1887

Abstract

A novel, Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, obligately anaerobic bacterium, designated strain ZHW00191, was isolated from human faeces and characterized by using a polyphasic taxonomic approach. Growth occurred at 25–45 °C (optimum, 37–42 °C), at pH 5.5–10.0 (optimum, pH 6.5–7.0) and with 0–2 % (w/v) NaCl (optimum, 0 %). The end products of glucose fermentation were acetic acid, isobutyric acid and isovaleric acid and a small amount of propionic acid. The dominant cellular fatty acids (>10 %) of strain ZHW00191 were C, C 9 and Cω6,9. Its polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and ten unidentified glycolipids. Respiratory quinones were not detected. The cell-wall peptidoglycan contained -2,6-diaminopimelic acid, and the whole-cell sugars were ribose and glucose. The genomic DNA G+C content was 32.8 mol%. Analysis of the 16S rRNA gene sequence indicated that ZHW00191 was most closely related to TO-931 (95.3 % similarity). Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) analyses with closely related reference strains indicated that reassociation values were both well below the thresholds of 95–96% and 70 % for species delineation, respectively. Based on phenotypic, chemotaxonomic and genetic studies, a novel genus, gen. nov., is proposed. The novel isolate ZHW00191 (=JCM 33482=GDMCC 1.1530) is proposed as the type strain of the type species gen. nov., sp. nov. of the proposed new genus. Furthermore, it is proposed that be transferred to this novel genus, as comb. nov.

Funding
This study was supported by the:
  • Hong-Wei Zhou , State Key Laboratory for Diagnosis and Treatment of Infectious Diseases (CN) , (Award 2017ZX10103011006)
  • Hong-Wei Zhou , National Natural Science Foundation of China , (Award NSFC31570497)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003925
2020-05-05
2020-06-04
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/5/2988.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003925&mimeType=html&fmt=ahah

References

  1. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L et al. Diversity of the human intestinal microbial flora. Science 2005; 308:1635–1638 [CrossRef][PubMed]
    [Google Scholar]
  2. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 2008; 6:776–788 [CrossRef][PubMed]
    [Google Scholar]
  3. Kundu P, Blacher E, Elinav E, Pettersson S. Our gut microbiome: the evolving inner self. Cell 2017; 171:1481–1493 [CrossRef][PubMed]
    [Google Scholar]
  4. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV et al. Current understanding of the human microbiome. Nat Med 2018; 24:392–400 [CrossRef][PubMed]
    [Google Scholar]
  5. Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB et al. A new genomic blueprint of the human gut microbiota. Nature 2019; 568:499–504 [CrossRef][PubMed]
    [Google Scholar]
  6. 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 [CrossRef][PubMed]
    [Google Scholar]
  7. Wiegel J, Tanner R, Rainey FA. An Introduction to the Family Clostridiaceae . In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E. (editors) The Prokaryotes: Bacteria: Firmicutes, Cyanobacteria 4 New York, NY: Springer US; 2006 pp 654–678
    [Google Scholar]
  8. Yutin N, Galperin MY. A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia . Environ Microbiol 2013; 15:2631–2641 [CrossRef][PubMed]
    [Google Scholar]
  9. 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 [CrossRef][PubMed]
    [Google Scholar]
  10. Wiegel J. Family I. Clostridiaceae Pribham 1933, 90AL. In Vos PD, Garrity GM, Jones D, Krieg NR, Ludwig W. (editors) Bergey’s Manual of Systematic Bacteriology 3, 2nd ed. New York, NY: Springer US; 2009 pp 736–738
    [Google Scholar]
  11. Gerritsen J, Fuentes S, Grievink W, van Niftrik L, Tindall BJ et al. Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov. Int J Syst Evol Microbiol 2014; 64:1600–1616 [CrossRef][PubMed]
    [Google Scholar]
  12. Ezaki T. Family Ⅶ. Peptostreptococcaceae fam. nov.. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W. (editors) Bergey's Mannual of Systematic Bacteriology 3 ed., 2nd ed. New York: Springer; 2009 pp 738–828
    [Google Scholar]
  13. Lawson PA, Citron DM, Tyrrell KL, Finegold SM. Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O'Toole 1935) Prévot 1938. Anaerobe 2016; 40:95–99 [CrossRef][PubMed]
    [Google Scholar]
  14. Galperin MY, Brover V, Tolstoy I, Yutin N. Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov. Int J Syst Evol Microbiol 2016; 66:5506–5513 [CrossRef][PubMed]
    [Google Scholar]
  15. Li G, Zeng X, Liu X, Zhang X, Shao Z. Wukongibacter baidiensis gen. nov., sp. nov., an anaerobic bacterium isolated from hydrothermal sulfides, and proposal for the reclassification of the closely related Clostridium halophilum and Clostridium caminithermale within Maledivibacter gen. nov. and Paramaledivibacter gen. nov., respectively. Int J Syst Evol Microbiol 2016; 66:4355–4361 [CrossRef][PubMed]
    [Google Scholar]
  16. Holdeman LV, Cato EP, Moore WEC. Anaerobe Laboratory Manual, 4th edn. Blacksburg, VA: Virginia Polytechnic Institute and State University; 1977 pp 117–149
    [Google Scholar]
  17. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [CrossRef][PubMed]
    [Google Scholar]
  18. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  19. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  21. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  22. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  23. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 2004; 101:11030–11035 [CrossRef][PubMed]
    [Google Scholar]
  24. 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][PubMed]
    [Google Scholar]
  25. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from illumina MiSeq data. Bioinformatics 2015; 31:587–589 [CrossRef][PubMed]
    [Google Scholar]
  26. Blake JD, Cohen FE. Pairwise sequence alignment below the twilight zone. J Mol Biol 2001; 307:721–735 [CrossRef][PubMed]
    [Google Scholar]
  27. Conesa A, Götz S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008; 2008:61983212 [CrossRef][PubMed]
    [Google Scholar]
  28. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:W182–W185 [CrossRef][PubMed]
    [Google Scholar]
  29. Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res 2014; 42:D231–D239 [CrossRef][PubMed]
    [Google Scholar]
  30. Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics 2005; 21:537–539 [CrossRef][PubMed]
    [Google Scholar]
  31. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  32. 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 [CrossRef][PubMed]
    [Google Scholar]
  33. 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][PubMed]
    [Google Scholar]
  34. Fischer S, Brunk BP, Chen F, Gao X, Harb OS et al. Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinform 2011Chapter 6:Unit 6.12.1-19
    [Google Scholar]
  35. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  36. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [CrossRef]
    [Google Scholar]
  37. Letunic I, Bork P. Interactive tree of life (iTOL) V3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016; 44:W242–W245 [CrossRef]
    [Google Scholar]
  38. Lawson PA, Johnson CN, Bengtsson L, Charalampakis G, Dahlén G et al. Peptostreptococcus canis sp. nov., isolated from subgingival plaque from canine oral cavity. Anaerobe 2012; 18:597–601 [CrossRef][PubMed]
    [Google Scholar]
  39. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575–580[PubMed]
    [Google Scholar]
  40. Sasser M. 2011; Identification of bacteria by gas chromatography of cellular fatty acids. www.microbialid.com/PDF/TechNote_101.pdf
  41. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [CrossRef]
    [Google Scholar]
  42. Komagata K, Lipid SK-I. And cell-wall analysis in bacterial Systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  43. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [CrossRef]
    [Google Scholar]
  44. Howard G, Norah CJ. Membrane Lipids of Clostridia. In Dürre P. editor Handbook on Clostridia Boca Raton, Florida: CRC Press; 2005 pp 297–309
    [Google Scholar]
  45. Guan Z, Johnston NC, Raetz CRH, Johnson EA, Goldfine H. Lipid diversity among botulinum neurotoxin-producing clostridia . Microbiology 2012; 158:2577–2584 [CrossRef]
    [Google Scholar]
  46. Dewhirst FE, Klein EA, Thompson EC, Blanton JM, Chen T et al. The canine oral microbiome. PLoS One 2012; 7:e36067 [CrossRef][PubMed]
    [Google Scholar]
  47. Zhang H, Chen L. Phylogenetic analysis of 16S rRNA gene sequences reveals distal gut bacterial diversity in wild wolves (Canis lupus). Mol Biol Rep 2010; 37:4013–4022 [CrossRef][PubMed]
    [Google Scholar]
  48. Glad T, Kristiansen VF, Nielsen KM, Brusetti L, Wright AD et al. Ecological characterisation of the colonic microbiota in Arctic and sub-arctic seals. Microb Ecol 2010; 60:320–330 [CrossRef][PubMed]
    [Google Scholar]
  49. Li E, Hamm CM, Gulati AS, Sartor RB, Chen H et al. Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS One 2012; 7:e26284 [CrossRef]
    [Google Scholar]
  50. Kitahara M, Takamine F, Imamura T, Benno Y. Clostridium hiranonis sp. nov., a human intestinal bacterium with bile acid 7alpha-dehydroxylating activity. Int J Syst Evol Microbiol 2001; 51:39–44 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003925
Loading
/content/journal/ijsem/10.1099/ijsem.0.003925
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error