Microbial diversity and the genetic nature of microbial species (original) (raw)
Pace, N. R. Time for a change. Nature441, 289 (2006). Discourages the use of the term prokaryotes to cover Bacteria and Archaea. ArticleCASPubMed Google Scholar
Doolittle, W. F. & Papke, R. T. Genomics and the bacterial species problem. Genome Biol.7, 116 (2006). Questions whether microbial species represent a true biological grouping. ArticlePubMedPubMed CentralCAS Google Scholar
Mayr, E. Systematics and the Origin of Species — From the Viewpoint of a Zoologist (Harvard Univ. Press, Cambridge, 1942). Google Scholar
Coyne, J. A. & Orr, H. A. Speciation (Sinauer Associates, Sunderland, 2004). Google Scholar
Vandamme, P. et al. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev.60, 407–438 (1996). CASPubMedPubMed Central Google Scholar
de Queiroz, K. Ernst Mayr and the modern concept of species. Proc. Natl Acad. Sci. USA102 (Suppl. 1), 6600–6607 (2005). The source of the metapopulation lineage concept used in this Review. ArticleCASPubMedPubMed Central Google Scholar
Hey, J. On the failure of modern species concepts. Trends Ecol. Evol.21, 447–450 (2006). ArticlePubMed Google Scholar
Rossello-Mora, R. & Amann, R. The species concept for prokaryotes. FEMS Microbiol. Rev.25, 39–67 (2001). ArticleCASPubMed Google Scholar
Gevers, D. et al. Opinion: re-evaluating prokaryotic species. Nature Rev. Microbiol.3, 733–739 (2005). ArticleCAS Google Scholar
Stackebrandt, E. et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol.52, 1043–1047 (2002). CASPubMed Google Scholar
Konstantinidis, K. T., Ramette, A. & Tiedje, J. M. The bacterial species definition in the genomic era. Philos. Trans. R. Soc. Lond. B361, 1929–1940 (2006). Article Google Scholar
Buckley, M. & Roberts, R. J. Critical Issues Colloquia Reports. Reconciling Microbial Systematics and Genomics (American Academy of Microbiology, Washington DC, 2007). Google Scholar
Ley, R. E., Turnbaugh, P. J., Klein, S. & Gordon, J. I. Microbial ecology: human gut microbes associated with obesity. Nature444, 1022–1023 (2006). ArticleCASPubMed Google Scholar
Goris, J. et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol.57, 81–91 (2007). ArticleCASPubMed Google Scholar
Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature428, 37–43 (2004). ArticleCASPubMed Google Scholar
Strous, M. et al. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature440, 790–794 (2006). ArticlePubMed Google Scholar
Hallam, S. J. et al. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc. Natl Acad. Sci. USA103, 18296–18301 (2006). ArticleCASPubMedPubMed Central Google Scholar
Halpern, A. L. et al. The Sorcerer II global ocean sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol.5, e77 (2007). ArticlePubMedPubMed CentralCAS Google Scholar
Marcy, Y. et al. Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl Acad. Sci. USA104, 11889–11894 (2007). ArticleCASPubMedPubMed Central Google Scholar
Mussmann, M. et al. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol.5, e230 (2007). ArticlePubMedPubMed CentralCAS Google Scholar
Cohan, F. M. & Perry, E. B. A systematics for discovering the fundamental units of bacterial diversity. Curr. Biol.17, R373–R386 (2007). ArticleCASPubMed Google Scholar
Koeppel, A. et al. Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc. Natl Acad. Sci. USA105, 2504–2509 (2008). ArticleCASPubMedPubMed Central Google Scholar
Sikorski, J. & Nevo, E. Adaptation and incipient sympatric speciation of Bacillus simplex under microclimatic contrast at “Evolution Canyons” I and II, Israel. Proc. Natl Acad. Sci. USA102, 15924–15929 (2005). ArticleCASPubMedPubMed Central Google Scholar
Smith, N. H., Gordon, S. V., Rua-Domenech, R., Clifton-Hadley, R. S. & Hewinson, R. G. Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis. Nature Rev. Microbiol.4, 670–681 (2006). ArticleCAS Google Scholar
Polz, M. F., Hunt, D. E., Preheim, S. P. & Weinreich, D. M. Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos. Trans. R. Soc. Lond. B361, 2009–2021 (2006). Article Google Scholar
Coleman, M. L. et al. Genomic islands and the ecology and evolution of Prochlorococcus. Science311, 1768–1770 (2006). ArticleCASPubMed Google Scholar
Achtman, M. et al. Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl Acad. Sci. USA96, 14043–14048 (1999). ArticleCASPubMedPubMed Central Google Scholar
Achtman, M. et al. Microevolution and history of the plague bacillus, Yersinia pestis. Proc. Natl Acad. Sci. USA101, 17837–17842 (2004). ArticleCASPubMedPubMed Central Google Scholar
Linz, B., Schenker, M., Zhu, P. & Achtman, M. Frequent interspecific genetic exchange between commensal neisseriae and Neisseria meningitidis. Mol. Microbiol.36, 1049–1058 (2000). ArticleCASPubMed Google Scholar
Zhu, P. et al. Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis. Proc. Natl Acad. Sci. USA98, 5234–5239 (2001). ArticleCASPubMedPubMed Central Google Scholar
Selander, R. K. et al. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol.51, 873–884 (1986). CASPubMedPubMed Central Google Scholar
Maiden, M. C. Multilocus sequence typing of bacteria. Annu. Rev. Microbiol.60, 561–588 (2006). ArticleCASPubMed Google Scholar
Feil, E. J. Small change: keeping pace with microevolution. Nature Rev. Microbiol.2, 483–495 (2004). ArticleCAS Google Scholar
Maynard Smith, J., Smith, N. H., O'Rourke, M. & Spratt, B. G. How clonal are bacteria? Proc. Natl Acad. Sci. USA90, 4384–4388 (1993). A revolutionary publication that altered our thought processes on the importance of homologous recombination. Article Google Scholar
Vergin, K. L. et al. High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR11). Environ. Microbiol.9, 2430–2440 (2007). ArticleCASPubMed Google Scholar
Lodders, N., Stackebrandt, E. & Nübel, U. Frequent genetic recombination in natural populations of the marine cyanobacterium Microcoleus chthonoplastes. Environ. Microbiol.7, 434–442 (2005). ArticleCASPubMed Google Scholar
Whitaker, R. J. Allopatric origins of microbial species. Philos. Trans. R. Soc. Lond. B361, 1975–1984 (2006). Article Google Scholar
Linz, B. et al. An African origin for the intimate association between humans and Helicobacter pylori. Nature445, 915–918 (2007). Bacterial biogeography as a mirror of ancient human migrations. ArticlePubMedPubMed Central Google Scholar
Falush, D. et al. Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size and minimal age. Proc. Natl Acad. Sci. USA98, 15056–15061 (2001). ArticleCASPubMedPubMed Central Google Scholar
Falush, D. et al. Mismatch induced speciation in Salmonella: model and data. Philos. Trans. R. Soc. Lond. B361, 2045–2053 (2006). Article Google Scholar
Eppley, J. M., Tyson, G. W., Getz, W. M. & Banfield, J. F. Genetic exchange across a species boundary in the archaeal genus Ferroplasma. Genetics177, 407–416 (2007). ArticleCASPubMedPubMed Central Google Scholar
Hanage, W. P., Fraser, C. & Spratt, B. G. Sequences, sequence clusters and bacterial species. Philos. Trans. R. Soc. Lond. B361, 1917–1927 (2006). One of a number of articles from a special symposium that are cited here and that illustrate various aspects of diversity within microbial species. The whole symposium is highly recommended as background material. Article Google Scholar
Eppinger, M. et al. Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PLoS Genet.2, e120 (2006). ArticlePubMedPubMed CentralCAS Google Scholar
Keim, P., Johansson, A. & Wagner, D. M. Molecular epidemiology, evolution, and ecology of Francisella. Ann. NY Acad. Sci.1105, 30–66 (2007). ArticleCASPubMed Google Scholar
Retchless, A. C. & Lawrence, J. G. Temporal fragmentation of speciation in bacteria. Science317, 1093–1096 (2007). ArticleCASPubMed Google Scholar
Falush, D. et al. Traces of human migrations in Helicobacter pylori populations. Science299, 1582–1585 (2003). ArticleCASPubMed Google Scholar
Grundmann, H., Aires-de-Sousa, M., Boyce, J. & Tiemersma, E. Emergence and resurgence of meticillin-resistant Staphylococcus aureus as a public-health threat. Lancet368, 874–885 (2006). ArticlePubMed Google Scholar
Welch, R. A. et al. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl Acad. Sci. USA99, 17020–17024 (2002). ArticleCASPubMedPubMed Central Google Scholar
Lloyd, A. L., Rasko, D. A. & Mobley, H. L. Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli. J. Bacteriol.189, 3532–3546 (2007). ArticleCASPubMedPubMed Central Google Scholar
Hacker, J. & Carniel, E. Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep.2, 376–381 (2001). ArticleCASPubMedPubMed Central Google Scholar
Gal-Mor, O. & Finlay, B. B. Pathogenicity islands: a molecular toolbox for bacterial virulence. Cell. Microbiol.8, 1707–1719 (2006). ArticleCASPubMed Google Scholar
Mussmann, M. et al. Clustered genes related to sulfate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer. J. Bacteriol.187, 7126–7137 (2005). ArticleCASPubMedPubMed Central Google Scholar
Tettelin, H. et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc. Natl Acad. Sci. USA102, 13950–13955 (2005). ArticleCASPubMedPubMed Central Google Scholar
Dagan, T. & Martin, W. Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc. Natl Acad. Sci. USA104, 870–875 (2007). ArticleCASPubMedPubMed Central Google Scholar
Ochman, H. & Groisman, E. A. Distribution of pathogenicity islands in Salmonella spp. Infect. Immun.64, 5410–5412 (1996). CASPubMedPubMed Central Google Scholar
Vernikos, G. S. & Parkhill, J. Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics22, 2196–2203 (2006). ArticleCASPubMed Google Scholar
Shih, A. C., Hsiao, T. C., Ho, M. S. & Li, W. H. Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proc. Natl Acad. Sci. USA104, 6283–6288 (2007). ArticleCASPubMedPubMed Central Google Scholar
Gagneux, S. et al. The competitive cost of antibiotic resistance in Mycobacterium tuberculosis. Science312, 1944–1946 (2006). The role of fitness in natural microbial populations. ArticleCASPubMed Google Scholar
Weissman, S. J. et al. Differential stability and trade-off effects of pathoadaptive mutations in the Escherichia coli FimH adhesin. Infect. Immun.75, 3548–3555 (2007). ArticleCASPubMedPubMed Central Google Scholar
Smith, E. E. et al. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc. Natl Acad. Sci. USA103, 8487–8492 (2006). ArticleCASPubMedPubMed Central Google Scholar
Moran, N. A. & Plague, G. R. Genomic changes following host restriction in bacteria. Curr. Opin. Genet. Dev.14, 627–633 (2004). ArticleCASPubMed Google Scholar
Dethlefsen, L., McFall-Ngai, M. & Relman, D. A. An ecological and evolutionary perspective on human–microbe mutualism and disease. Nature449, 811–818 (2007). ArticleCASPubMed Google Scholar
Curtis, T. P., Sloan, W. T. & Scannell, J. W. Estimating prokaryotic diversity and its limits. Proc. Natl Acad. Sci. USA99, 10494–10499 (2002). ArticleCASPubMedPubMed Central Google Scholar
Huber, J. A. et al. Microbial population structure in the deep marine biosphere. Science318, 97–100 (2007). ArticleCASPubMed Google Scholar
Johnson, Z. I. et al. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science311, 1737–1740 (2006). ArticleCASPubMed Google Scholar
Thompson, J. R. et al. Genotypic diversity within a natural coastal bacterioplankton population. Science307, 1311–1313 (2005). ArticleCASPubMed Google Scholar
Wilhelm, L. J., Tripp, H. J., Givan, S. A., Smith, D. P. & Giovannoni, S. J. Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data. Biol. Direct2, 27 (2007). ArticlePubMedPubMed CentralCAS Google Scholar
Wayne, L. G. et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol.37, 463–464 (1987). Article Google Scholar
Stackebrandt, E. & Ebers, J. Taxonomic parameters revisited: tarnished gold standards. Microbiol. Today33, 152–155 (2006). Google Scholar
Murray, R. G. & Stackebrandt, E. Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int. J. Syst. Bacteriol.45, 186–187 (1995). ArticleCASPubMed Google Scholar
Staley, J. T. The bacterial species dilemma and the genomic–phylogenetic species concept. Philos. Trans. R. Soc. Lond. B361, 1899–1909 (2006). Article Google Scholar
Dykhuizen, D. Species numbers in bacteria. Proceedings Calif. Acad. Sci.56, 62–71 (2005). Google Scholar
Nesbø, C. L., Dlutek, M. & Doolittle, W. F. Recombination in Thermotoga: implications for species concepts and biogeography. Genetics172, 759–769 (2006). ArticlePubMedPubMed CentralCAS Google Scholar
Maiden, M. C. J. et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl Acad. Sci. USA95, 3140–3145 (1998). The first publication to describe the MLST concept. ArticleCASPubMedPubMed Central Google Scholar
Hugenholtz, P., Pitulle, C., Hershberger, K.L. & Pace, N. R. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol.180, 366–376 (1998). CASPubMedPubMed Central Google Scholar
Liolios, K., Tavernarakis, N., Hugenholtz, P. & Kyrpides, N. C. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res.34, D332–D334 (2006). ArticleCASPubMed Google Scholar
Ribosomal gene milestone met, already left in dust. ASM News71, 6–7 (2005).