and evolution across diverse taxa and ecosystems. Nematode worms are ubiquitous across most habitats on earth, yet little is known about host-associated microbial assemblages within the phylum. Free-living nematodes are globally abundant and diverse in marine sediments, with species exhibiting distinct buccal cavity (mouth) morphologies that are thought to play an important role in feeding ecology and life history strategies. Here, we investigated patterns in marine nematode microbiomes, by characterizing host-associated microbial taxa in 281 worms isolated from a range of habitat types (deep-sea, shallow water, methane seeps, Lophelia coral mounds, kelp holdfasts) across three distinct geographic regions (Arctic, Southern California and Gulf of Mexico). Microbiome profiles were generated from single worms spanning 33 distinct morphological genera, using a two-gene metabarcoding approach to amplify the V4 region of the 16S ribosomal RNA (rRNA) gene targeting bacteria/archaea and the V1-V2 region of the 18S rRNA gene targeting microbial eukaryotes. Contrary to our expectations, nematode microbiome profiles demonstrated no distinct patterns either globally (across depths and ocean basins) or locally (within site); prokaryotic and eukaryotic microbial assemblages did not correlate with nematode feeding morphology, host phylogeny or morphological identity, ocean region or marine habitat type. However, fine-scale analysis of nematode microbiomes revealed a variety of novel ecological interactions, including putative parasites and symbionts, and potential associations with bacterial/archaeal taxa involved in nitrogen and methane cycling. Our results suggest that in marine habitats, free-living nematodes may utilize diverse and generalist foraging strategies that are not correlated with host genotype or feeding morphology. Furthermore, some abiotic factors such as geographic region and habitat type do not appear to play an obvious role in structuring host-microbe associations or feeding preferences. © 2018 John Wiley & Sons Ltd.

Early-Life Host–Microbiome Interphase: The Key Frontier for Immune Development

PubMed Central

Amenyogbe, Nelly; Kollmann, Tobias R.; Ben-Othman, Rym

2017-01-01

Human existence can be viewed as an “animal in a microbial world.” A healthy interaction of the human host with the microbes in and around us heavily relies on a well-functioning immune system. As development of both the microbiota and the host immune system undergo rapid changes in early life, it is not surprising that even minor alterations during this co-development can have profound consequences. Scrutiny of existing data regarding pre-, peri-, as well as early postnatal modulators of newborn microbiota indeed suggest strong associations with several immune-mediated diseases with onset far beyond the newborn period. We here summarize these data and extract overarching themes. This same effort in turn sets the stage to guide effective countermeasures, such as probiotic administration. The objective of our review is to highlight the interaction of host immune ontogeny with the developing microbiome in early life as a critical window of susceptibility for lifelong disease, as well as to identify the enormous potential to protect and promote lifelong health by specifically targeting this window of opportunity. PMID:28596951

Immunomagnetic isolation of pathogen-containing phagosomes and apoptotic blebs from primary phagocytes.

PubMed

Steinhäuser, Christine; Dallenga, Tobias; Tchikov, Vladimir; Schaible, Ulrich E; Schütze, Stefan; Reiling, Norbert

2014-04-02

Macrophages and polymorphonuclear neutrophils are professional phagocytes essential in the initial host response against intracellular pathogens such as Mycobacterium tuberculosis. Phagocytosis is the first step in phagocyte-pathogen interaction, where the pathogen is engulfed into a membrane-enclosed compartment termed a phagosome. Subsequent effector functions of phagocytes result in killing and degradation of the pathogen by promoting phagosome maturation, and, terminally, phago-lysosome fusion. Intracellular pathogenic microbes use various strategies to avoid detection and elimination by phagocytes, including induction of apoptosis to escape host cells, thereby generating apoptotic blebs as shuttles to other cells for pathogens and antigens thereof. Hence, phagosomes represent compartments where host and pathogen become quite intimate, and apoptotic blebs are carrier bags of the pathogen's legacy. In order to investigate the molecular mechanisms underlying these interactions, both phagosomes and apoptotic blebs are required as purified subcellular fractions for subsequent analysis of their biochemical properties. Here, we describe a lipid-based procedure to magnetically label surfaces of either pathogenic mycobacteria or apoptotic blebs for purification by a strong magnetic field in a novel free-flow system. Copyright © 2014 John Wiley & Sons, Inc.

Uncovering the drivers of host-associated microbiota with joint species distribution modelling.

PubMed

Björk, Johannes R; Hui, Francis K C; O'Hara, Robert B; Montoya, Jose M

2018-06-01

In addition to the processes structuring free-living communities, host-associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host-specific factors, often spanning multiple levels of biological organization. Current statistical methods do not accommodate this hierarchical data structure and therefore cannot explicitly account for the effect of the host in structuring the microbiota. We introduce a novel extension of joint species distribution models (JSDMs) which can straightforwardly accommodate and discern between effects such as host phylogeny and traits, recorded covariates such as diet and collection site, among other ecological processes. Our proposed methodology includes powerful yet familiar outputs seen in community ecology overall, including (a) model-based ordination to visualize and quantify the main patterns in the data; (b) variance partitioning to assess how influential the included host-specific factors are in structuring the microbiota; and (c) co-occurrence networks to visualize microbe-to-microbe associations. © 2018 John Wiley & Sons Ltd.

Microbial small molecules - weapons of plant subversion.

PubMed

Stringlis, Ioannis A; Zhang, Hao; Pieterse, Corné M J; Bolton, Melvin D; de Jonge, Ronnie

2018-05-25

Covering: up to 2018 Plants live in close association with a myriad of microbes that are generally harmless. However, the minority of microbes that are pathogens can severely impact crop quality and yield, thereby endangering food security. By contrast, beneficial microbes provide plants with important services, such as enhanced nutrient uptake and protection against pests and diseases. Like pathogens, beneficial microbes can modulate host immunity to efficiently colonize the nutrient-rich niches within and around the roots and aerial tissues of a plant, a phenomenon mirroring the establishment of commensal microbes in the human gut. Numerous ingenious mechanisms have been described by which pathogenic and beneficial microbes in the plant microbiome communicate with their host, including the delivery of immune-suppressive effector proteins and the production of phytohormones, toxins and other bioactive molecules. Plants signal to their associated microbes via exudation of photosynthetically fixed carbon sources, quorum-sensing mimicry molecules and selective secondary metabolites such as strigolactones and flavonoids. Molecular communication thus forms an integral part of the establishment of both beneficial and pathogenic plant-microbe relations. Here, we review the current knowledge on microbe-derived small molecules that can act as signalling compounds to stimulate plant growth and health by beneficial microbes on the one hand, but also as weapons for plant invasion by pathogens on the other. As an exemplary case, we used comparative genomics to assess the small molecule biosynthetic capabilities of the Pseudomonas genus; a genus rich in both plant pathogenic and beneficial microbes. We highlight the biosynthetic potential of individual microbial genomes and the population at large, providing evidence for the hypothesis that the distinction between detrimental and beneficial microbes is increasingly fading. Knowledge on the biosynthesis and molecular activity of microbial small molecules will aid in the development of successful biological agents boosting crop resiliency in a sustainable manner and could also provide scientific routes to pathogen inhibition or eradication.

Fungi on the skin: dermatophytes and Malassezia.

PubMed

White, Theodore C; Findley, Keisha; Dawson, Thomas L; Scheynius, Annika; Boekhout, Teun; Cuomo, Christina A; Xu, Jun; Saunders, Charles W

2014-08-01

Several human skin diseases and disorders are associated with two groups of fungi, the dermatophytes and Malassezia. Although these skin-related problems are not generally life threatening, they are among the most common diseases and disorders of mankind. These fungi are phylogenetically divergent, with the dermatophytes within the Ascomycota and Malassezia within Basidiomycota. Genome analysis indicates that the adaptations to the skin environment are different in these two groups of fungi. Malassezia are dependent on host lipids and secrete lipases and phospholipases that likely release host fatty acids. The dermatophytes encode multiple enzymes with potential roles in modulating host interactions: polyketide synthases, nonribosomal peptide synthetases, LysM, proteases, kinases, and pseudokinases. These two fungal groups have maximized their interactions with the host using two very different mechanisms. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Role of the Microbiota in Immunity and inflammation

PubMed Central

Belkaid, Yasmine; Hand, Timothy

2014-01-01

The microbiota plays a fundamental role on the induction, training and function of the host immune system. In return, the immune system has largely evolved as a means to maintain the symbiotic relationship of the host with these highly diverse and evolving microbes. When operating optimally this immune system–microbiota alliance allows the induction of protective responses to pathogens and the maintenance of regulatory pathways involved in the maintenance of tolerance to innocuous antigens. However, in high-income countries overuse of antibiotics, changes in diet, and elimination of constitutive partners such as nematodes has selected for a microbiota that lack the resilience and diversity required to establish balanced immune responses. This phenomenon is proposed to account for some of the dramatic rise in autoimmune and inflammatory disorders in parts of the world where our symbiotic relationship with the microbiota has been the most affected. PMID:24679531

Is Drosophila-microbe association species-specific or region specific? A study undertaken involving six Indian Drosophila species.

PubMed

Singhal, Kopal; Khanna, Radhika; Mohanty, Sujata

2017-06-01

The present work aims to identify the microbial diversity associated with six Indian Drosophila species using next generation sequencing (NGS) technology and to discover the nature of their distribution across species and eco-geographic regions. Whole fly gDNA of six Drosophila species were used to generate sequences in an Illumina platform using NGS technology. De novo based assembled raw reads were blasted against the NR database of NCBI using BLASTn for identification of their bacterial loads. We have tried to include Drosophila species from different taxonomical groups and subgroups and from three different eco-climatic regions India; four species belong to Central India, while the rest two, D. melanogaster and D. ananassae, belong to West and South India to determine both their species-wise and region-wide distribution. We detected the presence of 33 bacterial genera across all six study species, predominated by the class Proteobacteria. Amongst all, D. melanogaster was found to be the most diverse by carrying around 85% of the bacterial diversity. Our findings infer both species-specific and environment-specific nature of the bacterial species inhabiting the Drosophila host. Though the present results are consistent with most of the earlier studies, they also remain incoherent with some. The present study outcome on the host-bacteria association and their species specific adaptation may provide some insight to understand the host-microbial interactions and the phenotypic implications of microbes on the host physiology. The knowledge gained may be importantly applied into the recent insect and pest population control strategy going to implement through gut microflora in India and abroad.

Gaian bottlenecks and planetary habitability maintained by evolving model biospheres: the ExoGaia model

NASA Astrophysics Data System (ADS)

Nicholson, Arwen E.; Wilkinson, David M.; Williams, Hywel T. P.; Lenton, Timothy M.

2018-06-01

The search for habitable exoplanets inspires the question - how do habitable planets form? Planet habitability models traditionally focus on abiotic processes and neglect a biotic response to changing conditions on an inhabited planet. The Gaia hypothesis postulates that life influences the Earth's feedback mechanisms to form a self-regulating system, and hence that life can maintain habitable conditions on its host planet. If life has a strong influence, it will have a role in determining a planet's habitability over time. We present the ExoGaia model - a model of simple `planets' host to evolving microbial biospheres. Microbes interact with their host planet via consumption and excretion of atmospheric chemicals. Model planets orbit a `star' that provides incoming radiation, and atmospheric chemicals have either an albedo or a heat-trapping property. Planetary temperatures can therefore be altered by microbes via their metabolisms. We seed multiple model planets with life while their atmospheres are still forming and find that the microbial biospheres are, under suitable conditions, generally able to prevent the host planets from reaching inhospitable temperatures, as would happen on a lifeless planet. We find that the underlying geochemistry plays a strong role in determining long-term habitability prospects of a planet. We find five distinct classes of model planets, including clear examples of `Gaian bottlenecks' - a phenomenon whereby life either rapidly goes extinct leaving an inhospitable planet or survives indefinitely maintaining planetary habitability. These results suggest that life might play a crucial role in determining the long-term habitability of planets.

Amoeba host-Legionella synchronization of amino acid auxotrophy and its role in bacterial adaptation and pathogenic evolution

PubMed Central

Price, Christopher T. D.; Richards, Ashley M.; Von Dwingelo, Juanita E.; Samara, Hala A.; Kwaik, Yousef Abu

2013-01-01

Summary Legionella pneumophila, the causative agent of Legionnaires’ disease, invades and proliferates within a diverse range of free-living amoeba in the environment but upon transmission to humans the bacteria hijack alveolar macrophages. Intracellular proliferation of L. pneumophila in two evolutionarily distant hosts is facilitated by bacterial exploitation of conserved host processes that are targeted by bacterial protein effectors injected into the host cell. A key aspect of microbe-host interaction is microbial extraction of nutrients from the host but understanding of this is still limited. AnkB functions as a nutritional virulence factor and promotes host proteasomal degradation of polyubiquitinated proteins generating gratuitous levels of limiting host cellular amino acids. L. pneumophila is auxotrophic for several amino acids including cysteine, which is a metabolically preferred source of carbon and energy during intracellular proliferation, but is limiting in both amoebae and humans. We propose that synchronization of bacterial amino acids auxotrophy with the host is a driving force in pathogenic evolution and nutritional adaptation of L. pneumophila and other intracellular bacteria to life within the host cell. Understanding microbial strategies of nutrient generation and acquisition in the host will provide novel antimicrobial strategies to disrupt pathogen access to essential sources of carbon and energy. PMID:24112119

Cuticular bacteria appear detrimental to social spiders in mixed but not monoculture exposure

PubMed Central

Keiser, Carl N.; Shearer, Taylor A.; DeMarco, Alexander E.; Brittingham, Hayley A.; Knutson, Karen A.; Kuo, Candice; Zhao, Katherine; Pruitt, Jonathan N.

2016-01-01

Abstract Much of an animal’s health status, life history, and behavior are dictated by interactions with its endogenous and exogenous bacterial communities. Unfortunately, interactions between hosts and members of their resident bacterial community are often ignored in animal behavior and behavioral ecology. Here, we aim to identify the nature of host–microbe interactions in a nonmodel organism, the African social spider Stegodyphus dumicola. We collected and identified bacteria from the cuticles of spiders in situ and then exposed spiders to bacterial monocultures cultures via topical application or injection. We also topically inoculated spiders with a concomitant “cocktail” of bacteria and measured the behavior of spiders daily for 24 days after inoculation. Lastly, we collected and identified bacteria from the cuticles of prey items in the capture webs of spiders, and then fed spiders domestic crickets which had been injected with these bacteria. We also injected 1 species of prey-borne bacteria into the hemolymph of spiders. Only Bacillus thuringiensis caused increased mortality when injected into the hemolymph of spiders, whereas no bacterial monocultures caused increased mortality when applied topically, relative to control solutions. However, a bacterial cocktail of cuticular bacteria caused weight loss and mortality when applied topically, yet did not detectibly alter spider behavior. Consuming prey injected with prey-borne bacteria was associated with an elongated lifespan in spiders. Thus, indirect evidence from multiple experiments suggests that the effects of these bacteria on spider survivorship appear contingent on their mode of colonization and whether they are applied in monoculture or within a mixed cocktail. We urge that follow-up studies should test these host–microbe interactions across different social contexts to determine the role that microbes play in colony performance. PMID:29491926

Recombinant Incretin-Secreting Microbe Improves Metabolic Dysfunction in High-Fat Diet Fed Rodents.

PubMed

Ryan, Paul M; Patterson, Elaine; Kent, Robert M; Stack, Helena; O'Connor, Paula M; Murphy, Kiera; Peterson, Veronica L; Mandal, Rupasri; Wishart, David S; Dinan, Timothy G; Cryan, John F; Seeley, Randy J; Stanton, Catherine; Ross, R Paul

2017-10-19

The gut hormone glucagon-like peptide (GLP)-1 and its analogues represent a new generation of anti-diabetic drugs, which have also demonstrated propensity to modulate host lipid metabolism. Despite this, drugs of this nature are currently limited to intramuscular administration routes due to intestinal degradation. The aim of this study was to design a recombinant microbial delivery vector for a GLP-1 analogue and assess the efficacy of the therapeutic in improving host glucose, lipid and cholesterol metabolism in diet induced obese rodents. Diet-induced obese animals received either Lactobacillus paracasei NFBC 338 transformed to express a long-acting analogue of GLP-1 or the isogenic control microbe which solely harbored the pNZ44 plasmid. Short-term GLP-1 microbe intervention in rats reduced serum low-density lipoprotein cholesterol, triglycerides and triglyceride-rich lipoprotein cholesterol substantially. Conversely, extended GLP-1 microbe intervention improved glucose-dependent insulin secretion, glucose metabolism and cholesterol metabolism, compared to the high-fat control group. Interestingly, the microbe significantly attenuated the adiposity associated with the model and altered the serum lipidome, independently of GLP-1 secretion. These data indicate that recombinant incretin-secreting microbes may offer a novel and safe means of managing cholesterol metabolism and diet induced dyslipidaemia, as well as insulin sensitivity in metabolic dysfunction.

Dipteran larvae and microbes facilitate nutrient sequestration in the Nepenthes gracilis pitcher plant host.

PubMed

Lam, Weng Ngai; Chong, Kwek Yan; Anand, Ganesh S; Tan, Hugh Tiang Wah

2017-03-01

The fluid-containing traps of Nepenthes carnivorous pitcher plants (Nepenthaceae) are often inhabited by organisms known as inquilines. Dipteran larvae are key components of such communities and are thought to facilitate pitcher nitrogen sequestration by converting prey protein into inorganic nitrogen, although this has never been demonstrated in Nepenthes Pitcher fluids are also inhabited by microbes, although the relationship(s) between these and the plant is still unclear. In this study, we examined the hypothesis of digestive mutualism between N. gracilis pitchers and both dipteran larvae and fluid microbes. Using dipteran larvae, prey and fluid volumes mimicking in situ pitcher conditions, we conducted in vitro experiments and measured changes in available fluid nitrogen in response to dipteran larvae and microbe presence. We showed that the presence of dipteran larvae resulted in significantly higher and faster releases of ammonium and soluble protein into fluids in artificial pitchers, and that the presence of fluid microbes did likewise for ammonium. We showed also that niche segregation occurs between phorid and culicid larvae, with the former fragmenting prey carcasses and the latter suppressing fluid microbe levels. These results clarify the relationships between several key pitcher-dwelling organisms, and show that pitcher communities facilitate nutrient sequestration in their host. © 2017 The Author(s).

Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies.

PubMed

Laforest-Lapointe, Isabelle; Arrieta, Marie-Claire

2018-01-01

Human-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health. In this perspective, we discuss new evidence on eukaryotes as fundamental species of the human gut and emphasize that future microbiome studies should characterize the multitrophic interactions between microeukaryotes, other microorganisms, and the host.

Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies

PubMed Central

2018-01-01

ABSTRACT Human-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health. In this perspective, we discuss new evidence on eukaryotes as fundamental species of the human gut and emphasize that future microbiome studies should characterize the multitrophic interactions between microeukaryotes, other microorganisms, and the host. PMID:29556538

Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions.

PubMed

Ceapă, Corina Diana; Vázquez-Hernández, Melissa; Rodríguez-Luna, Stefany Daniela; Cruz Vázquez, Angélica Patricia; Jiménez Suárez, Verónica; Rodríguez-Sanoja, Romina; Alvarez-Buylla, Elena R; Sánchez, Sergio

2018-01-01

Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte Streptomyces scabrisporus NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven Streptomyces and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The S. scabrisporus NF3 genome is larger than the average Streptomyces genome and not structured for an obligate endosymbiotic lifestyle; this and the fact that can grow in R2YE media implies that it could include a soil-living stage. The genome displays an enrichment of genes associated with amino acid production, protein secretion, secondary metabolite and antioxidants production and xenobiotic degradation, indicating that S. scabrisporus NF3 could contribute to the metabolic enrichment of soil microbial communities and of its hosts. Importantly, besides its metabolic advantages, the genome showed evidence for differential functional specificity and diversification of plant interaction molecules, including genes for the production of plant hormones, stress resistance molecules, chitinases, antibiotics and siderophores. Given the diversity of S. scabrisporus mechanisms for host upkeep, we propose that these strategies were necessary for its adaptation to plant hosts and to face changes in environmental conditions.

Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions

PubMed Central

Rodríguez-Luna, Stefany Daniela; Cruz Vázquez, Angélica Patricia; Jiménez Suárez, Verónica; Rodríguez-Sanoja, Romina; Alvarez-Buylla, Elena R.; Sánchez, Sergio

2018-01-01

Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte Streptomyces scabrisporus NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven Streptomyces and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The S. scabrisporus NF3 genome is larger than the average Streptomyces genome and not structured for an obligate endosymbiotic lifestyle; this and the fact that can grow in R2YE media implies that it could include a soil-living stage. The genome displays an enrichment of genes associated with amino acid production, protein secretion, secondary metabolite and antioxidants production and xenobiotic degradation, indicating that S. scabrisporus NF3 could contribute to the metabolic enrichment of soil microbial communities and of its hosts. Importantly, besides its metabolic advantages, the genome showed evidence for differential functional specificity and diversification of plant interaction molecules, including genes for the production of plant hormones, stress resistance molecules, chitinases, antibiotics and siderophores. Given the diversity of S. scabrisporus mechanisms for host upkeep, we propose that these strategies were necessary for its adaptation to plant hosts and to face changes in environmental conditions. PMID:29447216

A symbiosis-dedicated SYNTAXIN OF PLANTS 13II isoform controls the formation of a stable host-microbe interface in symbiosis.

PubMed

Huisman, Rik; Hontelez, Jan; Mysore, Kirankumar S; Wen, Jiangqi; Bisseling, Ton; Limpens, Erik

2016-09-01

Arbuscular mycorrhizal (AM) fungi and rhizobium bacteria are accommodated in specialized membrane compartments that form a host-microbe interface. To better understand how these interfaces are made, we studied the regulation of exocytosis during interface formation. We used a phylogenetic approach to identify target soluble N-ethylmaleimide-sensitive factor-attachment protein receptors (t-SNAREs) that are dedicated to symbiosis and used cell-specific expression analysis together with protein localization to identify t-SNAREs that are present on the host-microbe interface in Medicago truncatula. We investigated the role of these t-SNAREs during the formation of a host-microbe interface. We showed that multiple syntaxins are present on the peri-arbuscular membrane. From these, we identified SYNTAXIN OF PLANTS 13II (SYP13II) as a t-SNARE that is essential for the formation of a stable symbiotic interface in both AM and rhizobium symbiosis. In most dicot plants, the SYP13II transcript is alternatively spliced, resulting in two isoforms, SYP13IIα and SYP13IIβ. These splice-forms differentially mark functional and degrading arbuscule branches. Our results show that vesicle traffic to the symbiotic interface is specialized and required for its maintenance. Alternative splicing of SYP13II allows plants to replace a t-SNARE involved in traffic to the plasma membrane with a t-SNARE that is more stringent in its localization to functional arbuscules. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Interaction of the tick immune system with transmitted pathogens

PubMed Central

Hajdušek, Ondřej; Šíma, Radek; Ayllón, Nieves; Jalovecká, Marie; Perner, Jan; de la Fuente, José; Kopáček, Petr

2013-01-01

Ticks are hematophagous arachnids transmitting a wide variety of pathogens including viruses, bacteria, and protozoans to their vertebrate hosts. The tick vector competence has to be intimately linked to the ability of transmitted pathogens to evade tick defense mechanisms encountered on their route through the tick body comprising midgut, hemolymph, salivary glands or ovaries. Tick innate immunity is, like in other invertebrates, based on an orchestrated action of humoral and cellular immune responses. The direct antimicrobial defense in ticks is accomplished by a variety of small molecules such as defensins, lysozymes or by tick-specific antimicrobial compounds such as microplusin/hebraein or 5.3-kDa family proteins. Phagocytosis of the invading microbes by tick hemocytes is likely mediated by the primordial complement-like system composed of thioester-containing proteins, fibrinogen-related lectins and convertase-like factors. Moreover, an important role in survival of the ingested microbes seems to be played by host proteins and redox balance maintenance in the tick midgut. Here, we summarize recent knowledge about the major components of tick immune system and focus on their interaction with the relevant tick-transmitted pathogens, represented by spirochetes (Borrelia), rickettsiae (Anaplasma), and protozoans (Babesia). Availability of the tick genomic database and feasibility of functional genomics based on RNA interference greatly contribute to the understanding of molecular and cellular interplay at the tick-pathogen interface and may provide new targets for blocking the transmission of tick pathogens. PMID:23875177

The plant microbiome explored: implications for experimental botany

PubMed Central

Berg, Gabriele; Rybakova, Daria; Grube, Martin; Köberl, Martina

2017-01-01

The importance of microbial root inhabitants for plant growth and health was recognized as early as 100 years ago. Recent insights reveal a close symbiotic relationship between plants and their associated microorganisms, and high structural and functional diversity within plant microbiomes. Plants provide microbial communities with specific habitats, which can be broadly categorized as the rhizosphere, phyllosphere, and endosphere. Plant-associated microbes interact with their host in essential functional contexts. They can stimulate germination and growth, help plants fend off disease, promote stress resistance, and influence plant fitness. Therefore, plants have to be considered as metaorganisms within which the associated microbes usually outnumber the cells belonging to the plant host. The structure of the plant microbiome is determined by biotic and abiotic factors but follows ecological rules. Metaorganisms are co-evolved species assemblages. The metabolism and morphology of plants and their microbiota are intensively connected with each other, and the interplay of both maintains the functioning and fitness of the holobiont. Our study of the current literature shows that analysis of plant microbiome data has brought about a paradigm shift in our understanding of the diverse structure and functioning of the plant microbiome with respect to the following: (i) the high interplay of bacteria, archaea, fungi, and protists; (ii) the high specificity even at cultivar level; (iii) the vertical transmission of core microbiomes; (iv) the extraordinary function of endophytes; and (v) several unexpected functions and metabolic interactions. The plant microbiome should be recognized as an additional factor in experimental botany and breeding strategies. PMID:26547794

Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog (Polypedates megacephalus) and a Validation Using Probiotics

PubMed Central

Weng, Francis Cheng-Hsuan; Shaw, Grace Tzun-Wen; Weng, Chieh-Yin; Yang, Yi-Ju; Wang, Daryi

2017-01-01

The concerted activity of intestinal microbes is crucial to the health and development of their host organisms. Investigation of microbial interactions in the gut should deepen our understanding of how these micro-ecosystems function. Due to advances in Next Generation Sequencing (NGS) technologies, various bioinformatic strategies have been proposed to investigate these microbial interactions. However, due to the complexity of the intestinal microbial community and difficulties in monitoring their interactions, at present there is a gap between the theory and biological application. In order to construct and validate microbial relationships, we first induce a community shift from simple to complex by manipulating artificial hibernation (AH) in the treefrog Polypedates megacephalus. To monitor community growth and microbial interactions, we further performed a time-course screen using a 16S rRNA amplicon approach and a Lotka-Volterra model. Lotka-Volterra models, also known as predator–prey equations, predict the dynamics of microbial communities and how communities are structured and sustained. An interaction network of gut microbiota at the genus level in the treefrog was constructed using Metagenomic Microbial Interaction Simulator (MetaMIS) package. The interaction network obtained had 1,568 commensal, 1,737 amensal, 3,777 mutual, and 3,232 competitive relationships, e.g., Lactococcus garvieae has a commensal relationship with Corynebacterium variabile. To validate the interacting relationships, the gut microbe composition was analyzed after probiotic trials using single strain (L. garvieae, C. variabile, and Bacillus coagulans, respectively) and a combination of L. garvieae, C. variabile, and B. coagulans, because of the cooperative relationship among their respective genera identified in the interaction network. After a 2 week trial, we found via 16S rRNA amplicon analysis that the combination of cooperative microbes yielded significantly higher probiotic concentrations than single strains, and the immune response (interleukin-10 expression) also significantly changed in a manner consistent with improved probiotic effects. By taking advantage of microbial community shift from simple to complex, we thus constructed a reliable microbial interaction network, and validated it using probiotic strains as a test system. PMID:28424669

Human Gut Microbiota: Toward an Ecology of Disease

PubMed Central

Selber-Hnatiw, Susannah; Rukundo, Belise; Ahmadi, Masoumeh; Akoubi, Hayfa; Al-Bizri, Hend; Aliu, Adelekan F.; Ambeaghen, Tanyi U.; Avetisyan, Lilit; Bahar, Irmak; Baird, Alexandra; Begum, Fatema; Ben Soussan, Hélène; Blondeau-Éthier, Virginie; Bordaries, Roxane; Bramwell, Helene; Briggs, Alicia; Bui, Richard; Carnevale, Matthew; Chancharoen, Marisa; Chevassus, Talia; Choi, Jin H.; Coulombe, Karyne; Couvrette, Florence; D'Abreau, Samantha; Davies, Meghan; Desbiens, Marie-Pier; Di Maulo, Tamara; Di Paolo, Sean-Anthony; Do Ponte, Sabrina; dos Santos Ribeiro, Priscyla; Dubuc-Kanary, Laure-Anne; Duncan, Paola K.; Dupuis, Frédérique; El-Nounou, Sara; Eyangos, Christina N.; Ferguson, Natasha K.; Flores-Chinchilla, Nancy R.; Fotakis, Tanya; Gado Oumarou H D, Mariam; Georgiev, Metodi; Ghiassy, Seyedehnazanin; Glibetic, Natalija; Grégoire Bouchard, Julien; Hassan, Tazkia; Huseen, Iman; Ibuna Quilatan, Marlon-Francis; Iozzo, Tania; Islam, Safina; Jaunky, Dilan B.; Jeyasegaram, Aniththa; Johnston, Marc-André; Kahler, Matthew R.; Kaler, Kiranpreet; Kamani, Cedric; Karimian Rad, Hessam; Konidis, Elisavet; Konieczny, Filip; Kurianowicz, Sandra; Lamothe, Philippe; Legros, Karina; Leroux, Sebastien; Li, Jun; Lozano Rodriguez, Monica E.; Luponio-Yoffe, Sean; Maalouf, Yara; Mantha, Jessica; McCormick, Melissa; Mondragon, Pamela; Narayana, Thivaedee; Neretin, Elizaveta; Nguyen, Thi T. T.; Niu, Ian; Nkemazem, Romeo B.; O'Donovan, Martin; Oueis, Matthew; Paquette, Stevens; Patel, Nehal; Pecsi, Emily; Peters, Jackie; Pettorelli, Annie; Poirier, Cassandra; Pompa, Victoria R.; Rajen, Harshvardhan; Ralph, Reginald-Olivier; Rosales-Vasquez, Josué; Rubinshtein, Daria; Sakr, Surya; Sebai, Mohammad S.; Serravalle, Lisa; Sidibe, Fily; Sinnathurai, Ahnjana; Soho, Dominique; Sundarakrishnan, Adithi; Svistkova, Veronika; Ugbeye, Tsolaye E.; Vasconcelos, Megan S.; Vincelli, Michael; Voitovich, Olga; Vrabel, Pamela; Wang, Lu; Wasfi, Maryse; Zha, Cong Y.; Gamberi, Chiara

2017-01-01

Composed of trillions of individual microbes, the human gut microbiota has adapted to the uniquely diverse environments found in the human intestine. Quickly responding to the variances in the ingested food, the microbiota interacts with the host via reciprocal biochemical signaling to coordinate the exchange of nutrients and proper immune function. Host and microbiota function as a unit which guards its balance against invasion by potential pathogens and which undergoes natural selection. Disturbance of the microbiota composition, or dysbiosis, is often associated with human disease, indicating that, while there seems to be no unique optimal composition of the gut microbiota, a balanced community is crucial for human health. Emerging knowledge of the ecology of the microbiota-host synergy will have an impact on how we implement antibiotic treatment in therapeutics and prophylaxis and how we will consider alternative strategies of global remodeling of the microbiota such as fecal transplants. Here we examine the microbiota-human host relationship from the perspective of the microbial community dynamics. PMID:28769880

Leishmania parasites: could we consider them as living organisms per se?

PubMed

Milon, Geneviève

2008-07-01

Over the last 10 years - in Microbes and Infection - the publications dealing with protozoan parasites were mainly providing insights on the pathogenic processes leading to the local or systemic damages in the mammals, these parasitic organisms exploit/subvert as hosts. As a result, many investigators introduced the objectives of their analysis by referring to "host-pathogen" interactions. Though we, as investigators, are all determined to decipher the pathogenic processes which can indeed be coupled to the parasite uncontrolled development, I think that the parasites - alike the living organisms they subvert as hosts - need to be considered as living organisms per se, instead of being considered as "pathogens". Such a conceptual frame will promote research on the processes on which relies their perpetuation whatever the level under investigations - individual and/or population level. Only the unicellular protozoan parasites of the genus Leishmania known to be hosted by blood-feeding insects and mammals will be further considered in this brief contribution.

Symbiosis insights through metagenomic analysis of a microbial consortium.

PubMed

Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N; Huntemann, Marcel; Richter, Michael; Gloeckner, Frank Oliver; Boffelli, Dario; Anderson, Iain J; Barry, Kerrie W; Shapiro, Harris J; Szeto, Ernest; Kyrpides, Nikos C; Mussmann, Marc; Amann, Rudolf; Bergin, Claudia; Ruehland, Caroline; Rubin, Edward M; Dubilier, Nicole

2006-10-26

Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulphur-oxidizing and sulphate-reducing bacteria, all of which are capable of carbon fixation, thus providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits.

Copper Homeostasis at the Host-Pathogen Interface*

PubMed Central

Hodgkinson, Victoria; Petris, Michael J.

2012-01-01

The trace element copper is indispensable for all aerobic life forms. Its ability to cycle between two oxidation states, Cu1+ and Cu2+, has been harnessed by a wide array of metalloenzymes that catalyze electron transfer reactions. The metabolic needs for copper are sustained by a complex series of transporters and carrier proteins that regulate its intracellular accumulation and distribution in both pathogenic microbes and their animal hosts. However, copper is also potentially toxic due in part to its ability to generate reactive oxygen species. Recent studies suggest that the macrophage phagosome accumulates copper during bacterial infection, which may constitute an important mechanism of killing. Bacterial countermeasures include the up-regulation of copper export and detoxification genes during infection, which studies suggest are important determinants of virulence. In this minireview, we summarize recent developments that suggest an emerging role for copper as an unexpected component in determining the outcome of host-pathogen interactions. PMID:22389498

Symbiosis insights through metagenomic analysis of a microbialconsortium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N.

Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here, we used a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut, and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulfur-oxidizing and sulfate-reducing bacteria, all of which are capable of carbon fixation, providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the wormmore » could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model which describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments which it inhabits.« less

Differential carbohydrate utilization and organic acid production by honey bee symbionts.

PubMed

Lee, Fredrick J; Miller, Kayla I; McKinlay, James B; Newton, Irene L G

2018-06-06

The honey bee worker gut hosts a community of bacteria that comprises 8-10 core bacterial species, along with a set of more transient environmental microbes. Collectively, these microbes break down and ferment saccharides present in the host's diet, based on analyses of metagenomes, and metatranscriptomes from this environment. As part of this metabolism, the bacteria produce short-chain fatty acids that may serve as a food source for the host bee, stimulating biological processes that may contribute to host weight gain. To identify metabolic contributions of symbionts within the honey bee gut, we utilized a combination of molecular and biochemical approaches. We show significant variation in the metabolic capabilities of honey bee associated taxa, highlighting the fact that honey bee gut microbiota members of the same clade are highly variable in their ability to use specific carbohydrates and produce organic acids. Finally, we confirm that the honey bee core microbes are active in vivo, expressing key enzymatic genes critical for utilizing plant-derived molecules and producing organic acids (i.e. acetate and lactate). These results suggest that core taxa may contribute significantly to weight gain in the honey bee, specifically through the production of organic acids.

Microbial communities and bioactive compounds in marine sponges of the family irciniidae-a review.

PubMed

Hardoim, Cristiane C P; Costa, Rodrigo

2014-09-30

Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species-the vast majority of which are difficult to cultivate-and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.

Trichomonas vaginalis origins, molecular pathobiology and clinical considerations.

PubMed

Hirt, Robert P; Sherrard, Jackie

2015-02-01

To integrate a selection of the most recent data on Trichomonas vaginalis origins, molecular cell biology and T. vaginalis interactions with the urogenital tract microbiota with trichomoniasis symptoms and clinical management. Transcriptomics and proteomics datasets are accumulating, facilitating the identification and prioritization of key target genes to study T. vaginalis pathobiology. Proteins involved in host sensing and cytoskeletal plasticity during T. vaginalis amoeboid transformation were identified. T. vaginalis was shown to secrete exosomes and a macrophage migration inhibitory factor-like protein that both influence host-parasite interactions. T. vaginalis co-infections with Mycoplasma species and viruses were shown to modulate the inflammatory responses, whereas T. vaginalis interactions with various Lactobacillus species inhibit parasite interactions with human cells. T. vaginalis infections were also shown to be associated with bacterial vaginosis. A broader range of health sequelae is also becoming apparent. Diagnostics for both women and men based on the molecular approaches are being refined, in particular for men. New developments in the molecular and cellular basis of T. vaginalis pathobiology combined with data on the urogenital tract microbiota and immunology have enriched our knowledge on human-microbe interactions that will contribute to increasing our capacity to prevent and treat T. vaginalis and other sexually transmitted infections.

Microbe Hunting

PubMed Central

Lipkin, W. Ian

2010-01-01

Summary: Platforms for pathogen discovery have improved since the days of Koch and Pasteur; nonetheless, the challenges of proving causation are at least as daunting as they were in the late 1800s. Although we will almost certainly continue to accumulate low-hanging fruit, where simple relationships will be found between the presence of a cultivatable agent and a disease, these successes will be increasingly infrequent. The future of the field rests instead in our ability to follow footprints of infectious agents that cannot be characterized using classical microbiological techniques and to develop the laboratory and computational infrastructure required to dissect complex host-microbe interactions. I have tried to refine the criteria used by Koch and successors to prove linkage to disease. These refinements are working constructs that will continue to evolve in light of new technologies, new models, and new insights. What will endure is the excitement of the chase. Happy hunting! PMID:20805403

The influence of milk oligosaccharides on microbiota of infants: opportunities for formulas.

PubMed

Chichlowski, Maciej; German, J Bruce; Lebrilla, Carlito B; Mills, David A

2011-01-01

In addition to a nutritive role, human milk also guides the development of a protective intestinal microbiota in the infant. Human milk possesses an overabundance of complex oligosaccharides that are indigestible by the infant yet are consumed by microbial populations in the developing intestine. These oligosaccharides are believed to facilitate enrichment of a healthy infant gastrointestinal microbiota, often associated with bifidobacteria. Advances in glycomics have enabled precise determination of milk glycan structures as well as identification of the specific glycans consumed by various gut microbes. Furthermore, genomic analysis of bifidobacteria from infants has revealed specific genetic loci related to milk oligosaccharide import and processing, suggesting coevolution between the human host, milk glycans, and the microbes they enrich. This review discusses the current understanding of how human milk oligosaccharides interact with the infant microbiota and examines the opportunities for translating this knowledge to improve the functionality of infant formulas.

Rearing the Fruit Fly Drosophila melanogaster Under Axenic and Gnotobiotic Conditions.

PubMed

Koyle, Melinda L; Veloz, Madeline; Judd, Alec M; Wong, Adam C-N; Newell, Peter D; Douglas, Angela E; Chaston, John M

2016-07-30

The influence of microbes on myriad animal traits and behaviors has been increasingly recognized in recent years. The fruit fly Drosophila melanogaster is a model for understanding microbial interactions with animal hosts, facilitated by approaches to rear large sample sizes of Drosophila under microorganism-free (axenic) conditions, or with defined microbial communities (gnotobiotic). This work outlines a method for collection of Drosophila embryos, hypochlorite dechorionation and sterilization, and transfer to sterile diet. Sterilized embryos are transferred to sterile diet in 50 ml centrifuge tubes, and developing larvae and adults remain free of any exogenous microbes until the vials are opened. Alternatively, flies with a defined microbiota can be reared by inoculating sterile diet and embryos with microbial species of interest. We describe the introduction of 4 bacterial species to establish a representative gnotobiotic microbiota in Drosophila. Finally, we describe approaches for confirming bacterial community composition, including testing if axenic Drosophila remain bacteria-free into adulthood.

Oral delivery of dsRNA by microbes: Beyond pest control.

PubMed

Abrieux, Antoine; Chiu, Joanna C

2016-01-01

RNA interference (RNAi) by oral delivery of dsRNA in insects has great potential as a tool for integrated pest management (IPM), especially with respect to addressing the need to reduce off-target effect and slow down resistance development to chemical insecticides. Employing the natural association existing between insect and yeast, we developed a novel method to enable the knock down of vital genes in the pest insect Drosophila suzukii through oral delivery of species-specific dsRNA using genetically modified Saccharomyces cerevisae. D. suzukii that were fed with our "yeast biopesticide" showed a significant decrease in fitness. In this perspective article, we postulate that this approach could be adapted to a large number of species, given the great diversity of symbiotic interactions involving microorganisms and host species. Furthermore, we speculate that beyond its application as biopesticide, dsRNA delivery by genetically modified microbes can also serve to facilitate reverse genetic applications, specifically in non-model organisms.

Socializing, networking and development: a report from the second 'Young Microbiologists Symposium on Microbe Signalling, Organization and Pathogenesis'.

PubMed

Caly, Delphine L; Coulthurst, Sarah J; Geoghegan, Joan A; Malone, Jacob G; Ryan, Robert P

2012-11-01

In mid-June, the second Young Microbiologists Symposium took place under the broad title of 'Microbe signalling, organization and pathogenesis' on the picturesque campus of University College Cork, Ireland. The symposium attracted 150 microbiologists from 15 different countries. The key feature of this meeting was that it was specifically aimed at providing a platform for junior scientists to present their work to a broad audience. The meeting was principally supported by Science Foundation Ireland with further backing from the Society for General Microbiology, the American Society for Microbiology and the European Molecular Biology Organization. Sessions focused on microbial gene expression, biogenesis, pathogenicity and host interaction. In this MicroMeeting report, we highlight some of the most significant advances and exciting developments reported during various talks and poster presentations given by the young and talented microbiologists. © 2012 Blackwell Publishing Ltd.

Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome.

PubMed

Zhang, Yunzeng; Xu, Jin; Riera, Nadia; Jin, Tao; Li, Jinyun; Wang, Nian

2017-08-10

Roots are the primary site for plant-microbe interactions. Among the three root-associated layers (i.e., rhizosphere, rhizoplane, and endorhiza), the rhizoplane is a key component serving a critical gating role that controls microbial entry into plant roots. The microbial communities colonizing the three layers are believed to be gradually enriched from the bulk soil inoculum. However, it is unknown how this enrichment process, particularly the rhizosphere to rhizoplane step, is affected by biotic stresses, such as disease. In this study, we address this question using the citrus root-associated microbiome as a model. We identified the rhizosphere-to-rhizoplane-enriched taxonomic and functional properties of the citrus root-associated microbiome and determined how they were affected by Huanglongbing (HLB), a severe systemic disease caused by Candidatus Liberibacter asiaticus, using metagenomic and metatranscriptomic approaches. Multiple rhizoplane-enriched genera were identified, with Bradyrhizobium and Burkholderia being the most dominant. Plant-derived carbon sources are an important driving force for the enrichment process. The enrichment of functional attributes, such as motility, chemotaxis, secretion systems, and lipopolysaccharide (LPS) synthesis, demonstrated more active microbe-plant interactions on the rhizoplane than the rhizosphere. We observed that HLB impaired the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome in three ways: (1) by decreasing the relative abundance of most rhizoplane-enriched genera; (2) by reducing the relative abundance and/or expression activity of the functional attributes involved in microbe-plant interactions; and (3) by recruiting more functional features involved in autotrophic life cycle adaptation, such as carbon fixation and nitrogen nitrification in the HLB rhizoplane microbiome. Finally, our data showed that inoculation of Burkholderia strains isolated from the healthy citrus root-associated microbiome could trigger the expression of genes involved in induced systemic resistance in inoculated plants. HLB causes decreased relative abundance and/or expression activity of rhizoplane-enriched taxonomic and functional properties, collectively resulting in impaired plant host-microbiome interactions. Manipulation of the citrus root-associated microbiome, for instance, by inoculating citrus roots with beneficial Burkholderia strains, has potential to promote plant health. Our results provide novel insights for understanding the contributions of the community enrichment process of the root-associated microbiome to the plant hosts.

Interactions Between Stress and Sex in Microbial Responses Within the Microbiota-Gut-Brain Axis in a Mouse Model.

PubMed

Tsilimigras, Matthew C B; Gharaibeh, Raad Z; Sioda, Michael; Gray, Laura; Fodor, Anthony A; Lyte, Mark

2018-05-01

Animal models are frequently used to examine stress response, but experiments seldom include females. The connection between the microbiota-gut-brain axis and behavioral stress response is investigated here using a mixed-sex mouse cohort. CF-1 mice underwent alternating days of restraint and forced swim for 19 days (male n = 8, female n = 8) with matching numbers of control animals at which point the 16S rRNA genes of gut microbiota were sequenced. Mixed linear models accounting for stress status and sex with individuals nested in cage to control for cage effects evaluated these data. Murine behaviors in elevated plus-maze, open-field, and light/dark box were investigated. Community-level associations with sex, stress, and their interaction were significant. Males had higher microbial diversity than females (p = .025). Of the 638 operational taxonomic units detected in at least 25% of samples, 94 operational taxonomic units were significant: 31 (stress), 61 (sex), and 34 (sex-stress interaction). Twenty of the 39 behavioral measures were significant for stress, 3 for sex, and 6 for sex-stress. However, no significant associations between behavioral measures and specific microbes were detected. These data suggest sex influences stress response and the microbiota-gut-brain axis and that studies of behavior and the microbiome therefore benefit from consideration of how sex differences drive behavior and microbial community structure. Host stress resilience and absence of associations between stress-induced behaviors with specific microbes suggests that hypothalamic-pituitary-adrenal axis activation represents a threshold for microbial influence on host behavior. Future studies are needed in examining the intersection of sex, stress response, and the microbiota-gut-brain axis.

Probing Molecular Insights into Zika Virus–Host Interactions

PubMed Central

Lee, Ina; Li, Ge; Wang, Shusheng; Desprès, Philippe; Zhao, Richard Y.

2018-01-01

The recent Zika virus (ZIKV) outbreak in the Americas surprised all of us because of its rapid spread and association with neurologic disorders including fetal microcephaly, brain and ocular anomalies, and Guillain–Barré syndrome. In response to this global health crisis, unprecedented and world-wide efforts are taking place to study the ZIKV-related human diseases. Much has been learned about this virus in the areas of epidemiology, genetic diversity, protein structures, and clinical manifestations, such as consequences of ZIKV infection on fetal brain development. However, progress on understanding the molecular mechanism underlying ZIKV-associated neurologic disorders remains elusive. To date, we still lack a good understanding of; (1) what virologic factors are involved in the ZIKV-associated human diseases; (2) which ZIKV protein(s) contributes to the enhanced viral pathogenicity; and (3) how do the newly adapted and pandemic ZIKV strains alter their interactions with the host cells leading to neurologic defects? The goal of this review is to explore the molecular insights into the ZIKV–host interactions with an emphasis on host cell receptor usage for viral entry, cell innate immunity to ZIKV, and the ability of ZIKV to subvert antiviral responses and to cause cytopathic effects. We hope this literature review will inspire additional molecular studies focusing on ZIKV–host Interactions. PMID:29724036

Probing Molecular Insights into Zika Virus⁻Host Interactions.

PubMed

Lee, Ina; Bos, Sandra; Li, Ge; Wang, Shusheng; Gadea, Gilles; Desprès, Philippe; Zhao, Richard Y

2018-05-02

The recent Zika virus (ZIKV) outbreak in the Americas surprised all of us because of its rapid spread and association with neurologic disorders including fetal microcephaly, brain and ocular anomalies, and Guillain⁻Barré syndrome. In response to this global health crisis, unprecedented and world-wide efforts are taking place to study the ZIKV-related human diseases. Much has been learned about this virus in the areas of epidemiology, genetic diversity, protein structures, and clinical manifestations, such as consequences of ZIKV infection on fetal brain development. However, progress on understanding the molecular mechanism underlying ZIKV-associated neurologic disorders remains elusive. To date, we still lack a good understanding of; (1) what virologic factors are involved in the ZIKV-associated human diseases; (2) which ZIKV protein(s) contributes to the enhanced viral pathogenicity; and (3) how do the newly adapted and pandemic ZIKV strains alter their interactions with the host cells leading to neurologic defects? The goal of this review is to explore the molecular insights into the ZIKV⁻host interactions with an emphasis on host cell receptor usage for viral entry, cell innate immunity to ZIKV, and the ability of ZIKV to subvert antiviral responses and to cause cytopathic effects. We hope this literature review will inspire additional molecular studies focusing on ZIKV⁻host Interactions.

The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model.

PubMed

Dirksen, Philipp; Marsh, Sarah Arnaud; Braker, Ines; Heitland, Nele; Wagner, Sophia; Nakad, Rania; Mader, Sebastian; Petersen, Carola; Kowallik, Vienna; Rosenstiel, Philip; Félix, Marie-Anne; Schulenburg, Hinrich

2016-05-09

Host-microbe associations underlie many key processes of host development, immunity, and life history. Yet, none of the current research on the central model species Caenorhabditis elegans considers the worm's natural microbiome. Instead, almost all laboratories exclusively use the canonical strain N2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an E. coli strain as food. Here, we characterize for the first time the native microbiome of C. elegans and assess its influence on nematode life history characteristics. Nematodes sampled directly from their native habitats carry a species-rich bacterial community, dominated by Proteobacteria such as Enterobacteriaceae and members of the genera Pseudomonas, Stenotrophomonas, Ochrobactrum, and Sphingomonas. The C. elegans microbiome is distinct from that of the worm's natural environment and the congeneric species C. remanei. Exposure to a derived experimental microbiome revealed that bacterial composition is influenced by host developmental stage and genotype. These experiments also showed that the microbes enhance host fitness under standard and also stressful conditions (e.g., high temperature and either low or high osmolarity). Taking advantage of the nematode's transparency, we further demonstrate that several Proteobacteria are able to enter the C. elegans gut and that an Ochrobactrum isolate even seems to be able to persist in the intestines under stressful conditions. Moreover, three Pseudomonas isolates produce an anti-fungal effect in vitro which we show can contribute to the worm's defense against fungal pathogens in vivo. This first systematic analysis of the nematode's native microbiome reveals a species-rich bacterial community to be associated with C. elegans, which is likely of central importance for our understanding of the worm's biology. The information acquired and the microbial isolates now available for experimental work establishes C. elegans as a tractable model for the in-depth dissection of host-microbiome interactions.

Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis.

PubMed

Seal, John B; Alverdy, John C; Zaborina, Olga; An, Gary

2011-09-19

There is a growing realization that alterations in host-pathogen interactions (HPI) can generate disease phenotypes without pathogen invasion. The gut represents a prime region where such HPI can arise and manifest. Under normal conditions intestinal microbial communities maintain a stable, mutually beneficial ecosystem. However, host stress can lead to changes in environmental conditions that shift the nature of the host-microbe dialogue, resulting in escalation of virulence expression, immune activation and ultimately systemic disease. Effective modulation of these dynamics requires the ability to characterize the complexity of the HPI, and dynamic computational modeling can aid in this task. Agent-based modeling is a computational method that is suited to representing spatially diverse, dynamical systems. We propose that dynamic knowledge representation of gut HPI with agent-based modeling will aid in the investigation of the pathogenesis of gut-derived sepsis. An agent-based model (ABM) of virulence regulation in Pseudomonas aeruginosa was developed by translating bacterial and host cell sense-and-response mechanisms into behavioral rules for computational agents and integrated into a virtual environment representing the host-microbe interface in the gut. The resulting gut milieu ABM (GMABM) was used to: 1) investigate a potential clinically relevant laboratory experimental condition not yet developed--i.e. non-lethal transient segmental intestinal ischemia, 2) examine the sufficiency of existing hypotheses to explain experimental data--i.e. lethality in a model of major surgical insult and stress, and 3) produce behavior to potentially guide future experimental design--i.e. suggested sample points for a potential laboratory model of non-lethal transient intestinal ischemia. Furthermore, hypotheses were generated to explain certain discrepancies between the behaviors of the GMABM and biological experiments, and new investigatory avenues proposed to test those hypotheses. Agent-based modeling can account for the spatio-temporal dynamics of an HPI, and, even when carried out with a relatively high degree of abstraction, can be useful in the investigation of system-level consequences of putative mechanisms operating at the individual agent level. We suggest that an integrated and iterative heuristic relationship between computational modeling and more traditional laboratory and clinical investigations, with a focus on identifying useful and sufficient degrees of abstraction, will enhance the efficiency and translational productivity of biomedical research.

Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis

PubMed Central

2011-01-01

Background There is a growing realization that alterations in host-pathogen interactions (HPI) can generate disease phenotypes without pathogen invasion. The gut represents a prime region where such HPI can arise and manifest. Under normal conditions intestinal microbial communities maintain a stable, mutually beneficial ecosystem. However, host stress can lead to changes in environmental conditions that shift the nature of the host-microbe dialogue, resulting in escalation of virulence expression, immune activation and ultimately systemic disease. Effective modulation of these dynamics requires the ability to characterize the complexity of the HPI, and dynamic computational modeling can aid in this task. Agent-based modeling is a computational method that is suited to representing spatially diverse, dynamical systems. We propose that dynamic knowledge representation of gut HPI with agent-based modeling will aid in the investigation of the pathogenesis of gut-derived sepsis. Methodology/Principal Findings An agent-based model (ABM) of virulence regulation in Pseudomonas aeruginosa was developed by translating bacterial and host cell sense-and-response mechanisms into behavioral rules for computational agents and integrated into a virtual environment representing the host-microbe interface in the gut. The resulting gut milieu ABM (GMABM) was used to: 1) investigate a potential clinically relevant laboratory experimental condition not yet developed - i.e. non-lethal transient segmental intestinal ischemia, 2) examine the sufficiency of existing hypotheses to explain experimental data - i.e. lethality in a model of major surgical insult and stress, and 3) produce behavior to potentially guide future experimental design - i.e. suggested sample points for a potential laboratory model of non-lethal transient intestinal ischemia. Furthermore, hypotheses were generated to explain certain discrepancies between the behaviors of the GMABM and biological experiments, and new investigatory avenues proposed to test those hypotheses. Conclusions/Significance Agent-based modeling can account for the spatio-temporal dynamics of an HPI, and, even when carried out with a relatively high degree of abstraction, can be useful in the investigation of system-level consequences of putative mechanisms operating at the individual agent level. We suggest that an integrated and iterative heuristic relationship between computational modeling and more traditional laboratory and clinical investigations, with a focus on identifying useful and sufficient degrees of abstraction, will enhance the efficiency and translational productivity of biomedical research. PMID:21929759

Diet, gut microbes, and the pathogenesis of inflammatory bowel diseases.

PubMed

Dolan, Kyle T; Chang, Eugene B

2017-01-01

The rising incidence of inflammatory bowel diseases in recent decades has notably paralleled changing lifestyle habits in Western nations, which are now making their way into more traditional societies. Diet plays a key role in IBD pathogenesis, and there is a growing appreciation that the interaction between diet and microbes in a susceptible person contributes significantly to the onset of disease. In this review, we examine what is known about dietary and microbial factors that promote IBD. We summarize recent findings regarding the effects of diet in IBD epidemiology from prospective population cohort studies, as well as new insights into IBD-associated dysbiosis. Microbial metabolism of dietary components can influence the epithelial barrier and the mucosal immune system, and understanding how these interactions generate or suppress inflammation will be a significant focus of IBD research. Our knowledge of dietary and microbial risk factors for IBD provides important considerations for developing therapeutic approaches through dietary modification or re-shaping the microbiota. We conclude by calling for increased sophistication in designing studies on the role of diet and microbes in IBD pathogenesis and disease resolution in order to accelerate progress in response to the growing challenge posed by these complex disorders. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigating Microbe-Mineral Interactions: Recent Advances in X-Ray and Electron Microscopy and Redox-Sensitive Methods

NASA Astrophysics Data System (ADS)

Miot, Jennyfer; Benzerara, Karim; Kappler, Andreas

2014-05-01

Microbe-mineral interactions occur in diverse modern environments, from the deep sea and subsurface rocks to soils and surface aquatic environments. They may have played a central role in the geochemical cycling of major (e.g., C, Fe, Ca, Mn, S, P) and trace (e.g., Ni, Mo, As, Cr) elements over Earth's history. Such interactions include electron transfer at the microbe-mineral interface that left traces in the rock record. Geomicrobiology consists in studying interactions at these organic-mineral interfaces in modern samples and looking for traces of past microbe-mineral interactions recorded in ancient rocks. Specific tools are required to probe these interfaces and to understand the mechanisms of interaction between microbes and minerals from the scale of the biofilm to the nanometer scale. In this review, we focus on recent advances in electron microscopy, in particular in cryoelectron microscopy, and on a panel of electrochemical and synchrotron-based methods that have recently provided new understanding and imaging of the microbe-mineral interface, ultimately opening new fields to be explored.

Structural basis for the role of serine-rich repeat proteins from Lactobacillus reuteri in gut microbe–host interactions

PubMed Central

Sequeira, Saannya; Kavanaugh, Devon; MacKenzie, Donald A.; Walpole, Samuel; Leclaire, Charlotte; Gunning, A. Patrick; Latousakis, Dimitrios; Willats, William G. T.; Dong, Changjiang; Juge, Nathalie

2018-01-01

Lactobacillus reuteri, a Gram-positive bacterial species inhabiting the gastrointestinal tract of vertebrates, displays remarkable host adaptation. Previous mutational analyses of rodent strain L. reuteri 100-23C identified a gene encoding a predicted surface-exposed serine-rich repeat protein (SRRP100-23) that was vital for L. reuteri biofilm formation in mice. SRRPs have emerged as an important group of surface proteins on many pathogens, but no structural information is available in commensal bacteria. Here we report the 2.00-Å and 1.92-Å crystal structures of the binding regions (BRs) of SRRP100-23 and SRRP53608 from L. reuteri ATCC 53608, revealing a unique β-solenoid fold in this important adhesin family. SRRP53608-BR bound to host epithelial cells and DNA at neutral pH and recognized polygalacturonic acid (PGA), rhamnogalacturonan I, or chondroitin sulfate A at acidic pH. Mutagenesis confirmed the role of the BR putative binding site in the interaction of SRRP53608-BR with PGA. Long molecular dynamics simulations showed that SRRP53608-BR undergoes a pH-dependent conformational change. Together, these findings provide mechanistic insights into the role of SRRPs in host–microbe interactions and open avenues of research into the use of biofilm-forming probiotics against clinically important pathogens. PMID:29507249

Developmental biology in marine invertebrate symbioses.

PubMed

McFall-Ngai, M J; Ruby, E G

2000-12-01

Associations between marine invertebrates and their cooperative bacterial symbionts offer access to an understanding of the roots of host-microbe interaction; for example, several symbioses like the squid-vibrio light organ association serve as models for investigating how each partner affects the developmental biology of the other. Previous results have identified a program of specific developmental events that unfolds as the association is initiated. In the past year, published studies have focused primarily on describing the mechanisms underlying the signaling processes that occur between the juvenile squid and the luminous bacteria that colonize it.

Intercalation of paracetamol into the hydrotalcite-like host

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kovanda, Frantisek, E-mail: Frantisek.Kovanda@vscht.cz; Maryskova, Zuzana; Kovar, Petr

2011-12-15

Hydrotalcite-like compounds are often used as host structures for intercalation of various anionic species. The product intercalated with the nonionic, water-soluble pharmaceuticals paracetamol, N-(4-hydroxyphenyl)acetamide, was prepared by rehydration of the Mg-Al mixed oxide obtained by calcination of hydrotalcite-like precursor at 500 Degree-Sign C. The successful intercalation of paracetamol molecules into the interlayer space was confirmed by powder X-ray diffraction and infrared spectroscopy measurements. Molecular simulations showed that the phenolic hydroxyl groups of paracetamol interact with hydroxide sheets of the host via the hydroxyl groups of the positively charged sites of Al-containing octahedra; the interlayer water molecules are located mostly nearmore » the hydroxide sheets. The arrangement of paracetamol molecules in the interlayer is rather disordered and interactions between neighboring molecules cause their tilting towards the hydroxide sheets. Dissolution tests in various media showed slower release of paracetamol intercalated in the hydrotalcite-like host in comparison with tablets containing the powdered pharmaceuticals. - Graphical abstract: Molecular simulations showed disordered arrangement of paracetamol molecules in the interlayer; most of the interlayer water molecules are located near the hydroxide sheets. Black-Small-Square Highlights: Black-Right-Pointing-Pointer Paracetamol was intercalated in Mg-Al hydrotalcite-like host by rehydration/reconstruction procedure. Black-Right-Pointing-Pointer Paracetamol phenolic groups interact with positively charged sites in hydroxide sheets. Black-Right-Pointing-Pointer Molecular simulations showed disordered arrangement of guest molecules in the interlayer. Black-Right-Pointing-Pointer Slower release of paracetamol intercalated in the hydrotalcite-like host was observed.« less

Exploitation of the host cell ubiquitin machinery by microbial effector proteins.

PubMed

Lin, Yi-Han; Machner, Matthias P

2017-06-15

Pathogenic bacteria are in a constant battle for survival with their host. In order to gain a competitive edge, they employ a variety of sophisticated strategies that allow them to modify conserved host cell processes in ways that favor bacterial survival and growth. Ubiquitylation, the covalent attachment of the small modifier ubiquitin to target proteins, is such a pathway. Ubiquitylation profoundly alters the fate of a myriad of cellular proteins by inducing changes in their stability or function, subcellular localization or interaction with other proteins. Given the importance of ubiquitylation in cell development, protein homeostasis and innate immunity, it is not surprising that this post-translational modification is exploited by a variety of effector proteins from microbial pathogens. Here, we highlight recent advances in our understanding of the many ways microbes take advantage of host ubiquitylation, along with some surprising deviations from the canonical theme. The lessons learned from the in-depth analyses of these host-pathogen interactions provide a fresh perspective on an ancient post-translational modification that we thought was well understood.This article is part of a Minifocus on Ubiquitin Regulation and Function. For further reading, please see related articles: 'Mechanisms of regulation and diversification of deubiquitylating enzyme function' by Pawel Leznicki and Yogesh Kulathu ( J. Cell Sci. 130 , 1997-2006). 'Cell scientist to watch - Mads Gyrd-Hansen' ( J. Cell Sci. 130 , 1981-1983). © 2017. Published by The Company of Biologists Ltd.

Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants.

PubMed

Trujillo, Martha E; Riesco, Raúl; Benito, Patricia; Carro, Lorena

2015-01-01

For a long time, it was believed that a healthy plant did not harbor any microorganisms within its tissues, as these were often considered detrimental for the plant. In the last three decades, the numbers of studies on plant microbe-interactions has led to a change in our view and we now know that many of these invisible partners are essential for the overall welfare of the plant. The application of Next Generation Sequencing techniques is a powerful tool that has permitted the detection and identification of microbial communities in healthy plants. Among the new plant microbe interactions recently reported several actinobacteria such as Micromonospora are included. Micromonospora is a Gram-positive bacterium with a wide geographical distribution; it can be found in the soil, mangrove sediments, and freshwater and marine ecosistems. In the last years our group has focused on the isolation of Micromonospora strains from nitrogen fixing nodules of both leguminous and actinorhizal plants and reported for the first time its wide distribution in nitrogen fixing nodules of both types of plants. These studies have shown how this microoganism had been largely overlooked in this niche due to its slow growth. Surprisingly, the genetic diversity of Micromonospora strains isolated from nodules is very high and several new species have been described. The current data indicate that Micromonospora saelicesensis is the most frequently isolated species from the nodular tissues of both leguminous and actinorhizal plants. Further studies have also been carried out to confirm the presence of Micromonospora inside the nodule tissues, mainly by specific in situ hybridization. The information derived from the genome of the model strain, Micromonospora lupini, Lupac 08, has provided useful information as to how this bacterium may relate with its host plant. Several strategies potentially necessary for Micromonospora to thrive in the soil, a highly competitive, and rough environment, and as an endophytic bacterium with the capacity to colonize the internal plant tissues which are protected from the invasion of other soil microbes were identified. The genome data also revealed the potential of M. lupini Lupac 08 as a plant growth promoting bacterium. Several loci involved in plant growth promotion features such as the production of siderophores, phytohormones, and the degradation of chitin (biocontrol) were also located on the genome and the functionality of these genes was confirmed in the laboratory. In addition, when several host plants species were inoculated with Micromonospora strains, the plant growth enhancing effect was evident under greenhouse conditions. Unexpectedly, a high number of plant-cell wall degrading enzymes were also detected, a trait usually found only in pathogenic bacteria. Thus, Micromonospora can be added to the list of new plant-microbe interactions. The current data indicate that this microorganism may have an important application in agriculture and other biotechnological processes. The available information is promising but limited, much research is still needed to determine which is the ecological function of Micromonospora in interaction with nitrogen fixing plants.

Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants

PubMed Central

Trujillo, Martha E.; Riesco, Raúl; Benito, Patricia; Carro, Lorena

2015-01-01

For a long time, it was believed that a healthy plant did not harbor any microorganisms within its tissues, as these were often considered detrimental for the plant. In the last three decades, the numbers of studies on plant microbe-interactions has led to a change in our view and we now know that many of these invisible partners are essential for the overall welfare of the plant. The application of Next Generation Sequencing techniques is a powerful tool that has permitted the detection and identification of microbial communities in healthy plants. Among the new plant microbe interactions recently reported several actinobacteria such as Micromonospora are included. Micromonospora is a Gram-positive bacterium with a wide geographical distribution; it can be found in the soil, mangrove sediments, and freshwater and marine ecosistems. In the last years our group has focused on the isolation of Micromonospora strains from nitrogen fixing nodules of both leguminous and actinorhizal plants and reported for the first time its wide distribution in nitrogen fixing nodules of both types of plants. These studies have shown how this microoganism had been largely overlooked in this niche due to its slow growth. Surprisingly, the genetic diversity of Micromonospora strains isolated from nodules is very high and several new species have been described. The current data indicate that Micromonospora saelicesensis is the most frequently isolated species from the nodular tissues of both leguminous and actinorhizal plants. Further studies have also been carried out to confirm the presence of Micromonospora inside the nodule tissues, mainly by specific in situ hybridization. The information derived from the genome of the model strain, Micromonospora lupini, Lupac 08, has provided useful information as to how this bacterium may relate with its host plant. Several strategies potentially necessary for Micromonospora to thrive in the soil, a highly competitive, and rough environment, and as an endophytic bacterium with the capacity to colonize the internal plant tissues which are protected from the invasion of other soil microbes were identified. The genome data also revealed the potential of M. lupini Lupac 08 as a plant growth promoting bacterium. Several loci involved in plant growth promotion features such as the production of siderophores, phytohormones, and the degradation of chitin (biocontrol) were also located on the genome and the functionality of these genes was confirmed in the laboratory. In addition, when several host plants species were inoculated with Micromonospora strains, the plant growth enhancing effect was evident under greenhouse conditions. Unexpectedly, a high number of plant-cell wall degrading enzymes were also detected, a trait usually found only in pathogenic bacteria. Thus, Micromonospora can be added to the list of new plant-microbe interactions. The current data indicate that this microorganism may have an important application in agriculture and other biotechnological processes. The available information is promising but limited, much research is still needed to determine which is the ecological function of Micromonospora in interaction with nitrogen fixing plants. PMID:26648923

Brucella

USDA-ARS?s Scientific Manuscript database

The genus Brucella encompasses a group of gram negative bacteria that survive almost exclusively in infected hosts with preference for localization in intracellular compartments of cells. The genus has traditionally been divided into species based on microbe characteristics and host preference, bu...

Tracking microbial interactions with NanoSIMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Musat, Niculina; Musat, Florin; Weber, Peter Kilian

The combination of stable isotope probing (SIP), NanoSIMS imaging and microbe identification via fluorescence in situ hybridization (FISH) is often used to link identity to function at the cellular level in microbial communities. Many opportunities remain for nanoSIP to identify metabolic interactions and nutrient fluxes within syntrophic associations and obligate symbioses where exchanges can be extremely rapid. However, additional data, such as genomic potential, gene expression or other imaging modalities are often critical to deciphering the mechanisms underlying specific interactions, and researchers must keep sample preparation artefacts in mind. Here we focus on recent applications of nanoSIP, particularly where usedmore » to track exchanges of isotopically labelled molecules between organisms. Here, we highlight metabolic interactions within syntrophic consortia, carbon/nitrogen fluxes between phototrophs and their heterotrophic partners, and symbiont–host nutrient sharing.« less

The Functional Impact of the Intestinal Microbiome on Mucosal Immunity and Systemic Autoimmunity

PubMed Central

Longman, Randy S.; Littman, Dan R.

2016-01-01

Purpose of Review This review will highlight recent advances functionally linking the gut microbiome with mucosal and systemic immune cell activation potentially underlying autoimmunity. Recent Findings Dynamic interactions between the gut microbiome and environmental cues (including diet and medicines) shape the effector potential of the microbial organ. Key bacteria and viruses have emerged, that, in defined microenvironments, play a critical role in regulating effector lymphocyte functions. The coordinated interactions between these different microbial kingdoms—including bacteria, helminths, and viruses (termed transkingdom interactions)—play a critical role in shaping immunity. Emerging strategies to identify immunologically-relevant microbes with the potential to regulate immune cell functions both at mucosal sites and systemically will likely define key diagnostic and therapeutic targets. Summary The microbiome constitutes a critical microbial organ with coordinated interactions that shape host immunity. PMID:26002030

Tracking microbial interactions with NanoSIMS

DOE PAGES

Musat, Niculina; Musat, Florin; Weber, Peter Kilian; ...

2016-07-12

The combination of stable isotope probing (SIP), NanoSIMS imaging and microbe identification via fluorescence in situ hybridization (FISH) is often used to link identity to function at the cellular level in microbial communities. Many opportunities remain for nanoSIP to identify metabolic interactions and nutrient fluxes within syntrophic associations and obligate symbioses where exchanges can be extremely rapid. However, additional data, such as genomic potential, gene expression or other imaging modalities are often critical to deciphering the mechanisms underlying specific interactions, and researchers must keep sample preparation artefacts in mind. Here we focus on recent applications of nanoSIP, particularly where usedmore » to track exchanges of isotopically labelled molecules between organisms. Here, we highlight metabolic interactions within syntrophic consortia, carbon/nitrogen fluxes between phototrophs and their heterotrophic partners, and symbiont–host nutrient sharing.« less

Interactions of the Intestinal Epithelium with the Pathogen and the Indigenous Microbiota: A Three-Way Crosstalk

PubMed Central

Srikanth, C. V.; McCormick, Beth A.

2008-01-01

The mucosal surfaces of the gastrointestinal tract harbor a vast number of commensal microbiota that have coevolved with the host, and in addition display one of the most complex relationships with the host. This relationship affects several important aspects of the biology of the host including the synthesis of nutrients, protection against infection, and the development of the immune system. On the other hand, despite the existence of several lines of mucosal defense mechanisms, pathogenic organisms such as Shigella and Salmonella have evolved sophisticated virulence strategies for breaching these barriers. The constant challenge from these pathogens and the attempts by the host to counter them set up a dynamic equilibrium of cellular and molecular crosstalk. Even slight perturbations in this equilibrium may be detrimental to the host leading to severe bacterial infection or even autoimmune diseases like inflammatory bowel disease. Several experimental model systems, including germ-free mice and antibiotic-treated mice, have been used by various researchers to study this complex relationship. Although it is only the beginning, it promises to be an exciting era in the study of these host-microbe relationships. PMID:19259328

Potential applications of insect symbionts in biotechnology.

PubMed

Berasategui, Aileen; Shukla, Shantanu; Salem, Hassan; Kaltenpoth, Martin

2016-02-01

Symbiotic interactions between insects and microorganisms are widespread in nature and are often the source of ecological innovations. In addition to supplementing their host with essential nutrients, microbial symbionts can produce enzymes that help degrade their food source as well as small molecules that defend against pathogens, parasites, and predators. As such, the study of insect ecology and symbiosis represents an important source of chemical compounds and enzymes with potential biotechnological value. In addition, the knowledge on insect symbiosis can provide novel avenues for the control of agricultural pest insects and vectors of human diseases, through targeted manipulation of the symbionts or the host-symbiont associations. Here, we discuss different insect-microbe interactions that can be exploited for insect pest and human disease control, as well as in human medicine and industrial processes. Our aim is to raise awareness that insect symbionts can be interesting sources of biotechnological applications and that knowledge on insect ecology can guide targeted efforts to discover microorganisms of applied value.

Insights into teichoic acid biosynthesis by Bifidobacterium bifidum PRL2010.

PubMed

Colagiorgi, Angelo; Turroni, Francesca; Mancabelli, Leonardo; Serafini, Fausta; Secchi, Andrea; van Sinderen, Douwe; Ventura, Marco

2015-09-01

Bifidobacteria are colonizers of the human gut, where they are interacting with their host as well as with other members of the intestinal microbiota. Teichoic acids (TAs) have previously been shown to play an important role in modulating microbe-host interactions in the human gut. However, so far, there is a paucity of information regarding the presence of TAs in the cell envelope of bifidobacteria. In silico analyses targeting the chromosomes of all 48 (sub)species that currently represent the genus Bifidobacterium revealed the presence of genes responsible for TA biosynthesis, suggesting that bifidobacteria contain both wall TAs and lipoteichoic acids. Transcriptome analyses of the infant gut commensal Bifidobacterium bifidum PRL2010 highlighted that the transcription of the presumptive TA biosynthetic loci is modulated in response to environmental conditions reflecting those of the human gut. Furthermore, chemical characterization of TAs produced by PRL2010 indicates the presence of lipoteichoic acids. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Neisseria infection of rhesus macaques as a model to study colonization, transmission, persistence, and horizontal gene transfer.

PubMed

Weyand, Nathan J; Wertheimer, Anne M; Hobbs, Theodore R; Sisko, Jennifer L; Taku, Nyiawung A; Gregston, Lindsay D; Clary, Susan; Higashi, Dustin L; Biais, Nicolas; Brown, Lewis M; Planer, Shannon L; Legasse, Alfred W; Axthelm, Michael K; Wong, Scott W; So, Magdalene

2013-02-19

The strict tropism of many pathogens for man hampers the development of animal models that recapitulate important microbe-host interactions. We developed a rhesus macaque model for studying Neisseria-host interactions using Neisseria species indigenous to the animal. We report that Neisseria are common inhabitants of the rhesus macaque. Neisseria isolated from the rhesus macaque recolonize animals after laboratory passage, persist in the animals for at least 72 d, and are transmitted between animals. Neisseria are naturally competent and acquire genetic markers from each other in vivo, in the absence of selection, within 44 d after colonization. Neisseria macacae encodes orthologs of known or presumed virulence factors of human-adapted Neisseria, as well as current or candidate vaccine antigens. We conclude that the rhesus macaque model will allow studies of the molecular mechanisms of Neisseria colonization, transmission, persistence, and horizontal gene transfer. The model can potentially be developed further for preclinical testing of vaccine candidates.

Integrating Lung Physiology, Immunology, and Tuberculosis.

PubMed

Torrelles, Jordi B; Schlesinger, Larry S

2017-08-01

Lungs are directly exposed to the air, have enormous surface area, and enable gas exchange in air-breathing animals. They are constantly 'attacked' by microbes from both outside and inside and thus possess a unique, highly regulated local immune defense system which efficiently allows for microbial clearance while minimizing damaging inflammatory responses. As a prototypic host-adapted airborne pathogen, Mycobacterium tuberculosis traverses the lung and has several 'interaction points' (IPs) which it must overcome to cause infection. These interactions are critical, not only from a pathogenesis perspective but also in considering the effectiveness of therapies and vaccines in the lungs. Here we discuss emerging views on immunologic interactions occurring in the lungs for M. tuberculosis and their impact on infection and persistence. Copyright © 2017 Elsevier Ltd. All rights reserved.

Macrophage defense mechanisms against intracellular bacteria

PubMed Central

Weiss, Günter; Schaible, Ulrich E

2015-01-01

Macrophages and neutrophils play a decisive role in host responses to intracellular bacteria including the agent of tuberculosis (TB), Mycobacterium tuberculosis as they represent the forefront of innate immune defense against bacterial invaders. At the same time, these phagocytes are also primary targets of intracellular bacteria to be abused as host cells. Their efficacy to contain and eliminate intracellular M. tuberculosis decides whether a patient initially becomes infected or not. However, when the infection becomes chronic or even latent (as in the case of TB) despite development of specific immune activation, phagocytes have also important effector functions. Macrophages have evolved a myriad of defense strategies to combat infection with intracellular bacteria such as M. tuberculosis. These include induction of toxic anti-microbial effectors such as nitric oxide and reactive oxygen intermediates, the stimulation of microbe intoxication mechanisms via acidification or metal accumulation in the phagolysosome, the restriction of the microbe's access to essential nutrients such as iron, fatty acids, or amino acids, the production of anti-microbial peptides and cytokines, along with induction of autophagy and efferocytosis to eliminate the pathogen. On the other hand, M. tuberculosis, as a prime example of a well-adapted facultative intracellular bacterium, has learned during evolution to counter-balance the host's immune defense strategies to secure survival or multiplication within this otherwise hostile environment. This review provides an overview of innate immune defense of macrophages directed against intracellular bacteria with a focus on M. tuberculosis. Gaining more insights and knowledge into this complex network of host-pathogen interaction will identify novel target sites of intervention to successfully clear infection at a time of rapidly emerging multi-resistance of M. tuberculosis against conventional antibiotics. PMID:25703560

Amoeba host-Legionella synchronization of amino acid auxotrophy and its role in bacterial adaptation and pathogenic evolution.

PubMed

Price, Christopher T D; Richards, Ashley M; Von Dwingelo, Juanita E; Samara, Hala A; Abu Kwaik, Yousef

2014-02-01

Legionella pneumophila, the causative agent of Legionnaires' disease, invades and proliferates within a diverse range of free-living amoeba in the environment, but upon transmission to humans, the bacteria hijack alveolar macrophages. Intracellular proliferation of L. pneumophila in two evolutionarily distant hosts is facilitated by bacterial exploitation of conserved host processes that are targeted by bacterial protein effectors injected into the host cell. A key aspect of microbe-host interaction is microbial extraction of nutrients from the host, but understanding of this is still limited. AnkB functions as a nutritional virulence factor and promotes host proteasomal degradation of polyubiquitinated proteins generating gratuitous levels of limiting host cellular amino acids. Legionella pneumophila is auxotrophic for several amino acids including cysteine, which is a metabolically preferred source of carbon and energy during intracellular proliferation, but is limiting in both amoebae and humans. We propose that synchronization of bacterial amino acids auxotrophy with the host is a driving force in pathogenic evolution and nutritional adaptation of L. pneumophila and other intracellular bacteria to life within the host cell. Understanding microbial strategies of nutrient generation and acquisition in the host will provide novel antimicrobial strategies to disrupt pathogen access to essential sources of carbon and energy. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Potential roles for microbial endophytes in herbicide tolerance in plants.

PubMed

Tétard-Jones, Catherine; Edwards, Robert

2016-02-01

Herbicide tolerance in crops and weeds is considered to be monotrophic, i.e. determined by the relative susceptibility of the physiological process targeted and the plant's ability to metabolise and detoxify the agrochemical. A growing body of evidence now suggests that endophytes, microbes that inhabit plant tissues and provide a range of growth, health and defence enhancements, can contribute to other types of abiotic and biotic stress tolerance. The current evidence for herbicide tolerance being bitrophic, with both free-living and plant-associated endophytes contributing to tolerance in the host plant, has been reviewed. We propose that endophytes can directly contribute to herbicide detoxification through their ability to metabolise xenobiotics. In addition, we explore the paradigm that microbes can 'prime' resistance mechanisms in plants such that they enhance herbicide tolerance by inducing the host's stress responses to withstand the downstream toxicity caused by herbicides. This latter mechanism has the potential to contribute to the growth of non-target-site-based herbicide resistance in weeds. Microbial endophytes already contribute to herbicide detoxification in planta, and there is now significant scope to extend these interactions using synthetic biology approaches to engineer new chemical tolerance traits into crops via microbial engineering. © 2015 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Microbial Communities and Bioactive Compounds in Marine Sponges of the Family Irciniidae—A Review

PubMed Central

Hardoim, Cristiane C. P.; Costa, Rodrigo

2014-01-01

Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species—the vast majority of which are difficult to cultivate—and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed. PMID:25272328

An Introductory "How-to" Guide for Incorporating Microbiome Research into Integrative and Comparative Biology.

PubMed

Kohl, Kevin D

2017-10-01

Research on host-associated microbial communities has grown rapidly. Despite the great body of work, inclusion of microbiota-related questions into integrative and comparative biology is still lagging behind other disciplines. The purpose of this paper is to offer an introduction into the basic tools and techniques of host-microbe research. Specifically, what considerations should be made before embarking on such projects (types of samples, types of controls)? How is microbiome data analyzed and integrated with data measured from the hosts? How can researchers experimentally manipulate the microbiome? With this information, integrative and comparative biologists should be able to include host-microbe studies into their research and push the boundaries of both fields. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Chemosensation of Bacterial Secondary Metabolites Modulates Neuroendocrine Signaling and Behavior of C. elegans

PubMed Central

Meisel, Joshua D.; Panda, Oishika; Mahanti, Parag; Schroeder, Frank C.; Kim, Dennis H.

2014-01-01

Summary Discrimination among pathogenic and beneficial microbes is essential for host organism immunity and homeostasis. Here, we show that chemosensory detection of two secondary metabolites produced by Pseudomonas aeruginosa modulates a neuroendocrine signaling pathway that promotes avoidance behavior in the simple animal host Caenorhabditis elegans. Secondary metabolites phenazine-1-carboxamide and pyochelin activate a G protein-signaling pathway in the ASJ chemosensory neuron pair that induces expression of the neuromodulator DAF-7/TGF-β. DAF-7, in turn, activates a canonical TGF-β signaling pathway in adjacent interneurons to modulate aerotaxis behavior and promote avoidance of pathogenic P. aeruginosa. Our data provide a chemical, genetic, and neuronal basis for how the behavior and physiology of a simple animal host can be modified by the microbial environment, and suggest that secondary metabolites produced by microbes may provide environmental cues that contribute to pathogen recognition and host survival. PMID:25303524

What’s the Damage? The Impact of Pathogens on Pathways that Maintain Host Genome Integrity

PubMed Central

Weitzman, Matthew D.; Weitzman, Jonathan B.

2014-01-01

Maintaining genome integrity and transmission of intact genomes is critical for cellular, organismal, and species survival. Cells can detect damaged DNA, activate checkpoints, and either enable DNA repair or trigger apoptosis to eliminate the damaged cell. Aberrations in these mechanisms lead to somatic mutations and genetic instability, which are hallmarks of cancer. Considering the long history of host-microbe coevolution, an impact of microbial infection on host genome integrity is not unexpected, and emerging links between microbial infections and oncogenesis further reinforce this idea. In this review, we compare strategies employed by viruses, bacteria, and parasites to alter, subvert, or otherwise manipulate host DNA damage and repair pathways. We highlight how microbes contribute to tumorigenesis by directly inducing DNA damage, inactivating checkpoint controls, or manipulating repair processes. We also discuss indirect effects resulting from inflammatory responses, changes in cellular metabolism, nuclear architecture, and epigenome integrity, and the associated evolutionary tradeoffs. PMID:24629335

Diversification of Type VI Secretion System Toxins Reveals Ancient Antagonism among Bee Gut Microbes.

PubMed

Steele, Margaret I; Kwong, Waldan K; Whiteley, Marvin; Moran, Nancy A

2017-12-12

Microbial communities are shaped by interactions among their constituent members. Some Gram-negative bacteria employ type VI secretion systems (T6SSs) to inject protein toxins into neighboring cells. These interactions have been theorized to affect the composition of host-associated microbiomes, but the role of T6SSs in the evolution of gut communities is not well understood. We report the discovery of two T6SSs and numerous T6SS-associated Rhs toxins within the gut bacteria of honey bees and bumble bees. We sequenced the genomes of 28 strains of Snodgrassella alvi , a characteristic bee gut microbe, and found tremendous variability in their Rhs toxin complements: altogether, these strains appear to encode hundreds of unique toxins. Some toxins are shared with Gilliamella apicola , a coresident gut symbiont, implicating horizontal gene transfer as a source of toxin diversity in the bee gut. We use data from a transposon mutagenesis screen to identify toxins with antibacterial function in the bee gut and validate the function and specificity of a subset of these toxin and immunity genes in Escherichia coli Using transcriptome sequencing, we demonstrate that S. alvi T6SSs and associated toxins are upregulated in the gut environment. We find that S. alvi Rhs loci have a conserved architecture, consistent with the C-terminal displacement model of toxin diversification, with Rhs toxins, toxin fragments, and cognate immunity genes that are expressed and confer strong fitness effects in vivo Our findings of T6SS activity and Rhs toxin diversity suggest that T6SS-mediated competition may be an important driver of coevolution within the bee gut microbiota. IMPORTANCE The structure and composition of host-associated bacterial communities are of broad interest, because these communities affect host health. Bees have a simple, conserved gut microbiota, which provides an opportunity to explore interactions between species that have coevolved within their host over millions of years. This study examined the role of type VI secretion systems (T6SSs)-protein complexes used to deliver toxic proteins into bacterial competitors-within the bee gut microbiota. We identified two T6SSs and diverse T6SS-associated toxins in bacterial strains from bees. Expression of these genes is increased in bacteria in the bee gut, and toxin and immunity genes demonstrate antibacterial and protective functions, respectively, when expressed in Escherichia coli Our results suggest that coevolution among bacterial species in the bee gut has favored toxin diversification and maintenance of T6SS machinery, and demonstrate the importance of antagonistic interactions within host-associated microbial communities. Copyright © 2017 Steele et al.

Action on the Surface: Entomopathogenic Fungi versus the Insect Cuticle.

PubMed

Ortiz-Urquiza, Almudena; Keyhani, Nemat O

2013-07-16

Infections mediated by broad host range entomopathogenic fungi represent seminal observations that led to one of the first germ theories of disease and are a classic example of a co-evolutionary arms race between a pathogen and target hosts. These fungi are able to parasitize susceptible hosts via direct penetration of the cuticle with the initial and potentially determining interaction occurring between the fungal spore and the insect epicuticle. Entomogenous fungi have evolved mechanisms for adhesion and recognition of host surface cues that help direct an adaptive response that includes the production of: (a) hydrolytic, assimilatory, and/or detoxifying enzymes including lipase/esterases, catalases, cytochrome P450s, proteases, and chitinases; (b) specialized infectious structures, e.g., appressoria or penetrant tubes; and (c) secondary and other metabolites that facilitate infection. Aside from immune responses, insects have evolved a number of mechanisms to keep pathogens at bay that include: (a) the production of (epi) cuticular antimicrobial lipids, proteins, and metabolites; (b) shedding of the cuticle during development; and (c) behavioral-environmental adaptations such as induced fever, burrowing, and grooming, as well as potentially enlisting the help of other microbes, all intended to stop the pathogen before it can breach the cuticle. Virulence and host-defense can be considered to be under constant reciprocal selective pressure, and the action on the surface likely contributes to phenomena such as strain variation, host range, and the increased virulence often noted once a (low) virulent strain is "passaged" through an insect host. Since the cuticle represents the first point of contact and barrier between the fungus and the insect, the "action on the surface" may represent the defining interactions that ultimately can lead either to successful mycosis by the pathogen or successful defense by the host. Knowledge concerning the molecular mechanisms underlying this interaction can shed light on the ecology and evolution of virulence and can be used for rational design strategies at increasing the effectiveness of entomopathogenic fungi for pest control in field applications.

Salivary Biomarkers for Caries Risk Assessment

PubMed Central

Guo, Lihong; Shi, Wenyuan

2013-01-01

Saliva contains various microbes and host biological components that could be used for caries risk assessment. This review focuses on the research topics that connect dental caries with saliva, including both the microbial and host components within saliva. PMID:23505756

A radioisotope based methodology for plant-fungal interactions in the rhizosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weisenberger, A. G.; Bonito, G.; Lee, S.

In plant ecophysiology research there is interest in studying the biology of the rhizosphere because of its importance in plant nutrient-interactions. The rhizosphere is the zone of soil surrounding a plant's root system where microbes (such as fungi) are influenced by the root and the roots by the microbes. We are investigating a methodology for imaging the distribution of molecular compounds of interest in the rhizosphere without disturbing the root or soil habitat. Our intention is to develop a single photon emission computed tomography (SPECT) system (PhytoSPECT) to image the bio-distribution of fungi in association with a host plant's roots.more » The technique we are exploring makes use of radioactive isotopes as tracers to label molecules that bind to fungal-specific compounds of interest and to image the fungi distribution in the plant and/or soil. We report on initial experiments designed to test the ability of fungal-specific compounds labeled with an iodine radioisotope that binds to chitin monomers (N-acetylglucosamine). Chitin is a compound not found in roots but in fungal cell walls. We will test the ability to label the compound with radioactive isotopes of iodine ({sup 125}I, and {sup 123}I).« less

Surveillance for microbes and range expansion in house sparrows

PubMed Central

Martin, Lynn B.; Coon, Courtney A. C.; Liebl, Andrea L.; Schrey, Aaron W.

2014-01-01

Interactions between hosts and parasites influence the success of host introductions and range expansions post-introduction. However, the physiological mechanisms mediating these outcomes are little known. In some vertebrates, variation in the regulation of inflammation has been implicated, perhaps because inflammation imparts excessive costs, including high resource demands and collateral damage upon encounter with novel parasites. Here, we tested the hypothesis that variation in the regulation of inflammation contributed to the spread of house sparrows (Passer domesticus) across Kenya, one of the world's most recent invasions of this species. Specifically, we asked whether inflammatory gene expression declines with population age (i.e. distance from Mombasa (dfM), the site of introduction around 1950). We compared expression of two microbe surveillance molecules (Toll-like receptors, TLRs-2 and 4) and a proinflammatory cytokine (interleukin-6, IL-6) before and after an injection of an immunogenic component of Gram-negative bacteria (lipopolysaccharide, LPS) among six sparrow populations. We then used a best-subset model selection approach to determine whether population age (dfM) or other factors (e.g. malaria or coccidian infection, sparrow density or genetic group membership) best-explained gene expression. For baseline expression of TLR-2 and TLR-4, population age tended to be the best predictor with expression decreasing with population age, although other factors were also important. Induced expression of TLRs was affected by LPS treatment alone. For induced IL-6, only LPS treatment reliably predicted expression; baseline expression was not explained by any factor. These data suggest that changes in microbe surveillance, more so than downstream control of inflammation via cytokines, might have been important to the house sparrow invasion of Kenya. PMID:24258722

Glycoconjugates in Host-Helminth Interactions

PubMed Central

Prasanphanich, Nina Salinger; Mickum, Megan L.; Heimburg-Molinaro, Jamie; Cummings, Richard D.

2013-01-01

Helminths are multicellular parasitic worms that comprise a major class of human pathogens and cause an immense amount of suffering worldwide. Helminths possess an abundance of complex and unique glycoconjugates that interact with both the innate and adaptive arms of immunity in definitive and intermediate hosts. These glycoconjugates represent a major untapped reservoir of immunomodulatory compounds, which have the potential to treat autoimmune and inflammatory disorders, and antigenic glycans, which could be exploited as vaccines and diagnostics. This review will survey current knowledge of the interactions between helminth glycans and host immunity and highlight the gaps in our understanding which are relevant to advancing therapeutics, vaccine development, and diagnostics. PMID:24009607

Plants versus Fungi and Oomycetes: Pathogenesis, Defense and Counter-Defense in the Proteomics Era

PubMed Central

El Hadrami, Abdelbasset; El-Bebany, Ahmed F.; Yao, Zhen; Adam, Lorne R.; El Hadrami, Ismailx; Daayf, Fouad

2012-01-01

Plant-fungi and plant-oomycete interactions have been studied at the proteomic level for many decades. However, it is only in the last few years, with the development of new approaches, combined with bioinformatics data mining tools, gel staining, and analytical instruments, such as 2D-PAGE/nanoflow-LC-MS/MS, that proteomic approaches thrived. They allow screening and analysis, at the sub-cellular level, of peptides and proteins resulting from plants, pathogens, and their interactions. They also highlight post-translational modifications to proteins, e.g., glycosylation, phosphorylation or cleavage. However, many challenges are encountered during in planta studies aimed at stressing details of host defenses and fungal and oomycete pathogenicity determinants during interactions. Dissecting the mechanisms of such host-pathogen systems, including pathogen counter-defenses, will ensure a step ahead towards understanding current outcomes of interactions from a co-evolutionary point of view, and eventually move a step forward in building more durable strategies for management of diseases caused by fungi and oomycetes. Unraveling intricacies of more complex proteomic interactions that involve additional microbes, i.e., PGPRs and symbiotic fungi, which strengthen plant defenses will generate valuable information on how pathosystems actually function in nature, and thereby provide clues to solving disease problems that engender major losses in crops every year. PMID:22837691

Plants versus fungi and oomycetes: pathogenesis, defense and counter-defense in the proteomics era.

PubMed

El Hadrami, Abdelbasset; El-Bebany, Ahmed F; Yao, Zhen; Adam, Lorne R; El Hadrami, Ismailx; Daayf, Fouad

2012-01-01

Plant-fungi and plant-oomycete interactions have been studied at the proteomic level for many decades. However, it is only in the last few years, with the development of new approaches, combined with bioinformatics data mining tools, gel staining, and analytical instruments, such as 2D-PAGE/nanoflow-LC-MS/MS, that proteomic approaches thrived. They allow screening and analysis, at the sub-cellular level, of peptides and proteins resulting from plants, pathogens, and their interactions. They also highlight post-translational modifications to proteins, e.g., glycosylation, phosphorylation or cleavage. However, many challenges are encountered during in planta studies aimed at stressing details of host defenses and fungal and oomycete pathogenicity determinants during interactions. Dissecting the mechanisms of such host-pathogen systems, including pathogen counter-defenses, will ensure a step ahead towards understanding current outcomes of interactions from a co-evolutionary point of view, and eventually move a step forward in building more durable strategies for management of diseases caused by fungi and oomycetes. Unraveling intricacies of more complex proteomic interactions that involve additional microbes, i.e., PGPRs and symbiotic fungi, which strengthen plant defenses will generate valuable information on how pathosystems actually function in nature, and thereby provide clues to solving disease problems that engender major losses in crops every year.

Host plant associated enhancement of immunity and survival in virus infected caterpillars.

PubMed

Smilanich, Angela M; Langus, Tara C; Doan, Lydia; Dyer, Lee A; Harrison, Joshua G; Hsueh, Jennifer; Teglas, Mike B

2018-01-01

Understanding the interaction between host plant chemistry, the immune response, and insect pathogens can shed light on host plant use by insect herbivores. In this study, we focused on how interactions between the insect immune response and plant secondary metabolites affect the response to a viral pathogen. Based upon prior research, we asked whether the buckeye caterpillar, Junonia coenia (Nymphalidae), which specializes on plants containing iridoid glycosides (IGs), is less able to resist the pathogenic effects of a densovirus infection when feeding on plants with high concentrations of IGs. In a fully factorial design, individuals were randomly assigned to three treatments, each of which had two levels: (1) exposed to the densovirus versus control, (2) placed on a plant species with high concentrations of IGs (Plantago lanceolata, Plantaginaceae) versus low concentrations of IGs (P. major), and (3) control versus surface sterilized to exclude surface microbes that may contribute to viral resistance. We measured phenoloxidase (PO) activity, hemocyte counts, and gut bacterial diversity (16S ribosomal RNA) during the fourth larval instar, as well as development time, pupal weight, and survival to adult. Individuals infected with the virus were immune-suppressed (as measured by PO response and hemocyte count) and developed significantly faster than virus-free individuals. Contrary to our predictions,mortality was significantly less for virus challengedindividuals reared on the high IG plant compared to the low IG plant.This suggests that plant secondary metabolites can influence survival from viral infection and may be associated with activation of PO. Removing egg microbes did not affect the immune response or survival of the larvae. In summary, these results suggest that plant secondary metabolites are important for survival against a viral pathogen. Even though the PO response was better on the high IG plant, the extent to which this result contributes to survival against the virus needs further investigation. Copyright © 2017 Elsevier Inc. All rights reserved.

Emerging Role of D-Amino Acid Metabolism in the Innate Defense.

PubMed

Sasabe, Jumpei; Suzuki, Masataka

2018-01-01

Mammalian innate and adaptive immune systems use the pattern recognition receptors, such as toll-like receptors, to detect conserved bacterial and viral components. Bacteria synthesize diverse D-amino acids while eukaryotes and archaea generally produce two D-amino acids, raising the possibility that many of bacterial D-amino acids are bacteria-specific metabolites. Although D-amino acids have not been identified to bind to any known pattern recognition receptors, D-amino acids are enantioselectively recognized by some other receptors and enzymes including a flavoenzyme D-amino acid oxidase (DAO) in mammals. At host-microbe interfaces in the neutrophils and intestinal mucosa, DAO catalyzes oxidation of bacterial D-amino acids, such as D-alanine, and generates H 2 O 2 , which is linked to antimicrobial activity. Intestinal DAO also modifies the composition of microbiota through modulation of growth for some bacteria that are dependent on host nutrition. Furthermore, regulation and recognition of D-amino acids in mammals have additional meanings at various host-microbe interfaces; D-phenylalanine and D-tryptophan regulate chemotaxis of neutrophils through a G-coupled protein receptor, D-serine has a bacteriostatic role in the urinary tract, D-phenylalanine and D-leucine inhibit innate immunity through the sweet taste receptor in the upper airway, and D-tryptophan modulates immune tolerance in the lower airway. This mini-review highlights recent evidence supporting the hypothesis that D-amino acids are utilized as inter-kingdom communication at host-microbe interface to modulate bacterial colonization and host defense.

THE HUMAN MICROBIOME AND PROBIOTICS: IMPLICATIONS FOR PEDIATRICS

PubMed Central

Hsieh, Michael H.; Versalovic, James

2010-01-01

The “human super-organism” refers to the human body and the massive numbers of microbes which dwell within us and on the skin surface. Despite the large numbers of microbes co-existing within the human body, humans including infants and children achieve a physiologic state of equilibrium known as health in the context of this microbial world. These key concepts suggest that many individual members of the human microbiome, including bacterial and fungal species, confer different benefits on the human host. Probiotics, or beneficial microbes, may modulate immune responses, provide key nutrients, or suppress the proliferation and virulence of infectious agents. The human microbiome is in fact dynamic and often in flux, which may be indicative of the continuous interplay among commensal microbes, pathogens, and the human host. In this article we review the state-of-the-art regarding probiotics applications to prevent or treat diseases of the pediatric gastrointestinal and genitourinary systems. Additionally, probiotics may regulate local and systemic immunity, thereby reducing allergic disease severity and susceptibilities of infants and children to allergies and atopic diseases. In summary, beneficial microbes offer promising alternatives for new strategies in therapeutic microbiology with implications for different subspecialties within pediatrics. Instead of simply trying to counteract microbes with vaccines and antibiotics, a new field of medical microbiology is emerging that strives to translate human microbiome research into new probiotics strategies for promotion of health and prevention of disease in children. PMID:18992706

Cross-species Virus-host Protein-Protein Interactions Inhibiting Innate Immunity

DTIC Science & Technology

2016-07-01

Distribution A: Approved for public release; distribution is unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT The single- stranded negative sense RNA...focused upon members of three negative-sense single- stranded RNA (ssRNA(-)) virus families with know or suspected histories of changes in host-species...however, the N and C-termini are disordered extended strands . In contrast, our covariance analysis mapped hotspots for protein interaction to the

Host behaviour–parasite feedback: an essential link between animal behaviour and disease ecology

PubMed Central

Archie, Elizabeth A.; Craft, Meggan E.; Hawley, Dana M.; Martin, Lynn B.; Moore, Janice; White, Lauren

2016-01-01

Animal behaviour and the ecology and evolution of parasites are inextricably linked. For this reason, animal behaviourists and disease ecologists have been interested in the intersection of their respective fields for decades. Despite this interest, most research at the behaviour–disease interface focuses either on how host behaviour affects parasites or how parasites affect behaviour, with little overlap between the two. Yet, the majority of interactions between hosts and parasites are probably reciprocal, such that host behaviour feeds back on parasites and vice versa. Explicitly considering these feedbacks is essential for understanding the complex connections between animal behaviour and parasite ecology and evolution. To illustrate this point, we discuss how host behaviour–parasite feedbacks might operate and explore the consequences of feedback for studies of animal behaviour and parasites. For example, ignoring the feedback of host social structure on parasite dynamics can limit the accuracy of predictions about parasite spread. Likewise, considering feedback in studies of parasites and animal personalities may provide unique insight about the maintenance of variation in personality types. Finally, applying the feedback concept to links between host behaviour and beneficial, rather than pathogenic, microbes may shed new light on transitions between mutualism and parasitism. More generally, accounting for host behaviour–parasite feedbacks can help identify critical gaps in our understanding of how key host behaviours and parasite traits evolve and are maintained. PMID:27053751

Host behaviour-parasite feedback: an essential link between animal behaviour and disease ecology.

PubMed

Ezenwa, Vanessa O; Archie, Elizabeth A; Craft, Meggan E; Hawley, Dana M; Martin, Lynn B; Moore, Janice; White, Lauren

2016-04-13

Animal behaviour and the ecology and evolution of parasites are inextricably linked. For this reason, animal behaviourists and disease ecologists have been interested in the intersection of their respective fields for decades. Despite this interest, most research at the behaviour-disease interface focuses either on how host behaviour affects parasites or how parasites affect behaviour, with little overlap between the two. Yet, the majority of interactions between hosts and parasites are probably reciprocal, such that host behaviour feeds back on parasites and vice versa. Explicitly considering these feedbacks is essential for understanding the complex connections between animal behaviour and parasite ecology and evolution. To illustrate this point, we discuss how host behaviour-parasite feedbacks might operate and explore the consequences of feedback for studies of animal behaviour and parasites. For example, ignoring the feedback of host social structure on parasite dynamics can limit the accuracy of predictions about parasite spread. Likewise, considering feedback in studies of parasites and animal personalities may provide unique insight about the maintenance of variation in personality types. Finally, applying the feedback concept to links between host behaviour and beneficial, rather than pathogenic, microbes may shed new light on transitions between mutualism and parasitism. More generally, accounting for host behaviour-parasite feedbacks can help identify critical gaps in our understanding of how key host behaviours and parasite traits evolve and are maintained. © 2016 The Author(s).

A conserved chemical dialog of mutualism: lessons from squid and vibrio

PubMed Central

Schwartzman, Julia A.; Ruby, Edward G.

2015-01-01

Microorganisms shape, and are shaped by, their environment. In host-microbe associations, this environment is defined by tissue chemistry, which reflects local and organism-wide physiology, as well as inflammatory status. We review how, in the squid-vibrio mutualism, both partners shape tissue chemistry, revealing common themes governing tissue homeostasis in animal-microbe associations. PMID:26384815

The Fungal Mycobiome and Its Interaction with Gut Bacteria in the Host

PubMed Central

Sam, Qi Hui; Chang, Matthew Wook; Chai, Louis Yi Ann

2017-01-01

The advent of sequencing technology has endowed us with the capacity to study microbes constituting the human commensal community that were previously non-culturable. Much of the initial works have concentrated on the bacterial flora constituting the gut microbiome, since specimens are readily accessible in health and disease. Less, however, is understood of the “silent population”—the fungal species, also known as the mycobiome. Living in symbiosis with bacteria as commensals in our body, it is perceivable that the mycobiome exerts an inadvertent influence on the microbiome. We review here the recent knowledge gained from study of the interaction between the mycobiome and microbiome in health and disease susceptibility, immunity, and consequences from antimicrobial treatment. PMID:28165395

Microbiome and Malignancy

PubMed Central

Plottel, Claudia S.; Blaser, Martin J.

2011-01-01

Current knowledge is insufficient to explain why only a proportion of individuals exposed to environmental carcinogens or carrying a genetic predisposition to cancer develop disease. Clearly, other factors must be important and one such element that has recently received attention is the human microbiome, the residential microbes including Bacteria, Archaea, Eukaryotes, and viruses that colonize humans. Here, we review principles and paradigms of microbiome-related malignancy, as illustrated by three specific microbial-host interactions. We review the effects of the microbiota on local and adjacent-neoplasia, present the estrobolome model of distant effects, and discuss the complex interactions with a latent virus leading to malignancy. These are separate facets of a complex biology interfacing all the microbial species we harbor from birth onward toward early reproductive success and eventual senescence. PMID:22018233

Receptor Kinases in Plant-Pathogen Interactions: More Than Pattern Recognition[OPEN

PubMed Central

2017-01-01

Receptor-like kinases (RLKs) and Receptor-like proteins (RLPs) play crucial roles in plant immunity, growth, and development. Plants deploy a large number of RLKs and RLPs as pattern recognition receptors (PRRs) that detect microbe- and host-derived molecular patterns as the first layer of inducible defense. Recent advances have uncovered novel PRRs, their corresponding ligands, and mechanisms underlying PRR activation and signaling. In general, PRRs associate with other RLKs and function as part of multiprotein immune complexes at the cell surface. Innovative strategies have emerged for the rapid identification of microbial patterns and their cognate PRRs. Successful pathogens can evade or block host recognition by secreting effector proteins to “hide” microbial patterns or inhibit PRR-mediated signaling. Furthermore, newly identified pathogen effectors have been shown to manipulate RLKs controlling growth and development by mimicking peptide hormones of host plants. The ongoing studies illustrate the importance of diverse plant RLKs in plant disease resistance and microbial pathogenesis. PMID:28302675

Selective Imaging of Gram-Negative and Gram-Positive Microbiotas in the Mouse Gut.

PubMed

Wang, Wei; Zhu, Yuntao; Chen, Xing

2017-08-01

The diverse gut microbial communities are crucial for host health. How the interactions between microbial communities and between host and microbes influence the host, however, is not well understood. To facilitate gut microbiota research, selective imaging of specific groups of microbiotas in the gut is of great utility but remains technically challenging. Here we present a chemical approach that enables selective imaging of Gram-negative and Gram-positive microbiotas in the mouse gut by exploiting their distinctive cell wall components. Cell-selective labeling is achieved by the combined use of metabolic labeling of Gram-negative bacterial lipopolysaccharides with a clickable azidosugar and direct labeling of Gram-positive bacteria with a vancomycin-derivatized fluorescent probe. We demonstrated this strategy by two-color fluorescence imaging of Gram-negative and Gram-positive gut microbiotas in the mouse intestines. This chemical method should be broadly applicable to different gut microbiota research fields and other bacterial communities studied in microbiology.