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Volume 67, Issue 5

gen. nov., sp. nov., a new human-associated member of the family Free

Abstract

An anaerobic bacterium, strain AT2, was isolated from the fresh stool sample of a healthy French man using the culturomics approach. The 16S rRNA gene sequence analysis showed that strain AT2 had 95.2 % nucleotide sequence similarity with ATCC 27749, the phylogenetically closest species with standing in nomenclature. Cells are Gram-stain-negative, catalase- and oxidase-negative, obligately anaerobic, non-motile, non-spore-forming, rod-shaped, and the bacilli were mesothermophilic. The major fatty acids were C (43.8 %) and C (20 %). The DNA G+C content of the strain based on its genome sequence was 56.8 mol%. Based on the phenotypic, biochemical and phylogenetic analysis, we propose the creation of the genus gen. nov., which contains strain AT2 (=CSUR P2014=DSM 100451) as the type strain of the type species gen. nov., sp. nov.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): anaerobic bacteria , culturomics , Fournierella massiliensis , gut microbiota , human microbiome and taxonogenomics
© 2017 IUMS
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2017-05-01
2022-10-03
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References

  1. Lagier JC, Khelaifia S, Alou MT, Ndongo S, Dione N et al. Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol 2016; 1:16203 [View Article][PubMed]
     [Google Scholar]
  2. Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi M et al. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 2014; 64:384–391 [View Article][PubMed]
     [Google Scholar]
  3. Ramasamy D, Kokcha S, Lagier JC, Nguyen TT, Raoult D et al. Genome sequence and description of Aeromicrobium massiliense sp. nov. Stand Genomic Sci 2012; 7:246–257 [View Article][PubMed]
     [Google Scholar]
  4. Lagier JC, Elkarkouri K, Rivet R, Couderc C, Raoult D et al. Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov. Stand Genomic Sci 2013; 7:343–356 [View Article][PubMed]
     [Google Scholar]
  5. Rainey FA. Family VIII. Ruminococcaceae fam. nov. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W. et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 3 (The Firmicutes) Dordrecht, Heidelberg, London, New York: Springer; 2009 pp. 1016
     [Google Scholar]
  6. Duncan SH, Hold GL, Harmsen HJ, Stewart CS, Flint HJ. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int J Syst Evol Microbiol 2002; 52:2141–2146 [View Article][PubMed]
     [Google Scholar]
  7. Khan MT, Duncan SH, Stams AJ, van Dijl JM, Flint HJ et al. The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases. Isme J 2012; 6:1578–1585 [View Article][PubMed]
     [Google Scholar]
  8. Sadaghian Sadabad M, von Martels JZ, Khan MT, Blokzijl T, Paglia G et al. A simple coculture system shows mutualism between anaerobic Faecalibacteria and epithelial Caco-2 cells. Sci Rep 2015; 5:17906 [View Article][PubMed]
     [Google Scholar]
  9. Million M, Diallo A, Raoult D. Gut microbiota and malnutrition. Microb Pathog 201630212–30216 [View Article]
     [Google Scholar]
  10. Million M, Tidjani Alou M, Khelaifia S, Bachar D, Lagier JC et al. Increased gut redox and depletion of anaerobic and methanogenic prokaryotes in severe acute malnutrition. Sci Rep 2016; 6:26051 [View Article][PubMed]
     [Google Scholar]
  11. Hornef MW, Pabst O. Real friends: Faecalibacterium prausnitzii supports mucosal immune homeostasis. Gut 2016; 65:365–367 [View Article][PubMed]
     [Google Scholar]
  12. Miquel S, Martín R, Rossi O, Bermúdez-Humarán LG, Chatel JM et al. Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbiol 2013; 16:255–261 [View Article][PubMed]
     [Google Scholar]
  13. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 2009; 49:543–551 [View Article][PubMed]
     [Google Scholar]
  14. Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP et al. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 2000; 38:3623–3630[PubMed]
     [Google Scholar]
  15. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
     [Google Scholar]
  16. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  17. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article][PubMed]
     [Google Scholar]
  18. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  19. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
     [Google Scholar]
  20. Pattengale ND, Alipour M, Bininda-Emonds OR, Moret BM, Stamatakis A. How many bootstrap replicates are necessary?. J Comput Biol 2010; 17:337–354 [View Article][PubMed]
     [Google Scholar]
  21. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 B10. Sunderland: Sinauer Associates; 2002
     [Google Scholar]
  22. Halebian S, Harris B, Finegold SM, Rolfe RD. Rapid method that aids in distinguishing Gram-positive from Gram-negative anaerobic bacteria. J Clin Microbiol 1981; 13:444–448[PubMed]
     [Google Scholar]
  23. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining Gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995; 61:3756–3758[PubMed]
     [Google Scholar]
  24. Johnson MJ, Thatcher E, Cox ME. Techniques for controlling variability in Gram staining of obligate anaerobes. J Clin Microbiol 1995; 33:755–758[PubMed]
     [Google Scholar]
  25. Le Page S, van Belkum A, Fulchiron C, Huguet R, Raoult D et al. Evaluation of the PREVI® isola automated seeder system compared to reference manual inoculation for antibiotic susceptibility testing by the disk diffusion method. Eur J Clin Microbiol Infect Dis 2015; 34:1859–1869 [View Article][PubMed]
     [Google Scholar]
  26. Sasser M. Bacterial Identification by Gas Chromatographic Analysis of Fatty Acids Methyl Esters (GC-FAME), Technical Note 101. Newark, DE: MIDI Inc; 2006
     [Google Scholar]
  27. Dione N, Sankar SA, Lagier JC, Khelaifia S, Michele C et al. Genome sequence and description of Anaerosalibacter massiliensis sp. nov. New Microbes New Infect 2016; 10:66–76 [View Article][PubMed]
     [Google Scholar]
  28. Kläring K, Hanske L, Bui N, Charrier C, Blaut M et al. Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine. Int J Syst Evol Microbiol 2013; 63:4606–4612 [View Article][PubMed]
     [Google Scholar]
  29. Pfeiffer N, Desmarchelier C, Blaut M, Daniel H, Haller D et al. Acetatifactor muris gen. nov., sp. nov., a novel bacterium isolated from the intestine of an obese mouse. Arch Microbiol 2012; 194:901–907 [View Article][PubMed]
     [Google Scholar]
  30. Zhao G, Nyman M, Jönsson JA. Rapid determination of short-chain fatty acids in colonic contents and faeces of humans and rats by acidified water-extraction and direct-injection gas chromatography. Biomed Chromatogr 2006; 20:674–682 [View Article][PubMed]
     [Google Scholar]
  31. Illumina 2012; Illumina data processing of nextera® mate pair reads on illumina sequencing platforms. 2012. www.illumina.com/documents/products/technotes/technote_nextera_matepair_data_processing.pdf accessed 05 January 2017
  32. Nomenclatural changes validly published in the 2002 issues of the IJSEM www.bacterio.net/-changes-2002.html
  33. Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 2014; 58:212–220 [View Article][PubMed]
     [Google Scholar]
  34. Conway KR, Boddy CN. ClusterMine360: a database of microbial PKS/NRPS biosynthesis. Nucleic Acids Res 2013; 41:D402–D407 [View Article][PubMed]
     [Google Scholar]
  35. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article][PubMed]
     [Google Scholar]
  36. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article][PubMed]
     [Google Scholar]
  37. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
     [Google Scholar]
  38. Barcenilla A, Pryde SE, Martin JC, Duncan SH, Stewart CS et al. Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl Environ Microbiol 2000; 66:1654–1661 [View Article][PubMed]
     [Google Scholar]
  39. Duncan SH, Barcenilla A, Stewart CS, Pryde SE, Flint HJ. Acetate utilization and butyryl coenzyme a (CoA):acetate-CoA transferase in butyrate-producing bacteria from the human large intestine. Appl Environ Microbiol 2002; 68:5186–5190 [View Article][PubMed]
     [Google Scholar]
  40. Gossling J, Moore WEC. Gemmiger formicilis, n.gen., n.sp., an anaerobic budding bacterium from intestines. Int J Syst Bacteriol 1975; 25:202–207 [View Article]
     [Google Scholar]
  41. Holmstrøm K, Collins MD, Møller T, Falsen E, Lawson PA. Subdoligranulum variabile gen. nov., sp. nov. from human feces. Anaerobe 2004; 10:197–203 [View Article][PubMed]
     [Google Scholar]
  42. Zellner G, Stackebrandt E, Nagel D, Messner P, Weiss N et al. Anaerofilum pentosovorans gen. nov., sp. nov., and Anaerofilum agile sp. nov., two new, strictly anaerobic, mesophilic, acidogenic bacteria from anaerobic bioreactors. Int J Syst Bacteriol 1996; 46:871–875 [View Article][PubMed]
     [Google Scholar]
  43. Song L, Dong X. Hydrogenoanaerobacterium saccharovorans gen. nov., sp. nov., isolated from H2-producing UASB granules. Int J Syst Evol Microbiol 2009; 59:295–299 [View Article][PubMed]
     [Google Scholar]
  44. Chen S, Dong X. Acetanaerobacterium elongatum gen. nov., sp. nov., from paper mill waste water. Int J Syst Evol Microbiol 2004; 54:2257–2262 [View Article][PubMed]
     [Google Scholar]
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Fournierella massiliensis gen. nov., sp. nov., a new human-associated member of the family Ruminococcaceae
Int J Syst Evol Microbiol 67, 1393 (2017); https://doi.org/10.1099/ijsem.0.001826
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