1887

Abstract

A strain of obligately anaerobic, spore-forming, Gram-positive rods was isolated from child faeces and characterized both phenotypically and genotypically. Phylogenetic analysis based on 16S rRNA gene and whole genome sequencing revealed the strain to represent a member of the family distant from described species and genera. The strain was moderately saccharolytic with mannose as the preferred substrate and produced lactic acid, acetic acid and H as the end products. The major cellular long-chain fatty acids were C and C aldehyde. The genomic DNA G+C content was 52.3 mol%. On the basis of chemotaxonomic and genomic properties it was concluded that the strain represents a novel species in a new genus within the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is ASD2818 (=VKM B-3268=JCM 33295).

Funding
This study was supported by the:
  • Not Applicable , Russian Science Foundation , (Award 17-15-01488)
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2020-02-29
2020-06-03
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References

  1. Rainey FA. Family VIII. Ruminococcaceae fam. nov. Bergey’s Manual of Systematic Bacteriology 3 The Firmicutes; 2009 p 817
    [Google Scholar]
  2. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J et al. The Phylogeny of the Genus Clostridium: Proposal of Five New Genera and Eleven New Species Combinations. Int J Syst Bacteriol 1994 [CrossRef]
    [Google Scholar]
  3. Zhang X, Tu B, Dai LR, Lawson PA, Zheng ZZ et al. Petroclostridium xylanilyticum gen. nov., sp. nov., a xylan-degrading bacterium isolated from an oilfield, and reclassification of clostridial cluster III members into four novel genera in a new Hungateiclostridiaceae fam. nov. Int J Syst Evol Microbiol 2018; 68:3197–3211 [CrossRef]
    [Google Scholar]
  4. Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y et al. Population-Level analysis of gut microbiome variation. Science 2016; 352:560–564 [CrossRef]
    [Google Scholar]
  5. Shcherbakova VA, Chuvilskaya NA, Rivkina EM, Pecheritsyna SA, Laurinavichius KS et al. Novel psychrophilic anaerobic spore-forming bacterium from the overcooled water brine in permafrost: description Clostridium algoriphilum sp. nov. Extremophiles 2005; 9:239–246 [CrossRef]
    [Google Scholar]
  6. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477
    [Google Scholar]
  7. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [CrossRef]
    [Google Scholar]
  8. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS 2008; 12:137–141 [CrossRef]
    [Google Scholar]
  9. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [CrossRef]
    [Google Scholar]
  10. Lee I, Chalita M, Ha SM, Na SI, Yoon SH et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [CrossRef]
    [Google Scholar]
  11. Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 2013; 29:2933–2935 [CrossRef]
    [Google Scholar]
  12. Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E et al. Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res 2018; 46:D335–D342 [CrossRef]
    [Google Scholar]
  13. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189 [CrossRef]
    [Google Scholar]
  14. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [CrossRef]
    [Google Scholar]
  15. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [CrossRef]
    [Google Scholar]
  16. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [CrossRef]
    [Google Scholar]
  17. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [CrossRef]
    [Google Scholar]
  18. 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 [CrossRef]
    [Google Scholar]
  19. Koransky JR, Allen SD, Dowell VR. Use of ethanol for selective isolation of sporeforming microorganisms. Appl Environ Microbiol 1978; 35:762–765
    [Google Scholar]
  20. Jorgensen JH, Pfaller MA, Carroll KC, Funke G, Andry ML. Manual of Clinical Microbiology, 11th ed. American Society of Microbiology; 2015
    [Google Scholar]
  21. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [CrossRef]
    [Google Scholar]
  22. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [CrossRef]
    [Google Scholar]
  23. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006 [CrossRef]
    [Google Scholar]
  24. Mai V, Greenwald B, Morris JG, Raufman JP, Stine OC. Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition. Gut 2006; 55:1822–1823 [CrossRef]
    [Google Scholar]
  25. Li M, Wang B, Zhang M, Rantalainen M, Wang S et al. Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci 2008 [CrossRef]
    [Google Scholar]
  26. Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA et al. Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature 2016; 533:543–546 [CrossRef]
    [Google Scholar]
  27. Kong HH, Oh J, Deming C, Conlan S, Grice EA et al. Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res 2012; 22:850–859 [CrossRef]
    [Google Scholar]
  28. Guilhot E, Alou MT, Lagier JC, Labas N, Couderc C et al. Genome sequence and description of Anaeromassilibacillus senegalensis gen. nov., sp. nov., isolated from the gut of patient with kwashiorkor. New Microbes New Infect 2017; 17:54–64 [CrossRef]
    [Google Scholar]
  29. Kim BC, Seung Jeon B, Kim S, Kim H, Um Y et al. Caproiciproducens galactitolivorans gen. nov., sp. nov., a bacterium capable of producing caproic acid from galactitol, isolated from a wastewater treatment plant. Int J Syst Evol Microbiol 2015; 65:4902–4908 [CrossRef]
    [Google Scholar]
  30. Rainey FA, Hollen BJ, Small A, Genus I. Clostridium Prazmowski 1880. Bergey’s Manual of Systematic Bacteriology 3 The Firmicutes; 2009 p 817
    [Google Scholar]
  31. Lagier JC, Bibi F, Ramasamy D, Azhar EI, Robert C et al. Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov. Stand Genomic Sci 2014; 9:1003–1019 [CrossRef]
    [Google Scholar]
  32. Moore WEC, Johnson JL, Holdeman L V. Emendation of Bacteroidaceae and Butyrivibrio and Descriptions of Desulfomonas gen. nov. and Ten New Species in the Genera Desulfomonas, Butyrivibrio, Eubacterium, Clostridium, and Ruminococcus . Int J Syst Bacteriol 1976; 26:238–252 [CrossRef]
    [Google Scholar]
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