Genome and pan-genome analysis to classify emerging bacteria

Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol. 1977;31:107–33. Finegold SM, Attebery HR, Sutter VL. Effect of diet on human fecal flora: comparison of Japanese and American diets. Am J Clin Nutr. 1974;27:1456–69. Moore WE, Holdeman LV. Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl Microbiol. 1974;27:961–79. Lagier J-C, Edouard S, Pagnier I, Mediannikov O, Drancourt M, Raoult D. Current and past strategies for bacterial culture in clinical microbiology. Clin Microbiol Rev. 2015;28:208-36. Caputo A, Dubourg G, Croce O, Gupta S, Robert C, Papazian L, et al. Whole-genome assembly of Akkermansia muciniphila sequenced directly from human stool. Biol Direct. 2015;10:5. Lagier J-C, Million M, Hugon P, Armougom F, Raoult D. Human gut microbiota: repertoire and variations. Front Cell Infect Microbiol. 2012;2:136. Lagier J-C, Hugon P, Khelaifia S, Fournier P-E, La Scola B, Raoult D. The rebirth of culture in microbiology through the example of Culturomics to study human gut microbiota. Clin Microbiol Rev. 2015;28:237-64. Lagier J-C, Khelaifia S, Alou MT, Ndongo S, Dione N, Hugon P, et al. Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol. 2016;1:16203. Fournier P-E, Lagier J-C, Dubourg G, Raoult D. From culturomics to taxonomogenomics: a need to change the taxonomy of prokaryotes in clinical microbiology. Anaerobe. 2015;36:73–8. Caputo A, Lagier J-C, Azza S, Robert C, Mouelhi D, Fournier P-E, et al. Microvirga massiliensis sp. nov., the human commensal with the largest genome. MicrobiologyOpen. 2016;5:307–22. Staley JT. The bacterial species dilemma and the genomic-phylogenetic species concept. Philos Trans R Soc B Biol Sci. 2006;361:1899–909. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol. 2010;60:249–66. Kämpfer P, Glaeser SP. Prokaryotic taxonomy in the sequencing era--the polyphasic approach revisited. Environ Microbiol. 2012;14:291–317. Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev. 2001;25:39–67. Drancourt M, Berger P, Raoult D. Systematic 16S rRNA gene sequencing of atypical clinical isolates identified 27 new bacterial species associated with humans. J Clin Microbiol. 2004;42:2197–202. Drancourt M, Raoult D. Taxonomic position of the Rickettsiae: current knowledge. FEMS Microbiol Rev. 1994;13:13–24. Ogata H, Audic S, Renesto-Audiffren P, Fournier PE, Barbe V, Samson D, et al. Mechanisms of evolution in rickettsia conorii and R. Prowazekii. Science. 2001;293:2093–8. Sentausa E, Fournier P-E. Advantages and limitations of genomics in prokaryotic taxonomy. Clin Microbiol Infect. 2013;19:790–5. O’Malley MA, Koonin EV. How stands the tree of life a century and a half after the origin? Biol Direct. 2011;6:32. Dagan T, Roettger M, Stucken K, Landan G, Koch R, Major P, et al. Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol Evol. 2013;5:31–44. Pei AY, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, Gerz EA, et al. Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol. 2010;76:3886–97. Ochman H, Elwyn S, Moran NA. Calibrating bacterial evolution. Proc Natl Acad Sci U S A. 1999;96:12638–43. Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol. 2004;186:2629–35. Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol. 1975;94:441–8. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci. 1977;74:5463–7. Ambardar S, Gupta R, Trakroo D, Lal R, Vakhlu J. High throughput sequencing: an overview of sequencing chemistry. Indian J Microbiol. 2016;56:394–404. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome.”. Proc Natl Acad Sci U S A. 2005;102:13950–5. Tettelin H, Riley D, Cattuto C, Medini D. Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol. 2008;11:472–7. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev. 2005;15:589–94. Mira A, Martín-Cuadrado AB, D’Auria G, Rodríguez-Valera F. The bacterial pan-genome:a new paradigm in microbiology. Int Microbiol Off J Span Soc Microbiol. 2010;13:45–57. Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, et al. Origins of the E. Coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med. 2011;365:709–17. Chun J, Grim CJ, Hasan NA, Lee JH, Choi SY, Haley BJ, et al. Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae. Proc Natl Acad Sci U S A. 2009;106:15442–7. den Bakker HC, Cummings CA, Ferreira V, Vatta P, Orsi RH, Degoricija L, et al. Comparative genomics of the bacterial genus Listeria: genome evolution is characterized by limited gene acquisition and limited gene loss. BMC Genomics. 2010;11:688. Olivares J, Bernardini A, Garcia-Leon G, Corona F, B Sanchez M, Martinez JL. The intrinsic resistome of bacterial pathogens. Front Microbiol. 2013;4:103. Diene SM, Merhej V, Henry M, Filali AE, Roux V, Robert C, et al. The Rhizome of the Multidrug-Resistant Enterobacter aerogenes Genome Reveals How New “Killer Bugs” Are Created because of a Sympatric Lifestyle. Mol Biol Evol. 2012;30:mss236. Caputo A, Merhej V, Georgiades K, Fournier P-E, Croce O, Robert C, et al. Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the Klebsiella paradigm. Biol Direct. 2015;10:55. Camiolo S, Sablok G, Porceddu A. Altools: a user friendly NGS data analyser. Biol Direct. 2016;11:8. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, et al. Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol. 2006;24:680–6. Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, et al. One bacterial cell, one complete genome. PLoS One. 2010;5:e10314. Gawad C, Koh W, Quake SR. Single-cell genome sequencing: current state of the science. Nat Rev Genet. 2016;17:175–88. Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG, 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. 2007;104:11889–94. McLean JS, Lombardo M-J, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, et al. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc Natl Acad Sci. 2013;110:E2390–9. Lasken RS. Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol. 2012;10:631–40. Rappé MS, Giovannoni SJ. The uncultured microbial majority. Annu Rev Microbiol. 2003;57:369–94. Wang Y, Navin NE. Advances and applications of single cell sequencing technologies. Mol Cell. 2015;58:598–609. Doud DFR, Woyke T. Novel approaches in function-driven single-cell genomics. FEMS Microbiol Rev. 2017;41:538–48. Nasheri N, Petronella N, Ronholm J, Bidawid S, Corneau N. Characterization of the genomic diversity of norovirus in linked patients using a metagenomic deep sequencing approach. Front Microbiol. 2017;8:73. Weng FC-H, Shaw GT-W, Weng C-Y, Yang Y-J, Wang D. Inferring microbial interactions in the gut of the Hong Kong whipping frog (Polypedates megacephalus) and a validation using probiotics. Front Microbiol. 2017;8:525. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016;17:333–51. Ekblom R, Wolf JBW. A field guide to whole-genome sequencing, assembly and annotation. Evol Appl. 2014;7:1026–42. Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res. 1999;9:868–77. Idury RM, Waterman MS. A new algorithm for DNA sequence assembly. J Comput Biol J Comput Mol Cell Biol. 1995;2:291–306. Cabau C, Escudié F, Djari A, Guiguen Y, Bobe J, Klopp C. Compacting and correcting trinity and oases RNA-Seq de novo assemblies. PeerJ. 2017;5:e2988. Cao MD, Nguyen SH, Ganesamoorthy D, Elliott AG, Cooper MA, Coin LJM. Scaffolding and completing genome assemblies in real-time with nanopore sequencing. Nat Commun. 2017;8:14515. Bilen M, Beye M, Fonkou MDM, Khelaifia S, Cadoret F, Armstrong N, et al. Genomic and phenotypic description of the newly isolated human species Collinsella bouchesdurhonensis sp. nov. MicrobiologyOpen. 2018;7(5):e00580. Liu D, Hunt M, Tsai IJ. Inferring synteny between genome assemblies: a systematic evaluation. BMC Bioinformatics. 2018;19:26. Lugli GA, Milani C, Mancabelli L, van Sinderen D, Ventura M. MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation. FEMS Microbiol Lett. 2016;363. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10. Stein L. Genome annotation: from sequence to biology. Nat Rev Genet. 2001;2:493–503. Médigue C, Bocs S, Labarre L, Mathé C, Vallenet D. L’annotation in silico des séquences génomiques. médecine/sciences. 2002;18:237–50. Hernandez D, François P, Farinelli L, Osterås M, Schrenzel J. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 2008;18:802–9. Nishito Y, Osana Y, Hachiya T, Popendorf K, Toyoda A, Fujiyama A, et al. Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics. 2010;11:243. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008;18:1851–8. Bratcher HB, Corton C, Jolley KA, Parkhill J, Maiden MC. A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics. 2014;15:1138. Dubourg G, Lagier J-C, Armougom F, Robert C, Audoly G, Papazian L, et al. High-level colonisation of the human gut by Verrucomicrobia following broad-spectrum antibiotic treatment. Int J Antimicrob Agents. 2013;41:149–55. Lagier J-C, Armougom F, Million M, Hugon P, Pagnier I, Robert C, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect Off Publ Eur Soc Clin Microbiol Infect Dis. 2012;18:1185–93. Msaddak A, Rejili M, Durán D, Rey L, Imperial J, Palacios JM, et al. Members of microvirga and Bradyrhizobium genera are native endosymbiotic bacteria nodulating Lupinus luteus in northern Tunisian soils. FEMS Microbiol Ecol. 2017;93. Busquets A, Gomila M, Beiki F, Mulet M, Rahimian H, García-Valdés E, et al. Pseudomonas caspiana sp. nov., a citrus pathogen in the Pseudomonas syringae phylogenetic group. Syst Appl Microbiol. [cited 2017 Jun 13]; Available from: http://www.sciencedirect.com/science/article/pii/S0723202017300450 Vinuesa P, León-Barrios M, Silva C, Willems A, Jarabo-Lorenzo A, Pérez-Galdona R, et al. Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae: Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. Genistearum, Bradyrhizobium genospecies alpha and Bradyrhizobium genospecies beta. Int J Syst Evol Microbiol. 2005;55:569–75. Wang M, Cao B, Yu Q, Liu L, Gao Q, Wang L, et al. Analysis of the 16S–23S rRNA gene internal transcribed spacer region in Klebsiella species. J Clin Microbiol. 2008;46:3555–63. Gupta RS. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev MMBR. 1998;62:1435–91. Ramasamy D, Mishra AK, Lagier J-C, Padhmanabhan R, Rossi M, Sentausa E, et al. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol. 2014;64:384–91. Ramasamy D, Kokcha S, Lagier J-C, Nguyen T-T, Raoult D, Fournier P-E. Genome sequence and description of Aeromicrobium massiliense sp. nov. Stand Genomic Sci. 2012;7:246–57. Roux V, Lagier J-C, Gorlas A, Robert C, Raoult D. Non-contiguous finished genome sequence and description of Kurthia senegalensis sp. nov. Stand Genomic Sci. 2014;9:1319–30. Hugon P, Mishra AK, Lagier J-C, Nguyen TT, Couderc C, Raoult D, et al. Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov. Stand Genomic Sci. 2013;8:1–14. Kokcha S, Ramasamy D, Lagier J-C, Robert C, Raoult D, Fournier P-E. Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov. Stand Genomic Sci. 2012;7:233–45. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol. 2014;66:1–5. Lagier J-C, Armougom F, Mishra AK, Nguyen T-T, Raoult D, Fournier P-E. Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov. Stand Genomic Sci. 2012;6:315–24. Lagier J-C, El Karkouri K, Nguyen T-T, Armougom F, Raoult D, Fournier P-E. Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov. Stand Genomic Sci. 2012;6:116–25. Lagier J-C, Gimenez G, Robert C, Raoult D, Fournier P-E. Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. Stand Genomic Sci. 2012;7:200–9. Lagier J-C, El Karkouri K, Mishra AK, Robert C, Raoult D, Fournier P-E. Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov. Stand Genomic Sci. 2013;7:399–412. Lagier J-C, Elkarkouri K, Rivet R, Couderc C, Raoult D, Fournier P-E. Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. Nov., sp. nov. Stand Genomic Sci. 2013;7:343–56. Pei J, Chu C, Li X, Lu B, Wu Y. CLADES: A classification-based machine learning method for species delimitation from population genetic data. Mol Ecol Resour. 2018;18(5):1144–56. Paolozzi L, Liébart J-C, Sansonetti P. Microbiologie: biologie des procaryotes et de leurs virus. Paris: Dunod; 2015. Skerman VBD, McGowan V, Sneath PHA. Approved lists of bacterial names. Int J Syst Evol Microbiol. 1980;30:225–420. Reeves MW, Evins GM, Heiba AA, Plikaytis BD, Farmer JJ. Clonal nature of Salmonella typhi and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of Salmonella bongori comb. nov. J Clin Microbiol. 1989;27:313–20. Le Minor L, Popoff MY. Designation of Salmonella enterica sp. nov., nom. Rev., as the type and only species of the Genus Salmonella: request for an opinion. Int J Syst Evol Microbiol. 1987;37:465–8. Moore ERB, Mihaylova SA, Vandamme P, Krichevsky MI, Dijkshoorn L. Microbial systematics and taxonomy: relevance for a microbial commons. Res Microbiol. 2010;161:430–8. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, et al. Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol. 2005;3:733–9. Hugon P, Dufour J-C, Colson P, Fournier P-E, Sallah K, Raoult D. A comprehensive repertoire of prokaryotic species identified in human beings. Lancet Infect Dis. 2015;15:1211–9. Zakhia F, de Lajudie P. Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL). Can J Microbiol. 2006;52:169–81. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today. 2006;33:152–5. Krawiec S. Concept of a bacterial species. Int J Syst Bacteriol. 1985;35:217–20. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev. 1996;60:407–38. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol. 1987;37:463–4. Keswani J, Whitman WB. Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int J Syst Evol Microbiol. 2001;51:667–78. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA Reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol. 1994;44:846–9. Ritari J, Salojärvi J, Lahti L, de Vos WM. Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database. BMC Genomics. 2015;16:1056. Rainey FA, Ward-Rainey NL, Janssen PH, Hippe H, Stackebrandt E. Clostridium paradoxum DSM 7308T contains multiple 16S rRNA genes with heterogeneous intervening sequences. Microbiol Read Engl. 1996;142(Pt 8):2087–95. Dagan T, Martin W. The tree of one percent. Genome Biol. 2006;7:118. Gándara B, Merino AL, Rogel MA, Martı́nez-Romero E. Limited Genetic Diversity ofBrucella spp. J Clin Microbiol. 2001;39:235–40. Větrovský T, Baldrian P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One. 2013;8:e57923. Marchandin H, Teyssier C, Siméon De Buochberg M, Jean-Pierre H, Carriere C, Jumas-Bilak E. Intra-chromosomal heterogeneity between the four 16S rRNA gene copies in the genus Veillonella: implications for phylogeny and taxonomy. Microbiol Read Engl. 2003;149:1493–501. van Berkum P, Terefework Z, Paulin L, Suomalainen S, Lindström K, Eardly BD. Discordant phylogenies within the rrn loci of rhizobia. J Bacteriol. 2003;185:2988–98. Fitz-Gibbon ST, House CH. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 1999;27:4218–22. Tekaia F, Lazcano A, Dujon B. The genomic tree as revealed from whole proteome comparisons. Genome Res. 1999;9:550–7. Rivera MC, Lake JA. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature. 2004;431:152–5. Montague MG, Hutchison CA. Gene content phylogeny of herpesviruses. Proc Natl Acad Sci U S A. 2000;97:5334–9. Gupta RS. The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Int Microbiol Off J Span Soc Microbiol. 2001;4:187–202. Coenye T, Vandamme P. Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case. Microbiol Read Engl. 2003;149:3507–17. Huson DH, Steel M. Phylogenetic trees based on gene content. Bioinforma Oxf Engl. 2004;20:2044–9. Snel B, Bork P, Huynen MA. Genome phylogeny based on gene content. Nat Genet. 1999;21:108–10. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007;57:81–91. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci. 2010;2:117–34. Auch AF, Klenk H-P, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci. 2010;2:142–8. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E, Thompson FL. Microbial genomic taxonomy. BMC Genomics. 2013;14:913. Bascomb S, Lapage SP, Willcox WR, Curtis MA. Numerical classification of the tribe Klebsielleae. J Gen Microbiol. 1971;66:279–95. Cowan ST, Steel M, Shaw C, Duguid JP. A classification of the Klebsiella group. J Gen Microbiol. 1960;23:601–12. Brenner DJ, Farmer JJ, Hickman FW, Asbury MA, Steigerwalt AG. Taxonomic and Nomenclature Changes in Enterobacteriaceae. [cited 2017 May 31]. Available from: https://www.abebooks.fr/Taxonomic-Nomenclature-Enterobacteriaceae-Don-Brenner-Farmer/4158251114/bd Klebsiella OI. Bergey’s man Syst Bacteriol; 1974. Orskov I, Genus V. Klebsiella. Bergey’s manual of systematic bacteriology. 1984:461–5. Rouli L, Merhej V, Fournier P-E, Raoult D. The bacterial pangenome as a new tool for analyzing pathogenic bacteria. New Microbes New Infect. [cited 2015 Jul 20]; Available from: http://www.sciencedirect.com/science/article/pii/S2052297515000529 Ereshefsky M. Eliminative Pluralism. Philos Sci. 1992;59:671–90.