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Abstract

A novel Gram-stain-positive, rod-shaped, obligately anaerobic, non-motile, spore-forming and binary fission encapsulated bacterium, designated strain JN500901, was isolated from a mud cellar which has been continuously used for the fermentation of Chinese strong-flavour baijiu for over 100 years. Growth of JN500901occurred at pH 4.5–8.0 (optimum, pH 5.0), 20–40 °C (37 °C), 0–2 % (w/v) NaCl and 0–10 % (v/v) ethanol. The Biolog assay revealed that strain JN500901 metabolized d-fructose, l-fucose, isomaltulose and l-rhamnose among the 95 studied carbon sources. p-Cresol was the predominant volatile metabolite in the fermentation broth of strain JN500901 incubated in liquid reinforced clostridial medium under anaerobic conditions. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JN500901 belongs to Clostridium sensu stricto, and shared the highest sequence similarity to Clostridium carboxidivorans DSM 15243 (94.2 %), followed by Clostridium scatologenes DSM 757 (94.1 %). The dominant cellular fatty acids (>10 %) were C16 : 0 FAME (36.6 %), C19 : 0 cyc 9,10 DMA (19.8 %) and C16 : 1 cis 9 DMA (11.8 %). The complete genome of strain JN500901 contained a circular chromosome of 2.812 Mb with 2611 genes and 31.0 mol% G+C content. Comparative genome analysis of the strain JN500901, Clostridium carboxidivorans DSM 15243 and Clostridium scatologenes DSM 757 revealed 74.5 and 74.8 % average nucleotide identity, respectively. Based on the phenotypic, biochemical and phylogenetic analyses presented here, strain JN500901 is considered to be a novel species of the genus Clostridium sensustricto, for which the name Clostridium fermenticellae sp. nov. is proposed. The type strain is JN500901 (=CICC 24501=JCM 32827).

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2019-02-08
2024-03-28
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References

  1. 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; 44:812–826 [View Article][PubMed]
    [Google Scholar]
  2. Lawson PA. The taxonomy of the genus Clostridium: current status and future perspectives. Microbiol China 2016; 43:1070–1074
    [Google Scholar]
  3. Lawson PA, Rainey FA. Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species. Int J Syst Evol Microbiol 2016; 66:1009–1016 [View Article][PubMed]
    [Google Scholar]
  4. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
    [Google Scholar]
  5. Gupta RS, Gao B. Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I). Int J Syst Evol Microbiol 2009; 59:285–294 [View Article][PubMed]
    [Google Scholar]
  6. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014; 42:D633–D642 [View Article][PubMed]
    [Google Scholar]
  7. Tao Y, Li J, Rui J, Xu Z, Zhou Y et al. Prokaryotic communities in pit mud from different-aged cellars used for the production of Chinese strong-flavored liquor. Appl Environ Microbiol 2014; 80:2254–2260 [View Article][PubMed]
    [Google Scholar]
  8. Yin Q, Tao Y, Zhu X, Zhou Y, He X et al. Clostridium liquoris sp. nov., isolated from a fermentation pit used for the production of Chinese strong-flavoured liquor. Int J Syst Evol Microbiol 2016; 66:749–754 [View Article][PubMed]
    [Google Scholar]
  9. Zhang J, Fang F, Chen J, Du G. The arginine deiminase pathway of koji bacteria is involved in ethyl carbamate precursor production in soy sauce. FEMS Microbiol Lett 2014; 358:91–97 [View Article][PubMed]
    [Google Scholar]
  10. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  11. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  14. Rzhetsky A, Nei M. A simple method for evaluating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  16. 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]
  17. 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]
  18. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  19. Küsel K, Dorsch T, Acker G, Stackebrandt E, Drake HL. Clostridium scatologenes strain SL1 isolated as an acetogenic bacterium from acidic sediments. Int J Syst Evol Microbiol 2000; 50:537–546 [View Article][PubMed]
    [Google Scholar]
  20. Liou JS, Balkwill DL, Drake GR, Tanner RS. Clostridium carboxidivorans sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov. Int J Syst Evol Microbiol 2005; 55:2085–2091 [View Article][PubMed]
    [Google Scholar]
  21. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  22. Rainey FA, Holley BJ, Small A. Genus I. Clostridium Prazmowski 1880. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W. (editors) Bergey's Manual of Systematic Bacteriology, The Firmicutes. vol. 3 USA: Springer; 2009 pp. 738–828
    [Google Scholar]
  23. Bochner B. “Breathprints” at the microbial level. ASM News 1989; 55:536–539
    [Google Scholar]
  24. Bochner BR. Sleuthing out bacterial identities. Nature 1989; 339:157–158 [View Article][PubMed]
    [Google Scholar]
  25. Y-J Y, Z-M L, N-H Y, Xu W LG-Q et al. HS-SPME/GC-MS and chemometrics for volatile composition of Chinese traditional aromatic vinegar in the Zhenjiang region. J I Brewing 2012; 118:133–141
    [Google Scholar]
  26. Du H, Liu B, Wang X, Xu Y. Exploring the microbial origins of p-cresol and its co-occurrence pattern in the Chinese liquor-making process. Int J Food Microbiol 2017; 260:27–35 [View Article][PubMed]
    [Google Scholar]
  27. Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C et al. Long-read, whole-genome shotgun sequence data for five model organisms. Sci Data 2014; 1:140045 [View Article][PubMed]
    [Google Scholar]
  28. Badouin H, Hood ME, Gouzy J, Aguileta G, Siguenza S et al. Chaos of rearrangements in the mating-type chromosomes of the anther-smut fungus Microbotryum lychnidis-dioicae. Genetics 2015; 200:1275–1284 [View Article][PubMed]
    [Google Scholar]
  29. Faino L, Seidl MF, Datema E, van den Berg GCM, Janssen A et al. Single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome. mBio 2015; 6:e0093615 [View Article][PubMed]
    [Google Scholar]
  30. Sit CS, Ruzzini AC, van Arnam EB, Ramadhar TR, Currie CR et al. Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants. Proc Natl Acad Sci USA 2015; 112:13150–13154 [View Article]
    [Google Scholar]
  31. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679 [View Article][PubMed]
    [Google Scholar]
  32. Li N, Yang J, Chai C, Yang S, Jiang W et al. Complete genome sequence of Clostridium carboxidivorans P7(T), a syngas-fermenting bacterium capable of producing long-chain alcohols. J Biotechnol 2015; 211:44–45 [View Article][PubMed]
    [Google Scholar]
  33. Zhu Z, Guo T, Zheng H, Song T, Ouyang P et al. Complete genome sequence of a malodorant-producing acetogen, Clostridium scatologenes ATCC 25775(T). J Biotechnol 2015; 212:19–20 [View Article][PubMed]
    [Google Scholar]
  34. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12 [View Article][PubMed]
    [Google Scholar]
  35. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R et al. Circos: an information aesthetic for comparative genomics. Genome Res 2009; 19:1639–1645 [View Article][PubMed]
    [Google Scholar]
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