1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 9

sp. nov., a resveratrol-metabolizing bacterium isolated from human faeces and emended description of the genus Open Access

Abstract

The novel, anaerobic, Gram-positive, rod-shaped bacterial strain, ResAG-91, was isolated from a faecal sample of a male human volunteer. Analysis of the 16S rRNA gene sequence revealed that strain ResAG-91 showed high similarity to the type strains of subsp. and subsp. . Analysis of the whole draft genome sequences, i.e. digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI), of strain ResAG-91 and the type strains of species revealed that strain ResAG-91 represents a novel species of the genus . The genome size of strain ResAG-91 is 2.8 Mbp and the G+C content is 63.3 mol%. The major respiratory quinone of strain ResAG-91 was MMK-5 (methylmenaquinone). Major cellular fatty acids were C15 : 0 anteiso, C14 : 0 iso and C14 : 0 2-OH. Galactose and ribose were detected as major whole cell sugars. Furthermore, the peptidoglycan type of strain ResAG-91 was A1γ with meso-diaminopimelic acid. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid, three unidentified phospholipids and five unidentified glycolipids. Strain ResAG-91 was able to metabolize the stilbene resveratrol into dihydroresveratrol. On the basis of this polyphasic approach, including phenotypical, molecular (16S rRNA gene and whole genome sequencing) and biochemical (fatty acids, quinones, polar lipids, peptidoglycan, whole cell sugars, Rapid ID32A and API20A) analyses, we propose the novel species sp. nov. with the type and only strain ResAG-91 (=DSM 111416=JCM 34176=LMG 31897).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Adlercreutzia , anaerobic , Eggerthellaceae , faeces and taxonomy
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004987
2021-09-08
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/9/ijsem004987.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004987&mimeType=html&fmt=ahah

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. Gupta RS, Chen WJ, Adeolu M, Chai Y. Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales, containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthellales ord. nov., containing the family Eggerthellaceae fam. nov. Int J Syst Evol Microbiol 2013; 63:3379–3397 [View Article] [PubMed]
     [Google Scholar]
  3. Nouioui I, Carro L, Garcia-Lopez 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]
  4. Clavel T, Duck W, Charrier C, Wenning M, Elson C. 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]
  5. 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]
  6. 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]
  7. 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; 1:16131 [View Article] [PubMed]
     [Google Scholar]
  8. Stoll DA, Danylec N, Grimmler C, Kulling SE, Huch M. Genome analysis reveals that the correct name of type strain Adlercreutzia caecicola DSM 22242T is Parvibacter caecicola Clavel et al. 2013. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  9. 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 [View Article] [PubMed]
     [Google Scholar]
  10. Danylec N, Gobl A, Stoll DA, Hetzer B, Kulling SE et al. Rubneribacter badeniensis gen. nov., sp. nov. and Enteroscipio rubneri gen. nov., sp. nov., new members of the Eggerthellaceae isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:1533–1540 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. Lawson PA, Greetham HL, Gibson GR, Giffard C, Falsen E et al. Slackia faecicanis sp. nov., isolated from canine faeces. Int J Syst Evol Microbiol 2005; 55:1243–1246 [View Article] [PubMed]
     [Google Scholar]
  13. Lanigan GW. Peptococcus heliotrinreducans, sp. nov., a cytochrome-producing anaerobe which metabolizes pyrrolizidine alkaloids. J Gen Microbiol 1976; 94:1–10 [View Article] [PubMed]
     [Google Scholar]
  14. Koppel N, Bisanz JE, Pandelia ME, Turnbaugh PJ, Balskus EP. Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins. eLife 2018; 7: [View Article] [PubMed]
     [Google Scholar]
  15. Selma MV, Beltrán D, García-Villalba R, Espín JC, Tomás-Barberán FA. Description of urolithin production capacity from ellagic acid of two human intestinal Gordonibacter species. Food & function 2014; 5:1779–1784
     [Google Scholar]
  16. Bode LM, Bunzel D, Huch M, Cho GS, Ruhland D et al. In vivo and in vitro metabolism of trans-resveratrol by human gut microbiota. Am J Clin Nutr 2013; 97:295–309 [View Article] [PubMed]
     [Google Scholar]
  17. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods 2012; 9:671–675 [View Article] [PubMed]
     [Google Scholar]
  18. Nagai F, Watanabe Y, Morotomi M. Slackia piriformis sp. nov. and Collinsella tanakaei sp. nov., new members of the family Coriobacteriaceae, isolated from human faeces. Int J Syst Evol Microbiol 2010; 60:2639–2646 [View Article] [PubMed]
     [Google Scholar]
  19. Wade WG, Downes J, Dymock D, Hiom SJ, Weightman AJ. The family Coriobacteriaceae: reclassification of Eubacterium exiguum (Poco et al. 1996) and Peptostreptococcus heliotrinreducens (Lanigan 1976) as Slackia exigua gen. nov., comb. nov. and Slackia heliotrinireducens gen. nov., comb. nov., and Eubacterium lentum (Prevot 1938) as Eggerthella lenta gen. nov., comb. nov. Int J Syst Evol Microbiol 1999; 49:595–600
     [Google Scholar]
  20. Danylec N, Stoll DA, Gobl A, Huch M. Draft genome sequences of 13 isolates of Adlercreutzia equolifaciens, Eggerthella lenta, and Gordonibacter urolithinfaciens, isolated from Human Fecal Samples in Karlsruhe, Germany. Microbiol Resour Announc 2020; 9:e00017-00020 [View Article] [PubMed]
     [Google Scholar]
  21. Danylec N, Stoll DA, Dotsch A, Huch M. Draft genome sequences of type strains of Gordonibacter faecihominis, Paraeggerthella hongkongensis, Parvibacter caecicola, Slackia equolifaciens, Slackia faecicanis, and Slackia isoflavoniconvertens. Microbiol Resour Announc 2019; 8:e01532-01518 [View Article] [PubMed]
     [Google Scholar]
  22. Danylec N, Stoll DA, Huch M. Draft genome sequences of type strains of Adlercreutzia muris and Ellagibacter urolithinifaciens, belonging to the family Eggerthellaceae. Microbiol Resour Announc 2019; 8:e01306-01319 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. Richter M, Rossello-Mora 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]
  25. 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]
  26. 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]
  27. 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]
  28. Lee I, Ouk Kim Y, Park S-C, 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]
  29. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res 2017; 45:D535–D542 [View Article] [PubMed]
     [Google Scholar]
  30. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004987
Loading
Adlercreutzia rubneri sp. nov., a resveratrol-metabolizing bacterium isolated from human faeces and emended description of the genus Adlercreutzia
Int J Syst Evol Microbiol 71, 004987 (2021); https://doi.org/10.1099/ijsem.0.004987
/content/journal/ijsem/10.1099/ijsem.0.004987
/content/journal/ijsem/10.1099/ijsem.0.004987
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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