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Chapter 25 : Metamicrobiology: Analyzing Microbial Behavior at the Community Level

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Metamicrobiology: Analyzing Microbial Behavior at the Community Level, Page 1 of 2

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Abstract:

This chapter explores the intersection of stress biology, community ecology, and meta-level molecular sciences. The understanding of bacterial life is more sophisticated than that of any other group of organisms, despite the tremendous physiological complexity that is the hallmark of the prokaryotes. Much of microbial cell and molecular biology is based on the assumption that the behaviors of individuals and populations of cells are the same and this is often the case. Communities can be thought of as collections of organisms, each conducting a living in the context of the rest of the community. Metagenomics provides a system-level approach to studying communities of microorganisms. In studies of gene discovery based on functional expression, metagenomics can facilitate analysis of genes in both the culturable and unculturable portions of the community. The gut microbial community is emerging as one of the most influential organs in the human body. The fusion of reductionism and systems biology can be found in metagenetics, which is the application of classical bacterial genetics to understanding communities as systems. An interesting mixture of diffusible signals and direct contact comprises the arsenal of messages used by bacteria and fungi in the mouth. Future research will need to unite metagenomics with many other approaches, including metagenetics. The richness of the interplay is particularly well illustrated by the application of genomics and mutant analysis to community-level events in the oral biofilm.

Citation: Handelsman J. 2011. Metamicrobiology: Analyzing Microbial Behavior at the Community Level, p 419-424. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch25

Key Concept Ranking

Bacterial Genetics
0.51274073
Soil Microbial Communities
0.4459573
Viruses
0.43055555
Actinomyces naeslundii
0.40000004
Streptococcus oralis
0.40000004
Actinomyces naeslundii
0.40000004
Streptococcus oralis
0.40000004
Actinomyces naeslundii
0.40000004
0.51274073
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References

/content/book/10.1128/9781555816841.ch25
1. Allen, H. K.,, K.A. Cloud-Hansen,, J.M. Wolinski,, C. Guan,, S. Greene,, S. lu,, M. Boeyink,, N. A. Broderick,, K. F. Raffa,, and J. Handelsman. 2009. Resident microbiota of the gypsy moth midgut harbors antibiotic resistance determinants. DNA Cell Biol. 28:109117.
2. Andersson, A. F., and, J.F. Banfield. 2008. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320:10471050.
3. Bamford, C. V.,, A. d’Mello, A. H. Nobbs,, L.C. Dutton, M. M. Vickerman, and, H.F. Jenkinson. 2009. Streptococcus gordonii modulates Candida albicans biofilm formation through intergeneric communication. Infect. Immun. 77:36963704.
4. Barkai, N., and, S. Leibler. 1997. Robustness in simple biochemical networks. Nature 387:913917.
5. Barsch, A., T. Patschkowski, and, K. Niehaus. 2004. Comprehensive metabolite profiling of Sinorhizobium meliloti using gas chromatography-mass spectrometry. Funct. Integr. Genomics 4:219230.
6. Beja, O.,, E.N. Spudich,, J.L. Spudich,, M. Leclerc, and, E.F. Delong. 2001. Proteorhodopsin phototrophy in the ocean. Nature 411:786789.
7. Blehert, D. S.,, R.J. Palmer,, Jr., J.B. Xavier, J. S. Almeida, and, P.E. Kolenbrander. 2003. Autoinducer 2 production by Streptococcus gordonii DL1 and the biofilm phenotype of a luxS mutant are influenced by nutritional conditions. J. Bacteriol. 185:48514860.
8. Coleman, M. L.,, M. B. Sullivan,, A.C. Martiny,, C. Steglich,, K. Barry,, E. F. Delong, and, S.W. chisholm. 2006. Genomic islands and the ecology and evolution of Prochlorococcus. Science 311:17681770.
9. Davey, M. E., and, G.A. O’Toole. 2000. Microbial biofilms: from ecology to molecular genetics. Microbiol. Mol. Biol. Rev. 64:847867.
10. DeLong, E. F. 2002. Towards microbial systems science: integrating microbial perspective, from genomes to biomes. Environ. Microbiol. 4:910.
11. Eldar, A., and, M. Elowitz. 2005. Deviations in mating. Nature 437:631632.
12. Elowitz, M. B.,, A.J. Levine,, E.D. Siggia, and, P.S. Swain. 2002. Stochastic gene expression in a single cell. Science 297:11831186.
13. Fuqua, C., and, E.P. Greenberg. 1998. Self perception in bacteria: quorum sensing with acylated homoserine lactones. Curr. Opin. Microbiol. 1:183189.
14. Fuqua, C.,, S. C. Winans, and, E.P. Greenberg. 1996. Census and consensus in bacterial ecosystems: the LuxR-Luxi family of quorum-sensing transcriptional regulators. Annu. Rev. Microbiol. 50:727751.
15. Fuqua, W. c., S. C. Winans, and, E.P. Greenberg. 1994. Quorum sensing in bacteria: the LuxR-Luxi family of cell density-responsive transcriptional regulators. J. Bacteriol. 176:269275.
16. Ghosh, D.,, K. Roy,, K.E. Williamson,, S. Srinivasiah,, K. E. Wommack,, and M. Radosevich. 2009. Acyl-homoserine lactones can induce virus production in lysogenic bacteria: an alternative paradigm for prophage induction. Appl. Environ. Microbiol. 75:71427152.
17. Gill, S. R.,, M. Pop,, R. T. Deboy,, P.B. Eckburg,, P. J. Turnbaugh,, B. S. Samuel,, J.I. Gordon,, D.A. Relman,, C. M. Fraser-Liggett, and, K.E. Nelson. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312:13551359.
18. Goh, E.-B.,, G. Yim,, W. Tsui,, J. McClure,, M.G. Surette,, and J. Davies. 2002. Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics. Proc. Natl. Acad. Sci. USA 99:1702517030.
19. Handelsman, J.,, M.R. Rondon,, S.F. Brady,, J. clardy, and, R.M. Goodman. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural productKs. Chem. Biol. 5: R245R249.
20. Johnson, B. P.,, B.J. Jensen,, E.M. Ransom,, K. A. Heinemann,, K. M. Vannatta,, K. A. Egland, and, P.G. Egland. 2009. Interspecies signaling between Veillonella atypica and Streptococcus gordonii requires the transcription factor CcpA. J. Bacteriol. 191:55635565.
21. Ley, R. E.,, F. Backhed,, P. Turnbaugh,, C.A. Lozupone,, R. D. Knight, and, J.I. Gordon. 2005. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA 102:1107011075.
22. Ley, R. E.,, P.J. Turnbaugh,, S. Klein, and, J.I. Gordon. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444:10221023.
23. Man, D.,, W. Wang,, G. Sabehi,, L. Aravind,, A.F. Post,, and R. Massana. 2003. Diversification and spectral tuning in marine proteorhodopsins. EMBO J. 22:17251731.
24. Parsek, M. R., and, E.P. Greenberg. 2005. Sociomicrobiology: the connections between quorum sensing and biofilms. Trends Microbiol. 13:2733.
25. Pazos, F., A. Valencia, and, V. De Lorenzo. 2003. The organization of the microbial biodegradation network from a systemsbiology perspective. EMBO Rep. 4:994999.
26. Periasamy, S.,, N. I. chalmers,, L. Du-Thumm, and, P.E. Kolenbrander. 2009. Fusobacterium nucleatum ATCC 10953 requires Actinomyces naeslundii ATCC 43146 for growth on saliva in a three-species community that includes Streptococcus oralis 34. Appl. Environ. Microbiol. 75:32503257.
27. Phillips, J. 1931. The biotic community. J. Ecol. 19:124.
28. Rajagopala, S. V.,, B. Titz,, J. Goll,, J.R. Parrish,, K. Wohlbold,, M. T. McKevitt,, T. Palzkill,, H. Mori,, R. L. Finley, Jr.,, and P. Uetz. 2007. The protein network of bacterial motility. Mol. Syst. Biol. 3:128.
29. Riesenfeld, C. S.,, P.D. Schloss, and, J. Handelsman. 2004. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38:525552.
30. Shapiro, J. A. 1998. Thinking about bacterial populations as multicellular organisms. Annu. Rev. Microbiol. 52:81104.
31. Swain, P. S., M. B. Elowitz, and, E.D. Siggia. 2002. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl. Acad. Sci. USA 99:1279512800.
32. Turnbaugh, P. J.,, R.E. Ley,, M.A. Mahowald,, V. Magrini,, E. R. Mardis, and, J.I. Gordon. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:10271031.
33. Yus, E.,, T. Maier,, K. Michalodimitrakis,, V. Van Noort,, T. Yamada,, W. H. Chen,, J. A. Wodke,, M. Guell,, S. Martinez,, R. Bourgeois,, S. Kuhner,, E. Raineri,, I. Letunic,, O. V. Kalinina,, M. Rode,, R. Herrmann,, R. Gutierrez-Gallego,, R. B. Russell,, A. C. Gavin,, P. Bork,, and L. Serrano. 2009. Impact of genome reduction on bacterial metabolism and its regulation. Science 326:12631268.

Tables

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Table 1.

Examples of habitats that harbor complex microbial communities

Citation: Handelsman J. 2011. Metamicrobiology: Analyzing Microbial Behavior at the Community Level, p 419-424. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch25
Generic image for table
Table 2.

Metamicrobiology approaches

Citation: Handelsman J. 2011. Metamicrobiology: Analyzing Microbial Behavior at the Community Level, p 419-424. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch25

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