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Testing culture purity in prokaryotes: criteria and challenges

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Abstract

Reliance on pure cultures was introduced at the beginning of microbiology as a discipline and has remained significant although their adaptive properties are essentially dissimilar from those of mixed cultures and environmental populations. They are needed for (i) taxonomic identification; (ii) diagnostics of pathogens; (iii) virulence and pathogenicity studies; (iv) elucidation of metabolic properties; (v) testing sensitivity to antibiotics; (vi) full-length genome assembly; (vii) strain deposition in microbial collections; and (viii) description of new species with name validation. Depending on the specific task there are alternative claims for culture purity, i.e., when conventional criteria are satisfied or when looking deeper is necessary. Conventional proof (microscopic and plating controls) has a low resolution and depends on the observer’s personal judgement. Phenotypic criteria alone cannot prove culture purity and should be complemented with genomic criteria. We consider the possible use of DNA high-throughput culture sequencing data to define criteria for only one genospecies, axenic state detection panel and only one genome. The second and third of these are preferable, although their resolving capacity (depth) is limited. Because minor contaminants may go undetected, even with deep sequencing, the reliably pure culture would be a clonal culture launched from a single cell or trichome (multicellular bacterium). Although this type of culture is associated with technical difficulties and cannot be employed on a large scale (the corresponding inoculums may have low chances of growth when transferred to solid media), it is hoped that the high-throughput culturing methods introduced by ‘culturomics’ will overcome this obstacle.

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References

  • Adékambi T, Drancourt M (2004) Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing. Int J Syst Evol Microbiol 54:2095–2105

    Article  PubMed  Google Scholar 

  • Amann RI, Ludwig W, Schleifer K-H (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    PubMed  PubMed Central  CAS  Google Scholar 

  • Austin B (2017) The value of cultures to modern microbiology. Antonie Van Leeuwenhoek. https://doi.org/10.1007/s10482-017-0840-8

    Article  PubMed  Google Scholar 

  • Babenzien HD, Glöckner FO, Head IM (2005) Genus II. Achromatium Schewiakoff 1893, 1 AL. In: Brenner DJ, Krieg NR, Staley JT (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, pp 142–147

    Google Scholar 

  • Borneman J, Skroch PW, Sullivan KM, Palus JA, Rumjanek NG et al (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62:1935–1942

    PubMed  PubMed Central  CAS  Google Scholar 

  • Bragg J, Stone G, Imelfort M, Hugenholtz P, Tyson GW (2012) Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nat Methods 9:425–426

    Article  PubMed  CAS  Google Scholar 

  • Bryant MP, Wolin EA, Wolin MJ, Wolfe RS (1967) Methanobacillus omelianskii, a symbiotic association of two species of bacteria. Arch Mikrobiol 59:20–31

    Article  PubMed  CAS  Google Scholar 

  • Bulaev AG, Pivovarova TA, Melamud VS, Bumazhkin BK, Patutina EO et al (2011) Species composition of the association of acidophilic chemolithotrophic microorganisms participating in the oxidation of gold-arsenic ore concentrate. Microbiology 80:842–849

    Article  CAS  Google Scholar 

  • Case RJ, Boucher Y, Dahllöf I, Holmström C, Doolittle WF, Kjelleber GS (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73:278–288

    Article  PubMed  CAS  Google Scholar 

  • Castenholz RW (1988) Culturing methods for cyanobacteria. Meth Enzymol 167:68–93

    Article  CAS  Google Scholar 

  • Chattaway MA, Schaefer U, Tewolde R, Dallman TJ, Jenkins C (2017) Identification of Escherichia coli and Shigella species from whole-genome sequences. J Clin Microbiol 55:616–623

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen CH, Cho SH, Chiang H-I, Tsai F, Zhang K et al (2011) Specific sorting of single bacterial cells with microfabricated fluorescence-activated cell sorting and tyramide signal amplification fluorescence in situ hybridization. Anal Chem 83:7269–7275

    Article  PubMed  CAS  Google Scholar 

  • Chick H (1905) The biological limitations of the method of pure culture. New Phytol 4:120–124

    Article  Google Scholar 

  • Christensen H, Kuhnert P, Olsen JE, Biscaard M (2004) Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae. Int J Syst Evol Microbiol 54:1601–1609

    Article  PubMed  CAS  Google Scholar 

  • Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten J, Graf J (2014) Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. mBio. https://doi.org/10.1128/mbio.02136-14

    Article  PubMed  PubMed Central  Google Scholar 

  • Creecy JP, Conway T (2015) Quantitative bacterial transcriptomics with RNA-seq. Curr Opin Microbiol. https://doi.org/10.1016/j.mib.2014.11.011

    Article  PubMed  Google Scholar 

  • Cummings CA, Bormann Chung CA, Fang R, Barker M et al (2010) Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing. Investig Genet. https://doi.org/10.1186/2041-2223-1-5

    Article  PubMed  PubMed Central  Google Scholar 

  • da Mota FF, Gomes EA, Paiva E, Rosado AS, Seldin L (2004) Use of rpoB gene analysis for identification of nitrogen-fixing Paenibacillus species as an alternative to the 16S rRNA gene. Lett Appl Microbiol 39:34–40

    Article  PubMed  Google Scholar 

  • Dahllöf I, Baillie H, Kjelleberg S (2000) rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66:3376–3380

    Article  PubMed  PubMed Central  Google Scholar 

  • de Las Rivas B, Marcobal A, Muñoz R (2006) Development of a multilocus sequence typing method for analysis of Lactobacillus plantarum strains. Microbiology 152:85–93

    Article  Google Scholar 

  • Dridi B, Raoult D, Drancourt M (2011) Archaea as emerging organisms in complex human microbiomes. Anaerobe 17:56–63

    Article  PubMed  Google Scholar 

  • Duda VI, Suzina NE, Esikova TZ, Akimov VN, Oleinikov RR et al (2009) A cytological characterization of the parasitic action of ultramicrobacteria NF1 and NF3 of the genus Kaistia on chemoorganotrophic and phototrophic bacteria. FEMS Microbiol Ecol 69:180–193

    Article  PubMed  CAS  Google Scholar 

  • Elahi E, Ronaghi M (2004) Pyrosequencing: a tool for DNA sequencing analysis. Methods Mol Biol 255:211–219

    PubMed  CAS  Google Scholar 

  • Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z et al (1996) Laser capture microdissection. Science 274:998–1001

    Article  PubMed  CAS  Google Scholar 

  • Epstein SS (2013) The phenomenon of microbial uncultivability. Curr Opin Microbiol 16:636–642

    Article  PubMed  CAS  Google Scholar 

  • Fournier P-E, Lagier J-C, Dubourg G, Raoult D (2015) From culturomics to taxonomogenomics: a need to change the taxonomy of prokaryotes in clinical microbiology. Anaerobe. https://doi.org/10.1016/j.anaerobe.2015.10.011

    Article  PubMed  Google Scholar 

  • Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G et al (2015) Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling. Nat Rev Microbiol. https://doi.org/10.1038/nrmicro3451

    Article  PubMed  PubMed Central  Google Scholar 

  • Gawad C, Koh W, Quake SR (2016) Single-cell genome sequencing: current state of the science. Nat Rev Genet 17:175–188

    Article  PubMed  CAS  Google Scholar 

  • Goodfellow M (2012) Class I. Actinobacteria Stackebrandt, Rainey and Ward-Rainey 1998, 483. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K et al (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, pp 34–35

    Chapter  Google Scholar 

  • Gottschalk JC, Herder W, Prins RA (1992) Principles of enrichment, isolation, cultivation, and preservation of bacteria. In: Balows A, Trüper HG, Dworkin M, Harder W et al (eds) The Prokaryotes, 2nd edn. Springer, New York, pp 149–196

    Google Scholar 

  • Greub G (2012) Culturomics: a new approach to study the human microbiome. Clin Microbiol Infect 18:1157–1159

    Article  PubMed  CAS  Google Scholar 

  • Guay R, Silver M (1975) Thiobacillus acidophilus sp. nov., isolation and some physiological characteristics. Can J Microbiol 21:281–288

    Article  PubMed  CAS  Google Scholar 

  • Gupta RS (2016) Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin’s views on classification. FEMS Microbiol Rev 40:520–553

    Article  PubMed  CAS  Google Scholar 

  • Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249

    Article  PubMed  CAS  Google Scholar 

  • Harrison AP Jr (1981) Acidiphilium cryptum gen. nov., sp. nov., heterotrophic bacterium from acidic mineral environments. Int J Syst Bacteriol 31:327–332

    Article  Google Scholar 

  • Harrison AP Jr, Jarvis BW, Johnson JL (1980) Heterotrophic bacteria from cultures of autotrophic Thiobacillus ferrooxidans: relationships as studied by means of deoxyribonucleic acid homology. J Bacteriol 43:448–454

    Google Scholar 

  • Hobbie JE, Daley RD, Jasper S (1977) Use of nuclepore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol 33:1225–1228

    PubMed  PubMed Central  CAS  Google Scholar 

  • Holmes DE, Nevin KP, Lovley DR (2004) Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes wthin he family Geobacteraceae fam. nov. Int J Syst Evol Microbiol 54:1591–1599

    Article  PubMed  CAS  Google Scholar 

  • Hu P, Zhang W, Xin H, Deng G (2016) Single cell isolation and analysis. Front Cell Dev Biol. https://doi.org/10.3389/fcell.2016.00116

    Article  PubMed  PubMed Central  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    PubMed  PubMed Central  CAS  Google Scholar 

  • Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17:377–386

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hutchinson CA III, Venter C (2006) Single-cell genomics. Nat Biotechnol 24:657–658

    Article  Google Scholar 

  • Itoh S, Kazumi Y, Abe C, Takahashi M (2003) Heterogeneity of RNA polymerase gene (rpoB) sequences of Mycobacterium gordonae clinical isolates identified with a DNA probe kit and by conventional methods. J Clin Microbiol 41:1656–1663

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Jansen van Regensburg MJ, Swift C, Cody AJ, Jenkins C, Maiden MC (2016) Exploiting bacterial whole-genome sequencing data for evaluation of diagnostic assays: Campylobacter species identification as a case study. J Clin Microbiol 54:2882–2890

    Article  Google Scholar 

  • Joensen KG, Tetzschner AMM, Iguchi A, Aaarestrup FM, Scheutz F (2015) Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data. J Clin Microbio 53:2410–2426

    Article  CAS  Google Scholar 

  • Jørgensen B, Teske A, Ahmad A (2005) Genus VII Thioploca Lauterborn 1907, 242AL. In: Brenner DJ, Krieg NR, Staley JT (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, pp 171–178

    Google Scholar 

  • Kaeberlein T, Lewis K, Epstein SS (2002) Isolating ‘uncultivable’ microorganisms in pure culture in a stimulated natural environment. Science 296:1127–1129

    Article  PubMed  CAS  Google Scholar 

  • Kempf VA, Trebesius K, Autenbrieth IB (2000) Fluorescent in situ hybridization allows rapid identification of microorganisms in blood cultures. J Clin Microbiol 38:830–838

    PubMed  PubMed Central  CAS  Google Scholar 

  • Kennedy K, Hall MW, Lynch MDJ, Moreno-Hagelsieb G, Neufeld JD (2014) Evaluating bias of Illumina-based bacterial 16S rRNA gene profiles. Appl Environ Microbiol 80:5717–5722

    Article  PubMed  PubMed Central  Google Scholar 

  • Kim M, Yu Z (2014) Variations in 16S rRNA-based microbiome profiling between pyrosequencing runs and between pyrosequencing facilities. J Microbiol 52:355–365

    Article  PubMed  CAS  Google Scholar 

  • Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    Article  PubMed  CAS  Google Scholar 

  • Koch R (1893) Über den augenblicklichen Stand der bakteriologischen Choleradiagnose. Z Hyg Infektionskr 14:319–333

    Article  Google Scholar 

  • Köhler W (1998) Was Robert Koch inspired by William Shakespeare? Some remarks on an article by William Fry: Prince Hamlet and Professor Koch. Zbl Bakteriol 288:161–165

    Article  Google Scholar 

  • Kouzuma A, Kato S, Watanabe K (2015) Microbial interspecies interactions: recent findings in syntrophic consortia. Front Microbiol. https://doi.org/10.3389/fmicb.2015.00477

    Article  PubMed  PubMed Central  Google Scholar 

  • Krieg NR (2001) Identification of procaryotes. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, pp 33–38

    Chapter  Google Scholar 

  • Kunin V, Engelbrektson A, Ochman H, Hugenholtz P (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12:118–123

    Article  PubMed  CAS  Google Scholar 

  • Küpfer M, Kuhnert P, Korczak BM, Peduzzi R, Demarta A (2006) Genetic relationships of Aeromonas strains inferred from 16S rRNA, gyrB and rpoB gene sequences. Int J Syst Evol Microbiol 56:2743–2751

    Article  PubMed  Google Scholar 

  • Kyrpides NC, Hugenholtz P, Eisen JA, Wyoke T, Göker M et al (2014) Genomic Encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol. https://doi.org/10.1371/journal.pbio.1001920

    Article  PubMed  PubMed Central  Google Scholar 

  • Lagier J-C, Armougom F, Million M, Hugon P, Pagnier I et al (2012) Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 18:1185–1193

    Article  PubMed  CAS  Google Scholar 

  • Lagier J-C, Edouard S, Pagnier I, Mediannikov O, Drancourt M, Raoult D (2015a) Current and past strategies for bacterial culture in clinical microbiology. Clin Microbiol Rev 28:208–235

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lagier J-C, Hugon P, Khelaifia S, Fournier P-E, La Scola B, Raoult D (2015b) The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 28:237–263

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lange JL, Thorne PS, Lynch N (1997) Application of flow cytometry and fluorescent in situ hybridization for assessment of exposures to airborne bacteria. Appl Environ Microbiol 63:1557–1563

    PubMed  PubMed Central  CAS  Google Scholar 

  • Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR et al (eds) (1975) International Code of Nomenclature of Bacteria. American Society for Microbiology, Washington, DC

    Google Scholar 

  • Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H et al (2012) Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355–1361

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Laurence M, Hatzis C, Brash DE (2014) Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes. PLoS ONE. https://doi.org/10.1371/journal.pone.0097876

    Article  PubMed  PubMed Central  Google Scholar 

  • Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ et al (2012) Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS ONE. https://doi.org/10.1371/journal.pone.0044224

    Article  PubMed  PubMed Central  Google Scholar 

  • Lurie-Weinberger MN, Gophna U (2015) Archaea in and on the human body: health implications and future directions. PLoS Pathog. https://doi.org/10.1371/journal.ppat.1004833

    Article  PubMed  PubMed Central  Google Scholar 

  • Lux M, Krüger J, Rinke C, Maus I, Schlüter A et al (2016) ACDC—Automated Contamination Detection and Confidence estimation for single-cell genome data. BMC Bioinform. https://doi.org/10.1186/s12859-016-1397-7

    Article  Google Scholar 

  • Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE et al (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140–3145

    Article  PubMed  CAS  Google Scholar 

  • Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A et al (2012) The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS ONE. https://doi.org/10.1371/journal.pone.0048837

    Article  PubMed  PubMed Central  Google Scholar 

  • McVeigh N, Munro J, Embley TM (1996) Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil. J Industr Microbiol 17:197–204

    Article  CAS  Google Scholar 

  • Murray RGE, Schleifer KH (1994) Taxonomic note: a proposal for recording the properties of putative taxa of prokaryotes. Int J Syst Bacteriol 44:174–176

    Article  PubMed  CAS  Google Scholar 

  • Nai C, Meyer V (2017) From axenic to mixed cultures: technological advances accelerating a paradigm shift in microbiology. Trends Microbiol. https://doi.org/10.1016/j.tim.2017.11.004

    Article  PubMed  Google Scholar 

  • Nakagawa Y (2011) Genus I. Cytophaga Winogradsky 1929, 577AL emend. Nakagawa and Yamasato 1996, 600VP. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ et al (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, pp 371–375

    Google Scholar 

  • Nguyen-Hieu T, Khelaifia S, Aboudharam G, Drancourt M (2012) Methanogenic archaea in subgingival sites: a review. APMIS 121:467–477

    Article  PubMed  Google Scholar 

  • Olson ND, Zook JM, Morrow JB, Lin NJ (2017) Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data. Peer J. https://doi.org/10.7717/peerj.3729

    Article  PubMed  Google Scholar 

  • Ørskov J (1922) Methods for the isolation of bacteria in pure culture from single cells and procedure for the direct tracing of bacterial growth on a solid medium. J Bacteriol 7:537–549

    PubMed  PubMed Central  Google Scholar 

  • Overmann J (2006) Principles of enrichment, isolation, cultivation and preservation of prokaryotes. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes, 3rd edn. Springer, New York, pp 80–136

    Chapter  Google Scholar 

  • Parker CT, Tindall BJ, Garrity GM (2015) International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.000778

    Article  PubMed  Google Scholar 

  • Pinto AJ, Raskin L (2012) PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS ONE. https://doi.org/10.1371/journal.pone.0043093

    Article  PubMed  PubMed Central  Google Scholar 

  • Prosser JI (2010) Replicate or lie. Environ Microbiol 12:1806–1810

    Article  PubMed  CAS  Google Scholar 

  • Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinform 12:38

    Article  Google Scholar 

  • Rajwar A, Sahgal M (2016) Phylogenetic relationships of fluorescent pseudomonads deduced from the sequence analysis of 16S rRNA, Pseudomonas-specific and rpoD genes. J Biotechnol. https://doi.org/10.1007/s13205-016-0386-x

    Article  Google Scholar 

  • Rippka R, Coursin T, Hess W, Lichtlé C, Scanlan D et al (2000) Prochlorococcus marinus Chisholm et al. 1992 subsp. pastoris subsp. nov. strain PCC 9511, the first axenic chlorophyll a 2/b 2-containing cyanobacterium (Oxyphotobacteria). Int J Syst Evol Microbiol 50:1833–1847

    Article  PubMed  CAS  Google Scholar 

  • Rodrigues-Luiz GF, Cardoso MS, Valdivia HO, Ayala EV, Contijo CMF et al (2017) TipMT: identification of PCR-based taxon-specific markers. BMC Bioinform. https://doi.org/10.1186/s12859-017-1485-3

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Rosselló-Mora R, Kämpfer P (2004) Defining microbial diversity—the species concept for prokaryotic and eukaryotic microorganisms. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, DC, pp 29–39

    Chapter  Google Scholar 

  • Roux S, Enault F, Bronner G, Debroas D (2011) Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems. FEMS Microbiol Ecol 78:617–628

    Article  PubMed  CAS  Google Scholar 

  • Schulz HN, Jørgensen BB (2005) Genus VI Thiomargarita Schulz, Brinkhoff, Ferdelman, Hernández Mariné, Teske and Jørgensen 1999b, 1325 VP. In: Brenner DJ, Krieg NR, Staley JT (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, pp 169–171

    Google Scholar 

  • Segata N, Börnigen D, Morgan XC, Huttenhower C (2014) PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun. https://doi.org/10.1038/ncomms3304

    Article  PubMed  PubMed Central  Google Scholar 

  • Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE et al (2009) Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 49:543–551

    Article  PubMed  CAS  Google Scholar 

  • Shrestha PM, Nevin KP, Shrestha M, Lovely DR (2013) When is a microbial culture ‘pure’? Persistent contaminant escapes detection even with deep genome sequencing. mBio. https://doi.org/10.1128/mBio.00591-12

    Article  PubMed  PubMed Central  Google Scholar 

  • Singh S, Eldin C, Kowalczewska M, Raoult D (2013) Axenic culture of fastidious and intracellular bacteria. Trends Microbiol 21:92–99

    Article  PubMed  CAS  Google Scholar 

  • Stackebrandt E (2006) Defining taxonomic ranks. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes, 3rd edn. Springer, New York, pp 20–57

    Google Scholar 

  • Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Ann Rev Microbiol 39:321–346

    Article  CAS  Google Scholar 

  • Stewart EJ (2012) Growing unculturable bacteria. J Bacteriol 194:4151–4160

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Strohl WR (2005) Genus III. Beggiatoa Trevisan 1842, 56 AL. In: Brenner DJ, Krieg NR, Staley JT (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, pp 148–161

    Google Scholar 

  • Strous M, Kuenen JG, Fuerst JA, Wagner M, Jetten MSM (2002) The anammox case—a new experimental manifesto for microbiological eco-physiology. Ant van Leeuwenhoek 81:693–702

    Article  CAS  Google Scholar 

  • Sun D-L, Jiang X, Wu QL, Zhou N-Y (2012) Intragenomic heterogeneity of 16S rRNA genes causes overestimation of prokaryotic diversity. Appl Environ Microbiol 79:5962–5969

    Article  Google Scholar 

  • Sung Y, Ritalahti KM, Apkarian RP, Löffler FE (2006) Quantitative RCR confirms purity of strain GT, a novel Dehalococcoides isolate. Appl Environ Microbiol 72:1980–1987

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tewolde R, Dallman T, Schaefer U, Sheppard CL, Ashton P et al (2016) MOST: a modified MLST typing tool based on short read sequencing. Peer J. https://doi.org/10.7717/peerj.2308

    Article  PubMed  Google Scholar 

  • Theron J, Cloete TE (2000) Molecular techniques for determining microbial diversity and community structure in natural environments. Crit Rev Microbiol 26:37–57

    Article  PubMed  CAS  Google Scholar 

  • Tian RM, Cai L, Zhang WP, Cao HL, Qian PY (2015) Rare events of intragenus and intraspecies horizontal transfer of the 16S rRNA gene. Genome Biol Evol 7:2310–2320

    Article  PubMed  PubMed Central  Google Scholar 

  • Tindall BJ, Rosselló-Mora R, Busse H-J, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266

    Article  PubMed  CAS  Google Scholar 

  • Tsang AKL, Lee HH, Yiu SM, Lau SKP, Woo PCY (2017) Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny. Sci Rep. https://doi.org/10.1038/s41598-017-04707-4

    Article  PubMed  PubMed Central  Google Scholar 

  • Valiunas D, Jomantiene R, Davis RE (2013) Evaluation of the DNA-dependent RNA polymerase β-subunit gene (rpoB) for phytoplasma classification and phylogeny. Int J Syst Evol Microbiol 63:3904–3914

    Article  PubMed  CAS  Google Scholar 

  • Vandamme P, Pot B, Gillis M, De Vos P, Kersters K et al (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438

    PubMed  PubMed Central  CAS  Google Scholar 

  • Vartoukian SR, Palmer RM, Wade WG (2010) Strategies for culture of ‘unculturable’ bacteria. FEMS Microbiol Lett 309:1–7

    PubMed  CAS  Google Scholar 

  • Veda T, Suga Y, Matsuguchi T (1995) Molecular phylogenetic analysis of a soil microbial community in a soybean field. Eur J Soil Sci 46:415–421

    Article  Google Scholar 

  • Velichko N, Chernyaeva E, Averina S, Gavrilova O, Lapidus A et al (2015) Consortium of the ‘bichlorophyllous’ cyanobacterium Prochlorothrix hollandica and chemoheterotrophic partner bacteria: culture and metagenome-based description. Environ Microbiol Rep 7:623–633

    Article  PubMed  CAS  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74

    Article  PubMed  CAS  Google Scholar 

  • Větrovský T, Baldrian P (2013) The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS ONE. https://doi.org/10.1371/journal.pone.0057923

    Article  PubMed  PubMed Central  Google Scholar 

  • Vos M, Quince C, Pijl AS, De Hollander M, Kowalchuk GA (2012) A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity. PLoS ONE. https://doi.org/10.1371/journal.pone.0030600

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequence into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wang M, Ye Y, Tang H (2012) A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community. J Comput Biol 19:814–825

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Waterbury JB (2006) The cyanobacteria—purification and identification. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes, 3rd edn. Springer, New York, pp 1053–1073

    Chapter  Google Scholar 

  • Wayne LG, Brenner DG, Colwell RR, Grimont PAD, Kandler O et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 347:463–464

    Article  Google Scholar 

  • Whitman WB (2016) Modest proposals to expand the type material for naming of prokaryotes. Int J Syst Evol Microbiol 66:2108–2112

    Article  PubMed  CAS  Google Scholar 

  • Zhang SV, Zhuo L, Hahn MW (2016) AGOUTI: improving genome assembly and annotation using transcriptome data. GigaScience. https://doi.org/10.1186/s13742-016-0136-3

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The work was supported by St. Petersburg State University Grant No 1.40.540.2017 (AVP), and Russian Scientific Foundation Grant No 14-26-00094P (EEA). We thank St. Petersburg State University research centres “Molecular and Cell Technologies” and “Culture Collection of Microorganisms” for technical assistance. We are grateful to Helena Kozhenkova for useful discussions. We especially thank the anonymous reviewers for their criticism and for offering valuable suggestions that have strongly improved the manuscript.

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  1. Saint Petersburg State University, Universitetskaya Quay, 7/9, P.O. Box 199034, St. Petersburg, Russia

    Alexander V. Pinevich, Agnia A. Pinevich & Helena Y. Dmitrieva

  2. All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Russian Academy of Sciences, Podbelskogo Highway, 3, P.O. Box 196608, St. Petersburg–Pushkin, Russia

    Eugeny E. Andronov & Elizaveta V. Pershina

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  1. Alexander V. Pinevich
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  2. Eugeny E. Andronov
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  3. Elizaveta V. Pershina
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  4. Agnia A. Pinevich
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Correspondence to Alexander V. Pinevich.

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Pinevich, A.V., Andronov, E.E., Pershina, E.V. et al. Testing culture purity in prokaryotes: criteria and challenges. Antonie van Leeuwenhoek 111, 1509–1521 (2018). https://doi.org/10.1007/s10482-018-1054-4

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