1
|
Kumar M, Sarma DK, Shubham S, Kumawat M, Verma V, Nina PB, JP D, Kumar S, Singh B, Tiwari RR. Futuristic Non-antibiotic Therapies to Combat Antibiotic Resistance: A Review. Front Microbiol 2021; 12:609459. [PMID: 33574807 PMCID: PMC7870489 DOI: 10.3389/fmicb.2021.609459] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/04/2021] [Indexed: 12/26/2022] Open
Abstract
The looming problem of resistance to antibiotics in microorganisms is a global health concern. The drug-resistant microorganisms originating from anthropogenic sources and commercial livestock farming have posed serious environmental and health challenges. Antibiotic-resistant genes constituting the environmental "resistome" get transferred to human and veterinary pathogens. Hence, deciphering the origin, mechanism and extreme of transfer of these genetic factors into pathogens is extremely important to develop not only the therapeutic interventions to curtail the infections, but also the strategies to avert the menace of microbial drug-resistance. Clinicians, researchers and policymakers should jointly come up to develop the strategies to prevent superfluous exposure of pathogens to antibiotics in non-clinical settings. This article highlights the present scenario of increasing antimicrobial-resistance in pathogenic bacteria and the clinical importance of unconventional or non-antibiotic therapies to thwart the infectious pathogenic microorganisms.
Collapse
Affiliation(s)
- Manoj Kumar
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | | | - Swasti Shubham
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Manoj Kumawat
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Vinod Verma
- Stem Cell Research Centre, Department of Hematology, SGPGIMS, Lucknow, India
| | | | - Devraj JP
- ICMR- National Institute of Nutrition, Hyderabad, India
| | - Santosh Kumar
- ICMR- National Institute of Nutrition, Hyderabad, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, India
| | | |
Collapse
|
2
|
Metagenomic analysis of the cow, sheep, reindeer and red deer rumen. Sci Rep 2021; 11:1990. [PMID: 33479378 PMCID: PMC7820578 DOI: 10.1038/s41598-021-81668-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
The rumen microbiota comprises a community of microorganisms which specialise in the degradation of complex carbohydrates from plant-based feed. These microbes play a highly important role in ruminant nutrition and could also act as sources of industrially useful enzymes. In this study, we performed a metagenomic analysis of samples taken from the ruminal contents of cow (Bos Taurus), sheep (Ovis aries), reindeer (Rangifer tarandus) and red deer (Cervus elaphus). We constructed 391 metagenome-assembled genomes originating from 16 microbial phyla. We compared our genomes to other publically available microbial genomes and found that they contained 279 novel species. We also found significant differences between the microbiota of different ruminant species in terms of the abundance of microbial taxonomies, carbohydrate-active enzyme genes and KEGG orthologs. We present a dataset of rumen-derived genomes which in combination with other publicly-available rumen genomes can be used as a reference dataset in future metagenomic studies.
Collapse
|
3
|
Are Vaccines the Solution for Methane Emissions from Ruminants? A Systematic Review. Vaccines (Basel) 2020; 8:vaccines8030460. [PMID: 32825375 PMCID: PMC7565300 DOI: 10.3390/vaccines8030460] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/13/2020] [Accepted: 08/15/2020] [Indexed: 11/16/2022] Open
Abstract
Ruminants produce considerable amounts of methane during their digestive process, which makes the livestock industry as one of the largest sources of anthropogenic greenhouse gases. To tackle this situation, several solutions have been proposed, including vaccination of ruminants against microorganisms responsible for methane synthesis in the rumen. In this review, we summarize the research done on this topic and describe the state of the art of this strategy. The different steps implied in this approach are described: experimental design, animal model (species, age), antigen (whole cells, cell parts, recombinant proteins, peptides), adjuvant (Freund's, Montanide, saponin, among others), vaccination schedule (booster intervals and numbers) and measurements of treatment success (immunoglobulin titers and/or effects on methanogens and methane production). Highlighting both the advances made and knowledge gaps in the use of vaccines to inhibit ruminant methanogen activity, this research review opens the door to future studies. This will enable improvements in the methodology and systemic approaches so as to ensure the success of this proposal for the sustainable mitigation of methane emission.
Collapse
|
4
|
Markowiak P, Śliżewska K. The role of probiotics, prebiotics and synbiotics in animal nutrition. Gut Pathog 2018; 10:21. [PMID: 29930711 PMCID: PMC5989473 DOI: 10.1186/s13099-018-0250-0] [Citation(s) in RCA: 264] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/26/2018] [Indexed: 12/15/2022] Open
Abstract
Along with the intensive development of methods of livestock breeding, breeders' expectations are growing concerning feed additives that would guarantee such results as accelerating growth rate, protection of health from pathogenic infections and improvement of other production parameters such as: absorption of feed and quality of meat, milk, eggs. The main reason for their application would be a strive to achieve some beneficial effects comparable to those of antibiotic-based growth stimulators, banned on 01 January 2006. High hopes are being associated with the use of probiotics, prebiotics and synbiotics. Used mainly for maintenance of the equilibrium of the intestinal microbiota of livestock, they turn out to be an effective method in fight against pathogens posing a threat for both animals and consumers. This paper discusses definitions of probiotics, prebiotics and synbiotics. Criteria that have to be met by those kinds of formulas are also presented. The paper offers a list of the most commonly used probiotics and prebiotics and some examples of their combinations in synbiotic formulas used in animal feeding. Examples of available study results on the effect of probiotics, prebiotics and synbiotics on animal health are also summarised.
Collapse
Affiliation(s)
- Paulina Markowiak
- Department of Biotechnology and Food Sciences, Institute of Fermentation Technology and Microbiology, Lodz University of Technology, ul. Wólczańska 171/173, 90-924 Lodz, Poland
| | - Katarzyna Śliżewska
- Department of Biotechnology and Food Sciences, Institute of Fermentation Technology and Microbiology, Lodz University of Technology, ul. Wólczańska 171/173, 90-924 Lodz, Poland
| |
Collapse
|
5
|
Kumar M, Yadav AK, Verma V, Singh B, Mal G, Nagpal R, Hemalatha R. Bioengineered probiotics as a new hope for health and diseases: an overview of potential and prospects. Future Microbiol 2016; 11:585-600. [PMID: 27070955 DOI: 10.2217/fmb.16.4] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Despite the use of microorganisms as therapeutics for over a century, the scientific and clinical admiration of their potential is a recent phenomenon. Genome sequencing and genetic engineering has enabled researchers to develop novel strategies, such as bioengineered probiotics or pharmabiotics, which may become a therapeutic strategy. Bioengineered probiotics with multiple immunogenic or antagonistic properties could be a viable option to improve human health. The bacteria are tailored to deliver drugs, therapeutic proteins or gene therapy vectors with precision and a higher degree of site specificity than conventional drug administration regimes. This article provides an overview of methodological concepts, thereby encouraging research and interest in this topic, with the ultimate goal of using designer probiotics as therapeutics in clinical practice.
Collapse
Affiliation(s)
- Manoj Kumar
- Department of Clinical Microbiology & Immunology, National Institute of Nutrition, ICMR Hyderabad, India
| | - Ashok Kumar Yadav
- Department of Clinical Microbiology & Immunology, National Institute of Nutrition, ICMR Hyderabad, India
| | - Vinod Verma
- Centre of Biotechnology, Nehru Science Complex, University of Allahabad, Allahabad, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, India
| | - Gorakh Mal
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, India
| | - Ravinder Nagpal
- Probiotics Research Laboratory, Graduate School of Medicine, Juntendo University, Tokyo
| | - Rajkumar Hemalatha
- Department of Clinical Microbiology & Immunology, National Institute of Nutrition, ICMR Hyderabad, India
| |
Collapse
|
6
|
Dubinkina VB, Ischenko DS, Ulyantsev VI, Tyakht AV, Alexeev DG. Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis. BMC Bioinformatics 2016; 17:38. [PMID: 26774270 PMCID: PMC4715287 DOI: 10.1186/s12859-015-0875-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/14/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. "Shotgun" metagenome is an analytically challenging type of genomic data - containing sequences of all genes from the totality of a complex microbial community. Recently, researchers started to analyze metagenomes using reference-free methods based on the analysis of oligonucleotides (k-mers) frequency spectrum previously applied to isolated genomes. However, little is known about their correlation with the existing approaches for metagenomic feature extraction, as well as the limits of applicability. Here we evaluated a metagenomic pairwise dissimilarity measure based on short k-mer spectrum using the example of human gut microbiota, a biomedically significant object of study. RESULTS We developed a method for calculating pairwise dissimilarity (beta-diversity) of "shotgun" metagenomes based on short k-mer spectra (5 ≤ k ≤ 11). The method was validated on simulated metagenomes and further applied to a large collection of human gut metagenomes from the populations of the world (n=281). The k-mer spectrum-based measure was found to behave similarly to one based on mapping to a reference gene catalog, but different from one using a genome catalog. This difference turned out to be associated with a significant presence of viral reads in a number of metagenomes. Simulations showed limited impact of bacterial genetic variability as well as sequencing errors on k-mer spectra. Specific differences between the datasets from individual populations were identified. CONCLUSIONS Our approach allows rapid estimation of pairwise dissimilarity between metagenomes. Though we applied this technique to gut microbiota, it should be useful for arbitrary metagenomes, even metagenomes with novel microbiota. Dissimilarity measure based on k-mer spectrum provides a wider perspective in comparison with the ones based on the alignment against reference sequence sets. It helps not to miss possible outstanding features of metagenomic composition, particularly related to the presence of an unknown bacteria, virus or eukaryote, as well as to technical artifacts (sample contamination, reads of non-biological origin, etc.) at the early stages of bioinformatic analysis. Our method is complementary to reference-based approaches and can be easily integrated into metagenomic analysis pipelines.
Collapse
Affiliation(s)
- Veronika B Dubinkina
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology (State University), Institutskiy per., Dolgoprudny, 141700, Russia.
| | - Dmitry S Ischenko
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology (State University), Institutskiy per., Dolgoprudny, 141700, Russia.
| | | | - Alexander V Tyakht
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology (State University), Institutskiy per., Dolgoprudny, 141700, Russia.
| | - Dmitry G Alexeev
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology (State University), Institutskiy per., Dolgoprudny, 141700, Russia.
| |
Collapse
|
7
|
Culligan EP, Sleator RD, Marchesi JR, Hill C. Metagenomics and novel gene discovery: promise and potential for novel therapeutics. Virulence 2014; 5:399-412. [PMID: 24317337 PMCID: PMC3979868 DOI: 10.4161/viru.27208] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/21/2013] [Accepted: 11/14/2013] [Indexed: 02/06/2023] Open
Abstract
Metagenomics provides a means of assessing the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. It has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. Herein, we review both sequence-based and functional metagenomic methods to uncover novel genes and outline some of the associated problems of each type of approach, as well as potential solutions. Furthermore, we discuss the potential for metagenomic biotherapeutic discovery, with a particular focus on the human gut microbiome and finally, we outline how the discovery of novel genes may be used to create bioengineered probiotics.
Collapse
Affiliation(s)
- Eamonn P Culligan
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- School of Microbiology; University College Cork; Cork, Ireland
| | - Roy D Sleator
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- Department of Biological Sciences; Cork Institute of Technology; Bishopstown, Cork, Ireland
| | - Julian R Marchesi
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- Cardiff School of Biosciences; Cardiff University; Cardiff, UK
- Department of Hepatology and Gastroenterology; Imperial College London; London, UK
| | - Colin Hill
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- School of Microbiology; University College Cork; Cork, Ireland
| |
Collapse
|
8
|
Kumar M, Nagpal R, Verma V, Kumar A, Kaur N, Hemalatha R, Gautam SK, Singh B. Probiotic metabolites as epigenetic targets in the prevention of colon cancer. Nutr Rev 2012; 71:23-34. [PMID: 23282249 DOI: 10.1111/j.1753-4887.2012.00542.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Dietary interventions for preventing colon cancer have recently attracted increased attention from researchers and clinicians. The probiotics have emerged as potential therapeutic agents but are also regarded as healthy dietary supplements for nutrition and health applications. The probiotic metabolome may interfere with various cellular and molecular processes, including the onset and progression of colon cancer. Probiotic metabolites may lead to the modulation of diverse cellular signal transduction and metabolic pathways. The gut microbial metabolites (organic acids, bacteriocins, peptides, etc.) have been noted to interact with multiple key targets in various metabolic pathways that regulate cellular proliferation, differentiation, apoptosis, inflammation, angiogenesis, and metastasis. Progress in this field suggests that epigenetic alterations will be widely used in the near future to manage colon cancer. The present review provides insights into the molecular basis of the therapeutic applications and the chemopreventive activities of certain probiotic metabolites, with emphasis on the interaction between these metabolites and the molecular signaling cascades that are considered to be epigenetic targets in preventing colon cancer.
Collapse
Affiliation(s)
- Manoj Kumar
- Department of Microbiology and Immunology, National Institute of Nutrition, Hyderabad, India.
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Lu HP, Wang YB, Huang SW, Lin CY, Wu M, Hsieh CH, Yu HT. Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena). BMC Genomics 2012; 13:466. [PMID: 22963241 PMCID: PMC3527328 DOI: 10.1186/1471-2164-13-466] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 09/07/2012] [Indexed: 02/01/2023] Open
Abstract
Background Animals co-evolve with their gut microbiota; the latter can perform complex metabolic reactions that cannot be done independently by the host. Although the importance of gut microbiota has been well demonstrated, there is a paucity of research regarding its role in foliage-foraging mammals with a specialized digestive system. Results In this study, a 16S rRNA gene survey and metagenomic sequencing were used to characterize genetic diversity and functional capability of cecal microbiota of the folivorous flying squirrel (Petaurista alborufus lena). Phylogenetic compositions of the cecal microbiota derived from 3 flying squirrels were dominated by Firmicutes. Based on end-sequences of fosmid clones from 1 flying squirrel, we inferred that microbial metabolism greatly contributed to intestinal functions, including degradation of carbohydrates, metabolism of proteins, and synthesis of vitamins. Moreover, 33 polysaccharide-degrading enzymes and 2 large genomic fragments containing a series of carbohydrate-associated genes were identified. Conclusions Cecal microbiota of the leaf-eating flying squirrel have great metabolic potential for converting diverse plant materials into absorbable nutrients. The present study should serve as the basis for future investigations, using metagenomic approaches to elucidate the intricate mechanisms and interactions between host and gut microbiota of the flying squirrel digestive system, as well as other mammals with similar adaptations.
Collapse
Affiliation(s)
- Hsiao-Pei Lu
- Institute of Zoology and Department of Life Science, National Taiwan University, Taipei, Taiwan, ROC
| | | | | | | | | | | | | |
Collapse
|
10
|
Bhatt VD, Ahir VB, Koringa PG, Jakhesara SJ, Rank DN, Nauriyal DS, Kunjadia AP, Joshi CG. Milk microbiome signatures of subclinical mastitis-affected cattle analysed by shotgun sequencing. J Appl Microbiol 2012; 112:639-50. [PMID: 22277077 DOI: 10.1111/j.1365-2672.2012.05244.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
AIMS Metagenomic analysis of milk samples collected from Kankrej, Gir (Bos indicus) and crossbred (Bos taurus × B. indicus) cattle harbouring subclinical mastitis was carried out by next-generation sequencing 454 GS-FLX technology to elucidate the microbial community structure of cattle milk. METHODS AND RESULTS Milk samples from Kankrej, Gir and crossbred cattle were subjected to metagenomic profiling by pyrosequencing. The Metagenomic analysis produced 63·07, 11·09 and 7·87 million base pairs (Mb) of sequence data, assembled in 264 798, 56 114 and 36 762 sequences with an average read length of 238, 197 and 214 nucleotides in Kankrej, Gir and crossbred cattle, respectively. Phylogenetic and metabolic profiles by the web-based tool MG-RAST revealed that the members of Enterobacteriales were predominant in mastitic milk followed by Pseudomonadales, Bacillales and Lactobacillales. Around 56 different species with varying abundance were detected in the subclinically infected milk. Escherichia coli was found to be the most predominant species in Kankrej and Gir cattle followed by Pseudomonas aeruginosa, Pseudomonas mendocina, Shigella flexneri and Bacillus cereus. In crossbred cattle, Staphylococcus aureus followed by Klebsiella pneumoniae, Staphylococcus epidermidis and E. coli were detected in descending order. Metabolic profiling indicated fluoroquinolones, methicillin, copper, cobalt-zinc-cadmium as the groups of antibiotics and toxic compounds to which the organisms showed resistance. Sequences indicating potential of organisms exhibiting multidrug resistance against antibiotics and resistance to toxic compounds were also present. Interestingly, presence of bacteriophages against Staph. aureus, E. coli, Enterobacter and Yersinia species was also observed. CONCLUSIONS The analysis identified potential infectious organisms in mastitis, resistance of organisms to antibiotics and chemical compounds and the natural resistance potential of dairy cows. SIGNIFICANCE AND IMPACT OF THE STUDY The findings of this study may help in formulating strategies for the prevention and treatment of mastitis in dairy animals and consequently in reducing economic losses incurred because of it.
Collapse
Affiliation(s)
- V D Bhatt
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, Anand, Gujarat, India.
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Singh B, Bhat T, Sharma O, Kanwar S, Rahi P, Gulati A. Isolation of tannase-producing Enterobacter ludwigii GRT-1 from the rumen of migratory goats. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2011.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
12
|
Gilbert J, Li LL, Taghavi S, McCorkle SM, Tringe S, van der Lelie D. Bioprospecting metagenomics for new glycoside hydrolases. Methods Mol Biol 2012; 908:141-151. [PMID: 22843397 DOI: 10.1007/978-1-61779-956-3_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
To efficiently deconstruct recalcitrant plant biomass to fermentable sugars in industrial processes, biocatalysts of higher performance and lower cost are required. The genetic diversity found in the metagenomes of natural microbial biomass decay communities may harbor such enzymes. The aim of this chapter is to describe strategies, based on metagenomic approaches, for the discovery of glycoside hydrolases (GHases) from microbial biomass decay communities, especially those from unknown or never-been-cultivated microorganisms.
Collapse
Affiliation(s)
- Jack Gilbert
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, USA
| | | | | | | | | | | |
Collapse
|
13
|
Ekkers DM, Cretoiu MS, Kielak AM, van Elsas JD. The great screen anomaly--a new frontier in product discovery through functional metagenomics. Appl Microbiol Biotechnol 2011; 93:1005-20. [PMID: 22189864 PMCID: PMC3264863 DOI: 10.1007/s00253-011-3804-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 11/27/2011] [Accepted: 11/29/2011] [Indexed: 11/25/2022]
Abstract
Functional metagenomics, the study of the collective genome of a microbial community by expressing it in a foreign host, is an emerging field in biotechnology. Over the past years, the possibility of novel product discovery through metagenomics has developed rapidly. Thus, metagenomics has been heralded as a promising mining strategy of resources for the biotechnological and pharmaceutical industry. However, in spite of innovative work in the field of functional genomics in recent years, yields from function-based metagenomics studies still fall short of producing significant amounts of new products that are valuable for biotechnological processes. Thus, a new set of strategies is required with respect to fostering gene expression in comparison to the traditional work. These new strategies should address a major issue, that is, how to successfully express a set of unknown genes of unknown origin in a foreign host in high throughput. This article is an opinionating review of functional metagenomic screening of natural microbial communities, with a focus on the optimization of new product discovery. It first summarizes current major bottlenecks in functional metagenomics and then provides an overview of the general metagenomic assessment strategies, with a focus on the challenges that are met in the screening for, and selection of, target genes in metagenomic libraries. To identify possible screening limitations, strategies to achieve optimal gene expression are reviewed, examining the molecular events all the way from the transcription level through to the secretion of the target gene product.
Collapse
Affiliation(s)
- David Matthias Ekkers
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Mariana Silvia Cretoiu
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anna Maria Kielak
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| |
Collapse
|
14
|
Ardura A, Planes S, Garcia-Vazquez E. Beyond biodiversity: fish metagenomes. PLoS One 2011; 6:e22592. [PMID: 21829636 PMCID: PMC3150381 DOI: 10.1371/journal.pone.0022592] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 06/29/2011] [Indexed: 11/18/2022] Open
Abstract
Biodiversity and intra-specific genetic diversity are interrelated and determine the potential of a community to survive and evolve. Both are considered together in Prokaryote communities treated as metagenomes or ensembles of functional variants beyond species limits.Many factors alter biodiversity in higher Eukaryote communities, and human exploitation can be one of the most important for some groups of plants and animals. For example, fisheries can modify both biodiversity and genetic diversity (intra specific). Intra-specific diversity can be drastically altered by overfishing. Intense fishing pressure on one stock may imply extinction of some genetic variants and subsequent loss of intra-specific diversity. The objective of this study was to apply a metagenome approach to fish communities and explore its value for rapid evaluation of biodiversity and genetic diversity at community level. Here we have applied the metagenome approach employing the barcoding target gene coi as a model sequence in catch from four very different fish assemblages exploited by fisheries: freshwater communities from the Amazon River and northern Spanish rivers, and marine communities from the Cantabric and Mediterranean seas.Treating all sequences obtained from each regional catch as a biological unit (exploited community) we found that metagenomic diversity indices of the Amazonian catch sample here examined were lower than expected. Reduced diversity could be explained, at least partially, by overexploitation of the fish community that had been independently estimated by other methods.We propose using a metagenome approach for estimating diversity in Eukaryote communities and early evaluating genetic variation losses at multi-species level.
Collapse
Affiliation(s)
- Alba Ardura
- Department of Functional Biology, University of Oviedo, Oviedo, Spain.
| | | | | |
Collapse
|
15
|
Li LL, Taghavi S, McCorkle SM, Zhang YB, Blewitt MG, Brunecky R, Adney WS, Himmel ME, Brumm P, Drinkwater C, Mead DA, Tringe SG, Lelie DVD. Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases. BIOTECHNOLOGY FOR BIOFUELS 2011; 4:23. [PMID: 21816041 PMCID: PMC3171299 DOI: 10.1186/1754-6834-4-23] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 08/04/2011] [Indexed: 05/16/2023]
Abstract
BACKGROUND To efficiently deconstruct recalcitrant plant biomass to fermentable sugars in industrial processes, biocatalysts of higher performance and lower cost are required. The genetic diversity found in the metagenomes of natural microbial biomass decay communities may harbor such enzymes. Our goal was to discover and characterize new glycoside hydrolases (GHases) from microbial biomass decay communities, especially those from unknown or never previously cultivated microorganisms. RESULTS From the metagenome sequences of an anaerobic microbial community actively decaying poplar biomass, we identified approximately 4,000 GHase homologs. Based on homology to GHase families/activities of interest and the quality of the sequences, candidates were selected for full-length cloning and subsequent expression. As an alternative strategy, a metagenome expression library was constructed and screened for GHase activities. These combined efforts resulted in the cloning of four novel GHases that could be successfully expressed in Escherichia coli. Further characterization showed that two enzymes showed significant activity on p-nitrophenyl-α-L-arabinofuranoside, one enzyme had significant activity against p-nitrophenyl-β-D-glucopyranoside, and one enzyme showed significant activity against p-nitrophenyl-β-D-xylopyranoside. Enzymes were also tested in the presence of ionic liquids. CONCLUSIONS Metagenomics provides a good resource for mining novel biomass degrading enzymes and for screening of cellulolytic enzyme activities. The four GHases that were cloned may have potential application for deconstruction of biomass pretreated with ionic liquids, as they remain active in the presence of up to 20% ionic liquid (except for 1-ethyl-3-methylimidazolium diethyl phosphate). Alternatively, ionic liquids might be used to immobilize or stabilize these enzymes for minimal solvent processing of biomass.
Collapse
Affiliation(s)
- Luen-Luen Li
- Brookhaven National Laboratory, Upton, NY, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Safiyh Taghavi
- Brookhaven National Laboratory, Upton, NY, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sean M McCorkle
- Brookhaven National Laboratory, Upton, NY, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | | | - Roman Brunecky
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- National Renewable Energy Laboratory, Golden, CO, USA
| | - William S Adney
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- National Renewable Energy Laboratory, Golden, CO, USA
| | - Michael E Himmel
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- National Renewable Energy Laboratory, Golden, CO, USA
| | - Phillip Brumm
- Lucigen Corporation, Middleton, WI, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA
| | - Colleen Drinkwater
- Lucigen Corporation, Middleton, WI, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA
| | - David A Mead
- Lucigen Corporation, Middleton, WI, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA
| | | | - Daniel van der Lelie
- Brookhaven National Laboratory, Upton, NY, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Center for Agriculture and Environmental Biotechnology, RTI International, Research Triangle Park, NC, USA
| |
Collapse
|
16
|
Wang G, Luo H, Meng K, Wang Y, Huang H, Shi P, Pan X, Yang P, Diao Q, Zhang H, Yao B. High genetic diversity and different distributions of glycosyl hydrolase family 10 and 11 xylanases in the goat rumen. PLoS One 2011; 6:e16731. [PMID: 21304822 PMCID: PMC3033422 DOI: 10.1371/journal.pone.0016731] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 12/24/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The rumen harbors a complex microbial ecosystem for efficient hydrolysis of plant polysaccharides which are the main constituent of the diet. Xylanase is crucial for hemicellulose hydrolysis and plays an important role in the plant cell wall degradation. Xylanases of ruminal strains were widely studied, but few studies have focused on their diversity in rumen microenvironment. METHODOLOGY/PRINCIPAL FINDINGS We explored the genetic diversity of xylanases belonging to two major glycosyl hydrolase families (GH 10 and 11) in goat rumen contents by analyzing the amplicons generated with two degenerate primer sets. Fifty-two distinct GH 10 and 35 GH 11 xylanase gene fragments (similarity <95%) were retrieved, and most had low identities with known sequences. Based on phylogenetic analysis, all GH 10 xylanase sequences fell into seven clusters, and 88.5% of them were related to xylanases from Bacteroidetes. Five clusters of GH 11 xylanase sequences were identified. Of these, 85.7% were related to xylanases from Firmicutes, and 14.3% were related to those of rumen fungi. Two full-length xylanase genes (one for each family) were directly cloned and expressed in Escherichia coli. Both the recombinant enzymes showed substantial xylanase activity, and were purified and characterized. Combined with the results of sheep rumen, Bacteroidetes and Firmicutes are the two major phyla of xylan-degrading microorganisms in rumen, which is distinct from the representatives of other environments such as soil and termite hindgut, suggesting that xylan-degrading microorganisms are environment specific. CONCLUSION/SIGNIFICANCE The numerous new xylanase genes suggested the functional diversity of xylanase in the rumen microenvironment which may have great potential applications in industry and agriculture. The phylogenetic diversity and different distributions of xylanase genes will help us understand their roles in plant cell wall degradation in the rumen microenvironment.
Collapse
Affiliation(s)
- Guozeng Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Kun Meng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yaru Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Pengjun Shi
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Xia Pan
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Peilong Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Qiyu Diao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Hongfu Zhang
- State Key Lab of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
- * E-mail:
| |
Collapse
|
17
|
Bretschger O, Osterstock JB, Pinchak WE, Ishii S, Nelson KE. Microbial fuel cells and microbial ecology: applications in ruminant health and production research. MICROBIAL ECOLOGY 2010; 59:415-27. [PMID: 20024685 PMCID: PMC2855437 DOI: 10.1007/s00248-009-9623-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 11/27/2009] [Indexed: 05/28/2023]
Abstract
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.
Collapse
Affiliation(s)
- Orianna Bretschger
- J. Craig Venter Institute, 10355 Science Center Dr., San Diego, CA 92121 USA
| | | | | | - Shun’ichi Ishii
- J. Craig Venter Institute, 10355 Science Center Dr., San Diego, CA 92121 USA
| | | |
Collapse
|
18
|
Ghazanfar S, Azim A. Metagenomics and its Application in Rumen Ecosystem: Potential Biotechnological Prospects. ACTA ACUST UNITED AC 2009. [DOI: 10.3923/pjn.2009.1309.1315] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
19
|
Plant biomass degradation by gut microbiomes: more of the same or something new? Curr Opin Biotechnol 2009; 20:358-63. [PMID: 19515552 DOI: 10.1016/j.copbio.2009.05.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2009] [Revised: 05/13/2009] [Accepted: 05/14/2009] [Indexed: 11/21/2022]
Abstract
Herbivores retain within their gastrointestinal tract a microbiome that specializes in the rapid hydrolysis and fermentation of lignocellulosic plant biomass. With the emergence of high-throughput DNA sequencing technologies and related 'omics' approaches, along with demands to better utilize lignocellulose materials as a feedstock for second-generation biofuels, these gut microbiomes are thought to be a potential source of novel biotechnologies relevant to meeting these needs. This review provides an insight into the new findings that have arisen from the (meta)genomic analysis of specialist cellulolytic bacteria and gut microbiomes of herbivorous insects, ruminants, native Australian marsupials, and other obligate herbivores. In addition to there being more of the same in terms of cellulases and cellulosomes, there also appears to be something 'new' in terms of the compositional and functional attributes of the plant cell wall deconstruction systems employed by these bacteria. However, future dissection and capture of useful biotechnologies via metagenomics will need more than the production of data using next generation sequencing technologies.
Collapse
|