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Abstract

Cultivation and isolation of gut bacteria are necessary for understanding their role in the intestinal ecosystem. We isolated a novel bacterium, designated strain BG01, from the faeces of a patient with Crohn's disease. Strain BG01 was a strictly anaerobic, rod-shaped, Gram-variable and endospore-forming bacterium. Strain BG01 possessed C, C dimethyl aldehyde (DMA) and C 9 DMA as predominant cellular fatty acids and -diaminopimelic acid as a diagnostic diamino acid. Strain BG01 grew at 15–45 °C (optimum, 37 °C), with 0–4 % (w/v) NaCl (optimum, 0–1 %), at pH 6–10 (optimum, pH 7) and was resistant to bile salt, but not to ampicillin, metronidazole, vancomycin and cefoperazone. Butyrate, propionate, oxalacetate and fumarate were produced as fermentation end products from Gifu anaerobic medium broth. Strain BG01 showed 97.7 % 16S rRNA gene sequence similarity, and 92.0 and 48.5 % of average nucleotide identity and digital DNA–DNA hybridization values, respectively, with KCTC 15019. Genomic analysis indicated that strain BG01 had a butyrate-producing pathway. The genomic G+C content of the strain was 43.5 mol%. Results of the phenotypic, phylogenetic and genotypic analyses indicated that strain BG01 represents a novel butyrate-producing species of the genus , for which the name sp. nov. is proposed. The type strain is BG01 (=KCTC 15617=JCM 32275).

Funding
This study was supported by the:
  • Korea Research Institute of Bioscience and Biotechnology (Award KGM5232113)
    • Principle Award Recipient: Na-RiShin
  • Ministry of Science & ICT (KR) (Award NRF-2017M3A9F3046549)
    • Principle Award Recipient: Jin-WooBae
  • National Research Foundation of Korea (Award NRF-2020R1A2C3012797)
    • Principle Award Recipient: Jin-WooBae
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2021-12-06
2022-01-29
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References

  1. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 2009; 9:313–323 [View Article] [PubMed]
    [Google Scholar]
  2. Manichanh C, Borruel N, Casellas F, Guarner F. The gut microbiota in IBD. Nat Rev Gastroenterol Hepatol 2012; 9:599–608 [View Article] [PubMed]
    [Google Scholar]
  3. Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology 2008; 134:577–594 [View Article] [PubMed]
    [Google Scholar]
  4. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 2007; 104:13780–13785 [View Article] [PubMed]
    [Google Scholar]
  5. Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 2012; 13:R79 [View Article] [PubMed]
    [Google Scholar]
  6. Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA et al. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol 2017; 2:17004 [View Article] [PubMed]
    [Google Scholar]
  7. Walker AW, Duncan SH, Louis P, Flint HJ. Phylogeny, culturing, and metagenomics of the human gut microbiota. Trends Microbiol 2014; 22:267–274 10.1016/j.tim.2014.03.001 [PubMed]
    [Google Scholar]
  8. Schwiertz A, Hold GL, Duncan SH, Gruhl B, Collins MD et al. Anaerostipes caccae gen. nov., sp. nov., a new saccharolytic, acetate-utilising, butyrate-producing bacterium from human faeces. Syst Appl Microbiol 2002; 25:46–51 [View Article] [PubMed]
    [Google Scholar]
  9. Allen-Vercoe E, Daigneault M, White A, Panaccione R, Duncan SH. Anaerostipes hadrus comb. nov., a dominant species within the human colonic microbiota; reclassification of Eubacterium hadrum Moore et al. 1976. Anaerobe 2012; 18:523–529 [PubMed]
    [Google Scholar]
  10. Bui TPN, de Vos WM, Plugge CM. Anaerostipes rhamnosivorans sp. nov., a human intestinal, butyrate-forming bacterium. Int J Syst Evol Microbiol 2014; 64:787–793 [View Article] [PubMed]
    [Google Scholar]
  11. Eeckhaut V, Van Immerseel F, Pasmans F, De Brandt E, Haesebrouck F et al. Anaerostipes butyraticus sp. nov., an anaerobic, butyrate-producing bacterium from Clostridium cluster XIVa isolated from broiler chicken caecal content, and emended description of the genus Anaerostipes. Int J Syst Evol Microbiol 2010; 60:1108–1112 [View Article] [PubMed]
    [Google Scholar]
  12. Duncan SH, Louis P, Flint HJ. Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl Environ Microbiol 2004; 70:5810–5817 [View Article] [PubMed]
    [Google Scholar]
  13. Kim PS, Shin N-R, Kim JY, Yun J-H, Hyun D-W et al. Gibbsiella papilionis sp. nov., isolated from the intestinal tract of the butterfly Mycalesis gotama, and emended description of the genus Gibbsiella. Int J Syst Evol Microbiol 2013; 63:2607–2611 [View Article] [PubMed]
    [Google Scholar]
  14. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991 pp 115–175
    [Google Scholar]
  15. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
  16. 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 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Systematic Zoology 1969; 18:1 [View Article]
    [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  20. 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]
  21. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575–580 [View Article] [PubMed]
    [Google Scholar]
  22. MIDI Sherlock Microbial Identification System Operating Manual, version 3.0. Newark, DE: MIDI, Inc; 1999
  23. Bousfield GR, Sugino H, Ward DN. Demonstration of a COOH-terminal extension on equine lutropin by means of a common acid-labile bond in equine lutropin and equine chorionic gonadotropin. J Biol Chem 1985; 260:9531–9533 [View Article] [PubMed]
    [Google Scholar]
  24. Collins MD, Jones D. A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 1981; 51:129–134 [View Article] [PubMed]
    [Google Scholar]
  25. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 10.2323/jgam.42.457
    [Google Scholar]
  26. Hyun DW, Jeong YS, Lee JY, Sung H, Lee SY et al. Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish). J Microbiol 2021; 59:552–562
    [Google Scholar]
  27. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd. edn American Society of Microbiology; 2007 pp 330–393
    [Google Scholar]
  28. Shin N-R, Kang W, Tak EJ, Hyun D-W, Kim PS et al. Blautia hominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:1059–1064 [View Article] [PubMed]
    [Google Scholar]
  29. 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 [View Article] [PubMed]
    [Google Scholar]
  30. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
    [Google Scholar]
  31. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  32. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  33. 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 [View Article] [PubMed]
    [Google Scholar]
  34. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
    [Google Scholar]
  35. Chen I-MA, Chu K, Palaniappan K, Pillay M, Ratner A et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res 2019; 47:D666–D677 [View Article] [PubMed]
    [Google Scholar]
  36. Shetty SA, Boeren S, Bui TPN, Smidt H, de Vos WM. Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics. Environ Microbiol 2020; 22:4863–4875 [View Article] [PubMed]
    [Google Scholar]
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