Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6:431–440. doi: 10.1038/nrmicro1872

Alvarez-Pérez S, de Vega C, Herrera CM (2013) Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns. PLoS One 8:e75797. doi: 10.1371/journal.pone.0075797

Amaral GRS, Dias GM, Wellington-Oguri M et al (2014) Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences. Int J Syst Evol Microbiol 64:357–365. doi: 10.1099/ijs.0.057927-0

Auch AF, von Jan M, Klenk H-P, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134. doi: 10.4056/sigs.531120

Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75

Bayjanov JR, Molenaar D, Tzeneva V et al (2012) PhenoLink—a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains. BMC Genomics 13:170. doi: 10.1186/1471-2164-13-170

Brown JR, Douady CJ, Italia MJ et al (2001) Universal trees based on large combined protein sequence data sets. Nat Genet 28:281–285. doi: 10.1038/90129

Brown MV, Lauro FM, DeMaere MZ et al (2012) Global biogeography of SAR11 marine bacteria. Mol Syst Biol 8:595. doi: 10.1038/msb.2012.28

Cadillo-Quiroz H, Didelot X, Held NL et al (2012) Patterns of gene flow define species of thermophilic Archaea. PLoS Biol 10:e1001265. doi: 10.1371/journal.pbio.1001265

Caro-Quintero A, Konstantinidis KT (2012) Bacterial species may exist, metagenomics reveal. Environ Microbiol 14:347–355. doi: 10.1111/j.1462-2920.2011.02668.x

Chun J, Rainey FA (2014) Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 64:316–324. doi: 10.1099/ijs.0.054171-0

Coenye T, Vandamme P (2003) Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case. Microbiology 149:3507–3517. doi: 10.1099/mic.0.26515-0

Coenye T, Gevers D, Van de Peer Y et al (2005) Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 29:147–167

Cohan F (2001) Bacterial species and speciation. Syst Biol 50:513–524

Colwell RR (1970) Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol 104:410–433

Cordero OX, Polz MF (2014) Explaining microbial genomic diversity in light of evolutionary ecology. Nat Rev Microbiol 12:263–273. doi: 10.1038/nrmicro3218

Cordero OX, Ventouras LA, DeLong EF, Polz MF (2012) Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations. Proc Natl Acad Sci USA 109:20059–20064. doi: 10.1073/pnas.1213344109

Cuevas DA, Garza D, Sanchez SE et al (2014) Elucidating genomic gaps using phenotypic profiles [v1; ref status: approved with reservations 1, http://f1000r.es/488 ]. F1000Research 3:210. doi: 10.12688/f1000research.5140.1

De Ley J (1970) Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. J Bacteriol 101:738–754

De Queiroz K (2005) Ernst Mayr and the modern concept of species. Proc Natl Acad Sci USA 102(Suppl1):6600–6607. doi: 10.1073/pnas.0502030102

Denef VJ, Mueller RS, Banfield JF (2010) AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J 4:599–610. doi: 10.1038/ismej.2009.158

Didelot X, Bowden R, Wilson DJ et al (2012) Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 13:601–612. doi: 10.1038/nrg3226

Doi Y, Hazen TH, Boitano M, et al (2014) Whole genome assembly of Klebsiella pneumoniae co-producing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing. Antimicrob Agents Chemother 58(10):5947–5953. doi: 10.1128/AAC.03180-14

Doolittle WF, Papke RT (2006) Genomics and the bacterial species problem. Genome Biol 7:116. doi: 10.1186/gb-2006-7-9-116

Doolittle WF, Zhaxybayeva O (2009) On the origin of prokaryotic species. Genome Res 19:744–756. doi: 10.1101/gr.086645.108

Dutilh BE, Backus L, Edwards RA et al (2013) Explaining microbial phenotypes on a genomic scale: GWAS for microbes. Brief Funct Genomics 12:366–380. doi: 10.1093/bfgp/elt008

Dutilh BE, Thompson CC, Vicente AC et al (2014) Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions. BMC Genomics 15:654. doi: 10.1186/1471-2164-15-654

Dykhuizen D (2005) Species numbers in bacteria. Proc Calif Acad Sci 56:62–71

Ellegaard KM, Klasson L, Näslund K et al (2013) Comparative genomics of Wolbachia and the bacterial species concept. PLoS Genet 9:e1003381. doi: 10.1371/journal.pgen.1003381

Forde BM, Ben Zakour NL, Stanton-Cook M et al (2014) The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. PLoS One 9:e104400. doi: 10.1371/journal.pone.0104400

Franzosa EA, Morgan XC, Segata N et al (2014) Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci USA. doi: 10.1073/pnas.1319284111

Fraser C, Hanage WP, Spratt BG (2007) Recombination and the nature of bacterial speciation. Science 315:476–480. doi: 10.1126/science.1127573.Recombination

Fraser C, Alm EJ, Polz MF et al (2009) The bacterial species challenge: ecological diversity. Science 323:741–746

Gevers D, Cohan FM, Lawrence JG et al (2005) Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733–739

Giovannoni SJ, Tripp HJ, Givan S et al (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:1242–1245. doi: 10.1126/science.1114057

Haley BJ, Grim CJ, Hasan NA et al (2010) Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae. BMC Microbiol 10:154. doi: 10.1186/1471-2180-10-154

Hanage WP (2013) Fuzzy species revisited. BMC Biol 11:41. doi: 10.1186/1741-7007-11-41

Hanage WP, Fraser C, Spratt BG (2005) Fuzzy species among recombinogenic bacteria. BMC Biol 3:6. doi: 10.1186/1741-7007-3-6

Huang K, Brady A, Mahurkar A et al (2014) MetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acids Res 42:D617–D624. doi: 10.1093/nar/gkt1078

Hunt DE, David LA, Gevers D et al (2008) Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 320:1081–1085. doi: 10.1126/science.1157890

Kämpfer P, Glaeser SP (2012) Prokaryotic taxonomy in the sequencing era—the polyphasic approach revisited. Environ Microbiol 14:291–317. doi: 10.1111/j.1462-2920.2011.02615.x

Karlin S, Burge C (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends Genet 11:283–290

Karp PD, Ouzounis CA, Moore-Kochlacs C et al (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33:6083–6089. doi: 10.1093/nar/gki892

Kashtan N, Roggensack SE, Rodrigue S et al (2014) Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344:416–420. doi: 10.1126/science.1248575

Klenk H-P, Göker M (2010) En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 33:175–182. doi: 10.1016/j.syapm.2010.03.003

Konstantinidis KT, DeLong EF (2008) Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J 2:1052–1065. doi: 10.1038/ismej.2008.62

Konstantinidis KT, Stackebrandt E (2013) Defining taxonomic ranks. In: Rosenberg E, DeLong EF, Lory S, et al (eds) Prokaryotes (4th ed). Prokaryotic Biol. Symbiotic Assoc., 4th edn p 229

Konstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258–6264. doi: 10.1128/JB.187.18.6258

Kyrpides NC (1999) Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. Bioinformatics 15:773–774

Lan R, Reeves PR (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8:396–401

Larsen MV, Cosentino S, Lukjancenko O et al (2014) Benchmarking of methods for genomic taxonomy. J Clin Microbiol 52:1529–1539. doi: 10.1128/JCM.02981-13

Li J, Jia H, Cai X et al (2014) An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol. doi: 10.1038/nbt.2942

Mallet J (2008) Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation. Philos Trans R Soc Lond B Biol Sci 363:2971–2986. doi: 10.1098/rstb.2008.0081

Markowitz VM, Korzeniewski F, Palaniappan K et al (2006) The integrated microbial genomes (IMG) system. Nucleic Acids Res 34:D344–D348. doi: 10.1093/nar/gkj024

Markowitz VM, Chen I-MA, Palaniappan K et al (2014) IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42:D560–D567. doi: 10.1093/nar/gkt963

Mayr E (1942) Systematics and the origin of species—from the viewpoint of a zoologist. Harvard Univ. Press, Cambridge

Mick E, Sorek R (2014) High-resolution metagenomics. Nat Biotechnol 32:750–751. doi: 10.1038/nbt.2962

Moreira APB, Duytschaever G, Tonon LAC et al (2014a) Photobacterium sanctipauli sp. nov. isolated from bleached Madracis decactis (Scleractinia) in the St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil. Peer J 2:e427. doi: 10.7717/peerj.427

Moreira APB, Duytschaever G, Tonon LAC et al (2014b) Vibrio madracius sp. nov. isolated from Madracis decactis (Scleractinia) in St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil. Curr Microbiol 2:e427. doi: 10.1007/s00284-014-0600-1

Nesbø CL, Dlutek M, Doolittle WF (2006) Recombination in Thermotoga: implications for species concepts and biogeography. Genetics 172:759–769. doi: 10.1534/genetics.105.049312

Nielsen HB, Almeida M, Juncker AS et al (2014) Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol. doi: 10.1038/nbt.2939

Overbeek R, Olson R, Pusch GD et al (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–D214. doi: 10.1093/nar/gkt1226

Pagani I, Liolios K, Jansson J et al (2012) The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 40:D571–D579. doi: 10.1093/nar/gkr1100

Polz MF, Hunt DE, Preheim SP, Weinreich DM (2006) Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos Trans R Soc Lond B Biol Sci 361:2009–2021. doi: 10.1098/rstb.2006.1928

Polz MF, Alm EJ, Hanage WP (2013) Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet 29:170–175. doi: 10.1016/j.tig.2012.12.006

Preheim SP, Timberlake S, Polz MF (2011) Merging taxonomy with ecological population prediction in a case study of Vibrionaceae. Appl Environ Microbiol 77:7195–7206. doi: 10.1128/AEM.00665-11

Ramasamy D, Mishra AK, Lagier J-C et al (2014) A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 64:384–391. doi: 10.1099/ijs.0.057091-0

Rinke C, Schwientek P, Sczyrba A et al (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437. doi: 10.1038/nature12352

Rodriguez-Valera F, Martin-Cuadrado A-B, Rodriguez-Brito B et al (2009) Explaining microbial population genomics through phage predation. Nat Rev Microbiol 7:828–836. doi: 10.1038/nrmicro2235

Rohwer F, Edwards R (2002) The phage proteomic tree: a genome-based taxonomy for phage. J Bacteriol 184:4529–4535. doi: 10.1128/JB.184.16.4529

Romero P, Wagg J, Green ML et al (2005) Computational prediction of human metabolic pathways from the complete human genome. Genome Biol 6:R2. doi: 10.1186/gb-2004-6-1-r2

Rosselló-Móra R (2012) Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories. Environ Microbiol 14:318–334. doi: 10.1111/j.1462-2920.2011.02599.x

Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67

Sen A, Daubin V, Abrouk D, Gifford I, Berry AM, Normand P (2014) Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. Int J Syst Evol Microbiol 64:3821–3832. doi: 10.1099/ijs.0.063966-0

Shapiro BJ, Polz MF (2014) Ordering microbial diversity into ecologically and genetically cohesive units. Trends Microbiol 22:235–247. doi: 10.1016/j.tim.2014.02.006

Shapiro BJ, Friedman J, Cordero OX et al (2012) Population genomics of early events in the ecological differentiation of bacteria. Science 336:48–51. doi: 10.1126/science.1218198

Shiwa Y, Yanase H, Hirose Y et al (2014) Complete genome sequence of Enterococcus mundtii QU 25, an efficient l-(+)-Lactic Acid-producing bacterium. DNA Res 21:369–377. doi: 10.1093/dnares/dsu003

Sneath PHA, Sokal RR (1973) The principles and practice of numerical classification. Numer. Taxon

Snipen L, Ussery DW (2010) Standard operating procedure for computing pangenome trees. Stand Genomic Sci 2:135–141. doi: 10.4056/sigs.38923

Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155

Stackebrandt E, Frederiksen W, Garrity GM et al (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047. doi: 10.1099/ijs.0.02360-0.02360

Stackebrandt E, Smith D, Casaregola S et al (2014) Deposit of microbial strains in public service collections as part of the publication process to underpin good practice in science. Springerplus 3:208. doi: 10.1186/2193-1801-3-208

Staley JT (2006) The bacterial species dilemma and the genomic–phylogenetic species concept. Philos Trans R Soc Lond B Biol Sci 361:1899–1909. doi: 10.1098/rstb.2006.1914

Staley JT (2009) Universal species concept: Pipe dream or a step toward unifying biology? J Ind Microbiol Biotechnol 36:1331–1336. doi: 10.1007/s10295-009-0642-8

Tamames J, Rosselló-Móra R (2012) On the fitness of microbial taxonomy. Trends Microbiol 20:514–516. doi: 10.1016/j.tim.2012.08.012

Thompson CC, Vicente ACP, Souza RC et al (2009) Genomic taxonomy of vibrios. BMC Evol Biol 9:258. doi: 10.1186/1471-2148-9-258

Thompson C, Vieira NM, Vicente A, Thompson F (2011a) Towards a genome based taxonomy of Mycoplasmas. Infect Genet Evol 11:1798–1804. doi: 10.1016/j.meegid.2011.07.020

Thompson FL, Thompson CC, Dias GM et al (2011b) The genus Listonella MacDonell and Colwell 1986 is a later heterotypic synonym of the genus Vibrio Pacini 1854 (Approved Lists 1980)—a taxonomic opinion. Int J Syst Evol Microbiol 61:3023–3027. doi: 10.1099/ijs.0.030015-0

Thompson CC, Chimetto L, Edwards RA et al (2013a) Microbial genomic taxonomy. BMC Genomics 14:913. doi: 10.1186/1471-2164-14-913

Thompson CC, Emmel VE, Fonseca EL et al (2013b) Streptococcal taxonomy based on genome sequence analyses. F1000Res 2:67. doi: 10.12688/f1000research.2-67.v1

Thompson CC, Silva GZ, Vieira NM et al (2013c) Genomic taxonomy of the genus Prochlorococcus. Microb Ecol 66:752–762. doi: 10.1007/s00248-013-0270-8

Tindall BJ, Rosselló-Móra R, Busse H-J et al (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266. doi: 10.1099/ijs.0.016949-0

Vandamme P, Peeters C (2014) Time to revisit polyphasic taxonomy. Antonie Van Leeuwenhoek 106:57–65

Wayne LG, Brenner DJ, Colwell RR, et al (1987) International Committee on Systematic Bacteriology announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Bacteriol 463–464

Whitman WB (2009) The modern concept of the procaryote. J Bacteriol 191:2000–2005. doi: 10.1128/JB.00962-08 Discussion 2006–2007

Wiedenbeck J, Cohan FM (2011) Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev 35:957–976. doi: 10.1111/j.1574-6976.2011.00292.x

Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090

Woyke T, Xie G, Copeland A et al (2009) Assembling the marine metagenome, one cell at a time. PLoS One 4:e5299. doi: 10.1371/journal.pone.0005299

Wright F (1990) The effective number of codons used in a gene. Gene 87:23–29

Wu D, Hugenholtz P, Mavromatis K et al (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:1056–1060. doi: 10.1038/nature08656.A

Yarza P, Richter M, Peplies J et al (2008) The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250

Zhi X-Y, Zhao W, Li W-J, Zhao G-P (2012) Prokaryotic systematics in the genomics era. Antonie Van Leeuwenhoek 101:21–34. doi: 10.1007/s10482-011-9667-x