1887

Abstract

An oval to rod-shaped, Gram-stain-positive, strictly anaerobic bacterium, designated LFL-14, was isolated from the faeces of a healthy Chinese woman. Cells of the strain were non-spore-forming, grew optimally at 37 °C (growth range 30–45 °C) and pH 7.0 (growth range 6.0–9.0) under anaerobic conditions in the liquid modified Gifu anaerobic medium (mGAM). The result of 16S rRNA gene-based analysis indicated that LFL-14 shared an identity of 94.7 0% with ATCC 27560, indicating LFL-14 represented a novel taxon. The results of genome-based analysis revealed that the average nucleotide identity (ANI), the digital DNA–DNA hybridisation (dDDH) and average amino acid identity (AAI) between LFL-14 and its phylogenetically closest neighbour, ATCC 27560, were 77.0 %, 24.6 and 70.9 %, respectively, indicating that LFL-14 represents a novel species of the genus . The genome size of LFL-14 was 2.92 Mbp and the DNA G+C content was 33.14 mol%. We analysed the distribution of the genome of LFL-14 in cohorts of healthy individuals, type 2 diabetes patients (T2D) and patients with non-alcoholic fatty liver disease (NAFLD). We found that its abundance was higher in the T2D cohort, but it had a low average abundance of less than 0.2 % in all three cohorts. The percentages of frequency of occurrence in the T2D, healthy and NAFLD cohorts were 48.87 %, 16.72 % and 13.10 % respectively. The major cellular fatty acids of LFL-14 were C (34.4 %), C 2-OH (21.4 %) and C (11.7 %). Additionally, the strain contained diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE), as well as unidentified phospholipids and unidentified glycolipids. The glucose fermentation products of LFL-14 were acetate and butyrate. In summary, On the basis of its chemotaxonomic, phenotypic, phylogenetic and phylogenomic properties, strain LFL-14 (= CGMCC 1.18005 = KCTC 25580) is identified as representing a novel species of the genus , for which the name sp. nov. is proposed.

Funding
This study was supported by the:
  • Innovative Research Group Project of the National Natural Science Foundation of China (Award No. 82030116)
    • Principle Award Recipient: Shuang-JiangLiu
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006380
2024-05-13
2024-05-26
Loading full text...

Full text loading...

References

  1. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464:59–65 [View Article] [PubMed]
    [Google Scholar]
  2. Liu C, Du M-X, Abuduaini R, Yu H-Y, Li D-H et al. Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank. Microbiome 2021; 9:119 [View Article] [PubMed]
    [Google Scholar]
  3. Cato EP, Holdeman LV, Moore WEC. Designation of Eubacterium limosum (Eggerth) prevot as the type species of Eubacterium request for an opinion. Int J Syst Bacteriol 1981; 31:209–210 [View Article]
    [Google Scholar]
  4. Mukherjee A, Lordan C, Ross RP, Cotter PD. Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health. Gut Microbes 2020; 12:1802866 [View Article] [PubMed]
    [Google Scholar]
  5. Poco SE, Nakazawa F, Sato M, Hoshino E. Eubacterium minutum sp. nov., isolated from human periodontal pockets. Int J Syst Bacteriol 1996; 46:31–34 [View Article] [PubMed]
    [Google Scholar]
  6. Cheeseman SL, Hiom SJ, Weightman AJ, Wade WG. Phylogeny of oral asaccharolytic Eubacterium species determined by 16S ribosomal DNA sequence comparison and proposal of Eubacterium infirmum sp. nov. and Eubacterium tardum sp. nov. Int J Syst Bacteriol 1996; 46:957–959 [View Article] [PubMed]
    [Google Scholar]
  7. Poco SE, Nakazawa F, Ikeda T, Sato M, Sato T et al. Eubacterium exiguum sp. nov., isolated from human oral lesions. Int J Syst Bacteriol 1996; 46:1120–1124 [View Article] [PubMed]
    [Google Scholar]
  8. Feng Y, Stams AJM, Sánchez-Andrea I, de Vos WM. Eubacterium maltosivorans sp. nov., a novel human intestinal acetogenic and butyrogenic bacterium with a versatile metabolism. Int J Syst Evol Microbiol 2018; 68:3546–3550 [View Article] [PubMed]
    [Google Scholar]
  9. Fekry MI, Engels C, Zhang J, Schwab C, Lacroix C et al. The strict anaerobic gut microbe Eubacterium hallii transforms the carcinogenic dietary heterocyclic amine 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). Environ Microbiol Rep 2016; 8:201–209 [View Article] [PubMed]
    [Google Scholar]
  10. Markowiak-Kopeć P, Śliżewska K. The effect of probiotics on the production of short-chain fatty acids by human intestinal microbiome. Nutrients 2020; 12:1107 [View Article] [PubMed]
    [Google Scholar]
  11. Lu H, Xu X, Fu D, Gu Y, Fan R et al. Butyrate-producing Eubacterium rectale suppresses lymphomagenesis by alleviating the TNF-induced TLR4/MyD88/NF-κB axis. Cell Host Microbe 2022; 30:1139–1150 [View Article]
    [Google Scholar]
  12. Freier TA, Beitz DC, Li L, Hartman PA. Characterization of Eubacterium coprostanoligenes sp. nov., a cholesterol-reducing anaerobe. Int J Syst Bacteriol 1994; 44:137–142 [View Article] [PubMed]
    [Google Scholar]
  13. Islam SMS, Ryu H-M, Sayeed HM, Byun H-O, Jung J-Y et al. Eubacterium rectale attenuates HSV-1 induced systemic inflammation in mice by inhibiting CD83. Front Immunol 2021; 12:712312 [View Article] [PubMed]
    [Google Scholar]
  14. Kanauchi O, Fukuda M, Matsumoto Y, Ishii S, Ozawa T et al. Eubacterium limosum ameliorates experimental colitis and metabolite of microbe attenuates colonic inflammatory action with increase of mucosal integrity. World J Gastroenterol 2006; 12:1071–1077 [View Article] [PubMed]
    [Google Scholar]
  15. Wang Y, Wan X, Wu X, Zhang C, Liu J et al. Eubacterium rectale contributes to colorectal cancer initiation via promoting colitis. Gut Pathog 2021; 13:2 [View Article] [PubMed]
    [Google Scholar]
  16. Berger FK, Schwab N, Glanemann M, Bohle RM, Gärtner B et al. Flavonifractor (Eubacterium) plautii bloodstream infection following acute cholecystitis. IDCases 2018; 14:e00461 [View Article]
    [Google Scholar]
  17. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R et al. The human microbiome project. Nature 2007; 449:804–810 [View Article] [PubMed]
    [Google Scholar]
  18. Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y et al. The “most wanted” taxa from the human microbiome for whole genome sequencing. PLoS One 2012; 7:e41294 [View Article] [PubMed]
    [Google Scholar]
  19. Abdugheni R, Wang Y-J, Li D-H, Du M-X, Liu C et al. Pararoseburia lenta gen. nov., sp. nov. isolated from human faeces. Int J Syst Evol Microbiol 2022; 72:1–9 [View Article]
    [Google Scholar]
  20. Abdugheni R, Li D-H, Wang Y-J, Du M-X, Zhou N et al. Acidaminococcus hominis sp. nov., Amedibacillus hominis sp. nov., Lientehia hominis gen. nov. sp. nov., Merdimmobilis hominis gen. nov. sp. nov., and Paraeggerthella hominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2023; 73:1–21 [View Article]
    [Google Scholar]
  21. Khelifi N, Ben Romdhane E, Hedi A, Postec A, Fardeau M-L et al. Characterization of Microaerobacter geothermalis gen. nov., sp. nov., a novel microaerophilic, nitrate- and nitrite-reducing thermophilic bacterium isolated from a terrestrial hot spring in Tunisia. Extremophiles 2010; 14:297–304 [View Article]
    [Google Scholar]
  22. Fukuoka H, Taskin M, Teii K, Kato Y. Measurement of oxygen concentration in atmospheric air using ultrasound time of flight with humidity compensation. Rev Sci Instrum 2023; 94:035001 [View Article] [PubMed]
    [Google Scholar]
  23. Wikins TD, Holdeman LV, Abramson IJ, Moore WE. Standardized single-disc method for antibiotic susceptibility testing of anaerobic bacteria. Antimicrob Agents Chemother 1972; 1:451–459 [View Article] [PubMed]
    [Google Scholar]
  24. Preston-Mafham J, Boddy L, Randerson PF. Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles - a critique. FEMS Microbiol Ecol 2002; 42:1–14 [View Article] [PubMed]
    [Google Scholar]
  25. Wang Y-J, Xu X-J, Zhou N, Sun Y, Liu C et al. Parabacteroides acidifaciens sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2019; 69:761–766 [View Article] [PubMed]
    [Google Scholar]
  26. Abdugheni R, Wang WZ, Wang YJ, Du MX, Liu FL et al. Metabolite profiling of human‐originated Lachnospiraceae at the strain level. iMeta 2022; 1:e58 [View Article]
    [Google Scholar]
  27. 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]
  28. 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]
  29. 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]
  30. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  31. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  32. Yan Z, Cao Z, Liu Y, Ogilvie HA, Nakhleh L. Maximum parsimony inference of phylogenetic networks in the presence of polyploid complexes. Syst Biol 2022; 71:706–720 [View Article] [PubMed]
    [Google Scholar]
  33. Abdugheni R, Liu C, Liu F-L, Zhou N, Jiang C-Y et al. Comparative genomics reveals extensive intra-species genetic divergence of the prevalent gut commensal Ruminococcus gnavus. Microb Genom 2023; 9:1–12 [View Article] [PubMed]
    [Google Scholar]
  34. 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 [View Article] [PubMed]
    [Google Scholar]
  35. 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]
  36. Kim J, Na S-I, Kim D, Chun J. UBCG2: up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 2021; 59:609–615 [View Article] [PubMed]
    [Google Scholar]
  37. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  38. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  39. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
    [Google Scholar]
  40. Dai D, Zhu J, Sun C, Li M, Liu J et al. GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison. Nucleic Acids Res 2022; 50:D777–D784 [View Article] [PubMed]
    [Google Scholar]
  41. Villanueva RAM, Chen ZJ. ggplot2: Elegant Graphics for Data Analysis Taylor & Francis; 2019; 17160–167 [View Article]
    [Google Scholar]
  42. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
    [Google Scholar]
  43. 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]
  44. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  45. Diaz HF, Nunez CG, Sineriz F. Eubacterium tucumanense sp. nov.: an Anaerobic Gram-positive Non-sporeformer Isolated from an Anaerobic Digester. Microbiology 1989; 135:2537–2541 [View Article]
    [Google Scholar]
  46. The Prokaryotes. New York, NY: 2006 https://doi.org/10.1007/0-387-30744-3
  47. Kim W, Yang S-H, Park M-J, Oh J, Lee J-H et al. Anaerosacchariphilus polymeriproducens gen. nov., sp. nov., an anaerobic bacterium isolated from a salt field. Int J Syst Evol Microbiol 2019; 69:1934–1940 [View Article]
    [Google Scholar]
  48. Van Gylswyk N, Van Der Toorn J. Eubacterium uniforme sp. nov. and Eubacterium xylanophilum sp. nov., fiber-digesting bacteria from the rumina of sheep fed corn stover. Int J Syst Evol Bacteriol 1985; 35:323–326 [View Article]
    [Google Scholar]
  49. Sakamoto M, Iino T, Ohkuma M. Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov. Int J Syst Evol Microbiol 2017; 67:1219–1227 [View Article] [PubMed]
    [Google Scholar]
  50. Holdeman LV, Cato EP, Moore WEC. Eubacterium contortum (Prevot) comb. nov.: emendation of description and designation of the type strain. Int J Syst Bacteriol 1971; 21:304–306 [View Article]
    [Google Scholar]
  51. Taylor MM. Eubacterium fissicatena sp.nov. isolated from the alimentary tract of the goat. J Gen Microbiol 1972; 71:457–463 [View Article] [PubMed]
    [Google Scholar]
  52. Krumholz LR, Bryant MP. Eubacterium oxidoreducens sp. nov. requiring H2 or formate to degrade gallate, pyrogallol, phloroglucinol and quercetin. Arch Microbiol 1986; 144:8–14 [View Article]
    [Google Scholar]
  53. Li Y, Zhang L-L, Liu L, Tian Y-Q, Liu X-F et al. Paludicola psychrotolerans gen. nov., sp. nov., a novel psychrotolerant chitinolytic anaerobe of the family Ruminococcaceae. Int J Syst Evol Microbiol 2017; 67:4100–4103 [View Article]
    [Google Scholar]
  54. Wallace R, McKain N, McEwan NR, Miyagawa E, Chaudhary LC et al. Eubacterium pyruvativorans sp. nov., a novel non-saccharolytic anaerobe from the rumen that ferments pyruvate and amino acids, forms caproate and utilizes acetate and propionate. Int J Syst Evol Microbiol 2003; 53:965–970 [View Article] [PubMed]
    [Google Scholar]
  55. Wilkins TD, Fulghum RS, Wilkins JH. Eubacterium plexicaudatum sp. nov., an anaerobic bacterium with a subpolar tuft of flagella, isolated from a mouse cecum. Int J Syst Evol Microbiol 1974; 24:408–411 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006380
Loading
/content/journal/ijsem/10.1099/ijsem.0.006380
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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