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Sample records for microbial natural products

  1. Bioactive natural products from novel microbial sources.

    PubMed

    Challinor, Victoria L; Bode, Helge B

    2015-09-01

    Despite the importance of microbial natural products for human health, only a few bacterial genera have been mined for the new natural products needed to overcome the urgent threat of antibiotic resistance. This is surprising, given that genome sequencing projects have revealed that the capability to produce natural products is not a rare feature among bacteria. Even the bacteria occurring in the human microbiome produce potent antibiotics, and thus potentially are an untapped resource for novel compounds, potentially with new activities. This review highlights examples of bacteria that should be considered new sources of natural products, including anaerobes, pathogens, and symbionts of humans, insects, and nematodes. Exploitation of these producer strains, combined with advances in modern natural product research methodology, has the potential to open the way for a new golden age of microbial therapeutics.

  2. Natural products: Hunting microbial metabolites

    NASA Astrophysics Data System (ADS)

    Schmidt, Eric W.

    2015-05-01

    Symbiotic bacteria synthesize many specialized small molecules; however, establishing the role these chemicals play in human health and disease has been difficult. Now, the chemical structure and mechanism of the Escherichia coli product colibactin provides insight into the link between this secondary metabolite and colorectal cancer.

  3. Microbial production of natural raspberry ketone.

    PubMed

    Beekwilder, Jules; van der Meer, Ingrid M; Sibbesen, Ole; Broekgaarden, Mans; Qvist, Ingmar; Mikkelsen, Joern D; Hall, Robert D

    2007-10-01

    Raspberry ketone is an important compound for the flavour industry. It is frequently used in products such as soft drinks, sweets, puddings and ice creams. The compound can be produced by organic synthesis. Demand for "natural" raspberry ketone is growing considerably. However, this product is extremely expensive. Consequently, there is a remaining desire to better understand how raspberry ketone is synthesized in vivo, and which genes and enzymes are involved. With this information we will then be in a better position to design alternative production strategies such as microbial fermentation. This article focuses on the identification and application of genes potentially linked to raspberry ketone synthesis. We have isolated candidate genes from both raspberry and other plants, and these have been introduced into bacterial and yeast expression systems. Conditions have been determined that result in significant levels of raspberry ketone, up to 5 mg/L. These results therefore lay a strong foundation for a potentially renewable source of "natural" flavour compounds making use of plant genes.

  4. Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities

    PubMed Central

    Milshteyn, Aleksandr; Schneider, Jessica S.; Brady, Sean F.

    2014-01-01

    Summary Microbial-derived natural products provide the foundation for most of the chemotherapeutic arsenal available to contemporary medicine. In the face of a dwindling pipeline of new lead structures identified by traditional culturing techniques and an increasing need for new therapeutics, surveys of microbial biosynthetic diversity across environmental metabiomes have revealed enormous reservoirs of as yet untapped natural products chemistry. In this review we touch on the historical context of microbial natural product discovery and discuss innovations and technological advances that are facilitating culture-dependent and culture-independent access to new chemistry from environmental microbiomes with the goal of re-invigorating the small molecule therapeutics discovery pipeline. We highlight the successful strategies that have emerged and some of the challenges that must be overcome to enable the development of high-throughput methods for natural product discovery from complex microbial communities. PMID:25237864

  5. Microbial genomics for the improvement of natural product discovery.

    PubMed

    Van Lanen, Steven G; Shen, Ben

    2006-06-01

    The quest for the discovery of novel natural products has entered a new chapter with the enormous wealth of genetic data that is now available. This information has been exploited by using whole-genome sequence mining to uncover cryptic pathways, or biosynthetic pathways for previously undetected metabolites. Alternatively, using known paradigms for secondary metabolite biosynthesis, genetic information has been 'fished out' of DNA libraries resulting in the discovery of new natural products and isolation of gene clusters for known metabolites. Novel natural products have been discovered by expressing genetic data from uncultured organisms or difficult-to-manipulate strains in heterologous hosts. Furthermore, improvements in heterologous expression have not only helped to identify gene clusters but have also made it easier to manipulate these genes in order to generate new compounds. Finally, and perhaps the most crucial aspect of the efficient and prosperous use of the abundance of genetic information, novel enzyme chemistry continues to be discovered, which has aided our understanding of how natural products are biosynthesized de novo, and enabled us to rework the current paradigms for natural product biosynthesis.

  6. Systematics-guided bioprospecting for bioactive microbial natural products.

    PubMed

    Liu, Xueting; Bolla, Krishna; Ashforth, Elizabeth Jane; Zhuo, Ying; Gao, Hong; Huang, Pei; Stanley, Sarah A; Hung, Deborah T; Zhang, Lixin

    2012-01-01

    Advances in the taxonomic characterization of microorganisms have accelerated the rate at which new producers of natural products can be understood in relation to known organisms. Yet for many reasons, chemical efforts to characterize new compounds from new microbes have not kept pace with taxonomic advances. That there exists an ever-widening gap between the biological versus chemical characterization of new microorganisms creates tremendous opportunity for the discovery of novel natural products through the calculated selection and study of organisms from unique, untapped, ecological niches. A systematics-guided bioprospecting, including the construction of high quality libraries of marine microbes and their crude extracts, investigation of bioactive compounds, and increasing the active compounds by precision engineering, has become an efficient approach to drive drug leads discovery. This review outlines the recent advances in these issues and shares our experiences on anti-infectious drug discovery and improvement of avermectins production as well.

  7. Discovery of New Compounds Active against Plasmodium falciparum by High Throughput Screening of Microbial Natural Products.

    PubMed

    Pérez-Moreno, Guiomar; Cantizani, Juan; Sánchez-Carrasco, Paula; Ruiz-Pérez, Luis Miguel; Martín, Jesús; El Aouad, Noureddine; Pérez-Victoria, Ignacio; Tormo, José Rubén; González-Menendez, Víctor; González, Ignacio; de Pedro, Nuria; Reyes, Fernando; Genilloud, Olga; Vicente, Francisca; González-Pacanowska, Dolores

    2016-01-01

    Due to the low structural diversity within the set of antimalarial drugs currently available in the clinic and the increasing number of cases of resistance, there is an urgent need to find new compounds with novel modes of action to treat the disease. Microbial natural products are characterized by their large diversity provided in terms of the chemical complexity of the compounds and the novelty of structures. Microbial natural products extracts have been underexplored in the search for new antiparasitic drugs and even more so in the discovery of new antimalarials. Our objective was to find new druggable natural products with antimalarial properties from the MEDINA natural products collection, one of the largest natural product libraries harboring more than 130,000 microbial extracts. In this work, we describe the optimization process and the results of a phenotypic high throughput screen (HTS) based on measurements of Plasmodium lactate dehydrogenase. A subset of more than 20,000 extracts from the MEDINA microbial products collection has been explored, leading to the discovery of 3 new compounds with antimalarial activity. In addition, we report on the novel antiplasmodial activity of 4 previously described natural products.

  8. [Strategies on the construction of high-quality microbial natural product library--a review].

    PubMed

    Bian, Jiang; Song, Fuhang; Zhang, Lixin

    2008-08-01

    The microbial secondary metabolites are always the main source of the natural drugs. The historical paradigm of the deep ocean as a biological 'desert' has shifted to one of a 'rainforest' owing to the isolation of many novel microbes and their associated bioactive compounds. A high quality microbial and its natural product library are crucial for successful drug and other screenings. However, how to build up the library efficiently is still faced with many bottlenecks. To overcome the difficulties and limitations, we reviewed the following strategies: (1) diversifying microbial sources and dereplication; (2) diversifying gene sources and dereplication; (3) diversifying microbial metabolite sources and dereplication; (4) novel methods and technologies for bioactive secondary metabolites, especially the high-throughput synergy screening for multi-target drugs. Bioactive compounds isolated using the above chemical microbiology strategies have not only shown importance in biotechnological and pharmaceutical applications but also increased our understanding of the diversity of microbe, ecosystem functions and the exploitable biology.

  9. The historical delivery of antibiotics from microbial natural products--can history repeat?

    PubMed

    Peláez, Fernando

    2006-03-30

    Microbial natural products are the origin of most of the antibiotics on the market today. However, research in antibiotics and natural products has declined significantly during the last decade as a consequence of diverse factors, among which the lack of interest of industry in the field and the strong competition from collections of synthetic compounds as source of drug leads. As a consequence, there is an alarming scarcity of new antibiotic classes in the pipelines of the pharmaceutical industry. Still, microbial natural products remain the most promising source of novel antibiotics, although new approaches are required to improve the efficiency of the discovery process. The impact of microbial biodiversity, the influence of growth conditions on the production of secondary metabolites, the choice of the best approach at the screening step and the challenges faced during the isolation and identification of the active compounds are examined in this review as the critical factors contributing to success in the effort of antibiotic discovery from microbial natural products.

  10. Microbial biotransformation as a tool for drug development based on natural products from mevalonic acid pathway: A review

    PubMed Central

    Hegazy, Mohamed-Elamir F.; Mohamed, Tarik A.; ElShamy, Abdelsamed I.; Mohamed, Abou-El-Hamd H.; Mahalel, Usama A.; Reda, Eman H.; Shaheen, Alaa M.; Tawfik, Wafaa A.; Shahat, Abdelaaty A.; Shams, Khalid A.; Abdel-Azim, Nahla S.; Hammouda, Fayza M.

    2014-01-01

    Natural products are structurally and biologically interesting metabolites, but they have been isolated in minute amounts. The syntheses of such natural products help in obtaining them in bulk amounts. The recognition of microbial biotransformation as important manufacturing tool has increased in chemical and pharmaceutical industries. In recent years, microbial transformation is increasing significantly from limited interest into highly active area in green chemistry including preparation of pharmaceutical products. This is the first review published on the usage of microbial biocatalysts for some natural product classes and natural product drugs. PMID:25685541

  11. Bioprospecting microbial natural product libraries from the marine environment for drug discovery.

    PubMed

    Liu, Xiangyang; Ashforth, Elizabeth; Ren, Biao; Song, Fuhang; Dai, Huanqin; Liu, Mei; Wang, Jian; Xie, Qiong; Zhang, Lixin

    2010-08-01

    Marine microorganisms are fascinating resources due to their production of novel natural products with antimicrobial activities. Increases in both the number of new chemical entities found and the substantiation of indigenous marine actinobacteria present a fundamental difficulty in the future discovery of novel antimicrobials, namely dereplication of those compounds already discovered. This review will share our experience on the taxonomic-based construction of a highly diversified and low redundant marine microbial natural product library for high-throughput antibiotic screening. We anticipate that libraries such as these can drive the drug discovery process now and in the future.

  12. Use of in situ solid-phase adsorption in microbial natural product fermentation development.

    PubMed

    Phillips, Thomas; Chase, Matthew; Wagner, Stephanie; Renzi, Chris; Powell, Marcella; DeAngelo, Joseph; Michels, Peter

    2013-05-01

    It has been half a century since investigators first began experimenting with adding ion exchange resins during the fermentation of microbial natural products. With the development of nonionic polymeric adsorbents in the 1970s, the application of in situ product adsorption in bioprocessing has grown slowly, but steadily. To date, in situ product adsorption strategies have been used in biotransformations, plant cell culture, the production of biofuels, and selected bulk chemicals, such as butanol and lactic acid, as well as in more traditional natural product fermentation within the pharmaceutical industry. Apart from the operational gains in efficiency from the integration of fermentation and primary recovery, the addition of adsorbents during fermentation has repeatedly demonstrated the capacity to significantly increase titers by sequestering the product and preventing or mitigating degradation, feedback inhibition and/or cytotoxic effects. Adoption of in situ product adsorption has been particularly valuable in the early stages of natural product-based drug discovery programs, where quickly and cost-effectively generating multigram quantities of a lead compound can be challenging when using a wild-type strain and fermentation conditions that have not been optimized. While much of the literature involving in situ adsorption describes its application early in the drug development process, this does not imply that the potential for scale-up is limited. To date, commercial-scale processes utilizing in situ product adsorption have reached batch sizes of at least 30,000 l. Here we present examples where in situ product adsorption has been used to improve product titers or alter the ratios among biosynthetically related natural products, examine some of the relevant variables to consider, and discuss the mechanisms by which in situ adsorption may impact the biosynthesis of microbial natural products.

  13. Microbial production of natural gas from coal and organic-rich shale

    USGS Publications Warehouse

    Orem, William

    2013-01-01

    Natural gas is an important component of the energy mix in the United States, producing greater energy yield per unit weight and less pollution compared to coal and oil. Most of the world’s natural gas resource is thermogenic, produced in the geologic environment over time by high temperature and pressure within deposits of oil, coal, and shale. About 20 percent of the natural gas resource, however, is produced by microorganisms (microbes). Microbes potentially could be used to generate economic quantities of natural gas from otherwise unexploitable coal and shale deposits, from coal and shale from which natural gas has already been recovered, and from waste material such as coal slurry. Little is known, however, about the microbial production of natural gas from coal and shale.

  14. Current challenges in the discovery of novel antibacterials from microbial natural products.

    PubMed

    Genilloud, Olga

    2012-12-01

    Microbial natural products have been for decades one of the most successful sources of drugs to treat infectious diseases. The high occurrence of resistances to all major classes of known antibiotics represents today a new challenge and new classes of antibacterial compounds are urgently needed to respond to this unmet clinical need. While natural products discovery programs have been gradually abandoned by big pharma, smaller biotechnology companies and other research organizations are taking the lead in the discovery of novel antibacterials. A survey of recent patents has shown that in spite of the efforts, few novel compounds are being developed that can overcome most of the emerging multi-resistant and pan-resistant pathogens. In order to respond to the current challenges of discovering novel antibiotics, new approaches are required to be developed to further exploit the microbial resources and their biosynthetic potential as an untapped source of novel metabolites. Strategies to mine microbial collections for orphan biosynthetic pathways and novel species thought to be uncultivable, are emerging as a need within antibacterial drug discovery programs, in combination with high throughput screening and chemical dereplication of novel compounds. Different innovative methods that are being developed to respond to the new challenges that are faced today by drug discovery programs will ensure the evolution of these strategies into a completely new framework that will address the renovated interest in the discovery of novel classes of antibiotics.

  15. A macrophage-stimulating compound from a screen of microbial natural products.

    PubMed

    Perry, Julie A; Koteva, Kalinka; Verschoor, Chris P; Wang, Wenliang; Bowdish, Dawn M E; Wright, Gerry D

    2015-01-01

    Rising rates of antibiotic resistance in bacterial pathogens is a medical crisis of global concern that necessitates the development of new treatment strategies. We have isolated a natural product with macrophage-stimulating activity from a screen of microbially produced bioactive molecules. Streptazolin increased bacterial killing and elaboration of immunostimulatory cytokines by macrophages in vitro. Furthermore, we show that streptazolin stimulates the macrophage nuclear factor κB (NF-κB) pathway via phosphatidylinositide 3-kinase (PI3K) signaling, and that the conjugated diene moiety is essential for stimulatory activity. Immunostimulatory molecules like streptazolin represent entries into new treatment paradigms to address the challenge of antibiotic resistance.

  16. Bio-mining the microbial treasures of the ocean: new natural products.

    PubMed

    Imhoff, Johannes F; Labes, Antje; Wiese, Jutta

    2011-01-01

    The biological resources of the oceans have been exploited since ancient human history, mainly by catching fish and harvesting algae. Research on natural products with special emphasis on marine animals and also algae during the last decades of the 20th century has revealed the importance of marine organisms as producers of substances useful for the treatment of human diseases. Though a large number of bioactive substances have been identified, some many years ago, only recently the first drugs from the oceans were approved. Quite astonishingly, the immense diversity of microbes in the marine environments and their almost untouched capacity to produce natural products and therefore the importance of microbes for marine biotechnology was realized on a broad basis by the scientific communities only recently. This has strengthened worldwide research activities dealing with the exploration of marine microorganisms for biotechnological applications, which comprise the production of bioactive compounds for pharmaceutical use, as well as the development of other valuable products, such as enzymes, nutraceuticals and cosmetics. While the focus in these fields was mainly on marine bacteria, also marine fungi now receive growing attention. Although culture-dependent studies continue to provide interesting new chemical structures with biological activities at a high rate and represent highly promising approaches for the search of new drugs, exploration and use of genomic and metagenomic resources are considered to further increase this potential. Many efforts are made for the sustainable exploration of marine microbial resources. Large culture collections specifically of marine bacteria and marine fungi are available. Compound libraries of marine natural products, even of highly purified substances, were established. The expectations into the commercial exploitation of marine microbial resources has given rise to numerous institutions worldwide, basic research facilities as

  17. Recent Advances in the Discovery and Development of Marine Microbial Natural Products

    PubMed Central

    Xiong, Zhi-Qiang; Wang, Jian-Feng; Hao, Yu-You; Wang, Yong

    2013-01-01

    Marine microbial natural products (MMNPs) have attracted increasing attention from microbiologists, taxonomists, ecologists, agronomists, chemists and evolutionary biologists during the last few decades. Numerous studies have indicated that diverse marine microbes appear to have the capacity to produce an impressive array of MMNPs exhibiting a wide variety of biological activities such as antimicrobial, anti-tumor, anti-inflammatory and anti-cardiovascular agents. Marine microorganisms represent an underexplored reservoir for the discovery of MMNPs with unique scaffolds and for exploitation in the pharmaceutical and agricultural industries. This review focuses on MMNPs discovery and development over the past decades, including innovative isolation and culture methods, strategies for discovering novel MMNPs via routine screenings, metagenomics, genomics, combinatorial biosynthesis, and synthetic biology. The potential problems and future directions for exploring MMNPs are also discussed. PMID:23528949

  18. Recombinant Environmental Libraries Provide Access to Microbial Diversity for Drug Discovery from Natural Products

    PubMed Central

    Courtois, Sophie; Cappellano, Carmela M.; Ball, Maria; Francou, Francois-Xavier; Normand, Philippe; Helynck, Gérard; Martinez, Asuncion; Kolvek, Steven J.; Hopke, Joern; Osburne, Marcia S.; August, Paul R.; Nalin, Renaud; Guérineau, Michel; Jeannin, Pascale; Simonet, Pascal; Pernodet, Jean-Luc

    2003-01-01

    To further explore possible avenues for accessing microbial biodiversity for drug discovery from natural products, we constructed and screened a 5,000-clone “shotgun” environmental DNA library by using an Escherichia coli-Streptomyces lividans shuttle cosmid vector and DNA inserts from microbes derived directly (without cultivation) from soil. The library was analyzed by several means to assess diversity, genetic content, and expression of heterologous genes in both expression hosts. We found that the phylogenetic content of the DNA library was extremely diverse, representing mostly microorganisms that have not been described previously. The library was screened by PCR for sequences similar to parts of type I polyketide synthase genes and tested for the expression of new molecules by screening of live colonies and cell extracts. The results revealed new polyketide synthase genes in at least eight clones. In addition, at least five additional clones were confirmed by high-pressure liquid chromatography analysis and/or biological activity to produce heterologous molecules. These data reinforce the idea that exploiting previously unknown or uncultivated microorganisms for the discovery of novel natural products has potential value and, most importantly, suggest a strategy for developing this technology into a realistic and effective drug discovery tool. PMID:12513976

  19. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products.

    PubMed

    Courtois, Sophie; Cappellano, Carmela M; Ball, Maria; Francou, Francois-Xavier; Normand, Philippe; Helynck, Gérard; Martinez, Asuncion; Kolvek, Steven J; Hopke, Joern; Osburne, Marcia S; August, Paul R; Nalin, Renaud; Guérineau, Michel; Jeannin, Pascale; Simonet, Pascal; Pernodet, Jean-Luc

    2003-01-01

    To further explore possible avenues for accessing microbial biodiversity for drug discovery from natural products, we constructed and screened a 5,000-clone "shotgun" environmental DNA library by using an Escherichia coli-Streptomyces lividans shuttle cosmid vector and DNA inserts from microbes derived directly (without cultivation) from soil. The library was analyzed by several means to assess diversity, genetic content, and expression of heterologous genes in both expression hosts. We found that the phylogenetic content of the DNA library was extremely diverse, representing mostly microorganisms that have not been described previously. The library was screened by PCR for sequences similar to parts of type I polyketide synthase genes and tested for the expression of new molecules by screening of live colonies and cell extracts. The results revealed new polyketide synthase genes in at least eight clones. In addition, at least five additional clones were confirmed by high-pressure liquid chromatography analysis and/or biological activity to produce heterologous molecules. These data reinforce the idea that exploiting previously unknown or uncultivated microorganisms for the discovery of novel natural products has potential value and, most importantly, suggest a strategy for developing this technology into a realistic and effective drug discovery tool.

  20. Engineering and comparison of non-natural pathways for microbial phenol production.

    PubMed

    Thompson, Brian; Machas, Michael; Nielsen, David R

    2016-08-01

    The non-renewable petrochemical phenol is used as a precursor to produce numerous fine and commodity chemicals, including various pharmaceuticals and phenolic resins. Microbial phenol biosynthesis has previously been established, stemming from endogenous tyrosine via tyrosine phenol lyase (TPL). TPL, however, suffers from feedback inhibition and equilibrium limitations, both of which contribute to reduced flux through the overall pathway. To address these limitations, two novel and non-natural phenol biosynthesis pathways, both stemming instead from chorismate, were constructed and comparatively evaluated. The first proceeds to phenol in one heterologous step via the intermediate p-hydroxybenzoic acid, while the second involves two heterologous steps and the associated intermediates isochorismate and salicylate. Maximum phenol titers achieved via these two alternative pathways reached as high as 377 ± 14 and 259 ± 31 mg/L in batch shake flask cultures, respectively. In contrast, under analogous conditions, phenol production via the established TPL-dependent route reached 377 ± 23 mg/L, which approaches the maximum achievable output reported to date under batch conditions. Additional strain development and optimization of relevant culture conditions with respect to each individual pathway is ultimately expected to result in further improved phenol production. Biotechnol. Bioeng. 2016;113: 1745-1754. © 2016 Wiley Periodicals, Inc.

  1. Phylogeny-guided (meta)genome mining approach for the targeted discovery of new microbial natural products.

    PubMed

    Kang, Hahk-Soo

    2017-02-01

    Genomics-based methods are now commonplace in natural products research. A phylogeny-guided mining approach provides a means to quickly screen a large number of microbial genomes or metagenomes in search of new biosynthetic gene clusters of interest. In this approach, biosynthetic genes serve as molecular markers, and phylogenetic trees built with known and unknown marker gene sequences are used to quickly prioritize biosynthetic gene clusters for their metabolites characterization. An increase in the use of this approach has been observed for the last couple of years along with the emergence of low cost sequencing technologies. The aim of this review is to discuss the basic concept of a phylogeny-guided mining approach, and also to provide examples in which this approach was successfully applied to discover new natural products from microbial genomes and metagenomes. I believe that the phylogeny-guided mining approach will continue to play an important role in genomics-based natural products research.

  2. Microbial Flocculant for Nature Soda

    SciTech Connect

    Qin, Peiyong; Zhang, Tong; Chen, Cuixian

    2004-03-31

    Microbial flocculant for nature soda has been studied. Lactobacillus TRJ21, which was able to produce an excellent biopolymer flocculant for nature soda, was obtained in our lab. The microbial flocculant was mainly produced when the bacteria laid in stationary growth phase. Fructose or glucose, as carbon sources, were more favorable for the bacterial growth and flocculant production. The bacteria was able to use ammonium sulfate or Urea as nitrogen to produce flocculant, but was not able to use peptone effectively. High C/N ratio was more favorable to Lactobacillus TRJ21 growth and flocculant production than low C/N ratio. The biopolymer flocculant was mainly composed of polysaccharide and protein with a molecular weight 1.38x106 by gel permeation chromatography. It was able to be easily purified from the culture medium by acetone. Protein in the flocculant was tested for the flocculating activity ingredient by heating the flocculant.

  3. Microbial Strain Prioritization Using Metabolomics Tools for the Discovery of Natural Products

    PubMed Central

    2012-01-01

    Natural products profoundly impact many research areas, including medicine, organic chemistry, and cell biology. However, discovery of new natural products suffers from a lack of high throughput analytical techniques capable of identifying structural novelty in the face of a high degree of chemical redundancy. Methods to select bacterial strains for drug discovery have historically been based on phenotypic qualities or genetic differences and have not been based on laboratory production of secondary metabolites. Therefore, untargeted LC/MS-based secondary metabolomics was evaluated to rapidly and efficiently analyze marine-derived bacterial natural products using LC/MS-principal component analysis (PCA). A major goal of this work was to demonstrate that LC/MS-PCA was effective for strain prioritization in a drug discovery program. As proof of concept, we evaluated LC/MS-PCA for strain selection to support drug discovery, for the discovery of unique natural products, and for rapid assessment of regulation of natural product production. PMID:22519562

  4. A Tropical Marine Microbial Natural Products Geobibliography as an Example of Desktop Exploration of Current Research Using Web Visualisation Tools

    PubMed Central

    Mukherjee, Joydeep; Llewellyn, Lyndon E; Evans-Illidge, Elizabeth A

    2008-01-01

    Microbial marine biodiscovery is a recent scientific endeavour developing at a time when information and other technologies are also undergoing great technical strides. Global visualisation of datasets is now becoming available to the world through powerful and readily available software such as Worldwind™, ArcGIS Explorer™ and Google Earth™. Overlaying custom information upon these tools is within the hands of every scientist and more and more scientific organisations are making data available that can also be integrated into these global visualisation tools. The integrated global view that these tools enable provides a powerful desktop exploration tool. Here we demonstrate the value of this approach to marine microbial biodiscovery by developing a geobibliography that incorporates citations on tropical and near-tropical marine microbial natural products research with Google Earth™ and additional ancillary global data sets. The tools and software used are all readily available and the reader is able to use and install the material described in this article. PMID:19172194

  5. Advancement in bioprocess technology: parallels between microbial natural products and cell culture biologics.

    PubMed

    Bandyopadhyay, Arpan A; Khetan, Anurag; Malmberg, Li-Hong; Zhou, Weichang; Hu, Wei-Shou

    2017-02-09

    The emergence of natural products and industrial microbiology nearly eight decades ago propelled an era of bioprocess innovation. Half a century later, recombinant protein technology spurred the tremendous growth of biologics and added mammalian cells to the forefront of industrial producing cells in terms of the value of products generated. This review highlights the process technology of natural products and protein biologics. Despite the separation in time, there is a remarkable similarity in their progression. As the new generation of therapeutics for gene and cell therapy emerges, its process technology development can take inspiration from that of natural products and biologics.

  6. Distributing a metabolic pathway among a microbial consortium enhances production of natural products.

    PubMed

    Zhou, Kang; Qiao, Kangjian; Edgar, Steven; Stephanopoulos, Gregory

    2015-04-01

    Metabolic engineering of microorganisms such as Escherichia coli and Saccharomyces cerevisiae to produce high-value natural metabolites is often done through functional reconstitution of long metabolic pathways. Problems arise when parts of pathways require specialized environments or compartments for optimal function. Here we solve this problem through co-culture of engineered organisms, each of which contains the part of the pathway that it is best suited to hosting. In one example, we divided the synthetic pathway for the acetylated diol paclitaxel precursor into two modules, expressed in either S. cerevisiae or E. coli, neither of which can produce the paclitaxel precursor on their own. Stable co-culture in the same bioreactor was achieved by designing a mutualistic relationship between the two species in which a metabolic intermediate produced by E. coli was used and functionalized by yeast. This synthetic consortium produced 33 mg/L oxygenated taxanes, including a monoacetylated dioxygenated taxane. The same method was also used to produce tanshinone precursors and functionalized sesquiterpenes.

  7. Distributing a metabolic pathway among a microbial consortium enhances production of natural products

    PubMed Central

    Zhou, Kang; Qiao, Kangjian; Edgar, Steven; Stephanopoulos, Gregory

    2016-01-01

    Metabolic engineering of microorganisms such as Escherichia coli and Saccharomyces cerevisiae to produce high-value natural metabolites is often done through functional reconstitution of long metabolic pathways. Problems arise when parts of pathways require specialized environments or compartments for optimal function. Here we solve this problem through co-culture of engineered organisms, each of which contains the part of the pathway that it is best suited to hosting. In one example, we divided the synthetic pathway for the acetylated diol paclitaxel precursor into two modules, expressed in either S. cerevisiae or E. coli, neither of which can produce the paclitaxel precursor on their own. Stable co-culture in the same bioreactor was achieved by designing a mutualistic relationship between the two species in which a metabolic intermediate produced by E. coli was used and functionalized by yeast. This synthetic consortium produced 33 mg/L oxygenated taxanes, including a monoacetylated dioxygenated taxane. The same method was also used to produce tanshinone precursors and functionalized sesquiterpenes. PMID:25558867

  8. A survey of phytotoxic microbial and plant metabolites as potential natural products for pest management.

    PubMed

    Schrader, Kevin K; Andolfi, Anna; Cantrell, Charles L; Cimmino, Alessio; Duke, Stephen O; Osbrink, Weste; Wedge, David E; Evidente, Antonio

    2010-09-01

    Phytotoxic microbial metabolites produced by certain phytopathogenic fungi and bacteria, and a group of phytotoxic plant metabolites including Amaryllidacea alkaloids and some derivatives of these compounds were evaluated for algicide, bactericide, insecticide, fungicide, and herbicide activities in order to discover natural compounds for potential use in the management and control of several important agricultural and household structural pests. Among the various compounds evaluated: i) ophiobolin A was found to be the most promising for potential use as a selective algicide; ii) ungeremine was discovered to be bactericidal against certain species of fish pathogenic bacteria; iii) cycasin caused significant mortality in termites; iv) cavoxin, ophiobolin A, and sphaeropsidin A were most active towards species of plant pathogenic fungi; and v) lycorine and some of its analogues (1-O-acetyllycorine and lycorine chlorohydrate) were highly phytotoxic in the herbicide bioassay. Our results further demonstrated that plants and microbes can provide a diverse and natural source of compounds with potential use as pesticides.

  9. Meta-omic characterization of the marine invertebrate microbial consortium that produces the chemotherapeutic natural product ET-743.

    PubMed

    Rath, Christopher M; Janto, Benjamin; Earl, Josh; Ahmed, Azad; Hu, Fen Z; Hiller, Luisa; Dahlgren, Meg; Kreft, Rachael; Yu, Fengan; Wolff, Jeremy J; Kweon, Hye Kyong; Christiansen, Michael A; Håkansson, Kristina; Williams, Robert M; Ehrlich, Garth D; Sherman, David H

    2011-11-18

    In many macroorganisms, the ultimate source of potent biologically active natural products has remained elusive due to an inability to identify and culture the producing symbiotic microorganisms. As a model system for developing a meta-omic approach to identify and characterize natural product pathways from invertebrate-derived microbial consortia, we chose to investigate the ET-743 (Yondelis) biosynthetic pathway. This molecule is an approved anticancer agent obtained in low abundance (10(-4)-10(-5) % w/w) from the tunicate Ecteinascidia turbinata and is generated in suitable quantities for clinical use by a lengthy semisynthetic process. On the basis of structural similarities to three bacterial secondary metabolites, we hypothesized that ET-743 is the product of a marine bacterial symbiont. Using metagenomic sequencing of total DNA from the tunicate/microbial consortium, we targeted and assembled a 35 kb contig containing 25 genes that comprise the core of the NRPS biosynthetic pathway for this valuable anticancer agent. Rigorous sequence analysis based on codon usage of two large unlinked contigs suggests that Candidatus Endoecteinascidia frumentensis produces the ET-743 metabolite. Subsequent metaproteomic analysis confirmed expression of three key biosynthetic proteins. Moreover, the predicted activity of an enzyme for assembly of the tetrahydroisoquinoline core of ET-743 was verified in vitro. This work provides a foundation for direct production of the drug and new analogues through metabolic engineering. We expect that the interdisciplinary approach described is applicable to diverse host-symbiont systems that generate valuable natural products for drug discovery and development.

  10. Meta-omic characterization of the marine invertebrate microbial consortium that produces the chemotherapeutic natural product ET-743

    PubMed Central

    Rath, Christopher M.; Janto, Benjamin; Earl, Josh; Ahmed, Azad; Hu, Fen Z.; Hiller, Luisa; Dahlgren, Meg; Kreft, Rachael; Yu, Fengan; Wolff, Jeremy J.; Kweon, Hye Kyong; Christiansen, Michael A.; Håkansson, Kristina; Williams, Robert M.; Ehrlich, Garth D.; Sherman, David H.

    2011-01-01

    In many macroorganisms, the ultimate source of potent biologically active natural products has remained elusive due to an inability to identify and culture the producing symbiotic microorganisms. As a model system for developing a meta-omic approach to identify and characterize natural product pathways from invertebrate-derived microbial consortia we chose to investigate the ET-743 (Yondelis®) biosynthetic pathway. This molecule is an approved anti-cancer agent obtained in low abundance (10−4–10−5% w/w) from the tunicate Ecteinascidia turbinata, and is generated in suitable quantities for clinical use by a lengthy semi-synthetic process. Based on structural similarities to three bacterial secondary metabolites, we hypothesized that ET-743 is the product of a marine bacterial symbiont. Using metagenomic sequencing of total DNA from the tunicate/microbial consortium we targeted and assembled a 35 kb contig containing 25 genes that comprise the core of the NRPS biosynthetic pathway for this valuable anti-cancer agent. Rigorous sequence analysis based on codon usage of two large unlinked contigs suggests that Candidatus Endoecteinascidia frumentensis produces the ET-743 metabolite. Subsequent metaproteomic analysis confirmed expression of three key biosynthetic proteins. Moreover, the predicted activity of an enzyme for assembly of the tetrahydroisoquinoline core of ET-743 was verified in vitro. This work provides a foundation for direct production of the drug and new analogs through metabolic engineering. We expect that the interdisciplinary approach described is applicable to diverse host-symbiont systems that generate valuable natural products for drug discovery and development. PMID:21875091

  11. Pest management with natural products

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The 2012 Philadelphia ACS Symposium on Natural Products for Pest Management introduced recent discoveries and applications of natural products from insect, terrestrial plant, microbial, and synthetic sources for the management of insects, weeds, plant pathogenic microbes, and nematodes. The symposiu...

  12. A survey of phytotoxic microbial and plant metabolites as potential natural products for pest management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phytotoxic microbial metabolites produced by certain phytopathogenic fungi and bacteria and a group of a phytotoxic plant metabolites including Amayllidaceae alkaloids and some derivatives of these compounds were evaluated for algicide, bactericide, insecticide, fungicide, and herbicide activities i...

  13. Microbial production of 1-octanol: A naturally excreted biofuel with diesel-like properties

    PubMed Central

    Akhtar, M. Kalim; Dandapani, Hariharan; Thiel, Kati; Jones, Patrik R.

    2014-01-01

    The development of sustainable, bio-based technologies to convert solar energy and carbon dioxide into fuels is a grand challenge. A core part of this challenge is to produce a fuel that is compatible with the existing transportation infrastructure. This task is further compounded by the commercial desire to separate the fuel from the biotechnological host. Based on its fuel characteristics, 1-octanol was identified as an attractive metabolic target with diesel-like properties. We therefore engineered a synthetic pathway specifically for the biosynthesis of 1-octanol in Escherichia coli BL21(DE3) by over-expression of three enzymes (thioesterase, carboxylic acid reductase and aldehyde reductase) and one maturation factor (phosphopantetheinyl transferase). Induction of this pathway in a shake flask resulted in 4.4 mg 1-octanol L−1 h−1 which exceeded the productivity of previously engineered strains. Furthermore, the majority (73%) of the fatty alcohol was localised within the media without the addition of detergent or solvent overlay. The deletion of acrA reduced the production and excretion of 1-octanol by 3-fold relative to the wild-type, suggesting that the AcrAB–TolC complex may be responsible for the majority of product efflux. This study presents 1-octanol as a potential fuel target that can be synthesised and naturally accumulated within the media using engineered microbes. PMID:27066394

  14. Microbial hydrogen production

    SciTech Connect

    Weaver, P.F.; Maness, P.C.; Martin, S.

    1995-09-01

    Photosynthetic bacteria inhabit an anaerobic or microaerophilic world where H{sub 2} is produced and consumed as a shared intermediary metabolite. Within a given bacterial isolate there are as many as 4 to 6 distinct enzymes that function to evolve or consume H{sub 2}. Three of the H{sub 2}-evolving physiologies involving three different enzymes from photosynthetic bacteria have been examined in detail for commercial viability. Nitrogenase-mediated H{sub 2} production completely dissimilates many soluble organic compounds to H{sub 2} and CO{sub 2} at rates up to 131 {mu}mol H{sub 2}{sm_bullet}min{sup -1}{sm_bullet}g cdw{sup -1} and can remain active for up to 20 days. This metabolism is very energy intensive, however, which limits solar conversion efficiencies. Fermentative hydrogenase can produce H{sub 2} at rates of 440 {mu}mol{sm_bullet}min{sup -1}{sm_bullet}g cdw{sup -1} at low levels of irradiation over indefinite periods. The equilibrium for this activity is low (<0.15 atmospheres), thereby requiring gas sparging, vacuuming, or microbial scavenging to retain prolonged activity. Microbial H{sub 2} production from the CO component of synthesis or producer gases maximally reaches activities of 1.5 mmol{sm_bullet}min{sup -1}{sm_bullet}g cdw{sup -1}. Mass transport of gaseous CO into an aqueous bacterial suspension is the rate-limiting step. Increased gas pressure strongly accelerates these rates. Immobilized bacteria on solid supports at ambient pressures also show enhanced shift activity when the bulk water is drained away. Scaled-up bioreactors with 100-200 cc bed volume have been constructed and tested. The near-term goal of this portion of the project is to engineer and economically evaluate a prototype system for the biological production of H{sub 2} from biomass. The CO shift enables a positive selection technique for O{sub 2}-resistant, H{sub 2}-evolving bacterial enzymes from nature.

  15. A High-Throughput Screening Platform of Microbial Natural Products for the Discovery of Molecules with Antibiofilm Properties against Salmonella

    PubMed Central

    Paytubi, Sonia; de La Cruz, Mercedes; Tormo, Jose R.; Martín, Jesús; González, Ignacio; González-Menendez, Victor; Genilloud, Olga; Reyes, Fernando; Vicente, Francisca; Madrid, Cristina; Balsalobre, Carlos

    2017-01-01

    In this report, we describe a High-Throughput Screening (HTS) to identify compounds that inhibit biofilm formation or cause the disintegration of an already formed biofilm using the Salmonella Enteritidis 3934 strain. Initially, we developed a new methodology for growing Salmonella biofilms suitable for HTS platforms. The biomass associated with biofilm at the solid-liquid interface was quantified by staining both with resazurin and crystal violet, to detect living cells and total biofilm mass, respectively. For a pilot project, a subset of 1120 extracts from the Fundación MEDINA's collection was examined to identify molecules with antibiofilm activity. This is the first validated HTS assay of microbial natural product extracts which allows for the detection of four types of activities which are not mutually exclusive: inhibition of biofilm formation, detachment of the preformed biofilm and antimicrobial activity against planktonic cells or biofilm embedded cells. Currently, several extracts have been selected for further fractionation and purification of the active compounds. In one of the natural extracts patulin has been identified as a potent molecule with antimicrobial activity against both, planktonic cells and cells within the biofilm. These findings provide a proof of concept that the developed HTS can lead to the discovery of new natural compounds with antibiofilm activity against Salmonella and its possible use as an alternative to antimicrobial therapies and traditional disinfectants. PMID:28303128

  16. A High-Throughput Screening Platform of Microbial Natural Products for the Discovery of Molecules with Antibiofilm Properties against Salmonella.

    PubMed

    Paytubi, Sonia; de La Cruz, Mercedes; Tormo, Jose R; Martín, Jesús; González, Ignacio; González-Menendez, Victor; Genilloud, Olga; Reyes, Fernando; Vicente, Francisca; Madrid, Cristina; Balsalobre, Carlos

    2017-01-01

    In this report, we describe a High-Throughput Screening (HTS) to identify compounds that inhibit biofilm formation or cause the disintegration of an already formed biofilm using the Salmonella Enteritidis 3934 strain. Initially, we developed a new methodology for growing Salmonella biofilms suitable for HTS platforms. The biomass associated with biofilm at the solid-liquid interface was quantified by staining both with resazurin and crystal violet, to detect living cells and total biofilm mass, respectively. For a pilot project, a subset of 1120 extracts from the Fundación MEDINA's collection was examined to identify molecules with antibiofilm activity. This is the first validated HTS assay of microbial natural product extracts which allows for the detection of four types of activities which are not mutually exclusive: inhibition of biofilm formation, detachment of the preformed biofilm and antimicrobial activity against planktonic cells or biofilm embedded cells. Currently, several extracts have been selected for further fractionation and purification of the active compounds. In one of the natural extracts patulin has been identified as a potent molecule with antimicrobial activity against both, planktonic cells and cells within the biofilm. These findings provide a proof of concept that the developed HTS can lead to the discovery of new natural compounds with antibiofilm activity against Salmonella and its possible use as an alternative to antimicrobial therapies and traditional disinfectants.

  17. BIOTIGER, A NATURAL MICROBIAL PRODUCT FOR ENHANCED HYDROCARBON RECOVERY FROM OIL SANDS.

    SciTech Connect

    Brigmon, R; Topher Berry, T; Whitney Jones, W; Charles Milliken, C

    2008-05-27

    BioTiger{trademark} is a unique microbial consortia that resulted from over 8 years of extensive microbiology screening and characterization of samples collected from a century-old Polish waste lagoon. BioTiger{trademark} shows rapid and complete degradation of aliphatic and aromatic hydrocarbons, produces novel surfactants, is tolerant of both chemical and metal toxicity and shows good activity at temperature and pH extremes. Although originally developed and used by the U.S. Department of Energy for bioremediation of oil-contaminated soils, recent efforts have proven that BioTiger{trademark} can also be used to increase hydrocarbon recovery from oil sands. This enhanced ex situ oil recovery process utilizes BioTiger{trademark} to optimize bitumen separation. A floatation test protocol with oil sands from Ft. McMurray, Canada was used for the BioTiger{trademark} evaluation. A comparison of hot water extraction/floatation test of the oil sands performed with BioTiger{trademark} demonstrated a 50% improvement in separation as measured by gravimetric analysis in 4 h and a five-fold increase at 25 hr. Since BioTiger{trademark} performs well at high temperatures and process engineering can enhance and sustain metabolic activity, it can be applied to enhance recovery of hydrocarbons from oil sands or other complex recalcitrant matrices.

  18. Application of 13C-labeling and 13C-13C COSY NMR experiments in the structure determination of a microbial natural product.

    PubMed

    Kwon, Yun; Park, Sunghyouk; Shin, Jongheon; Oh, Dong-Chan

    2014-08-01

    The elucidation of the structures of complex natural products bearing many quaternary carbons remains challenging, even in this advanced spectroscopic era. (13)C-(13)C COSY NMR spectroscopy shows direct couplings between (13)C and (13)C, which comprise the backbone of a natural product. Thus, this type of experiment is particularly useful for natural products bearing consecutive quaternary carbons. However, the low sensitivity of (13)C-based NMR experiments, due to the low natural abundance of the (13)C nucleus, is problematic when applying these techniques. Our efforts in the (13)C labeling of a microbial natural product, cyclopiazonic acid (1), by feeding (13)C-labeled glucose to the fungal culture, enabled us to acquire (13)C-(13)C COSY NMR spectra on a milligram scale that clearly show the carbon backbone of the compound. This is the first application of (13)C-(13)C COSY NMR experiments for a natural product. The results suggest that (13)C-(13)C COSY NMR spectroscopy can be routinely used for the structure determination of microbial natural products by (13)C-enrichment of a compound with (13)C-glucose.

  19. Microbial production of propanol.

    PubMed

    Walther, Thomas; François, Jean Marie

    2016-01-01

    Both, n-propanol and isopropanol are industrially attractive value-added molecules that can be produced by microbes from renewable resources. The development of cost-effective fermentation processes may allow using these alcohols as a biofuel component, or as a precursor for the chemical synthesis of propylene. This review reports and discusses the recent progress which has been made in the biochemical production of propanol. Several synthetic propanol-producing pathways were developed that vary with respect to stoichiometry and metabolic entry point. These pathways were expressed in different host organisms and enabled propanol production from various renewable feedstocks. Furthermore, it was shown that the optimization of fermentation conditions greatly improved process performance, in particular, when continuous product removal prevented accumulation of toxic propanol levels. Although these advanced metabolic engineering and fermentation strategies have facilitated significant progress in the biochemical production of propanol, the currently achieved propanol yields and productivities appear to be insufficient to compete with chemical propanol synthesis. The development of biosynthetic pathways with improved propanol yields, the breeding or identification of microorganisms with higher propanol tolerance, and the engineering of propanol producer strains that efficiently utilize low-cost feedstocks are the major challenges on the way to industrially relevant microbial propanol production processes.

  20. Microbial production of fatty alcohols.

    PubMed

    Fillet, Sandy; Adrio, José L

    2016-09-01

    Fatty alcohols have numerous commercial applications, including their use as lubricants, surfactants, solvents, emulsifiers, plasticizers, emollients, thickeners, and even fuels. Fatty alcohols are currently produced by catalytic hydrogenation of fatty acids from plant oils or animal fats. Microbial production of fatty alcohols may be a more direct and environmentally-friendly strategy since production is carried out by heterologous enzymes, called fatty acyl-CoA reductases, able to reduce different acyl-CoA molecules to their corresponding primary alcohols. Successful examples of metabolic engineering have been reported in Saccharomyces cerevisiae and Escherichia coli in which the production of fatty alcohols ranged from 1.2 to 1.9 g/L, respectively. Due to their metabolic advantages, oleaginous yeasts are considered the best hosts for production of fatty acid-derived chemicals. Some of these species can naturally produce, under specific growth conditions, lipids at high titers (>50 g/L) and therefore provide large amounts of fatty acyl-CoAs or fatty acids as precursors. Very recently, taking advantage of such features, over 8 g/L of C16-C18 fatty alcohols have been produced in Rhodosporidium toruloides. In this review we summarize the different metabolic engineering strategies, hosts and cultivation conditions used to date. We also point out some future trends and challenges for the microbial production of fatty alcohols.

  1. Microbial Production of Biovanillin

    PubMed Central

    Converti, A.; Aliakbarian, B.; Domínguez, J.M.; Bustos Vázquez, G.; Perego, P.

    2010-01-01

    This review aims at providing an overview on the microbial production of vanillin, a new alternative method for the production of this important flavor of the food industry, which has the potential to become economically competitive in the next future. After a brief description of the applications of vanillin in different industrial sectors and of its physicochemical properties, we described the traditional ways of providing vanillin, specifically extraction and chemical synthesis (mainly oxidation) and compared them with the new biotechnological options, i.e., biotransformations of caffeic acid, veratraldehyde and mainly ferulic acid. In the second part of the review, emphasis has been addressed to the factors most influencing the bioproduction of vanillin, specifically the age of inoculum, pH, temperature, type of co-substrate, as well as the inhibitory effects exerted either by excess substrate or product. The final part of the work summarized the downstream processes and the related unit operations involved in the recovery of vanillin from the bioconversion medium. PMID:24031526

  2. Microbial Production of Isoprene

    SciTech Connect

    Ray Fall

    2007-07-29

    Isoprene is a volatile hydrocarbon of unknown function, produced by certain bacteria, plants and animals, sometimes in huge amounts—the Earth’s forests are estimated to emit >500 x 106 tons of isoprene per year. With funding from this program we explored the biochemistry and regulation of isoprene formation in the model bacterial system, Bacillus subtilis, with the goals of explaining the biological rationale for isoprene biogenesis and constructing an isoprene-overproducing microbial system. Although the role for isoprene formation in B. subtilis is still uncertain, our current model for regulation of this hydrocarbon’s synthesis is that isoprene production in B. subtilis is controlled by a combination of i) rapid regulation of isoprene synthase activity and ii) supply of the substrate for isoprene synthase, dimethyallyl diphosphate (DMAPP). This model parallels our current thinking about the control of isoprene formation in plant chloroplasts. In this reporting period we have been working to test part ii) of this model; this work has produced new results using genetic and analytical approaches. For examples, we have developed an analytical method to resolve DMAPP and its isomer, isopentenyl diphosphate, from each other in bacteria and plants. We have also shown that the IPP isomerase (type 2) of B. subtilis is not the source of “isoprene synthase” activity, and discovered that B. subtilis releases C5 isoprenoid alcohols to the medium, suggesting that isoprene plus other C5 isoprenoids may be common by-products of metabolism. In addition, we have continued to work on our discovery that wild type B. subtilis strains form prolific biofilms, are normal components of plant root microflora, and are testing the idea that B. subtilis growing in biofilms uses isoprene to induce plant root exudation.

  3. Natural products as aromatase inhibitors.

    PubMed

    Balunas, Marcy J; Su, Bin; Brueggemeier, Robert W; Kinghorn, A Douglas

    2008-08-01

    With the clinical success of several synthetic aromatase inhibitors (AIs) in the treatment of postmenopausal estrogen receptor-positive breast cancer, researchers have also been investigating the potential of natural products as AIs. Natural products from terrestrial and marine organisms provide a chemically diverse array of compounds not always available through current synthetic chemistry techniques. Natural products that have been used traditionally for nutritional or medicinal purposes (e.g., botanical dietary supplements) may also afford AIs with reduced side effects. A thorough review of the literature regarding natural product extracts and secondary metabolites of plant, microbial, and marine origin that have been shown to exhibit aromatase inhibitory activity is presented herein.

  4. NATURAL CO2 FLOW FROM THE LOIHI VENT: IMPACT ON MICROBIAL PRODUCTION AND FATE OF THE CO2

    SciTech Connect

    Richard B. Coffin; Thomas J. Boyd; David L. Knies; Kenneth S. Grabowski; John W. Pohlman; Clark S. Mitchell

    2004-02-27

    The program for International Collaboration on CO{sub 2} Ocean Sequestration was initiated December 1997. Preliminary steps involved surveying a suite of biogeochemical parameters off the coast of Kona on the Big Island of Hawaii. The preliminary survey was conducted twice, in 1999 and 2000, to obtain a thorough data set including measurements of pH, current profiles, CO{sub 2} concentrations, microbial activities, and water and sediment chemistries. These data were collected in order to interpret a planned CO{sub 2} injection experiment. After these preliminary surveys were completed, local environment regulation forced moving the project to the coast north east of Bergen, Norway. The preliminary survey along the Norwegian Coast was conducted during 2002. However, Norwegian government revoked a permit, approved by the Norwegian State Pollution Control Authority, for policy reasons regarding the CO{sub 2} injection experiment. As a result the research team decided to monitor the natural CO{sub 2} flow off the southern coast of the Big Island. From December 3rd-13th 2002 scientists from four countries representing the Technical Committee of the International Carbon Dioxide Sequestration Experiment examined the hydrothermal venting at Loihi Seamount (Hawaiian Islands, USA). Work focused on tracing the venting gases, the impacts of the vent fluids on marine organisms, and CO{sub 2} influence on biogeochemical cycles. The cruise on the R/V Ka'imikai-O-Kanaloa (KOK) included 8 dives by the PISCES V submarine, 6 at Loihi and 2 at a nearby site in the lee of the Big Island. Data for this final report is from the last 2 dives on Loihi.

  5. Microbial production of value-added nutraceuticals.

    PubMed

    Wang, Jian; Guleria, Sanjay; Koffas, Mattheos A G; Yan, Yajun

    2016-02-01

    Nutraceuticals are important natural bioactive compounds that confer health-promoting and medical benefits to humans. Globally growing demands for value-added nutraceuticals for prevention and treatment of human diseases have rendered nutraceuticals a multi-billion dollar market. However, supply limitations and extraction difficulties from natural sources such as plants, animals or fungi, restrict the large-scale use of nutraceuticals. Metabolic engineering via microbial production platforms has been advanced as an eco-friendly alternative approach for production of value-added nutraceuticals from simple carbon sources. Microbial platforms like the most widely used Escherichia coli and Saccharomyces cerevisiae have been engineered as versatile cell factories for production of diverse and complex value-added chemicals such as phytochemicals, prebiotics, polysaccaharides and poly amino acids. This review highlights the recent progresses in biological production of value-added nutraceuticals via metabolic engineering approaches.

  6. Lack of the programmed death-1 receptor renders host susceptible to enteric microbial infection through impairing the production of the mucosal natural killer cell effector molecules.

    PubMed

    Solaymani-Mohammadi, Shahram; Lakhdari, Omar; Minev, Ivelina; Shenouda, Steve; Frey, Blake F; Billeskov, Rolf; Singer, Steven M; Berzofsky, Jay A; Eckmann, Lars; Kagnoff, Martin F

    2016-03-01

    The programmed death-1 receptor is expressed on a wide range of immune effector cells, including T cells, natural killer T cells, dendritic cells, macrophages, and natural killer cells. In malignancies and chronic viral infections, increased expression of programmed death-1 by T cells is generally associated with a poor prognosis. However, its role in early host microbial defense at the intestinal mucosa is not well understood. We report that programmed death-1 expression is increased on conventional natural killer cells but not on CD4(+), CD8(+) or natural killer T cells, or CD11b(+) or CD11c(+) macrophages or dendritic cells after infection with the mouse pathogen Citrobacter rodentium. Mice genetically deficient in programmed death-1 or treated with anti-programmed death-1 antibody were more susceptible to acute enteric and systemic infection with Citrobacter rodentium. Wild-type but not programmed death-1-deficient mice infected with Citrobacter rodentium showed significantly increased expression of the conventional mucosal NK cell effector molecules granzyme B and perforin. In contrast, natural killer cells from programmed death-1-deficient mice had impaired expression of those mediators. Consistent with programmed death-1 being important for intracellular expression of natural killer cell effector molecules, mice depleted of natural killer cells and perforin-deficient mice manifested increased susceptibility to acute enteric infection with Citrobacter rodentium. Our findings suggest that increased programmed death-1 signaling pathway expression by conventional natural killer cells promotes host protection at the intestinal mucosa during acute infection with a bacterial gut pathogen by enhancing the expression and production of important effectors of natural killer cell function.

  7. MICROBIAL RESISTANT GYPSUM PRODUCTS

    EPA Science Inventory

    Gypsum building materials often become wet, resulting in mold growth that leads to health and productivity impacts. A major source of mold growth is gypsum wallboard since nearly 90% of the interior finished surfaces of buildings are covered with gypsum products. It has been est...

  8. Commercial production of microbial enzymes

    SciTech Connect

    Munro, I.G.

    1985-01-01

    The advantages and uses of industrially produced microbial enzymes are described. The processes involved in the production of these enzymes, cultivation techniques, enzyme extraction, enzyme purification and immobilization are outlined. Both the history of enzyme technology and its future development are discussed.

  9. Combining microbial cultures for efficient production of electricity from butyrate in a microbial electrochemical cell.

    PubMed

    Miceli, Joseph F; Garcia-Peña, Ines; Parameswaran, Prathap; Torres, César I; Krajmalnik-Brown, Rosa

    2014-10-01

    Butyrate is an important product of anaerobic fermentation; however, it is not directly used by characterized strains of the highly efficient anode respiring bacteria (ARB) Geobacter sulfurreducens in microbial electrochemical cells. By combining a butyrate-oxidizing community with a Geobacter rich culture, we generated a microbial community which outperformed many naturally derived communities found in the literature for current production from butyrate and rivaled the highest performing natural cultures in terms of current density (∼ 11A/m(2)) and Coulombic efficiency (∼ 70%). Microbial community analyses support the shift in the microbial community from one lacking efficient ARB in the marine hydrothermal vent community to a community consisting of ∼ 80% Geobacter in the anode biofilm. This demonstrates the successful production and adaptation of a novel microbial culture for generating electrical current from butyrate with high current density and high Coulombic efficiency, by combining two mixed microbial cultures containing complementing biochemical pathways.

  10. Microbial utilisation of natural organic wastes.

    PubMed

    Ilyin, V K; Smirnov, I A; Soldatov, P E; Korniushenkova, I N; Grinin, A S; Lykov, I N; Safronova, S A

    2004-03-01

    The waste management strategy for the future should meet the benefits of humanity safety, respect principals of planet ecology, and compatibility with other habitability systems. For these purpose the waste management technologies, relevant to application of the biodegradation properties of bacteria are of great value. The biological treatment method is based upon the biodegradation of organic substances by various microorganisms. The advantage of the biodegradation waste management in general: it allows to diminish the volume of organic wastes, the biological hazard of the wastes is controlled, and this system may be compatible with the other systems. The objectives of our study were: to evaluate effectiveness of microbial biodegradation of non-pretreated substrate, to construct phneumoautomatic digester for organic wastes biodegradation, and to study microbial characteristics of active sludge samples used as inoculi in biodegradation experiment. The technology of vegetable wastes treatment was elaborated in IBMP and BMSTU. For this purpose the special unit was created where the degradation process is activated by enforced reinvention of portions of elaborated biogas into digester. This technology allows to save energy normally used for electromechanical agitation and to create optimal environment for anaerobic bacteria growth. The investigations were performed on waste simulator, which imitates physical and chemical content of food wastes calculated basing on the data on food wastes of moderate Russian city. The volume of created experimental sample of digester is 40 l. The basic system elements of device are digesters, gas receiver, remover of drops and valve monitoring and thermal control system. In our testing we used natural food wastes to measure basic parameters and time of biodegradation process. The diminution rate of organic gained 76% from initial mass taking part within 9 days of fermentation. The biogas production achieved 46 l per 1 kg of substrate

  11. Microbial utilisation of natural organic wastes

    NASA Astrophysics Data System (ADS)

    Ilyin, V. K.; Smirnov, I. A.; Soldatov, P. E.; Korniushenkova, I. N.; Grinin, A. S.; Lykov, I. N.; Safronova, S. A.

    2004-03-01

    The waste management strategy for the future should meet the benefits of humanity safety, respect principals of planet ecology, and compatibility with other habitability systems. For these purpose the waste management technologies, relevant to application of the biodegradation properties of bacteria are of great value. The biological treatment method is based upon the biodegradation of organic substances by various microorganisms. The advantage of the biodegradation waste management in general: it allows to diminish the volume of organic wastes, the biological hazard of the wastes is controlled and this system may be compatible with the other systems. The objectives of our study were: to evaluate effectiveness of microbial biodegradation of non-pretreated substrate, to construct phneumoautomatic digester for organic wastes biodegradation and to study microbial characteristics of active sludge samples used as inoculi in biodegradation experiment. The technology of vegetable wastes treatment was elaborated in IBMP and BMSTU. For this purpose the special unit was created where the degradation process is activated by enforced reinvention of portions of elaborated biogas into digester. This technology allows to save energy normally used for electromechanical agitation and to create optimal environment for anaerobic bacteria growth. The investigations were performed on waste simulator, which imitates physical and chemical content of food wastes calculated basing on the data on food wastes of moderate Russian city. The volume of created experimental sample of digester is 40 l. The basic system elements of device are digesters, gas receiver, remover of drops and valve monitoring and thermal control system. In our testing we used natural food wastes to measure basic parameters and time of biodegradation process. The diminution rate of organic gained 76% from initial mass taking part within 9 days of fermentation. The biogas production achieved 46 l per 1 kg of substrate

  12. Microbial Degradation of Natural Rubber Vulcanizates

    PubMed Central

    Tsuchii, Akio; Suzuki, Tomoo; Takeda, Kiyoshi

    1985-01-01

    An actinomycete, Nocardia sp. strain 835A, grows well on unvulcanized natural rubber and synthetic isoprene rubber, but not on other types of synthetic rubber. Not only unvulcanized but also various kinds of vulcanized natural rubber products were more or less utilized by the organism as the sole source of carbon and energy. The thin film from a latex glove was rapidly degraded, and the weight loss reached 75% after a 2-week cultivation period. Oligomers with molecular weights from 104 to 103 were accumulated during microbial growth on the latex glove. The partially purified oligomers were examined by infrared and 1H nuclear magnetic resonance and 13C nuclear magnetic resonance spectroscopy, and the spectra were those expected of cis-1, 4-polyisoprene with the structure, OHC—CH2—[—CH2—C(—CH3)=CH —CH2—]n—CH2—C(=O)— CH3, with average values of n of about 114 and 19 for the two oligomers. PMID:16346923

  13. Microbial production of primary metabolites

    NASA Astrophysics Data System (ADS)

    Demain, Arnold L.

    1980-12-01

    Microbial production of primary metabolites contributes significantly to the quality of life. Through fermentation, microorganisms growing on inexpensive carbon sources can produce valuable products such as amino acids, nucleotides, organic acids, and vitamins which can be added to food to enhance its flavor or increase its nutritive value. The contribution of microorganisms will go well beyond the food industry with the renewed interest in solvent fermentations. Microorganisms have the potential to provide many petroleum-derived products as well as the ethanol necessary for liquid fuel. The role of primary metabolites and the microbes which produce them will certainly increase in importance.

  14. Natural Products as Aromatase Inhibitors

    PubMed Central

    Balunas, Marcy J.; Su, Bin; Brueggemeier, Robert W.; Kinghorn, A. Douglas

    2010-01-01

    With the clinical success of several synthetic aromatase inhibitors (AIs) in the treatment of postmenopausal estrogen receptor-positive breast cancer, researchers have also been investigating also the potential of natural products as AIs. Natural products from terrestrial and marine organisms provide a chemically diverse array of compounds not always available through current synthetic chemistry techniques. Natural products that have been used traditionally for nutritional or medicinal purposes (e.g., botanical dietary supplements) may also afford AIs with reduced side effects. A thorough review of the literature regarding natural product extracts and secondary metabolites of plant, microbial, and marine origin that have been shown to exhibit aromatase inhibitory activity is presented herein. PMID:18690828

  15. The Biogeography of Putative Microbial Antibiotic Production.

    PubMed

    Morlon, Hélène; O'Connor, Timothy K; Bryant, Jessica A; Charkoudian, Louise K; Docherty, Kathryn M; Jones, Evan; Kembel, Steven W; Green, Jessica L; Bohannan, Brendan J M

    2015-01-01

    Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics.

  16. The Biogeography of Putative Microbial Antibiotic Production

    PubMed Central

    Bryant, Jessica A.; Charkoudian, Louise K.; Docherty, Kathryn M.; Jones, Evan; Kembel, Steven W.; Green, Jessica L.; Bohannan, Brendan J. M.

    2015-01-01

    Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics. PMID:26102275

  17. Engineering microbial factories for synthesis of value-added products

    PubMed Central

    Du, Jing; Shao, Zengyi; Zhao, Huimin

    2011-01-01

    Microorganisms have become an increasingly important platform for the production of drugs, chemicals, and biofuels from renewable resources. Advances in protein engineering, metabolic engineering, and synthetic biology enable redesigning microbial cellular networks and fine-tuning physiological capabilities, thus generating industrially viable strains for the production of natural and unnatural value-added compounds. In this review, we describe the recent progress on engineering microbial factories for synthesis of valued-added products including alkaloids, terpenoids, flavonoids, polyketides, non-ribosomal peptides, biofuels, and chemicals. Related topics on lignocellulose degradation, sugar utilization, and microbial tolerance improvement will also be discussed. PMID:21526386

  18. Engineering microbial factories for synthesis of value-added products.

    PubMed

    Du, Jing; Shao, Zengyi; Zhao, Huimin

    2011-08-01

    Microorganisms have become an increasingly important platform for the production of drugs, chemicals, and biofuels from renewable resources. Advances in protein engineering, metabolic engineering, and synthetic biology enable redesigning microbial cellular networks and fine-tuning physiological capabilities, thus generating industrially viable strains for the production of natural and unnatural value-added compounds. In this review, we describe the recent progress on engineering microbial factories for synthesis of valued-added products including alkaloids, terpenoids, flavonoids, polyketides, non-ribosomal peptides, biofuels, and chemicals. Related topics on lignocellulose degradation, sugar utilization, and microbial tolerance improvement will also be discussed.

  19. Production Methods for Microbial Biocontrol Agents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A critical constraint to the commercial use of microbial biopesticides is the development of an economic production process. The production process must be cost-effective and yield a microbial propagule that is stable and efficacious under field conditions. Currently, the commercial production of ...

  20. Marine actinomycete diversity and natural product discovery.

    PubMed

    Jensen, Paul R; Mincer, Tracy J; Williams, Philip G; Fenical, William

    2005-01-01

    Microbial natural products remain an important resource for drug discovery yet the microorganisms inhabiting the world's oceans have largely been overlooked in this regard. The recent discovery of novel secondary metabolites from taxonomically unique populations of marine actinomycetes suggests that these bacteria add an important new dimension to microbial natural product research. Continued efforts to characterize marine actinomycete diversity and how adaptations to the marine environment affect secondary metabolite production will create a better understanding of the potential utility of these bacteria as a source of useful products for biotechnology.

  1. Understanding Bacteriophage Specificity in Natural Microbial Communities

    PubMed Central

    Koskella, Britt; Meaden, Sean

    2013-01-01

    Studying the coevolutionary dynamics between bacteria and the bacteriophage viruses that infect them is critical to understanding both microbial diversity and ecosystem functioning. Phages can play a key role in shaping bacterial population dynamics and can significantly alter both intra- and inter-specific competition among bacterial hosts. Predicting how phages might influence community stability and apparent competition, however, requires an understanding of how bacteria-phage interaction networks evolve as a function of host diversity and community dynamics. Here, we first review the progress that has been made in understanding phage specificity, including the use of experimental evolution, we then introduce a new dataset on natural bacteriophages collected from the phyllosphere of horse chestnut trees, and finally we highlight that bacterial sensitivity to phage is rarely a binary trait and that this variation should be taken into account and reported. We emphasize that there is currently insufficient evidence to make broad generalizations about phage host range in natural populations, the limits of phage adaptation to novel hosts, or the implications of phage specificity in shaping microbial communities. However, the combination of experimental and genomic approaches with the study of natural communities will allow new insight to the evolution and impact of phage specificity within complex bacterial communities. PMID:23478639

  2. Microbial production of lactate-containing polyesters

    PubMed Central

    Yang, Jung Eun; Choi, So Young; Shin, Jae Ho; Park, Si Jae; Lee, Sang Yup

    2013-01-01

    Due to our increasing concerns on environmental problems and limited fossil resources, biobased production of chemicals and materials through biorefinery has been attracting much attention. Optimization of the metabolic performance of microorganisms, the key biocatalysts for the efficient production of the desired target bioproducts, has been achieved by metabolic engineering. Metabolic engineering allowed more efficient production of polyhydroxyalkanoates, a family of microbial polyesters. More recently, non-natural polyesters containing lactate as a monomer have also been produced by one-step fermentation of engineered bacteria. Systems metabolic engineering integrating traditional metabolic engineering with systems biology, synthetic biology, protein/enzyme engineering through directed evolution and structural design, and evolutionary engineering, enabled microorganisms to efficiently produce natural and non-natural products. Here, we review the strategies for the metabolic engineering of microorganisms for the in vivo biosynthesis of lactate-containing polyesters and for the optimization of whole cell metabolism to efficiently produce lactate-containing polyesters. Also, major problems to be solved to further enhance the production of lactate-containing polyesters are discussed. PMID:23718266

  3. Method Analysis of Microbial Resistant Gypsum Products

    EPA Science Inventory

    Abstract: Several commercially available gypsum products are marketed as microbial-resistant. During previous test method research on a microbial resistant gypsum wallboard study, a common theme from both stakeholders and product vendors was the need for a unified and accepted m...

  4. Uranium Biomineralization By Natural Microbial Phosphatase Activities in the Subsurface

    SciTech Connect

    Taillefert, Martial

    2015-04-01

    This project investigated the geochemical and microbial processes associated with the biomineralization of radionuclides in subsurface soils. During this study, it was determined that microbial communities from the Oak Ridge Field Research subsurface are able to express phosphatase activities that hydrolyze exogenous organophosphate compounds and result in the non-reductive bioimmobilization of U(VI) phosphate minerals in both aerobic and anaerobic conditions. The changes of the microbial community structure associated with the biomineralization of U(VI) was determined to identify the main organisms involved in the biomineralization process, and the complete genome of two isolates was sequenced. In addition, it was determined that both phytate, the main source of natural organophosphate compounds in natural environments, and polyphosphate accumulated in cells could also be hydrolyzed by native microbial population to liberate enough orthophosphate and precipitate uranium phosphate minerals. Finally, the minerals produced during this process are stable in low pH conditions or environments where the production of dissolved inorganic carbon is moderate. These findings suggest that the biomineralization of U(VI) phosphate minerals is an attractive bioremediation strategy to uranium bioreduction in low pH uranium-contaminated environments. These efforts support the goals of the SBR long-term performance measure by providing key information on "biological processes influencing the form and mobility of DOE contaminants in the subsurface".

  5. Biotechnological Processes in Microbial Amylase Production

    PubMed Central

    Arshad, M. K. Md; Lakshmipriya, Thangavel; Hashim, Uda; Chinni, Suresh V.

    2017-01-01

    Amylase is an important and indispensable enzyme that plays a pivotal role in the field of biotechnology. It is produced mainly from microbial sources and is used in many industries. Industrial sectors with top-down and bottom-up approaches are currently focusing on improving microbial amylase production levels by implementing bioengineering technologies. The further support of energy consumption studies, such as those on thermodynamics, pinch technology, and environment-friendly technologies, has hastened the large-scale production of the enzyme. Herein, the importance of microbial (bacteria and fungi) amylase is discussed along with its production methods from the laboratory to industrial scales. PMID:28280725

  6. Microbial pathogen quality criteria of rendered products.

    PubMed

    Pandey, Pramod K; Biswas, Sagor; Kass, Philip

    2016-06-01

    The North American rendering industry processes approximately 24 million metric tons (Mt) of raw materials and produces more than 8 million Mt of rendered products. More than 85 % of rendered products produced annually in the USA are used for producing animal feed. Pathogen contamination in rendered products is an important and topical issue. Although elevated temperatures (115-140 °C) for 40-90 min during the standard rendering processes are mathematically sufficient to completely destroy commonly found pathogens, the presence of pathogens in rendered products has nevertheless been reported. Increased concern over the risk of microbial contamination in rendered products may require additional safeguards for producing pathogen-free rendered products. This study provides an overview of rendered products, existing microbial pathogen quality criteria of rendered products (MPQCR), limitations, and the scope of improving the MPQCR.

  7. Microbial Production of Isoprenoids Enabled by Synthetic Biology

    PubMed Central

    Immethun, Cheryl M.; Hoynes-O’Connor, Allison G.; Balassy, Andrea; Moon, Tae Seok

    2013-01-01

    Microorganisms transform inexpensive carbon sources into highly functionalized compounds without toxic by-product generation or significant energy consumption. By redesigning the natural biosynthetic pathways in an industrially suited host, microbial cell factories can produce complex compounds for a variety of industries. Isoprenoids include many medically important compounds such as antioxidants and anticancer and antimalarial drugs, all of which have been produced microbially. While a biosynthetic pathway could be simply transferred to the production host, the titers would become economically feasible when it is rationally designed, built, and optimized through synthetic biology tools. These tools have been implemented by a number of research groups, with new tools pledging further improvements in yields and expansion to new medically relevant compounds. This review focuses on the microbial production of isoprenoids for the health industry and the advancements though synthetic biology. PMID:23577007

  8. Natural Products for Antithrombosis

    PubMed Central

    Chen, Cen; Zhang, Qian; Wang, Feng-Qin; Hu, Yuan-Jia; Xia, Zhi-Ning

    2015-01-01

    Thrombosis is considered to be closely related to several diseases such as atherosclerosis, ischemic heart disease and stroke, as well as rheumatoid arthritis, hyperuricemia, and various inflammatory conditions. More and more studies have been focused on understanding the mechanism of molecular and cellular basis of thrombus formation as well as preventing thrombosis for the treatment of thrombotic diseases. In reality, there is considerable interest in the role of natural products and their bioactive components in the prevention and treatment of thrombosis related disorders. This paper briefly describes the mechanisms of thrombus formation on three aspects, including coagulation system, platelet activation, and aggregation, and change of blood flow conditions. Furthermore, the natural products for antithrombosis by anticoagulation, antiplatelet aggregation, and fibrinolysis were summarized, respectively. PMID:26075003

  9. Hydrogen production from microbial strains

    DOEpatents

    Harwood, Caroline S; Rey, Federico E

    2012-09-18

    The present invention is directed to a method of screening microbe strains capable of generating hydrogen. This method involves inoculating one or more microbes in a sample containing cell culture medium to form an inoculated culture medium. The inoculated culture medium is then incubated under hydrogen producing conditions. Once incubating causes the inoculated culture medium to produce hydrogen, microbes in the culture medium are identified as candidate microbe strains capable of generating hydrogen. Methods of producing hydrogen using one or more of the microbial strains identified as well as the hydrogen producing strains themselves are also disclosed.

  10. Microbial production of scleroglucan and downstream processing.

    PubMed

    Castillo, Natalia A; Valdez, Alejandra L; Fariña, Julia I

    2015-01-01

    Synthetic petroleum-based polymers and natural plant polymers have the disadvantage of restricted sources, in addition to the non-biodegradability of the former ones. In contrast, eco-sustainable microbial polysaccharides, of low-cost and standardized production, represent an alternative to address this situation. With a strong global market, they attracted worldwide attention because of their novel and unique physico-chemical properties as well as varied industrial applications, and many of them are promptly becoming economically competitive. Scleroglucan, a β-1,3-β-1,6-glucan secreted by Sclerotium fungi, exhibits high potential for commercialization and may show different branching frequency, side-chain length, and/or molecular weight depending on the producing strain or culture conditions. Water-solubility, viscosifying ability and wide stability over temperature, pH and salinity make scleroglucan useful for different biotechnological (enhanced oil recovery, food additives, drug delivery, cosmetic and pharmaceutical products, biocompatible materials, etc.), and biomedical (immunoceutical, antitumor, etc.) applications. It can be copiously produced at bioreactor scale under standardized conditions, where a high exopolysaccharide concentration normally governs the process optimization. Operative and nutritional conditions, as well as the incidence of scleroglucan downstream processing will be discussed in this chapter. The relevance of using standardized inocula from selected strains and experiences concerning the intricate scleroglucan scaling-up will be also herein outlined.

  11. Microbial production of scleroglucan and downstream processing

    PubMed Central

    Castillo, Natalia A.; Valdez, Alejandra L.; Fariña, Julia I.

    2015-01-01

    Synthetic petroleum-based polymers and natural plant polymers have the disadvantage of restricted sources, in addition to the non-biodegradability of the former ones. In contrast, eco-sustainable microbial polysaccharides, of low-cost and standardized production, represent an alternative to address this situation. With a strong global market, they attracted worldwide attention because of their novel and unique physico-chemical properties as well as varied industrial applications, and many of them are promptly becoming economically competitive. Scleroglucan, a β-1,3-β-1,6-glucan secreted by Sclerotium fungi, exhibits high potential for commercialization and may show different branching frequency, side-chain length, and/or molecular weight depending on the producing strain or culture conditions. Water-solubility, viscosifying ability and wide stability over temperature, pH and salinity make scleroglucan useful for different biotechnological (enhanced oil recovery, food additives, drug delivery, cosmetic and pharmaceutical products, biocompatible materials, etc.), and biomedical (immunoceutical, antitumor, etc.) applications. It can be copiously produced at bioreactor scale under standardized conditions, where a high exopolysaccharide concentration normally governs the process optimization. Operative and nutritional conditions, as well as the incidence of scleroglucan downstream processing will be discussed in this chapter. The relevance of using standardized inocula from selected strains and experiences concerning the intricate scleroglucan scaling-up will be also herein outlined. PMID:26528259

  12. Metabolic engineering for the microbial production of marine bioactive compounds.

    PubMed

    Mao, Xiangzhao; Liu, Zhen; Sun, Jianan; Lee, Sang Yup

    2017-03-06

    Many marine bioactive compounds have medicinal and nutritional values. These bioactive compounds have been prepared using solvent-based extraction from marine bio-resources or chemical synthesis, which are costly, inefficient with low yields, and environmentally unfriendly. Recent advances in metabolic engineering allowed to some extent more efficient production of these compounds, showing promises to meet the increasing demand of marine natural bioactive compounds. In this paper, we review the strategies and statuses of metabolic engineering applied to microbial production of marine natural bioactive compounds including terpenoids and their derivatives, omega-3 polyunsaturated fatty acids, and marine natural drugs, and provide perspectives.

  13. Microbial production of energy sources from biomass

    NASA Astrophysics Data System (ADS)

    Righelato, R. C.

    1980-02-01

    The biochemical options available for the microbial production of energy sources from biomass is reviewed and some of the technology available for microbial conversion is discussed with particular reference to present limitations and how they may be overcome. Attention is given to the chemical process of anaerobic fermentation emphasizing the chemical reaction of glucose into pyruvic acid. The capital costs and energy consumption of ethanol and methane and their production are discussed. It is concluded that anaerobic fermentation of carbohydrates and digestion of biomass-containing effluents can be used as methods for achieving greater energy availability.

  14. [Progress in microbial production of succinic acid].

    PubMed

    Liu, Rongming; Liang, Liya; Wu, Mingke; Jiang, Min

    2013-10-01

    Succinic acid is one of the key intermediates in the tricarboxylic acid cycle (TCA)and has huge potentials in biopolymer, food, medicine applications. This article reviews recent research progress in the production of succinic acid by microbial fermentation, including discovery and screening of the succinic-acid-producing microbes, the progress of genetic engineering strategy and metabolic engineering technology for construction of succinic acid-producing strains, and fermentation process control and optimization. Finally, we discussed the limitation of current progress and proposed the future research needs for microbial production of succinic acid.

  15. Systems Biology of Microbial Exopolysaccharides Production

    PubMed Central

    Ates, Ozlem

    2015-01-01

    Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran. PMID:26734603

  16. Microbial Content of Nonsterile Therapeutic Agents Containing Natural or Seminatural Active Ingredients

    PubMed Central

    Schiller, I.; Kuntscher, H.; Wolff, A.; Nekola, M.

    1968-01-01

    The relationship was investigated between various chemical or pharmaceutical production processes and the extent of microbial contamination, of natural origin, of the resulting products. The products contained active ingredients of vegetable, enzymatic, or animal origin. It was concluded that (i) vegetable products practically free from microbes can be produced if the proper manufacturing steps are taken; (ii) sterilization of the media used to manufacture antibiotics, etc., produces products with little contamination; and (iii) products containing extracts of animal organs require careful refrigeration and addition of preservatives to produce acceptable levels of microbial contamination. PMID:5726165

  17. Marine natural products.

    PubMed

    Blunt, John W; Copp, Brent R; Keyzers, Robert A; Munro, Murray H G; Prinsep, Michèle R

    2015-02-01

    This review covers the literature published in 2013 for marine natural products (MNPs), with 982 citations (644 for the period January to December 2013) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1163 for 2013), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.

  18. Marine natural products.

    PubMed

    Blunt, John W; Copp, Brent R; Keyzers, Robert A; Munro, Murray H G; Prinsep, Michèle R

    2014-01-17

    This review covers the literature published in 2012 for marine natural products, with 1035 citations (673 for the period January to December 2012) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1241 for 2012), together with the relevant biological activities, source organisms and country of origin. Biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.

  19. Production of novel microbial biopolymers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microorganisms are well known to produce a wide variety of biobased polymers. These biopolymers have found a wide range of commercial uses, including food, feed, and consumer and industrial products. The production and possible uses of several novel biopolymers from both bacteria and fungi will be d...

  20. Microbial production of amino acids in Japan.

    PubMed

    Kumagai, H

    2000-01-01

    The microbial biotechnology of amino acids production which was developed and industrialized in Japan have been summarized. The amino acids include L-glutamic acid, L-lysine, L-threonine, L-aspartic acid, L-alanine, L-cysteine, L-dihydroxyphenylalanine, D-p-hydroxyphenyl-glycine, and hydroxy-L-proline.

  1. Natural Product Molecular Fossils.

    PubMed

    Falk, Heinz; Wolkenstein, Klaus

    2017-01-01

    The natural products synthesized by organisms that were living a long time ago gave rise to their molecular fossils. These can consist of either the original unchanged compounds or they may undergo peripheral transformations in which their skeletons remain intact. In cases when molecular fossils can be traced to their organismic source, they are termed "geological biomarkers".This contribution describes apolar and polar molecular fossils and, in particular biomarkers, along the lines usually followed in organic chemistry textbooks, and points to their bioprecursors when available. Thus, the apolar compounds are divided in linear and branched alkanes followed by alicyclic compounds and aromatic and heterocyclic molecules, and, in particular, the geoporphyrins. The polar molecular fossils contain as functional groups or constituent units ethers, alcohols, phenols, carbonyl groups, flavonoids, quinones, and acids, or are polymers like kerogen, amber, melanin, proteins, or nucleic acids. The final sections discuss the methodology used and the fundamental processes encountered by the biomolecules described, including diagenesis, catagenesis, and metagenesis.

  2. Microbial bioinformatics for food safety and production.

    PubMed

    Alkema, Wynand; Boekhorst, Jos; Wels, Michiel; van Hijum, Sacha A F T

    2016-03-01

    In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput 'omics' technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety.

  3. Microbial bioinformatics for food safety and production

    PubMed Central

    Alkema, Wynand; Boekhorst, Jos; Wels, Michiel

    2016-01-01

    In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput ‘omics’ technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety. PMID:26082168

  4. Natural selection for costly nutrient recycling in simulated microbial metacommunities.

    PubMed

    Boyle, Richard A; Williams, Hywel T P; Lenton, Timothy M

    2012-11-07

    Recycling of essential nutrients occurs at scales from microbial communities to global biogeochemical cycles, often in association with ecological interactions in which two or more species utilise each others' metabolic by-products. However, recycling loops may be unstable; sequences of reactions leading to net recycling may be parasitised by side-reactions causing nutrient loss, while some reactions in any closed recycling loop are likely to be costly to participants. Here we examine the stability of nutrient recycling loops in an individual-based ecosystem model based on microbial functional types that differ in their metabolism. A supplied nutrient is utilised by a "source" functional type, generating a secondary nutrient that is subsequently used by two other types-a "mutualist" that regenerates the initial nutrient at a growth rate cost, and a "parasite" that produces a refractory waste product but does not incur any additional cost. The three functional types are distributed across a metacommunity in which separate patches are linked by a stochastic diffusive migration process. Regions of high mutualist abundance feature high levels of nutrient recycling and increased local population density leading to greater export of individuals, allowing the source-mutualist recycling loop to spread across the system. Individual-level selection favouring parasites is balanced by patch-level selection for high productivity, indirectly favouring mutualists due to the synergistic productivity benefits of the recycling loop they support. This suggests that multi-level selection may promote nutrient cycling and thereby help to explain the apparent ubiquity and stability of nutrient recycling in nature.

  5. Maximizing efficiency of rumen microbial protein production

    PubMed Central

    Hackmann, Timothy J.; Firkins, Jeffrey L.

    2015-01-01

    Rumen microbes produce cellular protein inefficiently partly because they do not direct all ATP toward growth. They direct some ATP toward maintenance functions, as long-recognized, but they also direct ATP toward reserve carbohydrate synthesis and energy spilling (futile cycles that dissipate heat). Rumen microbes expend ATP by vacillating between (1) accumulation of reserve carbohydrate after feeding (during carbohydrate excess) and (2) mobilization of that carbohydrate thereafter (during carbohydrate limitation). Protozoa account for most accumulation of reserve carbohydrate, and in competition experiments, protozoa accumulated nearly 35-fold more reserve carbohydrate than bacteria. Some pure cultures of bacteria spill energy, but only recently have mixed rumen communities been recognized as capable of the same. When these communities were dosed glucose in vitro, energy spilling could account for nearly 40% of heat production. We suspect that cycling of glycogen (a major reserve carbohydrate) is a major mechanism of spilling; such cycling has already been observed in single-species cultures of protozoa and bacteria. Interconversions of short-chain fatty acids (SCFA) may also expend ATP and depress efficiency of microbial protein production. These interconversions may involve extensive cycling of intermediates, such as cycling of acetate during butyrate production in certain butyrivibrios. We speculate this cycling may expend ATP directly or indirectly. By further quantifying the impact of reserve carbohydrate accumulation, energy spilling, and SCFA interconversions on growth efficiency, we can improve prediction of microbial protein production and guide efforts to improve efficiency of microbial protein production in the rumen. PMID:26029197

  6. A Natural Love of Natural Products

    PubMed Central

    2008-01-01

    Recent research on the chemistry of natural products from the author’s group that led to the receipt of the ACS Ernest Guenther Award in the Chemistry of Natural Products is reviewed. REDOR NMR and synthetic studies established the T-taxol conformation as the bioactive tubulin-binding conformation, and these results were confirmed by the synthesis of compounds which clearly owed their activity or lack of activity to whether or not they could adopt the T-taxol conformation. Similar studies with the epothilones suggest that the current tubulin-binding model needs to be modified. Examples of natural products discovery and biodiversity conservation in Suriname and Madagascar are also presented, and it is concluded that natural products chemistry will continue to make significant contributions to drug discovery. PMID:18459734

  7. Computational approaches to natural product discovery

    PubMed Central

    Medema, Marnix H.; Fischbach, Michael A.

    2016-01-01

    From the earliest Streptomyces genome sequences, the promise of natural product genome mining has been captivating: genomics and bioinformatics would transform compound discovery from an ad hoc pursuit to a high-throughput endeavor. Until recently, however, genome mining has advanced natural product discovery only modestly. Here, we argue that the development of algorithms to mine the continuously increasing amounts of (meta)genomic data will enable the promise of genome mining to be realized. We review computational strategies that have been developed to identify biosynthetic gene clusters in genome sequences and predict the chemical structures of their products. We then discuss networking strategies that can systematize large volumes of genetic and chemical data, and connect genomic information to metabolomic and phenotypic data. Finally, we provide a vision of what natural product discovery might look like in the future, specifically considering long-standing questions in microbial ecology regarding the roles of metabolites in interspecies interactions. PMID:26284671

  8. Computational approaches to natural product discovery.

    PubMed

    Medema, Marnix H; Fischbach, Michael A

    2015-09-01

    Starting with the earliest Streptomyces genome sequences, the promise of natural product genome mining has been captivating: genomics and bioinformatics would transform compound discovery from an ad hoc pursuit to a high-throughput endeavor. Until recently, however, genome mining has advanced natural product discovery only modestly. Here, we argue that the development of algorithms to mine the continuously increasing amounts of (meta)genomic data will enable the promise of genome mining to be realized. We review computational strategies that have been developed to identify biosynthetic gene clusters in genome sequences and predict the chemical structures of their products. We then discuss networking strategies that can systematize large volumes of genetic and chemical data and connect genomic information to metabolomic and phenotypic data. Finally, we provide a vision of what natural product discovery might look like in the future, specifically considering longstanding questions in microbial ecology regarding the roles of metabolites in interspecies interactions.

  9. Perspectives of microbial oils for biodiesel production.

    PubMed

    Li, Qiang; Du, Wei; Liu, Dehua

    2008-10-01

    Biodiesel has become more attractive recently because of its environmental benefits, and the fact that it is made from renewable resources. Generally speaking, biodiesel is prepared through transesterification of vegetable oils or animal fats with short chain alcohols. However, the lack of oil feedstocks limits the large-scale development of biodiesel to some extent. Recently, much attention has been paid to the development of microbial, oils and it has been found that many microorganisms, such as algae, yeast, bacteria, and fungi, have the ability to accumulate oils under some special cultivation conditions. Compared to other plant oils, microbial oils have many advantages, such as short life cycle, less labor required, less affection by venue, season and climate, and easier to scale up. With the rapid expansion of biodiesel, microbial oils might become one of potential oil feedstocks for biodiesel production in the future, though there are many works associated with microorganisms producing oils need to be carried out further. This review is covering the related research about different oleaginous microorganisms producing oils, and the prospects of such microbial oils used for biodiesel production are also discussed.

  10. 7 CFR 3201.105 - Microbial cleaning products.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 15 2014-01-01 2014-01-01 false Microbial cleaning products. 3201.105 Section 3201... PROCUREMENT Designated Items § 3201.105 Microbial cleaning products. (a) Definition. (1) Cleaning agents that... include organisms that digest protein, starch, fat, and cellulose. (2) Microbial cleaning products...

  11. Utilization of wastewater originated from naturally fermented virgin coconut oil manufacturing process for bioextract production: physico-chemical and microbial evolution.

    PubMed

    Tripetchkul, Sudarut; Kusuwanwichid, Sasithorn; Koonsrisuk, Songpon; Akeprathumchai, Saengchai

    2010-08-01

    Production of virgin coconut oil via natural fermentation has led to large amount of wastes being generated, i.e., coconut pulp and wastewater containing coconut crème. Objective of this study is to gain more insight into the feasibility of utilization of such wastes as raw materials together with several types of wastes such as fish waste and/or pineapple peel for bioextract production. Chemical, physico-chemical and biological changes including phytotoxicity of the fermented mixture were closely monitored. Physical observation suggested that fermentation of bioextract obtained with fish waste appeared to be complete within the first month of fermentation while bioextract obtained using pineapple waste seemed to be complete after 8 months post-fermentation. Fermentation broth is of blackish color with alcoholic as well as acidic odour with no gas bubble and/or yeast film present on top of the surface. During the whole fermentation interval, several attributes of both bioextracts, e.g., pH, chemical oxygen demand (COD) and organic acids, were statistically different. Further, the total bacteria and lactic acid bacteria present in pineapple bioextract were statistically higher than those of the fish bioextract (p<0.01). The highest germination indices of 123 and 106 were obtained at 21 and 14 days post-fermentation for fish and pineapple bioextracts, respectively. In addition, qualities of both bioextracts conformed well with those specified by the Thai standard for liquid biofertilizer after 1 month fermentation. Results further showed that wastewater derived from virgin coconut oil manufacturing process could effectively be employed together with other types of wastes such as fish waste and pineapple peel for bioextract production. However, for the best bioextract quality, fermentation should be carefully planned since over fermentation led to bioextract of low qualities.

  12. Microbial production of hyaluronic acid: current state, challenges, and perspectives

    PubMed Central

    2011-01-01

    Hyaluronic acid (HA) is a natural and linear polymer composed of repeating disaccharide units of β-1, 3-N-acetyl glucosamine and β-1, 4-glucuronic acid with a molecular weight up to 6 million Daltons. With excellent viscoelasticity, high moisture retention capacity, and high biocompatibility, HA finds a wide-range of applications in medicine, cosmetics, and nutraceuticals. Traditionally HA was extracted from rooster combs, and now it is mainly produced via streptococcal fermentation. Recently the production of HA via recombinant systems has received increasing interest due to the avoidance of potential toxins. This work summarizes the research history and current commercial market of HA, and then deeply analyzes the current state of microbial production of HA by Streptococcus zooepidemicus and recombinant systems, and finally discusses the challenges facing microbial HA production and proposes several research outlines to meet the challenges. PMID:22088095

  13. Microbial methanol formation: A major end product of pectin metabolism

    SciTech Connect

    Schink, B.; Zeikus, J.G.

    1980-01-01

    Various pectinolytic strains of Clostridium, Erwinia, and Pseudomonas species produced methanol as a major end product during growth on pectin but not on glucose of polygalacturonic acid. Pectin metabolism of Clostridium butyricum strain 4PI correlated with a final product concentration of 16 mM at the end of growth, and a 1:1 stoichiometry for methanol production and percent initial substrate methoxylation. Growth on pectin was associated with high activity of pectin methylesterase and the absence of methanol consumption. The ecological significance of pectin metabolism and the establishment of microbial methylotrophic metabolism in nature is discussed.

  14. Comparison of microbial communities in Lake Tahoe surface sample with Tonga Trench water column samples using High Pressure Liquid Chromatography - Electrospray Ionization - Mass Spectroscopy (HPLC - ESI - MS) and Global Natural Products Social Molecular Network (GNPS)

    NASA Astrophysics Data System (ADS)

    Belmonte, M. A.

    2015-12-01

    Intact polar lipids (IPLs) are lipids composed of a head group, a glycerol, and a fatty acid chain that make up the lipid bilayer of cell membranes in living cells; and the varying head groups can be indicative of the type of microbes present in the environment (Van Mooy 2010). So by distinguishing and identifying the IPL distribution in an environment one can make inferences about the microbial communities in the said environment. In this study, we used High Pressure Liquid Chromatography-Electrospray Ionization- Mass Spectroscopy (HPLC-ESI-MS) and Global Natural Products Social Molecular Networking (GNPS) to compare the IPL distributions of two oligotrophic environments: surface waters of Lake Tahoe in the Sierra Nevada Mountains, and the water column of the Tonga Trench in the South Pacific. We hypothesized that the similar nutrient dynamics of the two oligotrophic environments would result in similar eukaryotic and prokaryotic communities, which would be reflected in the IPL composition of suspended particulate organic matter (POM). For simplicity we focused on the classes of IPLs most commonly observed in the marine environment: phosphotidylglycerol (PG), phosphotidylethanolamine (PE), diacylglyceryl-trimethyl-homoserine (DGTS), diacylglyceryl-hydroxymethyl-trimethylalanine (DGTA), sulfoquinovosyldiacylglycerol (SQDG), monoglycosyldiacylglycerol (MGDG) and diglycosyldiacylglycerol (DGDG). Our results showed that all of the marine IPLs of interest were present in Lake Tahoe which confirms that there are many of the same microbial communities in the fresh waters of Lake Tahoe and the salt waters Tonga Trench.

  15. Microbial production strategies and applications of lycopene and other terpenoids.

    PubMed

    Ma, Tian; Deng, Zixin; Liu, Tiangang

    2016-01-01

    Terpenoids are a large class of compounds that have far-reaching applications and economic value, particularly those most commonly found in plants; however, the extraction and synthesis of these compounds is often expensive and technically challenging. Recent advances in microbial metabolic engineering comprise a breakthrough that may enable the efficient, cost-effective production of these limited natural resources. Via the engineering of safe, industrial microorganisms that encode product-specific enzymes, and even entire metabolic pathways of interest, microbial-derived semisynthetic terpenoids may soon replace plant-derived terpenoids as the primary source of these valuable compounds. Indeed, the recent metabolic engineering of an Escherichia coli strain that produces the precursor to lycopene, a commercially and medically important compound, with higher yields than those in tomato plants serves as a successful example. Here, we review the recent developments in the metabolic engineering of microbes for the production of certain terpenoid compounds, particularly lycopene, which has been increasingly used in pharmaceuticals, nutritional supplements, and cosmetics. Furthermore, we summarize the metabolic engineering strategies used to achieve successful microbial production of some similar compounds. Based on this overview, there is a reason to believe that metabolic engineering comprises an optimal approach for increasing the production of lycopene and other terpenoids.

  16. Microbial biomass and productivity in seagrass beds

    NASA Technical Reports Server (NTRS)

    Moriarty, D. J.; Boon, P. I.; Hansen, J. A.; Hunt, W. G.; Poiner, I. R.; Pollard, P. C.; Skyring, G. W.; White, D. C.

    1985-01-01

    Different methods for measuring the rates of processes mediated by bacteria in sediments and the rates of bacterial cell production have been compared. In addition, net production of the seagrass Zostera capricorni and bacterial production have been compared and some interrelationships with the nitrogen cycle discussed. Seagrass productivity was estimated by measuring the plastochrone interval using a leaf stapling technique. The average productivity over four seasons was 1.28 +/- 0.28 g C m-2 day-1 (mean +/- standard deviation, n = 4). Bacterial productivity was measured five times throughout a year using the rate of tritiated thymidine incorporated into DNA. Average values were 33 +/- 12 mg C m-2 day-1 for sediment and 23 +/- 4 for water column (n = 5). Spatial variability between samples was greater than seasonal variation for both seagrass productivity and bacterial productivity. On one occasion, bacterial productivity was measured using the rate of 32P incorporated into phospholipid. The values were comparable to those obtained with tritiated thymidine. The rate of sulfate reduction was 10 mmol SO4(-2) m-2 day-1. The rate of methanogenesis was low, being 5.6 mg CH4 produced m-2 day-1. A comparison of C flux measured using rates of sulfate reduction and DNA synthesis indicated that anaerobic processes were predominant in these sediments. An analysis of microbial biomass and community structure, using techniques of phospholipid analysis, showed that bacteria were predominant members of the microbial biomass and that of these, strictly anaerobic bacteria were the main components. Ammonia concentration in interstitial water varied from 23 to 71 micromoles. Estimates of the amount of ammonia required by seagrass showed that the ammonia would turn over about once per day. Rapid recycling of nitrogen by bacteria and bacterial grazers is probably important.

  17. Natural product discovery: past, present, and future.

    PubMed

    Katz, Leonard; Baltz, Richard H

    2016-03-01

    Microorganisms have provided abundant sources of natural products which have been developed as commercial products for human medicine, animal health, and plant crop protection. In the early years of natural product discovery from microorganisms (The Golden Age), new antibiotics were found with relative ease from low-throughput fermentation and whole cell screening methods. Later, molecular genetic and medicinal chemistry approaches were applied to modify and improve the activities of important chemical scaffolds, and more sophisticated screening methods were directed at target disease states. In the 1990s, the pharmaceutical industry moved to high-throughput screening of synthetic chemical libraries against many potential therapeutic targets, including new targets identified from the human genome sequencing project, largely to the exclusion of natural products, and discovery rates dropped dramatically. Nonetheless, natural products continued to provide key scaffolds for drug development. In the current millennium, it was discovered from genome sequencing that microbes with large genomes have the capacity to produce about ten times as many secondary metabolites as was previously recognized. Indeed, the most gifted actinomycetes have the capacity to produce around 30-50 secondary metabolites. With the precipitous drop in cost for genome sequencing, it is now feasible to sequence thousands of actinomycete genomes to identify the "biosynthetic dark matter" as sources for the discovery of new and novel secondary metabolites. Advances in bioinformatics, mass spectrometry, proteomics, transcriptomics, metabolomics and gene expression are driving the new field of microbial genome mining for applications in natural product discovery and development.

  18. [Microbial silage production from eviscerated fish].

    PubMed

    Bello, R; Cardillo, E; Martínez, R

    1993-09-01

    Microbial fish silage was produced from a mixture of several fish species that belong to the shrimp by-catch. They were mixed with molasses, fruits (pineapple and papaya), sorbate and a starter of Lactobacillus plantarum ATCC8014. Process was evaluated by pH, acidity, consistency, exudate liquid, non-protein nitrogen, total volatile bases, microbial and toxicological tests. Results indicated that acid production and pH reduction occurs during the first two days of processing, later these values were maintained stable during 64 storage days. Total volatile bases increased during storage period. Consistency, non-protein nitrogen and exudate liquid showed that hydrolysis and liquefaction occurs during the first 8 days of processing. Raw material showed high counts of aerobic mesophilic and psicrotrophic organisms, in addition to Pseudomonas, coliform and S. aureus. However silage showed only a few aerobic mesophilic organisms due to low pH values and development of lactic acid bacteria. Silage dehydration reduces possibilities of microbial growth, and only spores of Bacillus were observed. Low levels of lead, mercury and chrome were detected in the dry silage. Proximal analysis values did not change during process and storage period.

  19. Carbonate Precipitation through Microbial Activities in Natural Environment, and Their Potential in Biotechnology: A Review

    PubMed Central

    Zhu, Tingting; Dittrich, Maria

    2016-01-01

    Calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. Microbial carbonate precipitation, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. This natural process occurring in various geological settings can be mimicked and used for a number of biotechnologies, such as metal remediation, carbon sequestration, enhanced oil recovery, and construction restoration. In this study, different metabolic activities leading to calcium carbonate precipitation, their native environment, and potential applications and challenges are reviewed. PMID:26835451

  20. Disturbance Increases Microbial Community Diversity and Production in Marine Sediments

    PubMed Central

    Galand, Pierre E.; Lucas, Sabrina; Fagervold, Sonja K.; Peru, Erwan; Pruski, Audrey M.; Vétion, Gilles; Dupuy, Christine; Guizien, Katell

    2016-01-01

    Disturbance strongly impacts patterns of community diversity, yet the shape of the diversity-disturbance relationship remains a matter of debate. The topic has been of interest in theoretical ecology for decades as it has practical implications for the understanding of ecosystem services in nature. One of these processes is the remineralization of organic matter by microorganisms in coastal marine sediments, which are periodically impacted by disturbances across the sediment-water interface. Here we set up an experiment to test the hypothesis that disturbance impacts microbial diversity and function during the anaerobic degradation of organic matter in coastal sediments. We show that during the first 3 weeks of the experiment, disturbance increased both microbial production, derived from the increase in microbial abundance, and diversity of the active fraction of the community. Both community diversity and phylogenetic diversity increased, which suggests that disturbance promoted the cohabitation of ecologically different microorganisms. Metagenome analysis also showed that disturbance increased the relative abundance of genes diagnostic of metabolism associated with the sequential anaerobic degradation of organic matter. However, community composition was not impacted in a systematic way and changed over time. In nature, we can hypothesize that moderate storm disturbances, which impact coastal sediments, promote diverse, and productive communities. These events, rather than altering the decomposition of organic matter, may increase the substrate turnover and, ultimately, remineralization rates. PMID:27994581

  1. Problems with the microbial production of butanol.

    PubMed

    Zheng, Yan-Ning; Li, Liang-Zhi; Xian, Mo; Ma, Yu-Jiu; Yang, Jian-Ming; Xu, Xin; He, Dong-Zhi

    2009-09-01

    With the incessant fluctuations in oil prices and increasing stress from environmental pollution, renewed attention is being paid to the microbial production of biofuels from renewable sources. As a gasoline substitute, butanol has advantages over traditional fuel ethanol in terms of energy density and hygroscopicity. A variety of cheap substrates have been successfully applied in the production of biobutanol, highlighting the commercial potential of biobutanol development. In this review, in order to better understand the process of acetone-butanol-ethanol production, traditional clostridia fermentation is discussed. Sporulation is probably induced by solvent formation, and the molecular mechanism leading to the initiation of sporulation and solventogenesis is also investigated. Different strategies are employed in the metabolic engineering of clostridia that aim to enhancing solvent production, improve selectivity for butanol production, and increase the tolerance of clostridia to solvents. However, it will be hard to make breakthroughs in the metabolic engineering of clostridia for butanol production without gaining a deeper understanding of the genetic background of clostridia and developing more efficient genetic tools for clostridia. Therefore, increasing attention has been paid to the metabolic engineering of E. coli for butanol production. The importation and expression of a non-clostridial butanol-producing pathway in E. coli is probably the most promising strategy for butanol biosynthesis. Due to the lower butanol titers in the fermentation broth, simultaneous fermentation and product removal techniques have been developed to reduce the cost of butanol recovery. Gas stripping is the best technique for butanol recovery found so far.

  2. Strategies to diagnose and control microbial souring in natural gas storage reservoirs and produced water systems

    SciTech Connect

    Morris, E.A.; Derr, R.M.; Pope, D.H.

    1995-12-31

    Hydrogen sulfide production (souring) in natural gas storage reservoirs and produced water systems is a safety and environmental problem that can lead to operational shutdown when local hydrogen sulfide standards are exceeded. Systems affected by microbial souring have historically been treated using biocides that target the general microbial community. However, requirements for more environmentally friendly solutions have led to treatment strategies in which sulfide production can be controlled with minimal impact to the system and environment. Some of these strategies are based on microbial and/or nutritional augmentation of the sour environment. Through research sponsored by the Gas Research Institute (GRI) in Chicago, Illinois, methods have been developed for early detection of microbial souring in natural gas storage reservoirs, and a variety of mitigation strategies have been evaluated. The effectiveness of traditional biocide treatment in gas storage reservoirs was shown to depend heavily on the methods by which the chemical is applied. An innovative strategy using nitrate was tested and proved ideal for produced water and wastewater systems. Another strategy using elemental iodine was effective for sulfide control in evaporation ponds and is currently being tested in microbially sour natural gas storage wells.

  3. Microbial protein production: maximizing protein production efficiency in Space habitats

    NASA Astrophysics Data System (ADS)

    Clauwaert, Peter; Alloul, Abbas; Muys, Maarten; Sui, Yixing; Boon, Nico; Luther, Amanda; Christiaens, Marlies E. R.; Ilgrande, Chiara; Lindeboom, Ralph E. F.; Rabaey, Korneel; Vlaeminck, Siegfried

    2016-07-01

    On top of the goal of a closed material cycle for Space habitats or deep Space missions with food production, extreme requirements apply to such Life Support Systems (LSS) in terms of mass, volume, crew time, energy consumption and controllability. Although relatively high water recovery efficiencies (~70-90%) can be achieved, all Space missions until now have relied on terrestrial food resupply and thus no nutrient recovery has been achieved so far. Researchers and Space agencies have typically been focussing on the cultivation of higher plants to produce food for crew members for future Space LSS. It can be assumed that the required surface area (50-500 m2 per crew member), plant evaporation rates (~200 kg per crew member per day), power consumption (~65 kW per crew member) and the degree of controllability of a higher plant compartment will have a great impact on the feasibility of realizing a future closed loop LSS in Space for the first time. As the food production density is so critical in a LSS, a combination of higher plant cultivation and microbial protein production might increase the chances of success of future Space LSS's since the production densities are significantly higher. Higher plants in Space LSS's would typically have an average specific protein production rate in the order of 0-4 kg protein m-3 year-1 (calculated from Do, Owens et al. (2016)), whereas bacterial biomass can be produced continuously at a rate up to ~1000 kg protein m-3 year-1. Several routes for microbial food production will be discussed in this presentation, ranging from aerobic heterotrophic production with for instance Candida ingens (Strayer, Finger et al. 1997), photoheterotrophic production with PNSB such as Rhodospirillum rubrum (Hendrickx, De Wever et al. 2006) and hydrogenotrophic production with HOB such as Cupriavidus necator (Matassa, Boon et al. 2015)) and photoautotrophic production of oxygen and microbial food (e.g. Arthrospira sp. (Hendrickx, De Wever et al

  4. Natural products and diabetes treatment.

    PubMed

    Gori, M; Campbell, R K

    1998-01-01

    Many natural products are promoted to improve the health status of patients with diabetes by people making a profit on these products. Few of these claims have any scientific basis. Certain natural products are potentially damaging to patients with chronic diseases, especially if the products are used instead of proven scientific treatment regimens. Many individuals believe that if a product is natural it must be effective and safe. What is ironic is that if the products were safe and effective, and if studies would have been done on humans to prove safety and effectiveness, the sales of the products would greatly increase (as opposed to present limited sales as herbs from health food stores). Some of the products do have a beneficial effect, especially as a placebo if the patient believes that the product is going to work. As can be seen from the summary of products that are listed here that claim to improve the treatment of patients with diabetes, very few are available in a standard form that would produce a known positive effect. The few products that do have a mild impact on lowering blood glucose levels are much less effective than standard treatments. In a recent review of the role of plant-derived drugs and herbal medicines in healthcare, no natural products were listed as having a beneficial effect on diabetes. Diabetes care providers need to confront the issue of the use of natural products with their patients. Patients should be taught the importance of using proven, effective treatment regimens. Any patient who decides to use a natural product should be followed closely to make sure that no toxic effects occur and that treatment objectives are achieved.

  5. High impact technologies for natural products screening.

    PubMed

    Koehn, Frank E

    2008-01-01

    Natural products have historically been a rich source of lead molecules in drug discovery. However, natural products have been de-emphasized as high throughput screening resources in the recent past, in part because of difficulties in obtaining high quality natural products screening libraries, or in applying modern screening assays to these libraries. In addition, natural products programs based on screening of extract libraries, bioassay-guided isolation, structure elucidation and subsequent production scale-up are challenged to meet the rapid cycle times that are characteristic of the modern HTS approach. Fortunately, new technologies in mass spectrometry, NMR and other spectroscopic techniques can greatly facilitate the first components of the process - namely the efficient creation of high-quality natural products libraries, bimolecular target or cell-based screening, and early hit characterization. The success of any high throughput screening campaign is dependent on the quality of the chemical library. The construction and maintenance of a high quality natural products library, whether based on microbial, plant, marine or other sources is a costly endeavor. The library itself may be composed of samples that are themselves mixtures - such as crude extracts, semi-pure mixtures or single purified natural products. Each of these library designs carries with it distinctive advantages and disadvantages. Crude extract libraries have lower resource requirements for sample preparation, but high requirements for identification of the bioactive constituents. Pre-fractionated libraries can be an effective strategy to alleviate interferences encountered with crude libraries, and may shorten the time needed to identify the active principle. Purified natural product libraries require substantial resources for preparation, but offer the advantage that the hit detection process is reduced to that of synthetic single component libraries. Whether the natural products library

  6. Production, purification and properties of microbial phytases.

    PubMed

    Pandey, A; Szakacs, G; Soccol, C R; Rodriguez-Leon, J A; Soccol, V T

    2001-05-01

    Phytases (myo-inositol hexakisphosphate phosphohydrolase, EC 3.1.3.8) catalyse the release of phosphate from phytate (mycoinositol hexakiphosphate). Several cereal grains, legumes and oilseeds, etc., store phosphorus as phytate. Environmental pollution due to the high-phosphate manure, resulting in the accumulation of P at various locations has raised serious concerns. Phytases appear of significant value in effectively controlling P pollution. They can be produced from a host of sources including plants, animals and micro-organisms. Microbial sources, however, are promising for their commercial exploitations. Strains of Aspergillus sp., chiefly A. ficuum and A. niger have most commonly been employed for industrial purposes. Phytases are considered as a monomeric protein, generally possessing a molecular weight between 40 and 100 kDa. They show broad substrate specificity and have generally pH and temperature optima around 4.5-6.0 and 45-60 degrees C. The crystal structure of phytase has been determined at 2.5 A resolution. Immobilization of phytase has been found to enhance its thermostability. This article reviews recent trends on the production, purification and properties of microbial phytases.

  7. Bioactive natural products from Lysobacter

    PubMed Central

    Xie, Yunxuan; Wright, Stephen; Shen, Yuemao

    2012-01-01

    The gliding Gram-negative Lysobacter bacteria are emerging as a promising source of new bioactive natural products. These ubiquitous freshwater and soil microorganisms are fast growing, simple to use and maintain, and genetically amenable for biosynthetic engineering. This Highlight reviews a group of biologically active and structurally distinct natural products from the genus Lysobacter, with a focus on their biosyntheses. Although Lysobacter sp. are known as prolific producers of bioactive natural products, detailed molecular mechanistic studies of their enzymatic assembly have been surprisingly scarce. We hope to provide a snapshot of the important work done on the lysobacterial natural products and to provide useful information for future biosynthetic engineering of novel antibiotics in Lysobacter. PMID:22898908

  8. Microbial production of 1,3-propanediol.

    PubMed

    Sauer, Michael; Marx, Hans; Mattanovich, Diethard

    2008-01-01

    The introduction of economic production processes for 1,3-propanediol is a success story for the creation of a new market for a (bulk) chemical. The compound and its favorable properties have long been known; also the fermentation of glycerol to 1,3-propanediol had been described more than 120 years ago. Nevertheless, the product remained a specialty chemical until recently, when two new processes were introduced, providing 1,3-propanediol at a competitive price. Remarkably, one of the processes is in the field of white biotechnology and based on microbial fermentation, converting a renewable carbon source into a bulk chemical. This review covers the most important patents that led to the commercialization of bio-based 1,3-propanediol. Furthermore, some of the recent developments towards a sustainable industry are addressed. Similar questions arise for a variety of products if they are to be produced bio-based in large scale. However, special emphasis is given to 1,3-propanediol production.

  9. Microbial products from sweet potato wastes

    SciTech Connect

    Nghiem, N.P.

    1982-01-01

    Microbial production of methane from alkaline sweet potato wastes was studied. Assessment of methane production potential was based on total COD of the wastes. A single-stage and a two-stage system were studied. In both systems, to ensure stable operation and high performance, methane fermenters had to be initially seeded with large quantities of methane formers. A 50% inoculum (based on total fermenter volume) was found to be most effective. Methane formers tended to aggregate to form spherical particles which had extremely high settling rates, this eliminated the requirement of cell recycle. In both single-stage and two-stage systems the rates of gas production was sufficiently fast to induce thorough mixing of the fermenter contents. At low residence times of two and four days the two-stage system achieved significantly higher conversions. Gas production started almost immediately after feeding the methane fermenter of the two-stage system. The conversions in the methane fermenter of a two-stage system could be predicted by a model based on Contois' kinetics. The composition of the gas produced in this fermenter could also be predicted from the distribution of the organic acids in the effluent from the acid fermenter. The acid formation stage was studied in a chemostat operated at a fixed residence time of 5.5 hours. The highest yield of 0.09 g protein/g glucose consumed was obtained at pH 5.5 and 37/sup 0/C.

  10. Coastal Microbial Mat Diversity along a Natural Salinity Gradient

    PubMed Central

    Bolhuis, Henk; Fillinger, Lucas; Stal, Lucas J.

    2013-01-01

    The North Sea coast of the Dutch barrier island of Schiermonnikoog is covered by microbial mats that initiate a succession of plant communities that eventually results in the development of a densely vegetated salt marsh. The North Sea beach has a natural elevation running from the low water mark to the dunes resulting in gradients of environmental factors perpendicular to the beach. These gradients are due to the input of seawater at the low water mark and of freshwater from upwelling groundwater at the dunes and rainfall. The result is a natural and dynamic salinity gradient depending on the tide, rainfall and wind. We studied the microbial community composition in thirty three samples taken every ten meters along this natural salinity gradient by using denaturing gradient gel electrophoresis (DGGE) of rRNA gene fragments. We looked at representatives from each Domain of life (Bacteria, Archaea and Eukarya) and with a particular emphasis on Cyanobacteria. Analysis of the DGGE fingerprints together with pigment composition revealed three distinct microbial mat communities, a marine community dominated by diatoms as primary producers, an intermediate brackish community dominated by Cyanobacteria as primary producers and a freshwater community with Cyanobacteria and freshwater green algae. PMID:23704895

  11. Coastal microbial mat diversity along a natural salinity gradient.

    PubMed

    Bolhuis, Henk; Fillinger, Lucas; Stal, Lucas J

    2013-01-01

    The North Sea coast of the Dutch barrier island of Schiermonnikoog is covered by microbial mats that initiate a succession of plant communities that eventually results in the development of a densely vegetated salt marsh. The North Sea beach has a natural elevation running from the low water mark to the dunes resulting in gradients of environmental factors perpendicular to the beach. These gradients are due to the input of seawater at the low water mark and of freshwater from upwelling groundwater at the dunes and rainfall. The result is a natural and dynamic salinity gradient depending on the tide, rainfall and wind. We studied the microbial community composition in thirty three samples taken every ten meters along this natural salinity gradient by using denaturing gradient gel electrophoresis (DGGE) of rRNA gene fragments. We looked at representatives from each Domain of life (Bacteria, Archaea and Eukarya) and with a particular emphasis on Cyanobacteria. Analysis of the DGGE fingerprints together with pigment composition revealed three distinct microbial mat communities, a marine community dominated by diatoms as primary producers, an intermediate brackish community dominated by Cyanobacteria as primary producers and a freshwater community with Cyanobacteria and freshwater green algae.

  12. Biohydrogen Production: Strategies to Improve Process Efficiency through Microbial Routes

    PubMed Central

    Chandrasekhar, Kuppam; Lee, Yong-Jik; Lee, Dong-Woo

    2015-01-01

    The current fossil fuel-based generation of energy has led to large-scale industrial development. However, the reliance on fossil fuels leads to the significant depletion of natural resources of buried combustible geologic deposits and to negative effects on the global climate with emissions of greenhouse gases. Accordingly, enormous efforts are directed to transition from fossil fuels to nonpolluting and renewable energy sources. One potential alternative is biohydrogen (H2), a clean energy carrier with high-energy yields; upon the combustion of H2, H2O is the only major by-product. In recent decades, the attractive and renewable characteristics of H2 led us to develop a variety of biological routes for the production of H2. Based on the mode of H2 generation, the biological routes for H2 production are categorized into four groups: photobiological fermentation, anaerobic fermentation, enzymatic and microbial electrolysis, and a combination of these processes. Thus, this review primarily focuses on the evaluation of the biological routes for the production of H2. In particular, we assess the efficiency and feasibility of these bioprocesses with respect to the factors that affect operations, and we delineate the limitations. Additionally, alternative options such as bioaugmentation, multiple process integration, and microbial electrolysis to improve process efficiency are discussed to address industrial-level applications. PMID:25874756

  13. Biohydrogen production: strategies to improve process efficiency through microbial routes.

    PubMed

    Chandrasekhar, Kuppam; Lee, Yong-Jik; Lee, Dong-Woo

    2015-04-14

    The current fossil fuel-based generation of energy has led to large-scale industrial development. However, the reliance on fossil fuels leads to the significant depletion of natural resources of buried combustible geologic deposits and to negative effects on the global climate with emissions of greenhouse gases. Accordingly, enormous efforts are directed to transition from fossil fuels to nonpolluting and renewable energy sources. One potential alternative is biohydrogen (H2), a clean energy carrier with high-energy yields; upon the combustion of H2, H2O is the only major by-product. In recent decades, the attractive and renewable characteristics of H2 led us to develop a variety of biological routes for the production of H2. Based on the mode of H2 generation, the biological routes for H2 production are categorized into four groups: photobiological fermentation, anaerobic fermentation, enzymatic and microbial electrolysis, and a combination of these processes. Thus, this review primarily focuses on the evaluation of the biological routes for the production of H2. In particular, we assess the efficiency and feasibility of these bioprocesses with respect to the factors that affect operations, and we delineate the limitations. Additionally, alternative options such as bioaugmentation, multiple process integration, and microbial electrolysis to improve process efficiency are discussed to address industrial-level applications.

  14. Recent advances in amino acid production by microbial cells.

    PubMed

    Hirasawa, Takashi; Shimizu, Hiroshi

    2016-12-01

    Amino acids have been utilized for the production of foods, animal feeds and pharmaceuticals. After the discovery of the glutamic acid-producing bacterium Corynebacterium glutamicum by Japanese researchers, the production of amino acids, which are primary metabolites, has been achieved using various microbial cells as hosts. Recently, metabolic engineering studies on the rational design of amino acid-producing microbial cells have been successfully conducted. Moreover, the technology of systems biology has been applied to metabolic engineering for the creation of amino acid-producing microbial cells. Currently, new technologies including synthetic biology, single-cell analysis, and evolutionary engineering have been utilized to create amino acid-producing microbial cells. In addition, useful compounds from amino acids have been produced by microbial cells. Here, current researches into the metabolic engineering of microbial cells toward production of amino acids and amino acid-related compounds are reviewed.

  15. Metabolomics and dereplication strategies in natural products.

    PubMed

    Tawfike, Ahmed Fares; Viegelmann, Christina; Edrada-Ebel, Ruangelie

    2013-01-01

    Metabolomic methods can be utilized to screen diverse biological sources of potentially novel and sustainable sources of antibiotics and pharmacologically-active drugs. Dereplication studies by high resolution Fourier transform mass spectrometry coupled to liquid chromatography (LC-HRFTMS) and nuclear magnetic resonance (NMR) spectroscopy can establish the chemical profile of endophytic and/or endozoic microbial extracts and their plant or animal sources. Identifying the compounds of interest at an early stage will aid in the isolation of the bioactive components. Therefore metabolite profiling is important for functional genomics and in the search for new pharmacologically active compounds. Using the tools of metabolomics through the employment of LC-HRFTMS as well as high resolution NMR will be a very efficient approach. Metabolomic profiling has found its application in screening extracts of macroorganisms as well as in the isolation and cultivation of suspected microbial producers of bioactive natural products.Metabolomics is being applied to identify and biotechnologically optimize the production of pharmacologically active secondary metabolites. The links between metabolome evolution during optimization and processing factors can be identified through metabolomics. Information obtained from a metabolomics dataset can efficiently establish cultivation and production processes at a small scale which will be finally scaled up to a fermenter system, while maintaining or enhancing synthesis of the desired compounds. MZmine (BMC Bioinformatics 11:395-399, 2010; http://mzmine.sourceforge.net/download.shtml ) and SIEVE ( http://www.vastscientific.com/resources/index.html ; Rapid Commun Mass Spectrom 22:1912-1918, 2008) softwares are utilized to perform differential analysis of sample populations to find significant expressed features of complex biomarkers between parameter variables. Metabolomes are identified with the aid of existing high resolution MS and NMR

  16. Genomic Prospecting for Microbial Biodiesel Production

    SciTech Connect

    Lykidis, Athanasios; Lykidis, Athanasios; Ivanova, Natalia

    2008-03-20

    Biodiesel is defined as fatty acid mono-alkylesters and is produced from triacylglycerols. In the current article we provide an overview of the structure, diversity and regulation of the metabolic pathways leading to intracellular fatty acid and triacylglycerol accumulation in three types of organisms (bacteria, algae and fungi) of potential biotechnological interest and discuss possible intervention points to increase the cellular lipid content. The key steps that regulate carbon allocation and distribution in lipids include the formation of malonyl-CoA, the synthesis of fatty acids and their attachment onto the glycerol backbone, and the formation of triacylglycerols. The lipid biosynthetic genes and pathways are largely known for select model organisms. Comparative genomics allows the examination of these pathways in organisms of biotechnological interest and reveals the evolution of divergent and yet uncharacterized regulatory mechanisms. Utilization of microbial systems for triacylglycerol and fatty acid production is in its infancy; however, genomic information and technologies combined with synthetic biology concepts provide the opportunity to further exploit microbes for the competitive production of biodiesel.

  17. Recognition of Microbial Glycolipids by Natural Killer T Cells

    PubMed Central

    Zajonc, Dirk M.; Girardi, Enrico

    2015-01-01

    T cells can recognize microbial antigens when presented by dedicated antigen-presenting molecules. While peptides are presented by classical members of the major histocompatibility complex (MHC) family (MHC I and II), lipids, glycolipids, and lipopeptides can be presented by the non-classical MHC member, CD1. The best studied subset of lipid-reactive T cells are type I natural killer T (iNKT) cells that recognize a variety of different antigens when presented by the non-classical MHCI homolog CD1d. iNKT cells have been shown to be important for the protection against various microbial pathogens, including B. burgdorferi, the causative agents of Lyme disease, and S. pneumoniae, which causes pneumococcal meningitis and community-acquired pneumonia. Both pathogens carry microbial glycolipids that can trigger the T cell antigen receptor (TCR), leading to iNKT cell activation. iNKT cells have an evolutionary conserved TCR alpha chain, yet retain the ability to recognize structurally diverse glycolipids. They do so using a conserved recognition mode, in which the TCR enforces a conserved binding orientation on CD1d. TCR binding is accompanied by structural changes within the TCR binding site of CD1d, as well as the glycolipid antigen itself. In addition to direct recognition of microbial antigens, iNKT cells can also be activated by a combination of cytokines (IL-12/IL-18) and TCR stimulation. Many microbes carry TLR antigens, and microbial infections can lead to TLR activation. The subsequent cytokine response in turn lower the threshold of TCR-mediated iNKT cell activation, especially when weak microbial or even self-antigens are presented during the cause of the infection. In summary, iNKT cells can be directly activated through TCR triggering of strong antigens, while cytokines produced by the innate immune response may be necessary for TCR triggering and iNKT cell activation in the presence of weak antigens. Here, we will review the molecular basis of iNKT cell

  18. Synthesis of Polycyclic Natural Products

    SciTech Connect

    Nguyen, Tuan Hoang

    2003-01-01

    With the continuous advancements in molecular biology and modern medicine, organic synthesis has become vital to the support and extension of those discoveries. The isolations of new natural products allow for the understanding of their biological activities and therapeutic value. Organic synthesis is employed to aid in the determination of the relationship between structure and function of these natural products. The development of synthetic methodologies in the course of total syntheses is imperative for the expansion of this highly interdisciplinary field of science. In addition to the practical applications of total syntheses, the structural complexity of natural products represents a worthwhile challenge in itself. The pursuit of concise and efficient syntheses of complex molecules is both gratifying and enjoyable.

  19. Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems.

    PubMed

    Perez-Garcia, Octavio; Lear, Gavin; Singhal, Naresh

    2016-01-01

    We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can

  20. Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

    PubMed Central

    Perez-Garcia, Octavio; Lear, Gavin; Singhal, Naresh

    2016-01-01

    We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can

  1. Microbial fuel cells and microbial ecology: applications in ruminant health and production research.

    PubMed

    Bretschger, Orianna; Osterstock, Jason B; Pinchak, William E; Ishii, Shun'ichi; Nelson, Karen E

    2010-04-01

    Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H(2)) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H(2)in the rumen. Given the crucial role that H(2) plays in ruminant digestion, it is desirable to understand the microbial relationships that control H(2) partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research.

  2. Microbial Fuel Cells and Microbial Ecology: Applications in Ruminant Health and Production Research

    PubMed Central

    Osterstock, Jason B.; Pinchak, William E.; Ishii, Shun’ichi; Nelson, Karen E.

    2009-01-01

    Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H2) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H2in the rumen. Given the crucial role that H2 plays in ruminant digestion, it is desirable to understand the microbial relationships that control H2 partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research. PMID:20024685

  3. Microbial community structure of three traditional zambian fermented products: mabisi, chibwantu and munkoyo.

    PubMed

    Schoustra, Sijmen E; Kasase, Chitundu; Toarta, Cristian; Kassen, Rees; Poulain, Alexandre J

    2013-01-01

    Around the world, raw materials are converted into fermented food products through microbial and enzymatic activity. Products are typically produced using a process known as batch culture, where small volumes of an old culture are used to initiate a fresh culture. Repeated over many years, and provided samples are not shared among producers, batch culture techniques allow for the natural evolution of independent microbial ecosystems. While these products form an important part of the diets of many people because of their nutritional, organoleptic and food safety properties, for many traditional African fermented products the microbial communities responsible for fermentation are largely unknown. Here we describe the microbial composition of three traditional fermented non-alcoholic beverages that are widely consumed across Zambia: the milk based product Mabisi and the cereal based products Munkoyo and Chibwantu. Using culture and non-culture based techniques, we found that six to eight lactic acid bacteria predominate in all products. We then used this data to investigate in more detail the factors affecting community structure. We found that products made from similar raw materials do not harbor microbial communities that are more similar to each other than those made from different raw materials. We also found that samples from the same product taken at the same location were as different from each other in terms of microbial community structure and composition, as those from geographically very distant locations. These results suggest that microbial community structure in these products is neither a simple consequence of the raw materials used, nor the particular suite of microbes available in the environment but that anthropogenic variables (e.g., competition among sellers or organoleptic preferences by different tribes) are important in shaping the microbial community structures.

  4. Natural products: DNA double whammy

    NASA Astrophysics Data System (ADS)

    Gates, Kent S.

    2014-06-01

    The lomaiviticins are exceedingly potent antibiotic agents, but the mechanism responsible for this activity has so far been unclear. Now, efficient generation of double-strand breaks in DNA by lomaiviticin A has been linked to the remarkable cytotoxicity of these diazobenzofluorene-containg natural products.

  5. EIA's Natural Gas Production Data

    EIA Publications

    2009-01-01

    This special report examines the stages of natural gas processing from the wellhead to the pipeline network through which the raw product becomes ready for transportation and eventual consumption, and how this sequence is reflected in the data published by the Energy Information Administration (EIA).

  6. Chemical diversity of microbial volatiles and their potential for plant growth and productivity.

    PubMed

    Kanchiswamy, Chidananda Nagamangala; Malnoy, Mickael; Maffei, Massimo E

    2015-01-01

    Microbial volatile organic compounds (MVOCs) are produced by a wide array of microorganisms ranging from bacteria to fungi. A growing body of evidence indicates that MVOCs are ecofriendly and can be exploited as a cost-effective sustainable strategy for use in agricultural practice as agents that enhance plant growth, productivity, and disease resistance. As naturally occurring chemicals, MVOCs have potential as possible alternatives to harmful pesticides, fungicides, and bactericides as well as genetic modification. Recent studies performed under open field conditions demonstrate that efficiently adopting MVOCs may contribute to sustainable crop protection and production. We review here the chemical diversity of MVOCs by describing microbial-plants and microbial-microbial interactions. Furthermore, we discuss MVOCs role in inducing phenotypic plant responses and their potential physiological effects on crops. Finally, we analyze potential and actual limitations for MVOC use and deployment in field conditions as a sustainable strategy for improving productivity and reducing pesticide use.

  7. White Paper on Natural Products.

    PubMed

    Gabay, Michael; Smith, Judith A; Chavez, Mary L; Goldwire, Micheline; Walker, Scot; Coon, Scott A; Gosser, Rena; Hume, Anne L; Musselman, Megan; Phillips, Jennifer; Abe, Andrew M

    2017-01-01

    The American College of Clinical Pharmacy (ACCP) published an initial white paper on herbal products in 2000. Since then, the global market for natural products has continued to expand, with tens of millions of consumers using such products on an annual basis in the United States alone. However, despite this expansion, natural products remain largely unregulated compared with prescription medications, have moderate- to low-level clinical evidence for efficacy, and continue to have safety concerns, including adulteration and misbranding. As comprehensive medication management experts, clinical pharmacists are uniquely qualified to navigate these concerns and advise patients appropriately. To develop and recommend a suitable care plan involving natural products, clinical pharmacists must establish a strong pharmacist-patient relationship, assess the appropriateness of therapy, educate the patient regarding key issues, and continuously monitor and follow up on the effectiveness of the care plan. This process should not only occur in an individual community or hospital setting, but also whenever a patient transitions from one care setting to another in cooperation with other clinicians.

  8. Natural and Heterologous Production of Bacteriocins

    NASA Astrophysics Data System (ADS)

    Cintas, Luis M.; Herranz, Carmen; Hernández, Pablo E.

    Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria, and their use as natural and nontoxic food preservatives has been the source of considerable interest for the research community. In addition, bacteriocins have been investigated for their potential use in human and veterinary applications and in the animal production field. In the native bacterial strain, most bacteriocins are synthesized as biologically inactive precursors, with N-terminal extensions, that are cleaved concomitantly during export of the bacteriocin by dedicated ABC transporters, or the general secretory pathway (GSP) or Sec-dependent pathway. However, a few bacteriocins are synthesized without an N-terminal extension, and others are circularized through a head-to-tail peptide bond, complicating the elucidation of their processing and transport across the cytoplasmic membrane. The high cost of synthetic bacteriocin synthesis and their low yields from many natural producers recommends the exploration of recombinant microbial systems for the heterologous production of bacteriocins. Other advantages of such systems include production of bacteriocins in safer hosts, increased bacteriocin production, control of bacteriocin gene expression, production of food ingredients with antimicrobial activity, construction of multibacteriocinogenic strains with a wider antagonistic spectrum, a better adaptation of the selected hosts to food environments, and providing antagonistic properties to lactic acid bacteria (LAB) used as starter, protective, or probiotic cultures. The recombinant production of bacteriocins mostly relies on the use of expression vectors that replicate in Gram-negative bacteria, Gram-positive bacteria, and yeasts, whereas the production of bacteriocins in heterologous LAB hosts may be essentially based on the expression of native biosynthetic genes, by exchanging or replacing leader peptides and/or dedicated processing and secretion systems (ABC transporters

  9. Bioactive natural products from Papua New Guinea marine sponges.

    PubMed

    Noro, Jeffery C; Kalaitzis, John A; Neilan, Brett A

    2012-10-01

    The discovery of novel natural products for drug development relies heavily upon a rich biodiversity, of which the marine environment is an obvious example. Marine natural product research has spawned several drugs and many other candidates, some of which are the focus of current clinical trials. The sponge megadiversity of Papua New Guinea is a rich but underexplored source of bioactive natural products. Here, we review some of the many natural products derived from PNG sponges with an emphasis on those with interesting biological activity and, therefore, drug potential. Many bioactive natural products discussed here appear to be derived from non-ribosomal peptide and polyketide biosynthesis pathways, strongly suggesting a microbial origin of these compounds. With this in mind, we also explore the notion of sponge-symbiont biosynthesis of these bioactive compounds and present examples to support the working hypothesis.

  10. A microbial biomanufacturing platform for natural and semisynthetic opioids.

    PubMed

    Thodey, Kate; Galanie, Stephanie; Smolke, Christina D

    2014-10-01

    Opiates and related molecules are medically essential, but their production via field cultivation of opium poppy Papaver somniferum leads to supply inefficiencies and insecurity. As an alternative production strategy, we developed baker's yeast Saccharomyces cerevisiae as a microbial host for the transformation of opiates. Yeast strains engineered to express heterologous genes from P. somniferum and bacterium Pseudomonas putida M10 convert thebaine to codeine, morphine, hydromorphone, hydrocodone and oxycodone. We discovered a new biosynthetic branch to neopine and neomorphine, which diverted pathway flux from morphine and other target products. We optimized strain titer and specificity by titrating gene copy number, enhancing cosubstrate supply, applying a spatial engineering strategy and performing high-density fermentation, which resulted in total opioid titers up to 131 mg/l. This work is an important step toward total biosynthesis of valuable benzylisoquinoline alkaloid drug molecules and demonstrates the potential for developing a sustainable and secure yeast biomanufacturing platform for opioids.

  11. NATURAL PRODUCTS: A CONTINUING SOURCE OF NOVEL DRUG LEADS

    PubMed Central

    Cragg, Gordon M.; Newman, David J.

    2013-01-01

    1. Background Nature has been a source of medicinal products for millennia, with many useful drugs developed from plant sources. Following discovery of the penicillins, drug discovery from microbial sources occurred and diving techniques in the 1970s opened the seas. Combinatorial chemistry (late 1980s), shifted the focus of drug discovery efforts from Nature to the laboratory bench. 2. Scope of Review This review traces natural products drug discovery, outlining important drugs from natural sources that revolutionized treatment of serious diseases. It is clear Nature will continue to be a major source of new structural leads, and effective drug development depends on multidisciplinary collaborations. 3. Major Conclusions The explosion of genetic information led not only to novel screens, but the genetic techniques permitted the implementation of combinatorial biosynthetic technology and genome mining. The knowledge gained has allowed unknown molecules to be identified. These novel bioactive structures can be optimized by using combinatorial chemistry generating new drug candidates for many diseases. 4 General Significance: The advent of genetic techniques that permitted the isolation / expression of biosynthetic cassettes from microbes may well be the new frontier for natural products lead discovery. It is now apparent that biodiversity may be much greater in those organisms. The numbers of potential species involved in the microbial world are many orders of magnitude greater than those of plants and multi-celled animals. Coupling these numbers to the number of currently unexpressed biosynthetic clusters now identified (>10 per species) the potential of microbial diversity remains essentially untapped. PMID:23428572

  12. Microbial production of lactic acid: the latest development.

    PubMed

    Juturu, Veeresh; Wu, Jin Chuan

    2016-12-01

    Lactic acid is an important platform chemical for producing polylactic acid (PLA) and other value-added products. It is naturally produced by a wide spectrum of microbes including bacteria, yeast and filamentous fungi. In general, bacteria ferment C5 and C6 sugars to lactic acid by either homo- or hetero-fermentative mode. Xylose isomerase, phosphoketolase, transaldolase, l- and d-lactate dehydrogenases are the key enzymes that affect the ways of lactic acid production. Metabolic engineering of microbial strains are usually needed to produce lactic acid from unconventional carbon sources. Production of d-LA has attracted much attention due to the demand for producing thermostable PLA, but large scale production of d-LA has not yet been commercialized. Thermophilic Bacillus coagulans strains are able to produce l-lactic acid from lignocellulose sugars homo-fermentatively under non-sterilized conditions, but the lack of genetic tools for metabolically engineering them severely affects their development for industrial applications. Pre-treatment of agriculture biomass to obtain fermentable sugars is a pre-requisite for utilization of the huge amounts of agricultural biomass to produce lactic acid. The major challenge is to obtain quality sugars of high concentrations in a cost effective-way. To avoid or minimize the use of neutralizing agents during fermentation, genetically engineering the strains to make them resist acidic environment and produce lactic acid at low pH would be very helpful for reducing the production cost of lactic acid.

  13. Unconventional food regeneration in space - Opportunities for microbial food production

    NASA Technical Reports Server (NTRS)

    Petersen, Gene R.; Schubert, Wayne W.; Seshan, P. K.; Dunlop, Eric H.

    1987-01-01

    The possible role of microbial species in regenerating food is considered, and three areas where microbial systems can be used in controlled ecological life support systems are discussed. Microbial species can serve as the biological portion of hybrid chemical/biological schemes for primary food products, as a means more fully to utilize waste materials from agronomical food production, and as a source of nutritional supplements to conventional plant foods. Work accomplished in each of these areas is described. The role of microgravity fermenters in this technology is addressed.

  14. Automated genome mining of ribosomal peptide natural products

    SciTech Connect

    Mohimani, Hosein; Kersten, Roland; Liu, Wei; Wang, Mingxun; Purvine, Samuel O.; Wu, Si; Brewer, Heather M.; Pasa-Tolic, Ljiljana; Bandeira, Nuno; Moore, Bradley S.; Pevzner, Pavel A.; Dorrestein, Pieter C.

    2014-07-31

    Ribosomally synthesized and posttranslationally modified peptides (RiPPs), especially from microbial sources, are a large group of bioactive natural products that are a promising source of new (bio)chemistry and bioactivity (1). In light of exponentially increasing microbial genome databases and improved mass spectrometry (MS)-based metabolomic platforms, there is a need for computational tools that connect natural product genotypes predicted from microbial genome sequences with their corresponding chemotypes from metabolomic datasets. Here, we introduce RiPPquest, a tandem mass spectrometry database search tool for identification of microbial RiPPs and apply it for lanthipeptide discovery. RiPPquest uses genomics to limit search space to the vicinity of RiPP biosynthetic genes and proteomics to analyze extensive peptide modifications and compute p-values of peptide-spectrum matches (PSMs). We highlight RiPPquest by connection of multiple RiPPs from extracts of Streptomyces to their gene clusters and by the discovery of a new class III lanthipeptide, informatipeptin, from Streptomyces viridochromogenes DSM 40736 as the first natural product to be identified in an automated fashion by genome mining. The presented tool is available at cy-clo.ucsd.edu.

  15. The chemical logic of plant natural product biosynthesis.

    PubMed

    Anarat-Cappillino, Gülbenk; Sattely, Elizabeth S

    2014-06-01

    Understanding the logic of plant natural product biosynthesis is important for three reasons: it guides the search for new natural products and pathways, illuminates the function of existing pathways in the context of host biology, and builds an enabling 'parts list' for plant and microbial metabolic engineering. In this review, we highlight the chemical themes that underlie a broad range of plant pathways, dividing pathways into two parts: scaffold-generating steps that draw on a limited set of chemistries, and tailoring reactions that produce a wide range of end products from a small number of common scaffolds.

  16. Synergistic microbial consortium for bioenergy generation from complex natural energy sources.

    PubMed

    Wang, Victor Bochuan; Yam, Joey Kuok Hoong; Chua, Song-Lin; Zhang, Qichun; Cao, Bin; Chye, Joachim Loo Say; Yang, Liang

    2014-01-01

    Microbial species have evolved diverse mechanisms for utilization of complex carbon sources. Proper combination of targeted species can affect bioenergy production from natural waste products. Here, we established a stable microbial consortium with Escherichia coli and Shewanella oneidensis in microbial fuel cells (MFCs) to produce bioenergy from an abundant natural energy source, in the form of the sarcocarp harvested from coconuts. This component is mostly discarded as waste. However, through its usage as a feedstock for MFCs to produce useful energy in this study, the sarcocarp can be utilized meaningfully. The monospecies S. oneidensis system was able to generate bioenergy in a short experimental time frame while the monospecies E. coli system generated significantly less bioenergy. A combination of E. coli and S. oneidensis in the ratio of 1:9 (v:v) significantly enhanced the experimental time frame and magnitude of bioenergy generation. The synergistic effect is suggested to arise from E. coli and S. oneidensis utilizing different nutrients as electron donors and effect of flavins secreted by S. oneidensis. Confocal images confirmed the presence of biofilms and point towards their importance in generating bioenergy in MFCs.

  17. Natural products for cancer chemotherapy

    PubMed Central

    Demain, Arnold L.; Vaishnav, Preeti

    2011-01-01

    Summary For over 40 years, natural products have served us well in combating cancer. The main sources of these successful compounds are microbes and plants from the terrestrial and marine environments. The microbes serve as a major source of natural products with anti‐tumour activity. A number of these products were first discovered as antibiotics. Another major contribution comes from plant alkaloids, taxoids and podophyllotoxins. A vast array of biological metabolites can be obtained from the marine world, which can be used for effective cancer treatment. The search for novel drugs is still a priority goal for cancer therapy, due to the rapid development of resistance to chemotherapeutic drugs. In addition, the high toxicity usually associated with some cancer chemotherapy drugs and their undesirable side‐effects increase the demand for novel anti‐tumour drugs active against untreatable tumours, with fewer side‐effects and/or with greater therapeutic efficiency. This review points out those technologies needed to produce the anti‐tumour compounds of the future. PMID:21375717

  18. Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

    SciTech Connect

    Sobecky, Patricia A.

    2015-04-06

    In this project, inter-disciplinary research activities were conducted in collaboration among investigators at The University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3 from the Oak Ridge Field Research Center result in solid U-phosphate precipitation in aerobic and anaerobic conditions; (ii) investigate the eventual competition between uranium biomineralization via U-phosphate precipitation and uranium bioreduction; (iii) determine subsurface microbial community structure changes of Area 2 soils following organophosphate amendments; (iv) obtain the complete genome sequences of the Rahnella sp. Y9-602 and the type-strain Rahnella aquatilis ATCC 33071 isolated from these soils; (v) determine if polyphosphate accumulation and phytate hydrolysis can be used to promote U(VI) biomineralization in subsurface sediments; (vi) characterize the effect of uranium on phytate hydrolysis by a new microorganism isolated from uranium-contaminated sediments; (vii) utilize positron-emission tomography to label and track metabolically-active bacteria in soil columns, and (viii) study the stability of the uranium phosphate mineral product. Microarray analyses and mineral precipitation characterizations were conducted in collaboration with DOE SBR-funded investigators at LBNL. Thus, microbial phosphorus metabolism has been shown to have a contributing role to uranium immobilization in the subsurface.

  19. A new perspective on microbial landscapes within food production.

    PubMed

    Bokulich, Nicholas A; Lewis, Zachery T; Boundy-Mills, Kyria; Mills, David A

    2016-02-01

    High-throughput, 'next-generation' sequencing tools offer many exciting new possibilities for food research. From investigating microbial dynamics within food fermentations to the ecosystem of the food-processing built environment, amplicon sequencing, metagenomics, and transcriptomics present novel applications for exploring microbial communities in, on, and around our foods. This review discusses the many uses of these tools for food-related and food facility-related research and highlights where they may yield nuanced insight into the microbial world of food production systems.

  20. Microbial Factories for the Production of Benzylisoquinoline Alkaloids.

    PubMed

    Narcross, Lauren; Fossati, Elena; Bourgeois, Leanne; Dueber, John E; Martin, Vincent J J

    2016-03-01

    Benzylisoquinoline alkaloids (BIAs) are a family of ∼2500 alkaloids with both potential and realized pharmaceutical value, including most notably the opiates such as codeine and morphine. Only a few BIAs accumulate readily in plants, which limits the pharmaceutical potential of the family. Shifting BIA production to microbial sources could provide a scalable and flexible source of these compounds in the future. This review details the current status of microbial BIA synthesis and derivatization, including rapid developments in the past 6 months culminating in the synthesis of opioids from glucose in a microbial host.

  1. A new perspective on microbial landscapes within food production

    PubMed Central

    Bokulich, Nicholas A; Lewis, Zachery T; Boundy-Mills, Kyria; Mills, David A

    2016-01-01

    High-throughput, ‘next-generation’ sequencing tools offer many exciting new possibilities for food research. From investigating microbial dynamics within food fermentations to the ecosystem of the food-processing built environment, amplicon sequencing, metagenomics, and transcriptomics present novel applications for exploring microbial communities in, on, and around our foods. This review discusses the many uses of these tools for food-related and food facility-related research and highlights where they may yield nuanced insight into the microbial world of food production systems. PMID:26773388

  2. Microbial response to single-cell protein production and brewery wastewater treatment

    PubMed Central

    Lee, Jackson Z; Logan, Andrew; Terry, Seth; Spear, John R

    2015-01-01

    As global fisheries decline, microbial single-cell protein (SCP) produced from brewery process water has been highlighted as a potential source of protein for sustainable animal feed. However, biotechnological investigation of SCP is difficult because of the natural variation and complexity of microbial ecology in wastewater bioreactors. In this study, we investigate microbial response across a full-scale brewery wastewater treatment plant and a parallel pilot bioreactor modified to produce an SCP product. A pyrosequencing survey of the brewery treatment plant showed that each unit process selected for a unique microbial community. Notably, flow equalization basins were dominated by Prevotella, methanogenesis effluent had the highest levels of diversity, and clarifier wet-well samples were sources of sequences for the candidate bacterial phyla of TM7 and BD1-5. Next, the microbial response of a pilot bioreactor producing SCP was tracked over 1 year, showing that two different production trials produced two different communities originating from the same starting influent. However, SCP production resulted generally in enrichment of several clades of rhizospheric diazotrophs of Alphaproteobacteria and Betaproteobacteria in the bioreactor and even more so in the final product. These diazotrophs are potentially useful as the basis of a SCP product for commercial feed production. PMID:24837420

  3. Biotechnological production of natural zero-calorie sweeteners.

    PubMed

    Philippe, Ryan N; De Mey, Marjan; Anderson, Jeff; Ajikumar, Parayil Kumaran

    2014-04-01

    The increasing public awareness of adverse health impacts from excessive sugar consumption has created increasing interest in plant-derived, natural low-calorie or zero-calorie sweeteners. Two plant species which contain natural sweeteners, Stevia rebaudiana and Siraitia grosvenorii, have been extensively profiled to identify molecules with high intensity sweetening properties. However, sweetening ability does not necessarily make a product viable for commercial applications. Some criteria for product success are proposed to identify which targets are likely to be accepted by consumers. Limitations of plant-based production are discussed, and a case is put forward for the necessity of biotechnological production methods such as plant cell culture or microbial fermentation to meet needs for commercial-scale production of natural sweeteners.

  4. Myxobacterial natural product assembly lines: fascinating examples of curious biochemistry.

    PubMed

    Wenzel, Silke Christine; Müller, Rolf

    2007-12-01

    Over the last 20 years myxobacteria have made their way from highly exotic organisms to one of the major sources of microbial natural products with interesting biological activities. Recent progress towards achieving a better understanding of the genetics and the biochemistry of myxobacterial secondary metabolism, revealed the involvement of numerous exceptional combinations of polyketide synthases and nonribosomal peptide synthetases operating far from textbook biosynthetic logic. In this Highlight, selected examples of recently described systems are discussed in comparison to all myxobacterial natural product assembly lines known to date.

  5. Spatial and temporal control of fungal natural product synthesis.

    PubMed

    Lim, Fang Yun; Keller, Nancy P

    2014-10-01

    Despite their oftentimes-elusive ecological role, fungal natural products have, for better or worse, impacted our daily lives tremendously owing to their diverse and potent bioactive properties. This Janus-faced nature of fungal natural products inevitably ushered in a field of research dedicated towards understanding the ecology, organisms, genes, enzymes, and biosynthetic pathways that give rise to this arsenal of diverse and complex chemistry. Ongoing research in fungal secondary metabolism has not only increased our appreciation for fungal natural products as an asset but also sheds light on the pivotal role that these once-regarded "metabolic wastes" play in fungal biology, defense, and stress response in addition to their potential contributions towards human mycoses. Full orchestration of secondary metabolism requires not only the seamless coordination between temporal and spatial control of SM-associated machineries (e.g. enzymes, cofactors, intermediates, and end-products) but also integration of these machineries into primary metabolic processes and established cellular mechanisms. An intriguing, but little known aspect of microbial natural product synthesis lies in the spatial organization of both pathway intermediates and enzymes responsible for the production of these compounds. In this highlight, we summarize some major breakthroughs in understanding the genes and regulation of fungal natural product synthesis and introduce the current state of knowledge on the spatial and temporal control of fungal natural product synthesis.

  6. Spatial and Temporal Control of Fungal Natural Product Synthesis

    PubMed Central

    Lim, Fang Yun; Keller, Nancy P.

    2014-01-01

    Despite their oftentimes-elusive ecological role, fungal natural products have, for better or worse, impacted our daily lives tremendously owing to their diverse and potent bioactive properties. This Janus-faced nature of fungal natural products inevitably ushered in a field of research dedicated towards understanding the ecology, organisms, genes, enzymes, and biosynthetic pathways that give rise to this arsenal of diverse and complex chemistry. Ongoing research in fungal secondary metabolism has not only increased our appreciation for fungal natural products as an asset but also sheds light on the pivotal role that these once-regarded “metabolic wastes” play in fungal biology, defense, and stress response in addition to their potential contributions towards human mycoses. Full orchestration of secondary metabolism requires not only the seamless coordination between temporal and spatial control of SM-associated machineries (e.g. enzymes, cofactors, intermediates, and end-products) but also integration of these machineries into primary metabolic processes and established cellular mechanisms. An intriguing, but little known aspect of microbial natural product synthesis lies in the spatial organization of both pathway intermediates and enzymes responsible for the production of these compounds. In this highlight, we summarize some major breakthroughs in understanding the genes and regulation of fungal natural product synthesis and introduce the current state of knowledge on the spatial and temporal control of fungal natural product synthesis. PMID:25142354

  7. Microbial control of hydrogen sulfide production

    SciTech Connect

    Montgomery, A.D.; Bhupathiraju, V.K.; Wofford, N.; McInerney, M.J.

    1995-12-31

    A sulfide-resistant strain of Thiobacillus denitrificans, strain F, prevented the accumulation of sulfide by Desulfovibrio desulfuricans when both organisms were grown in liquid medium. The wild-type strain of T. denitrificans did not prevent the accumulation of sulfide produced by D. desulfuricans. Strain F also prevented the accumulation of sulfide by a mixed population of sulfate-reducing bacteria enriched from an oil field brine. Fermentation balances showed that strain F stoichiometrically oxidized the sulfide produced by D. desulfuricans and the oil field brine enrichment to sulfate. The ability of a strain F to control sulfide production in an experimental system of cores and formation water from the Redfield, Iowa, natural gas storage facility was also investigated. A stable, sulfide-producing biofilm was established in two separate core systems, one of which was inoculated with strain F while the other core system (control) was treated in an identical manner, but was not inoculated with strain F. When formation water with 10 mM acetate and 5 mM nitrate was injected into both core systems, the effluent sulfide concentrations in the control core system ranged from 200 to 460 {mu}M. In the test core system inoculated with strain F, the effluent sulfide concentrations were lower, ranging from 70 to 110 {mu}M. In order to determine whether strain F could control sulfide production under optimal conditions for sulfate-reducing bacteria, the electron donor was changed to lactate and inorganic nutrients (nitrogen and phosphate sources) were added to the formation water. When nutrient-supplemented formation water with 3.1 mM lactate and 10 mM nitrate was used, the effluent sulfide concentrations of the control core system initially increased to about 3,800 {mu}M, and then decreased to about 1,100 {mu}M after 5 weeks. However, in the test core system inoculated with strain F, the effluent sulfide concentrations were much lower, 160 to 330 {mu}M.

  8. Hot springs and cool natural products.

    PubMed

    Kwon, Ho Jeong; Lee, Choong Hwan; Osada, Hiroyuki; Yoshida, Minoru; Imoto, Masaya

    2008-08-01

    Natural products have played a unique role in providing new tools and insights in chemical biology. The tremendous value of natural products was highlighted by scientists from Korea and Japan at the 4(th) Korea-Japan Chemical Biology symposium.

  9. Engineering microbial electrocatalysis for chemical and fuel production.

    PubMed

    Rosenbaum, Miriam A; Henrich, Alexander W

    2014-10-01

    In many biotechnological areas, metabolic engineering and synthetic biology have become core technologies for biocatalyst development. Microbial electrocatalysis for biochemical and fuel production is still in its infancy and reactions rates and the product spectrum are currently very low. Therefore, molecular engineering strategies will be crucial for the advancement and realization of many new bioproduction routes using electroactive microorganisms. The complex and unresolved biochemistry and physiology of extracellular electron transfer and the lack of molecular tools for these new non-model hosts for genetic engineering constitute the major challenges for this effort. This review is providing an insight into the current status, challenges and promising approaches of pathway engineering for microbial electrocatalysis.

  10. Enantiomeric Natural Products: Occurrence and Biogenesis**

    PubMed Central

    Finefield, Jennifer M.; Sherman, David H.; Kreitman, Martin; Williams, Robert M.

    2012-01-01

    In Nature, chiral natural products are usually produced in optically pure form; however, on occasion Nature is known to produce enantiomerically opposite metabolites. These enantiomeric natural products can arise in Nature from a single species, or from different genera and/or species. Extensive research has been carried out over the years in an attempt to understand the biogenesis of naturally occurring enantiomers, however, many fascinating puzzles and stereochemical anomalies still remain. PMID:22555867

  11. Production Strategies and Applications of Microbial Single Cell Oils

    PubMed Central

    Ochsenreither, Katrin; Glück, Claudia; Stressler, Timo; Fischer, Lutz; Syldatk, Christoph

    2016-01-01

    Polyunsaturated fatty acids (PUFAs) of the ω-3 and ω-6 class (e.g., α-linolenic acid, linoleic acid) are essential for maintaining biofunctions in mammalians like humans. Due to the fact that humans cannot synthesize these essential fatty acids, they must be taken up from different food sources. Classical sources for these fatty acids are porcine liver and fish oil. However, microbial lipids or single cell oils, produced by oleaginous microorganisms such as algae, fungi and bacteria, are a promising source as well. These single cell oils can be used for many valuable chemicals with applications not only for nutrition but also for fuels and are therefore an ideal basis for a bio-based economy. A crucial point for the establishment of microbial lipids utilization is the cost-effective production and purification of fuels or products of higher value. The fermentative production can be realized by submerged (SmF) or solid state fermentation (SSF). The yield and the composition of the obtained microbial lipids depend on the type of fermentation and the particular conditions (e.g., medium, pH-value, temperature, aeration, nitrogen source). From an economical point of view, waste or by-product streams can be used as cheap and renewable carbon and nitrogen sources. In general, downstream processing costs are one of the major obstacles to be solved for full economic efficiency of microbial lipids. For the extraction of lipids from microbial biomass cell disruption is most important, because efficiency of cell disruption directly influences subsequent downstream operations and overall extraction efficiencies. A multitude of cell disruption and lipid extraction methods are available, conventional as well as newly emerging methods, which will be described and discussed in terms of large scale applicability, their potential in a modern biorefinery and their influence on product quality. Furthermore, an overview is given about applications of microbial lipids or derived fatty

  12. Production Strategies and Applications of Microbial Single Cell Oils.

    PubMed

    Ochsenreither, Katrin; Glück, Claudia; Stressler, Timo; Fischer, Lutz; Syldatk, Christoph

    2016-01-01

    Polyunsaturated fatty acids (PUFAs) of the ω-3 and ω-6 class (e.g., α-linolenic acid, linoleic acid) are essential for maintaining biofunctions in mammalians like humans. Due to the fact that humans cannot synthesize these essential fatty acids, they must be taken up from different food sources. Classical sources for these fatty acids are porcine liver and fish oil. However, microbial lipids or single cell oils, produced by oleaginous microorganisms such as algae, fungi and bacteria, are a promising source as well. These single cell oils can be used for many valuable chemicals with applications not only for nutrition but also for fuels and are therefore an ideal basis for a bio-based economy. A crucial point for the establishment of microbial lipids utilization is the cost-effective production and purification of fuels or products of higher value. The fermentative production can be realized by submerged (SmF) or solid state fermentation (SSF). The yield and the composition of the obtained microbial lipids depend on the type of fermentation and the particular conditions (e.g., medium, pH-value, temperature, aeration, nitrogen source). From an economical point of view, waste or by-product streams can be used as cheap and renewable carbon and nitrogen sources. In general, downstream processing costs are one of the major obstacles to be solved for full economic efficiency of microbial lipids. For the extraction of lipids from microbial biomass cell disruption is most important, because efficiency of cell disruption directly influences subsequent downstream operations and overall extraction efficiencies. A multitude of cell disruption and lipid extraction methods are available, conventional as well as newly emerging methods, which will be described and discussed in terms of large scale applicability, their potential in a modern biorefinery and their influence on product quality. Furthermore, an overview is given about applications of microbial lipids or derived fatty

  13. Enrichment and characterization of microbial consortia degrading soluble microbial products discharged from anaerobic methanogenic bioreactors.

    PubMed

    Kim, Na-Kyung; Oh, Seungdae; Liu, Wen-Tso

    2016-03-01

    Soluble microbial products (SMP) produced in bioprocesses have been known as a main cause to decrease treatment efficiency, lower effluent quality, and promote membrane fouling in water reclamation plants. In this study, biological degradation of SMP using selectively enriched microbial consortia in a down-flow hanging sponge (DHS) reactor was introduced to remove SMP discharged from anaerobic methanogenic reactors. On average, 68.9-87.5% SMP removal was achieved by the enriched microbial consortia in the DHS reactor for >800 days. The influent SMP fed to the DHS reactor exhibited a bimodal molecular weight (MW) distribution with 14-20 kDa and <4 kDa. Between these two types of SMP, the small MW SMP were biodegraded in the upper part of the reactor, together with most of the large MW SMP. Using 16S rRNA gene pyrosequencing technology, the microbial community composition and structure were characterized and correlated with operational factors, such as hydraulic retention time, organic loading rate, and removal of soluble chemical oxygen demand at different depths of the reactor, by performing network and redundancy analyses. The results revealed that Saprospiraceae was strongly correlated to the increasing SMP loading condition, indicating positive co-occurrences with neighboring bacterial populations. Different microbial diversity along with the depth of the reactor implies that stratified microbial communities could participate in the process of SMP degradation. Taken together, these observations indicate that the spatial and temporal variability of the enriched microbial community in the DHS reactor could effectively treat SMP with respect to changes in the operational factors.

  14. Exploitation of genus Rhodosporidium for microbial lipid production.

    PubMed

    Xu, Jingyang; Liu, Dehua

    2017-03-01

    Oleaginous microorganisms are receiving significant attention worldwide for their utility in biodiesel production and the potentiality to produce some specialty-type lipids. There is an increasing interest in isolation/adaption of robust microbe strains and design of innovative fermentation processes to make microbial lipid production a more efficient and economically feasible bio-process. Currently, the genus Rhodosporidium has been considered an important candidate, for the reason that several strains belonging to this genus have shown excellent capabilities of lipid accumulation, broad adaptabilities to various substrates, and co-production of some carotenoids. This paper reviews the current trends in the exploitation of Rhodosporidium species for microbial lipid production, including the utilization of various (single or mixed, pure or waste-derived) substrates, progress of genetic modification and metabolic engineering, innovations in fermentation mode, lipid characterizations and their potential applications. Finally, the constraints and perspectives of cultivating Rhodosporidium species for lipid production are also discussed.

  15. Versatile microbial surface-display for environmental remediation and biofuels production

    SciTech Connect

    Wu, Cindy H.; Mulchandani, Ashok; Chen, wilfred

    2008-02-14

    Surface display is a powerful technique that utilizes natural microbial functional components to express proteins or peptides on the cell exterior. Since the reporting of the first surface-display system in the mid-1980s, a variety of new systems have been reported for yeast, Gram-positive and Gram-negative bacteria. Non-conventional display methods are emerging, eliminating the generation of genetically modified microorganisms. Cells with surface display are used as biocatalysts, biosorbents and biostimulants. Microbial cell-surface display has proven to be extremely important for numerous applications ranging from combinatorial library screening and protein engineering to bioremediation and biofuels production.

  16. Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although natural products have been a particularly rich source of human medicines, the rate at which new molecules are being discovered is declining precipitously. Based on the large number of natural product biosynthetic genes in microbial genomes, many have suggested “genome mining” as an approach...

  17. Microbial antibiotic production aboard the International Space Station.

    PubMed

    Benoit, M R; Li, W; Stodieck, L S; Lam, K S; Winther, C L; Roane, T M; Klaus, D M

    2006-04-01

    Previous studies examining metabolic characteristics of bacterial cultures have mostly suggested that reduced gravity is advantageous for microbial growth. As a consequence, the question of whether space flight would similarly enhance secondary metabolite production was raised. Results from three prior space shuttle experiments indicated that antibiotic production was stimulated in space for two different microbial systems, albeit under suboptimal growth conditions. The goal of this latest experiment was to determine whether the enhanced productivity would also occur with better growth conditions and over longer durations of weightlessness. Microbial antibiotic production was examined onboard the International Space Station during the 72-day 8A increment. Findings of increased productivity of actinomycin D by Streptomyces plicatus in space corroborated with previous findings for the early sample points (days 8 and 12); however, the flight production levels were lower than the matched ground control samples for the remainder of the mission. The overall goal of this research program is to elucidate the specific mechanisms responsible for the initial stimulation of productivity in space and translate this knowledge into methods for improving efficiency of commercial production facilities on Earth.

  18. Method Analysis of Microbial-Resistant Gypsum Products

    EPA Science Inventory

    Method Analysis of Microbial-Resistant Gypsum ProductsD.A. Betancourt1, T.R.Dean1, A. Evans2, and G.Byfield2 1. US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory; RTP, NC 277112. RTI International, RTP, NCSeveral...

  19. Production of microbial glycolipid biosurfactants and their antimicrobial activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial glycolipids produced by bacteria or yeast as secondary metabolites, such as sophorolipids (SLs), rhamnolipids (RLs) and mannosylerythritol lipids (MELs) are “green” biosurfactants desirable in a bioeconomy. High cost of production is a major hurdle toward widespread commercial use of bios...

  20. Production of biofuels from synthesis gas using microbial catalysts.

    PubMed

    Tirado-Acevedo, Oscar; Chinn, Mari S; Grunden, Amy M

    2010-01-01

    World energy consumption is expected to increase 44% in the next 20 years. Today, the main sources of energy are oil, coal, and natural gas, all fossil fuels. These fuels are unsustainable and contribute to environmental pollution. Biofuels are a promising source of sustainable energy. Feedstocks for biofuels used today such as grain starch are expensive and compete with food markets. Lignocellulosic biomass is abundant and readily available from a variety of sources, for example, energy crops and agricultural/industrial waste. Conversion of these materials to biofuels by microorganisms through direct hydrolysis and fermentation can be challenging. Alternatively, biomass can be converted to synthesis gas through gasification and transformed to fuels using chemical catalysts. Chemical conversion of synthesis gas components can be expensive and highly susceptible to catalyst poisoning, limiting biofuel yields. However, there are microorganisms that can convert the CO, H(2), and CO(2) in synthesis gas to fuels such as ethanol, butanol, and hydrogen. Biomass gasification-biosynthesis processing systems have shown promise as some companies have already been exploiting capable organisms for commercial purposes. The discovery of novel organisms capable of higher product yield, as well as metabolic engineering of existing microbial catalysts, makes this technology a viable option for reducing our dependency on fossil fuels.

  1. Frontiers in microbial 1-butanol and isobutanol production.

    PubMed

    Chen, Chang-Ting; Liao, James C

    2016-03-01

    The heavy dependence on petroleum-derived fuel has raised concerns about energy sustainability and climate change, which have prompted researchers to explore fuel production from renewable sources. 1-Butanol and isobutanol are promising biofuels that have favorable properties and can also serve as solvents or chemical feedstocks. Microbial production of these alcohols provides great opportunities to access a wide spectrum of renewable resources. In recent years, research has improved the native 1-butanol production and has engineered isobutanol production in various organisms to explore metabolic diversity and a broad range of substrates. This review focuses on progress in metabolic engineering for the production of these two compounds using various resources.

  2. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession

    NASA Astrophysics Data System (ADS)

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-05-01

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth’s biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

  3. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession

    PubMed Central

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-01-01

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth’s biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession. PMID:25943705

  4. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

    PubMed

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-05-06

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

  5. Studies on potential effects of fumaric acid on rumen microbial fermentation, methane production and microbial community.

    PubMed

    Riede, Susanne; Boguhn, Jeannette; Breves, Gerhard

    2013-01-01

    The greenhouse gas methane (CH4) contributes substantially to global climate change. As a potential approach to decrease ruminal methanogenesis, the effects of different dosages of fumaric acid (FA) on ruminal microbial metabolism and on the microbial community (archaea, bacteria) were studied using a rumen simulation technique (RUSITEC). FA acts as alternative hydrogen acceptor diverting 2H from methanogenesis of archaea towards propionate formation of bacteria. Three identical trials were conducted with 12 fermentation vessels over a period of 14 days. In each trial, four fermentation vessels were assigned to one of the three treatment groups differing in FA dosage: low fumaric acid (LFA), high fumaric acid (HFA) and without FA (control). FA was continuously infused with the buffer. Grass silage and concentrate served as substrate. FA led to decreases in pH and to higher production rates of total short chain fatty acids (SCFA) mediated by increases in propionate for LFA of 1.69 mmol d(-1) and in propionate and acetate production for HFA of 4.49 and 1.10 mmol d(-1), respectively. Concentrations of NH3-N, microbial crude protein synthesis, their efficiency, degradation of crude nutrients and detergent fibre fraction were unchanged. Total gas and CH4 production were not affected by FA. Effects of FA on structure of microbial community by means of single strand conformation polymorphism (SSCP) analyses could not be detected. Given the observed increase in propionate production and the unaffected CH4 production it can be supposed that the availability of reduction equivalents like 2H was not limited by the addition of FA in this study. It has to be concluded from the present study that the application of FA is not an appropriate approach to decrease the ruminal CH4 production.

  6. Microbials for the production of monoclonal antibodies and antibody fragments

    PubMed Central

    Spadiut, Oliver; Capone, Simona; Krainer, Florian; Glieder, Anton; Herwig, Christoph

    2014-01-01

    Monoclonal antibodies (mAbs) and antibody fragments represent the most important biopharmaceutical products today. Because full length antibodies are glycosylated, mammalian cells, which allow human-like N-glycosylation, are currently used for their production. However, mammalian cells have several drawbacks when it comes to bioprocessing and scale-up, resulting in long processing times and elevated costs. By contrast, antibody fragments, that are not glycosylated but still exhibit antigen binding properties, can be produced in microbial organisms, which are easy to manipulate and cultivate. In this review, we summarize recent advances in the expression systems, strain engineering, and production processes for the three main microbials used in antibody and antibody fragment production, namely Saccharomyces cerevisiae, Pichia pastoris, and Escherichia coli. PMID:24183828

  7. Microbial enhancement of oil production from carbonate reservoirs

    SciTech Connect

    Tanner, R.S.; Knapp, R.M.; McInerney, M.J.; Udegbunam, E.O.

    1991-01-01

    The goal of this work is to evaluate the potential for Microbial Enhanced Oil Recovery (MEOR) in carbonate reservoirs. Specific objectives include: review of the literature pertinent to MEOR in carbonate reservoirs, a study of the microbial ecology of carbonate reservoirs, isolation of microorganisms and their end-products of metabolism on carbonate pore structure, the recovery of residual oil from carbonates in model core systems, and development of models to examine and predict MEOR processes in carbonate reservoirs. 1 ref., 3 figs., 1 tab.

  8. Microbial Activation of Wooden Vats Used for Traditional Cheese Production and Evolution of Neoformed Biofilms.

    PubMed

    Gaglio, Raimondo; Cruciata, Margherita; Di Gerlando, Rosalia; Scatassa, Maria Luisa; Cardamone, Cinzia; Mancuso, Isabella; Sardina, Maria Teresa; Moschetti, Giancarlo; Portolano, Baldassare; Settanni, Luca

    2015-11-06

    Three Lactococcus lactis subsp. cremoris strains were used to develop ad hoc biofilms on the surfaces of virgin wooden vats used for cheese production. Two vats (TZ) were tested under controlled conditions (pilot plant), and two vats (TA) were tested under uncontrolled conditions (industrial plant). In each plant, one vat (TA1 and TZ1) was used for the control, traditional production of PDO Vastedda della Valle del Belìce (Vastedda) cheese, and one (TA2 and TZ2) was used for experimental production performed after lactococcal biofilm activation and the daily addition of a natural whey starter culture (NWSC). Microbiological and scanning electron microscopy analyses showed differences in terms of microbial levels and composition of the neoformed biofilms. The levels of the microbial groups investigated during cheese production showed significant differences between the control trials and between the control and experimental trials, but the differences were not particularly marked between the TA2 and TZ2 productions, which showed the largest numbers of mesophilic lactic acid bacterium (LAB) cocci. LAB populations were characterized phenotypically and genotypically, and 44 dominant strains belonging to 10 species were identified. Direct comparison of the polymorphic profiles of the LAB collected during cheese making showed that the addition of the NWSC reduced their biodiversity. Sensory evaluation showed that the microbial activation of the wooden vats with the multistrain Lactococcus culture generated cheeses with sensory attributes comparable to those of commercial cheese. Thus, neoformed biofilms enable a reduction of microbial variability and stabilize the sensorial attributes of Vastedda cheese.

  9. Natural product-based nanomedicine: recent advances and issues

    PubMed Central

    Watkins, Rebekah; Wu, Ling; Zhang, Chenming; Davis, Richey M; Xu, Bin

    2015-01-01

    Natural products have been used in medicine for many years. Many top-selling pharmaceuticals are natural compounds or their derivatives. These plant- or microorganism-derived compounds have shown potential as therapeutic agents against cancer, microbial infection, inflammation, and other disease conditions. However, their success in clinical trials has been less impressive, partly due to the compounds’ low bioavailability. The incorporation of nanoparticles into a delivery system for natural products would be a major advance in the efforts to increase their therapeutic effects. Recently, advances have been made showing that nanoparticles can significantly increase the bioavailability of natural products both in vitro and in vivo. Nanotechnology has demonstrated its capability to manipulate particles in order to target specific areas of the body and control the release of drugs. Although there are many benefits to applying nanotechnology for better delivery of natural products, it is not without issues. Drug targeting remains a challenge and potential nanoparticle toxicity needs to be further investigated, especially if these systems are to be used to treat chronic human diseases. This review aims to summarize recent progress in several key areas relevant to natural products in nanoparticle delivery systems for biomedical applications. PMID:26451111

  10. Natural product-based nanomedicine: recent advances and issues.

    PubMed

    Watkins, Rebekah; Wu, Ling; Zhang, Chenming; Davis, Richey M; Xu, Bin

    2015-01-01

    Natural products have been used in medicine for many years. Many top-selling pharmaceuticals are natural compounds or their derivatives. These plant- or microorganism-derived compounds have shown potential as therapeutic agents against cancer, microbial infection, inflammation, and other disease conditions. However, their success in clinical trials has been less impressive, partly due to the compounds' low bioavailability. The incorporation of nanoparticles into a delivery system for natural products would be a major advance in the efforts to increase their therapeutic effects. Recently, advances have been made showing that nanoparticles can significantly increase the bioavailability of natural products both in vitro and in vivo. Nanotechnology has demonstrated its capability to manipulate particles in order to target specific areas of the body and control the release of drugs. Although there are many benefits to applying nanotechnology for better delivery of natural products, it is not without issues. Drug targeting remains a challenge and potential nanoparticle toxicity needs to be further investigated, especially if these systems are to be used to treat chronic human diseases. This review aims to summarize recent progress in several key areas relevant to natural products in nanoparticle delivery systems for biomedical applications.

  11. Microbial production of plant hormones: Opportunities and challenges.

    PubMed

    Shi, Tian-Qiong; Peng, Hui; Zeng, Si-Yu; Ji, Rong-Yu; Shi, Kun; Huang, He; Ji, Xiao-Jun

    2017-03-04

    Plant hormones are a class of organic substances which are synthesized during the plant metabolism. They have obvious physiological effect on plant growth at very low concentrations. Generally, plant hormones are mainly divided into 5 categories: auxins, cytokinins, ethylene, gibberellins (GAs) and abscisic acid (ABA). With the deepening of research, some novel plant hormones such as brassinosteroid and salicylates have been found and identified. The plant hormone products are mainly obtained through plant extraction, chemical synthesis as well as microbial fermentation. However, the extremely low yield in plants and relatively complex chemical structure limit the development of the former 2 approaches. Therefore, more attention has been paid into the microbial fermentative production. In this commentary, the developments and technological achievements of the 2 important plant hormones (GAs and ABA) have been discussed. The discovery, producing strains, fermentation technologies, and their accumulation mechanisms are first introduced. Furthermore, progresses in the industrial mass scale production are discussed. Finally, guidelines for future studies for GAs and ABA production are proposed in light of the current progress, challenges and trends in the field. With the widespread use of plant hormones in agriculture, we believe that the microbial production of plant hormones will have a bright future.

  12. Natural atmospheric microbial conditions in a typical suburban area.

    PubMed Central

    Jones, B L; Cookson, J T

    1983-01-01

    Ambient outdoor concentrations and size distributions of airborne microbial particles were measured approximately weekly for 2 years in a Washington, D.C., suburban area. The study objective was to characterize microbial air quality in the vicinity of a proposed sewage sludge composting facility. During the study, 379 samples were taken at 17 stations, using Andersen microbial samplers. Concentration ranges (in viable particles per cubic meter) were as follows: airborne mesophilic fungi, 0 to 7,220 with a geometric mean of 273; thermophilic fungi, 0 to 193 with a median of 2.1; Aspergillus fumigatus, 0 to 71 with a median of 1.0; aerobic bacteria, 4.2 to 1,640 with a geometric mean of 79; and fecal streptococci, 0 to 5.7 with a median of 0. No fecal coliforms were recovered. The potentially respirable fraction (less than 8 microns) averaged 34% for total bacteria, 56% for mesophilic fungi, 91% for thermophilic fungi, and 95% for A. fumigatus. The specific sampling location was not a major factor affecting microbial particle concentrations or size distributions. Conversely, the time of year was an important determinant of viable particle concentrations for all groups of microorganisms studied. The highest concentrations were observed in summer and fall, with significantly lower levels detected in winter. In general, the microbial data did not correlate with other variables, including weather conditions, measured in this study. PMID:6342536

  13. Bioengineering natural product biosynthetic pathways for therapeutic applications.

    PubMed

    Wu, Ming-Cheng; Law, Brian; Wilkinson, Barrie; Micklefield, Jason

    2012-12-01

    With the advent of next-generation DNA sequencing technologies, the number of microbial genome sequences has increased dramatically, revealing a vast array of new biosynthetic gene clusters. Genomics data provide a tremendous opportunity to discover new natural products, and also to guide the bioengineering of new and existing natural product scaffolds for therapeutic applications. Notably, it is apparent that the vast majority of biosynthetic gene clusters are either silent or produce very low quantities of the corresponding natural products. It is imperative therefore to devise methods for activating unproductive biosynthetic pathways to provide the quantities of natural products needed for further development. Moreover, on the basis of our expanding mechanistic and structural knowledge of biosynthetic assembly-line enzymes, new strategies for re-programming biosynthetic pathways have emerged, resulting in focused libraries of modified products with potentially improved biological properties. In this review we will focus on the latest bioengineering approaches that have been utilised to optimise yields and increase the structural diversity of natural product scaffolds for future clinical applications.

  14. Potential contribution of microbial degradation to natural attenuation of MTBE in surface water systems

    USGS Publications Warehouse

    Bradley, P.M.; Chapelle, F.H.; Landmeyer, J.E.

    2001-01-01

    The potential contribution of in situ biodegradation as a mechanism for natural attenuation of MTBE in surface water was studied. Surface water sediments from streams and lakes at 11 sites throughout the US. Microbial degradation of [U-14C] MTBE was observed in surface-water-sediment microcosms under anaerobic conditions, but the efficiency and products of anaerobic MTBE biodegradation were strongly dependent on the predominant terminal electron accepting conditions. In the presence of substantial methanogenic activity, MTBE biodegradation was nominal and involved reduction of MTBE to t-butanol (TBA). Under more oxidizing conditions, minimal accumulation of 14C-TBA and significant mineralization of [U-14C] MTBE to 14CO2 were observed. Microorganisms inhabiting the bed sediments of streams and lakes could degrade MTBE effectively under a range of anaerobic terminal electron accepting conditions. Thus, anaerobic bed sediment microbial processes also might contribute to natural attenuation of MTBE in surface water systems throughout the US. This is an abstract of a paper presented at the 222nd ACS National Meting (Chicago, IL 8/26-30/2001).

  15. Method for redesign of microbial production systems

    DOEpatents

    Maranas, Costas D.; Burgard, Anthony P.; Pharkya, Priti

    2010-11-02

    A computer-assisted method for identifying functionalities to add to an organism-specific metabolic network to enable a desired biotransformation in a host includes accessing reactions from a universal database to provide stoichiometric balance, identifying at least one stoichiometrically balanced pathway at least partially based on the reactions and a substrate to minimize a number of non-native functionalities in the production host, and incorporating the at least one stoichiometrically balanced pathway into the host to provide the desired biotransformation. A representation of the metabolic network as modified can be stored.

  16. Method for redesign of microbial production systems

    DOEpatents

    Maranas, Costas D [State College, PA; Burgard, Anthony P [San Diego, CA; Pharkya, Priti [San Diego, CA

    2012-01-31

    A computer-assisted method for identifying functionalities to add to an organism-specific metabolic network to enable a desired biotransformation in a host includes accessing reactions from a universal database to provide stoichiometric balance, identifying at least one stoichiometrically balanced pathway at least partially based on the reactions and a substrate to minimize a number of non-native functionalities in the production host, and incorporating the at least one stoichiometrically balanced pathway into the host to provide the desired biotransformation. A representation of the metabolic network as modified can be stored.

  17. 40 CFR 158.2160 - Microbial pesticides product performance data requirements.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Microbial pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2160 Microbial pesticides product performance data requirements. Product performance data must be developed...

  18. 40 CFR 158.2160 - Microbial pesticides product performance data requirements.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Microbial pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2160 Microbial pesticides product performance data requirements. Product performance data must be developed...

  19. 40 CFR 158.2160 - Microbial pesticides product performance data requirements.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Microbial pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2160 Microbial pesticides product performance data requirements. Product performance data must be developed...

  20. 40 CFR 158.2160 - Microbial pesticides product performance data requirements.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Microbial pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2160 Microbial pesticides product performance data requirements. Product performance data must be developed...

  1. 40 CFR 158.2160 - Microbial pesticides product performance data requirements.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Microbial pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2160 Microbial pesticides product performance data requirements. Product performance data must be developed...

  2. Soil Microbial Substrate Properties and Microbial Community Responses under Irrigated Organic and Reduced-Tillage Crop and Forage Production Systems

    PubMed Central

    Ghimire, Rajan; Norton, Jay B.; Stahl, Peter D.; Norton, Urszula

    2014-01-01

    Changes in soil microbiotic properties such as microbial biomass and community structure in response to alternative management systems are driven by microbial substrate quality and substrate utilization. We evaluated irrigated crop and forage production in two separate four-year experiments for differences in microbial substrate quality, microbial biomass and community structure, and microbial substrate utilization under conventional, organic, and reduced-tillage management systems. The six different management systems were imposed on fields previously under long-term, intensively tilled maize production. Soils under crop and forage production responded to conversion from monocropping to crop rotation, as well as to the three different management systems, but in different ways. Under crop production, four years of organic management resulted in the highest soil organic C (SOC) and microbial biomass concentrations, while under forage production, reduced-tillage management most effectively increased SOC and microbial biomass. There were significant increases in relative abundance of bacteria, fungi, and protozoa, with two- to 36-fold increases in biomarker phospholipid fatty acids (PLFAs). Under crop production, dissolved organic C (DOC) content was higher under organic management than under reduced-tillage and conventional management. Perennial legume crops and organic soil amendments in the organic crop rotation system apparently favored greater soil microbial substrate availability, as well as more microbial biomass compared with other management systems that had fewer legume crops in rotation and synthetic fertilizer applications. Among the forage production management systems with equivalent crop rotations, reduced-tillage management had higher microbial substrate availability and greater microbial biomass than other management systems. Combined crop rotation, tillage management, soil amendments, and legume crops in rotations considerably influenced soil

  3. Soil microbial substrate properties and microbial community responses under irrigated organic and reduced-tillage crop and forage production systems.

    PubMed

    Ghimire, Rajan; Norton, Jay B; Stahl, Peter D; Norton, Urszula

    2014-01-01

    Changes in soil microbiotic properties such as microbial biomass and community structure in response to alternative management systems are driven by microbial substrate quality and substrate utilization. We evaluated irrigated crop and forage production in two separate four-year experiments for differences in microbial substrate quality, microbial biomass and community structure, and microbial substrate utilization under conventional, organic, and reduced-tillage management systems. The six different management systems were imposed on fields previously under long-term, intensively tilled maize production. Soils under crop and forage production responded to conversion from monocropping to crop rotation, as well as to the three different management systems, but in different ways. Under crop production, four years of organic management resulted in the highest soil organic C (SOC) and microbial biomass concentrations, while under forage production, reduced-tillage management most effectively increased SOC and microbial biomass. There were significant increases in relative abundance of bacteria, fungi, and protozoa, with two- to 36-fold increases in biomarker phospholipid fatty acids (PLFAs). Under crop production, dissolved organic C (DOC) content was higher under organic management than under reduced-tillage and conventional management. Perennial legume crops and organic soil amendments in the organic crop rotation system apparently favored greater soil microbial substrate availability, as well as more microbial biomass compared with other management systems that had fewer legume crops in rotation and synthetic fertilizer applications. Among the forage production management systems with equivalent crop rotations, reduced-tillage management had higher microbial substrate availability and greater microbial biomass than other management systems. Combined crop rotation, tillage management, soil amendments, and legume crops in rotations considerably influenced soil

  4. Alternative natural seasoning to improve the microbial stability of low-salt beef patties.

    PubMed

    García-Lomillo, Javier; González-SanJosé, M A Luisa; Del Pino-García, Raquel; Rivero-Pérez, M A Dolores; Muñiz-Rodríguez, Pilar

    2017-07-15

    The meat industry is seeking new strategies to reduce the sodium content of meat products without shortening their shelf-life. Natural seasonings as salt alternatives are more appreciated than chemical preservatives and also enable the incorporation of interesting nutrients. The present work studies the potential of a new red wine pomace seasoning (RWPS), derived from wine pomace, to inhibit spoilage growth in beef patties with different salt levels (2%, 1.5% and 1%) held in storage at 4°C. The use of RWPS (2% w/w) improved the microbial stability of the patties, delaying total aerobic mesophilic, and lactic acid bacteria growth, especially in samples with low salt levels. Satisfactory results were obtained in modified-atmosphere and air-packaged patties. RWPS also enabled the incorporation of fiber and phenolic compounds, and increased potassium and calcium levels. In summary, RWPS presented an interesting potential as a seasoning in meat products, enabling salt reduction without compromising their microbial stability.

  5. Counting on natural products for drug design

    NASA Astrophysics Data System (ADS)

    Rodrigues, Tiago; Reker, Daniel; Schneider, Petra; Schneider, Gisbert

    2016-06-01

    Natural products and their molecular frameworks have a long tradition as valuable starting points for medicinal chemistry and drug discovery. Recently, there has been a revitalization of interest in the inclusion of these chemotypes in compound collections for screening and achieving selective target modulation. Here we discuss natural-product-inspired drug discovery with a focus on recent advances in the design of synthetically tractable small molecules that mimic nature's chemistry. We highlight the potential of innovative computational tools in processing structurally complex natural products to predict their macromolecular targets and attempt to forecast the role that natural-product-derived fragments and fragment-like natural products will play in next-generation drug discovery.

  6. Chemical diversity of microbial volatiles and their potential for plant growth and productivity

    PubMed Central

    Kanchiswamy, Chidananda Nagamangala; Malnoy, Mickael; Maffei, Massimo E.

    2015-01-01

    Microbial volatile organic compounds (MVOCs) are produced by a wide array of microorganisms ranging from bacteria to fungi. A growing body of evidence indicates that MVOCs are ecofriendly and can be exploited as a cost-effective sustainable strategy for use in agricultural practice as agents that enhance plant growth, productivity, and disease resistance. As naturally occurring chemicals, MVOCs have potential as possible alternatives to harmful pesticides, fungicides, and bactericides as well as genetic modification. Recent studies performed under open field conditions demonstrate that efficiently adopting MVOCs may contribute to sustainable crop protection and production. We review here the chemical diversity of MVOCs by describing microbial–plants and microbial–microbial interactions. Furthermore, we discuss MVOCs role in inducing phenotypic plant responses and their potential physiological effects on crops. Finally, we analyze potential and actual limitations for MVOC use and deployment in field conditions as a sustainable strategy for improving productivity and reducing pesticide use. PMID:25821453

  7. Sampling natural biofilms: a new route to build efficient microbial anodes.

    PubMed

    Erable, Benjamin; Roncato, Marie-Anne; Achouak, Wafa; Bergel, Alain

    2009-05-01

    Electrochemically active biofilms were constructed on graphite anodes under constant polarization at -0.1V vs saturated calomel reference (SCE) with 10 mM acetate as substrate. The reactors were inoculated with three different microbial samples that were drawn from exactly the same place in a French Atlantic coastal port (i) by scraping the biofilm that had formed naturally on the surface of a floating bridge, (ii) by taking marine sediments just under the floating bridge, and (iii) by taking nearby beach sand. Current densities of 2.0 A/m2 were reached using the biofilm sample as inoculum while only 0.4 A/m2 and 0.8 A/m2 were obtained using the underlying sediments and the beach sand, respectively. The structure of bacterial communities forming biofilms was characterized by denaturing gradient gel electrophoresis (DGGE) analysis, and revealed differences between samples with the increase in relative intensities of some bands and the appearance of others. Bacteria close related to Bacteroidetes, Halomonas, and Marinobacterium were retrieved only from the efficient EA-biofilms formed from natural biofilms, whereas, bacteria close related to Mesoflavibacter were predominant on biofilm formed from sediments. The marine biofilm was selected as the inoculum to further optimize the microbial anode. Epifluorescence microscopy and SEM confirmed that maintaining the electrode under constant polarization promoted rapid settlement of the electrode surface by a bacterial monolayer film. The microbial anode was progressively adapted to the consumption of acetate by three serial additions of substrate, thus improving the Coulombic efficiency of acetate consumption from 31 to 89%. The possible oxidation of sulfide played only a very small part in the current production and the biofilm was not able to oxidize hydrogen. Graphite proved to be more efficient than dimensionally stable anode (DSA) or stainless steel butthis result might be due to differences in the surface roughness

  8. Culture-independent discovery of natural products from soil metagenomes.

    PubMed

    Katz, Micah; Hover, Bradley M; Brady, Sean F

    2016-03-01

    Bacterial natural products have proven to be invaluable starting points in the development of many currently used therapeutic agents. Unfortunately, traditional culture-based methods for natural product discovery have been deemphasized by pharmaceutical companies due in large part to high rediscovery rates. Culture-independent, or "metagenomic," methods, which rely on the heterologous expression of DNA extracted directly from environmental samples (eDNA), have the potential to provide access to metabolites encoded by a large fraction of the earth's microbial biosynthetic diversity. As soil is both ubiquitous and rich in bacterial diversity, it is an appealing starting point for culture-independent natural product discovery efforts. This review provides an overview of the history of soil metagenome-driven natural product discovery studies and elaborates on the recent development of new tools for sequence-based, high-throughput profiling of environmental samples used in discovering novel natural product biosynthetic gene clusters. We conclude with several examples of these new tools being employed to facilitate the recovery of novel secondary metabolite encoding gene clusters from soil metagenomes and the subsequent heterologous expression of these clusters to produce bioactive small molecules.

  9. Biotechnological Aspects and Perspective of Microbial Keratinase Production.

    PubMed

    Gopinath, Subash C B; Anbu, Periasamy; Lakshmipriya, Thangavel; Tang, Thean-Hock; Chen, Yeng; Hashim, Uda; Ruslinda, A Rahim; Arshad, M K Md

    2015-01-01

    Keratinases are proteolytic enzymes predominantly active when keratin substrates are available that attack disulfide bridges in the keratin to convert them from complex to simplified forms. Keratinases are essential in preparation of animal nutrients, protein supplements, leather manufacture, textile processing, detergent formulation, feather meal processing for feed and fertilizer, the pharmaceutical and biomedical industries, and waste management. Accordingly, it is necessary to develop a method for continuous production of keratinase from reliable sources that can be easily managed. Microbial keratinase is less expensive than conventionally produced keratinase and can be obtained from fungi, bacteria, and actinomycetes. In this overview, the expansion of information about microbial keratinases and important considerations in keratinase production are discussed.

  10. Biotechnological Aspects and Perspective of Microbial Keratinase Production

    PubMed Central

    Gopinath, Subash C. B.; Anbu, Periasamy; Lakshmipriya, Thangavel; Tang, Thean-Hock; Chen, Yeng; Hashim, Uda; Ruslinda, A. Rahim; Arshad, M. K. Md.

    2015-01-01

    Keratinases are proteolytic enzymes predominantly active when keratin substrates are available that attack disulfide bridges in the keratin to convert them from complex to simplified forms. Keratinases are essential in preparation of animal nutrients, protein supplements, leather manufacture, textile processing, detergent formulation, feather meal processing for feed and fertilizer, the pharmaceutical and biomedical industries, and waste management. Accordingly, it is necessary to develop a method for continuous production of keratinase from reliable sources that can be easily managed. Microbial keratinase is less expensive than conventionally produced keratinase and can be obtained from fungi, bacteria, and actinomycetes. In this overview, the expansion of information about microbial keratinases and important considerations in keratinase production are discussed. PMID:26180780

  11. Characterization of proton production and consumption associated with microbial metabolism

    PubMed Central

    2010-01-01

    Background Production or consumption of protons in growth medium during microbial metabolism plays an important role in determining the pH of the environment. Such pH changes resulting from microbial metabolism may influence the geochemical speciation of many elements in subsurface environments. Protons produced or consumed during microbial growth were measured by determining the amount of acid or base added in a 5 L batch bioreactor equipped with pH control for different species including Escherichia coli, Geobacter sulfurreducens, and Geobacter metallireducens. Results An in silico model was used to predict the proton secretion or consumption rates and the results were compared with the data. The data was found to confirm predictions of proton consumption during aerobic growth of E. coli with acetate as the carbon source. However, in contrast to proton consumption observed during aerobic growth of E. coli with acetate, proton secretion was observed during growth of Geobacter species with acetate as the donor and Fe(III) as the extracellular electron acceptor. Conclusions In this study, we have also shown that the final pH of the medium can be either acidic or basic depending on the choice of the electron acceptor for the same electron donor. In all cases, the in silico model could predict qualitatively the proton production/consumption rates obtained from the experimental data. Therefore, measurements of pH equivalents generated or consumed during growth can help characterize the microbial physiology further and can be valuable for optimizing practical applications such as microbial fuel cells, where growth associated pH changes can limit current generation rates. PMID:20089195

  12. Microbial xylanases: engineering, production and industrial applications.

    PubMed

    Juturu, Veeresh; Wu, Jin Chuan

    2012-01-01

    and paper industries for a longer time but more and more attention has been paid to using them in producing sugars and other chemicals from lignocelluloses in recent years. Mining new genes from nature, rational engineering of known genes and directed evolution of these genes are required to get tailor-made xylanases for various industrial applications.

  13. Optimization of supercritical carbon dioxide treatment for the inactivation of the natural microbial flora in cubed cooked ham.

    PubMed

    Ferrentino, Giovanna; Balzan, Sara; Spilimbergo, Sara

    2013-02-15

    This study aims to investigate the effects of supercritical carbon dioxide (SC-CO₂) treatment on the inactivation of the natural microbial flora in cubed cooked ham. Response surface methodology with a central composite design was applied to determine the optimal process conditions and investigate the effect of three independent variables (pressure, temperature and treatment time). Additionally, analyses of texture, pH and color together with a storage study of the product were performed to determine its microbial and qualitative stability. Response surface analysis revealed that 12 MPa, 50 °C, 5 min were the optimal conditions to obtain about 3.0, 1.6, and 2.5 Log(CFU/g) reductions of mesophilic aerobic bacteria, psychrophilic bacteria and lactic acid bacteria respectively. Inactivation to undetectable levels of yeasts and molds and coliforms was also obtained. A storage study of 30 days at 4 °C was carried out on the treated product (12 MPa, 50 °C, 5 min) monitoring microbial growth, pH, texture, and color parameters (L*, a*, b* and ΔE). Microbial loads slightly increased and after 30 days of storage reached the same levels detected in the fresh product. Color parameters (L*, a*, b*) showed slight variations while pH and texture did not change significantly. On the basis of the results obtained, SC-CO₂ can be considered a promising technique to microbiologically stabilize cubed cooked ham and, in general, cut/sliced meat products without affecting its quality attributes.

  14. Enhanced product formation in continuous fermentations with microbial cell recycle

    SciTech Connect

    Bull, D.N.; Young, M.D.

    1981-02-01

    The effect of partial recycle of microbial cells on the operation of a chemostat has been investigated for two fermentations. Stable steady states with and without partial cell recycle were obtained for the conversion of d-sorbitol to L-sorbose by Gluconobacter oxydans subsp. suboxydans 1916B and for the conversion of glucose to 2-ketogluconic acid by Serratia marcescens NRRl B-486. The employment of partial cell recycle dramatically increased product formation rates for both fermentations.

  15. Microbial products trigger amino acid exudation from plant roots.

    PubMed

    Phillips, Donald A; Fox, Tama C; King, Maria D; Bhuvaneswari, T V; Teuber, Larry R

    2004-09-01

    Plants naturally cycle amino acids across root cell plasma membranes, and any net efflux is termed exudation. The dominant ecological view is that microorganisms and roots passively compete for amino acids in the soil solution, yet the innate capacity of roots to recover amino acids present in ecologically relevant concentrations is unknown. We find that, in the absence of culturable microorganisms, the influx rates of 16 amino acids (each supplied at 2.5 microm) exceed efflux rates by 5% to 545% in roots of alfalfa (Medicago sativa), Medicago truncatula, maize (Zea mays), and wheat (Triticum aestivum). Several microbial products, which are produced by common soil microorganisms such as Pseudomonas bacteria and Fusarium fungi, significantly enhanced the net efflux (i.e. exudation) of amino acids from roots of these four plant species. In alfalfa, treating roots with 200 microm phenazine, 2,4-diacetylphloroglucinol, or zearalenone increased total net efflux of 16 amino acids 200% to 2,600% in 3 h. Data from (15)N tests suggest that 2,4-diacetylphloroglucinol blocks amino acid uptake, whereas zearalenone enhances efflux. Thus, amino acid exudation under normal conditions is a phenomenon that probably reflects both active manipulation and passive uptake by microorganisms, as well as diffusion and adsorption to soil, all of which help overcome the innate capacity of plant roots to reabsorb amino acids. The importance of identifying potential enhancers of root exudation lies in understanding that such compounds may represent regulatory linkages between the larger soil food web and the internal carbon metabolism of the plant.

  16. Final Technical Report: Microbial Production of Isoprene

    SciTech Connect

    Fall, Ray

    2003-09-12

    natural state (e.g. as biofilms on surfaces). (3) We successfully used on-line mass spectrometry methods to measure release of volatiles, including isoprene, from bioreactors during growth of B. subtilis. This methodology, still in its infancy, may provide a new means to assess physiological processes during industrial growth of Bacillus species, and use isoprene formation as a barometer of carbon flow in these bacteria. (4) We also addressed the question: is Bacillus isoprene formation analogous to chloroplast processes? This research was initiated because of the continuing interest in the puzzle of isoprene formation in leaf chloroplasts. In pursuit of linkages between bacterial and plant isoprene formation, we used our DMAPP assay to demonstrate that leaves of the isoprene-emitter (cottonwood) show a diurnal cycle, peaking at mid-day in parallel with isoprene release. Thus it appears that in two different biological systems isoprene formation is highly regulated, and linked to isoprenoid carbon availability. (5) We developed a new method to detect Bacillus species in plant root samples, and demonstrated that plant roots are a rich source of biofilm-forming B. subtilis. Furthermore, using cultured Arabidopsis roots as a test system, we were able to demonstrate the formation of stable, viable Bacillus biofilms on the roots. Such roots were protected from killing by a root pathogenic Pseudomonas syringae strain. We have now formulated a mechanism to explain how such biocontrol by B. subtilis occurs, and future work will explore the role of isoprene in signaling between different rhizobacteria and plant roots.

  17. Microbial fuel cells and microbial electrolysis cells for the production of bioelectricity and biomaterials.

    PubMed

    Zhou, Minghua; Yang, Jie; Wang, Hongyu; Jin, Tao; Xu, Dake; Gu, Tingyue

    2013-01-01

    Today's global energy crisis requires a multifaceted solution. Bioenergy is an important part of the solution. The microbial fuel cell (MFC) technology stands out as an attractive potential technology in bioenergy. MFCs can convert energy stored in organic matter directly into bioelectricity. MFCs can also be operated in the electrolysis mode as microbial electrolysis cells to produce bioproducts such as hydrogen and ethanol. Various wastewaters containing low-grade organic carbons that are otherwise unutilized can be used as feed streams for MFCs. Despite major advances in the past decade, further improvements in MFC power output and cost reduction are needed for MFCs to be practical. This paper analysed MFC operating principles using bioenergetics and bioelectrochemistry. Several major issues were explored to improve the MFC performance. An emphasis was placed on the use of catalytic materials for MFC electrodes. Recent advances in the production of various biomaterials using MFCs were also investigated.

  18. Microbial community structure accompanied with electricity production in a constructed wetland plant microbial fuel cell.

    PubMed

    Lu, Lu; Xing, Defeng; Ren, Zhiyong Jason

    2015-11-01

    This study reveals the complex structure of bacterial and archaeal communities associated with a Canna indica plant microbial fuel cell (PMFC) and its electricity production. The PMFC produced a maximum current of 105 mA/m(2) by utilizing rhizodeposits as the sole electron donor without any external nutrient or buffer supplements, which demonstrates the feasibility of PMFCs in practical oligotrophic conditions with low solution conductivity. The microbial diversity was significantly higher in the PMFC than non-plant controls or sediment-only controls, and pyrosequencing and clone library reveal that rhizodeposits conversion to current were carried out by syntrophic interactions between fermentative bacteria (e.g., Anaerolineaceae) and electrochemically active bacteria (e.g., Geobacter). Denitrifying bacteria and acetotrophic methanogens play a minor role in organics degradation, but abundant hydrogenotrophic methanogens and thermophilic archaea are likely main electron donor competitors.

  19. Fractionating soluble microbial products in the activated sludge process.

    PubMed

    Ni, Bing-Jie; Zeng, Raymond J; Fang, Fang; Xie, Wen-Ming; Sheng, Guo-Ping; Yu, Han-Qing

    2010-04-01

    Soluble microbial products (SMP) are the pool of organic compounds originating from microbial growth and decay, and are usually the major component of the soluble organic matters in effluents from biological treatment processes. In this work, SMP in activated sludge were characterized, fractionized, and quantified using integrated chemical analysis and mathematical approach. The utilization-associated products (UAP) in SMP, produced in the substrate-utilization process, were found to be carbonaceous compounds with a molecular weight (MW) lower than 290 kDa which were quantified separately from biomass-associated products (BAP). The BAP were mainly cellular macromolecules with an MW in a range of 290-5000 kDa, and for the first time were further classified into the growth-associated BAP (GBAP) with an MW of 1000 kDa, which were produced in the microbial growth phase, and the endogeny-associated BAP (EBAP) with an MW of 4500 kDa, which were generated in the endogenous phase. Experimental and modeling results reveal that the UAP could be utilized by the activated sludge and that the BAP would accumulate in the system. The GBAP and EBAP had different formation rates from the hydrolysis of extracellular polymeric substances and distinct biodegradation kinetics. This study provides better understanding of SMP formation mechanisms and becomes useful for subsequent effluent treatment.

  20. Macrolactam analogues of macrolide natural products.

    PubMed

    Hügel, Helmut M; Smith, Andrew T; Rizzacasa, Mark A

    2016-12-07

    The chemical modification of macrolide natural products into aza- or lactam analogues is a strategy employed to improve their metabolic stability and biological activity. The methods for the synthesis of several lactam analogues of macrolide natural products are highlighted and aspects of their biological properties presented.

  1. Functional chromatographic technique for natural product isolation†

    PubMed Central

    Lau, Eric C.; Mason, Damian J.; Eichhorst, Nicole; Engelder, Pearce; Mesa, Celestina; Kithsiri Wijeratne, E. M.; Gunaherath, G. M. Kamal B.; Leslie Gunatilaka, A. A.

    2015-01-01

    Natural product discovery arises through a unique interplay between chromatographic purification and biological assays. Currently, most techniques used for natural product purification deliver leads without a defined biological action. We now describe a technique, referred to herein as functional chromatography, that deploys biological affinity as the matrix for compound isolation. PMID:25588099

  2. Natural products against cancer angiogenesis.

    PubMed

    Khalid, El Bairi; Ayman, El-Meghawry El-Kenawy; Rahman, Heshu; Abdelkarim, Guaadaoui; Najda, Agnieszka

    2016-11-01

    The process of angiogenesis is quite well-known nowadays. Some medicines and extracts affecting this process are already used routinely in supporting the conventional treatment of many diseases that are considered angiogenic such as cancer. However, we must be aware that the area of currently used drugs of this type is much narrower than the theoretical possibilities existing in therapeutic angiogenesis. Plant substances are a large and diverse group of compounds that are found naturally in fruits, vegetables, spices, and medicinal plants. They also have different anticancer properties. The aim of this literature review article is to present the current state of knowledge concerning the molecular targets of tumor angiogenesis and the active substances (polyphenols, alkaloids, phytohormones, carbohydrates, and terpenes) derived from natural sources, whose activity against cancer angiogenesis has been confirmed.

  3. Mimicking a natural pathway for de novo biosynthesis: natural vanillin production from accessible carbon sources.

    PubMed

    Ni, Jun; Tao, Fei; Du, Huaiqing; Xu, Ping

    2015-09-02

    Plant secondary metabolites have been attracting people's attention for centuries, due to their potentials; however, their production is still difficult and costly. The rich diversity of microbes and microbial genome sequence data provide unprecedented gene resources that enable to develop efficient artificial pathways in microorganisms. Here, by mimicking a natural pathway of plants using microbial genes, a new metabolic route was developed in E. coli for the synthesis of vanillin, the most widely used flavoring agent. A series of factors were systematically investigated for raising production, including efficiency and suitability of genes, gene dosage, and culture media. The metabolically engineered strain produced 97.2 mg/L vanillin from l-tyrosine, 19.3 mg/L from glucose, 13.3 mg/L from xylose and 24.7 mg/L from glycerol. These results show that the metabolic route enables production of natural vanillin from low-cost substrates, suggesting that it is a good strategy to mimick natural pathways for artificial pathway design.

  4. Mimicking a natural pathway for de novo biosynthesis: natural vanillin production from accessible carbon sources

    PubMed Central

    Ni, Jun; Tao, Fei; Du, Huaiqing; Xu, Ping

    2015-01-01

    Plant secondary metabolites have been attracting people’s attention for centuries, due to their potentials; however, their production is still difficult and costly. The rich diversity of microbes and microbial genome sequence data provide unprecedented gene resources that enable to develop efficient artificial pathways in microorganisms. Here, by mimicking a natural pathway of plants using microbial genes, a new metabolic route was developed in E. coli for the synthesis of vanillin, the most widely used flavoring agent. A series of factors were systematically investigated for raising production, including efficiency and suitability of genes, gene dosage, and culture media. The metabolically engineered strain produced 97.2 mg/L vanillin from l-tyrosine, 19.3 mg/L from glucose, 13.3 mg/L from xylose and 24.7 mg/L from glycerol. These results show that the metabolic route enables production of natural vanillin from low-cost substrates, suggesting that it is a good strategy to mimick natural pathways for artificial pathway design. PMID:26329726

  5. Stereoselective Halogenation in Natural Product Synthesis.

    PubMed

    Chung, Won-jin; Vanderwal, Christopher D

    2016-03-24

    At last count, nearly 5000 halogenated natural products have been discovered. In approximately half of these compounds, the carbon atom to which the halogen is bound is sp(3) -hybridized; therefore, there are an enormous number of natural products for which stereocontrolled halogenation must be a critical component of any synthesis strategy. In this Review, we critically discuss the methods and strategies used for stereoselective introduction of halogen atoms in the context of natural product synthesis. Using the successes of the past, we also attempt to identify gaps in our synthesis technology that would aid the synthesis of halogenated natural products, as well as existing methods that have not yet seen application in complex molecule synthesis. The chemistry described herein demonstrates yet again how natural products continue to provide the inspiration for critical advances in chemical synthesis.

  6. 40 CFR 158.2120 - Microbial pesticides product analysis data requirements table.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Microbial pesticides product analysis... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2120 Microbial pesticides product analysis data requirements table. (a) General. Sections 158.100 through...

  7. 40 CFR 158.2120 - Microbial pesticides product analysis data requirements table.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Microbial pesticides product analysis... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2120 Microbial pesticides product analysis data requirements table. (a) General. Sections 158.100 through...

  8. 40 CFR 158.2120 - Microbial pesticides product analysis data requirements table.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Microbial pesticides product analysis... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2120 Microbial pesticides product analysis data requirements table. (a) General. Sections 158.100 through...

  9. Microbial-processing of fruit and vegetable wastes for production of vital enzymes and organic acids: Biotechnology and scopes.

    PubMed

    Panda, Sandeep K; Mishra, Swati S; Kayitesi, Eugenie; Ray, Ramesh C

    2016-04-01

    Wastes generated from fruits and vegetables are organic in nature and contribute a major share in soil and water pollution. Also, green house gas emission caused by fruit and vegetable wastes (FVWs) is a matter of serious environmental concern. This review addresses the developments over the last one decade on microbial processing technologies for production of enzymes and organic acids from FVWs. The advances in genetic engineering for improvement of microbial strains in order to enhance the production of the value added bio-products as well as the concept of zero-waste economy have been briefly discussed.

  10. Natural Microbial Assemblages Reflect Distinct Organismal and Functional Partitioning

    NASA Astrophysics Data System (ADS)

    Wilmes, P.; Andersson, A.; Kalnejais, L. H.; Verberkmoes, N. C.; Lefsrud, M. G.; Wexler, M.; Singer, S. W.; Shah, M.; Bond, P. L.; Thelen, M. P.; Hettich, R. L.; Banfield, J. F.

    2007-12-01

    The ability to link microbial community structure to function has long been a primary focus of environmental microbiology. With the advent of community genomic and proteomic techniques, along with advances in microscopic imaging techniques, it is now possible to gain insights into the organismal and functional makeup of microbial communities. Biofilms growing within highly acidic solutions inside the Richmond Mine (Iron Mountain, Redding, California) exhibit distinct macro- and microscopic morphologies. They are composed of microorganisms belonging to the three domains of life, including archaea, bacteria and eukarya. The proportion of each organismal type depends on sampling location and developmental stage. For example, mature biofilms floating on top of acid mine drainage (AMD) pools exhibit layers consisting of a densely packed bottom layer of the chemoautolithotroph Leptospirillum group II, a less dense top layer composed mainly of archaea, and fungal filaments spanning across the entire biofilm. The expression of cytochrome 579 (the most highly abundant protein in the biofilm, believed to be central to iron oxidation and encoded by Leptospirillum group II) is localized at the interface of the biofilm with the AMD solution, highlighting that biofilm architecture is reflected at the functional gene expression level. Distinct functional partitioning is also apparent in a biological wastewater treatment system that selects for distinct polyphosphate accumulating organisms. Community genomic data from " Candidatus Accumulibacter phosphatis" dominated activated sludge has enabled high mass-accuracy shotgun proteomics for identification of key metabolic pathways. Comprehensive genome-wide alignment of orthologous proteins suggests distinct partitioning of protein variants involved in both core-metabolism and specific metabolic pathways among the dominant population and closely related species. In addition, strain- resolved proteogenomic analysis of the AMD biofilms

  11. Targeting nuclear receptors with marine natural products.

    PubMed

    Yang, Chunyan; Li, Qianrong; Li, Yong

    2014-01-27

    Nuclear receptors (NRs) are important pharmaceutical targets because they are key regulators of many metabolic and inflammatory diseases, including diabetes, dyslipidemia, cirrhosis, and fibrosis. As ligands play a pivotal role in modulating nuclear receptor activity, the discovery of novel ligands for nuclear receptors represents an interesting and promising therapeutic approach. The search for novel NR agonists and antagonists with enhanced selectivities prompted the exploration of the extraordinary chemical diversity associated with natural products. Recent studies involving nuclear receptors have disclosed a number of natural products as nuclear receptor ligands, serving to re-emphasize the translational possibilities of natural products in drug discovery. In this review, the natural ligands of nuclear receptors will be described with an emphasis on their mechanisms of action and their therapeutic potentials, as well as on strategies to determine potential marine natural products as nuclear receptor modulators.

  12. Expanding the product profile of a microbial alkane biosynthetic pathway.

    PubMed

    Harger, Matthew; Zheng, Lei; Moon, Austin; Ager, Casey; An, Ju Hye; Choe, Chris; Lai, Yi-Ling; Mo, Benjamin; Zong, David; Smith, Matthew D; Egbert, Robert G; Mills, Jeremy H; Baker, David; Pultz, Ingrid Swanson; Siegel, Justin B

    2013-01-18

    Microbially produced alkanes are a new class of biofuels that closely match the chemical composition of petroleum-based fuels. Alkanes can be generated from the fatty acid biosynthetic pathway by the reduction of acyl-ACPs followed by decarbonylation of the resulting aldehydes. A current limitation of this pathway is the restricted product profile, which consists of n-alkanes of 13, 15, and 17 carbons in length. To expand the product profile, we incorporated a new part, FabH2 from Bacillus subtilis , an enzyme known to have a broader specificity profile for fatty acid initiation than the native FabH of Escherichia coli . When provided with the appropriate substrate, the addition of FabH2 resulted in an altered alkane product profile in which significant levels of n-alkanes of 14 and 16 carbons in length are produced. The production of even chain length alkanes represents initial steps toward the expansion of this recently discovered microbial alkane production pathway to synthesize complex fuels. This work was conceived and performed as part of the 2011 University of Washington international Genetically Engineered Machines (iGEM) project.

  13. Informatic search strategies to discover analogues and variants of natural product archetypes.

    PubMed

    Johnston, Chad W; Connaty, Alex D; Skinnider, Michael A; Li, Yong; Grunwald, Alyssa; Wyatt, Morgan A; Kerr, Russell G; Magarvey, Nathan A

    2016-03-01

    Natural products are a crucial source of antimicrobial agents, but reliance on low-resolution bioactivity-guided approaches has led to diminishing interest in discovery programmes. Here, we demonstrate that two in-house automated informatic platforms can be used to target classes of biologically active natural products, specifically, peptaibols. We demonstrate that mass spectrometry-based informatic approaches can be used to detect natural products with high sensitivity, identifying desired agents present in complex microbial extracts. Using our specialised software packages, we could elaborate specific branches of chemical space, uncovering new variants of trichopolyn and demonstrating a way forward in mining natural products as a valuable source of potential pharmaceutical agents.

  14. Natural gas production verification tests

    SciTech Connect

    Not Available

    1992-02-01

    This Environmental Assessment (EA) has been prepared by the Department of Energy (DOE) in compliance with the requirements of the National Environmental Policy Act of 1969. The Department of Energy (DOE) proposes to fund, through a contract with Petroleum Consulting Services, Inc. of Canton, Ohio, the testing of the effectiveness of a non-water based hydraulic fracturing treatment to increase gas recovery from low-pressure, tight, fractured Devonian Shale formations. Although Devonian Shales are found in the Appalachian, Michigan, and Illinois Basins, testing will be done only in the dominant, historical five state area of established production. The objective of this proposed project is to assess the benefits of liquid carbon dioxide (CO{sub 2})/sand stimulations in the Devonian Shale. In addition, this project would evaluate the potential nondamaging (to the formation) properties of this unique fracturing treatment relative to the clogging or chocking of pores and fractures that act as gas flow paths to the wellbore in the target gas-producing zones of the formation. This liquid CO{sub 2}/sand fracturing process is water-free and is expected to facilitate gas well cleanup, reduce the time required for post-stimulation cleanup, and result in improved production levels in a much shorter time than is currently experienced.

  15. New Synthetic Methods for Hypericum Natural Products

    SciTech Connect

    Jeon, Insik

    2006-01-01

    Organic chemistry has served as a solid foundation for interdisciplinary research areas, such as molecular biology and medicinal chemistry. An understanding of the biological activities and structural elucidations of natural products can lead to the development of clinically valuable therapeutic options. The advancements of modern synthetic methodologies allow for more elaborate and concise natural product syntheses. The theme of this study centers on the synthesis of natural products with particularly challenging structures and interesting biological activities. The synthetic expertise developed here will be applicable to analog syntheses and to other research problems.

  16. Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

    NASA Astrophysics Data System (ADS)

    Martinez, R.; Wu, C. H.; Beazley, M. J.; Andersen, G. L.; Hazen, T. C.; Taillefert, M.; Sobecky, P. A.

    2011-12-01

    Soils and groundwater contaminated with heavy metals and radionuclides remain a legacy of Cold War nuclear weapons development. Due to the scale of environmental contamination, in situ sequestration of heavy metals and radionuclides remain the most cost-effective strategy for remediation. We are currently investigating a remediation approach that utilizes periplasmic and extracellular microbial phosphatase activity of soil bacteria capable promoting in situ uranium phosphate sequestration. Our studies focus on the contaminated soils from the DOE Field Research Center (ORFRC) in Oak Ridge, TN. We have previously demonstrated that ORFRC strains with phosphatase-positive phenotypes were capable of promoting the precpitation of >95% U(VI) as a low solubility phosphate mineral during growth on glycerol phosphate as a sole carbon and phosphorus source. Here we present culture-independent soil slurry studies aimed at understanding microbial community dynamics resulting from exogenous organophosphate additions. Soil slurries containing glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P) and nitrate as the sole C, P and N sources were incubated under oxic growth conditions at pH 5.5 or pH 6.8. Following treatments, total DNA was extracted and prokaryotic diversity was assessed using high-density 16S oligonucleotide microarray (PhyloChip) analysis. Treatments at pH 5.5 and pH 6.8 amended with G2P required 36 days to accumulate 4.8mM and 2.2 mM phosphate, respectively. In contrast, treatments at pH 5.5 and pH 6.8 amended with G3P accumulated 8.9 mM and 8.7 mM phosphate, respectively, after 20 days. A total of 2120 unique taxa representing 46 phyla, 66 classes, 110 orders, and 186 families were detected among all treatment conditions. The phyla that significantly (P<0.05) increased in abundance relative to incubations lacking organophosphate amendments included: Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria. Members from the classes Bacteroidetes

  17. Microbial Forensics for Natural and Intentional Incidents of Infectious Disease Involving Animals

    DTIC Science & Technology

    2006-01-01

    Palabras clave Animal - Aplicaci6n de Ia ley - Bioterrorismo - Crimen biol6gico - Enfermedad infecciosa- Medicina forense - Microbiologia forense . II...t:t=S~5S6~ C-AO~l-YS 5 Rev. sci. tech. Off. int. Epiz .. 2006, 25 (1). 329-339 Microbial forensics for natural and intentional incidents of...Netherlands (6) Defence R&D Canada- Suffield, Box 4000, Station Main, Medicine Hat, Alberta, T1A BK6, Canada Summary .... Microbial forensics is a relatively

  18. Microbial production of nattokinase: current progress, challenge and prospect.

    PubMed

    Cai, Dongbo; Zhu, Chengjun; Chen, Shouwen

    2017-05-01

    Nattokinase (EC 3.4.21.62) is a profibrinolytic serine protease with a potent fibrin-degrading activity, and it has been produced by many host strains. Compared to other fibrinolytic enzymes (urokinase, t-PA and streprokinase), nattokinase shows the advantages of having no side effects, low cost and long life-time, and it has the potential to be used as a drug for treating cardiovascular disease and served as a functional food additive. In this review, we focused on screening of producing strains, genetic engineering, fermentation process optimization for microbial nattokinase production, and the extraction and purification of nattokinase were also discussed in this particular chapter. The selection of optimal nattokinase producing strain was the crucial starting element for improvement of nattokinase production. Genetic engineering, protein engineering, fermentation optimization and process control have been proved to be the effective strategies for enhancement of nattokinase production. Also, extraction and purification of nattokinase are critical for the quality evaluation of nattokinase. Finally, the prospect of microbial nattokinase production was also discussed regarding the recent progress, challenge, and trends in this field.

  19. Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM).

    PubMed

    Skinnider, Michael A; Dejong, Chris A; Rees, Philip N; Johnston, Chad W; Li, Haoxin; Webster, Andrew L H; Wyatt, Morgan A; Magarvey, Nathan A

    2015-11-16

    Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products. PRISM implements novel algorithms which render it uniquely capable of predicting type II polyketides, deoxygenated sugars, and starter units, making it a comprehensive genome-guided chemical structure prediction engine. A library of 57 tailoring reactions is leveraged for combinatorial scaffold library generation when multiple potential substrates are consistent with biosynthetic logic. We compare the accuracy of PRISM to existing genomic analysis platforms. PRISM is an open-source, user-friendly web application available at http://magarveylab.ca/prism/.

  20. Natural Products for the Treatment of Type 2 Diabetes Mellitus.

    PubMed

    Ríos, José Luis; Francini, Flavio; Schinella, Guillermo R

    2015-08-01

    Type 2 diabetes mellitus is a metabolic disease characterized by persistent hyperglycemia. High blood sugar can produce long-term complications such as cardiovascular and renal disorders, retinopathy, and poor blood flow. Its development can be prevented or delayed in people with impaired glucose tolerance by implementing lifestyle changes or the use of therapeutic agents. Some of these drugs have been obtained from plants or have a microbial origin, such as galegine isolated from Galega officinalis, which has a great similarity to the antidiabetic drug metformin. Picnogenol, acarbose, miglitol, and voglibose are other antidiabetic products of natural origin. This review compiles the principal articles on medicinal plants used for treating diabetes and its comorbidities, as well as mechanisms of natural products as antidiabetic agents. Inhibition of α-glucosidase and α-amylase, effects on glucose uptake and glucose transporters, modification of mechanisms mediated by the peroxisome proliferator-activated receptor, inhibition of protein tyrosine phosphatase 1B activity, modification of gene expression, and activities of hormones involved in glucose homeostasis such as adiponectin, resistin, and incretin, and reduction of oxidative stress are some of the mechanisms in which natural products are involved. We also review the most relevant clinical trials performed with medicinal plants and natural products such as aloe, banaba, bitter melon, caper, cinnamon, cocoa, coffee, fenugreek, garlic, guava, gymnema, nettle, sage, soybean, green and black tea, turmeric, walnut, and yerba mate. Compounds of high interest as potential antidiabetics are: fukugetin, palmatine, berberine, honokiol, amorfrutins, trigonelline, gymnemic acids, gurmarin, and phlorizin.

  1. Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM)

    PubMed Central

    Skinnider, Michael A.; Dejong, Chris A.; Rees, Philip N.; Johnston, Chad W.; Li, Haoxin; Webster, Andrew L. H.; Wyatt, Morgan A.; Magarvey, Nathan A.

    2015-01-01

    Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products. PRISM implements novel algorithms which render it uniquely capable of predicting type II polyketides, deoxygenated sugars, and starter units, making it a comprehensive genome-guided chemical structure prediction engine. A library of 57 tailoring reactions is leveraged for combinatorial scaffold library generation when multiple potential substrates are consistent with biosynthetic logic. We compare the accuracy of PRISM to existing genomic analysis platforms. PRISM is an open-source, user-friendly web application available at http://magarveylab.ca/prism/. PMID:26442528

  2. Microbial and Natural Metabolites That Inhibit Splicing: A Powerful Alternative for Cancer Treatment

    PubMed Central

    Rosas-Murrieta, Nora Hilda; Martínez-Montiel, Mónica; Gaspariano-Cholula, Mayra Patricia

    2016-01-01

    In eukaryotes, genes are frequently interrupted with noncoding sequences named introns. Alternative splicing is a nuclear mechanism by which these introns are removed and flanking coding regions named exons are joined together to generate a message that will be translated in the cytoplasm. This mechanism is catalyzed by a complex machinery known as the spliceosome, which is conformed by more than 300 proteins and ribonucleoproteins that activate and regulate the precision of gene expression when assembled. It has been proposed that several genetic diseases are related to defects in the splicing process, including cancer. For this reason, natural products that show the ability to regulate splicing have attracted enormous attention due to its potential use for cancer treatment. Some microbial metabolites have shown the ability to inhibit gene splicing and the molecular mechanism responsible for this inhibition is being studied for future applications. Here, we summarize the main types of natural products that have been characterized as splicing inhibitors, the recent advances regarding molecular and cellular effects related to these molecules, and the applications reported so far in cancer therapeutics. PMID:27610372

  3. Microbial and Natural Metabolites That Inhibit Splicing: A Powerful Alternative for Cancer Treatment.

    PubMed

    Martínez-Montiel, Nancy; Rosas-Murrieta, Nora Hilda; Martínez-Montiel, Mónica; Gaspariano-Cholula, Mayra Patricia; Martínez-Contreras, Rebeca D

    2016-01-01

    In eukaryotes, genes are frequently interrupted with noncoding sequences named introns. Alternative splicing is a nuclear mechanism by which these introns are removed and flanking coding regions named exons are joined together to generate a message that will be translated in the cytoplasm. This mechanism is catalyzed by a complex machinery known as the spliceosome, which is conformed by more than 300 proteins and ribonucleoproteins that activate and regulate the precision of gene expression when assembled. It has been proposed that several genetic diseases are related to defects in the splicing process, including cancer. For this reason, natural products that show the ability to regulate splicing have attracted enormous attention due to its potential use for cancer treatment. Some microbial metabolites have shown the ability to inhibit gene splicing and the molecular mechanism responsible for this inhibition is being studied for future applications. Here, we summarize the main types of natural products that have been characterized as splicing inhibitors, the recent advances regarding molecular and cellular effects related to these molecules, and the applications reported so far in cancer therapeutics.

  4. Cancer wars: natural products strike back

    PubMed Central

    Basmadjian, Christine; Zhao, Qian; Bentouhami, Embarek; Djehal, Amel; Nebigil, Canan G.; Johnson, Roger A.; Serova, Maria; de Gramont, Armand; Faivre, Sandrine; Raymond, Eric; Désaubry, Laurent G.

    2014-01-01

    Natural products have historically been a mainstay source of anticancer drugs, but in the 90's they fell out of favor in pharmaceutical companies with the emergence of targeted therapies, which rely on antibodies or small synthetic molecules identified by high throughput screening. Although targeted therapies greatly improved the treatment of a few cancers, the benefit has remained disappointing for many solid tumors, which revitalized the interest in natural products. With the approval of rapamycin in 2007, 12 novel natural product derivatives have been brought to market. The present review describes the discovery and development of these new anticancer drugs and highlights the peculiarities of natural product and new trends in this exciting field of drug discovery. PMID:24822174

  5. Cancer wars: natural products strike back.

    PubMed

    Basmadjian, Christine; Zhao, Qian; Bentouhami, Embarek; Djehal, Amel; Nebigil, Canan G; Johnson, Roger A; Serova, Maria; de Gramont, Armand; Faivre, Sandrine; Raymond, Eric; Désaubry, Laurent G

    2014-01-01

    Natural products have historically been a mainstay source of anticancer drugs, but in the 90's they fell out of favor in pharmaceutical companies with the emergence of targeted therapies, which rely on antibodies or small synthetic molecules identified by high throughput screening. Although targeted therapies greatly improved the treatment of a few cancers, the benefit has remained disappointing for many solid tumors, which revitalized the interest in natural products. With the approval of rapamycin in 2007, 12 novel natural product derivatives have been brought to market. The present review describes the discovery and development of these new anticancer drugs and highlights the peculiarities of natural product and new trends in this exciting field of drug discovery.

  6. Total synthesis of alkyl citrate natural products.

    PubMed

    Rizzacasa, Mark A; Sturgess, Dayna

    2014-03-07

    This review highlights the synthesis of members of the alkyl citrate family of natural products. The focus is on the stereoselective construction of the alkyl citrate moiety common to these compounds.

  7. Cancer wars: Natural products strike back

    NASA Astrophysics Data System (ADS)

    Basmadjian, Christine; Zhao, Qian; Djehal, Amel; Bentouhami, Embarek; Nebigil, Canan; Johnson, Roger; Serova, Maria; De Gramont, Armand; Faivre, Sandrine; Raymond, Eric; Désaubry, Laurent

    2014-05-01

    Natural products have historically been a mainstay source of anticancer drugs, but in the 90’s they fell out of favor in pharmaceutical companies with the emergence of targeted therapies, which rely on antibodies or small synthetic molecules identified by high throughput screening. Although targeted therapies greatly improved the treatment of a few cancers, the benefit has remained disappointing for many sol¬¬id tumors, which revitalized the interest in natural products. With the approval of rapamycin in 2007, twelve novel natural product derivatives have been brought to market. The present review describes the discovery and development of these new anticancer drugs and highlights the peculiarities of natural product and new trends in this exciting field of drug discovery.

  8. Microbial production and oxidation of methane in deep subsurface

    NASA Astrophysics Data System (ADS)

    Kotelnikova, Svetlana

    2002-10-01

    The goal of this review is to summarize present studies on microbial production and oxidation of methane in the deep subterranean environments. Methane is a long-living gas causing the "greenhouse" effect in the planet's atmosphere. Earlier, the deep "organic carbon poor" subsurface was not considered as a source of "biogenic" methane. Evidence of active methanogenesis and presence of viable methanogens including autotrophic organisms were obtained for some subsurface environments including water-flooded oil-fields, deep sandy aquifers, deep sea hydrothermal vents, the deep sediments and granitic groundwater at depths of 10 to 2000 m below sea level. As a rule, the deep subterranean microbial populations dwell at more or less oligotrophic conditions. Molecular hydrogen has been found in a variety of subsurface environments, where its concentrations were significantly higher than in the tested surface aquatic environments. Chemolithoautotrophic microorganisms from deep aquifers that could grow on hydrogen and carbon dioxide can act as primary producers of organic carbon, initiating heterotrophic food chains in the deep subterranean environments independent of photosynthesis. "Biogenic" methane has been found all over the world. On the basis of documented occurrences, gases in reservoirs and older sediments are similar and have the isotopic character of methane derived from CO 2 reduction. Groundwater representing the methanogenic end member are characterized by a relative depletion of dissolved organic carbon (DOC) in combination with an enrichment in 13C in inorganic carbon, which is consistent with the preferential reduction of 12CO 2 by autotrophic methanogens or acetogens. The isotopic composition of methane formed via CO 2 reduction is controlled by the δ13C of the original CO 2 substrate. Literature data shows that CH 4 as heavy as -40‰ or -50‰ can be produced by the microbial reduction of isotopically heavy CO 2. Produced methane may be oxidized

  9. Natural products from the genus tephrosia.

    PubMed

    Chen, Yinning; Yan, Tao; Gao, Chenghai; Cao, Wenhao; Huang, Riming

    2014-01-27

    The genus Tephrosia, belonging to the Leguminosae family, is a large pantropical genus of more than 350 species, many of which have important traditional uses in agriculture. This review not only outlines the source, chemistry and biological evaluations of natural products from the genus Tephrosia worldwide that have appeared in literature from 1910 to December 2013, but also covers work related to proposed biosynthetic pathways and synthesis of some natural products from the genus Tephrosia, with 105 citations and 168 new compounds.

  10. Microbial Activation of Wooden Vats Used for Traditional Cheese Production and Evolution of Neoformed Biofilms

    PubMed Central

    Gaglio, Raimondo; Cruciata, Margherita; Di Gerlando, Rosalia; Scatassa, Maria Luisa; Cardamone, Cinzia; Mancuso, Isabella; Sardina, Maria Teresa; Moschetti, Giancarlo; Portolano, Baldassare

    2015-01-01

    Three Lactococcus lactis subsp. cremoris strains were used to develop ad hoc biofilms on the surfaces of virgin wooden vats used for cheese production. Two vats (TZ) were tested under controlled conditions (pilot plant), and two vats (TA) were tested under uncontrolled conditions (industrial plant). In each plant, one vat (TA1 and TZ1) was used for the control, traditional production of PDO Vastedda della Valle del Belìce (Vastedda) cheese, and one (TA2 and TZ2) was used for experimental production performed after lactococcal biofilm activation and the daily addition of a natural whey starter culture (NWSC). Microbiological and scanning electron microscopy analyses showed differences in terms of microbial levels and composition of the neoformed biofilms. The levels of the microbial groups investigated during cheese production showed significant differences between the control trials and between the control and experimental trials, but the differences were not particularly marked between the TA2 and TZ2 productions, which showed the largest numbers of mesophilic lactic acid bacterium (LAB) cocci. LAB populations were characterized phenotypically and genotypically, and 44 dominant strains belonging to 10 species were identified. Direct comparison of the polymorphic profiles of the LAB collected during cheese making showed that the addition of the NWSC reduced their biodiversity. Sensory evaluation showed that the microbial activation of the wooden vats with the multistrain Lactococcus culture generated cheeses with sensory attributes comparable to those of commercial cheese. Thus, neoformed biofilms enable a reduction of microbial variability and stabilize the sensorial attributes of Vastedda cheese. PMID:26546430

  11. Microbial Resistance to Triclosan: A Case Study in Natural Selection

    ERIC Educational Resources Information Center

    Serafini, Amanda; Matthews, Dorothy M.

    2009-01-01

    Natural selection is the mechanism of evolution caused by the environmental selection of organisms most fit to reproduce, sometimes explained as "survival of the fittest." An example of evolution by natural selection is the development of bacteria that are resistant to antimicrobial agents as a result of exposure to these agents. Triclosan, which…

  12. A new approach to microbial production of gallic acid

    PubMed Central

    Bajpai, Bhakti; Patil, Shridhar

    2008-01-01

    In a new approach to microbial gallic acid production by Aspergillus fischeri MTCC 150, 40gL−1 of tannic acid was added in two installments during the bioconversion phase of the process (25gL−1 and 15gL−1 at 32 and 44h respectively). The optimum parameters for the bioconversion phase were found to be temperature: 35°C, pH: slightly acidic (3.3–3.5), aeration: nil and agitation: 250 rpm. A maximum of 71.4% conversion was obtained after 71h fermentation with 83.3% product recovery. The yield was 7.35 g of gallic acid per g of biomass accumulated and the fermenter productivity was 0.56 g of gallic acid produced per liter of medium per hour. PMID:24031294

  13. Soluble microbial products and their implications in mixed culture biotechnology.

    PubMed

    Ni, Bing-Jie; Rittmann, Bruce E; Yu, Han-Qing

    2011-09-01

    Soluble microbial products (SMP) are soluble organic compounds released during normal biomass metabolism in mixed culture biotechnology. In this review, we give the up-to-date status on several essential SMP issues: mechanisms of SMP formation, differentiation between utilization-associated products (UAP) and biomass-associated products (BAP), biodegradability of the SMP components, how formation of SMP by autotrophs controls effluent quality and supports a substantial population of heterotrophs, mathematical modeling that includes SMP, and improving effluent quality by controlling SMP. We also present two timely examples that highlight our current understanding and give an indication of how SMP affects the performance of modern mixed culture biotechnology: membrane fouling of membrane bioreactors (MBRs) and the dynamics of SMP in anaerobic systems.

  14. Automated identification of depsipeptide natural products by an informatic search algorithm.

    PubMed

    Skinnider, Michael A; Johnston, Chad W; Zvanych, Rostyslav; Magarvey, Nathan A

    2015-01-19

    Nonribosomal depsipeptides are a class of potent microbial natural products, which include several clinically approved pharmaceutical agents. Genome sequencing has revealed a large number of uninvestigated natural-product biosynthetic gene clusters. However, while novel informatic search methods to access these gene clusters have been developed to identify peptide natural products, depsipeptide detection has proven challenging. Herein, we present an improved version of our informatic search algorithm for natural products (iSNAP), which facilitates the detection of known and genetically predicted depsipeptides in complex microbial culture extracts. We validated this technology by identifying several depsipeptides from novel producers, and located a large number of novel depsipeptide gene clusters for future study. This approach highlights the value of chemoinformatic search methods for the discovery of genetically encoded metabolites by targeting specific areas of chemical space.

  15. Whey-derived valuable products obtained by microbial fermentation.

    PubMed

    Pescuma, Micaela; de Valdez, Graciela Font; Mozzi, Fernanda

    2015-08-01

    Whey, the main by-product of the cheese industry, is considered as an important pollutant due to its high chemical and biological oxygen demand. Whey, often considered as waste, has high nutritional value and can be used to obtain value-added products, although some of them need expensive enzymatic synthesis. An economical alternative to transform whey into valuable products is through bacterial or yeast fermentations and by accumulation during algae growth. Fermentative processes can be applied either to produce individual compounds or to formulate new foods and beverages. In the first case, a considerable amount of research has been directed to obtain biofuels able to replace those derived from petrol. In addition, the possibility of replacing petrol-derived plastics by biodegradable polymers synthesized during bacterial fermentation of whey has been sought. Further, the ability of different organisms to produce metabolites commonly used in the food and pharmaceutical industries (i.e., lactic acid, lactobionic acid, polysaccharides, etc.) using whey as growth substrate has been studied. On the other hand, new low-cost functional whey-based foods and beverages leveraging the high nutritional quality of whey have been formulated, highlighting the health-promoting effects of fermented whey-derived products. This review aims to gather the multiple uses of whey as sustainable raw material for the production of individual compounds, foods, and beverages by microbial fermentation. This is the first work to give an overview on the microbial transformation of whey as raw material into a large repertoire of industrially relevant foods and products.

  16. How EIA Estimates Natural Gas Production

    EIA Publications

    2004-01-01

    The Energy Information Administration (EIA) publishes estimates monthly and annually of the production of natural gas in the United States. The estimates are based on data EIA collects from gas producing states and data collected by the U. S. Minerals Management Service (MMS) in the Department of Interior. The states and MMS collect this information from producers of natural gas for various reasons, most often for revenue purposes. Because the information is not sufficiently complete or timely for inclusion in EIA's Natural Gas Monthly (NGM), EIA has developed estimation methodologies to generate monthly production estimates that are described in this document.

  17. Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues

    PubMed Central

    Warren, Lesley A.; Kendra, Kathryn E.

    2015-01-01

    Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers. PMID:25979895

  18. Microbial nitrogen cycling response to forest-based bioenergy production.

    PubMed

    Minick, Kevan J; Strahm, Brian D; Fox, Thomas R; Sucre, Eric B; Leggett, Zakiya H

    2015-12-01

    Concern over rising atmospheric CO2 and other greenhouse gases due to fossil fuel combustion has intensified research into carbon-neutral energy production. Approximately 15.8 million ha of pine plantations exist across the southeastern United States, representing a vast land area advantageous for bioenergy production without significant landuse change or diversion of agricultural resources from food production. Furthermore, intercropping of pine with bioenergy grasses could provide annually harvestable, lignocellulosic biomass feedstocks along with production of traditional wood products. Viability of such a system hinges in part on soil nitrogen (N) availability and effects of N competition between pines and grasses on ecosystem productivity. We investigated effects of intercropping loblolly pine (Pinus taeda) with switchgrass (Panicum virgatum) on microbial N cycling processes in the Lower Coastal Plain of North Carolina, USA. Soil samples were collected from bedded rows of pine and interbed space of two treatments, composed of either volunteer native woody and herbaceous vegetation (pine-native) or pure switchgrass (pine-switchgrass) in interbeds. An in vitro 15N pool-dilution technique was employed to quantify gross N transformations at two soil depths (0-5 and 5-15 cm) on four dates in 2012-2013. At the 0-5 cm depth in beds of the pine-switchgrass treatment, gross N mineralization was two to three times higher in November and February compared to the pine-native treatment, resulting in increased NH4(+) availability. Gross and net nitrification were also significantly higher in February in the same pine beds. In interbeds of the pine-switchgrass treatment, gross N mineralization was lower from April to November, but higher in February, potentially reflecting positive effects of switchgrass root-derived C inputs during dormancy on microbial activity. These findings indicate soil N cycling and availability has increased in pine beds of the pine

  19. Naturally occurring products in cancer therapy

    PubMed Central

    Rajesh, E.; Sankari, Leena S.; Malathi, L.; Krupaa, Jayasri R.

    2015-01-01

    Natural products have been used for the treatment of various diseases and are becoming an important research area for drug discovery. These products, especially phytochemicals have been extensively studies and have exhibited anti-carcinogenic activities by interfering with the initiation, development and progression of cancer through the modulation of various mechanisms including cellular proliferation, differentiation, apoptosis, angiogenesis, and metastasis. This concept is gaining attention because it is a cost-effective alternative to cancer treatment. In this article, we have discussed some of the naturally occurring products used in cancer treatment. PMID:26015704

  20. Natural milk cultures for the production of Argentinian cheeses.

    PubMed

    Reinheimer, J A; Binetti, A G; Quiberoni, A; Bailo, N B; Rubiolo, A C; Giraffa, G

    1997-01-01

    Samples (32) of natural milk cultures used in the Santa Fe, Argentina, area for soft and semihard cheese production were examined. The microbial composition (including lactic acid microflora characterization) and technological parameters (acidifying and proteolytic activities) were evaluated. The cultures contained mainly thermophilic lactic acid bacteria, identified as Streptococcus salivarius subsp. thermophilus (96.8% of the total strains) and Enterococcus spp. The strains showed a low proteolytic activity. The isolates of S. salivarius subsp. thermophilus exhibited a widespread phage resistance. The nonlactic microflora comprised coliforms, yeasts, spore-forming bacteria and lactate fermentative bacteria. The samples showed an acidity level from 0.38 to 0.69% lactic acid (pH from 4.25 to 5.75). The acidifying activity was optimal at 45 degrees C. The advantages and disadvantages of the employment of natural milk starters are discussed.

  1. Using Genomics for Natural Product Structure Elucidation.

    PubMed

    Tietz, Jonathan I; Mitchell, Douglas A

    2016-01-01

    Natural products (NPs) are the most historically bountiful source of chemical matter for drug development-especially for anti-infectives. With insights gleaned from genome mining, interest in natural product discovery has been reinvigorated. An essential stage in NP discovery is structural elucidation, which sheds light not only on the chemical composition of a molecule but also its novelty, properties, and derivatization potential. The history of structure elucidation is replete with techniquebased revolutions: combustion analysis, crystallography, UV, IR, MS, and NMR have each provided game-changing advances; the latest such advance is genomics. All natural products have a genetic basis, and the ability to obtain and interpret genomic information for structure elucidation is increasingly available at low cost to non-specialists. In this review, we describe the value of genomics as a structural elucidation technique, especially from the perspective of the natural product chemist approaching an unknown metabolite. Herein we first introduce the databases and programs of interest to the natural products chemist, with an emphasis on those currently most suited for general usability. We describe strategies for linking observed natural product-linked phenotypes to their corresponding gene clusters. We then discuss techniques for extracting structural information from genes, illustrated with numerous case examples. We also provide an analysis of the biases and limitations of the field with recommendations for future development. Our overview is not only aimed at biologically-oriented researchers already at ease with bioinformatic techniques, but also, in particular, at natural product, organic, and/or medicinal chemists not previously familiar with genomic techniques.

  2. Methane Production by Microbial Mats Under Low Sulfate Concentrations

    NASA Technical Reports Server (NTRS)

    Bebout, Brad M.; Hoehler, Tori M.; Thamdrup, Bo; Albert, Dan; Carpenter, Steven P.; Hogan, Mary; Turk, Kendra; DesMarais, David J.

    2003-01-01

    Cyanobacterial mats collected in hypersaline salterns were incubated in a greenhouse under low sulfate concentrations ([SO4]) and examined for their primary productivity and emissions of methane and other major carbon species. Atmospheric greenhouse warming by gases such as carbon dioxide and methane must have been greater during the Archean than today in order to account for a record of moderate to warm paleoclemates, despite a less luminous early sun. It has been suggested that decreased levels of oxygen and sulfate in Archean oceans could have significantly stimulated microbial methanogenesis relative to present marine rates, with a resultant increase in the relative importance of methane in maintaining the early greenhouse. We maintained modern microbial mats, models of ancient coastal marine communities, in artificial brine mixtures containing both modern [SO4=] (ca. 70 mM) and "Archean" [SO4] (less than 0.2 mM). At low [SO4], primary production in the mats was essentially unaffected, while rates of sulfate reduction decreased by a factor of three, and methane fluxes increased by up to ten-fold. However, remineralization by methanogenesis still amounted to less than 0.4 % of the total carbon released by the mats. The relatively low efficiency of conversion of photosynthate to methane is suggested to reflect the particular geometry and chemical microenvironment of hypersaline cyanobacterial mats. Therefore, such mats w-ere probably relatively weak net sources of methane throughout their 3.5 Ga history, even during periods of low- environmental levels oxygen and sulfate.

  3. Improving microbial biogasoline production in Escherichia coli using tolerance engineering

    DOE PAGES

    Foo, Jee Loon; Jensen, Heather M.; Dahl, Robert H.; ...

    2014-11-04

    Engineering microbial hosts for the production of fungible fuels requires mitigation of limitations posed on the production capacity. One such limitation arises from the inherent toxicity of solvent-like biofuel compounds to production strains, such as Escherichia coli. Here we show the importance of host engineering for the production of short-chain alcohols by studying the overexpression of genes upregulated in response to exogenous isopentenol. Using systems biology data, we selected 40 genes that were upregulated following isopentenol exposure and subsequently overexpressed them in E. coli. Overexpression of several of these candidates improved tolerance to exogenously added isopentenol. Genes conferring isopentenol tolerancemore » phenotypes belonged to diverse functional groups, such as oxidative stress response (soxS, fpr, and nrdH), general stress response (metR, yqhD, and gidB), heat shock-related response (ibpA), and transport (mdlB). To determine if these genes could also improve isopentenol production, we coexpressed the tolerance-enhancing genes individually with an isopentenol production pathway. Our data show that expression of 6 of the 8 candidates improved the production of isopentenol in E. coli, with the methionine biosynthesis regulator MetR improving the titer for isopentenol production by 55%. Additionally, expression of MdlB, an ABC transporter, facilitated a 12% improvement in isopentenol production. To our knowledge, MdlB is the first example of a transporter that can be used to improve production of a short-chain alcohol and provides a valuable new avenue for host engineering in biogasoline production.« less

  4. Improving Microbial Biogasoline Production in Escherichia coli Using Tolerance Engineering

    PubMed Central

    Foo, Jee Loon; Jensen, Heather M.; Dahl, Robert H.; George, Kevin; Keasling, Jay D.; Lee, Taek Soon; Leong, Susanna

    2014-01-01

    ABSTRACT Engineering microbial hosts for the production of fungible fuels requires mitigation of limitations posed on the production capacity. One such limitation arises from the inherent toxicity of solvent-like biofuel compounds to production strains, such as Escherichia coli. Here we show the importance of host engineering for the production of short-chain alcohols by studying the overexpression of genes upregulated in response to exogenous isopentenol. Using systems biology data, we selected 40 genes that were upregulated following isopentenol exposure and subsequently overexpressed them in E. coli. Overexpression of several of these candidates improved tolerance to exogenously added isopentenol. Genes conferring isopentenol tolerance phenotypes belonged to diverse functional groups, such as oxidative stress response (soxS, fpr, and nrdH), general stress response (metR, yqhD, and gidB), heat shock-related response (ibpA), and transport (mdlB). To determine if these genes could also improve isopentenol production, we coexpressed the tolerance-enhancing genes individually with an isopentenol production pathway. Our data show that expression of 6 of the 8 candidates improved the production of isopentenol in E. coli, with the methionine biosynthesis regulator MetR improving the titer for isopentenol production by 55%. Additionally, expression of MdlB, an ABC transporter, facilitated a 12% improvement in isopentenol production. To our knowledge, MdlB is the first example of a transporter that can be used to improve production of a short-chain alcohol and provides a valuable new avenue for host engineering in biogasoline production. PMID:25370492

  5. Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice

    PubMed Central

    Nachman, Michael W.

    2016-01-01

    There is a growing appreciation of the role of gut microbial communities in host biology. However, the nature of variation in microbial communities among different segments of the gastrointestinal (GI) tract is not well understood. Here, we describe microbial communities from ten different segments of the GI tract (mouth, esophagus, stomach, duodenum, ileum, proximal cecum, distal cecum, colon, rectum, and feces) in wild house mice using 16S rRNA gene amplicon sequencing. We also measured carbon and nitrogen stable isotopic ratios from hair samples of individual mice as a proxy for diet. We identified factors that may explain differences in microbial composition among gut segments, and we tested for differences among individual mice in the composition of the microbiota. Consistent with previous studies, the lower GI tract was characterized by a greater relative abundance of anaerobic bacteria and greater microbial diversity relative to the upper GI tract. The upper and lower GI tracts also differed in the relative abundances of predicted microbial gene functions, including those involved in metabolic pathways. However, when the upper and lower GI tracts were considered separately, gut microbial composition was associated with individual mice. Finally, microbial communities derived from fecal samples were similar to those derived from the lower GI tract of their respective hosts, supporting the utility of fecal sampling for studying the gut microbiota of mice. These results show that while there is substantial heterogeneity among segments of the GI tract, individual hosts play a significant role in structuring microbial communities within particular segments of the GI tract. PMID:27669007

  6. [Characteristics of soil microbial community under different vegetation types in Wuyishan National Nature Reserve, East China].

    PubMed

    Wu, Ze-yan; Lin, Wen-xiong; Chen, Zhi-fang; Fang, Chang-xun; Zhang, Zhi-xing; Wu, Lin-kun; Zhou, Ming-ming; Shen, Li-hua

    2013-08-01

    By using Biolog Ecoplate system, this paper studied the structure and functional diversity of soil microbial community under different vegetation types in Wuyishan National Nature Reserve, aimed to probe into the effects of vegetation type on the diversity of soil microbial community. The results showed that the soil chemical properties, soil enzyme activities, and average well color development (AWCD) were higher in natural forest than in planted forest, and were the lowest in abandoned field. The AWCD reflecting soil microbial activity and functional diversity was increased with increasing incubation time, but there existed significant differences among different vegetation types. The carbon sources mostly used by soil microbes were carbohydrates and carboxylic acids, followed by amino acids, phenolic acids and polymers, and amines had the lowest utilization rate. The Simpson index, Shannon index, Richness index and McIntosh index in natural forest were holistically higher than those in planted forest. Principal component analysis (PCA) identified 2 principal component factors in relation to carbon sources, explaining 56.3% and 30.2% of the variation, respectively. The carbon sources used by soil microbial community differed with vegetation types. Amino acids and amides were the two main carbon sources separating the 2 principal component factors. The results of this study could provide basis for further approaching the relationships between vegetation diversity and soil microbial community diversity.

  7. Recent insights into microbial catalases: isolation, production and purification.

    PubMed

    Sooch, Balwinder Singh; Kauldhar, Baljinder Singh; Puri, Munish

    2014-12-01

    Catalase, an oxidoreductase enzyme, works as a detoxification system inside living cells against reactive oxygen species formed as a by-product of different metabolic reactions. The enzyme is found in a wide range of aerobic and anaerobic organisms. Catalase has also been employed in various analytical and diagnostic methods in the form of biosensors and biomarkers in addition to its other applications in textile, paper, food and pharmaceutical industries. New applications for catalases are constantly emerging thanks to their high turnover rate, distinct evolutionary origin, relatively simple and well-defined reaction mechanisms. The following review provides comprehensive information on isolation, production and purification of catalases with different techniques from various microbial sources along with their types, structure, mechanism of action and applications.

  8. Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill.

    PubMed

    Redmond, Molly C; Valentine, David L

    2012-12-11

    Microbial communities present in the Gulf of Mexico rapidly responded to the Deepwater Horizon oil spill. In deep water plumes, these communities were initially dominated by members of Oceanospirillales, Colwellia, and Cycloclasticus. None of these groups were abundant in surface oil slick samples, and Colwellia was much more abundant in oil-degrading enrichment cultures incubated at 4 °C than at room temperature, suggesting that the colder temperatures at plume depth favored the development of these communities. These groups decreased in abundance after the well was capped in July, but the addition of hydrocarbons in laboratory incubations of deep waters from the Gulf of Mexico stimulated Colwellia's growth. Colwellia was the primary organism that incorporated (13)C from ethane and propane in stable isotope probing experiments, and given its abundance in environmental samples at the time that ethane and propane oxidation rates were high, it is likely that Colwellia was active in ethane and propane oxidation in situ. Colwellia also incorporated (13)C benzene, and Colwellia's abundance in crude oil enrichments without natural gas suggests that it has the ability to consume a wide range of hydrocarbon compounds or their degradation products. However, the fact that ethane and propane alone were capable of stimulating the growth of Colwellia, and to a lesser extent, Oceanospirillales, suggests that high natural gas content of this spill may have provided an advantage to these organisms.

  9. Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill

    PubMed Central

    Redmond, Molly C.; Valentine, David L.

    2012-01-01

    Microbial communities present in the Gulf of Mexico rapidly responded to the Deepwater Horizon oil spill. In deep water plumes, these communities were initially dominated by members of Oceanospirillales, Colwellia, and Cycloclasticus. None of these groups were abundant in surface oil slick samples, and Colwellia was much more abundant in oil-degrading enrichment cultures incubated at 4 °C than at room temperature, suggesting that the colder temperatures at plume depth favored the development of these communities. These groups decreased in abundance after the well was capped in July, but the addition of hydrocarbons in laboratory incubations of deep waters from the Gulf of Mexico stimulated Colwellia's growth. Colwellia was the primary organism that incorporated 13C from ethane and propane in stable isotope probing experiments, and given its abundance in environmental samples at the time that ethane and propane oxidation rates were high, it is likely that Colwellia was active in ethane and propane oxidation in situ. Colwellia also incorporated 13C benzene, and Colwellia's abundance in crude oil enrichments without natural gas suggests that it has the ability to consume a wide range of hydrocarbon compounds or their degradation products. However, the fact that ethane and propane alone were capable of stimulating the growth of Colwellia, and to a lesser extent, Oceanospirillales, suggests that high natural gas content of this spill may have provided an advantage to these organisms. PMID:21969552

  10. Natural products as sources for new pesticides.

    PubMed

    Cantrell, Charles L; Dayan, Franck E; Duke, Stephen O

    2012-06-22

    Natural products as pesticides have been reviewed from several perspectives in the past, but no prior treatment has examined the impact of natural product and natural product-based pesticides on the U.S. market, as a function of new active ingredient registrations with the Environmental Protection Agency (EPA). Thus, EPA registration details of new active ingredients for all conventional pesticide registrations and biopesticide registrations were compiled from the years 1997-2010. Conventional pesticide registrations and biopesticide registrations were examined both collectively and independently for all 277 new active ingredients (NAI) and subsequently categorized and sorted into four types: biological (B), natural product (NP), synthetic (S), and synthetic natural derived (SND). When examining conventional pesticides alone, the S category accounted for the majority of NAI registrations, with 78.0%, followed by SND with 14.7%, NP with 6.4%, and B with 0.9%. Biopesticides alone were dominated by NPs with 54.8%, followed by B with 44.6%, SND with 0.6%, and 0% for S. When examining conventional pesticides and biopesticides combined, NPs accounted for the majority of NAI registrations, with 35.7%, followed by S with 30.7%, B with 27.4%, and SND with 6.1%. Despite the common perception that natural products may not be the best sources for NAI as pesticides, when both conventional and biopesticides are examined collectively, and considering that NP, SND, and B all have origins from natural product research, it can be argued that their combined impact with the EPA from 1997 to 2010 accounted for 69.3% of all NAI registrations.

  11. A sea of biosynthesis: marine natural products meet the molecular age†

    PubMed Central

    Lane, Amy L.; Moore, Bradley S.

    2011-01-01

    The years 2000 through mid-2010 marked a transformational period in understanding of the biosynthesis of marine natural products. During this decade the field emerged from one largely dominated by chemical approaches to understanding biosynthetic pathways to one incorporating the full force of modern molecular biology and bioinformatics. Fusion of chemical and biological approaches yielded great advances in understanding the genetic and enzymatic basis for marine natural product biosynthesis. Progress was particularly pronounced for marine microbes, especially actinomycetes and cyanobacteria. During this single decade, both the first complete marine microbial natural product biosynthetic gene cluster sequence was released as well as the first entire genome sequence for a secondary metabolite-rich marine microbe. The decade also saw tremendous progress in recognizing the key role of marine microbial symbionts of invertebrates in natural product biosynthesis. Application of genetic and enzymatic knowledge led to genetic engineering of novel “unnatural” natural products during this time, as well as opportunities for discovery of novel natural products through genome mining. The current review highlights selected seminal studies from 2000 through to June 2010 that illustrate breakthroughs in understanding of marine natural product biosynthesis at the genetic, enzymatic, and small-molecule natural product levels. A total of 154 references are cited. PMID:21170424

  12. Synthetic Biological Approaches to Natural Product Biosynthesis

    PubMed Central

    Winter, Jaclyn M; Tang, Yi

    2012-01-01

    Small molecules produced in Nature continue to be an inspiration for the development of new therapeutic agents. These natural products possess exquisite chemical diversity, which gives rise to their wide range of biological activities. In their host organism, natural products are assembled and modified by dedicated biosynthetic pathways that Nature has meticulously developed. Often times, the complex structures or chemical modifications instated by these pathways are difficult to replicate using traditional synthetic methods. An alternative approach for creating or enhancing the structural variation of natural products is through combinatorial biosynthesis. By rationally reprogramming and manipulating the biosynthetic machinery responsible for their production, unnatural metabolites that were otherwise inaccessible can be obtained. Additionally, new chemical structures can be synthesized or derivatized by developing the enzymes that carry out these complicated chemical reactions into biocatalysts. In this review, we will discuss a variety of combinatorial biosynthetic strategies, their technical challenges, and highlight some recent (since 2007) examples of rationally designed unnatural metabolites, as well as platforms that have been established for the production and modification of clinically important pharmaceutical compounds. PMID:22221832

  13. Microbial evaluation and deterioration of paints and paint-products.

    PubMed

    Obidi, O F; Aboaba, O O; Makanjuola, M S; Nwachukwu, S C U

    2009-09-01

    The microbial quality of materials and final products of a reputable paint industry in Lagos area were analysed. The bacterial contaminants isolated in the paint-products included Bacillus brevis, B. polymyxa, B. laterosporus, Lactobacillus gasseri, L. brevis, Escherichia coli and Proteus mirabilis. The fungal contaminants detected in the paints were mainly Aspergillus niger, A. flavus and Penicillium citrinum. The microbial populations in the raw materials ranged from 1.0 x 10(6) - 9.5 x 10(6) cfu g(-1) for bacteria and between 1.25 x 10(4) and 6.8 x 10(4) cfu g(-1) for fungi while those present in packaging materials ranged from 3.45 x 10(6) - 7.65 x 10(6) cfu g(-1) for bacteria and 2.4 x 10(3) - 2.8 x 10(3) cfu g(-1) for fungi respectively. The bacterial populations in the fresh paint samples monitored every two weeks from the time of production ranged from 1.6 x 10(1) - 4.7 x 10(5) cfu ml(-1) while the fungal populations ranged from 1.0 x 10(1) - 5.5 x 10(3) cfu ml(-1) over a ten-month study period. The optical density at 600 nm increased while transmittance, pH, specific gravity and viscosity of the paint samples decreased over the period suggesting gradual deterioration of the aesthetic qualities of the paint-products with time as indicated by the measured parameters.

  14. Microbial food web dynamics during spring phytoplankton blooms in the naturally iron-fertilized Kerguelen area (Southern Ocean)

    NASA Astrophysics Data System (ADS)

    Christaki, U.; Lefèvre, D.; Georges, C.; Colombet, J.; Catala, P.; Courties, C.; Sime-Ngando, T.; Blain, S.; Obernosterer, I.

    2014-12-01

    Microbial food web dynamics were determined during the onset of several spring phytoplankton blooms induced by natural iron fertilization off Kerguelen Island in the Southern Ocean (KEOPS2). The abundances of heterotrophic bacteria and heterotrophic nanoflagellates, bacterial heterotrophic production, bacterial respiration, and bacterial growth efficiency, were consistently higher in surface waters of the iron-fertilized sites than at the reference site in HNLC (high nutrient low chlorophyll) waters. The abundance of virus-like particles remained unchanged, but viral production increased by a factor of 6 in iron-fertilized waters. Bacterial heterotrophic production was significantly related to heterotrophic nanoflagellate abundance and viral production across all sites, with bacterial production explaining about 70 and 85%, respectively, of the variance of each in the mixed layer (ML). Estimated rates of grazing and viral lysis, however, indicated that heterotrophic nanoflagellates accounted for a substantially higher loss of bacterial production (50%) than viruses (11%). Combining these results with rates of primary production and export determined for the study area, a budget for the flow of carbon through the microbial food web and higher trophic levels during the early (KEOPS2) and the late phase (KEOPS1) of the Kerguelen bloom is provided.

  15. Naturally Efficient Emitters: Luminescent Organometallic Complexes Derived from Natural Products

    NASA Astrophysics Data System (ADS)

    Zhang, Wen-Hua; Young, David J.

    2013-08-01

    Naturally occurring molecules offer intricate structures and functionality that are the basis of modern medicinal chemistry, but are under-represented in materials science. Herein, we review recent literature describing the use of abundant and relatively inexpensive, natural products for the synthesis of ligands for luminescent organometallic complexes used for organic light emitting diodes (OLEDs) and related technologies. These ligands are prepared from the renewable starting materials caffeine, camphor, pinene and cinchonine and, with the exception of caffeine, impart performance improvements to the emissive metal complexes and resulting OLED devices, with emission wavelengths that span the visible spectrum from blue to red. The advantages of these biologically-derived molecules include improved solution processibility and phase homogeneity, brighter luminescence, higher quantum efficiencies and lower turn-on voltages. While nature has evolved these carbon-skeletons for specific purposes, they also offer some intriguing benefits in materials science and technology.

  16. Biochar and microbial signaling: production conditions determine effects on microbial communication.

    PubMed

    Masiello, Caroline A; Chen, Ye; Gao, Xiaodong; Liu, Shirley; Cheng, Hsiao-Ying; Bennett, Matthew R; Rudgers, Jennifer A; Wagner, Daniel S; Zygourakis, Kyriacos; Silberg, Jonathan J

    2013-10-15

    Charcoal has a long soil residence time, which has resulted in its production and use as a carbon sequestration technique (biochar). A range of biological effects can be triggered by soil biochar that can positively and negatively influence carbon storage, such as changing the decomposition rate of organic matter and altering plant biomass production. Sorption of cellular signals has been hypothesized to underlie some of these effects, but it remains unknown whether the binding of biochemical signals occurs, and if so, on time scales relevant to microbial growth and communication. We examined biochar sorption of N-3-oxo-dodecanoyl-L-homoserine lactone, an acyl-homoserine lactone (AHL) intercellular signaling molecule used by many gram-negative soil microbes to regulate gene expression. We show that wood biochars disrupt communication within a growing multicellular system that is made up of sender cells that synthesize AHL and receiver cells that express green fluorescent protein in response to an AHL signal. However, biochar inhibition of AHL-mediated cell-cell communication varied, with the biochar prepared at 700 °C (surface area of 301 m(2)/g) inhibiting cellular communication 10-fold more than an equivalent mass of biochar prepared at 300 °C (surface area of 3 m(2)/g). These findings provide the first direct evidence that biochars elicit a range of effects on gene expression dependent on intercellular signaling, implicating the method of biochar preparation as a parameter that could be tuned to regulate microbial-dependent soil processes, like nitrogen fixation and pest attack of root crops.

  17. Biochar and microbial signaling: production conditions determine effects on microbial communication

    PubMed Central

    Masiello, Caroline A.; Chen, Ye; Gao, Xiaodong; Liu, Shirley; Cheng, Hsiao-Ying; Bennett, Matthew R.; Rudgers, Jennifer A.; Wagner, Daniel S.; Zygourakis, Kyriacos; Silberg, Jonathan J.

    2013-01-01

    Charcoal has a long soil residence time, which has resulted in its production and use as a carbon sequestration technique (biochar). A range of biological effects can be triggered by soil biochar that can positively and negatively influence carbon storage, such as changing the decomposition rate of organic matter and altering plant biomass production. Sorption of cellular signals has been hypothesized to underlie some of these effects, but it remains unknown whether the binding of biochemical signals occurs, and if so, on time scales relevant to microbial growth and communication. We examined biochar sorption of N-3-oxo-dodecanoyl-L-homoserine lactone, an acyl-homoserine lactone (AHL) intercellular signaling molecule used by many gram-negative soil microbes to regulate gene expression. We show that wood biochars disrupt communication within a growing multicellular system that is made up of sender cells that synthesize AHL and receiver cells that express green fluorescent protein in response to an AHL signal. However, biochar inhibition of AHL-mediated cell-cell communication varied, with the biochar prepared at 700°C (surface area of 301 m2/g) inhibiting cellular communication 10-fold more than an equivalent mass of biochar prepared at 300°C (surface area of 3 m2/g). These findings provide the first direct evidence that biochars elicit a range of effects on gene expression dependent on intercellular signaling, implicating the method of biochar preparation as a parameter that could be tuned to regulate microbial-dependent soil processes, like nitrogen fixation and pest attack of root crops. PMID:24066613

  18. C1-carbon sources for chemical and fuel production by microbial gas fermentation.

    PubMed

    Dürre, Peter; Eikmanns, Bernhard J

    2015-12-01

    Fossil resources for production of fuels and chemicals are finite and fuel use contributes to greenhouse gas emissions and global warming. Thus, sustainable fuel supply, security, and prices necessitate the implementation of alternative routes to the production of chemicals and fuels. Much attention has been focussed on use of cellulosic material, particularly through microbial-based processes. However, this is still costly and proving challenging, as are catalytic routes to biofuels from whole biomass. An alternative strategy is to directly capture carbon before incorporation into lignocellulosic biomass. Autotrophic acetogenic, carboxidotrophic, and methanotrophic bacteria are able to capture carbon as CO, CO2, or CH4, respectively, and reuse that carbon in products that displace their fossil-derived counterparts. Thus, gas fermentation represents a versatile industrial platform for the sustainable production of commodity chemicals and fuels from diverse gas resources derived from industrial processes, coal, biomass, municipal solid waste (MSW), and extracted natural gas.

  19. Microbial Metabolite Production for Accelerated Metal and Radionuclide Bioremediation (Microbial Metabolite Production Report)

    SciTech Connect

    TURICK, CHARLES

    2004-09-21

    Biogeochemical activity is an ongoing and dynamic process due to bacterial activity in the subsurface. Bacteria contribute significantly to biotransformation of metals and radionuclides. As basic science reveals more information about specific mechanisms of bacterial-metal reduction, an even greater contribution of bacteria to biogeochemical activities is realized. An understanding and application of the mechanisms of metal and radionuclide reduction offers tremendous potential for development into bioremedial processes and technologies. Most bacteria are capable of biogeochemical transformation as a result of meeting nutrient requirements. These assimilatory mechanisms for metals transformation include production of small molecules that serve as electron shuttles for metal reduction. This contribution to biogeochemistry is small however due to only trace requirements for minerals by bacteria. Dissimilatory metal reducing bacteria (DMRB) reduce oxidized metals and insoluble mineral oxides as a means for biological energy production during growth. These types of bacteria offer considerable potential for bioremediation of environments contaminated with toxic metals and radionuclides because of the relatively large amount of metal biotransformation they require for growth. One of the mechanisms employed by some DMRB for electron transfer to insoluble metal oxides is melanin production. The electrochemical properties of melanin provide this polymeric, humic-type compound with electron shuttling properties. Melanin, specifically, pyomelanin, increases the rate and degree of metal reduction in DMRB as a function of pyomelanin concentration. Due to its electron shuttling behavior, only low femtogram quantities per cell are required to significantly increase metal reduction capacity of DMRB. Melanin production is not limited to DMRB. In fact melanin is one of the most common pigments produced by biological systems. Numerous soil microorganisms produce melanin, contributing

  20. Early state research on antifungal natural products.

    PubMed

    Negri, Melyssa; Salci, Tânia P; Shinobu-Mesquita, Cristiane S; Capoci, Isis R G; Svidzinski, Terezinha I E; Kioshima, Erika Seki

    2014-03-07

    Nosocomial infections caused by fungi have increased greatly in recent years, mainly due to the rising number of immunocompromised patients. However, the available antifungal therapeutic arsenal is limited, and the development of new drugs has been slow. Therefore, the search for alternative drugs with low resistance rates and fewer side effects remains a major challenge. Plants produce a variety of medicinal components that can inhibit pathogen growth. Studies of plant species have been conducted to evaluate the characteristics of natural drug products, including their sustainability, affordability, and antimicrobial activity. A considerable number of studies of medicinal plants and alternative compounds, such as secondary metabolites, phenolic compounds, essential oils and extracts, have been performed. Thus, this review discusses the history of the antifungal arsenal, surveys natural products with potential antifungal activity, discusses strategies to develop derivatives of natural products, and presents perspectives on the development of novel antifungal drug candidates.

  1. Countercurrent Separation of Natural Products: An Update

    PubMed Central

    2015-01-01

    This work assesses the current instrumentation, method development, and applications in countercurrent chromatography (CCC) and centrifugal partition chromatography (CPC), collectively referred to as countercurrent separation (CCS). The article provides a critical review of the CCS literature from 2007 since our last review (J. Nat. Prod.2008, 71, 1489–1508), with a special emphasis on the applications of CCS in natural products research. The current state of CCS is reviewed in regard to three continuing topics (instrumentation, solvent system development, theory) and three new topics (optimization of parameters, workflow, bioactivity applications). The goals of this review are to deliver the necessary background with references for an up-to-date perspective of CCS, to point out its potential for the natural product scientist, and thereby to induce new applications in natural product chemistry, metabolome, and drug discovery research involving organisms from terrestrial and marine sources. PMID:26177360

  2. Countercurrent Separation of Natural Products: An Update.

    PubMed

    Friesen, J Brent; McAlpine, James B; Chen, Shao-Nong; Pauli, Guido F

    2015-07-24

    This work assesses the current instrumentation, method development, and applications in countercurrent chromatography (CCC) and centrifugal partition chromatography (CPC), collectively referred to as countercurrent separation (CCS). The article provides a critical review of the CCS literature from 2007 since our last review (J. Nat. Prod. 2008, 71, 1489-1508), with a special emphasis on the applications of CCS in natural products research. The current state of CCS is reviewed in regard to three continuing topics (instrumentation, solvent system development, theory) and three new topics (optimization of parameters, workflow, bioactivity applications). The goals of this review are to deliver the necessary background with references for an up-to-date perspective of CCS, to point out its potential for the natural product scientist, and thereby to induce new applications in natural product chemistry, metabolome, and drug discovery research involving organisms from terrestrial and marine sources.

  3. Novel fermentation processes for manufacturing plant natural products.

    PubMed

    Zhou, Jingwen; Du, Guocheng; Chen, Jian

    2014-02-01

    Microbial production of plant natural products (PNPs), such as terpenoids, flavonoids from renewable carbohydrate feedstocks offers sustainable and economically attractive alternatives to their petroleum-based production. Rapid development of metabolic engineering and synthetic biology of microorganisms shows many advantages to replace the current extraction of these useful high price chemicals from plants. Although few of them were actually applied on a large scale for PNPs production, continuous research on these high-price chemicals and the rapid growing global market of them, show the promising future for the production of these PNPs by microorganisms with a more economic and environmental friendly way. Introduction of novel pathways and optimization of the native cellular processes by metabolic engineering of microorganisms for PNPs production are rapidly expanding its range of cell-factory applications. Here we review recent progress in metabolic engineering of microorganisms for the production of PNPs. Besides, factors restricting the yield improvement and application of lab-scale achievements to industrial applications have also been discussed.

  4. Mining and engineering natural-product biosynthetic pathways.

    PubMed

    Wilkinson, Barrie; Micklefield, Jason

    2007-07-01

    Natural products continue to fulfill an important role in the development of therapeutic agents. In addition, with the advent of chemical genetics and high-throughput screening platforms, these molecules have become increasingly valuable as tools for interrogating fundamental aspects of biological systems. To access the vast portion of natural-product structural diversity that remains unexploited for these and other applications, genome mining and microbial metagenomic approaches are proving particularly powerful. When these are coupled with recombineering and related genetic tools, large biosynthetic gene clusters that remain intractable or cryptic in the native host can be more efficiently cloned and expressed in a suitable heterologous system. For lead optimization and the further structural diversification of natural-product libraries, combinatorial biosynthetic engineering has also become indispensable. However, our ability to rationally redesign biosynthetic pathways is often limited by our lack of understanding of the structure, dynamics and interplay between the many enzymes involved in complex biosynthetic pathways. Despite this, recent structures of fatty acid synthases should allow a more accurate prediction of the likely architecture of related polyketide synthase and nonribosomal peptide synthetase multienzymes.

  5. Natural Product Sugar Biosynthesis and Enzymatic Glycodiversification**

    PubMed Central

    Thibodeaux, Christopher J.; Melançon, Charles E.; Liu, Hung-wen

    2009-01-01

    Many biologically active small molecule natural products produced by microorganisms derive their activities from sugar substituents. Changing the structures of these sugars can have a profound impact on the biological properties of the parent compounds. This realization has inspired attempts to derivatize the sugar moieties of these natural products through exploitation of the sugar biosynthetic machinery. This approach requires an understanding of the biosynthetic pathway of each target sugar and detailed mechanistic knowledge of the key enzymes. Scientists have begun to unravel the biosynthetic logic behind the assembly of many glycosylated natural products, and have found that a core set of enzyme activities is mixed and matched to synthesize the diverse sugar structures observed in nature. Remarkably, many of these sugar biosynthetic enzymes and glycosyltransferases also exhibit relaxed substrate specificity. The promiscuity of these enzymes has prompted efforts to modify the sugar structures and/or alter the glycosylation patterns of natural products via metabolic pathway engineering and/or enzymatic glycodiversification. In applied biomedical research, these studies will enable the development of new glycosylation tools and generate novel glycoforms of secondary metabolites with useful biological activity. PMID:19058170

  6. Antiviral Natural Products and Herbal Medicines

    PubMed Central

    Lin, Liang-Tzung; Hsu, Wen-Chan; Lin, Chun-Ching

    2014-01-01

    Viral infections play an important role in human diseases, and recent outbreaks in the advent of globalization and ease of travel have underscored their prevention as a critical issue in safeguarding public health. Despite the progress made in immunization and drug development, many viruses lack preventive vaccines and efficient antiviral therapies, which are often beset by the generation of viral escape mutants. Thus, identifying novel antiviral drugs is of critical importance and natural products are an excellent source for such discoveries. In this mini-review, we summarize the antiviral effects reported for several natural products and herbal medicines. PMID:24872930

  7. Anaerobic methane oxidation driven by microbial reduction of natural organic matter in a tropical wetland.

    PubMed

    Valenzuela, Edgardo I; Prieto-Davó, Alejandra; López-Lozano, Nguyen E; Hernández-Eligio, Alberto; Vega-Alvarado, Leticia; Juárez, Katy; García-González, Ana Sarahí; López, Mercedes G; Cervantes, Francisco J

    2017-03-24

    Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers such as electron acceptors supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment along with water samples harvested from a tropical wetland, amended with (13)C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic methane oxidation (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g. quinones) present in NOM fueled AOM by serving as terminal electron acceptor. Indeed, while sulfate reduction was the predominant process accounting for up to 42.5% of the AOM activities, microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided complementary electron-accepting capacity, which reduction accounted for ∼100 nmol (13)C-CH4 oxidized cm(-3) d(-1) Spectroscopic evidence showed that quinone moieties were heterogeneously distributed in the wetland sediment, and that their reduction occurred during the course of AOM. Moreover, an enrichment derived from wetland sediments performing AOM linked to NOM reduction stoichiometrically oxidized methane coupled to the reduction of the humic analogue, anthraquinone-2,6-disulfonate. Microbial populations potentially involved in AOM coupled to microbial reduction of NOM were dominated by divergent biota from putative AOM-associated archaea. We estimate that this microbial process could potentially contribute to the suppression of up to 114 Tg CH4 yr(-1) in coastal wetlands and more than 1,300 Tg yr(-1) considering the global wetland area.Importance Identifying key processes governing methane emissions from natural systems is of major importance considering the global warming effects triggered by this greenhouse gas. AOM coupled

  8. Natural Product Chemistry Meets Genetics: When is a Genotype a Chemotype?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The chemotype of a microbial or plant species has traditionally been defined as its profile of natural products, and the genotype as its genetic constitution or DNA sequence. The purpose of this perspective is to discuss applications of DNA genotyping, particularly by PCR-amplification methods, to ...

  9. TNT Biodegradation by Natural Microbial Assemblages at Estuarine Frontal Boundaries

    DTIC Science & Technology

    2012-07-02

    nitrogen ( Fogg et al. 1985). Not only are these fronts important regulators of OM processing in the water column, but tidal fronts moving back and forth...ecosystems: A review. Limnol. Oceanogr. 55:2452-2462. 35 Floodgate, G. D., G. E. Fogg , D. A. Jones, K. Lochte, and C. M. Turley. 1981. Microbiological...and zooplankton activity at a front in Liverpool Bay. Nature 290:133-136. Fogg , G. E., B. Egan, G. D. Floodgate, D. A. Jones, J. Y. Kassab, K

  10. Natural computation meta-heuristics for the in silico optimization of microbial strains

    PubMed Central

    Rocha, Miguel; Maia, Paulo; Mendes, Rui; Pinto, José P; Ferreira, Eugénio C; Nielsen, Jens; Patil, Kiran Raosaheb; Rocha, Isabel

    2008-01-01

    Background One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metabolic phenotype which typically means having a high yield/productivity. This challenge is not only due to the inherent complexity of the metabolic and regulatory networks, but also to the lack of appropriate modelling and optimization tools. To this end, Evolutionary Algorithms (EAs) have been proposed for in silico metabolic engineering, for example, to identify sets of gene deletions towards maximization of a desired physiological objective function. In this approach, each mutant strain is evaluated by resorting to the simulation of its phenotype using the Flux-Balance Analysis (FBA) approach, together with the premise that microorganisms have maximized their growth along natural evolution. Results This work reports on improved EAs, as well as novel Simulated Annealing (SA) algorithms to address the task of in silico metabolic engineering. Both approaches use a variable size set-based representation, thereby allowing the automatic finding of the best number of gene deletions necessary for achieving a given productivity goal. The work presents extensive computational experiments, involving four case studies that consider the production of succinic and lactic acid as the targets, by using S. cerevisiae and E. coli as model organisms. The proposed algorithms are able to reach optimal/near-optimal solutions regarding the production of the desired compounds and presenting low variability among the several runs. Conclusion The results show that the proposed SA and EA both perform well in the optimization task. A comparison between them is favourable to the SA in terms of consistency in obtaining optimal solutions and faster convergence. In both cases, the use of variable size representations allows the automatic discovery of the approximate number of

  11. Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea.

    PubMed

    Raulf, Felix F; Fabricius, Katharina; Uthicke, Sven; de Beer, Dirk; Abed, Raeid M M; Ramette, Alban

    2015-10-01

    Natural CO2 venting systems can mimic conditions that resemble intermediate to high pCO2 levels as predicted for our future oceans. They represent ideal sites to investigate potential long-term effects of ocean acidification on marine life. To test whether microbes are affected by prolonged exposure to pCO2 levels, we examined the composition and diversity of microbial communities in oxic sandy sediments along a natural CO2 gradient. Increasing pCO2 was accompanied by higher bacterial richness and by a strong increase in rare members in both bacterial and archaeal communities. Microbial communities from sites with CO2 concentrations close to today's conditions had different structures than those of sites with elevated CO2 levels. We also observed increasing sequence abundance of several organic matter degrading types of Flavobacteriaceae and Rhodobacteraceae, which paralleled concurrent shifts in benthic cover and enhanced primary productivity. With increasing pCO2 , sequences related to bacterial nitrifying organisms such as Nitrosococcus and Nitrospirales decreased, and sequences affiliated to the archaeal ammonia-oxidizing Thaumarchaeota Nitrosopumilus maritimus increased. Our study suggests that microbial community structure and diversity, and likely key ecosystem functions, may be altered in coastal sediments by long-term CO2 exposure to levels predicted for the end of the century.

  12. Effects of Environmental Toxicants on Metabolic Activity of Natural Microbial Communities

    PubMed Central

    Barnhart, Carole L. H.; Vestal, J. Robie

    1983-01-01

    Two methods of measuring microbial activity were used to study the effects of toxicants on natural microbial communities. The methods were compared for suitability for toxicity testing, sensitivity, and adaptability to field applications. This study included measurements of the incorporation of 14C-labeled acetate into microbial lipids and microbial glucosidase activity. Activities were measured per unit biomass, determined as lipid phosphate. The effects of various organic and inorganic toxicants on various natural microbial communities were studied. Both methods were useful in detecting toxicity, and their comparative sensitivities varied with the system studied. In one system, the methods showed approximately the same sensitivities in testing the effects of metals, but the acetate incorporation method was more sensitive in detecting the toxicity of organic compounds. The incorporation method was used to study the effects of a point source of pollution on the microbiota of a receiving stream. Toxic doses were found to be two orders of magnitude higher in sediments than in water taken from the same site, indicating chelation or adsorption of the toxicant by the sediment. The microbiota taken from below a point source outfall was 2 to 100 times more resistant to the toxicants tested than was that taken from above the outfall. Downstream filtrates in most cases had an inhibitory effect on the natural microbiota taken from above the pollution source. The microbial methods were compared with commonly used bioassay methods, using higher organisms, and were found to be similar in ability to detect comparative toxicities of compounds, but were less sensitive than methods which use standard media because of the influences of environmental factors. PMID:16346432

  13. Microbial production of fatty acid-derived fuels and chemicals

    PubMed Central

    Lennen, Rebecca M; Pfleger, Brian F

    2013-01-01

    Fatty acid metabolism is an attractive route to produce liquid transportation fuels and commodity oleochemicals from renewable feedstocks. Recently, genes and enzymes, which comprise metabolic pathways for producing fatty acid-derived compounds (e.g. esters, alkanes, olefins, ketones, alcohols, polyesters) have been elucidated and used in engineered microbial hosts. The resulting strains often generate products at low percentages of maximum theoretical yields, leaving significant room for metabolic engineering. Economically viable processes will require strains to approach theoretical yields, particularly for replacement of petroleum-derived fuels. This review will describe recent progress toward this goal, highlighting the scientific discoveries of each pathway, ongoing biochemical studies to understand each enzyme, and metabolic engineering strategies that are being used to improve strain performance. PMID:23541503

  14. Metabolic Engineering for the Production of Natural Products

    PubMed Central

    Pickens, Lauren B.; Tang, Yi; Chooi, Yit-Heng

    2014-01-01

    Natural products and natural product derived compounds play an important role in modern healthcare as frontline treatments for many diseases and as inspiration for chemically synthesized therapeutics. With advances in sequencing and recombinant DNA technology, many of the biosynthetic pathways responsible for the production of these chemically complex and pharmaceutically valuable compounds have been elucidated. With an ever expanding toolkit of biosynthetic components, metabolic engineering is an increasingly powerful method to improve natural product titers and generate novel compounds. Heterologous production platforms have enabled access to pathways from difficult to culture strains; systems biology and metabolic modeling tools have resulted in increasing predictive and analytic capabilities; advances in expression systems and regulation have enabled the fine-tuning of pathways for increased efficiency, and characterization of individual pathway components has facilitated the construction of hybrid pathways for the production of new compounds. These advances in the many aspects of metabolic engineering have not only yielded fascinating scientific discoveries but also make it an increasingly viable approach for the optimization of natural product biosynthesis. PMID:22432617

  15. Chocolate: A Marvelous Natural Product of Chemistry

    ERIC Educational Resources Information Center

    Tannenbaum, Ginger

    2004-01-01

    The study of chocolate, a natural product, can be beneficial for the chemistry students as they ask frequently about the relevancy of their chemistry classes. The history of chocolate, its chemical and physical changes during processing, its composition, different crystalline forms, tempering and its viscosity are discussed.

  16. New Methodology for Natural Gas Production Estimates

    EIA Publications

    2010-01-01

    A new methodology is implemented with the monthly natural gas production estimates from the EIA-914 survey this month. The estimates, to be released April 29, 2010, include revisions for all of 2009. The fundamental changes in the new process include the timeliness of the historical data used for estimation and the frequency of sample updates, both of which are improved.

  17. Marine Natural Products as Prototype Agrochemical Agents

    PubMed Central

    Peng, Jiangnan; Shen, Xiaoyu; El Sayed, Khalid A.; Dunbar, D. C Harles; Perry, Tony L.; Wilkins, Scott P.; Hamann, Mark T.; Bobzin, Steve; Huesing, Joseph; Camp, Robin; Prinsen, Mike; Krupa, Dan; Wideman, Margaret A.

    2016-01-01

    In the interest of identifying new leads that could serve as prototype agrochemical agents, 18 structurally diverse marine-derived compounds were examined for insecticidal, herbicidal, and fungicidal activities. Several new classes of compounds have been shown to be insecticidal, herbicidal, and fungicidal, which suggests that marine natural products represent an intriguing source for the discovery of new agrochemical agents. PMID:12670165

  18. An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products

    PubMed Central

    Johnston, Chad W.; Skinnider, Michael A.; Wyatt, Morgan A.; Li, Xiang; Ranieri, Michael R. M.; Yang, Lian; Zechel, David L.; Ma, Bin; Magarvey, Nathan A.

    2015-01-01

    Bacterial natural products are a diverse and valuable group of small molecules, and genome sequencing indicates that the vast majority remain undiscovered. The prediction of natural product structures from biosynthetic assembly lines can facilitate their discovery, but highly automated, accurate, and integrated systems are required to mine the broad spectrum of sequenced bacterial genomes. Here we present a genome-guided natural products discovery tool to automatically predict, combinatorialize and identify polyketides and nonribosomal peptides from biosynthetic assembly lines using LC–MS/MS data of crude extracts in a high-throughput manner. We detail the directed identification and isolation of six genetically predicted polyketides and nonribosomal peptides using our Genome-to-Natural Products platform. This highly automated, user-friendly programme provides a means of realizing the potential of genetically encoded natural products. PMID:26412281

  19. Natural Products for Chemoprevention of Breast Cancer

    PubMed Central

    Ko, Eun-Yi; Moon, Aree

    2015-01-01

    Breast cancer is the primary cause of cancer death in women. Although current therapies have shown some promise against breast cancer, there is still no effective cure for the majority of patients in the advanced stages of breast cancer. Development of effective agents to slow, reduce, or reverse the incidence of breast cancer in high-risk women is necessary. Chemoprevention of breast cancer by natural products is advantageous, as these compounds have few side effects and low toxicity compared to synthetic compounds. In the present review, we summarize natural products which exert chemopreventive activities against breast cancer, such as curcumin, sauchinone, lycopene, denbinobin, genipin, capsaicin, and ursolic acid. This review examines the current knowledge about natural compounds and their mechanisms that underlie breast cancer chemopreventive activity both in vitro and in vivo. The present review may provide information on the use of these compounds for the prevention of breast cancer. PMID:26734584

  20. Natural products in modern life science.

    PubMed

    Bohlin, Lars; Göransson, Ulf; Alsmark, Cecilia; Wedén, Christina; Backlund, Anders

    2010-06-01

    With a realistic threat against biodiversity in rain forests and in the sea, a sustainable use of natural products is becoming more and more important. Basic research directed against different organisms in Nature could reveal unexpected insights into fundamental biological mechanisms but also new pharmaceutical or biotechnological possibilities of more immediate use. Many different strategies have been used prospecting the biodiversity of Earth in the search for novel structure-activity relationships, which has resulted in important discoveries in drug development. However, we believe that the development of multidisciplinary incentives will be necessary for a future successful exploration of Nature. With this aim, one way would be a modernization and renewal of a venerable proven interdisciplinary science, Pharmacognosy, which represents an integrated way of studying biological systems. This has been demonstrated based on an explanatory model where the different parts of the model are explained by our ongoing research. Anti-inflammatory natural products have been discovered based on ethnopharmacological observations, marine sponges in cold water have resulted in substances with ecological impact, combinatory strategy of ecology and chemistry has revealed new insights into the biodiversity of fungi, in depth studies of cyclic peptides (cyclotides) has created new possibilities for engineering of bioactive peptides, development of new strategies using phylogeny and chemography has resulted in new possibilities for navigating chemical and biological space, and using bioinformatic tools for understanding of lateral gene transfer could provide potential drug targets. A multidisciplinary subject like Pharmacognosy, one of several scientific disciplines bridging biology and chemistry with medicine, has a strategic position for studies of complex scientific questions based on observations in Nature. Furthermore, natural product research based on intriguing scientific

  1. Natural products in modern life science

    PubMed Central

    Göransson, Ulf; Alsmark, Cecilia; Wedén, Christina; Backlund, Anders

    2010-01-01

    With a realistic threat against biodiversity in rain forests and in the sea, a sustainable use of natural products is becoming more and more important. Basic research directed against different organisms in Nature could reveal unexpected insights into fundamental biological mechanisms but also new pharmaceutical or biotechnological possibilities of more immediate use. Many different strategies have been used prospecting the biodiversity of Earth in the search for novel structure–activity relationships, which has resulted in important discoveries in drug development. However, we believe that the development of multidisciplinary incentives will be necessary for a future successful exploration of Nature. With this aim, one way would be a modernization and renewal of a venerable proven interdisciplinary science, Pharmacognosy, which represents an integrated way of studying biological systems. This has been demonstrated based on an explanatory model where the different parts of the model are explained by our ongoing research. Anti-inflammatory natural products have been discovered based on ethnopharmacological observations, marine sponges in cold water have resulted in substances with ecological impact, combinatory strategy of ecology and chemistry has revealed new insights into the biodiversity of fungi, in depth studies of cyclic peptides (cyclotides) has created new possibilities for engineering of bioactive peptides, development of new strategies using phylogeny and chemography has resulted in new possibilities for navigating chemical and biological space, and using bioinformatic tools for understanding of lateral gene transfer could provide potential drug targets. A multidisciplinary subject like Pharmacognosy, one of several scientific disciplines bridging biology and chemistry with medicine, has a strategic position for studies of complex scientific questions based on observations in Nature. Furthermore, natural product research based on intriguing scientific

  2. Microbial isoprenoid production: an example of green chemistry through metabolic engineering.

    PubMed

    Maury, Jérôme; Asadollahi, Mohammad A; Møller, Kasper; Clark, Anthony; Nielsen, Jens

    2005-01-01

    Saving energy, cost efficiency, producing less waste, improving the biodegradability of products, potential for producing novel and complex molecules with improved properties, and reducing the dependency on fossil fuels as raw materials are the main advantages of using biotechnological processes to produce chemicals. Such processes are often referred to as green chemistry or white biotechnology. Metabolic engineering, which permits the rational design of cell factories using directed genetic modifications, is an indispensable strategy for expanding green chemistry. In this chapter, the benefits of using metabolic engineering approaches for the development of green chemistry are illustrated by the recent advances in microbial production of isoprenoids, a diverse and important group of natural compounds with numerous existing and potential commercial applications. Accumulated knowledge on the metabolic pathways leading to the synthesis of the principal precursors of isoprenoids is reviewed, and recent investigations into isoprenoid production using engineered cell factories are described.

  3. Effects of encapsulation of microorganisms on product formation during microbial fermentations.

    PubMed

    Westman, Johan O; Ylitervo, Päivi; Franzén, Carl Johan; Taherzadeh, Mohammad J

    2012-12-01

    This paper reviews the latest developments in microbial products by encapsulated microorganisms in a liquid core surrounded by natural or synthetic membranes. Cells can be encapsulated in one or several steps using liquid droplet formation, pregel dissolving, coacervation, and interfacial polymerization. The use of encapsulated yeast and bacteria for fermentative production of ethanol, lactic acid, biogas, L-phenylacetylcarbinol, 1,3-propanediol, and riboflavin has been investigated. Encapsulated cells have furthermore been used for the biocatalytic conversion of chemicals. Fermentation, using encapsulated cells, offers various advantages compared to traditional cultivations, e.g., higher cell density, faster fermentation, improved tolerance of the cells to toxic media and high temperatures, and selective exclusion of toxic hydrophobic substances. However, mass transfer through the capsule membrane as well as the robustness of the capsules still challenge the utilization of encapsulated cells. The history and the current state of applying microbial encapsulation for production processes, along with the benefits and drawbacks concerning productivity and general physiology of the encapsulated cells, are discussed.

  4. Renewable sustainable biocatalyzed electricity production in a photosynthetic algal microbial fuel cell (PAMFC).

    PubMed

    Strik, David P B T B; Terlouw, Hilde; Hamelers, Hubertus V M; Buisman, Cees J N

    2008-12-01

    Electricity production via solar energy capturing by living higher plants and microalgae in combination with microbial fuel cells are attractive because these systems promise to generate useful energy in a renewable, sustainable, and efficient manner. This study describes the proof of principle of a photosynthetic algal microbial fuel cell (PAMFC) based on naturally selected algae and electrochemically active microorganisms in an open system and without addition of instable or toxic mediators. The developed solar-powered PAMFC produced continuously over 100 days renewable biocatalyzed electricity. The sustainable performance of the PAMFC resulted in a maximum current density of 539 mA/m2 projected anode surface area and a maximum power production of 110 mW/m2 surface area photobioreactor. The energy recovery of the PAMFC can be increased by optimization of the photobioreactor, by reducing the competition from non-electrochemically active microorganisms, by increasing the electrode surface and establishment of a further-enriched biofilm. Since the objective is to produce net renewable energy with algae, future research should also focus on the development of low energy input PAMFCs. This is because current algae production systems have energy inputs similar to the energy present in the outcoming valuable products.

  5. Efficacy of natural biocide on control of microbial induced corrosion in oil pipelines mediated by Desulfovibrio vulgaris and Desulfovibrio gigas.

    PubMed

    Lavania, Meeta; Sarma, Priyangshu M; Mandal, Ajoy K; Cheema, Simrita; Lal, Banwari

    2011-01-01

    We compared the efficacy of a natural biocide with four chemical tetrakishydroxymethyl phosphonium sulfonate, benzyl trimethyl ammonium chloride, and formaldehyde, glutaraldehyde, to control microbial induced corrosion in oil pipelines. The efficacy of biocides were monitored against Desulfovibrio vulgaris and Desulfovibrio gigas in experimental pipes by measuring cell counts, H2S production, Fe(II) production, production of extracellular polymeric substances and structure of biofilm. The treatment with cow urine had minimum planktonic cell counts of 3 x 10(2) CFU/mL as well as biofilm cell counts of 9 x 10(1) CFU/mL as compared with tetrakishydroxyl methyl phosphonium sulfonate, benzyl trimethyl ammonium chloride, formaldehyde and glutaraldehyde. Sulfide production was the lowest with cow urine (0.08 mmol/L), followed by tetrakishydroxymethyl phosphonium sulfonate 0.72 mmol/L. On day 90 of treatment, Fe(II) production was also found to be the lowest with cow urine. The scanning electron microscopic studies indicated that the biofilm bacteria were killed by cow urine. These results demonstrate the cow urine mediated control of microbially induced corrosion, and this is indicative of its potential as a viable substitute of toxic biocides. To the best of our knowledge, this seems to be the first report which screens possible biocidal activity by cow urine as compared to the most common biocides which oil industry is currently using.

  6. Microbial transformations of natural organic compounds and radionuclides in subsurface environments

    SciTech Connect

    Francis, A.J.

    1985-10-01

    A major national concern in the subsurface disposal of energy wastes is the contamination of ground and surface waters by waste leachates containing radionuclides, toxic metals, and organic compounds. Microorganisms play an important role in the transformation of organic compounds, radionuclides, and toxic metals present in the waste and affect their mobility in subsurface environments. Microbial processes involved in dissolution, mobilization, and immobilization of toxic metals under aerobic and anaerobic conditions are briefly reviewed. Metal complexing agents and several organic acids produced by microbial action affect mobilization of radionuclides and toxic metals in subsurface environments. Information on the persistence of and biodegradation rates of synthetic as well as microbiologically produced complexing agents is scarce but important in determining the mobility of metal organic complexes in subsoils. Several gaps in knowledge in the area of microbial transformation of naturally occurring organics, radionuclides, and toxic metals have been identified, and further basic research has been suggested. 31 refs., 1 fig., 3 tabs.

  7. Electricity production coupled to ammonium in a microbial fuel cell.

    PubMed

    He, Zhen; Kan, Jinjun; Wang, Yanbing; Huang, Yuelong; Mansfeld, Florian; Nealson, Kenneth H

    2009-05-01

    The production of electricity from ammonium was examined using a rotating-cathode microbial fuel cell (MFC). The addition of ammonium chloride, ammonium sulfate, or ammonium phosphate (monobasic) resulted in electricity generation, while adding sodium chloride, nitrate, or nitrite did not cause any increase in current production. The peak current increased with increasing amount of ammonium addition up to 62.3 mM of ammonium chloride, suggesting that ammonium was involved in electricity generation either directly as the anodic fuel or indirectly as substrates for nitrifiers to produce organic compounds for heterotrophs. Adding nitrate or nitrite with ammonium increased current production compared to solely ammonium addition. Using 16S rRNA-linked molecular analyses, we found ammonium-oxidizing bacteria and denitrifying bacteria on both the anode and cathode electrodes, whereas no anammox bacteria were detected. The dominant ammonium-oxidizing bacteria were closely related to Nitrosomonas europaea. The present MFC achieved an ammonium removal efficiency of 49.2 +/- 5.9 or 69.7 +/- 3.6%, depending on hydraulic retention time, but exhibited a very low Coulombic efficiency.

  8. 40 CFR 158.2171 - Experimental use permit microbial pesticides product analysis data requirements table.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... pesticides product analysis data requirements table. 158.2171 Section 158.2171 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2171 Experimental use permit microbial pesticides product analysis data requirements...

  9. 40 CFR 158.2171 - Experimental use permit microbial pesticides product analysis data requirements table.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... pesticides product analysis data requirements table. 158.2171 Section 158.2171 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2171 Experimental use permit microbial pesticides product analysis data requirements...

  10. 40 CFR 158.2171 - Experimental use permit microbial pesticides product analysis data requirements table.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... pesticides product analysis data requirements table. 158.2171 Section 158.2171 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2171 Experimental use permit microbial pesticides product analysis data requirements...

  11. Influence of packaging conditions on natural microbial population growth of endive.

    PubMed

    Charles, Florence; Rugani, Nathalie; Gontard, Nathalie

    2005-05-01

    The influence of three packaging conditions, i.e., unmodified atmosphere packaging (UAP), passive modified atmosphere packaging (MAP), and active MAP, on the natural microbial population growth of endive was investigated at 20 degrees C. For UAP, endive was placed in macroperforated oriented polypropylene pouches that maintained gas composition close to that of air (21 kPa O2 and 0 kPa CO2) but also limited superficial product dehydration. For MAP, endive was placed in low-density polyethylene pouches that induced a 3 kPa O2 and 5 kPa CO2 equilibrium atmosphere composition. Steady state was reached after 25 h of storage with an oxygen absorbing packet (active MAP) compared with 100 h without the packet (passive MAP) and was maintained for 200 h. After 312 h of storage, both active and passive MAP reduced total aerobic mesophile, yeast, and mold population growth compared with endive in UAP. Active MAP accelerated and improved the inhibition of Pseudomonas spp. and Enterobacteriaceae, respectively, probably because of the rapid O2 depletion during the transition period. A shift in the Enterobacteriaceae subpopulation from Rhanella aquatilis to Enterobacter agglomerans was observed for both passive and active MAP.

  12. Microbial Interactions with Natural Organic Matter Extracted from the Oak Ridge FRC

    NASA Astrophysics Data System (ADS)

    Wu, X.; Jagadamma, S.; Lancaster, A.; Adams, M. W. W.; Hazen, T.; Justice, N.; Chakraborty, R.

    2015-12-01

    Natural organic matter (NOM) is central to microbial food webs; however, little is known about the interplay between the physical and chemical characteristics of NOM and its turnover by microbial communities based upon biotic and abiotic parameters (e.g., biogenic precursors, redox state, bioavailability). Microbial activity changes the structures and properties that influence further bioavailability of NOM. To date, our understanding of these interactions is insufficient, and indigenous microbial activities that regulate NOM turnover are poorly resolved. It is critical to identify NOM characteristics to the structure and composition of microbial communities and to the metabolic potential of that community. Towards that end, sediment samples collected from the background area well FW305 (Oak Ridge Field Research Center, Oak Ridge, TN) were tested for NOM extraction methods that used three mild solvents, e.g., phosphate buffered saline (PBS), pyrophosphate, and MilliQ-water. MilliQ-water was finally chosen for extracting sediment samples via shaking and sonication. Groundwater from well FW301 was used as an inoculum to which the extracted NOM was added as carbon sources to feed native microbes. To identify the specific functional groups of extracted NOM that are bioavailable to indigenous microbes, several techniques, including FTIR, LC-MS, EEM, were applied to characterize the extracted NOM as well as the transformed NOM metabolites. 16S rDNA amplicon sequencing was also performed to identify the specific microbial diversity that was enriched and microbial isolates that preferentially grew with these NOM was also cultivated in the lab for future detailed studies.

  13. Microbial colonization of biopolymeric thin films containing natural compounds and antibiotics fabricated by MAPLE

    NASA Astrophysics Data System (ADS)

    Cristescu, R.; Surdu, A. V.; Grumezescu, A. M.; Oprea, A. E.; Trusca, R.; Vasile, O.; Dorcioman, G.; Visan, A.; Socol, G.; Mihailescu, I. N.; Mihaiescu, D.; Enculescu, M.; Chifiriuc, M. C.; Boehm, R. D.; Narayan, R. J.; Chrisey, D. B.

    2015-05-01

    Although a great number of antibiotics are currently available, they are often rendered ineffective by the ability of microbial strains to develop genetic resistance and to grow in biofilms. Since many antimicrobial agents poorly penetrate biofilms, biofilm-associated infections often require high concentrations of antimicrobial agents for effective treatment. Among the various strategies that may be used to inhibit microbial biofilms, one strategy that has generated significant interest involves the use of bioactive surfaces that are resistant to microbial colonization. In this respect, we used matrix assisted pulsed laser evaporation (MAPLE) involving a pulsed KrF* excimer laser source (λ = 248 nm, τ = 25 ns, ν = 10 Hz) to obtain thin composite biopolymeric films containing natural (flavonoid) or synthetic (antibiotic) compounds as bioactive substances. Chemical composition and film structures were investigated by Fourier transform infrared spectroscopy and X-ray diffraction. Films morphology was studied by scanning electron microscopy and transmission electron microscopy. The antimicrobial assay of the microbial biofilms formed on these films was assessed by the viable cell counts method. The flavonoid-containing thin films showed increased resistance to microbial colonization, highlighting their potential to be used for the design of anti-biofilm surfaces.

  14. Contrasting microbial biogeographical patterns between anthropogenic subalpine grasslands and natural alpine grasslands.

    PubMed

    Geremia, Roberto A; Pușcaș, Mihai; Zinger, Lucie; Bonneville, Jean-Marc; Choler, Philippe

    2016-02-01

    The effect of plant species composition on soil microbial communities was studied at the multiregional level. We compared the soil microbial communities of alpine natural grasslands dominated by Carex curvula and anthropogenic subalpine pastures dominated by Nardus stricta. We conducted paired sampling across the Carpathians and the Alps and used Illumina sequencing to reveal the molecular diversity of soil microbes. We found that bacterial and fungal communities exhibited contrasting regional distributions and that the distribution in each grassland is well discriminated. Beta diversity of microbial communities was much higher in C. curvula grasslands due to a marked regional effect. The composition of grassland-type core microbiomes suggest that C. curvula, and N. stricta to a lesser extent, tend to select a cohort of microbes related to antibiosis/exclusion, pathogenesis and endophytism. We discuss these findings in light of the postglacial history of the studied grasslands, the habitat connectivity and the disturbance regimes. Human-induced disturbance in the subalpine belt of European mountains has led to homogeneous soil microbial communities at large biogeographical scales. Our results confirm the overarching role of the dominant grassland plant species in the distribution of microbial communities and highlight the relevance of biogeographical history.

  15. Natural gas production and consumption 1979

    SciTech Connect

    Not Available

    1981-01-01

    Total marketed production of natural gas in the United States during 1979 was 20,471 billion cubic feet, an increase of approximately 497 billion cubic feet, or 2.5 percent over 1978. Texas and Louisiana, the two leading producing states, accounted for 70.5 percent of total 1979 marketed production. In 1979, deliveries of natural gas to residential, commercial, industrial, electric utilities, and other consumers totaled 18,141 billion cubic feet. Total consumption, which includes lease, plant, and pipeline fuel in addition to deliveries to consumers, was 20,241 billion cubic feet in 1979 compared to 19,627 billion cubic feet in 1978, an increase of 3.1 percent. Movements of natural gas into and out of each state are presented. Louisiana accounted for the largest quantity of net deliveries, 5,107 billion cubic feet, followed by Texas and Oklahoma with net deliveries of 2,772 billion cubic feet and 914 billion cubic feet, respectively. Imports of natural gas by pipeline from Canada and as liquefied natural gas (LNG) from Algeria totaled 1,253 billion cubic feet in 1979. Total imports increased 288 billion cubic feet, or 29.8 percent, from 1978 levels. Exports of LNG to Japan and pipeline shipments to Canada and Mexico increased 6.0 percent from 52.5 billion cubic feet in 1978 to 55.7 billion cubic feet in 1979. LNG shipments to Japan accounted for 92.1 percent of total exports in 1979.

  16. Biologically active proteins from natural product extracts.

    PubMed

    O'Keefe, B R

    2001-10-01

    The term "biologically active proteins" is almost redundant. All proteins produced by living creatures are, by their very nature, biologically active to some extent in their homologous species. In this review, a subset of these proteins will be discussed that are biologically active in heterologous systems. The isolation and characterization of novel proteins from natural product extracts including those derived from microorganisms, plants, insects, terrestrial vertebrates, and marine organisms will be reviewed and grouped into several distinct classes based on their biological activity and their structure.

  17. Milk kefir: composition, microbial cultures, biological activities, and related products

    PubMed Central

    Prado, Maria R.; Blandón, Lina Marcela; Vandenberghe, Luciana P. S.; Rodrigues, Cristine; Castro, Guillermo R.; Thomaz-Soccol, Vanete; Soccol, Carlos R.

    2015-01-01

    In recent years, there has been a strong focus on beneficial foods with probiotic microorganisms and functional organic substances. In this context, there is an increasing interest in the commercial use of kefir, since it can be marketed as a natural beverage that has health promoting bacteria. There are numerous commercially available kefir based-products. Kefir may act as a matrix in the effective delivery of probiotic microorganisms in different types of products. Also, the presence of kefir’s exopolysaccharides, known as kefiran, which has biological activity, certainly adds value to products. Kefiran can also be used separately in other food products and as a coating film for various food and pharmaceutical products. This article aims to update the information about kefir and its microbiological composition, biological activity of the kefir’s microflora and the importance of kefiran as a beneficial health substance. PMID:26579086

  18. Natural product inhibitors of ocular angiogenesis

    PubMed Central

    Sulaiman, Rania S.; Basavarajappa, Halesha D.; Corson, Timothy W.

    2014-01-01

    Natural products are characterized by high chemical diversity and biochemical specificity; therefore, they are appealing as lead compounds for drug discovery. Given the importance of angiogenesis to many pathologies, numerous natural products have been explored as potential anti-angiogenic drugs. Ocular angiogenesis underlies blinding eye diseases such as retinopathy of prematurity (ROP) in children, proliferative diabetic retinopathy (DR) in adults of working age, and age-related macular degeneration (AMD) in the elderly. Despite the presence of effective therapy in many cases, these diseases are still a significant health burden. Anti-VEGF biologics are the standard of care, but may cause ocular or systemic side effects after intraocular administration and patients may be refractory. Many anti-angiogenic compounds inhibit tumor growth and metastasis alone or in combination therapy, but a more select subset of them has been tested in the context of ocular neovascular diseases. Here, we review the promise of natural products as anti-angiogenic agents, with a specific focus on retinal and choroidal neovascularization. The multifunctional curcumin and the chalcone isoliquiritigenin have demonstrated promising anti-angiogenic effects in mouse models of DR and choroidal neovascularization (CNV) respectively. The homoisoflavanone cremastranone and the flavonoid deguelin have been shown to inhibit ocular neovascularization in more than one disease model. The isoflavone genistein and the flavone apigenin on the other hand are showing potential in the prevention of retinal and choroidal angiogenesis with long-term administration. Many other products with antiangiogenic potential in vitro such as the lactone withaferin A, the flavonol quercetin, and the stilbenoid combretastatin A4 are awaiting investigation in different ocular disease relevant animal models. These natural products may serve as lead compounds for the design of more specific, efficacious, and affordable

  19. A natural view of microbial biodiversity within hot spring cyanobacterial mat communities

    NASA Technical Reports Server (NTRS)

    Ward, D. M.; Ferris, M. J.; Nold, S. C.; Bateson, M. M.

    1998-01-01

    This review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. Molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. For example, none of 31 unique 16S rRNA sequences detected in the Octopus Spring mat, Yellowstone National Park, matches that of any prokaryote previously cultivated from geothermal systems; 11 are contributed by genetically diverse cyanobacteria, even though a single cyanobacterial species was suspected based on morphologic and culture analysis. By studying the basis for the incongruity between culture and molecular samplings of community composition, we are beginning to cultivate isolates whose 16S rRNA sequences are readily detected. By placing the genetic diversity detected in context with the well-defined natural environmental gradients typical of hot spring mat systems, the relationship between gene and species diversity is clarified and ecological patterns of species occurrence emerge. By combining these ecological patterns with the evolutionary patterns inherently revealed by phylogenetic analysis of gene sequence data, we find that it may be possible to understand microbial biodiversity within these systems by using principles similar to those developed by evolutionary ecologists to understand biodiversity of larger species. We hope that such an approach guides microbial ecologists to a more realistic and predictive understanding of microbial species occurrence and responsiveness in both natural and disturbed habitats.

  20. A Natural View of Microbial Biodiversity within Hot Spring Cyanobacterial Mat Communities

    PubMed Central

    Ward, David M.; Ferris, Michael J.; Nold, Stephen C.; Bateson, Mary M.

    1998-01-01

    This review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. Molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. For example, none of 31 unique 16S rRNA sequences detected in the Octopus Spring mat, Yellowstone National Park, matches that of any prokaryote previously cultivated from geothermal systems; 11 are contributed by genetically diverse cyanobacteria, even though a single cyanobacterial species was suspected based on morphologic and culture analysis. By studying the basis for the incongruity between culture and molecular samplings of community composition, we are beginning to cultivate isolates whose 16S rRNA sequences are readily detected. By placing the genetic diversity detected in context with the well-defined natural environmental gradients typical of hot spring mat systems, the relationship between gene and species diversity is clarified and ecological patterns of species occurrence emerge. By combining these ecological patterns with the evolutionary patterns inherently revealed by phylogenetic analysis of gene sequence data, we find that it may be possible to understand microbial biodiversity within these systems by using principles similar to those developed by evolutionary ecologists to understand biodiversity of larger species. We hope that such an approach guides microbial ecologists to a more realistic and predictive understanding of microbial species occurrence and responsiveness in both natural and disturbed habitats. PMID:9841675

  1. Pharmaceuticals in the environment: biodegradation and effects on natural microbial communities. A review.

    PubMed

    Barra Caracciolo, Anna; Topp, Edward; Grenni, Paola

    2015-03-15

    Environmental microorganisms play a key role in fundamental ecological processes such as biogeochemical cycling and organic contaminant degradation. Microorganisms comprise a large unexplored reservoir of genetic diversity and metabolic capability providing several ecosystem services, most importantly the maintenance of soil and water quality. Pharmaceutical occurrence in the environment can compromise microbial community structure and activities in different ways. The fate of a pharmaceutical in soil or water depends on numerous factors, including its inherent physic-chemical properties (e.g. water solubility, lipophilicity, vapour pressure), environmental factors and climate conditions (e.g. temperature, incident radiation, pH) and most importantly the presence and activity of microorganisms that possess the ability to biodegrade it. The presence of a natural microbial community is a necessary prerequisite for an effective response to the various chemicals that can contaminate an ecosystem. The recovery from contamination is only possible if toxicity does not hamper microbial activity. This review presents current knowledge on the effects on natural microbial communities of some pharmaceuticals and of some biocides commonly found as environmental microcontaminants.

  2. Thoughts Toward a Theory of Natural Selection: The Importance of Microbial Experimental Evolution.

    PubMed

    Dykhuizen, Daniel

    2016-01-08

    Natural selection should no longer be thought of simply as a primitive (magical) concept that can be used to support all kinds of evolutionary theorizing. We need to develop causal theories of natural selection; how it arises. Because the factors contributing to the creation of natural selection are expected to be complex and intertwined, theories explaining the causes of natural selection can only be developed through the experimental method. Microbial experimental evolution provides many benefits that using other organisms does not. Microorganisms are small, so millions can be housed in a test tube; they have short generation times, so evolution over hundreds of generations can be easily studied; they can grow in chemically defined media, so the environment can be precisely defined; and they can be frozen, so the fitness of strains or populations can be directly compared across time. Microbial evolution experiments can be divided into two types. The first is to measure the selection coefficient of two known strains over the first 50 or so generations, before advantageous mutations rise to high frequency. This type of experiment can be used to directly test hypotheses. The second is to allow microbial cultures to evolve over many hundreds or thousands of generations and follow the genetic changes, to infer what phenotypes are selected. In the last section of this article, I propose that selection coefficients are not constant, but change as the population becomes fitter, introducing the idea of the selection space.

  3. Taxonomy, Physiology, and Natural Products of Actinobacteria.

    PubMed

    Barka, Essaid Ait; Vatsa, Parul; Sanchez, Lisa; Gaveau-Vaillant, Nathalie; Jacquard, Cedric; Klenk, Hans-Peter; Clément, Christophe; Ouhdouch, Yder; van Wezel, Gilles P

    2016-03-01

    Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.

  4. Taxonomy, Physiology, and Natural Products of Actinobacteria

    PubMed Central

    Vatsa, Parul; Sanchez, Lisa; Gaveau-Vaillant, Nathalie; Jacquard, Cedric; Klenk, Hans-Peter; Clément, Christophe; Ouhdouch, Yder

    2015-01-01

    SUMMARY Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum. PMID:26609051

  5. Microbial production and applications of 1,2-propanediol.

    PubMed

    Saxena, R K; Anand, Pinki; Saran, Saurabh; Isar, Jasmine; Agarwal, Lata

    2010-03-01

    1,2-Propanediol (propylene glycol) is an existing commodity chemical and can be produced from renewable resources using microbes. By virtue of being a natural product, relevant biochemical pathways can be harnessed into fermentation processes to produce 1,2-propanediol. In the present review, the chemical process and different biological strategies for the production of 1,2-propanediol are reviewed and compared with the potentials and limitations of all processes. For the successful commercial production of this diol, it is necessary to establish the metabolic pathways and production hosts (microorganisms), which are capable of delivering final product with high yields and volumetric productivity. Three pathways which have been recognized for 1,2-propanediol production are discussed here. In the first, de-oxy sugars like fucose and rhamnose are used as the carbon sources, while in the other route, the glycolytic intermediate-dihydroxyacetonephosphate (DHAP) is used to produce 1,2-propanediol via the formation of methylglyoxal. A new pathway of 1,2-propanediol production by lactic acid degradation under anoxic conditions and the enzymes involved is also discussed. The production of this diol has gained attention because of their newer applications in industries such as polymers, food, pharmaceuticals, textiles, etc. Furthermore, improvement in fermentation technology will permit its uses in other applications. Future prospect in the light of the current research and its potential as a major bulk chemical are discussed.

  6. Designer synthetic media for studying microbial-catalyzed biofuel production

    SciTech Connect

    Tang, Xiaoyu; da Costa Sousa, Leonardo; Jin, Mingjie; Chundawat, Shishir; Chambliss, Charles; Lau, Ming W; Xiao, Zeyi; Dale, Bruce E; Balan, Venkatesh

    2015-01-01

    Background: The fermentation inhibition of yeast or bacteria by lignocellulose-derived degradation products, during hexose/pentose co-fermentation, is a major bottleneck for cost-effective lignocellulosic biorefineries. To engineer microbial strains for improved performance, it is critical to understand the mechanisms of inhibition that affect fermentative organisms in the presence of major components of a lignocellulosic hydrolysate. The development of a synthetic lignocellulosic hydrolysate (SH) media with a composition similar to the actual biomass hydrolysate will be an important advancement to facilitate these studies. In this work, we characterized the nutrients and plant-derived decomposition products present in AFEX™ pretreated corn stover hydrolysate (ACH). The SH was formulated based on the ACH composition and was further used to evaluate the inhibitory effects of various families of decomposition products during Saccharomyces cerevisiae 424A (LNH-ST) fermentation. Results: The ACH contained high levels of nitrogenous compounds, notably amides, pyrazines, and imidazoles. In contrast, a relatively low content of furans and aromatic and aliphatic acids were found in the ACH. Though most of the families of decomposition products were inhibitory to xylose fermentation, due to their abundance, the nitrogenous compounds showed the most inhibition. From these compounds, amides (products of the ammonolysis reaction) contributed the most to the reduction of the fermentation performance. However, this result is associated to a concentration effect, as the corresponding carboxylic acids (products of hydrolysis) promoted greater inhibition when present at the same molar concentration as the amides. Due to its complexity, the formulated SH did not perfectly match the fermentation profile of the actual hydrolysate, especially the growth curve. However, the SH formulation was effective for studying the inhibitory effect of various compounds on yeast fermentation

  7. Designer synthetic media for studying microbial-catalyzed biofuel production

    DOE PAGES

    Tang, Xiaoyu; da Costa Sousa, Leonardo; Jin, Mingjie; ...

    2015-01-01

    Background: The fermentation inhibition of yeast or bacteria by lignocellulose-derived degradation products, during hexose/pentose co-fermentation, is a major bottleneck for cost-effective lignocellulosic biorefineries. To engineer microbial strains for improved performance, it is critical to understand the mechanisms of inhibition that affect fermentative organisms in the presence of major components of a lignocellulosic hydrolysate. The development of a synthetic lignocellulosic hydrolysate (SH) media with a composition similar to the actual biomass hydrolysate will be an important advancement to facilitate these studies. In this work, we characterized the nutrients and plant-derived decomposition products present in AFEX™ pretreated corn stover hydrolysate (ACH). Themore » SH was formulated based on the ACH composition and was further used to evaluate the inhibitory effects of various families of decomposition products during Saccharomyces cerevisiae 424A (LNH-ST) fermentation. Results: The ACH contained high levels of nitrogenous compounds, notably amides, pyrazines, and imidazoles. In contrast, a relatively low content of furans and aromatic and aliphatic acids were found in the ACH. Though most of the families of decomposition products were inhibitory to xylose fermentation, due to their abundance, the nitrogenous compounds showed the most inhibition. From these compounds, amides (products of the ammonolysis reaction) contributed the most to the reduction of the fermentation performance. However, this result is associated to a concentration effect, as the corresponding carboxylic acids (products of hydrolysis) promoted greater inhibition when present at the same molar concentration as the amides. Due to its complexity, the formulated SH did not perfectly match the fermentation profile of the actual hydrolysate, especially the growth curve. However, the SH formulation was effective for studying the inhibitory effect of various compounds on yeast

  8. Natural oil slicks fuel surface water microbial activities in the northern Gulf of Mexico.

    PubMed

    Ziervogel, Kai; D'Souza, Nigel; Sweet, Julia; Yan, Beizhan; Passow, Uta

    2014-01-01

    We conducted a series of roller tank incubations with surface seawater from the Green Canyon oil reservoir, northern Gulf of Mexico, amended with either a natural oil slick (GCS-oil) or pristine oil. The goal was to test whether bacterial activities of natural surface water communities facilitate the formation of oil-rich marine snow (oil snow). Although oil snow did not form during any of our experiments, we found specific bacterial metabolic responses to the addition of GCS-oil that profoundly affected carbon cycling within our 4-days incubations. Peptidase and β-glucosidase activities indicative of bacterial enzymatic hydrolysis of peptides and carbohydrates, respectively, were suppressed upon the addition of GCS-oil relative to the non-oil treatment, suggesting that ascending oil and gas initially inhibits bacterial metabolism in surface water. Biodegradation of physically dispersed GCS-oil components, indicated by the degradation of lower molecular weight n-alkanes as well as the rapid transformation of particulate oil-carbon (C: N >40) into the DOC pool, led to the production of carbohydrate- and peptide-rich degradation byproducts and bacterial metabolites such as transparent exopolymer particles (TEP). TEP formation was highest at day 4 in the presence of GCS-oil; in contrast, TEP levels in the non-oil treatment already peaked at day 2. Cell-specific enzymatic activities closely followed TEP concentrations in the presence and absence of GCS-oil. These results demonstrate that the formation of oil slicks and activities of oil-degrading bacteria result in a temporal offset of microbial cycling of organic matter, affecting food web interactions and carbon cycling in surface waters over cold seeps.

  9. Natural oil slicks fuel surface water microbial activities in the northern Gulf of Mexico

    PubMed Central

    Ziervogel, Kai; D'souza, Nigel; Sweet, Julia; Yan, Beizhan; Passow, Uta

    2014-01-01

    We conducted a series of roller tank incubations with surface seawater from the Green Canyon oil reservoir, northern Gulf of Mexico, amended with either a natural oil slick (GCS-oil) or pristine oil. The goal was to test whether bacterial activities of natural surface water communities facilitate the formation of oil-rich marine snow (oil snow). Although oil snow did not form during any of our experiments, we found specific bacterial metabolic responses to the addition of GCS-oil that profoundly affected carbon cycling within our 4-days incubations. Peptidase and β-glucosidase activities indicative of bacterial enzymatic hydrolysis of peptides and carbohydrates, respectively, were suppressed upon the addition of GCS-oil relative to the non-oil treatment, suggesting that ascending oil and gas initially inhibits bacterial metabolism in surface water. Biodegradation of physically dispersed GCS-oil components, indicated by the degradation of lower molecular weight n-alkanes as well as the rapid transformation of particulate oil-carbon (C: N >40) into the DOC pool, led to the production of carbohydrate- and peptide-rich degradation byproducts and bacterial metabolites such as transparent exopolymer particles (TEP). TEP formation was highest at day 4 in the presence of GCS-oil; in contrast, TEP levels in the non-oil treatment already peaked at day 2. Cell-specific enzymatic activities closely followed TEP concentrations in the presence and absence of GCS-oil. These results demonstrate that the formation of oil slicks and activities of oil-degrading bacteria result in a temporal offset of microbial cycling of organic matter, affecting food web interactions and carbon cycling in surface waters over cold seeps. PMID:24847314

  10. Clostridium ljungdahlii represents a microbial production platform based on syngas

    PubMed Central

    Köpke, Michael; Held, Claudia; Hujer, Sandra; Liesegang, Heiko; Wiezer, Arnim; Wollherr, Antje; Ehrenreich, Armin; Liebl, Wolfgang; Gottschalk, Gerhard; Dürre, Peter

    2010-01-01

    Clostridium ljungdahlii is an anaerobic homoacetogen, able to ferment sugars, other organic compounds, or CO2/H2 and synthesis gas (CO/H2). The latter feature makes it an interesting microbe for the biotech industry, as important bulk chemicals and proteins can be produced at the expense of CO2, thus combining industrial needs with sustained reduction of CO and CO2 in the atmosphere. Sequencing the complete genome of C. ljungdahlii revealed that it comprises 4,630,065 bp and is one of the largest clostridial genomes known to date. Experimental data and in silico comparisons revealed a third mode of anaerobic homoacetogenic metabolism. Unlike other organisms such as Moorella thermoacetica or Acetobacterium woodii, neither cytochromes nor sodium ions are involved in energy generation. Instead, an Rnf system is present, by which proton translocation can be performed. An electroporation procedure has been developed to transform the organism with plasmids bearing heterologous genes for butanol production. Successful expression of these genes could be demonstrated, leading to formation of the biofuel. Thus, C. ljungdahlii can be used as a unique microbial production platform based on synthesis gas and carbon dioxide/hydrogen mixtures. PMID:20616070

  11. Microbial production of surfactants and their commercial potential.

    PubMed Central

    Desai, J D; Banat, I M

    1997-01-01

    Many microorganisms, especially bacteria, produce biosurfactants when grown on water-immiscible substrates. Biosurfactants are more effective, selective, environmentally friendly, and stable than many synthetic surfactants. Most common biosurfactants are glycolipids in which carbohydrates are attached to a long-chain aliphatic acid, while others, like lipopeptides, lipoproteins, and heteropolysaccharides, are more complex. Rapid and reliable methods for screening and selection of biosurfactant-producing microorganisms and evaluation of their activity have been developed. Genes involved in rhamnolipid synthesis (rhlAB) and regulation (rhlI and rhlR) in Pseudomonas aeruginosa are characterized, and expression of rhlAB in heterologous hosts is discussed. Genes for surfactin production (sfp, srfA, and comA) in Bacillus spp. are also characterized. Fermentative production of biosurfactants depends primarily on the microbial strain, source of carbon and nitrogen, pH, temperature, and concentration of oxygen and metal ions. Addition of water-immiscible substrates to media and nitrogen and iron limitations in the media result in an overproduction of some biosurfactants. Other important advances are the use of water-soluble substrates and agroindustrial wastes for production, development of continuous recovery processes, and production through biotransformation. Commercialization of biosurfactants in the cosmetic, food, health care, pulp- and paper-processing, coal, ceramic, and metal industries has been proposed. However, the most promising applications are cleaning of oil-contaminated tankers, oil spill management, transportation of heavy crude oil, enhanced oil recovery, recovery of crude oil from sludge, and bioremediation of sites contaminated with hydrocarbons, heavy metals, and other pollutants. Perspectives for future research and applications are also discussed. PMID:9106364

  12. Trypanocidal Activity of Marine Natural Products

    PubMed Central

    Jones, Amy J.; Grkovic, Tanja; Sykes, Melissa L.; Avery, Vicky M.

    2013-01-01

    Marine natural products are a diverse, unique collection of compounds with immense therapeutic potential. This has resulted in these molecules being evaluated for a number of different disease indications including the neglected protozoan diseases, human African trypanosomiasis and Chagas disease, for which very few drugs are currently available. This article will review the marine natural products for which activity against the kinetoplastid parasites; Trypanosoma brucei brucei, T.b. rhodesiense and T. cruzi has been reported. As it is important to know the selectivity of a compound when evaluating its trypanocidal activity, this article will only cover molecules which have simultaneously been tested for cytotoxicity against a mammalian cell line. Compounds have been grouped according to their chemical structure and representative examples from each class were selected for detailed discussion. PMID:24152565

  13. New chemistry from natural product biosynthesis.

    PubMed

    Hubert, Catherine B; Barry, Sarah M

    2016-06-15

    Catalysts are a vital part of synthetic chemistry. However, there are still many important reactions for which catalysts have not been developed. The use of enzymes as biocatalysts for synthetic chemistry is growing in importance due to the drive towards sustainable methods for producing both bulk chemicals and high value compounds such as pharmaceuticals, and due to the ability of enzymes to catalyse chemical reactions with excellent stereoselectivity and regioselectivity. Such challenging transformations are a common feature of natural product biosynthetic pathways. In this mini-review, we discuss the potential to use biosynthetic pathways as a starting point for biocatalyst discovery. We introduce the reader to natural product assembly and tailoring, then focus on four classes of enzyme that catalyse C─H bond activation reactions to functionalize biosynthetic precursors. Finally, we briefly discuss the challenges involved in novel enzyme discovery.

  14. Genome Mining for Ribosomally Synthesized Natural Products

    PubMed Central

    Velásquez, Juan E.; van der Donk, Wilfred

    2011-01-01

    In recent years, the number of known peptide natural products that are synthesized via the ribosomal pathway has rapidly grown. Taking advantage of sequence homology among genes encoding precursor peptides or biosynthetic proteins, in silico mining of genomes combined with molecular biology approaches has guided the discovery of a large number of new ribosomal natural products, including lantipeptides, cyanobactins, linear thiazole/oxazole-containing peptides, microviridins, lasso peptides, amatoxins, cyclotides, and conopeptides. In this review, we describe the strategies used for the identification of these ribosomally-synthesized and posttranslationally modified peptides (RiPPs) and the structures of newly identified compounds. The increasing number of chemical entities and their remarkable structural and functional diversity may lead to novel pharmaceutical applications. PMID:21095156

  15. Microbial Diversity Associated with Odor Modification for Production of Fertilizers from Chicken Litter†

    PubMed Central

    Enticknap, Julie J.; Nonogaki, Hirofumi; Place, Allen R.; Hill, Russell T.

    2006-01-01

    Litter from the chicken industry can present several environmental challenges, including offensive odors and runoff into waterways leading to eutrophication. An economically viable solution to the disposal of waste from chicken houses is treatment to produce a natural, granulated fertilizer that can be commercially marketed for garden and commercial use. Odor of the final product is important in consumer acceptance, and an earthy odor is desirable. By understanding and manipulating the microbial processes occurring during this process, it may be possible to modify the odors produced. Geosmin and related volatiles produced by soil actinomycetes are responsible for earthy odors, and actinomycetes are likely to be present in the composting manure. Bacterial communities at each stage of the process were analyzed by culturing studies and denaturing gradient gel electrophoresis (DGGE). The processing steps changed the culturable bacterial community, but the total community was shown by DGGE to be stable throughout the process. A local agricultural soil was analyzed in parallel as a potential source of geosmin-producing actinomycetes. This agricultural soil had higher microbial diversity than the compost at both the culturable and the molecular levels. Actinomycete bacteria were isolated and analyzed by AromaTrax, a gas chromatography-olfactometry system. This system enables the odor production of individual isolates to be monitored, allowing for rational selection of strains for augmentation experiments to improve the odor of the final fertilizer product. PMID:16751521

  16. Microbially-Enhanced Coal Bed Methane: Strategies for Increased Biogenic Production

    NASA Astrophysics Data System (ADS)

    Davis, K.; Barhart, E. P.; Schweitzer, H. D.; Cunningham, A. B.; Gerlach, R.; Hiebert, R.; Fields, M. W.

    2014-12-01

    Coal is the largest fossil fuel resource in the United States. Most of this coal is deep in the subsurface making it costly and potentially dangerous to extract. However, in many of these deep coal seams, methane, the main component of natural gas, has been discovered and successfully harvested. Coal bed methane (CBM) currently accounts for approximately 7.5% of the natural gas produced in the U.S. Combustion of natural gas produces substantially less CO2 and toxic emissions (e.g. heavy metals) than combustion of coal or oil thereby making it a cleaner energy source. In the large coal seams of the Powder River Basin (PRB) in southeast Montana and northeast Wyoming, CBM is produced almost entirely by biogenic processes. The in situ conversion of coal to CBM by the native microbial community is of particular interest for present and future natural gas sources as it provides the potential to harvest energy from coal seams with lesser environmental impacts than mining and burning coal. Research at Montana State University has shown the potential for enhancing the subsurface microbial processes that produce CBM. Long-term batch enrichments have investigated the methane enhancement potential of yeast extract as well as algal and cyanobacterial biomass additions with increased methane production observed with all three additions when compared to no addition. Future work includes quantification of CBM enhancement and normalization of additions. This presentation addresses the options thus far investigated for increasing CBM production and the next steps for developing the enhanced in situ conversion of coal to CBM.

  17. A comparative evaluation of different types of microbial electrolysis desalination cells for malic acid production.

    PubMed

    Liu, Guangli; Zhou, Ying; Luo, Haiping; Cheng, Xing; Zhang, Renduo; Teng, Wenkai

    2015-12-01

    The aim of this study was to investigate different microbial electrolysis desalination cells for malic acid production. The systems included microbial electrolysis desalination and chemical-production cell (MEDCC), microbial electrolysis desalination cell (MEDC) with bipolar membrane and anion exchange membrane (BP-A MEDC), MEDC with bipolar membrane and cation exchange membrane (BP-C MEDC), and modified microbial desalination cell (M-MDC). The microbial electrolysis desalination cells performed differently in terms of malic acid production and energy consumption. The MEDCC performed best with the highest malic acid production rate (18.4 ± 0.6 mmol/Lh) and the lowest energy consumption (0.35 ± 0.14 kWh/kg). The best performance of MEDCC was attributable to the neutral pH condition in the anode chamber, the lowest internal resistance, and the highest Geobacter percentage of the anode biofilm population among all the reactors.

  18. Deep microbial life in the Altmark natural gas reservoir: baseline characterization prior CO2 injection

    NASA Astrophysics Data System (ADS)

    Morozova, Daria; Shaheed, Mina; Vieth, Andrea; Krüger, Martin; Kock, Dagmar; Würdemann, Hilke

    2010-05-01

    Within the framework of the CLEAN project (CO2 Largescale Enhanced gas recovery in the Altmark Natural gas field) technical basics with special emphasis on process monitoring are explored by injecting CO2 into a gas reservoir. Our study focuses on the investigation of the in-situ microbial community of the Rotliegend natural gas reservoir in the Altmark, located south of the city Salzwedel, Germany. In order to characterize the microbial life in the extreme habitat we aim to localize and identify microbes including their metabolism influencing the creation and dissolution of minerals. The ability of microorganisms to speed up dissolution and formation of minerals might result in changes of the local permeability and the long-term safety of CO2 storage. However, geology, structure and chemistry of the reservoir rock and the cap rock as well as interaction with saline formation water and natural gases and the injected CO2 affect the microbial community composition and activity. The reservoir located at the depth of about 3500m, is characterised by high salinity fluid and temperatures up to 127° C. It represents an extreme environment for microbial life and therefore the main focus is on hyperthermophilic, halophilic anaerobic microorganisms. In consequence of the injection of large amounts of CO2 in the course of a commercial EGR (Enhanced Gas Recovery) the environmental conditions (e.g. pH, temperature, pressure and solubility of minerals) for the autochthonous microorganisms will change. Genetic profiling of amplified 16S rRNA genes are applied for detecting structural changes in the community by using PCR- SSCP (PCR-Single-Strand-Conformation Polymorphism) and DGGE (Denaturing Gradient Gel Electrophoresis). First results of the baseline survey indicate the presence of microorganisms similar to representatives from other saline, hot, anoxic, deep environments. However, due to the hypersaline and hyperthermophilic reservoir conditions, cell numbers are low, so that

  19. Natural products from filamentous fungi and production by heterologous expression.

    PubMed

    Alberti, Fabrizio; Foster, Gary D; Bailey, Andy M

    2017-01-01

    Filamentous fungi represent an incredibly rich and rather overlooked reservoir of natural products, which often show potent bioactivity and find applications in different fields. Increasing the naturally low yields of bioactive metabolites within their host producers can be problematic, and yield improvement is further hampered by such fungi often being genetic intractable or having demanding culturing conditions. Additionally, total synthesis does not always represent a cost-effective approach for producing bioactive fungal-inspired metabolites, especially when pursuing assembly of compounds with complex chemistry. This review aims at providing insights into heterologous production of secondary metabolites from filamentous fungi, which has been established as a potent system for the biosynthesis of bioactive compounds. Numerous advantages are associated with this technique, such as the availability of tools that allow enhanced production yields and directing biosynthesis towards analogues of the naturally occurring metabolite. Furthermore, a choice of hosts is available for heterologous expression, going from model unicellular organisms to well-characterised filamentous fungi, which has also been shown to allow the study of biosynthesis of complex secondary metabolites. Looking to the future, fungi are likely to continue to play a substantial role as sources of new pharmaceuticals and agrochemicals-either as producers of novel natural products or indeed as platforms to generate new compounds through synthetic biology.

  20. A Novel Synthetic Pathway Enables Microbial Production of Polyphenols Independent from the Endogenous Aromatic Amino Acid Metabolism.

    PubMed

    Kallscheuer, Nicolai; Vogt, Michael; Marienhagen, Jan

    2016-12-14

    Numerous plant polyphenols have potential applications as pharmaceuticals or nutraceuticals. Stilbenes and flavonoids as most abundant polyphenols are synthesized from phenylpropanoids, which are exclusively derived from aromatic amino acids in nature. Several microorganisms were engineered for the synthesis of biotechnologically interesting plant polyphenols; however, low activity of heterologous ammonia lyases, linking endogenous microbial aromatic amino acid biosynthesis to phenylpropanoid synthesis, turned out to be the limiting step during microbial synthesis. We here developed an alternative strategy for polyphenol production from cheap benzoic acids by reversal of a β-oxidative phenylpropanoid degradation pathway avoiding any ammonia lyase activity. The synthetic pathway running in the non-natural direction is feasible with respect to thermodynamics and involved reaction mechanisms. Instantly, product titers of 5 mg/L resveratrol could be achieved in recombinant Corynebacterium glutamicum strains indicating that phenylpropanoid synthesis from 4-hydroxybenzoic acid can in principle be implemented independently from aromatic amino acids and ammonia lyase activity.

  1. Differences in Intertidal Microbial Assemblages on Urban Structures and Natural Rocky Reef

    PubMed Central

    Tan, Elisa L.-Y.; Mayer-Pinto, Mariana; Johnston, Emma L.; Dafforn, Katherine A.

    2015-01-01

    Global seascapes are increasingly modified to support high levels of human activity in the coastal zone. Modifications include the addition of defense structures and boating infrastructure, such as seawalls and marinas that replace natural habitats. Artificial structures support different macrofaunal communities to those found on natural rocky shores; however, little is known about differences in microbial community structure or function in urban seascapes. Understanding how artificial constructions in marine environments influence microbial communities is important as these assemblages contribute to many basic ecological processes. In this study, the bacterial communities of intertidal biofilms were compared between artificial structures (seawalls) and natural habitats (rocky shores) within Sydney Harbour. Plots were cleared on each type of habitat at eight locations. After 3 weeks the newly formed biofilm was sampled and the 16S rRNA gene sequenced using the Illumina Miseq platform. To account for differences in orientation and substrate material between seawalls and rocky shores that might have influenced our survey, we also deployed recruitment blocks next to the habitats at all locations for 3 weeks and then sampled and sequenced their microbial communities. Intertidal bacterial community structure sampled from plots differed between seawalls and rocky shores, but when substrate material, age and orientation were kept constant (with recruitment blocks) then bacterial communities were similar in composition and structure among habitats. This suggests that changes in bacterial communities on seawalls are not related to environmental differences between locations, but may be related to other intrinsic factors that differ between the habitats such as orientation, complexity, or predation. This is one of the first comparisons of intertidal microbial communities on natural and artificial surfaces and illustrates substantial ecological differences with potential

  2. Natural products discovery from micro-organisms in the post-genome era.

    PubMed

    Ikeda, Haruo

    2017-01-01

    With the decision to award the Nobel Prize in Physiology or Medicine to Drs. S. Ōmura, W.C. Campbell, and Y. Tu, the importance and usefulness of natural drug discovery and development have been revalidated. Since the end of the twentieth century, many genome analyses of organisms have been conducted, and accordingly, numerous microbial genomes have been decoded. In particular, genomic studies of actinomycetes, micro-organisms that readily produce natural products, led to the discovery of biosynthetic gene clusters responsible for producing natural products. New explorations for natural products through a comprehensive approach combining genomic information with conventional methods show great promise for the discovery of new natural products and even systematic generation of unnaturally occurring compounds.

  3. Marine microbial production of dimethylsulfide from dissolved dimethylsulfoniopropionate. Doctoral thesis

    SciTech Connect

    Ledyard, K.M.

    1993-02-01

    Dimethylsulfide (DMS) plays a central role in the transfer of sulfur from the ocean to the atmosphere, and ultimately to land. The most abundant volatile organosulfur compound in seawater, DMS is believed to account for the bulk of the sea-to-air biogenic sulfur flux. DMS has also been implicated as the major precursor of submicron-sized sulfate aerosol over the ocean. This aerosol acts as an effective site for cloud droplet condensation, suggesting a possibly important role for DMS in marine cloud formation. In the ocean, the precursor of DMS is presumed to be the zwitterionic sulfonium compound dimethylsulfoniopropionate (DMSP), a common osmoticum in certain classes of marine algae. While some algae can cleave DMSP intracellularly to form DMS, correlation of DMS concentrations with indicators of algal productivity on a local scale is poor. This thesis focuses on an alternative pathway of DMS formation: microbial cleavage of dissolved (extracellular) DMSP. In laboratory studies, bacteria able to cleave DMSP to form DMS were isolated from seawater by a DMSP enrichment technique, and the kinetics of DMSP uptake and DMS production were examined closely in pure cultures of a bacterial isolate from the Sargasso Sea. The isolate could grow with both DMSP and acrylic acid, one of the products of DMSP cleavage, as the sole source of carbon and energy, and the enzyme catalyzing DMSP cleavage appeared to be induced by both of these compounds. Kinetic parameters were estimated for DMSP uptake and cleavage by whole cells. Comparison of the 16S rRNA sequence of this isolate with that of known eubacteria showed that it was most closely related to Erythrobacter longus, an aerobic, bacteriochlorophyll-containing member of the alpha proteobacteria.

  4. Retro-Biosynthesis for the Microbial Production of Organic Compounds

    DTIC Science & Technology

    2008-05-31

    product of this natural biosynthetic route is L- ascorbic acid (vitamin C). Thus, we chose to propose rationally-designed pathways for the...is the oxidation of glucose to form glucodialdose. A galactose oxidase is known to catalyze the desired reaction using galactose as a substrate...higher activities than what has previously been reported. We received the first library, a control library, to screen for a new glucose oxidase

  5. Impacts of engineered nanomaterials on microbial community structure and function in natural and engineered ecosystems.

    PubMed

    Mohanty, Anee; Wu, Yichao; Cao, Bin

    2014-10-01

    In natural and engineered environments, microorganisms often exist as complex communities, which are key to the health of ecosystems and the success of bioprocesses in various engineering applications. With the rapid development of nanotechnology in recent years, engineered nanomaterials (ENMs) have been considered one type of emerging contaminants that pose great potential risks to the proper function of microbial communities in natural and engineered ecosystems. The impacts of ENMs on microorganisms have attracted increasing research attentions; however, most studies focused on the antimicrobial activities of ENMs at single cell and population level. Elucidating the influence of ENMs on microbial communities represents a critical step toward a comprehensive understanding of the ecotoxicity of ENMs. In this mini-review, we summarize and discuss recent research work on the impacts of ENMs on microbial communities in natural and engineered ecosystems, with an emphasis on their influences on the community structure and function. We also highlight several important research topics which may be of great interest to the research community.

  6. RMS Titanic and the emergence of new concepts on consortial nature of microbial events.

    PubMed

    Cullimore, D Roy; Pellegrino, Charles; Johnston, Lori

    2002-01-01

    The RMS Titanic sank in 1912 and created a historical event that still ripples through time. Stories were told and lessons learned but the science has only just begun. Today the fading remains of the ship resemble the hanging gardens of Babylon except that it is not plants that drape the walls but complex microbial growths called rusticles. These organisms have been found to be not a species, like plants and animals, but to be structures created by complex communities of bacterial species. Like the discovery of tube worms in the mid-oceanic vents, the nature of these rusticles presents another biological discovery of a fundamental nature. Essentially these microbial consortia on the RMS Titanic have generated structures of a mass that would rival whales and elephants while gradually extracting the iron from the steel. Rusticle-like consortia appear to play many roles within the environment, and it is perhaps the RMS Titanic that is showing that there is a new way to understand the form, function, and nature of microorganisms. This understanding would develop by considering the bacteria not as individual species functioning independently but as consortia of species functioning in community structures within a common habitat. This concept, if adopted, would change dramatically the manner in which a microbial ecologist and any scientist or engineer would view the occurrence of a slime, encrustation, biocolloid, rust flake, iron pan, salt deposit, and perhaps even some of the diseases that remain unexplained as a disease of unknown cause.

  7. Acceleration of Fe-silicate mineral dissolution for CO2 sequestration via microbial siderophore production

    NASA Astrophysics Data System (ADS)

    Torres, M. A.; Nealson, K. H.; West, A.

    2013-12-01

    While the dissolution of silicate minerals will ultimately neutralize anthropogenic CO2 emissions, the slow natural timescale of this process limits its ability to mitigate any of the societal impacts of high atmospheric pCO2. As a result, much research has been focused on developing ways to significantly accelerate silicate mineral dissolution rates. Harnessing the effects of microbial activity is one particularly attractive strategy because research has shown that microbes can appreciably accelerate mineral dissolution rates and they require little external energy input. At present, one major hurdle in the development of microbe-based CO2 sequestration techniques is the observation that bacteria only accelerate dissolution rates under particular culturing conditions. In this work, natural and genetic mutant strains of the bacterial genera Shewanella, Pseudomonas, and Marinobacter are used to identify the geochemical and genetic factors that underlie the 'accelerated-weathering phenotype' in order to support the development of microbe-based CO2 sequestration techniques using olivine as a model mineral. Preliminary results suggest that microbial siderophore production at circum-neutral pH results in significantly accelerated olivine dissolution rates.

  8. Membrane bioreactors fed with different COD/N ratio wastewater: impacts on microbial community, microbial products, and membrane fouling.

    PubMed

    Han, Xiaomeng; Wang, Zhiwei; Ma, Jinxing; Zhu, Chaowei; Li, Yaxin; Wu, Zhichao

    2015-08-01

    It is known that an increase of COD/N ratio can result in an enhanced removal of nutrients in membrane bioreactors (MBRs); however, impacts of doing so on membrane filtration performance remain unclear. In this work, comparison of membrane filtration performance, microbial community, and microbial products under low temperature was carried out in anoxic/oxic (A/O) MBRs with COD/N ratios of 9.9 and 5.5 g COD/g N in influent. There was no doubt that an improvement of nitrogen removal under high COD/N ratio was observed; however, severer membrane fouling was found compared to the MBR fed with low COD/N ratio wastewater. The increase of COD/N ratio resulted in an elevated production of humic acids in soluble microbial product (SMP) and carbohydrates, proteins, and humic acids in loosely bound extracellular polymeric substance (LB-EPS). Quartz crystal microbalance with dissipation monitoring (QCM-D) analysis showed that the adsorption capability of SMP and LB-EPS was higher in the MBR with higher COD/N ratio. Four hundred fifty four high-throughput pyrosequencing revealed that the higher COD/N ratio led to the enrichment of Bacteroidetes at phylum level and Azospira, Thauera, Zoogloea, etc. at genus level. Bacteroidetes are considered to potentially release EPS, and Azospira, Thauera, and Zoogloea, etc. have denitrification activity. The change in microbial communities is consistent with MBR performance.

  9. Use of proteomic tools in microbial engineering for biofuel production.

    PubMed

    Mao, Shaoming; Jia, Kaizhi; Zhang, Yanping; Li, Yin

    2012-01-01

    The production of biofuels from renewable sources by microbial engineering has gained increased attention due to energy and environmental concerns. Butanol is one of the important gasoline-substitute fuels and can be produced by native microorganism Clostridium acetobutylicum. To develop a fundamental tool to understand C. acetobutylicum, a high resolution proteome reference map for this species has been established. To better understand the relationship between butanol tolerance and butanol yield, we performed a comparative proteomic analysis between the wild-type strain DSM 1731 and its mutant Rh8 at acidogenic and solventogenic phases, respectively. The 102 differentially expressed proteins that are mainly involved in protein folding, solvent formation, amino acid metabolism, protein synthesis, nucleotide metabolism, transport, and others were detected. Hierarchical clustering analysis revealed that over 70% of the 102 differentially expressed proteins in mutant Rh8 were either upregulated (e.g., chaperones and solvent formation related) or downregulated (e.g., amino acid metabolism and protein synthesis related) in both acidogenic and solventogenic phase, which, respectively, are only upregulated or downregulated in solventogenic phase in the wild-type strain.

  10. Bioelectricity production from soil using microbial fuel cells.

    PubMed

    Wolińska, Agnieszka; Stępniewska, Zofia; Bielecka, Arletta; Ciepielski, Jakub

    2014-08-01

    Microbial fuel cells (MFCs) are a device using microorganisms as biocatalysts for transforming chemical energy into bioelectricity. As soil is an environment with the highest number of microorganisms and diversity, we hypothesized that it should have the potential for energy generation. The soil used for the study was Mollic Gleysol collected from the surface layer (0-20 cm). Four combinations of soil MFC differing from each other in humidity (full water holding capacity [WHC] and flooding) and the carbon source (glucose and straw) were constructed. Voltage (mV) and current intensity (μA) produced by the MFCs were recorded every day or at 2-day intervals. The fastest and the most effective MFCs in voltage generation (372.2 ± 5 mV) were those constructed on the basis of glucose (MFC-G). The efficiency of straw MFCs (MFC-S) was noticeable after 2 weeks (319.3 ± 4 mV). Maximal power density (P max = 32 mW m(-2)) was achieved by the MFC-G at current density (CD) of 100 mA m(-2). Much lower values of P max (10.6-10.8 mW m(-2)) were noted in the MFC-S at CD of ca. 60-80 mA m(-2). Consequently, soil has potential for production of renewable energy.

  11. Engineering Escherichia coli for Microbial Production of Butanone

    PubMed Central

    Srirangan, Kajan; Liu, Xuejia; Akawi, Lamees; Bruder, Mark; Moo-Young, Murray

    2016-01-01

    To expand the chemical and molecular diversity of biotransformation using whole-cell biocatalysts, we genetically engineered a pathway in Escherichia coli for heterologous production of butanone, an important commodity ketone. First, a 1-propanol-producing E. coli host strain with its sleeping beauty mutase (Sbm) operon being activated was used to increase the pool of propionyl-coenzyme A (propionyl-CoA). Subsequently, molecular heterofusion of propionyl-CoA and acetyl-CoA was conducted to yield 3-ketovaleryl-CoA via a CoA-dependent elongation pathway. Lastly, 3-ketovaleryl-CoA was channeled into the clostridial acetone formation pathway for thioester hydrolysis and subsequent decarboxylation to form butanone. Biochemical, genetic, and metabolic factors affecting relative levels of ketogenesis, acidogenesis, and alcohologenesis under selected fermentative culture conditions were investigated. Using the engineered E. coli strain for batch cultivation with 30 g liter−1 glycerol as the carbon source, we achieved coproduction of 1.3 g liter−1 butanone and 2.9 g liter−1 acetone. The results suggest that approximately 42% of spent glycerol was utilized for ketone biosynthesis, and thus they demonstrate potential industrial applicability of this microbial platform. PMID:26896132

  12. Neurotrophic Natural Products: Chemistry and Biology

    PubMed Central

    Xu, Jing; Lacoske, Michelle H.

    2014-01-01

    Neurodegenerative diseases and spinal cord injury affect approximately 50 million people worldwide, bringing the total healthcare cost to over 600 billion dollars per year. Nervous system growth factors, that is, neurotrophins, are a potential solution to these disorders, since they could promote nerve regeneration. An average of 500 publications per year attests to the significance of neurotrophins in biomedical sciences and underlines their potential for therapeutic applications. Nonetheless, the poor pharmacokinetic profile of neurotrophins severely restricts their clinical use. On the other hand, small molecules that modulate neurotrophic activity offer a promising therapeutic approach against neurological disorders. Nature has provided an impressive array of natural products that have potent neurotrophic activities. This Review highlights the current synthetic strategies toward these compounds and summarizes their ability to induce neuronal growth and rehabilitation. It is anticipated that neurotrophic natural products could be used not only as starting points in drug design but also as tools to study the next frontier in biomedical sciences: the brain activity map project. PMID:24353244

  13. Natural products as potential anticonvulsants: caffeoylquinic acids.

    PubMed

    Kim, Hyo Geun; Oh, Myung Sook

    2012-03-01

    Current anticonvulsant therapies are generally directed at symptomatic treatment by suppressing excitability within the brain. Consequently, they have adverse effects such as cognitive impairment, dependence, and abuse. The need for more effective and less toxic anticonvulsants has generated renewed interest in natural products for the treatment of convulsions. Caffeoylquinic acids (CQs) are naturally occurring phenolic acids that are distributed widely in plants. There has been increasing interest in the biological activities of CQs in diseases of the central nervous system. In this issue, Nugroho et al. give evidence for the anticonvulsive effect of a CQ-rich extract from Aster glehni Franchet et Sckmidt. They optimized the extract solvent conditions, resulting in high levels of CQs and peroxynitrite-scavenging activity. Then, they investigated the sedative and anticonvulsive effects in pentobarbital- and pentylenetetrazole-induced models in mice. The CQ-rich extract significantly inhibited tonic convulsions as assessed by onset time, tonic extent, and mortality. They suggested that the CQ-rich extract from A. glehni has potential for treating convulsions. This report provides preclinical data which may be used for the development of anticonvulsants from natural products.

  14. Determining microbial products and identifying molecular targets in the human microbiome.

    PubMed

    Joice, Regina; Yasuda, Koji; Shafquat, Afrah; Morgan, Xochitl C; Huttenhower, Curtis

    2014-11-04

    Human-associated microbes are the source of many bioactive microbial products (proteins and metabolites) that play key functions both in human host pathways and in microbe-microbe interactions. Culture-independent studies now provide an accelerated means of exploring novel bioactives in the human microbiome; however, intriguingly, a substantial fraction of the microbial metagenome cannot be mapped to annotated genes or isolate genomes and is thus of unknown function. Meta'omic approaches, including metagenomic sequencing, metatranscriptomics, metabolomics, and integration of multiple assay types, represent an opportunity to efficiently explore this large pool of potential therapeutics. In combination with appropriate follow-up validation, high-throughput culture-independent assays can be combined with computational approaches to identify and characterize novel and biologically interesting microbial products. Here we briefly review the state of microbial product identification and characterization and discuss possible next steps to catalog and leverage the large uncharted fraction of the microbial metagenome.

  15. Microbial desalination cells for improved performance in wastewater treatment, electricity production, and desalination.

    PubMed

    Luo, Haiping; Xu, Pei; Roane, Timberley M; Jenkins, Peter E; Ren, Zhiyong

    2012-02-01

    The low conductivity and alkalinity in municipal wastewater significantly limit power production from microbial fuel cells (MFCs). This study integrated desalination with wastewater treatment and electricity production in a microbial desalination cell (MDC) by utilizing the mutual benefits among the above functions. When using wastewater as the sole substrate, the power output from the MDC (8.01 W/m(3)) was four times higher than a control MFC without desalination function. In addition, the MDC removed 66% of the salts and improved COD removal by 52% and Coulombic efficiency by 131%. Desalination in MDCs improved wastewater characteristics by increasing the conductivity by 2.5 times and stabilizing anolyte pH, which therefore reduced system resistance and maintained microbial activity. Microbial community analysis revealed a more diverse anode microbial structure in the MDC than in the MFC. The results demonstrated that MDC can serve as a viable option for integrated wastewater treatment, energy production, and desalination.

  16. Historical and Recent Achievements in the Field of Microbial Degradation of Natural and Synthetic Rubber

    PubMed Central

    Yikmis, Meral

    2012-01-01

    This review intends to provide an overview of historical and recent achievements in studies of microbial degradation of natural and synthetic rubber. The main scientific focus is on the key enzymes latex-clearing protein (Lcp) from the Gram-positive Streptomyces sp. strain K30 and rubber oxygenase A (RoxA) from the Gram-negative Xanthomonas sp. strain 35Y, which has been hitherto the only known rubber-degrading bacterium that does not belong to the actinomycetes. We also emphasize the importance of knowledge of biodegradation in industrial and environmental biotechnology for waste natural rubber disposal. PMID:22504822

  17. Historical and recent achievements in the field of microbial degradation of natural and synthetic rubber.

    PubMed

    Yikmis, Meral; Steinbüchel, Alexander

    2012-07-01

    This review intends to provide an overview of historical and recent achievements in studies of microbial degradation of natural and synthetic rubber. The main scientific focus is on the key enzymes latex-clearing protein (Lcp) from the Gram-positive Streptomyces sp. strain K30 and rubber oxygenase A (RoxA) from the Gram-negative Xanthomonas sp. strain 35Y, which has been hitherto the only known rubber-degrading bacterium that does not belong to the actinomycetes. We also emphasize the importance of knowledge of biodegradation in industrial and environmental biotechnology for waste natural rubber disposal.

  18. Growth and element flux at fine taxonomic resolution in natural microbial communities

    NASA Astrophysics Data System (ADS)

    Hungate, Bruce; Mau, Rebecca; Schwartz, Egbert; Caporaso, J. Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa; Marks, Jane C.; Morrissey, Ember; Price, Lance B.

    2015-04-01

    Microorganisms are the engines of global biogeochemical cycles, driving half of all photosynthesis and nearly all decomposition. Yet, quantifying the rates at which uncultured microbial taxa grow and transform elements in intact and highly diverse natural communities in the environment remains among the most pressing challenges in microbial ecology today. Here, we show how shifts in the density of DNA caused by stable isotope incorporation can be used to estimate the growth rates of individual bacterial taxa in intact soil communities. We found that the distribution of growth rates followed the familiar lognormal distribution observed for the abundances, biomasses, and traits of many organisms. Growth rates of most bacterial taxa increased in response to glucose amendment, though the increase in growth observed for many taxa was larger than could be explained by direct utilization of the added glucose for growth, illustrating that glucose addition indirectly stimulated the utilization of other substrates. Variation in growth rates and phylogenetic distances were quantitatively related, connecting evolutionary history and biogeochemical function in intact soil microbial communities. Our approach has the potential to identify biogeochemically significant taxa in the microbial community and quantify their contributions to element transformations and ecosystem processes.

  19. Direct Microbial Reduction and Subsequent Preservation of Uranium in Natural Near-Surface Sediment

    PubMed Central

    Suzuki, Yohey; Kelly, Shelly D.; Kemner, Kenneth M.; Banfield, Jillian F.

    2005-01-01

    The fate of uranium in natural systems is of great environmental importance. X-ray absorption near-edge spectroscopy (XANES) revealed that U(VI) was reduced to U(IV) in shallow freshwater sediment at an open pit in an inactive uranium mine. Geochemical characterization of the sediment showed that nitrate, Fe(III), and sulfate had also been reduced in the sediment. Observations of the sediment particles and microbial cells by scanning and transmission electron microscopy, coupled with elemental analysis by energy dispersive spectroscopy, revealed that uranium was concentrated at microbial cell surfaces. U(IV) was not associated with framboidal pyrite or nanometer-scale iron sulfides, which are presumed to be of microbial origin. Uranium concentrations were not detected in association with algal cells. Phylogenetic analyses of microbial populations in the sediment by the use of 16S rRNA and dissimilatory sulfite reductase gene sequences detected organisms belonging to the families Geobacteraceae and Desulfovibrionaceae. Cultivated members of these lineages reduce U(VI) and precipitate iron sulfides. The association of uranium with cells, but not with sulfide surfaces, suggests that U(VI) is reduced by the enzymatic activities of microorganisms. Uranium was highly enriched (760 ppm) in a subsurface black layer in unsaturated sediment sampled from a pit which was exposed to seasonal fluctuations in the pond level. XANES analysis showed that the majority of uranium in this layer was U(IV), indicating that uranium is preserved in its reduced form after burial. PMID:15812002

  20. Applications of microbial fermentations for production of gluten-free products and perspectives.

    PubMed

    Zannini, Emanuele; Pontonio, Erica; Waters, Deborah M; Arendt, Elke K

    2012-01-01

    A gluten-free (GF) diet is recognised as being the only accepted treatment for celiac disease-a permanent autoimmune enteropathy triggered by the ingestion of gluten-containing cereals. The bakery products available in today's gluten-free market are characterised by lower palatability than their conventional counterparts and may lead to nutritional deficiencies of vitamins, minerals and fibre. Thus, the production of high-quality gluten-free products has become a very important socioeconomical issue. Microbial fermentation by means of lactic acid bacteria and yeast is one of the most ecological/economical methods of producing and preserving food. In this review, the role of a fermentation process for improving the quality of GF products and for developing a new concept of GF products with nutraceutical and health-promoting characteristics will be examined.

  1. Evidence of soluble microbial products accelerating chloramine decay in nitrifying bulk water samples.

    PubMed

    Bal Krishna, K C; Sathasivan, Arumugam; Chandra Sarker, Dipok

    2012-09-01

    The discovery of a microbially derived soluble product that accelerates chloramine decay is described. Nitrifying bacteria are believed to be wholly responsible for rapid chloramine loss in drinking water systems. However, a recent investigation showed that an unidentified soluble agent significantly accelerated chloramine decay. The agent was suspected to be either natural organic matter (NOM) or soluble microbial products (SMPs). A laboratory scale reactor was fed chloraminated reverse osmosis (RO) treated water to eliminate the interference from NOM. Once nitrification had set in, experiments were conducted on the reactor and feed waters to determine the identity of the component. The study showed the presence of SMPs released by microbes in severely nitrified waters. Further experiments proved that the SMPs significantly accelerated chloramine decay, probably through catalytic reaction. Moreover, application of common protein denaturing techniques stopped the reaction implying that the compound responsible was likely to be a protein. This significant finding will pave the way for better control of chloramine in the distribution systems.

  2. Enhanced Microbial Pathways for Methane Production from Oil Shale

    SciTech Connect

    Paul Fallgren

    2009-02-15

    Methane from oil shale can potentially provide a significant contribution to natural gas industry, and it may be possible to increase and continue methane production by artificially enhancing methanogenic activity through the addition of various substrate and nutrient treatments. Western Research Institute in conjunction with Pick & Shovel Inc. and the U.S. Department of Energy conducted microcosm and scaled-up reactor studies to investigate the feasibility and optimization of biogenic methane production from oil shale. The microcosm study involving crushed oil shale showed the highest yield of methane was produced from oil shale pretreated with a basic solution and treated with nutrients. Incubation at 30 C, which is the estimated temperature in the subsurface where the oil shale originated, caused and increase in methane production. The methane production eventually decreased when pH of the system was above 9.00. In the scaled-up reactor study, pretreatment of the oil shale with a basic solution, nutrient enhancements, incubation at 30 C, and maintaining pH at circumneutral levels yielded the highest rate of biogenic methane production. From this study, the annual biogenic methane production rate was determined to be as high as 6042 cu. ft/ton oil shale.

  3. Hydrogen production from proteins via electrohydrogenesis in microbial electrolysis cells.

    PubMed

    Lu, Lu; Xing, Defeng; Xie, Tianhui; Ren, Nanqi; Logan, Bruce E

    2010-08-15

    Microorganisms can produce hydrogen gas (H(2)) at high rates by fermentation of carbohydrates, but not from proteins. However, it is possible to produce H(2) at high rates and yields from proteins by electrohydrogenesis in microbial electrolysis cells (MECs). Hydrogen gas was generated using bovine serum albumin (BSA, 700 mg/L) in a single-chamber MEC at a rate of Q=0.42+/-0.07 m(3)/m(3)/day and a yield of Y(H2) = 21.0 +/- 5.0 mmol-H2/g-COD, with an energy recovery (relative to electrical input) of eta(E)=75+/-12% (applied voltage of 0.6 V). Hydrogen production was substantially reduced using a complex protein (peptone) under the same conditions, to Q=0.05+/-0.01 m(3)/m(3)/day, YH2 = 2.6 +/- 0.1 mmol-H2/g-COD, and eta(E)=14+/-3%. There was good removal of organic matter for both substrates in terms of either protein (87+/-6 -97 +/-2%) or total COD (86+/-2 - 91+/-2%). Electron recycling likely occurred as Coulombic efficiencies exceeded 100% using BSA. The use of a two-chamber design, with either a CEM or AEM membrane, reduced the hydrogen production rate, but did not appreciably affect the hydrogen yield or energy efficiency. When an MEC was first acclimated to acetate, and then switched to BSA, performance was substantially reduced and was similar to that obtained using peptone. These results demonstrate that electrohydrogenesis can be used to produce H(2) from proteins, and it can also be used as a method for treatment of protein-containing wastewaters.

  4. Rational synthetic pathway refactoring of natural products biosynthesis in actinobacteria.

    PubMed

    Tan, Gao-Yi; Liu, Tiangang

    2017-01-01

    Natural products (NPs) and their derivatives are widely used as frontline treatments for many diseases. Actinobacteria spp. are used to produce most of NP antibiotics and have also been intensively investigated for NP production, derivatization, and discovery. However, due to the complicated transcriptional and metabolic regulation of NP biosynthesis in Actinobacteria, especially in the cases of genome mining and heterologous expression, it is often difficult to rationally and systematically engineer synthetic pathways to maximize biosynthetic efficiency. With the emergence of new tools and methods in metabolic engineering, the synthetic pathways of many chemicals, such as fatty acids and biofuels, in model organisms (e.g. Escherichia coli ), have been refactored to realize precise and flexible control of production. These studies also offer a promising approach for synthetic pathway refactoring in Actinobacteria. In this review, the great potential of Actinobacteria as a microbial cell factory for biosynthesis of NPs is discussed. To this end, recent progress in metabolic engineering of NP synthetic pathways in Actinobacteria are summarized and strategies and perspectives to rationally and systematically refactor synthetic pathways in Actinobacteria are highlighted.

  5. Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production

    PubMed Central

    Wohlbach, Dana J.; Rovinskiy, Nikolay; Lewis, Jeffrey A.; Sardi, Maria; Schackwitz, Wendy S.; Martin, Joel A.; Deshpande, Shweta; Daum, Christopher G.; Lipzen, Anna; Sato, Trey K.; Gasch, Audrey P.

    2014-01-01

    Lignocellulosic plant material is a viable source of biomass to produce alternative energy including ethanol and other biofuels. However, several factors—including toxic byproducts from biomass pretreatment and poor fermentation of xylose and other pentose sugars—currently limit the efficiency of microbial biofuel production. To begin to understand the genetic basis of desirable traits, we characterized three strains of Saccharomyces cerevisiae with robust growth in a pretreated lignocellulosic hydrolysate or tolerance to stress conditions relevant to industrial biofuel production, through genome and transcriptome sequencing analysis. All stress resistant strains were highly mosaic, suggesting that genetic admixture may contribute to novel allele combinations underlying these phenotypes. Strain-specific gene sets not found in the lab strain were functionally linked to the tolerances of particular strains. Furthermore, genes with signatures of evolutionary selection were enriched for functional categories important for stress resistance and included stress-responsive signaling factors. Comparison of the strains’ transcriptomic responses to heat and ethanol treatment—two stresses relevant to industrial bioethanol production—pointed to physiological processes that were related to particular stress resistance profiles. Many of the genotype-by-environment expression responses occurred at targets of transcription factors with signatures of positive selection, suggesting that these strains have undergone positive selection for stress tolerance. Our results generate new insights into potential mechanisms of tolerance to stresses relevant to biofuel production, including ethanol and heat, present a backdrop for further engineering, and provide glimpses into the natural variation of stress tolerance in wild yeast strains. PMID:25364804

  6. Production of natural products through metabolic engineering of Saccharomyces cerevisiae.

    PubMed

    Krivoruchko, Anastasia; Nielsen, Jens

    2015-12-01

    Many high-value metabolites are produced in nature by organisms that are not ideal for large-scale production. Therefore, interest exists in expressing the biosynthetic pathways of these compounds in organisms that are more suitable for industrial production. Recent years have seen developments in both the discovery of various biosynthetic pathways, as well as development of metabolic engineering tools that allow reconstruction of complex pathways in microorganisms. In the present review we discuss recent advances in reconstruction of the biosynthetic pathways of various high-value products in the yeast Saccharomyces cerevisiae, a commonly used industrial microorganism. Key achievements in the production of different isoprenoids, aromatics and polyketides are presented and the metabolic engineering strategies underlying these accomplishments are discussed.

  7. Modeling of Sustainable Base Production by Microbial Electrolysis Cell.

    PubMed

    Blatter, Maxime; Sugnaux, Marc; Comninellis, Christos; Nealson, Kenneth; Fischer, Fabian

    2016-07-07

    A predictive model for the microbial/electrochemical base formation from wastewater was established and compared to experimental conditions within a microbial electrolysis cell. A Na2 SO4 /K2 SO4 anolyte showed that model prediction matched experimental results. Using Shewanella oneidensis MR-1, a strong base (pH≈13) was generated using applied voltages between 0.3 and 1.1 V. Due to the use of bicarbonate, the pH value in the anolyte remained unchanged, which is required to maintain microbial activity.

  8. Composition and pathogenic potential of a microbial bioremediation product used for crude oil degradation.

    PubMed

    Tayabali, Azam F; Coleman, Gordon; Crosthwait, Jennifer; Nguyen, Kathy C; Zhang, Yan; Shwed, Philip

    2017-01-01

    A microbial bioremediation product (MBP) used for large-scale oil degradation was investigated for microbial constituents and possible pathogenicity. Aerobic growth on various media yielded >108 colonies mL-1. Full-length 16S rDNA sequencing and fatty acid profiling from morphologically distinct colonies revealed ≥13 distinct genera. Full-length 16S rDNA library sequencing, by either Sanger or long-read PacBio technology, suggested that up to 21% of the MBP was composed of Arcobacter. Other high abundance microbial constituents (>6%) included the genera Proteus, Enterococcus, Dysgonomonas and several genera in the order Bacteroidales. The MBP was most susceptible to ciprofloxacin, doxycycline, gentamicin, and meropenam. MBP exposure of human HT29 and A549 cells caused significant cytotoxicity, and bacterial growth and adherence. An acellular MBP filtrate was also cytotoxic to HT29, but not A549. Both MBP and filtrate exposures elevated the neutrophil chemoattractant IL-8. In endotracheal murine exposures, bacterial pulmonary clearance was complete after one-week. Elevation of pro-inflammatory cytokines IL-1β, IL-6, and TNF-α, and chemokines KC and MCP-1 occurred between 2h and 48h post-exposure, followed by restoration to baseline levels at 96h. Cytokine/chemokine signalling was accompanied by elevated blood neutrophils and monocytes at 4h and 48h, respectively. Peripheral acute phase response markers were maximal at 24h. All indicators examined returned to baseline values by 168h. In contrast to HT29, but similar to A549 observations, MBP filtrate did not induce significant murine effects with the indicators examined. The results demonstrated the potentially complex nature of MBPs and transient immunological effects during exposure. Products containing microbes should be scrutinized for pathogenic components and subjected to characterisation and quality validation prior to commercial release.

  9. Composition and pathogenic potential of a microbial bioremediation product used for crude oil degradation

    PubMed Central

    Tayabali, Azam F.; Coleman, Gordon; Crosthwait, Jennifer; Nguyen, Kathy C.; Zhang, Yan; Shwed, Philip

    2017-01-01

    A microbial bioremediation product (MBP) used for large-scale oil degradation was investigated for microbial constituents and possible pathogenicity. Aerobic growth on various media yielded >108 colonies mL-1. Full-length 16S rDNA sequencing and fatty acid profiling from morphologically distinct colonies revealed ≥13 distinct genera. Full-length 16S rDNA library sequencing, by either Sanger or long-read PacBio technology, suggested that up to 21% of the MBP was composed of Arcobacter. Other high abundance microbial constituents (>6%) included the genera Proteus, Enterococcus, Dysgonomonas and several genera in the order Bacteroidales. The MBP was most susceptible to ciprofloxacin, doxycycline, gentamicin, and meropenam. MBP exposure of human HT29 and A549 cells caused significant cytotoxicity, and bacterial growth and adherence. An acellular MBP filtrate was also cytotoxic to HT29, but not A549. Both MBP and filtrate exposures elevated the neutrophil chemoattractant IL-8. In endotracheal murine exposures, bacterial pulmonary clearance was complete after one-week. Elevation of pro-inflammatory cytokines IL-1β, IL-6, and TNF-α, and chemokines KC and MCP-1 occurred between 2h and 48h post-exposure, followed by restoration to baseline levels at 96h. Cytokine/chemokine signalling was accompanied by elevated blood neutrophils and monocytes at 4h and 48h, respectively. Peripheral acute phase response markers were maximal at 24h. All indicators examined returned to baseline values by 168h. In contrast to HT29, but similar to A549 observations, MBP filtrate did not induce significant murine effects with the indicators examined. The results demonstrated the potentially complex nature of MBPs and transient immunological effects during exposure. Products containing microbes should be scrutinized for pathogenic components and subjected to characterisation and quality validation prior to commercial release. PMID:28178315

  10. A quantitative analysis of microbially-induced calcite precipitation employing artificial and naturally-occurring sediments

    NASA Astrophysics Data System (ADS)

    Lokier, Stephen; Krieg Dosier, Ginger

    2013-04-01

    Microbially-induced calcite precipitation is a strong candidate for the production of sustainable construction materials. The process employs the microbe Sporosarcina pasteurii as an agent to microbially mediate the precipitation of calcium carbonate to bind unconsolidated sediment. As this process can be achieved under ambient temperature conditions and can utilise a wide variety of easily-available sediments, potentially including waste materials, it is envisioned that this procedure could significantly reduce carbon-dioxide emissions in the construction industry. This study describes and quantifies the precipitation of calcite cement in a range of naturally-occurring sediments compared with a control matrix. The study establishes the optimum treatment time for effective cement precipitation in order to produce a material that meets the standards required for construction whilst keeping economic and environmental outlays at a minimum. The 'control sediment' employed industrial-grade glass beads with a grain size range of 595-1180 microns (16-30 US mesh). Sporosarcina pasteurii were mixed in a solution of urea and calcium chloride and then inoculated into the control sediment. The microbes attach to the surface of the sediment grains and employ urea as a source of energy to produce ammonia and carbon dioxide. By so doing, they increase the pH of the solution allowing calcium carbonate to precipitate at the cell walls to act as nucleation points facilitating the precipitation of cements as a grain-coating and biocementing the unconsolidated sediment. The solution treatment was repeated at eight hour intervals with samples removed for detailed analysis after each every five consecutive treatments (i.e. 40 hours). The process was repeated to produce 20 samples with treatment times between 40 and 800 hours. Cemented samples were impregnated with blue epoxy and examined petrographically to monitor cement development. Modal analysis was undertaken on each cemented

  11. Gas extrusion in natural products total synthesis.

    PubMed

    Jiang, Xuefeng; Shi, Lei; Liu, Hui; Khan, Akbar H; Chen, Jason S

    2012-11-14

    The thermodynamic driving force from the release of a gaseous molecule drives a broad range of synthetic transformations. This review focuses on gas expulsion in key reactions within natural products total syntheses, selected from the past two decades. The highlighted examples survey transformations that generate sulfur dioxide, carbon dioxide, carbonyl sulfide, or nitrogen through polar, radical, pericyclic, photochemical, or organometallic mechanisms. Of particular interest are applications wherein the gas extrusion enables formation of a synthetically challenging motif, such as an unusually hindered or strained bond.

  12. Natural products from microbes associated with insects

    PubMed Central

    Guo, Huijuan; Rischer, Maja; Poulsen, Michael

    2016-01-01

    Summary Here we review discoveries of secondary metabolites from microbes associated with insects. We mainly focus on natural products, where the ecological role has been at least partially elucidated, and/or the pharmaceutical properties evaluated, and on compounds with unique structural features. We demonstrate that the exploration of specific microbial–host interactions, in combination with multidisciplinary dereplication processes, has emerged as a successful strategy to identify novel chemical entities and to shed light on the ecology and evolution of defensive associations. PMID:26977191

  13. Effects of shearing on biogas production and microbial community structure during anaerobic digestion with recuperative thickening.

    PubMed

    Yang, Shufan; Phan, Hop V; Bustamante, Heriberto; Guo, Wenshan; Ngo, Hao H; Nghiem, Long D

    2017-03-12

    Recuperative thickening can intensify anaerobic digestion to produce more biogas and potentially reduce biosolids odour. This study elucidates the effects of sludge shearing during the thickening process on the microbial community structure and its effect on biogas production. Medium shearing resulted in approximately 15% increase in biogas production. By contrast, excessive or high shearing led to a marked decrease in biogas production, possibly due to sludge disintegration and cell lysis. Microbial analysis using 16S rRNA gene amplicon sequencing showed that medium shearing increased the evenness and diversity of the microbial community in the anaerobic digester, which is consistent with the observed improved biogas production. By contrast, microbial diversity decreased under either excessive shearing or high shearing condition. In good agreement with the observed decrease in biogas production, the abundance of Bacteroidales and Syntrophobaterales (which are responsible for hydrolysis and acetogenesis) decreased due to high shearing during recuperative thickening.

  14. Multimodular biocatalysts for natural product assembly

    NASA Astrophysics Data System (ADS)

    Schwarzer, Dirk; Marahiel, Mohamed A.

    2001-03-01

    Nonribosomal peptides and polyketides represent a large class of natural products that show an extreme structural diversity and broad pharmacological relevance. They are synthesized from simple building blocks such as amino or carboxy acids and malonate derivatives on multimodular enzymes called nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), respectively. Although utilizing different substrates, NRPSs and PKSs show striking similarities in the modular architecture of their catalytic domains and product assembly-line mechanism. Among these compounds are well known antibiotics (penicillin, vancomycin and erythromycin) as well as potent immunosuppressive agents (cyclosporin, rapamycin and FK 506). This review focuses on the modular organization of NRPSs, PKSs and mixed NRPS/PKS systems and how modules and domains that build up the biosynthetic templates can be exploited for the rational design of recombinant enzymes capable of synthesizing novel compounds.

  15. Identification of a potent microbial lipid antigen for diverse Natural Killer T cells1

    PubMed Central

    Wolf, Benjamin J.; Tatituri, Raju V. V.; Almeida, Catarina F.; Le Nours, Jérôme; Bhowruth, Veemal; Johnson, Darryl; Uldrich, Adam P.; Hsu, Fong-Fu; Brigl, Manfred; Besra, Gurdyal S.; Rossjohn, Jamie; Godfrey, Dale I.; Brenner, Michael B.

    2016-01-01

    Invariant Natural Killer T (iNKT) cells are a well-characterized CD1d-restricted T cell subset. The availability of potent antigens and tetramers for iNKT cells has allowed this population to be extensively studied and has revealed their central roles in infection, autoimmunity, and tumor immunity. In contrast, diverse Natural Killer T (dNKT) cells are poorly understood because the lipid antigens they recognize are largely unknown. We sought to identify dNKT cell lipid antigen(s) by interrogating a panel of dNKT mouse cell hybridomas with lipid extracts from the pathogen Listeria monocytogenes. We identified Listeria phosphatidylglycerol (PG) as a microbial antigen that was significantly more potent than a previously characterized dNKT cell antigen, mammalian PG. Further, while mammalian PG loaded CD1d tetramers did not stain dNKT cells, the Listeria-derived PG loaded tetramers did. The structure of Listeria PG was distinct from mammalian PG since it contained shorter, fully-saturated anteiso fatty acid lipid tails. CD1d binding lipid displacement studies revealed that the microbial PG antigen binds significantly better to CD1d than counterparts with the same headgroup. These data reveal a highly-potent microbial lipid antigen for a subset of dNKT cells and provide an explanation for its increased antigen potency compared to the mammalian counterpart. PMID:26254340

  16. Direct Capture Technologies for Genomics-Guided Discovery of Natural Products

    PubMed Central

    Chan, Andrew N.; Santa Maria, Kevin C.; Li, Bo

    2016-01-01

    Microbes are important producers of natural products, which have played key roles in understanding biology and treating disease. However, the full potential of microbes to produce natural products has yet to be realized; the overwhelming majority of natural product gene clusters encoded in microbial genomes remain “cryptic”, and have not been expressed or characterized. In contrast to the fast-growing number of genomic sequences and bioinformatic tools, methods to connect these genes to natural product molecules are still limited, creating a bottleneck in genome-mining efforts to discover novel natural products. Here we review developing technologies that leverage the power of homologous recombination to directly capture natural product gene clusters and express them in model hosts for isolation and structural characterization. Although direct capture is still in its early stages of development, it has been successfully utilized in several different classes of natural products. These early successes will be reviewed, and the methods will be compared and contrasted with existing traditional technologies. Lastly, we will discuss the opportunities for the development of direct capture in other organisms, and possibilities to integrate direct capture with emerging genome-editing techniques to accelerate future study of natural products. PMID:26456469

  17. Bioprospecting for Microbial Endophytes and Their Natural Products

    PubMed Central

    Strobel, Gary; Daisy, Bryn

    2003-01-01

    Endophytic microorganisms are to be found in virtually every plant on earth. These organisms reside in the living tissues of the host plant and do so in a variety of relationships, ranging from symbiotic to slightly pathogenic. Because of what appears to be their contribution to the host plant, the endophytes may produce a plethora of substances of potential use to modern medicine, agriculture, and industry. Novel antibiotics, antimycotics, immunosuppressants, and anticancer compounds are only a few examples of what has been found after the isolation, culture, purification, and characterization of some choice endophytes in the recent past. The potential prospects of finding new drugs that may be effective candidates for treating newly developing diseases in humans, plants, and animals are great. PMID:14665674

  18. Microbial interactions with naturally occurring hydrophobic sediments: Influence on sediment and associated contaminant mobility.

    PubMed

    Droppo, I G; Krishnappan, B G; Lawrence, J R

    2016-04-01

    The erosion, transport and fate of sediments and associated contaminants are known to be influenced by both particle characteristics and the flow dynamics imparted onto the sediment. The influential role of bitumen containing hydrophobic sediments and the microbial community on sediment dynamics are however less understood. This study links an experimental evaluation of sediment erosion with measured sediment-associated contaminant concentrations and microbial community analysis to provide an estimate of the potential for sediment to control the erosion, transport and fate of contaminants. Specifically the paper addresses the unique behaviour of hydrophobic sediments and the role that the microbial community associated with hydrophobic sediment may play in the transport of contaminated sediment. Results demonstrate that the hydrophobic cohesive sediment demonstrates unique transport and particle characteristics (poor settling and small floc size). Biofilms were observed to increase with consolidation/biostabilization times and generated a unique microbial consortium relative to the eroded flocs. Natural oil associated with the flocs appeared to be preferentially associated with microbial derived extracellular polymeric substances. While PAHs and naphthenic acid increased with increasing shear (indicative of increasing loads), they tended to decrease with consolidation/biostabilization (CB) time at similar shears suggesting a chemical and/or biological degradation. PAH and napthenic acid degrading microbes decreased with time as well, which may suggest that there was a reduced pool of PAHs and naphthenic acids available resulting in their die off. This study emphasizes the importance that any management strategies and operational assessments for the protection of human and aquatic health incorporate the sediment (suspended and bed sediment) and biological (biofilm) compartments and the energy dynamics within the system in order to better predict contaminant

  19. Resolution of natural microbial community dynamics by community fingerprinting, flow cytometry, and trend interpretation analysis.

    PubMed

    Bombach, Petra; Hübschmann, Thomas; Fetzer, Ingo; Kleinsteuber, Sabine; Geyer, Roland; Harms, Hauke; Müller, Susann

    2011-01-01

    Natural microbial communities generally have an unknown structure and composition because of their still not yet cultivable members. Therefore, understanding the relationships among the bacterial members, prediction of their behaviour, and controlling their functions are difficult and often only partly successful endeavours to date. This study aims to test a new idea that allows to follow community dynamics on the basis of a simple concept. Terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S ribosomal RNA genes was used to describe a community profile that we define as composition of a community. Flow cytometry and analysis of DNA contents and forward scatter characteristics of the single cells were used to describe a community profile, which we define as structure of a community. Both approaches were brought together by a non-metric multidimensional scaling (n-MDS) for trend interpretation of changes in the complex community data sets. This was done on the basis of a graphical evaluation of the cytometric data, leading to the newly developed Dalmatian plot tool, which gave an unexpected insight into the dynamics of the unknown bacterial members of the investigated natural microbial community. The approach presented here was compared with other techniques described in the literature. The microbial community investigated in this study was obtained from a BTEX contaminated anoxic aquifer. The indigenous bacteria were allowed to colonise in situ microcosms consisting of activated carbon. These microcosms were amended with benzene and one of the electron acceptors nitrate, sulphate or ferric iron to stimulate microbial growth. The data obtained in this study indicated that the composition (via T-RFLP) and structure (via flow cytometry) of the natural bacterial community were influenced by the hydro-geochemical conditions in the test site, but also by the supplied electron acceptors, which led to distinct shifts in relative abundances of

  20. Microbial ecology involved in the ripening of naturally fermented llama meat sausages. A focus on lactobacilli diversity.

    PubMed

    Fontana, Cecilia; Bassi, Daniela; López, Constanza; Pisacane, Vincenza; Otero, Maria Claudia; Puglisi, Edoardo; Rebecchi, Annalisa; Cocconcelli, Pier Sandro; Vignolo, Graciela

    2016-11-07

    Llama represents for the Andean regions a valid alternative to bovine and pork meat and thanks to the high proteins and low fat content; it can constitute a good product for the novel food market. In this study, culture-dependent and independent methods were applied to investigate the microbial ecology of naturally fermented llama sausages produced in Northwest Argentina. Two different production technologies of llama sausage were investigated: a pilot-plant scale (P) and an artisanal one (A). Results obtained by High-Throughput Sequencing (HTS) of 16S rRNA amplicons showed that the production technologies influenced the development of microbial communities with a different composition throughout the entire fermentation process. Both sequencing and microbiological counts demonstrated that Lactic Acid Bacteria (LAB) contributed largely to the dominant microbiota. When a total of 230 isolates were approached by RAPD-PCR, presumptive LAB strains from P production exhibited an initial variability in RAPD fingerprints switching to a single profile at the final of ripening, while A production revealed a more heterogeneous RAPD pattern during the whole fermentation process. The constant presence of Lactobacillus sakei along the fermentation in both productions was revealed by HTS and confirmed by species-specific PCR from isolated strains. The technological characterization of Lb. sakei isolates evidenced their ability to grow at 15°C, pH4.5 and 5% NaCl (95%). Most strains hydrolyzed myofibrillar and sarcoplasmic proteins. Bacteriocins encoding genes and antimicrobial resistance were found in 35% and 42.5% of the strains, respectively. An appropriate choice of a combination of autochthonous strains in a starter formulation is fundamental to improve and standardize llama sausages safety and quality.

  1. Amorfrutins are potent antidiabetic dietary natural products.

    PubMed

    Weidner, Christopher; de Groot, Jens C; Prasad, Aman; Freiwald, Anja; Quedenau, Claudia; Kliem, Magdalena; Witzke, Annabell; Kodelja, Vitam; Han, Chung-Ting; Giegold, Sascha; Baumann, Matthias; Klebl, Bert; Siems, Karsten; Müller-Kuhrt, Lutz; Schürmann, Annette; Schüler, Rita; Pfeiffer, Andreas F H; Schroeder, Frank C; Büssow, Konrad; Sauer, Sascha

    2012-05-08

    Given worldwide increases in the incidence of obesity and type 2 diabetes, new strategies for preventing and treating metabolic diseases are needed. The nuclear receptor PPARγ (peroxisome proliferator-activated receptor gamma) plays a central role in lipid and glucose metabolism; however, current PPARγ-targeting drugs are characterized by undesirable side effects. Natural products from edible biomaterial provide a structurally diverse resource to alleviate complex disorders via tailored nutritional intervention. We identified a family of natural products, the amorfrutins, from edible parts of two legumes, Glycyrrhiza foetida and Amorpha fruticosa, as structurally new and powerful antidiabetics with unprecedented effects for a dietary molecule. Amorfrutins bind to and activate PPARγ, which results in selective gene expression and physiological profiles markedly different from activation by current synthetic PPARγ drugs. In diet-induced obese and db/db mice, amorfrutin treatment strongly improves insulin resistance and other metabolic and inflammatory parameters without concomitant increase of fat storage or other unwanted side effects such as hepatoxicity. These results show that selective PPARγ-activation by diet-derived ligands may constitute a promising approach to combat metabolic disease.

  2. Amorfrutins are potent antidiabetic dietary natural products

    PubMed Central

    Weidner, Christopher; de Groot, Jens C.; Prasad, Aman; Freiwald, Anja; Quedenau, Claudia; Kliem, Magdalena; Witzke, Annabell; Kodelja, Vitam; Han, Chung-Ting; Giegold, Sascha; Baumann, Matthias; Klebl, Bert; Siems, Karsten; Müller-Kuhrt, Lutz; Schürmann, Annette; Schüler, Rita; Pfeiffer, Andreas F. H.; Schroeder, Frank C.; Büssow, Konrad; Sauer, Sascha

    2012-01-01

    Given worldwide increases in the incidence of obesity and type 2 diabetes, new strategies for preventing and treating metabolic diseases are needed. The nuclear receptor PPARγ (peroxisome proliferator-activated receptor gamma) plays a central role in lipid and glucose metabolism; however, current PPARγ-targeting drugs are characterized by undesirable side effects. Natural products from edible biomaterial provide a structurally diverse resource to alleviate complex disorders via tailored nutritional intervention. We identified a family of natural products, the amorfrutins, from edible parts of two legumes, Glycyrrhiza foetida and Amorpha fruticosa, as structurally new and powerful antidiabetics with unprecedented effects for a dietary molecule. Amorfrutins bind to and activate PPARγ, which results in selective gene expression and physiological profiles markedly different from activation by current synthetic PPARγ drugs. In diet-induced obese and db/db mice, amorfrutin treatment strongly improves insulin resistance and other metabolic and inflammatory parameters without concomitant increase of fat storage or other unwanted side effects such as hepatoxicity. These results show that selective PPARγ-activation by diet-derived ligands may constitute a promising approach to combat metabolic disease. PMID:22509006

  3. Natural Products: Insights into Leishmaniasis Inflammatory Response

    PubMed Central

    Rodrigues, Igor A.; Mazotto, Ana Maria; Cardoso, Verônica; Alves, Renan L.; Amaral, Ana Claudia F.; Silva, Jefferson Rocha de Andrade; Pinheiro, Anderson S.; Vermelho, Alane B.

    2015-01-01

    Leishmaniasis is a vector-borne disease that affects several populations worldwide, against which there are no vaccines available and the chemotherapy is highly toxic. Depending on the species causing the infection, the disease is characterized by commitment of tissues, including the skin, mucous membranes, and internal organs. Despite the relevance of host inflammatory mediators on parasite burden control, Leishmania and host immune cells interaction may generate an exacerbated proinflammatory response that plays an important role in the development of leishmaniasis clinical manifestations. Plant-derived natural products have been recognized as bioactive agents with several properties, including anti-protozoal and anti-inflammatory activities. The present review focuses on the antileishmanial activity of plant-derived natural products that are able to modulate the inflammatory response in vitro and in vivo. The capability of crude extracts and some isolated substances in promoting an anti-inflammatory response during Leishmania infection may be used as part of an effective strategy to fight the disease. PMID:26538837

  4. Biotransformation of Furanic and Phenolic Compounds with Hydrogen Gas Production in a Microbial Electrolysis Cell.

    PubMed

    Zeng, Xiaofei; Borole, Abhijeet P; Pavlostathis, Spyros G

    2015-11-17

    Furanic and phenolic compounds are problematic byproducts resulting from the breakdown of lignocellulosic biomass during biofuel production. The capacity of a microbial electrolysis cell (MEC) to produce hydrogen gas (H2) using a mixture of two furanic (furfural, FF; 5-hydroxymethyl furfural, HMF) and three phenolic (syringic acid, SA; vanillic acid, VA; and 4-hydroxybenzoic acid, HBA) compounds as the substrate in the bioanode was assessed. The rate and extent of biotransformation of the five compounds and efficiency of H2 production, as well as the structure of the anode microbial community, were investigated. The five compounds were completely transformed within 7-day batch runs and their biotransformation rate increased with increasing initial concentration. At an initial concentration of 1200 mg/L (8.7 mM) of the mixture of the five compounds, their biotransformation rate ranged from 0.85 to 2.34 mM/d. The anode Coulombic efficiency was 44-69%, which is comparable to that of wastewater-fed MECs. The H2 yield varied from 0.26 to 0.42 g H2-COD/g COD removed in the anode, and the bioanode volume-normalized H2 production rate was 0.07-0.1 L/L-d. The biotransformation of the five compounds took place via fermentation followed by exoelectrogenesis. The major identified fermentation products that did not transform further were catechol and phenol. Acetate was the direct substrate for exoelectrogenesis. Current and H2 production were inhibited at an initial substrate concentration of 1200 mg/L, resulting in acetate accumulation at a much higher level than that measured in other batch runs conducted with a lower initial concentration of the five compounds. The anode microbial community consisted of exoelectrogens, putative degraders of the five compounds, and syntrophic partners of exoelectrogens. The MEC H2 production demonstrated in this study is an alternative to the currently used process of reforming natural gas to supply H2 needed to upgrade bio-oils to stable

  5. Biotransformation of furanic and phenolic compounds with hydrogen gas production in a microbial electrolysis cell

    DOE PAGES

    Zeng, Xiaofei; Borole, Abhijeet P.; Pavlostathis, Spyros G.

    2015-10-27

    In this study, furanic and phenolic compounds are problematic byproducts resulting from the decomposition of lignocellulosic biomass during biofuel production. This study assessed the capacity of a microbial electrolysis cell (MEC) to produce hydrogen gas (H2) using a mixture of two furanic (furfural, FF; 5-hydroxymethyl furfural, HMF) and three phenolic (syringic acid, SA; vanillic acid, VA; and 4-hydroxybenzoic acid, HBA) compounds as the sole carbon and energy source in the bioanode. The rate and extent of biotransformation of the five compounds, efficiency of H2 production, as well as the anode microbial community structure were investigated. The five compounds were completelymore » transformed within 7-day batch runs and their biotransformation rate increased with increasing initial concentration. At an initial concentration of 1,200 mg/L (8.7 mM) of the mixture of the five compounds, their biotransformation rate ranged from 0.85 to 2.34 mM/d. The anode coulombic efficiency was 44-69%, which is comparable to wastewater-fed MECs. The H2 yield varied from 0.26 to 0.42 g H2-COD/g COD removed in the anode, and the bioanode volume-normalized H2 production rate was 0.07-0.1 L/L-d. The major identified fermentation products that did not transform further were catechol and phenol. Acetate was the direct substrate for exoelectrogenesis. Current and H2 production were inhibited at an initial substrate concentration of 1,200 mg/L, resulting in acetate accumulation at a much higher level than that measured in other batch runs conducted with a lower initial concentration of the five compounds. The anode microbial community consisted of exoelectrogens, putative degraders of the five compounds, and syntrophic partners of exoelectrogens. The H2 production route demonstrated in this study has proven to be an alternative to the currently used process of reforming natural gas to supply H2 needed to upgrade bio-oils to stable hydrocarbon fuels.« less

  6. Biotransformation of furanic and phenolic compounds with hydrogen gas production in a microbial electrolysis cell

    SciTech Connect

    Zeng, Xiaofei; Borole, Abhijeet P.; Pavlostathis, Spyros G.

    2015-10-27

    In this study, furanic and phenolic compounds are problematic byproducts resulting from the decomposition of lignocellulosic biomass during biofuel production. This study assessed the capacity of a microbial electrolysis cell (MEC) to produce hydrogen gas (H2) using a mixture of two furanic (furfural, FF; 5-hydroxymethyl furfural, HMF) and three phenolic (syringic acid, SA; vanillic acid, VA; and 4-hydroxybenzoic acid, HBA) compounds as the sole carbon and energy source in the bioanode. The rate and extent of biotransformation of the five compounds, efficiency of H2 production, as well as the anode microbial community structure were investigated. The five compounds were completely transformed within 7-day batch runs and their biotransformation rate increased with increasing initial concentration. At an initial concentration of 1,200 mg/L (8.7 mM) of the mixture of the five compounds, their biotransformation rate ranged from 0.85 to 2.34 mM/d. The anode coulombic efficiency was 44-69%, which is comparable to wastewater-fed MECs. The H2 yield varied from 0.26 to 0.42 g H2-COD/g COD removed in the anode, and the bioanode volume-normalized H2 production rate was 0.07-0.1 L/L-d. The major identified fermentation products that did not transform further were catechol and phenol. Acetate was the direct substrate for exoelectrogenesis. Current and H2 production were inhibited at an initial substrate concentration of 1,200 mg/L, resulting in acetate accumulation at a much higher level than that measured in other batch runs conducted with a lower initial concentration of the five compounds. The anode microbial community consisted of exoelectrogens, putative degraders of the five compounds, and syntrophic partners of exoelectrogens. The H2 production route demonstrated in this study has proven to be an alternative to the currently used process of reforming natural gas to supply H2 needed to

  7. 40 CFR 158.2120 - Microbial pesticides product analysis data requirements table.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...-use product; EP=End-use product; TEP=Typical end-use product; TGAI=Technical grade of the active...: (c) Table. The following table shows the data requirements for microbial pesticides product analysis....6319 Miscibility R MP EP 2 830.6320 Corrosion Characteristics R MP EP 3 830.7000 pH R TGAI TGAI --...

  8. Plant cell culture strategies for the production of natural products

    PubMed Central

    Ochoa-Villarreal, Marisol; Howat, Susan; Hong, SunMi; Jang, Mi Ok; Jin, Young-Woo; Lee, Eun-Kyong; Loake, Gary J.

    2016-01-01

    Plants have evolved a vast chemical cornucopia to support their sessile lifestyles. Man has exploited this natural resource since Neolithic times and currently plant-derived chemicals are exploited for a myriad of applications. However, plant sources of most high-value natural products (NPs) are not domesticated and therefore their production cannot be undertaken on an agricultural scale. Further, these plant species are often slow growing, their populations limiting, the concentration of the target molecule highly variable and routinely present at extremely low concentrations. Plant cell and organ culture constitutes a sustainable, controllable and environmentally friendly tool for the industrial production of plant NPs. Further, advances in cell line selection, biotransformation, product secretion, cell permeabilisation, extraction and scale-up, among others, are driving increases in plant NP yields. However, there remain significant obstacles to the commercial synthesis of high-value chemicals from these sources. The relatively recent isolation, culturing and characterisation of cambial meristematic cells (CMCs), provides an emerging platform to circumvent many of these potential difficulties. [BMB Reports 2016; 49(3): 149-158] PMID:26698871

  9. Plant cell culture strategies for the production of natural products.

    PubMed

    Ochoa-Villarreal, Marisol; Howat, Susan; Hong, SunMi; Jang, Mi Ok; Jin, Young-Woo; Lee, Eun-Kyong; Loake, Gary J

    2016-03-01

    Plants have evolved a vast chemical cornucopia to support their sessile lifestyles. Man has exploited this natural resource since Neolithic times and currently plant-derived chemicals are exploited for a myriad of applications. However, plant sources of most high-value natural products (NPs) are not domesticated and therefore their production cannot be undertaken on an agricultural scale. Further, these plant species are often slow growing, their populations limiting, the concentration of the target molecule highly variable and routinely present at extremely low concentrations. Plant cell and organ culture constitutes a sustainable, controllable and environmentally friendly tool for the industrial production of plant NPs. Further, advances in cell line selection, biotransformation, product secretion, cell permeabilisation, extraction and scale-up, among others, are driving increases in plant NP yields. However, there remain significant obstacles to the commercial synthesis of high-value chemicals from these sources. The relatively recent isolation, culturing and characterisation of cambial meristematic cells (CMCs), provides an emerging platform to circumvent many of these potential difficulties. [BMB Reports 2016; 49(3): 149-158].

  10. Interfacing microbial styrene production with a biocompatible cyclopropanation reaction.

    PubMed

    Wallace, Stephen; Balskus, Emily P

    2015-06-08

    The introduction of new reactivity into living organisms is a major challenge in synthetic biology. Despite an increasing interest in both the development of small-molecule catalysts that are compatible with aqueous media and the engineering of enzymes to perform new chemistry in vitro, the integration of non-native reactivity into metabolic pathways for small-molecule production has been underexplored. Herein we report a biocompatible iron(III) phthalocyanine catalyst capable of efficient olefin cyclopropanation in the presence of a living microorganism. By interfacing this catalyst with E. coli engineered to produce styrene, we synthesized non-natural phenyl cyclopropanes directly from D-glucose in single-vessel fermentations. This process is the first example of the combination of nonbiological carbene-transfer reactivity with cellular metabolism for small-molecule production.

  11. Effects of phosphate limitation on soluble microbial products and microbial community structure in semi-continuous Synechocystis-based photobioreactors.

    PubMed

    Zevin, Alexander S; Nam, Taekgul; Rittmann, Bruce; Krajmalnik-Brown, Rosa

    2015-09-01

    All bacteria release organic compounds called soluble microbial products (SMP) as a part of their normal metabolism. In photobioreactor (PBR) settings, SMP produced by cyanobacteria represent a major pool of carbon and electrons available to heterotrophic bacteria. Thus, SMP in PBRs are a major driver for the growth of heterotrophic bacteria, and understanding the distribution of SMP in PBRs is an important step toward proper management of PBR microbial communities. Here, we analyzed the SMP and microbial communities in two Synechocystis sp. PCC6803-based PBRs. The first PBR (PBRP0) became phosphate limited after several days of operation, while the second PBR (PBRP+) did not have phosphate limitation. Heterotrophic bacteria were detected in both PBRs, but PBRP0 had a much higher proportion of heterotrophic bacteria than PBRP+. Furthermore, PBRP+ had greater biomass production and lower SMP production per unit biomass than PBRP0. Carbohydrates that were most likely derived from hydrolysis of extracellular polymeric substances (EPS) dominated the SMP in PBRP0, while products resulting from cell lysis or decay dominated the SMP in PBRP+. Together, our data support that maintaining phosphate availability in Synechocystis-based PBRs is important for managing SMP and, thus, the heterotrophic community.

  12. Biorefinery of corn cob for microbial lipid and bio-ethanol production: An environmental friendly process.

    PubMed

    Cai, Di; Dong, Zhongshi; Wang, Yong; Chen, Changjing; Li, Ping; Qin, Peiyong; Wang, Zheng; Tan, Tianwei

    2016-07-01

    Microbial lipid and bio-ethanol were co-generated by an integrated process using corn cob bagasse as raw material. After pretreatment, the acid hydrolysate was used as substrate for microbial lipid fermentation, while the solid residue was further enzymatic hydrolysis for bio-ethanol production. The effect of acid loading and pretreatment time on microbial lipid and ethanol production were evaluated. Under the optimized condition for ethanol production, ∼131.3g of ethanol and ∼11.5g of microbial lipid were co-generated from 1kg raw material. On this condition, ∼71.6% of the overall fermentable sugars in corn cob bagasse could be converted into valuable products. At the same time, at least 33% of the initial COD in the acid hydrolysate was depredated.

  13. [Fermentation production of microbial catalase and its application in textile industry].

    PubMed

    Zhang, Dongxu; Du, Guocheng; Chen, Jian

    2010-11-01

    Microbial catalase is an important industrial enzyme that catalyzes the decomposition of hydrogen peroxide to water and oxygen. This enzyme has great potential of application in food, textile and pharmaceutical industries. The production of microbial catalase has been significantly improved thanks to advances in bioprocess engineering and genetic engineering. In this paper, we review the progresses in fermentation production of microbial catalase and its application in textile industry. Among these progresses, we will highlight strain isolation, substrate and environment optimization, enzyme induction, construction of engineering strains and application process optimization. Meanwhile, we also address future research trends for microbial catalase production and its application in textile industry. Molecular modification (site-directed mutagenesis and directed revolution) will endue catalase with high pH and temperature stabilities. Improvement of catalase production, based on the understanding of induction mechanism and the process control of recombinant stain fermentation, will further accelerate the application of catalase in textile industry.

  14. RESEARCH PLAN FOR MICROBIAL PATHOGENS AND DISINFECTION BY-PRODUCTS IN DRINKING WATER

    EPA Science Inventory

    This research plan was developed to describe research needed to support EPA's development of drinking water regulations concerning disinfectants, disinfection by-products (DBPs) and microbial pathogens, focusing on key scientific and technical information needed. The research pl...

  15. Electricity production from municipal solid waste using microbial fuel cells.

    PubMed

    Chiu, H Y; Pai, T Y; Liu, M H; Chang, C A; Lo, F C; Chang, T C; Lo, H M; Chiang, C F; Chao, K P; Lo, W Y; Lo, S W; Chu, Y L

    2016-07-01

    The organic content of municipal solid waste has long been an attractive source of renewable energy, mainly as a solid fuel in waste-to-energy plants. This study focuses on the potential to use microbial fuel cells to convert municipal solid waste organics into energy using various operational conditions. The results showed that two-chamber microbial fuel cells with carbon felt and carbon felt allocation had a higher maximal power density (20.12 and 30.47 mW m(-2) for 1.5 and 4 L, respectively) than those of other electrode plate allocations. Most two-chamber microbial fuel cells (1.5 and 4 L) had a higher maximal power density than single-chamber ones with corresponding electrode plate allocations. Municipal solid waste with alkali hydrolysis pre-treatment and K3Fe(CN)6 as an electron acceptor improved the maximal power density to 1817.88 mW m(-2) (~0.49% coulomb efficiency, from 0.05-0.49%). The maximal power density from experiments using individual 1.5 and 4 L two-chamber microbial fuel cells, and serial and parallel connections of 1.5 and 4 L two-chamber microbial fuel cells, was found to be in the order of individual 4 L (30.47 mW m(-2)) > serial connection of 1.5 and 4 L (27.75) > individual 1.5 L (20.12) > parallel connection of 1.5 and 4 L (17.04) two-chamber microbial fuel cells . The power density using municipal solid waste microbial fuel cells was compared with information in the literature and discussed.

  16. Microbial Competition in Polar Soils: A Review of an Understudied but Potentially Important Control on Productivity

    PubMed Central

    Bell, Terrence H.; Callender, Katrina L.; Whyte, Lyle G.; Greer, Charles W.

    2013-01-01

    Intermicrobial competition is known to occur in many natural environments, and can result from direct conflict between organisms, or from differential rates of growth, colonization, and/or nutrient acquisition. It has been difficult to extensively examine intermicrobial competition in situ, but these interactions may play an important role in the regulation of the many biogeochemical processes that are tied to microbial communities in polar soils. A greater understanding of how competition influences productivity will improve projections of gas and nutrient flux as the poles warm, may provide biotechnological opportunities for increasing the degradation of contaminants in polar soil, and will help to predict changes in communities of higher organisms, such as plants. PMID:24832797

  17. Natural Products from Plant-associated Microorganisms: Distribution, Structural Diversity, Bioactivity, and Implications of Their Occurrence⊥

    PubMed Central

    Gunatilaka, A. A. Leslie

    2012-01-01

    A growing body of evidence suggests that plant-associated microorganisms, especially endophytic and rhizosphere bacteria and fungi, represent a huge and largely untapped resource of natural products with chemical structures that have been optimized by evolution for biological and ecological relevance. A diverse array of bioactive small molecule natural products has been encountered in these microorganisms. The structures of over 230 metabolites isolated and characterized from over 70 plant-associated microbial strains during the past four years are presented with information on their hosts, culture conditions, and biological activities. Some significant biological and ecological implications of their occurrence are also reviewed. PMID:16562864

  18. Natural product synthesis at the interface of chemistry and biology

    PubMed Central

    2014-01-01

    Nature has evolved to produce unique and diverse natural products that possess high target affinity and specificity. Natural products have been the richest sources for novel modulators of biomolecular function. Since the chemical synthesis of urea by Wöhler, organic chemists have been intrigued by natural products, leading to the evolution of the field of natural product synthesis over the past two centuries. Natural product synthesis has enabled natural products to play an essential role in drug discovery and chemical biology. With the introduction of novel, innovative concepts and strategies for synthetic efficiency, natural product synthesis in the 21st century is well poised to address the challenges and complexities faced by natural product chemistry and will remain essential to progress in biomedical sciences. PMID:25043880

  19. Natural product synthesis at the interface of chemistry and biology.

    PubMed

    Hong, Jiyong

    2014-08-11

    Nature has evolved to produce unique and diverse natural products that possess high target affinity and specificity. Natural products have been the richest sources for novel modulators of biomolecular function. Since the chemical synthesis of urea by Wöhler, organic chemists have been intrigued by natural products, leading to the evolution of the field of natural product synthesis over the past two centuries. Natural product synthesis has enabled natural products to play an essential role in drug discovery and chemical biology. With the introduction of novel, innovative concepts and strategies for synthetic efficiency, natural product synthesis in the 21st century is well poised to address the challenges and complexities faced by natural product chemistry and will remain essential to progress in biomedical sciences.

  20. Antibacterial natural products in medicinal chemistry--exodus or revival?

    PubMed

    von Nussbaum, Franz; Brands, Michael; Hinzen, Berthold; Weigand, Stefan; Häbich, Dieter

    2006-08-04

    To create a drug, nature's blueprints often have to be improved through semisynthesis or total synthesis (chemical postevolution). Selected contributions from industrial and academic groups highlight the arduous but rewarding path from natural products to drugs. Principle modification types for natural products are discussed herein, such as decoration, substitution, and degradation. The biological, chemical, and socioeconomic environments of antibacterial research are dealt with in context. Natural products, many from soil organisms, have provided the majority of lead structures for marketed anti-infectives. Surprisingly, numerous "old" classes of antibacterial natural products have never been intensively explored by medicinal chemists. Nevertheless, research on antibacterial natural products is flagging. Apparently, the "old fashioned" natural products no longer fit into modern drug discovery. The handling of natural products is cumbersome, requiring nonstandardized workflows and extended timelines. Revisiting natural products with modern chemistry and target-finding tools from biology (reversed genomics) is one option for their revival.

  1. Microbial production of 1,3-propanediol: Recent developments and emerging opportunities.

    PubMed

    Saxena, R K; Anand, Pinki; Saran, Saurabh; Isar, Jasmine

    2009-01-01

    1,3-Propanediol, a valuable bifunctional molecule, can be produced from renewable resources using microorganisms. It has several promising properties for many synthetic reactions, particularly for polymer and cosmetic industries. By virtue of being a natural product, relevant biochemical pathways can be harnessed into fermentation processes to produce 1,3-propanediol. Various strategies for the microbial production of 1,3-propanediol are reviewed and compared in this article with their promises and constraints. Furthermore, genetic and metabolic engineering could significantly improve product yields and overcome the limitations of fermentation technology. Present review gives an overview on 1,3-propanediol production by wild and recombinant strains. It also attempts to encompass the various issues concerned in utilization of crude glycerol for 1,3-propanediol production, with particular emphasis laid on biodiesel industries. This review also summarizes the present state of strategies studied for the downstream processing and purification of biologically produced 1,3-propanediol. The future prospect of 1,3-propanediol and its potential as a major bulk chemical are discussed under the light of the current research.

  2. Natural products - modifying metabolite pathways in plants.

    PubMed

    Staniek, Agata; Bouwmeester, Harro; Fraser, Paul D; Kayser, Oliver; Martens, Stefan; Tissier, Alain; van der Krol, Sander; Wessjohann, Ludger; Warzecha, Heribert

    2013-10-01

    The diversity of plant natural product (PNP) molecular structures is reflected in the variety of biochemical and genetic pathways that lead to their formation and accumulation. Plant secondary metabolites are important commodities, and include fragrances, colorants, and medicines. Increasing the extractable amount of PNP through plant breeding, or more recently by means of metabolic engineering, is a priority. The prerequisite for any attempt at metabolic engineering is a detailed knowledge of the underlying biosynthetic and regulatory pathways in plants. Over the past few decades, an enormous body of information about the biochemistry and genetics of biosynthetic pathways involved in PNPs production has been generated. In this review, we focus on the three large classes of plant secondary metabolites: terpenoids (or isoprenoids), phenylpropanoids, and alkaloids. All three provide excellent examples of the tremendous efforts undertaken to boost our understanding of biosynthetic pathways, resulting in the first successes in plant metabolic engineering. We further consider what essential information is still missing, and how future research directions could help achieve the rational design of plants as chemical factories for high-value products.

  3. Design of a microbial fuel cell and its transition to microbial electrolytic cell for hydrogen production by electrohydrogenesis.

    PubMed

    Gupta, Pratima; Parkhey, Piyush; Joshi, Komal; Mahilkar, Anjali

    2013-10-01

    Anaerobic bacteria were isolated from industrial wastewater and soil samples and tested for exoelectrogenic activity by current production in double chambered microbial fuel cell (MFC), which was further transitioned into a single chambered microbial electrolytic cell to test hydrogen production by electrohydrogenesis. Of all the cultures, the isolate from industrial water sample showed the maximum values for current = 0.161 mA, current density = 108.57 mA/m2 and power density = 48.85 mW/m2 with graphite electrode. Maximum voltage across the cell, however, was reported by the isolate from sewage water sample (506 mv) with copper as electrode. Tap water with KMnO4 was the best cathodic electrolyte as the highest values for all the measured MFC parameters were reported with it. Once the exoelectrogenic activity of the isolates was confirmed by current production, these were tested for hydrogen production in a single chambered microbial electrolytic cell (MEC) modified from the MFC. Hydrogen production was reported positive from co-culture of isolates of both the water samples and co-culture of one soil and one water sample. The maximum rate and yield of hydrogen production was 0.18 m3H2/m3/d and 3.2 mol H2/mol glucose respectively with total hydrogen production of 42.4 mL and energy recovery of 57.4%. Cumulative hydrogen production for a five day cycle of MEC operation was 0.16 m3H2/m3/d.

  4. Microbial community analysis in a long-term membrane-less microbial electrolysis cell with hydrogen and methane production.

    PubMed

    Rago, Laura; Ruiz, Yolanda; Baeza, Juan A; Guisasola, Albert; Cortés, Pilar

    2015-12-01

    A single-chamber microbial electrolysis cell (MEC) aiming at hydrogen production with acetate as sole carbon source failed due to methanogenesis build-up despite the significant amount of 2-bromoethanesulfonate (BES) dosage, 50 mM. Specific batch experiments and a thorough microbial community analysis, pyrosequencing and qPCR, of cathode, anode and medium were performed to understand these observations. The experimental data rebuts different hypothesis and shows that methanogenesis at high BES concentration was likely due to the capacity of some Archaea (hydrogen-oxidizing genus Methanobrevibacter) to resist high BES concentration up to 200 mM. Methanobrevibacter, of the Methanobacteriales order, represented almost the 98% of the total Archaea in the cathode whereas Geobacter was highly abundant in the anode (72% of bacteria). Moreover, at higher BES concentration (up to 200 mM), methanogenesis activity decreased resulting in an increase of homoacetogenic activity, which challenged the performance of the MEC for H2 production.

  5. Towards efficient bioethanol production from agricultural and forestry residues: Exploration of unique natural microorganisms in combination with advanced strain engineering.

    PubMed

    Zhao, Xinqing; Xiong, Liang; Zhang, Mingming; Bai, Fengwu

    2016-09-01

    Production of fuel ethanol from lignocellulosic feedstocks such as agricultural and forestry residues is receiving increasing attention due to the unsustainable supply of fossil fuels. Three key challenges include high cellulase production cost, toxicity of the cellulosic hydrolysate to microbial strains, and poor ability of fermenting microorganisms to utilize certain fermentable sugars in the hydrolysate. In this article, studies on searching of natural microbial strains for production of unique cellulase for biorefinery of agricultural and forestry wastes, as well as development of strains for improved cellulase production were reviewed. In addition, progress in the construction of yeast strains with improved stress tolerance and the capability to fully utilize xylose and glucose in the cellulosic hydrolysate was also summarized. With the superior microbial strains for high titer cellulase production and efficient utilization of all fermentable sugars in the hydrolysate, economic biofuels production from agricultural residues and forestry wastes can be realized.

  6. A microbial functional group-based module for simulating methane production and consumption: Application to an incubated permafrost soil

    SciTech Connect

    Xu, Xiaofeng; Elias, Dwayne A.; Graham, David E.; Phelps, Tommy J.; Carroll, Sue L.; Wullschleger, Stan D.; Thornton, Peter E.

    2015-07-23

    In this study, accurately estimating methane (CH4) flux is critically important for investigating and predicting the biogeochemistry-climate feedback. Better simulating CH4 flux requires explicit representations of microbial processes on CH4 dynamics because all processes for CH4 production and consumption are actually carried out by microbes. A microbial functional group based module was developed and tested against an incubation experiment. The module considers four key mechanisms for CH4 production and consumption: methanogenesis from acetate or single-carbon compounds and CH4 oxidation using molecular oxygen or other inorganic electron acceptors. These four processes were carried out by four microbial functional groups: acetoclastic methanogens, hydrogenotrophic methanogens, aerobic methanotrophs, and anaerobic methanotrophs. This module was then linked with the decomposition subroutine of the Community Land Model, and was further used to simulate dynamics of carbon dioxide (CO2) and CH4 concentrations from an incubation experiment with permafrost soils. The results show that the model could capture the dynamics of CO2 and CH4 concentrations in microcosms with top soils, mineral layer soils and permafrost soils under natural and saturated moisture conditions and a temperature gradient of -2°C, 3°C, and 5°C. Sensitivity analysis confirmed the importance of acetic acid's direct contribution as substrate and indirect effects through pH feedback on CO2 and CH4 production and consumption. This study suggests that representing the microbial mechanisms is critical for modeling CH4 production and consumption; it is urgent to incorporate microbial mechanisms into Earth system models for better predicting the behavior of the climate system.

  7. A microbial functional group-based module for simulating methane production and consumption: Application to an incubated permafrost soil

    DOE PAGES

    Xu, Xiaofeng; Elias, Dwayne A.; Graham, David E.; ...

    2015-07-23

    In this study, accurately estimating methane (CH4) flux is critically important for investigating and predicting the biogeochemistry-climate feedback. Better simulating CH4 flux requires explicit representations of microbial processes on CH4 dynamics because all processes for CH4 production and consumption are actually carried out by microbes. A microbial functional group based module was developed and tested against an incubation experiment. The module considers four key mechanisms for CH4 production and consumption: methanogenesis from acetate or single-carbon compounds and CH4 oxidation using molecular oxygen or other inorganic electron acceptors. These four processes were carried out by four microbial functional groups: acetoclastic methanogens,more » hydrogenotrophic methanogens, aerobic methanotrophs, and anaerobic methanotrophs. This module was then linked with the decomposition subroutine of the Community Land Model, and was further used to simulate dynamics of carbon dioxide (CO2) and CH4 concentrations from an incubation experiment with permafrost soils. The results show that the model could capture the dynamics of CO2 and CH4 concentrations in microcosms with top soils, mineral layer soils and permafrost soils under natural and saturated moisture conditions and a temperature gradient of -2°C, 3°C, and 5°C. Sensitivity analysis confirmed the importance of acetic acid's direct contribution as substrate and indirect effects through pH feedback on CO2 and CH4 production and consumption. This study suggests that representing the microbial mechanisms is critical for modeling CH4 production and consumption; it is urgent to incorporate microbial mechanisms into Earth system models for better predicting the behavior of the climate system.« less

  8. Pyrosequencing reveals highly diverse microbial communities in microbial electrolysis cells involved in enhanced H2 production from waste activated sludge.

    PubMed

    Lu, Lu; Xing, Defeng; Ren, Nanqi

    2012-05-01

    Renewable H(2) production from a plentiful biomass, waste activated sludge (WAS), can be achieved by fermentation, but the yields are low. The use of a microbial electrolysis cell (MEC) can increase the H(2) production yields to several times that of fermentation. We have proved that the enhancement of H(2) production was due to the ability of MECs to use a wider range of organic matter in WAS than in fermentation. To support this result strongly, we here investigated the microbial community structures of WAS and anode biofilms in WAS-fed MECs. A pyrosequencing analysis based on the bacterial 16S rRNA gene showed that dominant populations in MECs were more diverse than those in WAS (inoculum and substrate) after enrichment, and there was a clear distinction between MECs and WAS in microbial community structure. Diverse acid-producing bacteria and exoelectrogens (predominance of Geobacter) were detected in MECs but they were only rarely found in WAS. It has been reported that these acid-producing bacteria can ferment various sugars and amines with acetate, propionate, and butyrate as their major by-products. This was consistent with our chemical analyses. Detected exoelectrogens are known to use these organic acids (mainly acetate) and certain sugars to directly produce current for H(2) generation at the cathodes in the MECs. Using quantitative real-time PCR, we demonstrated that a consistent feed of alkaline-pretreated WAS containing large amounts of acetate led to a predominance of acetoclastic methanogens, while hydrogenotrophic methanogens were abundant in MECs fed both raw and alkaline-pretreated WAS. Syntrophic interactions between phylogenetically diverse microbial populations in anodophilic biofilms were found to drive the efficient cascade utilization of organic matter in WAS.

  9. Microbial biodegradation of proteinaceous tannery solid waste and production of a novel value added product - Metalloprotease.

    PubMed

    Ravindran, Balasubramani; Wong, Jonathan W C; Selvam, Ammaiyappan; Thirunavukarasu, Kathirvel; Sekaran, Ganesan

    2016-10-01

    In this study, animal fleshing (ANFL) was utilized as a substrate for the production of extracellular protease by Clostridium limosum through central composite rotatable design (CCRD) and response surface methodology (RSM). Optimum protease production of 433U/ml was achieved and the purified enzyme was identified as acidic metalloprotease, a monomeric protein. The molecular weight of the enzyme was 71kDa, whose activity was enhanced by bivalent metals such as Zn(2+) and Mg(2+). Scanning electron microscopy (SEM) examination also revealed the hydrolysis/microbial degradation of ANFL through protease activity in the anaerobic fermentation process. Simultaneous hydrolysis of ANFL and production of an enzyme with the potential for different industrial applications provide an attractive methodology for the disposal of tannery solid waste.

  10. Role of discontinuous chlorination on microbial production by drinking water biofilms.

    PubMed

    Codony, Francesc; Morató, Jordi; Mas, Jordi

    2005-05-01

    Microbial quality in water distribution systems is strongly affected by the development of microbial biofilms. Production and release of microbial cells by the biofilm affect microbial levels in the water column and in some cases this fact constitutes a public health concern. In this study, we attempt to analyze in which way the existence of different episodes of chlorine depletion affects both biofilm formation and microbial load of an artificial laboratory system. The work was carried out using two parallel packed bed reactors both supplied with running tap water. One of the reactors was used as a control and was permanently exposed to the action of chlorine. In the other reactor, chlorine was neutralized at selected times during the experiment and for periods of variable length. During the experiment the concentration of total and viable cells from the effluent was monitored at the exit of each of the reactors. The data obtained were used to estimate microbial production from the biofilms. As an average, release of microbial cells to the water phase increased tenfold in the absence of chlorine. The results also indicate that disinfectant efficiency against the biofilm was not recovered when chlorine returned to normal levels after each event of chlorine neutralization. Cell viability in the water phase in the presence of chlorine was low at the beginning of the experiment but increased 4 orders of magnitude after five neutralization periods. Therefore, subsequent episodes of chlorine depletion may accelerate the development of microbial communities with reduced susceptibility to disinfection in real drinking water systems.

  11. Environmental proteomics of microbial plankton in a highly productive coastal upwelling system

    SciTech Connect

    Sowell, Sarah; Abraham, Paul E; Shah, Manesh B; Verberkmoes, Nathan C; Smith, Daniel; Barofsky, Douglas; Giovannoni, Stephen

    2011-01-01

    Metaproteomics is one of a suite of new approaches providing insights into the activities of microorganisms in natural environments. Proteins, the final products of gene expression, indicate cellular priorities, taking into account both transcriptional and posttranscriptional control mechanisms that control adaptive responses. Here, we report the proteomic composition of the o 1.2 lm fraction of a microbial community from Oregon coast summer surface waters, detected with two-dimensional liquid chromatography coupled with electrospray tandem mass spectrometry. Spectra corresponding to proteins involved in protein folding and biosynthesis, transport, and viral capsid structure were the most frequently detected. A total of 36% of all the detected proteins were best matches to the SAR11 clade, and other abundant coastal microbial clades were also well represented, including the Roseobacter clade (17%), oligotrophic marine gammaproteobacteria group (6%), OM43 clade (1%). Viral origins were attributed to 2.5% of proteins. In contrast to oligotrophic waters, phosphate transporters were not highly detected in this nutrient-rich system. However, transporters for amino acids, taurine, polyamines and glutamine synthetase were among the most highly detected proteins, supporting predictions that carbon and nitrogen are more limiting than phosphate in this environment. Intriguingly, one of the highly detected proteins was methanol dehydrogenase originating from the OM43 clade, providing further support for recent reports that the metabolism of one-carbon compounds by these streamlined methylotrophs might be an important feature of coastal ocean biogeochemistry.

  12. Microbially-Enhanced Redox Solution Reoxidation for Sour Natural Gas Sweetening

    SciTech Connect

    Kenneth Brezinsky

    2008-01-15

    The specific objective of this project are to advance the technology and improve the economics of the commercial iron-based chelate processes such as LO-CAT II and SulFerox process utilizing biologically enhanced reoxidation of the redox solutions used in these processes. The project is based on the use of chelated ferric iron as the catalyst for the production of elemental sulfur, and then oxidizing bacteria, such as Thiobacillus Ferrooxidans (ATCC 23270) as an oxidizer. The regeneration of Fe{sup 3+} - chelate is accomplished by the use of these same microbes under mild conditions at 25-30 C and at atmospheric pressure to minimize the chelate degradation process. The pH of the redox solution was observed to be a key process parameter. Other parameters such as temperature, total iron concentration, gas to liquid ratio and bacterial cell densities also influence the overall process. The second part of this project includes experimental data and a kinetic model of microbial H{sub 2}S removal from sour natural gas using thiobacillus species. In the experimental part, a series of experiments were conducted with a commercial chelated iron catalyst at pH ranges from 8.7 to 9.2 using a total iron concentration range from 925 ppm to 1050 ppm in the solution. Regeneration of the solution was carried out by passing air through the solution. Iron oxidizing bacteria were used at cell densities of 2.3 x 10{sup 7}cells/ml for optimum effective performance. In the modeling part, oxidation of Fe{sup 2+} ions by the iron oxidizing bacteria - Thiobacillus Ferrooxidans was studied for application to a continuous stirred tank reactor (CSTR). The factors that can directly affect the oxidation rate such as dilution rate, temperature, and pH were analyzed. The growth of the microorganism was assumed to follow Monod type of growth kinetics. Dilution rate had influence on the rate of oxidation of ferrous iron. Higher dilution rates caused washout of the biomass. The oxidation rate was

  13. Quantitative microbial risk assessment for Staphylococcus aureus in natural and processed cheese in Korea.

    PubMed

    Lee, Heeyoung; Kim, Kyunga; Choi, Kyoung-Hee; Yoon, Yohan

    2015-09-01

    This study quantitatively assessed the microbial risk of Staphylococcus aureus in cheese in Korea. The quantitative microbial risk assessment was carried out for natural and processed cheese from factory to consumption. Hazards for S. aureus in cheese were identified through the literature. For exposure assessment, the levels of S. aureus contamination in cheeses were evaluated, and the growth of S. aureus was predicted by predictive models at the surveyed temperatures, and at the time of cheese processing and distribution. For hazard characterization, a dose-response model for S. aureus was found, and the model was used to estimate the risk of illness. With these data, simulation models were prepared with @RISK (Palisade Corp., Ithaca, NY) to estimate the risk of illness per person per day in risk characterization. Staphylococcus aureus cell counts on cheese samples from factories and markets were below detection limits (0.30-0.45 log cfu/g), and pert distribution showed that the mean temperature at markets was 6.63°C. Exponential model [P=1 - exp(7.64×10(-8) × N), where N=dose] for dose-response was deemed appropriate for hazard characterization. Mean temperature of home storage was 4.02°C (log-logistic distribution). The results of risk characterization for S. aureus in natural and processed cheese showed that the mean values for the probability of illness per person per day were higher in processed cheese (mean: 2.24×10(-9); maximum: 7.97×10(-6)) than in natural cheese (mean: 7.84×10(-10); maximum: 2.32×10(-6)). These results indicate that the risk of S. aureus-related foodborne illness due to cheese consumption can be considered low under the present conditions in Korea. In addition, the developed stochastic risk assessment model in this study can be useful in establishing microbial criteria for S. aureus in cheese.

  14. Microbial Diversity in Natural Asphalts of the Rancho La Brea Tar Pits▿

    PubMed Central

    Kim, Jong-Shik; Crowley, David E.

    2007-01-01

    Bacteria commonly inhabit subsurface oil reservoirs, but almost nothing is known yet about microorganisms that live in naturally occurring terrestrial oil seeps and natural asphalts that are comprised of highly recalcitrant petroleum hydrocarbons. Here we report the first survey of microbial diversity in ca. 28,000-year-old samples of natural asphalts from the Rancho La Brea Tar Pits in Los Angeles, CA. Microbiological studies included analyses of 16S rRNA gene sequences and DNA encoding aromatic ring-hydroxylating dioxygenases from two tar pits differing in chemical composition. Our results revealed a wide range of phylogenetic groups within the Archaea and Bacteria domains, in which individual taxonomic clusters were comprised of sets of closely related species within novel genera and families. Fluorescent staining of asphalt-soil particles using phylogenetic probes for Archaea, Bacteria, and Pseudomonas showed coexistence of mixed microbial communities at high cell densities. Genes encoding dioxygenases included three novel clusters of enzymes. The discovery of life in the tar pits provides an avenue for further studies of the evolution of enzymes and catabolic pathways for bacteria that have been exposed to complex hydrocarbons for millennia. These bacteria also should have application for industrial microbiology and bioremediation. PMID:17416692

  15. Spectroscopic Characterization of a Natural Product: Anethole

    NASA Astrophysics Data System (ADS)

    Barber, Victoria P.; Newby, Josh J.

    2013-06-01

    Anethole [(E)-1-methoxy-4-(1-propenyl)benzene] is a natural product molecule that is commonly recognized as the flavor component of anise, fennel, and licorice. Early jet-cooled spectroscopy of anethole showed the existence of two possible conformations, but did not address details of the vibronic structure. Here, we report the jet-cooled, laser-induced fluorescence and single vibronic level fluorescence spectra of anethole. Analysis of the spectra confirms the existence of two rotamers in the expansion that differ by the relative orientation of the methoxy and propenyl groups. The observed vibronic activity is similar to that of styrene and indicates planar symmetry of both rotamers. Vibrational assignments of anethole are assisted by density functional theory calculations and the results are compared with the analogous motions in styrene. V. H. Grassian, E. R. Bernstein, H. V. Secor and J. I. Seeman J. Phys. Chem. {93, 3470 (1989).

  16. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    USGS Publications Warehouse

    Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D. Kirk; McCleskey, R. Blaine; Shah, Menesh B.; VerBekmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

  17. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    SciTech Connect

    Muller, R; Denef, Vincent; Kalnejals, Linda; Suttle, K Blake; Thomas, Brian; Wilmes, P; Smith, Richard L.; Nordstrom, D Kirk; McCleskey, R Blaine; Shah, Manesh B; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems.We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism s metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ

  18. Response of Soil Properties and Microbial Communities to Agriculture: Implications for Primary Productivity and Soil Health Indicators

    PubMed Central

    Trivedi, Pankaj; Delgado-Baquerizo, Manuel; Anderson, Ian C.; Singh, Brajesh K.

    2016-01-01

    Agricultural intensification is placing tremendous pressure on the soil’s capacity to maintain its functions leading to large-scale ecosystem degradation and loss of productivity in the long term. Therefore, there is an urgent need to find early indicators of soil health degradation in response to agricultural management. In recent years, major advances in soil meta-genomic and spatial studies on microbial communities and community-level molecular characteristics can now be exploited as ‘biomarker’ indicators of ecosystem processes for monitoring and managing sustainable soil health under global change. However, a continental scale, cross biome approach assessing soil microbial communities and their functional potential to identify the unifying principles governing the susceptibility of soil biodiversity to land conversion is lacking. We conducted a meta-analysis from a dataset generated from 102 peer-reviewed publications as well as unpublished data to explore how properties directly linked to soil nutritional health (total C and N; C:N ratio), primary productivity (NPP) and microbial diversity and composition (relative abundance of major bacterial phyla determined by next generation sequencing techniques) are affected in response to agricultural management across the main biomes of Earth (arid, continental, temperate and tropical). In our analysis, we found strong statistical trends in the relative abundance of several bacterial phyla in agricultural (e.g., Actinobacteria and Chloroflexi) and natural (Acidobacteria, Proteobacteria, and Cyanobacteria) systems across all regions and these trends correlated well with many soil properties. However, main effects of agriculture on soil properties and productivity were biome-dependent. Our meta-analysis provides evidence on the predictable nature of the microbial community responses to vegetation type. This knowledge can be exploited in future for developing a new set of indicators for primary productivity and

  19. Investigations of mechanisms of microbial enhanced oil recovery by microbes and their metabolic products

    SciTech Connect

    Chase, K.L.; Bryant, R.S.; Bertus, K.M.; Stepp, A.K.

    1990-12-01

    Experiments at NIPER have demonstrated that oil mobilization by microbial formulations is not merely the result of the effects of the metabolic products from the in situ fermentation of nutrient. A combination of two microorganisms, Bacillus licheniformis, NIPER and a Clostridium species (NIPER 6) was determined to be an effective microbial formulation for the recovery of residual crude oil in porous media. Flask tests with various nutrients and environmental conditions were used to evaluate the growth and metabolite production of NIPER 1 and 6. Several interfacial tension (IFT) measurements were conducted using certain metabolic products from the combined microbial cultures NIPER 1 and NIPER 6. Nonane was used as the oil for these experiments, since crude oil from Delaware-Childers field emulsifies very easily. The IFT of a selected microbial formulation were measured with two different crude oils using brines of varying salinities. Comparisons were made with saline brines containing only the nutrient and with microbial metabolite solutions from which the active cells have been removed by filtration to isolate the specific effects of the microbial cells. Etched-glass micromodel studies showed that the microbial formulation effectively mobilized crude oil trapped after waterflooding. Wettability alteration and unsteady-state relative permeability tests were performed in Berea Sandstone cores. 16 refs., 17 figs., 12 tabs.

  20. Electrodic voltages in the presence of dissolved sulfide: Implications for monitoring natural microbial activity

    SciTech Connect

    Slater, L.; Ntarlagiannis, D.; Yee, N.; O'Brien, M.; Zhang, C.; Williams, K. H.

    2008-10-01

    There is growing interest in the development of new monitoring strategies for obtaining spatially extensive data diagnostic of microbial processes occurring in the earth. Open-circuit potentials arising from variable redox conditions in the fluid local-to-electrode surfaces (electrodic potentials) were recorded for a pair of silver-silver chloride electrodes in a column experiment, whereby a natural wetland soil containing a known community of sulfate reducers was continuously fed with a sulfate-rich nutrient medium. Measurements were made between five electrodes equally spaced along the column and a reference electrode placed on the column inflow. The presence of a sulfate reducing microbial population, coupled with observations of decreasing sulfate levels, formation of black precipitate (likely iron sulfide),elevated solid phase sulfide, and a characteristic sulfurous smell, suggest microbial-driven sulfate reduction (sulfide generation) in our column. Based on the known sensitivity of a silver electrode to dissolved sulfide concentration, we interpret the electrodic potentials approaching 700 mV recorded in this experiment as an indicator of the bisulfide (HS-) concentration gradients in the column. The measurement of the spatial and temporal variation in these electrodic potentials provides a simple and rapid method for monitoring patterns of relative HS- concentration that are indicative of the activity of sulfate-reducing bacteria. Our measurements have implications both for the autonomous monitoring of anaerobic microbial processes in the subsurface and the performance of self-potential electrodes, where it is critical to isolate, and perhaps quantify, electrochemical interfaces contributing to observed potentials.

  1. Characterization of the deep microbial life in the Altmark natural gas reservoir

    NASA Astrophysics Data System (ADS)

    Morozova, D.; Alawi, M.; Vieth-Hillebrand, A.; Kock, D.; Krüger, M.; Wuerdemann, H.; Shaheed, M.

    2010-12-01

    Within the framework of the CLEAN project (CO2 Largescale Enhanced gas recovery in the Altmark Natural gas field) technical basics with special emphasis on process monitoring are explored by injecting CO2 into a gas reservoir. Our study focuses on the investigation of the in-situ microbial community of the Rotliegend natural gas reservoir in the Altmark, located south of the city Salzwedel, Germany. In order to characterize the microbial life in the extreme habitat we aim to localize and identify microbes including their metabolism influencing the creation and dissolution of minerals. The ability of microorganisms to speed up dissolution and formation of minerals might result in changes of the local permeability and the long-term safety of CO2 storage. However, geology, structure and chemistry of the reservoir rock and the cap rock as well as interaction with saline formation water and natural gases and the injected CO2 affect the microbial community composition and activity. The reservoir located at the depth of approximately 3500 m, is characterised by high salinity (420 g/l) and temperatures up to 127°C. It represents an extreme environment for microbial life and therefore the main focus is on hyperthermophilic, halophilic anaerobic microorganisms. In consequence of the injection of large amounts of CO2 in the course of a commercial EGR (Enhanced Gas Recovery), the environmental conditions (e.g. pH, temperature, pressure and solubility of minerals) for the autochthonous microorganisms will change. Genetic profiling of amplified 16S rRNA genes are applied for detecting structural changes in the community by using PCR- SSCP (PCR-Single-Strand-Conformation Polymorphism), DGGE (Denaturing Gradient Gel Electrophoresis) and 16S rRNA cloning. First results of the baseline survey indicate the presence of microorganisms similar to representatives from other deep environments. The sequence analyses revealed the presence of several H2-oxidising bacteria (Hydrogenophaga sp

  2. Chocolate: A Marvelous Natural Product of Chemistry

    NASA Astrophysics Data System (ADS)

    Tannenbaum, Ginger

    2004-08-01

    Chocolate is a natural product as ubiquitous as television. Of course, it is eaten, but it is also found in air fresheners, marking pens, flavoring in a multitude of products including soda pop, and as an aroma in "chocolate-dyed" T-shirts. However, most of us are completely unaware of the complex chemical reactions that take place to produce chocolate and the necessary technology that has evolved to produce chocolate and all its byproducts. Processing results in a mixture of many components, an interesting contrast to most of the simple, one-step reactions introduced at the high school level. This article is a survey of chocolate from tree to table. After a brief introduction to the history of chocolate and how and where it is grown, the manufacturing process is examined, and the chemistry is explored. A bit of the jargon used in the industry is mentioned. Cocoa butter is a significant ingredient in chocolate, and an investigation of it introduces triglycerides, fatty acids, polymorphic behavior, and molecular packing of the fats in chocolate and how they affect the tempering process. There is a brief discussion of chocolate's non-Newtonian behavior and the resulting challenges presented in the manufacturing process. See Featured Molecules Featured on the Cover

  3. Use of natural health products in children

    PubMed Central

    Pike, Andrea; Etchegary, Holly; Godwin, Marshall; McCrate, Farah; Crellin, John; Mathews, Maria; Law, Rebecca; Newhook, Leigh Anne; Kinden, Jody

    2013-01-01

    Abstract Objective To gain a more thorough understanding of why parents choose to give their children natural health products (NHPs), parents’ sources of information about NHPs, and the extent of disclosure and conversation with family doctors about the use of NHPs. Design Qualitative study. Setting Newfoundland and Labrador. Participants Parents of children who were using NHPs (N = 20). Methods Individual, semistructured interviews were carried out with parents to obtain a better understanding of the reasoning behind the use of NHPs. Key themes emerging from the qualitative data were identified according to a number of criteria, including relevance to the research objectives, frequency with which a theme was mentioned, relative importance of the themes based on the amount of text taken up to address an issue, and emphasis (eg, emphatic or emotional speech). Main findings The types of NHPs used by parents participating in this study varied, except for the use of multivitamins. In addition, use of the products themselves was variable and inconsistent. Parents reported few concerns about the use of NHPs. The most commonly reported source of information about NHPs was family and friends. Most participants had not spoken to their family doctors about the use of NHPs. Conclusion Participants considered NHPs to be “natural” and seemed to equate this assessment with safety. This might explain why these parents sought advice and information from family and friends rather than from their family doctors and often failed to disclose the use of NHPs to their children’s family doctors. PMID:23946044

  4. Natural Products as a Foundation for Drug Discovery

    PubMed Central

    Beutler, John A.

    2009-01-01

    Natural products have contributed to the development of many drugs for diverse indications. While most U.S. pharmaceutical companies have reduced or eliminated their in-house natural product groups, new paradigms and new enterprises have evolved to carry on a role for natural products in the pharmaceutical industry. Many of the reasons for the decline in popularity of natural products are being addressed by the development of new techniques for screening and production. This overview aims to inform pharmacologists of current strategies and techniques that make natural products a viable strategic choice for inclusion in drug discovery programs. PMID:20161632

  5. Glucose-based microbial production of the hormone melatonin in yeast Saccharomyces cerevisiae.

    PubMed

    Germann, Susanne M; Baallal Jacobsen, Simo A; Schneider, Konstantin; Harrison, Scott J; Jensen, Niels B; Chen, Xiao; Stahlhut, Steen G; Borodina, Irina; Luo, Hao; Zhu, Jiangfeng; Maury, Jérôme; Forster, Jochen

    2016-05-01

    Melatonin is a natural mammalian hormone that plays an important role in regulating the circadian cycle in humans. It is a clinically effective drug exhibiting positive effects as a sleep aid and a powerful antioxidant used as a dietary supplement. Commercial melatonin production is predominantly performed by complex chemical synthesis. In this study, we demonstrate microbial production of melatonin and related compounds, such as serotonin and N-acetylserotonin. We generated Saccharomyces cerevisiae strains that comprise heterologous genes encoding one or more variants of an L-tryptophan hydroxylase, a 5-hydroxy-L-tryptophan decarboxylase, a serotonin acetyltransferase, an acetylserotonin O-methyltransferase, and means for providing the cofactor tetrahydrobiopterin via heterologous biosynthesis and recycling pathways. We thereby achieved de novo melatonin biosynthesis from glucose. We furthermore accomplished increased product titers by altering expression levels of selected pathway enzymes and boosting co-factor supply. The final yeast strain produced melatonin at a titer of 14.50 ± 0.57 mg L(-1) in a 76h fermentation using simulated fed-batch medium with glucose as sole carbon source. Our study lays the basis for further developing a yeast cell factory for biological production of melatonin.

  6. 40 CFR 158.2120 - Microbial pesticides product analysis data requirements table.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Microbial pesticides product analysis data requirements table. 158.2120 Section 158.2120 Protection of Environment ENVIRONMENTAL PROTECTION... Product Chemistry and Composition 885.1100 Product Identity R MP EP -- 885.1200 Manufacturing process...

  7. A cobalt complex of a microbial arene oxidation product

    PubMed Central

    2011-01-01

    We report the first synthesis of a cobalt Cp diene complex wherein the diene is derived by microbial dearomatising dihydroxylation of an aromatic ring. The complex has been characterised crystallographically and its structure is compared to that of an uncomplexed diene precursor. PMID:22152033

  8. A microbial functional group-based module for simulating methane production and consumption: Application to an incubated permafrost soil

    NASA Astrophysics Data System (ADS)

    Xu, Xiaofeng; Elias, Dwayne A.; Graham, David E.; Phelps, Tommy J.; Carroll, Sue L.; Wullschleger, Stan D.; Thornton, Peter E.

    2015-07-01

    Accurately estimating methane (CH4) flux in terrestrial ecosystems is critically important for investigating and predicting biogeochemistry-climate feedbacks. Improved simulations of CH4 flux require explicit representations of the microbial processes that account for CH4 dynamics. A microbial functional group-based module was developed, building on the decomposition subroutine of the Community Land Model 4.5. This module considers four key mechanisms for CH4 production and consumption: methanogenesis from acetate or from single-carbon compounds and CH4 oxidation using molecular oxygen or other inorganic electron acceptors. Four microbial functional groups perform these processes: acetoclastic methanogens, hydrogenotrophic methanogens, aerobic methanotrophs, and anaerobic methanotrophs. This module was used to simulate dynamics of carbon dioxide (CO2) and CH4 concentrations from an incubation experiment with permafrost soils. The results show that the model captures the dynamics of CO2 and CH4 concentrations in microcosms with top soils, mineral layer soils, and permafrost soils under natural and saturated moisture conditions and three temperature conditions of -2°C, 3°C, and 5°C (R2 > 0.67 P < 0.001). The biases for modeled results are less than 30% across the soil samples and moisture and temperature conditions. Sensitivity analysis confirmed the importance of acetic acid's direct contribution as substrate and indirect effects through pH feedback on CO2 and CH4 production and consumption. This study suggests that representing the microbial mechanisms is critical for modeling CH4 production and consumption; it is urgent to incorporate microbial mechanisms into Earth system models for better predicting trace gas dynamics and the behavior of the climate system.

  9. Integrated hydrogen production process from cellulose by combining dark fermentation, microbial fuel cells, and a microbial electrolysis cell.

    PubMed

    Wang, Aijie; Sun, Dan; Cao, Guangli; Wang, Haoyu; Ren, Nanqi; Wu, Wei-Min; Logan, Bruce E

    2011-03-01

    Hydrogen gas production from cellulose was investigated using an integrated hydrogen production process consisting of a dark fermentation reactor and microbial fuel cells (MFCs) as power sources for a microbial electrolysis cell (MEC). Two MFCs (each 25 mL) connected in series to an MEC (72 mL) produced a maximum of 0.43 V using fermentation effluent as a feed, achieving a hydrogen production rate from the MEC of 0.48 m(3) H(2)/m(3)/d (based on the MEC volume), and a yield of 33.2 mmol H(2)/g COD removed in the MEC. The overall hydrogen production for the integrated system (fermentation, MFC and MEC) was increased by 41% compared with fermentation alone to 14.3 mmol H(2)/g cellulose, with a total hydrogen production rate of 0.24 m(3) H(2)/m(3)/d and an overall energy recovery efficiency of 23% (based on cellulose removed) without the need for any external electrical energy input.

  10. Use of natural health products in children

    PubMed Central

    Godwin, Marshall; Crellin, John; Mathews, Maria; Chowdhury, Nurun L.; Newhook, Leigh Anne; Pike, Andrea; McCrate, Farah; Law, Rebecca

    2013-01-01

    Abstract Objective To determine how common it is for parents to give natural health products (NHPs) to their children, which NHPs are being used, why they are being used, and parents’ assessments of the benefits and side effects of NHPs. Design Survey. Setting Newfoundland and Labrador. Participants Parents waiting in their family doctors’ offices. Main outcome measures Parent and child demographic characteristics; pediatric chronic medical conditions affecting the children; prescribed medications, over-the-counter medications, and NHPs used by the children; why the medications and NHPs were being used, the dose, and parents’ assessments of the effectiveness and side effects; and where parents had heard about the NHPs, whether they had told their physicians that the children were taking the products, and where they had obtained the products. Results A total of 202 (53.4%) of the 378 eligible adults who were approached completed the survey. This represented 333 children. Mean (SD) age of the children was 5.1 (3.3) years. Overall, 28.7% of parents reported using nonvitamin NHPs for their children. A total of 137 children (41.1%) had taken NHPs (including vitamins); 61.1% of the NHPs being used were vitamins. The remainder fell under teas (primarily chamomile and green teas), echinacea, fish or omega-3 oils, and a large category of “other” products. These NHPs were most commonly used to improve general health, improve immunity, and prevent colds and infections. Approximately half of the parents (51.7%) believed their children had benefited from taking NHPs, and 4.4% believed their children had experienced adverse side effects. Slightly less than half of the parents (45.0%) had informed their physicians that their children were taking NHPs. Conclusion Overall, 45.5% of parents attending physicians’ offices reported using NHPs in their children. If vitamins are not included in the definition of NHPs, this rate drops to 28.7%. Parents most commonly use NHPs

  11. The Rhizosphere Zone: A Hot Spot of Microbial Activity and Methylmercury Production in Saltmarsh Sediments of San Francisco Bay, California

    NASA Astrophysics Data System (ADS)

    Windham-Myers, L.; Marvin-Dipasquale, M.; Voytek, M.; Kirshtein, J.; Krabbenhoft, D. P.; Agee, J. L.; Cox, M.; Kakouros, E.; Collins, J. N.; Yee, D.

    2008-12-01

    Tidal marshes of varying hydrology and salinity have been shown to have high rates of microbial methylmercury (MeHg) production, especially the periodically flooded, higher elevations which are densely vegetated with shallowly rooted plants. The specific influence of emergent wetland plants and their active rhizosphere (root zone) on mercury (Hg) biogeochemistry, however, is poorly understood. Seasonal and spatial patterns of Hg biogeochemistry were examined in 2005 and 2006 at three marshes along a salinity gradient of the Petaluma River, in Northern San Francisco Bay, California. In addition, to directly examine the influence of rhizosphere activity on MeHg production, a suite of devegetation experiments was conducted in 2006 within each marsh using paired vegetated and devegetated plots in two marsh subhabitats: poorly- drained interior sites and well-drained "edge" sites near slough channels. Surface sediment (0-2cm) was sampled in both April and August from these plots, as well as from 1st and 3rd order slough channels that were naturally free of vegetation. Vegetated marsh sites produced 3- to19-fold more MeHg than did slough sites, and MeHg production rates were greater in marsh interior sites compared to more oxic marsh "edge" sites. Microbial biomass (ng DNA gdrysed) was greater in vegetated marsh settings, compared to slough channels, and increased significantly between April and August at all marsh sites. Despite this seasonal increase in microbial biomass, MeHg concentrations and production rates decreased from April to August in vegetated surface sediments. Microbial indicators of methylation also decreased from April to August, including rates of microbial sulfate reduction and the abundance of iron- and sulfate- reducing bacterial DNA. Results from the devegetated plots suggest that root exudation of fermentative labile carbon to surface soils is responsible for the higher microbial biomass, and the higher relative abundance of iron- and sulfate

  12. What heat is telling us about microbial conversions in nature and technology: from chip‐ to megacalorimetry

    PubMed Central

    Maskow, Thomas; Kemp, Richard; Buchholz, Friederike; Schubert, Torsten; Kiesel, Baerbel; Harms, Hauke

    2010-01-01

    Summary The exploitation of microorganisms in natural or technological systems calls for monitoring tools that reflect their metabolic activity in real time and, if necessary, are flexible enough for field application. The Gibbs energy dissipation of assimilated substrates or photons often in the form of heat is a general feature of life processes and thus, in principle, available to monitor and control microbial dynamics. Furthermore, the combination of measured heat fluxes with material fluxes allows the application of Hess' law to either prove expected growth stoichiometries and kinetics or identify and estimate unexpected side reactions. The combination of calorimetry with respirometry is theoretically suited for the quantification of the degree of coupling between catabolic and anabolic reactions. New calorimeter developments overcome the weaknesses of conventional devices, which hitherto limited the full exploitation of this powerful analytical tool. Calorimetric systems can be integrated easily into natural and technological systems of interest. They are potentially suited for high‐throughput measurements and are robust enough for field deployment. This review explains what information calorimetric analyses provide; it introduces newly emerging calorimetric techniques and it exemplifies the application of calorimetry in different fields of microbial research. PMID:21255327

  13. Investigation of Microbial Respirometry for Monitoring Natural Sulfide Abatement in Geothermal Cooling Tower Basins

    SciTech Connect

    Peter A. Pryfogle

    2005-09-01

    Geothermal plant operators are interested in investigating the ability of micro-organisms found in the cooling tower basin to metabolize and cycle sulfide to less toxic sulfur compounds. If the growth or activity of the organisms participating in sulfur-oxidation could be selectively enhanced, then hydrogen sulfide could be naturally abated in the cooling basin, substantially reducing the costs associated with the chemicals used for abatement. The use of respirometry has been proposed as a technique for monitoring the response of the microbial populations found in geothermal cooling towers to various conditions, including the addition of nutrients such as nitrogen and phosphorus. Respiro-metry is a manometric measurement of dissolved gases that are in equilibrium in a con-fined sample volume. Since microbes expire varying amounts of carbon dioxide or oxygen as they metabolize nutrients, this technique can be used to evaluate their activities in process streams. This report describes a series of experiments designed to determine the suitability of respirometry for tracking microbial activity for evaluating and enhancing natural abatement processes in geothermal cooling basins.

  14. Hydrogen production from switchgrass via an integrated pyrolysis-microbial electrolysis process.

    PubMed

    Lewis, A J; Ren, S; Ye, X; Kim, P; Labbe, N; Borole, A P

    2015-11-01

    A new approach to hydrogen production using an integrated pyrolysis-microbial electrolysis process is described. The aqueous stream generated during pyrolysis of switchgrass was used as a substrate for hydrogen production in a microbial electrolysis cell, achieving a maximum hydrogen production rate of 4.3 L H2/L anode-day at a loading of 10 g COD/L-anode-day. Hydrogen yields ranged from 50±3.2% to 76±0.5% while anode Coulombic efficiency ranged from 54±6.5% to 96±0.21%, respectively. Significant conversion of furfural, organic acids and phenolic molecules was observed under both batch and continuous conditions. The electrical and overall energy efficiency ranged from 149-175% and 48-63%, respectively. The results demonstrate the potential of the pyrolysis-microbial electrolysis process as a sustainable and efficient route for production of renewable hydrogen with significant implications for hydrocarbon production from biomass.

  15. Hydrogen production from switchgrass via a hybrid pyrolysis-microbial electrolysis process

    SciTech Connect

    Lewis, Alex J.; Ren, Shoujie; Ye, Philip; Kim, Pyoungchung; Labbe, Niki; Borole, Abhijeet P.

    2015-06-30

    A new approach to hydrogen production using a hybrid pyrolysis-microbial electrolysis process is described. The aqueous stream generated during pyrolysis of switchgrass was used as a substrate for hydrogen production in a microbial electrolysis cell, achieving a maximum hydrogen production rate of 4.3 L H2/L-day at a loading of 10 g COD/L-anode-day. Hydrogen yields ranged from 50 3.2% to76 0.5% while anode coulombic efficiency ranged from 54 6.5% to 96 0.21%, respectively. Significant conversion of furfural, organic acids and phenolic molecules was observed under both batch and continuous conditions. The electrical and overall energy efficiency ranged from 149-175% and 48-63%, respectively. The results demonstrate the potential of the pyrolysis-microbial electrolysis process as a sustainable and efficient route for production of renewable hydrogen with significant implications for hydrocarbon production from biomass.

  16. Effects of natural microbial preparations on the electrokinetic potential of bacterial cells and clay minerals.

    PubMed

    Kiremidjian, L; Stotzky, G

    1973-06-01

    A complex mixture of fermentation residues and eutrophication products used commercially as a soil amendment and in various phases of sewage treatment was effective in reducing the electrophoretic mobility of clay minerals (kaolinite and montmorillonite) and cells of Agrobacterium radiobacter. The active fraction(s), which is active at very low concentrations, appears to be a stable (to heat, dialysis, concentration, and storage), net negatively charged polymer which may have several positively charged sites. The material does not significantly alter the viscosity or surface tension of aqueous systems and is probably a microbial metabolite(s).

  17. Identification of natural inhibitors of Entamoeba histolytica cysteine synthase from microbial secondary metabolites

    PubMed Central

    Mori, Mihoko; Jeelani, Ghulam; Masuda, Yui; Sakai, Kazunari; Tsukui, Kumiko; Waluyo, Danang; Tarwadi; Watanabe, Yoshio; Nonaka, Kenichi; Matsumoto, Atsuko; Ōmura, Satoshi; Nozaki, Tomoyoshi; Shiomi, Kazuro

    2015-01-01

    Amebiasis is a common worldwide diarrheal disease, caused by the protozoan parasite, Entamoeba histolytica. Metronidazole has been a drug of choice against amebiasis for decades despite its known side effects and low efficacy against asymptomatic cyst carriers. E. histolytica is also capable of surviving sub-therapeutic levels of metronidazole in vitro. Novel drugs with different mode of action are therefore urgently needed. The sulfur assimilatory de novo L-cysteine biosynthetic pathway is essential for various cellular activities, including the proliferation and anti-oxidative defense of E. histolytica. Since the pathway, consisting of two reactions catalyzed by serine acetyltransferase (SAT) and cysteine synthase (CS, O-acetylserine sulfhydrylase), does not exist in humans, it is a rational drug target against amebiasis. To discover inhibitors against the CS of E. histolytica (EhCS), the compounds of Kitasato Natural Products Library were screened against two recombinant CS isozymes: EhCS1 and EhCS3. Nine compounds inhibited EhCS1 and EhCS3 with IC50 values of 0.31–490 μM. Of those, seven compounds share a naphthoquinone moiety, indicating the structural importance of the moiety for binding to the active site of EhCS1 and EhCS3. We further screened >9,000 microbial broths for CS inhibition and purified two compounds, xanthofulvin and exophillic acid from fungal broths. Xanthofulvin inhibited EhCS1 and EhCS3. Exophillic acid showed high selectivity against EhCS1, but exhibited no inhibition against EhCS3. In vitro anti-amebic activity of the 11 EhCS inhibitors was also examined. Deacetylkinamycin C and nanaomycin A showed more potent amebicidal activity with IC50 values of 18 and 0.8 μM, respectively, in the cysteine deprived conditions. The differential sensitivity of trophozoites against deacetylkinamycin C in the presence or absence of L-cysteine in the medium and the IC50 values against EhCS suggest the amebicidal effect of deacetylkinamycin C is due to

  18. Volatile organic compound production and consumption by microbial plankton communities on the NOAA WACS cruise

    NASA Astrophysics Data System (ADS)

    Giovannoni, S. J.; Halsey, K.; Thrash, J. C.; De Gouw, J. A.; Graus, M.

    2013-12-01

    Information about biological sources and sinks of volatile organic compounds (VOCs) in the ocean surface could result in a better understanding of the underlying causes of variation in air/sea VOC fluxes, and potentially could alter predictions about the impact of climate change on ocean surface ecology and air/sea interactions. The goal of this work was to measure rates of biological production, oxidation and assimilation of volatile organic compounds (VOCs) by microbial plankton communities along the WACS cruise transect from Boston to Bermuda in August 2013. Tangential flow filtration was used to concentrate microbial plankton communities for incubation in environmentally controlled dynamic stripping chambers under simulated ocean surface layer conditions. Gas streams exiting the chambers were monitored in real time with proton transfer reaction mass spectrometry (PTR-MS). In separate experiments aliquots of plankton suspensions were incubated with 14C-methanol, 14C-TMAO, and 14C-pyruvate, and the assimilation of 14C into biomass and the production of 14C-CO2 were measured. Results showed that the highly productive George's Bank plankton community has a high capacity for methanol and trimethylamine oxide (TMAO) oxidation. Biomass was estimated by counting cells. The rate of incorporation of methanol-carbon into biomass was only 21% of the rate of methanol oxidation to CO2. Similar results were observed for TMAO. These experiments also allowed estimates of kinetic constants for both compounds. The half-saturation constants (Ks) for methanol oxidation were similar in natural populations collected at George's Bank and the Sargasso Sea (12.8 and 9.9 μM, respectively). Interestingly, the Ks values for TMAO oxidation were an order of magnitude lower than for methanol in plankton communities sampled from both sites (0.5 and 0.3 μM, respectively). These results provide additional evidence that microbial plankton have a high capacity for oxidation of these low

  19. Microbial Reverse-Electrodialysis Electrolysis and Chemical-Production Cell for H2 Production and CO2 Sequestration

    PubMed Central

    2014-01-01

    Natural mineral carbonation can be accelerated using acid and alkali solutions to enhance atmospheric CO2 sequestration, but the production of these solutions needs to be carbon-neutral. A microbial reverse-electrodialysis electrolysis and chemical-production cell (MRECC) was developed to produce these solutions and H2 gas using only renewable energy sources (organic matter and salinity gradient). Using acetate (0.82 g/L) as a fuel for microorganisms to generate electricity in the anode chamber (liquid volume of 28 mL), 0.45 mmol of acid and 1.09 mmol of alkali were produced at production efficiencies of 35% and 86%, respectively, along with 10 mL of H2 gas. Serpentine dissolution was enhanced 17–87-fold using the acid solution, with approximately 9 mL of CO2 absorbed and 4 mg of CO2 fixed as magnesium or calcium carbonates. The operational costs, based on mineral digging and grinding, and water pumping, were estimated to be only $25/metric ton of CO2 fixed as insoluble carbonates. Considering the additional economic benefits of H2 generation and possible wastewater treatment, this method may be a cost-effective and environmentally friendly method for CO2 sequestration. PMID:24741666

  20. Distribution of Toxin Genes and Enterotoxins in Bacillus thuringiensis Isolated from Microbial Insecticide Products.

    PubMed

    Cho, Seung-Hak; Kang, Suk-Ho; Lee, Yea-Eun; Kim, Sung-Jo; Yoo, Young-Bin; Bak, Yeong-Seok; Kim, Jung-Beom

    2015-12-28

    Bacillus thuringiensis microbial insecticide products have been applied worldwide. Although a few cases of B. thuringiensis foodborne illness have been reported, little is known about the toxigenic properties of B. thuringiensis isolates. The aims of this study were to estimate the pathogenic potential of B. thuringiensis selected from microbial insecticide products, based on its possession of toxin genes and production of enterotoxins. Fifty-two B. thuringiensis strains selected from four kinds of microbial insecticide products were analyzed. PCR assay for detection of toxin genes and immunoassay for detection of enterotoxins were performed. The hemolysin BL complex as a major enterotoxin was produced by 17 (32.7%), whereas the nonhemolytic enterotoxin complex was detected in 1 (1.9%) of 52 B. thuringiensis strains. However, cytK, entFM, and ces genes were not detected in any of the tested B. thuringiensis strains. The potential risk of food poisoning by B. thuringiensis along with concerns over B. thuringiensis microbial insecticide products has gained attention recently. Thus, microbial insecticide products based on B. thuringiensis should be carefully controlled.

  1. Microbial oils as food additives: recent approaches for improving microbial oil production and its polyunsaturated fatty acid content.

    PubMed

    Bellou, Stamatia; Triantaphyllidou, Irene-Eva; Aggeli, Dimitra; Elazzazy, Ahmed Mohammed; Baeshen, Mohammed Nabih; Aggelis, George

    2016-02-01

    In this short review, we summarize the latest research in the production of polyunsaturated microbial oils that are of interest in food technology. The current research targets the productivity of oleaginous microorganisms, as well as the biosynthesis of particular polyunsaturated fatty acids (PUFAs). The most important efforts target the efficiency of the oleaginous machinery, via overexpression of key-enzymes involved in lipid biosynthesis, as well as the minimization of lipid degradation, by repressing genes involved in the β-oxidation pathway. The production of specific PUFAs is approached by homologous or heterologous expression of specific desaturases and elongases involved in PUFA biosynthesis in oleaginous microorganisms. New perspectives, such as the production of triacylglycerols of specific structure and the employment of adaptive experimental evolution for creating robust oleaginous strains able to produce PUFAs are also discussed.

  2. Oxygen-containing fragments in natural products.

    PubMed

    Titarenko, Zoya; Vasilevich, Natalya; Zernov, Vladimir; Kirpichenok, Michael; Genis, Dmitry

    2013-02-01

    An analysis of the chemical environment of the oxygen atoms in the DNP database compared to the CMC and SCD databases was performed. Some structural clusters were identified which are predominant among the natural products and can be considered as distinctive features of NPs. Fifty-three oxygen-containing structural fragments that are distinctive for the DNP (distinctive set of fragments DSF) in comparison with the SCD have been identified. A new descriptor Mc was introduced for describing the ratio of atoms involved in the DSF to the total number of heavy atoms. A significant difference in the Mc values among the reference databases allowed the use of a specific cluster of the DSF as a tool for performing similarity searches for oxygen-containing NP molecules, or for evaluation or comparison of databases according to their NP-likeness. An example illustrating that the suggested approach could allow not only estimating the NP-likeness, but also serve as a tool for designing new NP-like compounds is provided. The suggested approach for NP-likeness evaluation moves away from the traditional ideas of scaffolds, cycles, linkers and substituents.

  3. Natural products and combinatorial chemistry: back to the future.

    PubMed

    Ortholand, Jean-Yves; Ganesan, A

    2004-06-01

    The introduction of high-throughput synthesis and combinatorial chemistry has precipitated a global decline in the screening of natural products by the pharmaceutical industry. Some companies terminated their natural products program, despite the unproven success of the new technologies. This was a premature decision, as natural products have a long history of providing important medicinal agents. Furthermore, they occupy a complementary region of chemical space compared with the typical synthetic compound library. For these reasons, the interest in natural products has been rekindled. Various approaches have evolved that combine the power of natural products and organic chemistry, ranging from the combinatorial total synthesis of analogues to the exploration of natural product scaffolds and the design of completely unnatural molecules that resemble natural products in their molecular characteristics.

  4. A Historical Overview of Natural Products in Drug Discovery

    PubMed Central

    Dias, Daniel A.; Urban, Sylvia; Roessner, Ute

    2012-01-01

    Historically, natural products have been used since ancient times and in folklore for the treatment of many diseases and illnesses. Classical natural product chemistry methodologies enabled a vast array of bioactive secondary metabolites from terrestrial and marine sources to be discovered. Many of these natural products have gone on to become current drug candidates. This brief review aims to highlight historically significant bioactive marine and terrestrial natural products, their use in folklore and dereplication techniques to rapidly facilitate their discovery. Furthermore a discussion of how natural product chemistry has resulted in the identification of many drug candidates; the application of advanced hyphenated spectroscopic techniques to aid in their discovery, the future of natural product chemistry and finally adopting metabolomic profiling and dereplication approaches for the comprehensive study of natural product extracts will be discussed. PMID:24957513

  5. [Electricity production from surplus sludge using microbial fuel cells].

    PubMed

    Jia, Bin; Liu, Zhi-Hua; Li, Xiao-Ming; Yang, Yong-Lin; Yang, Qi; Zeng, Guang-Ming; Liu, Yi-Lin; Liu, Qian-Qian; Zheng, Shi-Wen

    2009-04-15

    A single-chamber and membrane-less microbial fuel cells were successfully started up using anaerobic sludge as inoculums without any chemical substance for 20 d. The electricity generation of the microbial fuel cell using surplus sludge as fuel and the change of substrate were investigated. The results showed that the obtained maximum voltage and power density were 495 mV and 44 mW x m(-2) (fixed 1,000 Omega), and the internal resistance was about 300 Omega during steady state. In a cycle, the removal efficiency of SS and VSS were 27.3% and 28.7%, pH was 6.5-8.0. In addition, the COD increased from 617 mg x L(-1) to 1,150 mg x L(-1) and decreased afterwards with time. The change of glucose was similar to that of COD, glucose increased from 47 mg x L(-1) to 60 mg x L(-1) and decreased afterwards with time. Consequently, the microbial fuel cell can transform chemical energy of surplus sludge into the cleanest electrical energy, and it provides a new way of sludge recycling.

  6. Examining the Fish Microbiome: Vertebrate-Derived Bacteria as an Environmental Niche for the Discovery of Unique Marine Natural Products

    PubMed Central

    Sanchez, Laura M.; Wong, Weng Ruh; Riener, Romina M.; Schulze, Christopher J.; Linington, Roger G.

    2012-01-01

    Historically, marine invertebrates have been a prolific source of unique natural products, with a diverse array of biological activities. Recent studies of invertebrate-associated microbial communities are revealing microorganisms as the true producers of many of these compounds. Inspired by the human microbiome project, which has highlighted the human intestine as a unique microenvironment in terms of microbial diversity, we elected to examine the bacterial communities of fish intestines (which we have termed the fish microbiome) as a new source of microbial and biosynthetic diversity for natural products discovery. To test the hypothesis that the fish microbiome contains microorganisms with unique capacity for biosynthesizing natural products, we examined six species of fish through a combination of dissection and culture-dependent evaluation of intestinal microbial communities. Using isolation media designed to enrich for marine Actinobacteria, we have found three main clades that show taxonomic divergence from known strains, several of which are previously uncultured. Extracts from these strains exhibit a wide range of activities against both Gram-positive and Gram-negative human pathogens, as well as several fish pathogens. Exploration of one of these extracts has identified the novel bioactive lipid sebastenoic acid as an anti-microbial agent, with activity against Staphylococcus aureus, Bacillus subtilis, Enterococcus faecium, and Vibrio mimicus. PMID:22574119

  7. A new approach to drug discovery: high-throughput screening of microbial natural extracts against Aspergillus fumigatus using resazurin.

    PubMed

    Monteiro, Maria Cândida; de la Cruz, Mercedes; Cantizani, Juan; Moreno, Catalina; Tormo, José R; Mellado, Emilia; De Lucas, J Ramón; Asensio, Francisco; Valiante, Vito; Brakhage, Axel A; Latgé, Jean-Paul; Genilloud, Olga; Vicente, Francisca

    2012-04-01

    Natural products are an inexhaustible source for drug discovery. However, the validation and selection of primary screening assays are vital to guarantee a selection of extracts or molecules with relevant pharmacological action and worthy of following up. The assay must be rapid, simple, easy to implement, and produce quick results and preferably at a low cost. In this work, we developed and validated a colorimetric microtiter assay using the resazurin viability dye. The parameters of the resazurin method for high-throughput screening (HTS) using natural extracts against Aspergillus fumigatus were optimized and set up. The extracts plus RPMI-1640 modified medium containing the spores and 0.002% resazurin were added per well. The fluorescence was read after 24 to 30 h of incubation. The resazurin proved to be as suitable as Alamar Blue for determining the minimal inhibitory concentration of different antifungals against A. fumigatus and effective to analyze fungicidal and fungistatic compounds. An HTS of 12 000 microbial extracts was carried out against two A. fumigatus strains, and 2.7% of the extracts displayed antifungal activity. Our group has been the first to use this methodology for screening a collection of natural extracts to identify compounds with antifungal activity against the medically important human pathogen A. fumigatus.

  8. Microbial production of specialty organic acids from renewable and waste materials.

    PubMed

    Alonso, Saúl; Rendueles, Manuel; Díaz, Mario

    2015-01-01

    Microbial production of organic acids has become a fast-moving field due to the increasing role of these compounds as platform chemicals. In recent years, the portfolio of specialty fermentation-derived carboxylic acids has increased considerably, including the production of glyceric, glucaric, succinic, butyric, xylonic, fumaric, malic, itaconic, lactobionic, propionic and adipic acid through innovative fermentation strategies. This review summarizes recent trends in the use of novel microbial platforms as well as renewable and waste materials for efficient and cost-effective bio-based production of emerging high-value organic acids. Advances in the development of robust and efficient microbial bioprocesses for producing carboxylic acids from low-cost feedstocks are also discussed. The industrial market scenario is also reviewed, including the latest information on the stage of development for producing these emerging bio-products via large-scale fermentation.

  9. Effect of pretreatment by a microbial consortium on methane production of waste paper and cardboard.

    PubMed

    Yuan, Xufeng; Cao, Yanzhuan; Li, Jiajia; Wen, Boting; Zhu, Wanbin; Wang, Xiaofen; Cui, Zongjun

    2012-08-01

    A microbial consortium MC1 was used to pretreat filter paper, office paper, newspaper, and cardboard to enhance methane production. The results of pretreatment indicated that sCOD of hydrolysates of the four substrates increased significantly in the early stage, and peaked on day 7. During pretreatment, ethanol, acetic acid, propionic acid, butyric acid, and glycerol were the predominant volatile organic products in hydrolysates. MC1 had strong degradation ability on the four substrates, and the weight loss of filter paper, office paper, newspaper, and cardboard reached 78.3%, 80.5%, 39.7%, and 49.7%, respectively. The results of anaerobic digestion showed that methane production yields and rates of the four substrates significantly increased after pretreatment. This study is the first attempt to explore the microbial pretreatment method for anaerobic digestion of waste paper and cardboard. Microbial consortium pretreatment could be an effective method for enhancing methane production of waste paper and cardboard into bioenergy.

  10. Fluorescently Labeled Virus Probes Show that Natural Virus Populations Can Control the Structure of Marine Microbial Communities.

    PubMed

    Hennes, K P; Suttle, C A; Chan, A M

    1995-10-01

    Fluorescently stained viruses were used as probes to label, identify, and enumerate specific strains of bacteria and cyanobacteria in mixed microbial assemblages. Several marine virus isolates were fluorescently stained with YOYO-1 or POPO-1 (Molecular Probes, Inc.) and added to seawater samples that contained natural microbial communities. Cells to which the stained viruses adsorbed were easily distinguished from nonhost cells; typically, there was undetectable binding of stained viruses to natural microbial assemblages containing >10(sup6) bacteria ml(sup-1) but to which host cells were not added. Host cells that were added to natural seawater were quantified with 99% (plusmn) 2% (mean (plusmn) range) efficiency with fluorescently labeled virus probes (FLVPs). A marine bacterial isolate (strain PWH3a), tentatively identified as Vibrio natriegens, was introduced into natural microbial communities that were either supplemented with nutrients or untreated, and changes in the abundance of the isolate were monitored with FLVPs. Simultaneously, the concentrations of viruses that infected strain PWH3a were monitored by plaque assay. Following the addition of PWH3a, the concentration of viruses infecting this strain increased from undetectable levels (<1 ml(sup-1)) to 2.9 x 10(sup7) and 8.3 x 10(sup8) ml(sup-1) for the untreated and nutrient-enriched samples, respectively. The increase in viruses was associated with a collapse in populations of strain PWH3a from ca. 30 to 2% and 43 to 0.01% of the microbial communities in untreated and nutrient-enriched samples, respectively. These results clearly demonstrate that FLVPs can be used to identify and quantify specific groups of bacteria in mixed microbial communities. The data show as well that viruses which are present at low abundances in natural aquatic viral communities can control microbial community structure.

  11. Fluorescently Labeled Virus Probes Show that Natural Virus Populations Can Control the Structure of Marine Microbial Communities

    PubMed Central

    Hennes, K. P.; Suttle, C. A.; Chan, A. M.

    1995-01-01

    Fluorescently stained viruses were used as probes to label, identify, and enumerate specific strains of bacteria and cyanobacteria in mixed microbial assemblages. Several marine virus isolates were fluorescently stained with YOYO-1 or POPO-1 (Molecular Probes, Inc.) and added to seawater samples that contained natural microbial communities. Cells to which the stained viruses adsorbed were easily distinguished from nonhost cells; typically, there was undetectable binding of stained viruses to natural microbial assemblages containing >10(sup6) bacteria ml(sup-1) but to which host cells were not added. Host cells that were added to natural seawater were quantified with 99% (plusmn) 2% (mean (plusmn) range) efficiency with fluorescently labeled virus probes (FLVPs). A marine bacterial isolate (strain PWH3a), tentatively identified as Vibrio natriegens, was introduced into natural microbial communities that were either supplemented with nutrients or untreated, and changes in the abundance of the isolate were monitored with FLVPs. Simultaneously, the concentrations of viruses that infected strain PWH3a were monitored by plaque assay. Following the addition of PWH3a, the concentration of viruses infecting this strain increased from undetectable levels (<1 ml(sup-1)) to 2.9 x 10(sup7) and 8.3 x 10(sup8) ml(sup-1) for the untreated and nutrient-enriched samples, respectively. The increase in viruses was associated with a collapse in populations of strain PWH3a from ca. 30 to 2% and 43 to 0.01% of the microbial communities in untreated and nutrient-enriched samples, respectively. These results clearly demonstrate that FLVPs can be used to identify and quantify specific groups of bacteria in mixed microbial communities. The data show as well that viruses which are present at low abundances in natural aquatic viral communities can control microbial community structure. PMID:16535146

  12. Exploring anti-TB leads from natural products library originated from marine microbes and medicinal plants.

    PubMed

    Liu, Xueting; Chen, Caixia; He, Wenni; Huang, Pei; Liu, Miaomiao; Wang, Qian; Guo, Hui; Bolla, Krishna; Lu, Yan; Song, Fuhang; Dai, Huanqin; Liu, Mei; Zhang, Lixin

    2012-10-01

    Multidrug-resistant tuberculosis (MDR-TB) and TB-HIV co-infection have become a great threat to global health. However, the last truly novel drug that was approved for the treatment of TB was discovered 40 years ago. The search for new effective drugs against TB has never been more intensive. Natural products derived from microbes and medicinal plants have been an important source of TB therapeutics. Recent advances have been made to accelerate the discovery rate of novel TB drugs including diversifying strategies for environmental strains, high-throughput screening (HTS) assays, and chemical diversity. This review will discuss the challenges of finding novel natural products with anti-TB activity from marine microbes and plant medicines, including biodiversity- and taxonomy-guided microbial natural products library construction, target- and cell-based HTS, and bioassay-directed isolation of anti-TB substances from traditional medicines.

  13. Construction of a 3D-shaped, natural product like fragment library by fragmentation and diversification of natural products.

    PubMed

    Prescher, Horst; Koch, Guido; Schuhmann, Tim; Ertl, Peter; Bussenault, Alex; Glick, Meir; Dix, Ina; Petersen, Frank; Lizos, Dimitrios E

    2017-02-01

    A fragment library consisting of 3D-shaped, natural product-like fragments was assembled. Library construction was mainly performed by natural product degradation and natural product diversification reactions and was complemented by the identification of 3D-shaped, natural product like fragments available from commercial sources. In addition, during the course of these studies, novel rearrangements were discovered for Massarigenin C and Cytochalasin E. The obtained fragment library has an excellent 3D-shape and natural product likeness, covering a novel, unexplored and underrepresented chemical space in fragment based drug discovery (FBDD).

  14. Microbial Diversity-Based Novel Crop Protection Products

    SciTech Connect

    Pioneer Hi-Bred International Inc.; DuPont Experimental Station; Yalpani, Ronald Flannagan, Rafael Herrmann, James Presnail, Tamas Torok, and Nasser; Herrmann, Rafael; Presnail, James; Torok, Tamas; Yalpani, Nasser

    2007-05-10

    Extremophilic microorganisms are adapted to survive in ecological niches with high temperatures, extremes of pH, high salt concentrations, high pressure, radiation, etc. Extremophiles produce unique biocatalysts and natural products that function under extreme conditions comparab le to those prevailing in various industrial processes. Therefore, there is burgeoning interest in bioprospecting for extremophiles with potential immediate use in agriculture, the food, chemical, and pharm aceutical industries, and environmental biotechnology. Over the years, several thousand extremophilic bacteria, archaea, and filamentous fungi were collected at extreme environmental sites in the USA, the Chernobyl Exclusion Zone surrounding the faeild nuclear power plant in Ukraine, in and around Lake Baikal in Siberia, and at geothermal sites on the Kamchatka peninsula in Russia. These organisms were cultured under proprietary conditions, and the cell- free supernatants were screened for biological activities against plant pathogenic fungi and major crop damaging insects. Promising peptide lead molecules were isolated, characterized, and sequenced. Relatively high hit rates characterized the tested fermentation broths. Of the 26,000 samples screened, over thousand contained biological activity of interest. A fair number of microorganisms expressed broad- spectrum antifungal or insecticidal activity. Two- dozen broadly antifungal peptides (AFPs) are alr eady patent protected, and many more tens are under further investigation. Tapping the gene pool of extremophilic microorganisms to provide novel ways of crop protection proved a successful strategy.

  15. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

    PubMed Central

    Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M.; Wells, George F.

    2012-01-01

    Nitrous oxide (N2O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH) or the reduction of nitrite (NO−2) to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO−2 to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO−2, NH2OH, and nitroxyl (HNO). Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build

  16. Microbial screening and analytical methods for the production of polyol oils from soybean oil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study is to develop a new useful method including microbial screening and product identification for a bioprocess to produce polyol oils from soybean oil. Methods for separating of product polyol oils from soybean oil substrate and free fatty acid byproducts using HPLC and TLC...

  17. Hit identification of IKKβ natural product inhibitor

    PubMed Central

    2013-01-01

    Background The nuclear factor-κB (NF-κB) proteins are a small group of heterodimeric transcription factors that play an important role in regulating the inflammatory, immune, and apoptotic responses. NF-κB activity is suppressed by association with the inhibitor IκB. Aberrant NF-κB signaling activity has been associated with the development of cancer, chronic inflammatory diseases and auto-immune diseases. The IKK protein complex is comprised of IKKα, IKKβ and NEMO subunits, with IKKβ thought to play the dominant role in modulating NF-κB activity. Therefore, the discovery of new IKKβ inhibitors may offer new therapeutic options for the treatment of cancer and inflammatory diseases. Results A structure-based molecular docking approach has been employed to discover novel IKKβ inhibitors from a natural product library of over 90,000 compounds. Preliminary screening of the 12 highest-scoring compounds using a luciferase reporter assay identified 4 promising candidates for further biological study. Among these, the benzoic acid derivative (1) showed the most promising activity at inhibiting IKKβ phosphorylation and TNF-α-induced NF-κB signaling in vitro. Conclusions In this study, we have successfully identified a benzoic acid derivative (1) as a novel IKKβ inhibitor via high-throughput molecular docking. Compound 1 was able to inhibit IKKβ phosphorylation activity in vitro, and block IκBα protein degradation and subsequent NF-κB activation in human cells. Further in silico optimization of the compound is currently being conducted in order to generate more potent analogues for biological tests. PMID:23294515

  18. Quantitative Microbial Risk Assessment for Clostridium perfringens in Natural and Processed Cheeses

    PubMed Central

    Lee, Heeyoung; Lee, Soomin; Kim, Sejeong; Lee, Jeeyeon; Ha, Jimyeong; Yoon, Yohan

    2016-01-01

    This study evaluated the risk of Clostridium perfringens (C. perfringens) foodborne illness from natural and processed cheeses. Microbial risk assessment in this study was conducted according to four steps: hazard identification, hazard characterization, exposure assessment, and risk characterization. The hazard identification of C. perfringens on cheese was identified through literature, and dose response models were utilized for hazard characterization of the pathogen. For exposure assessment, the prevalence of C. perfringens, storage temperatures, storage time, and annual amounts of cheese consumption were surveyed. Eventually, a simulation model was developed using the collected data and the simulation result was used to estimate the probability of C. perfringens foodborne illness by cheese consumption with @RISK. C. perfringens was determined to be low risk on cheese based on hazard identification, and the exponential model (r = 1.82×10−11) was deemed appropriate for hazard characterization. Annual amounts of natural and processed cheese consumption were 12.40±19.43 g and 19.46±14.39 g, respectively. Since the contamination levels of C. perfringens on natural (0.30 Log CFU/g) and processed cheeses (0.45 Log CFU/g) were below the detection limit, the initial contamination levels of natural and processed cheeses were estimated by beta distribution (α1 = 1, α2 = 91; α1 = 1, α2 = 309)×uniform distribution (a = 0, b = 2; a = 0, b = 2.8) to be −2.35 and −2.73 Log CFU/g, respectively. Moreover, no growth of C. perfringens was observed for exposure assessment to simulated conditions of distribution and storage. These data were used for risk characterization by a simulation model, and the mean values of the probability of C. perfringens foodborne illness by cheese consumption per person per day for natural and processed cheeses were 9.57×10−14 and 3.58×10−14, respectively. These results indicate that probability of C. perfringens foodborne illness

  19. Quantitative Microbial Risk Assessment for Clostridium perfringens in Natural and Processed Cheeses.

    PubMed

    Lee, Heeyoung; Lee, Soomin; Kim, Sejeong; Lee, Jeeyeon; Ha, Jimyeong; Yoon, Yohan

    2016-08-01

    This study evaluated the risk of Clostridium perfringens (C. perfringens) foodborne illness from natural and processed cheeses. Microbial risk assessment in this study was conducted according to four steps: hazard identification, hazard characterization, exposure assessment, and risk characterization. The hazard identification of C. perfringens on cheese was identified through literature, and dose response models were utilized for hazard characterization of the pathogen. For exposure assessment, the prevalence of C. perfringens, storage temperatures, storage time, and annual amounts of cheese consumption were surveyed. Eventually, a simulation model was developed using the collected data and the simulation result was used to estimate the probability of C. perfringens foodborne illness by cheese consumption with @RISK. C. perfringens was determined to be low risk on cheese based on hazard identification, and the exponential model (r = 1.82×10(-11)) was deemed appropriate for hazard characterization. Annual amounts of natural and processed cheese consumption were 12.40±19.43 g and 19.46±14.39 g, respectively. Since the contamination levels of C. perfringens on natural (0.30 Log CFU/g) and processed cheeses (0.45 Log CFU/g) were below the detection limit, the initial contamination levels of natural and processed cheeses were estimated by beta distribution (α 1 = 1, α 2 = 91; α 1 = 1, α 2 = 309)×uniform distribution (a = 0, b = 2; a = 0, b = 2.8) to be -2.35 and -2.73 Log CFU/g, respectively. Moreover, no growth of C. perfringens was observed for exposure assessment to simulated conditions of distribution and storage. These data were used for risk characterization by a simulation model, and the mean values of the probability of C. perfringens foodborne illness by cheese consumption per person per day for natural and processed cheeses were 9.57×10(-14) and 3.58×10(-14), respectively. These results indicate that probability of C. perfringens foodborne illness

  20. Natural product proteomining, a quantitative proteomics platform, allows rapid discovery of biosynthetic gene clusters for different classes of natural products.

    PubMed

    Gubbens, Jacob; Zhu, Hua; Girard, Geneviève; Song, Lijiang; Florea, Bogdan I; Aston, Philip; Ichinose, Koji; Filippov, Dmitri V; Choi, Young H; Overkleeft, Herman S; Challis, Gregory L; van Wezel, Gilles P

    2014-06-19

    Information on gene clusters for natural product biosynthesis is accumulating rapidly because of the current boom of available genome sequencing data. However, linking a natural product to a specific gene cluster remains challenging. Here, we present a widely applicable strategy for the identification of gene clusters for specific natural products, which we name natural product proteomining. The method is based on using fluctuating growth conditions that ensure differential biosynthesis of the bioactivity of interest. Subsequent combination of metabolomics and quantitative proteomics establishes correlations between abundance of natural products and concomitant changes in the protein pool, which allows identification of the relevant biosynthetic gene cluster. We used this approach to elucidate gene clusters for different natural products in Bacillus and Streptomyces, including a novel juglomycin-type antibiotic. Natural product proteomining does not require prior knowledge of the gene cluster or secondary metabolite and therefore represents a general strategy for identification of all types of gene clusters.

  1. Role of natural product diversity in chemical biology.

    PubMed

    Hong, Jiyong

    2011-06-01

    Through the natural selection process, natural products possess a unique and vast chemical diversity and have been evolved for optimal interactions with biological macromolecules. Owing to their diversity, target affinity, and specificity, natural products have demonstrated enormous potential as modulators of biomolecular function, been an essential source for drug discovery, and provided design principles for combinatorial library development.

  2. Development of the microbial electrolysis desalination and chemical-production cell for desalination as well as acid and alkali productions.

    PubMed

    Chen, Shanshan; Liu, Guangli; Zhang, Renduo; Qin, Bangyu; Luo, Yong

    2012-02-21

    By combining the microbial electrolysis cell and the microbial desalination cell, the microbial electrolysis desalination cell (MEDC) becomes a novel device to desalinate salty water. However, several factors, such as sharp pH decrease and Cl(-) accumulation in the anode chamber, limit the MEDC development. In this study, a microbial electrolysis desalination and chemical-production cell (MEDCC) was developed with four chambers using a bipolar membrane. Results showed that the pH in the anode chamber of the MEDCC always remained near 7.0, which greatly enhanced the microbial activities in the cell. With applied voltages of 0.3-1.0 V, 62%-97% of Coulombic efficiencies were achieved from the MEDCC, which were 1.5-2.0 times of those from the MEDC. With 10 mL of 10 g/L NaCl in the desalination chamber, desalination rates of the MEDCC reached 46%-86% within 18 h. Another unique feature of the MEDCC was the simultaneous production of HCl and NaOH in the cell. With 1.0 V applied voltage, the pH values at 18 h in the acid-production chamber and cathode chamber were 0.68 and 12.9, respectively. With the MEDCC, the problem with large pH changes in the anode chamber was resolved, and products of the acid and alkali were obtained.

  3. Microbial electrolysis desalination and chemical-production cell for CO2 sequestration.

    PubMed

    Zhu, Xiuping; Logan, Bruce E

    2014-05-01

    Mineral carbonation can be used for CO2 sequestration, but the reaction rate is slow. In order to accelerate mineral carbonation, acid generated in a microbial electrolysis desalination and chemical-production cell (MEDCC) was examined to dissolve natural minerals rich in magnesium/calcium silicates (serpentine), and the alkali generated by the same process was used to absorb CO2 and precipitate magnesium/calcium carbonates. The concentrations of Mg(2+) and Ca(2+) dissolved from serpentine increased 20 and 145 times by using the acid solution. Under optimal conditions, 24 mg of CO2 was absorbed into the alkaline solution and 13 mg of CO2 was precipitated as magnesium/calcium carbonates over a fed-batch cycle (24h). Additionally, the MEDCC removed 94% of the COD (initially 822 mg/L) and achieved 22% desalination (initially 35 g/L NaCl). These results demonstrate the viability of this process for effective CO2 sequestration using renewable organic matter and natural minerals.

  4. Use of natural compounds to improve the microbial stability of Amaranth-based homemade fresh pasta.

    PubMed

    Del Nobile, M A; Di Benedetto, N; Suriano, N; Conte, A; Lamacchia, C; Corbo, M R; Sinigaglia, M

    2009-04-01

    A study on the use of natural antimicrobial compounds to improve the microbiological stability of refrigerated amaranth-based homemade fresh pasta is presented in this work. In particular, the antimicrobial activity of thymol, lemon extract, chitosan and grapefruit seed extract (GFSE) has been tested against mesophilic and psychrotrophic bacteria, total coliforms, Staphylococcus spp., yeasts and moulds. A sensory analysis on both fresh and cooked pasta was also run. Results suggest that chitosan and GFSE strongly increase the microbial acceptability limit of the investigated spoilage microorganisms, being the former the most effective. Thymol efficiently reduces the growth of mesophilic bacteria, psychrotrophic bacteria and Staphylococcus spp., whereas it does not affect, substantially, the growth cycle of total coliforms. Lemon extract is the less effective in preventing microbial growth. In fact, it is able to delay only total mesophilic and psychrotrophic bacterial evolution. From a sensorial point of view no significant differences were recorded between the control samples and all the types of loaded amaranth-based pasta.

  5. Natural Product Biosynthetic Diversity and Comparative Genomics of the Cyanobacteria.

    PubMed

    Dittmann, Elke; Gugger, Muriel; Sivonen, Kaarina; Fewer, David P

    2015-10-01

    Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with intricate chemical structures and potent biological activities. The bulk of these natural products are known from just a handful of genera. Recent efforts have elucidated the mechanisms underpinning the biosynthesis of a diverse array of natural products from cyanobacteria. Many of the biosynthetic mechanisms are unique to cyanobacteria or rarely described from other organisms. Advances in genome sequence technology have precipitated a deluge of genome sequences for cyanobacteria. This makes it possible to link known natural products to biosynthetic gene clusters but also accelerates the discovery of new natural products through genome mining. These studies demonstrate that cyanobacteria encode a huge variety of cryptic gene clusters for the production of natural products, and the known chemical diversity is likely to be just a fraction of the true biosynthetic capabilities of this fascinating and ancient group of organisms.

  6. Microbial lipids from renewable resources: production and characterization.

    PubMed

    Subramaniam, Ramalingam; Dufreche, Stephen; Zappi, Mark; Bajpai, Rakesh

    2010-12-01

    A number of microorganisms belonging to the genera of algae, yeast, bacteria, and fungi have ability to accumulate neutral lipids under specific cultivation conditions. The microbial lipids contain high fractions of polyunsaturated fatty acids and have the potential to serve as a source of significant quantities of transportation fuels. This paper reviews the current state of the art of this field. It summarizes the various microorganism used, feed stocks available, environmental factors that influence growth of cells and accumulation of lipids, major fatty acid composition of lipids, and the technology.

  7. Synthetic biology for microbial production of lipid-based biofuels.

    PubMed

    d'Espaux, Leo; Mendez-Perez, Daniel; Li, Rachel; Keasling, Jay D

    2015-12-01

    The risks of maintaining current CO2 emission trends have led to interest in producing biofuels using engineered microbes. Microbial biofuels reduce emissions because CO2 produced by fuel combustion is offset by CO2 captured by growing biomass, which is later used as feedstock for biofuel fermentation. Hydrocarbons found in petroleum fuels share striking similarity with biological lipids. Here we review synthetic metabolic pathways based on fatty acid and isoprenoid metabolism to produce alkanes and other molecules suitable as biofuels. We further discuss engineering strategies to optimize engineered biosynthetic routes, as well as the potential of synthetic biology for sustainable manufacturing.

  8. Natural products as a foundation for drug discovery.

    PubMed

    Beutler, John A

    2009-09-01

    Natural products have provided chemical leads for the development of many drugs for diverse indications. While most U.S. pharmaceutical firms have reduced or eliminated their in-house natural product groups, there is a renewed interest in this source of new chemical entities. Many of the reasons for the past decline in popularity of natural products are being addressed by the development of new techniques for screening and production. The aim of this unit is to review current strategies and techniques that increase the value of natural products as a source for novel drug candidates.

  9. Removal of soluble microbial products as the precursors of disinfection by-products in drinking water supplies.

    PubMed

    Liu, Jin-Lin; Li, Xiao-Yan

    2015-01-01

    Water pollution worsens the problem of disinfection by-products (DBPs) in drinking water supply. Biodegradation of wastewater organics produces soluble microbial products (SMPs), which can be important DBP precursors. In this laboratory study, a number of enhanced water treatment methods for DBP control, including enhanced coagulation, ozonation, and activated carbon adsorption, were evaluated for their effectiveness in treating SMP-containing water for the DBP reduction purpose. The results show that enhanced coagulation with alum could remove SMPs only marginally and decrease the DBP formation potential (DBPFP) of the water by less than 20%. Although ozone could cause destruction of SMPs in water, the overall DBPFP of the water did not decrease but increased after ozonation. In contrast, adsorption by granular activated carbon could remove the SMP organics from water by more than 60% and reduce the DBPFP by more than 70%. It is apparent that enhanced coagulation and ozonation are not suitable for the removal of SMPs as DBP precursors from polluted water, although enhanced coagulation has been commonly used to reduce the DBP formation caused by natural organic matter. In comparison, activated carbon adsorption is shown as a more effective means to remove the SMP content from water and hence to control the wastewater-derived DBP problem in water supply.

  10. Microbial diversity during maturation and natural processing of coffee cherries of Coffea arabica in Brazil.

    PubMed

    Silv, C F; Schwan, R F; Sousa Dias, E S; Wheals, A E

    2000-09-25

    The magnitude and diversity of the microbial population associated with dry (natural) processing of coffee (Coffea arabica) has been assessed during a 2-year period on 15 different farms in the Sul de Minas region of Brazil. Peptone water-washed samples were taken of maturing cherries on trees (cherries, raisins and dried cherries) and from ground fermentations. The microbial load varied from 3 x 10(4) to 2.2 x 10(9) cfu/cherry with a median value of 1.6 x 10(7) cfu/cherry. The microbial load increased after heavy rainfall on cherries that were drying on the ground. At all stages, bacteria were usually the most abundant group, followed by filamentous fungi and finally yeasts. Counts of bacteria, yeasts and fungi varied considerably between farms and at different stages of maturation and processing and no consistent pattern could be seen. Yeasts showed an increase during the fermentation process. Median counts were not significantly different for fungi, yeasts and bacteria between the 2 years although Gram-negative bacteria dominated in the wet year and Gram-positive bacteria dominated in the dry year. Of a total of 754 isolates, 626 were identified to at least genus level comprising 44 genera and 64 different species. The 164 isolates of Gram-negative bacteria included 17 genera and 26 species, the most common of which were members of the genera Aeromonas, Pseudomonas, Enterobacter and Serratia. Of 191 isolates of Gram-positive bacteria, 23 were spore-forming and included six Bacillus species, and 118 were non-spore-formers of which over half were Cellulomonas with lesser numbers of Arthrobacter, Microbacterium, Brochothrix, Dermabacter and Lactobacillus. Of the 107 yeast isolates, 90 were identified into 12 genera and 24 different species and almost all were fermentative. The most common genera, in decreasing frequency, were Pichia, Candida, Arxula and Saccharomycopsis. There were many rarely described yeasts including Pichia lynferdii and Arxula adeninivorans

  11. Quantitation of microbial products and their effectiveness in enhanced oil recovery. Final report

    SciTech Connect

    Zhang, X.; Knapp, R.M.; McInerney, M.J.

    1995-02-01

    A three-dimensional, three-phase, multiple-component numerical simulator was developed to investigate transport and growth of microorganisms in porous media and the impacts of microbial activities on oil recovery. The microbial activities modeled in this study included: (1) growth, retention, chemotaxis, and end product inhibition of growth, (2) the formation of metabolic products, and (3) the consumption of nutrients. Major mechanisms for microbial enhanced oil recovery (MEOR) processes were modeled as follows: (1) improvement in sweep efficiency of a displacement process due to in situ plugging of highly-permeable production zones by cell mass or due to improved mobility control achieved by increasing the viscosity of the displacing fluid with a biopolymer, and (2) solubilization and mobilization of residual oil in porous media due to the reduction of the interfacial tension between oleic and aqueous phases by the production of a biosurfactant. The numerical solutions for mathematical models involved two steps. The distributions of pressure and phase saturations were solved from continuity equations and Darcy flow velocities for the aqueous phase were computed. This was followed by the solution of convection-dispersion equations for individual components. Numerical solutions from the proposed model were compared to results obtained from analytical equations, commercial simulators, and laboratory experiments. The comparison indicated that the model accurately quantified microbial transport and metabolism in porous media, and predicted additional crude oil recovery due to microbial processes. 50 refs., 41 figs., 26 tabs.

  12. Anoxic Biodegradation of Isosaccharinic Acids at Alkaline pH by Natural Microbial Communities

    PubMed Central

    Rout, Simon P.; Charles, Christopher J.; Doulgeris, Charalampos; McCarthy, Alan J.; Rooks, Dave J.; Loughnane, J. Paul; Laws, Andrew P.; Humphreys, Paul N.

    2015-01-01

    One design concept for the long-term management of the UK’s intermediate level radioactive wastes (ILW) is disposal to a cementitious geological disposal facility (GDF). Under the alkaline (10.013.0) anoxic conditions expected within a GDF, cellulosic wastes will undergo chemical hydrolysis. The resulting cellulose degradation products (CDP) are dominated by α- and β-isosaccharinic acids (ISA), which present an organic carbon source that may enable subsequent microbial colonisation of a GDF. Microcosms established from neutral, near-surface sediments demonstrated complete ISA degradation under methanogenic conditions up to pH 10.0. Degradation decreased as pH increased, with β-ISA fermentation more heavily influenced than α-ISA. This reduction in degradation rate was accompanied by a shift in microbial population away from organisms related to Clostridium sporosphaeroides to a more diverse Clostridial community. The increase in pH to 10.0 saw an increase in detection of Alcaligenes aquatilis and a dominance of hydrogenotrophic methanogens within the Archaeal population. Methane was generated up to pH 10.0 with acetate accumulation at higher pH values reflecting a reduced detection of acetoclastic methanogens. An increase in pH to 11.0 resulted in the accumulation of ISA, the absence of methanogenesis and the loss of biomass from the system. This study is the first to demonstrate methanogenesis from ISA by near surface microbial communities not previously exposed to these compounds up to and including pH 10.0. PMID:26367005

  13. Microbial and chemical factors influencing methane production in laboratory incubations of low-rank subsurface coals

    USGS Publications Warehouse

    Harris, Stephen H.; Smith, Richard L.; Barker, Charles E.

    2008-01-01

    Lignite and subbituminous coals were investigated for their ability to support microbial methane production in laboratory incubations. Results show that naturally-occurring microorganisms associated with the coals produced substantial quantities of methane, although the factors influencing this process were variable among different samples tested. Methanogenic microbes in two coals from the Powder River Basin, Wyoming, USA, produced 140.5-374.6 mL CH4/kg ((4.5-12.0 standard cubic feet (scf)/ton) in response to an amendment of H2/CO2. The addition of high concentrations (5-10 mM) of acetate did not support substantive methane production under the laboratory conditions. However, acetate accumulated in control incubations where methanogenesis was inhibited, indicating that acetate was produced and consumed during the course of methane production. Acetogenesis from H2/CO2 was evident in these incubations and may serve as a competing metabolic mode influencing the cumulative amount of methane produced in coal. Two low-rank (lignite A) coals from Fort Yukon, Alaska, USA, demonstrated a comparable level of methane production (131.1-284.0 mL CH4/kg (4.2-9.1 scf/ton)) in the presence of an inorganic nutrient amendment, indicating that the source of energy and organic carbon was derived from the coal. The concentration of chloroform-extractable organic matter varied by almost three orders of magnitude among all the coals tested, and appeared to be related to methane production potential. These results indicate that substrate availability within the coal matrix and competition between different groups of microorganisms are two factors that may exert a profound influence on methanogenesis in subsurface coal beds.

  14. Microbial production of vitamin B12: a review and future perspectives.

    PubMed

    Fang, Huan; Kang, Jie; Zhang, Dawei

    2017-01-30

    Vitamin B12 is an essential vitamin that is widely used in medical and food industries. Vitamin B12 biosynthesis is confined to few bacteria and archaea, and as such its production relies on microbial fermentation. Rational strain engineering is dependent on efficient genetic tools and a detailed knowledge of metabolic pathways, regulation of which can be applied to improve product yield. Recent advances in synthetic biology and metabolic engineering have been used to efficiently construct many microbial chemical factories. Many published reviews have probed the vitamin B12 biosynthetic pathway. To maximize the potential of microbes for vitamin B12 production, new strategies and tools are required. In this review, we provide a comprehensive understanding of advances in the microbial production of vitamin B12, with a particular focus on establishing a heterologous host for the vitamin B12 production, as well as on strategies and tools that have been applied to increase microbial cobalamin production. Several worthy strategies employed for other products are also included.

  15. Industrial natural product chemistry for drug discovery and development.

    PubMed

    Bauer, Armin; Brönstrup, Mark

    2014-01-01

    Covering: up to March 2013. In addition to their prominent role in basic biological and chemical research, natural products are a rich source of commercial products for the pharmaceutical and other industries. Industrial natural product chemistry is of fundamental importance for successful product development, as the vast majority (ca. 80%) of commercial drugs derived from natural products require synthetic efforts, either to enable economical access to bulk material, and/or to optimize drug properties through structural modifications. This review aims to illustrate issues on the pathway from lead to product, and how they have been successfully addressed by modern natural product chemistry. It is focused on natural products of current relevance that are, or are intended to be, used as pharmaceuticals.

  16. Characterization of soluble microbial products as precursors of disinfection byproducts in drinking water supply.

    PubMed

    Liu, Jin-Lin; Li, Xiao-Yan; Xie, Yue-Feng; Tang, Hao

    2014-02-15

    Water pollution by wastewater discharge can cause the problem of disinfection byproducts (DBPs) in drinking water supply. In this study, DBP formation characteristics of soluble microbial products (SMPs) as the main products of wastewater organic biodegradation were investigated. The results show that SMPs can act as DBP precursors in simulated wastewater biodegradation process. Under the experimental conditions, stabilized SMPs had DBPFP (DBP formation potential) yield of around 5.6 μmol mmol(-1)-DOC (dissolved organic carbon) and DBP speciation profile different from that of the conventional precursor, natural organic matter (NOM). SMPs contained polysaccharides, proteins, and humic-like substances, and the latter two groups can act as reactive DBP precursors. SMP fraction with molecular weight of <1 kDa accounted for 85% of the organic carbon and 65% of the DBP formation. As small SMP molecules are more difficult to remove by conventional water treatment processes, more efforts are needed to control wastewater-derived DBP problem in water resource management.

  17. Biotechnological production of phenyllactic acid and biosurfactants from trimming vine shoot hydrolyzates by microbial coculture fermentation.

    PubMed

    Rodríguez-Pazo, Noelia; Salgado, José Manuel; Cortés-Diéguez, Sandra; Domínguez, José Manuel

    2013-04-01

    Coculture fermentations show advantages for producing food additives from agroindustrial wastes, considering that different specified microbial strains are combined to improve the consumption of mixed sugars obtained by hydrolysis. This technology dovetails with both the growing interest of consumers towards the use of natural food additives and with stricter legislations and concern in developed countries towards the management of wastes. The use of this technology allows valorization of both cellulosic and hemicellulosic fractions of trimming vine shoots for the production of lactic acid (LA), phenyllactic acid (PLA), and biosurfactants (BS). This work compares the study of the potential of hemicellulosic and cellulosic fractions of trimming vine shoots as cheaper and renewable carbon sources for PLA and BS production by independent or coculture fermentations. The highest LA and PLA concentrations, 43.0 g/L and 1.58 mM, respectively, were obtained after 144 h during the fermentation of hemicellulosic sugars and simultaneous saccharification and fermentation (SSF) carried out by cocultures of Lactobacillus plantarum and Lactobacillus pentosus. Additionally, cell-bond BS decreased the surface tension (ST) in 17.2 U; meanwhile, cell-free supernatants (CFS) showed antimicrobial activity against Salmonella enterica and Listeria monocytogenes with inhibition halos of 12.1±0.6 mm and 11.5±0.9 mm, respectively.

  18. Recent advances in awakening silent biosynthetic gene clusters and linking orphan clusters to natural products in microorganisms.

    PubMed

    Chiang, Yi-Ming; Chang, Shu-Lin; Oakley, Berl R; Wang, Clay C C

    2011-02-01

    Secondary metabolites from microorganisms have a broad spectrum of applications, particularly in therapeutics. The growing number of sequenced microbial genomes has revealed a remarkably large number of natural product biosynthetic clusters for which the products are still unknown. These cryptic clusters are potentially a treasure house of medically useful compounds. The recent development of new methodologies has made it possible to begin unlock this treasure house, to discover new natural products and to determine their biosynthesis pathways. This review will highlight some of the most recent strategies to activate silent biosynthetic gene clusters and to elucidate their corresponding products and pathways.

  19. Deep-sea hydrothermal vents: potential hot spots for natural products discovery?

    PubMed

    Thornburg, Christopher C; Zabriskie, T Mark; McPhail, Kerry L

    2010-03-26

    Deep-sea hydrothermal vents are among the most extreme and dynamic environments on Earth. However, islands of highly dense and biologically diverse communities exist in the immediate vicinity of hydrothermal vent flows, in stark contrast to the surrounding bare seafloor. These communities comprise organisms with distinct metabolisms based on chemosynthesis and growth rates comparable to those from shallow water tropical environments, which have been rich sources of biologically active natural products. The geological setting and geochemical nature of deep-sea vents that impact the biogeography of vent organisms, chemosynthesis, and the known biological and metabolic diversity of Eukarya, Bacteria, and Archaea, including the handful of natural products isolated to date from deep-sea vent organisms, are considered here in an assessment of deep-sea hydrothermal vents as potential hot spots for natural products investigations. Of critical importance too are the logistics of collecting deep vent organisms, opportunities for re-collection considering the stability and longevity of vent sites, and the ability to culture natural product-producing deep vent organisms in the laboratory. New cost-effective technologies in deep-sea research and more advanced molecular techniques aimed at screening a more inclusive genetic assembly are poised to accelerate natural product discoveries from these microbial diversity hot spots.

  20. Use of natural health products in children

    PubMed Central

    Godwin, Marshall; McCrate, Farah; Newhook, Leigh Anne; Pike, Andrea; Crellin, John; Law, Rebecca; Mathews, Maria; Chowdhury, Nurun L.

    2013-01-01

    Abstract Objective To determine the experiences of family physicians in Newfoundland and Labrador with parents’ use of natural health products (NHPs) for their children and to assess physicians’ attitudes toward use of NHPs in children. Design A survey using the Dillman approach. Setting Newfoundland and Labrador. Participants All family physicians in the province. Main outcome measures Physician demographic characteristics; whether physicians inquire about the use of NHPs in children; the degree to which they think patients disclose use of NHPs in children; whether they counsel parents about the potential benefits or harms of NHPs; their own opinions about the usefulness of NHPs; whether they recommend NHPs in children and for what reasons; and the particular NHPs they have seen used in children and for what reasons. Results A total of 159 (33.1%) family physicians responded; 65.4% were men, 71.7% were Canadian medical graduates, and 46.5% practised in rural areas. Overall, 18.8% of family physicians said they regularly or frequently asked about NHP use; 24.7% counseled patients about potential harms. Only 1.9% of physicians believed NHPs were usually beneficial, but a similarly small number (8.4%) thought they were usually harmful. Most respondents were somewhat neutral; 59.7% said they never recommend NHPs for children, and a further 37.0% said they would only “sometimes” recommend NHPs. Conclusion Most physicians believed that NHPs were probably of little benefit but not likely to be harmful. Most NHPs used were vitamins and minerals. Physicians recognized that NHPs were often used by parents for children, but in general they believed NHPs had little effect on their day-to-day medical practices. Thirty-eight (24.7%) of the 154 physicians had at least once recommended an NHP (including vitamins) for their pediatric patients. Physicians believed that parents did not often disclose use of NHPs for their children, but at the same time physicians generally

  1. Efficacy of natural wetlands to retain nutrient, sediment and microbial pollutants.

    PubMed

    Knox, A K; Dahlgren, R A; Tate, K W; Atwill, E R

    2008-01-01

    Wetlands can improve water quality through natural processes including sedimentation, nutrient transformations, and microbial and plant uptake. Tailwater from irrigated pastures may contribute to nonpoint source water pollution in the form of sediments, nutrients, and pathogens that degrade downstream water quality. We examined benefits to water quality provided by a natural, flow-through wetland and a degraded, channelized wetland situated within the flood-irrigation agricultural landscape of the Sierra Nevada foothills of Northern California. The non-degraded, reference wetland significantly improved water quality by reducing loads of total suspended sediments, nitrate, and Escherichia coli on average by 77, 60, and 68%, respectively. Retention of total N, total P, and soluble reactive P (SRP) was between 35 and 42% of loads entering the reference wetland. Retention of pollutant loads by the channelized wetland was significantly lower than by the reference wetland for all pollutants except SRP. A net export of sediment and nitrate was observed from the channelized wetland. Decreased irrigation inflow rates significantly improved retention efficiencies for nitrate, E. coli, and sediments in the reference wetland. We suggest that maintenance of these natural wetlands and regulation of inflow rates can be important aspects of a best management plan to improve water quality as water runs off of irrigated pastures.

  2. Plant natural products: back to the future or into extinction?

    PubMed

    McChesney, James D; Venkataraman, Sylesh K; Henri, John T

    2007-07-01

    Natural product substances have historically served as the most significant source of new leads for pharmaceutical development. However, with the advent of robotics, bioinformatics, high throughput screening (HTS), molecular biology-biotechnology, combinatorial chemistry, in silico (molecular modeling) and other methodologies, the pharmaceutical industry has largely moved away from plant derived natural products as a source for leads and prospective drug candidates. Can, or will, natural products ever recapture the preeminent position they once held as a foundation for drug discovery and development? The challenges associated with development of natural products as pharmaceuticals are illustrated by the Taxol story. Several misconceptions, which constrain utilization of plant natural products, for discovery and development of pharmaceuticals, are addressed to return natural products to the forefront.

  3. Microbial and nutritional aspects on the production of live feeds in a fish farming industry.

    PubMed

    De Donno, A; Lugoli, F; Bagordo, F; Vilella, S; Campa, A; Grassi, T; Guido, M

    2010-03-01

    Aquaculture is an enterprise in constant development, in particular relating to its effect on the environment and also the quality of its products. It represents a valid alternative to traditional fishing, facing the increasing demand for fish products. To guarantee to the consumer a product of high nutritional, organoleptic and hygienic quality, it is fundamental to monitor every phase of the fish farming industry, isolating the potential risk points. For this reason there has been a rapid evolution of productive technique, particularly in the technology, artificial reproduction and feed sectors. The aim of this research has been the monitoring of the evolution of certain microbial and nutritional quality indexes (total microbial counts and lipid analysis on suspensions of Rotifers and Artemia, used as live feed) in the larval phase of the productive cycle of the farm raised fish, in an intensive system. The study has shown an increment in the total microbial counts in the fish farming industry within the production of Rotifers and Artemia, more evident in the suspensions of Rotifers. In addition the study has demonstrated that the maintenance phase, in the enrichment protocol, can reduce the EPA and DHA content. The results confirm the importance of microbial and nutritional control of the live feeds before they get supplied to fish larvae.

  4. Microbial abundance and community composition influence production performance in a low-temperature petroleum reservoir.

    PubMed

    Li, Guoqiang; Gao, Peike; Wu, Yunqiang; Tian, Huimei; Dai, Xuecheng; Wang, Yansen; Cui, Qingfeng; Zhang, Hongzuo; Pan, Xiaoxuan; Dong, Hanping; Ma, Ting

    2014-05-06

    Enhanced oil recovery using indigenous microorganisms has been successfully applied in the petroleum industry, but the role of microorganisms remains poorly understood. Here, we investigated the relationship between microbial population dynamics and oil production performance during a water flooding process coupled with nutrient injection in a low-temperature petroleum reservoir. Samples were collected monthly over a two-year period. The microbial composition of samples was determined using 16S rRNA gene pyrosequencing and real-time quantitative polymerase chain reaction analyses. Our results indicated that the microbial community structure in each production well microhabitat was dramatically altered during flooding with eutrophic water. As well as an increase in the density of microorganisms, biosurfactant producers, such as Pseudomonas, Alcaligenes, Rhodococcus, and Rhizobium, were detected in abundance. Furthermore, the density of these microorganisms was closely related to the incremental oil production. Oil emulsification and changes in the fluid-production profile were also observed. In addition, we found that microbial community structure was strongly correlated with environmental factors, such as water content and total nitrogen. These results suggest that injected nutrients increase the abundance of microorganisms, particularly biosurfactant producers. These bacteria and their metabolic products subsequently emulsify oil and alter fluid-production profiles to enhance oil recovery.

  5. Marine natural products: a way to new drugs.

    PubMed

    Stonik, V A

    2009-07-01

    The investigation of marine natural products (low molecular weight bioregulators) is a rapidly developing scientific field at the intersection of biology and chemistry. Investigations aimed at detecting, identifying, and understanding the structure of marine natural products have led to the discovery of 20,000 new substances, including those characterized by an extremely high physiological activity. Some results and prospects of works aimed at creating new drugs on the basis of marine natural products are discussed herein.

  6. Dearomatization Strategies in the Synthesis of Complex Natural Products

    PubMed Central

    Roche, Stéphane P.; Porco, John A.

    2014-01-01

    Evolution in the field of the total synthesis of natural products has led to exciting developments over the last decade. Numerous chemo-selective and enantioselective methodologies have emerged from total syntheses, resulting in efficient access to many important natural product targets. This Review highlights recent developments concerning dearomatization, a powerful strategy for the total synthesis of architecturally complex natural products wherein planar, aromatic scaffolds are converted to three-dimensional molecular architectures. PMID:21506209

  7. Marine Natural Products: A Way to New Drugs

    PubMed Central

    2009-01-01

    The investigation of marine natural products (low molecular weight bioregulators) is a rapidly developing scientific field at the intersection of biology and chemistry. Investigations aimed at detecting, identifying, and understanding the structure of marine natural products have led to the discovery of 20,000 new substances, including those characterized by an extremely high physiological activity. Some results and prospects of works aimed at creating new drugs on the basis of marine natural products are discussed herein. PMID:22649599

  8. Biosynthesis of therapeutic natural products using synthetic biology.

    PubMed

    Awan, Ali R; Shaw, William M; Ellis, Tom

    2016-10-01

    Natural products are a group of bioactive structurally diverse chemicals produced by microorganisms and plants. These molecules and their derivatives have contributed to over a third of the therapeutic drugs produced in the last century. However, over the last few decades traditional drug discovery pipelines from natural products have become far less productive and far more expensive. One recent development with promise to combat this trend is the application of synthetic biology to therapeutic natural product biosynthesis. Synthetic biology is a young discipline with roots in systems biology, genetic engineering, and metabolic engineering. In this review, we discuss the use of synthetic biology to engineer improved yields of existing therapeutic natural products. We further describe the use of synthetic biology to combine and express natural product biosynthetic genes in unprecedented ways, and how this holds promise for opening up completely new avenues for drug discovery and production.

  9. Natural products as sources of new drugs over the 30 years from 1981 to 2010.

    PubMed

    Newman, David J; Cragg, Gordon M

    2012-03-23

    This review is an updated and expanded version of the three prior reviews that were published in this journal in 1997, 2003, and 2007. In the case of all approved therapeutic agents, the time frame has been extended to cover the 30 years from January 1, 1981, to December 31, 2010, for all diseases worldwide, and from 1950 (earliest so far identified) to December 2010 for all approved antitumor drugs worldwide. We have continued to utilize our secondary subdivision of a "natural product mimic" or "NM" to join the original primary divisions and have added a new designation, "natural product botanical" or "NB", to cover those botanical "defined mixtures" that have now been recognized as drug entities by the FDA and similar organizations. From the data presented, the utility of natural products as sources of novel structures, but not necessarily the final drug entity, is still alive and well. Thus, in the area of cancer, over the time frame from around the 1940s to date, of the 175 small molecules, 131, or 74.8%, are other than "S" (synthetic), with 85, or 48.6%, actually being either natural products or directly derived therefrom. In other areas, the influence of natural product structures is quite marked, with, as expected from prior information, the anti-infective area being dependent on natural products and their structures. Although combinatorial chemistry techniques have succeeded as methods of optimizing structures and have been used very successfully in the optimization of many recently approved agents, we are able to identify only one de novo combinatorial compound approved as a drug in this 30-year time frame. We wish to draw the attention of readers to the rapidly evolving recognition that a significant number of natural product drugs/leads are actually produced by microbes and/or microbial interactions with the "host from whence it was isolated", and therefore we consider that this area of natural product research should be expanded significantly.

  10. Natural Products as Sources of New Drugs from 1981 to 2014.

    PubMed

    Newman, David J; Cragg, Gordon M

    2016-03-25

    This contribution is a completely updated and expanded version of the four prior analogous reviews that were published in this journal in 1997, 2003, 2007, and 2012. In the case of all approved therapeutic agents, the time frame has been extended to cover the 34 years from January 1, 1981, to December 31, 2014, for all diseases worldwide, and from 1950 (earliest so far identified) to December 2014 for all approved antitumor drugs worldwide. As mentioned in the 2012 review, we have continued to utilize our secondary subdivision of a "natural product mimic", or "NM", to join the original primary divisions and the designation "natural product botanical", or "NB", to cover those botanical "defined mixtures" now recognized as drug entities by the U.S. FDA (and similar organizations). From the data presented in this review, the utilization of natural products and/or their novel structures, in order to discover and develop the final drug entity, is still alive and well. For example, in the area of cancer, over the time frame from around the 1940s to the end of 2014, of the 175 small molecules approved, 131, or 75%, are other than "S" (synthetic), with 85, or 49%, actually being either natural products or directly derived therefrom. In other areas, the influence of natural product structures is quite marked, with, as expected from prior information, the anti-infective area being dependent on natural products and their structures. We wish to draw the attention of readers to the rapidly evolving recognition that a significant number of natural product drugs/leads are actually produced by microbes and/or microbial interactions with the "host from whence it was isolated", and therefore it is considered that this area of natural product research should be expanded significantly.

  11. Microbial metabolic engineering for L-threonine production.

    PubMed

    Dong, Xunyan; Quinn, Peter J; Wang, Xiaoyuan

    2012-01-01

    L-threonine, one of the three major amino acids produced throughout the world, has a wide application in industry, as an additive or as a precursor for the biosynthesis of other chemicals. It is predominantly produced through microbial fermentation the efficiency of which largely depends on the quality of strains. Metabolic engineering based on a cogent understanding of the metabolic pathways of L-threonine biosynthesis and regulation provides an effective alternative to the traditional breeding for strain development. Continuing efforts have been made in revealing the mechanisms and regulation of L-threonine producing strains, as well as in metabolic engineering of suitable organisms whereby genetically-defined, industrially competitive L-threonine producing strains have been successfully constructed. This review focuses on the global metabolic and regulatory networks responsible for L-threonine biosynthesis, the molecular mechanisms of regulation, and the strategies employed in strain engineering.

  12. Recent advances in lactic acid production by microbial fermentation processes.

    PubMed

    Abdel-Rahman, Mohamed Ali; Tashiro, Yukihiro; Sonomoto, Kenji

    2013-11-01

    Fermentative production of optically pure lactic acid has roused interest among researchers in recent years due to its high potential for applications in a wide range of fields. More specifically, the sharp increase in manufacturing of biodegradable polylactic acid (PLA) materials, green alternatives to petroleum-derived plastics, has significantly increased the global interest in lactic acid production. However, higher production costs have hindered the large-scale application of PLA because of the high price of lactic acid. Therefore, reduction of lactic acid production cost through utilization of inexpensive substrates and improvement of lactic acid production and productivity has become an important goal. Various methods have been employed for enhanced lactic acid production, including several bioprocess techniques facilitated by wild-type and/or engineered microbes. In this review, we will discuss lactic acid producers with relation to their fermentation characteristics and metabolism. Inexpensive fermentative substrates, such as dairy products, food and agro-industrial wastes, glycerol, and algal biomass alternatives to costly pure sugars and food crops are introduced. The operational modes and fermentation methods that have been recently reported to improve lactic acid production in terms of concentrations, yields, and productivities are summarized and compared. High cell density fermentation through immobilization and cell-recycling techniques are also addressed. Finally, advances in recovery processes and concluding remarks on the future outlook of lactic acid production are presented.

  13. Cell immobilization for microbial production of 1,3-propanediol.

    PubMed

    Gungormusler-Yilmaz, Mine; Cicek, Nazim; Levin, David B; Azbar, Nuri

    2016-01-01

    Cell and enzyme immobilization are often used for industrial production of high-value products. In recent years, immobilization techniques have been applied to the production of value-added chemicals such as 1,3-Propanediol (1,3-PDO). Biotechnological fermentation is an attractive alternative to current 1,3-PDO production methods, which are primarily thermochemical processes, as it generates high volumetric yields of 1,3-PDO, is a much less energy intensive process, and generates lower amounts of environmental organic pollutants. Although several approaches including: batch, fed-batch, continuous-feed and two-step continuous-feed were tested in suspended systems, it has been well demonstrated that cell immobilization techniques can significantly enhance 1,3-PDO production and allow robust continuous production in smaller bioreactors. This review covers various immobilization methods and their application for 1,3-PDO production.

  14. Changes in microbial activity of soils during the natural restoration of abandoned lands in central Russia

    NASA Astrophysics Data System (ADS)

    Ovsepyan, Lilit; Mostovaya, Anna; Lopes de Gerenyu, Valentin; Kurganova, Irina

    2015-04-01

    Most changes in land use affect significantly the amount of soil organic carbon (SOC) and alter the nutrition status of soil microbial community. The arable lands withdrawal induced usually the carbon sequestration in soil, the significant shifts in quality of soil organic matter and structure of microbial community. This study was aimed to determine the microbial activity of the abandoned lands in Central Russia due to the process of natural self-restoration. For the study, two representative chronosequences were selected in Central Russia: (1) deciduous forest area, DFA (Moscow region, 54o49N'; 37o34'E; Haplic Luvisols) and (2) forest steppe area, FSA (Belgorod region 50o36'N, 36o01'E Luvic Phaeozems). Each chronosequence included current arable, abandoned lands of different age, and forest plots. The total soil organic carbon (Corg, automatic CHNS analyzer), carbon immobilized in microbial biomass (Cmic, SIR method), and respiratory activity (RA) were determined in the topsoil (0-5, 5-10, 10-20 and 20-30 cm layers) for each plots. Relationships between Corg, Cmic, and RA were determined by liner regression method. Our results showed that the conversion of croplands to the permanent forest induced the progressive accumulation Corg, Cmic and acceleration of RA in the top 10-cm layer for both chronosequences. Carbon stock increased from 24.1 Mg C ha-1 in arable to 45.3 Mg C ha-1 in forest soil (Luvic Phaeozems, Belgorod region). In Haplic Luvisols (Moscow region), SOC build up was 2 time less: from 13.5 Mg C ha-1 in arable to 27.9 Mg C ha-1 in secondary forest. During post-agrogenic evolution, Cmic also increased significantly: from 0.34 to 1.43 g C kg-1 soil in Belgorod region and from 0.34 to 0.64 g C kg-1 soil in Moscow region. RA values varied widely in soils studied: from 0.54-0.63 mg C kg-1h-1 in arable plots to 2.02-3.4 mg C kg-1h-1 in forest ones. The close correlations between Cmic, RA and Corg in the top 0-5cm layer (R2 = 0.81-0.90; P<0.01-0.05) were

  15. Microbial electrolysis cells for high yield hydrogen gas production from organic matter.

    PubMed

    Logan, Bruce E; Call, Douglas; Cheng, Shaoan; Hamelers, Hubertus V M; Sleutels, Tom H J A; Jeremiasse, Adriaan W; Rozendal, René A

    2008-12-01

    The use of electrochemically active bacteria to break down organic matter, combined with the addition of a small voltage (> 0.2 V in practice) in specially designed microbial electrolysis cells (MECs), can result in a high yield of hydrogen gas. While microbial electrolysis was invented only a few years ago, rapid developments have led to hydrogen yields approaching 100%, energy yields based on electrical energy input many times greater than that possible by water electrolysis, and increased gas production rates. MECs used to make hydrogen gas are similar in design to microbial fuel cells (MFCs) that produce electricity, but there are important differences in architecture and analytical methods used to evaluate performance. We review here the materials, architectures, performance, and energy efficiencies of these MEC systems that show promise as a method for renewable and sustainable energy production, and wastewater treatment.

  16. Engineered Biosynthesis of Natural Products in Heterologous Hosts

    PubMed Central

    Luo, Yunzi; Li, Bing-Zhi; Liu, Duo; Zhang, Lu; Chen, Yan; Jia, Bin; Zeng, Bo-Xuan; Zhao, Huimin; Yuan, Ying-Jin

    2015-01-01

    Natural products produced by microorganisms and plants are a major resource of antibacterial and anticancer drugs as well as industrially useful compounds. However, the native producers often suffer from low productivity and titers. Here we summarize the recent applications of heterologous biosynthesis for the production of several important classes of natural products such as terpenoids, flavonoids, alkaloids, and polyketides. In addition, we will discuss the new tools and strategies at multi-scale levels including gene, pathway, genome and community levels for highly efficient heterologous biosynthesis of natural products. PMID:25960127

  17. Natural organic matter as global antennae for primary production.

    PubMed

    Van Trump, J Ian; Rivera Vega, Fransheska J; Coates, John D

    2013-05-01

    Humic substances (HS) are high-molecular-weight complex refractory organics that are ubiquitous in terrestrial and aquatic environments. While resistant to microbial degradation, these compounds nevertheless support microbial metabolism via oxidation or reduction of their (hydro)quinone moieties. As such, they are known to be important electron sinks for respiratory and fermentative bacteria and electron sources for denitrifying and perchlorate-reducing bacteria. HS also strongly promote abiotic reduction of Fe(III) when irradiated with light. Here, we show that HS-enhanced Fe(III) photoreduction can also drive chemolithotrophic microbial respiration by producing Fe(II), which functions as a respiratory electron donor. Due to their molecular complexity, HS absorb most of the electromagnetic spectrum and can act as broad-spectrum antennae converting radiant energy into bioavailable chemical energy. The finding that chemolithotrophic organisms can utilize this energy has important implications for terrestrial, and possibly extraterrestrial, microbial processes and offers an alternative mechanism of radiation-driven primary productivity to that of phototrophy.

  18. Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir.

    PubMed

    Walsh, Aaron M; Crispie, Fiona; Kilcawley, Kieran; O'Sullivan, Orla; O'Sullivan, Maurice G; Claesson, Marcus J; Cotter, Paul D

    2016-01-01

    Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides. Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand

  19. Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

    PubMed Central

    Walsh, Aaron M.; Crispie, Fiona; Kilcawley, Kieran; O’Sullivan, Orla; O’Sullivan, Maurice G.; Claesson, Marcus J.

    2016-01-01

    ABSTRACT Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L.