Synonyms
Host-microbiota interactions
Definition
Functional analysis of a metagenome (combined genomes of a defined system) with the aim to understand and/or identify single components of the interaction of a microbe with specific cells.
Introduction
Complex ecosystems often exert several niche-specific functions. Dependent on their entanglement and the accessibility of the ecosystem, the identification and analysis of these single functions can be challenging.
Cultivability and metabolic interdependence of microbes in their ecosystems have confronted microbial ecologist with “the great plate-count anomaly” (Staley and Konopka 1985) since the beginning of their studies. The term summarizes the great discrepancy between the loads of microscopically observed bacteria in an environmental sample and the lower numbers obtained using culture-dependent counting techniques, indicating the lack of representativeness of culture-dependent techniques in the study of most complex bacterial...
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References
Albers S-V, Jonuscheit M, Dinkelaker S, Urich T, Kletzin A, Tampé R, et al. Production of recombinant and tagged proteins in the hyperthermophilic archaeon Sulfolobus solfataricus. Appl Environ Microbiol [Internet]. 2006 [cited 2011 Aug 21];72(1):102–11. Available from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1352248&tool=pmcentrez&rendertype=abstract
Barinov A, Loux V, Hammani A, Nicolas P, Langella P, Ehrlich D, et al. Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria. Proteomics [Internet]. 2009 [cited 2012 Sep 5];9(1):61–73. Available from http://www.ncbi.nlm.nih.gov/pubmed/19053137
Cerf-Bensussan N, Gaboriau-Routhiau V. The immune system and the gut microbiota: friends or foes? Nature Rev Immunol [Internet]. Nature Publishing Group; 2010 [cited 2011 Jul 20];10(10):735–44. Available from http://www.ncbi.nlm.nih.gov/pubmed/20865020
Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Reyes-Duarte D, Santos V a PM Dos, et al. Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environ Microbiol [Internet]. 2005 [cited 2013 Jan 28];7(12):1996–2010. Available from http://www.ncbi.nlm.nih.gov/pubmed/16309396
Gabor EM, Alkema WBL, Janssen DB. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ Microbiol [Internet]. 2004 [cited 2011 Jun 22];6(9):879–86. Available from http://www.ncbi.nlm.nih.gov/pubmed/15305913
Gloux K, Berteau O, El Oumami H, Béguet F, Leclerc M, Doré J. A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome. Proc Natl Acad Sci U S A [Internet]. 2011 [cited 2011 Jul 29];108(Suppl):4539–46. Available from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3063586&tool=pmcentrez&rendertype=abstract
Gloux K, Leclerc M, Iliozer H, L’Haridon R, Manichanh C, Corthier G, et al. Development of high-throughput phenotyping of metagenomic clones from the human gut microbiome for modulation of eukaryotic cell growth. Appl Environ Microbiol [Internet]. 2007 [cited 2011 Jun 22];73(11):3734–7. Available from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1932692&tool=pmcentrez&rendertype=abstract
Hayashi H, Sakamoto M, Benno Y. Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods. Microbiol Immunol [Internet]. 2002 [cited 2011 Apr 21];46(8):535–48. Available from http://www.ncbi.nlm.nih.gov/pubmed/12363017
Healy FG, Ray RM, Aldrich HC, Wilkie AC, Ingram LO, Shanmugam KT. Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose. Appl Microbiol Biotechnol [Internet]. 1995 [cited 2011 Aug 17];43(4):667–74. Available from http://www.ncbi.nlm.nih.gov/pubmed/7546604
Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, et al. Structure, function and diversity of the healthy human microbiome. Nature [Internet]. Nature Publishing Group; 2012 [cited 2012 Jun 13];486(7402):207–14. Available from http://www.nature.com/doifinder/10.1038/nature11234
Jones BV, Begley M, Hill C, Gahan CGM, Marchesi JR. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S Am [Internet]. 2008 [cited 2011 Aug 20];105(36):13580–5. Available from http://www.pnas.org/cgi/content/abstract/105/36/13580
Lakhdari O, Cultrone A, Tap J, Gloux K, Bernard F, Ehrlich SD, et al. Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut. Sturtevant J, editor. PLoS ONE [Internet]. 2010 [cited 2010 Oct 1];5(9):e13092. Available from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2948039&tool=pmcentrez&rendertype=abstract
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature [Internet]. 2010;464(7285):59–65. Available from http://www.ncbi.nlm.nih.gov/pubmed/20203603
Staley JT, Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Ann Rev Microbiol [Internet]. 1985 [cited 2011 Aug 13];39:321–46. Available from http://www.ncbi.nlm.nih.gov/pubmed/3904603
Suau A, Bonnet R, Sutren M, Godon JJ, Gibson GR, Collins MD, et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol [Internet]. 1999;65(11):4799–807. Available from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=91647&tool=pmcentrez&rendertype=abstract
Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, et al. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res [Internet]. 2010 [cited 2010 Sep 18];20(11):1605–12. Available from http://www.ncbi.nlm.nih.gov/pubmed/20841432
Walter J, Mangold M, Tannock GW, Icrobiol APPLENM. Construction, analysis, and beta-glucanase screening of a bacterial artificial chromosome library from the large-bowel microbiota of mice. Appl Environ Microbiol. 2005;71(5):2347–54.
Wang GY, Graziani E, Waters B, Pan W, Li X, McDermott J, et al. Novel natural products from soil DNA libraries in a streptomycete host. Organ Lett [Internet]. 2000 [cited 2011 Aug 21];2(16):2401–4. Available from http://www.ncbi.nlm.nih.gov/pubmed/10956506
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de Wouters, T., Lapaque, N., Maguin, E., Doré, J., Blottière, H.M. (2015). Functional Metagenomics of Bacterial-Cell Crosstalk. In: Nelson, K.E. (eds) Encyclopedia of Metagenomics. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-7478-5_773
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DOI: https://doi.org/10.1007/978-1-4899-7478-5_773
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