1887

Abstract

Two obligately anaerobic, Gram-stain-positive, rod-shaped bacteria were isolated from faecal samples of healthy humans in Japan. 16S rRNA gene sequence analysis indicated that these two strains (8CFCBH1 and 9CBH6) belonged to the genus , which is known as an equol-producing bacterium. The closest neighbours of strain 8CFCBH1 were subsp. DSM 19450 (98.6%), subsp. do03 (98.4%), WCA-131-CoC-2 (96.6%), NR06 (96.4%), B7 (95.3%) and Mt1B8 (95.3%). The closest relatives to strain 9CBH6 were subsp. DSM 19450 (99.8%), subsp. do03 (99.6%) and WCA-131-CoC-2 (96.8%). Strain 8CFCBH1 showed 22.3–53.5% digital DNA–DNA hybridization (dDDH) values with its related species. In addition, the average nucleotide identity (ANI) values between strain 8CFCBH1 and its related species ranged from 75.4 to 93.3%. On the other hand, strain 9CBH6 was considered as based on the dDDH and ANI values (>70% dDDH and >95–96% ANI). Strain 9CBH6 showed daidzein-converting activity, as expected from the result of genome analysis. The genome of strain 8CFCBH1 lacked four genes involved in equol production. Growing cells of strain 8CFCBH1 were not capable of converting daidzein. Based on the collected data, strain 8CFCBH1 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain of is 8CFCBH1 (=JCM 34083=DSM 112284).

Funding
This study was supported by the:
  • Japan Society for the Promotion of Science (Award 19H05679)
    • Principle Award Recipient: MoriyaOhkuma
  • Japan Agency for Medical Research and Development (Award JP21gm1010006)
    • Principle Award Recipient: HiroshiMori
  • Japan Agency for Medical Research and Development (Award JP19gm6010007)
    • Principle Award Recipient: MitsuoSakamoto
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2021-12-06
2022-01-29
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References

  1. Maruo T, Sakamoto M, Ito C, Toda T, Benno Y. Adlercreutzia equolifaciens gen. nov., sp. nov., an equol-producing bacterium isolated from human faeces, and emended description of the genus Eggerthella. Int J Syst Evol Microbiol 2008; 58:1221–1227 [View Article] [PubMed]
    [Google Scholar]
  2. Day AJ, Cañada FJ, Díaz JC, Kroon PA, Mclauchlan R et al. Dietary flavonoid and isoflavone glycosides are hydrolysed by the lactase site of lactase phlorizin hydrolase. FEBS Lett 2000; 468:166–170 [View Article] [PubMed]
    [Google Scholar]
  3. Setchell KDR, Brown NM, Zimmer-Nechemias L, Brashear WT, Wolfe BE et al. Evidence for lack of absorption of soy isoflavone glycosides in humans, supporting the crucial role of intestinal metabolism for bioavailability. Am J Clin Nutr 2002; 76:447–453 [View Article] [PubMed]
    [Google Scholar]
  4. Chang YC, Nair MG. Metabolism of daidzein and genistein by intestinal bacteria. J Nat Prod 1995; 58:1892–1896 [View Article] [PubMed]
    [Google Scholar]
  5. Joannou GE, Kelly GE, Reeder AY, Waring M, Nelson C. A urinary profile study of dietary phytoestrogens. The identification and mode of metabolism of new isoflavonoids. J Steroid Biochem Mol Biol 1995; 54:167–184 [View Article] [PubMed]
    [Google Scholar]
  6. Sathyamoorthy N, Wang TT. Differential effects of dietary phyto-oestrogens daidzein and equol on human breast cancer MCF-7 cells. Eur J Cancer 1997; 33:2384–2389 [View Article] [PubMed]
    [Google Scholar]
  7. Schmitt E, Dekant W, Stopper H. Assaying the estrogenicity of phytoestrogens in cells of different estrogen sensitive tissues. Toxicol In Vitro 2001; 15:433–439 [View Article] [PubMed]
    [Google Scholar]
  8. Arai Y, Uehara M, Sato Y, Kimira M, Eboshida A et al. Comparison of isoflavones among dietary intake, plasma concentration and urinary excretion for accurate estimation of phytoestrogen intake. J Epidemiol 2000; 10:127–135 [View Article] [PubMed]
    [Google Scholar]
  9. Setchell KDR, Brown NM, Desai PB, Zimmer-Nechimias L, Wolfe B et al. Bioavailability, disposition, and dose-response effects of soy isoflavones when consumed by healthy women at physiologically typical dietary intakes. J Nutr 2003; 133:1027–1035 [View Article] [PubMed]
    [Google Scholar]
  10. Ogata Y, Sakamoto M, Ohkuma M, Hattori M, Suda W. Complete genome sequence of Adlercreutzia sp. strain 8CFCBH1, a potent producer of equol, isolated from healthy Japanese feces. Microbiol Resour Announc 2020; 9:e01240-20 [View Article] [PubMed]
    [Google Scholar]
  11. Sakamoto M, Suzuki M, Umeda M, Ishikawa I, Benno Y. Reclassification of Bacteroides forsythus (Tanner et al. 1986) as Tannerella forsythensis corrig., gen. nov., comb. nov. Int J Syst Evol Microbiol 2002; 52:841–849 [View Article] [PubMed]
    [Google Scholar]
  12. 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]
  13. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
  14. 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 [View Article] [PubMed]
    [Google Scholar]
  15. 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]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  17. Stecher G, Tamura K, Kumar S. Molecular Evolutionary Genetics Analysis (MEGA) for macOS. Mol Biol Evol 2020; 37:1237–1239 [View Article] [PubMed]
    [Google Scholar]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  19. Minamida K, Ota K, Nishimukai M, Tanaka M, Abe A et al. Asaccharobacter celatus gen. nov., sp. nov., isolated from rat caecum. Int J Syst Evol Microbiol 2008; 58:1238–1240 [View Article] [PubMed]
    [Google Scholar]
  20. Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP et al. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol 2016; 51:16131
    [Google Scholar]
  21. Clavel T, Duck W, Charrier C, Wenning M, Elson C et al. Enterorhabdus caecimuris sp. nov., a member of the family Coriobacteriaceae isolated from a mouse model of spontaneous colitis, and emended description of the genus Enterorhabdus Clavel et al. 2009. Int J Syst Evol Microbiol 2010; 60:1527–1531 [View Article] [PubMed]
    [Google Scholar]
  22. Clavel T, Charrier C, Braune A, Wenning M, Blaut M et al. Isolation of bacteria from the ileal mucosa of TNFdeltaARE mice and description of Enterorhabdus mucosicola gen. nov., sp. nov. Int J Syst Evol Microbiol 2009; 59:1805–1812 [View Article] [PubMed]
    [Google Scholar]
  23. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:2007 [View Article] [PubMed]
    [Google Scholar]
  24. Clavel T, Charrier C, Wenning M, Haller D. Parvibacter caecicola gen. nov., sp. nov., a bacterium of the family Coriobacteriaceae isolated from the caecum of a mouse. Int J Syst Evol Microbiol 2013; 63:2642–2648 [View Article] [PubMed]
    [Google Scholar]
  25. Stoll DA, Danylec N, Grimmler C, Kulling SE, Huch M. Genome analysis reveals that the correct name of the type strain Adlercreutzia caecicola DSM 22242T is Parvibacter caecicola Clavel et al. 2013. Int J Syst Evol Microbiol 2021; 71:004814
    [Google Scholar]
  26. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article] [PubMed]
    [Google Scholar]
  27. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  28. Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. DFAST and DAGA: web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 2016; 35:173–184 [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  30. 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 [View Article] [PubMed]
    [Google Scholar]
  31. 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] [PubMed]
    [Google Scholar]
  32. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  33. Shimada Y, Takahashi M, Miyazawa N, Abiru Y, Uchiyama S et al. Identification of a novel dihydrodaidzein racemase essential for biosynthesis of equol from daidzein in Lactococcus sp. strain 20-92. Appl Environ Microbiol 2012; 78:4902–4907 [View Article] [PubMed]
    [Google Scholar]
  34. Toh H, Oshima K, Suzuki T, Hattori M, Morita H. Complete genome sequence of the equol-producing bacterium Adlercreutzia equolifaciens DSM 19450T. Genome Announc 2013; 1:e00742-13 [View Article] [PubMed]
    [Google Scholar]
  35. Takahashi H, Yang J, Yamamoto H, Fukuda S, Arakawa K. Complete genome sequence of Adlercreutzia equolifaciens subsp. celatus DSM 18785. Microbiol Resour Announc 2021; 10:e00354-21 [View Article] [PubMed]
    [Google Scholar]
  36. Takahasi H, Yang J, Yamamoto H, Fukuda S, Arakawa K. Correction for Takahashi et al., “Complete genome sequence of Adlercreutzia equolifaciens subsp. celatus JCM 14811T.”. Microbiol Resour Announc 2021; 10:e00507–21
    [Google Scholar]
  37. 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]
  38. Pramono AK, Sakamoto M, Iino T, Hongoh Y, Ohkuma M. Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus. Int J Syst Evol Microbiol 2015; 65:681–685 [View Article] [PubMed]
    [Google Scholar]
  39. Kuykendall LD, Roy MA, O’Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  40. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
    [Google Scholar]
  41. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  42. Hein S, von Irmer J, Gallei M, Meusinger R, Simon J. Two dedicated class C radical S-adenosylmethionine methyltransferases concertedly catalyse the synthesis of 7,8-dimethylmenaquinone. Biochim Biophys Acta Bioenerg 2018; 1859:300–308 [View Article] [PubMed]
    [Google Scholar]
  43. Akasaka H, Ueki A, Hanada S, Kamagata Y, Ueki K. Propionicimonas paludicola gen. nov., sp. nov., a novel facultatively anaerobic, Gram-positive, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil. Int J Syst Evol Microbiol 2003; 53:1991–1998 [View Article] [PubMed]
    [Google Scholar]
  44. Schoefer L, Mohan R, Braune A, Birringer M, Blaut M. Anaerobic C-ring cleavage of genistein and daidzein by Eubacterium ramulus. FEMS Microbiol Lett 2002; 208:197–202 [View Article] [PubMed]
    [Google Scholar]
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