Skip to main content

Collinsella ihumii sp. nov., a new anaerobic bacterium isolated from human stool

Abstract

Strain GD8 is a new species belonging to the order Coriobacteriales that was isolated from fresh stool of a French volunteer. It is an anaerobic Gram-positive bacterium isolated from human gut microbiota. The sequence analysis of the 16S rRNA gene showed that our strain GD8 was 96.2% of similarity with Collinsella massiliensis strain An5 which was the phylogenetically related species. Its genome size is 2,836,446 bp with 64.1 mol% of G + C content. Strain GD8T (= CSUR P2019 = DSM 101062) is the type strain of the new species Collinsella ihumii sp. nov.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3

References

  1. Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  2. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  3. Chen J, Wright K, Davis JM et al (2016) An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis. Genome Med 8:43. https://doi.org/10.1186/s13073-016-0299-7

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  4. Clark K, Karsch-Mizrachi I, Lipman DJ et al (2016) GenBank. Nucleic Acids Res 44:D67–D72. https://doi.org/10.1093/nar/gkv1276

    Article  PubMed  CAS  Google Scholar 

  5. Dione N, Sankar SA, Lagier JC et al (2016) Genome sequence and description of Anaerosalibacter massiliensis sp. nov. New Microbes New Infect 10:66–76. https://doi.org/10.1016/j.nmni.2016.01.002

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Diop A, Diop K, Tomei E et al (2019a) Collinsella vaginalis sp. nov. strain Marseille-P2666T, a new member of the Collinsella genus isolated from the genital tract of a patient suffering from bacterial vaginosis. Int J Syst Evol Microbiol 69:949–956. https://doi.org/10.1099/ijsem.0.003221

    Article  PubMed  CAS  Google Scholar 

  7. Diop K, Diop A, Michelle C et al (2019b) Description of three new Peptoniphilus species cultured in the vaginal fluid of a woman diagnosed with bacterial vaginosis: Peptoniphilus pacaensis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilus vaginalis sp. nov. MicrobiologyOpen 8:1–16. https://doi.org/10.1002/mbo3.661

    Article  CAS  Google Scholar 

  8. Durand GA, Cadoret F, Lagier JC et al (2017) Description of ‘Gorbachella massiliensis’ gen. nov., sp. nov., ‘Fenollaria timonensis’ sp. nov., ‘Intestinimonas timonensis’ sp. nov. and ‘Collinsella ihuae’ sp. nov. isolated from healthy fresh stools with culturomics. New Microbes New Infect 16:60–62. https://doi.org/10.1016/j.nmni.2017.01.005

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. Grant JR, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:181–184. https://doi.org/10.1093/nar/gkn179

    Article  CAS  Google Scholar 

  10. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 6:1–8

    Google Scholar 

  11. Kageyama A, Benno Y (2000) Emendation of genus Collinsella and proposal of Collinsella stercoris sp. nov. and Collinsella intestinalis sp. nov. Int J Syst Evol Microbiol 50:1767–1774. https://doi.org/10.1099/00207713-50-5-1767

    Article  PubMed  CAS  Google Scholar 

  12. Kageyama A, Benno Y, Nakase T (1999) Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsella as Collinsella aerofaciens gen. nov., comb. nov. Int J Syst Bacteriol 49:557–565. https://doi.org/10.1099/00207713-49-2-557

    Article  PubMed  Google Scholar 

  13. Lagesen K, Hallin P, Rødland EA et al (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. https://doi.org/10.1093/nar/gkm160

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  14. Lagier JC, Armougom F, Million M et al (2012) Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 18:1185–1193. https://doi.org/10.1111/1469-0691.12023

    Article  PubMed  CAS  Google Scholar 

  15. Lagier JC, Hugon P, Khelaifia S et al (2015) The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 28:237–264. https://doi.org/10.1128/CMR.00014-14

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  16. Lee BJ, Bak YT (2011) Irritable bowel syndrome, gut microbiota and probiotics. J Neurogastroenterol Motil 17:252–266. https://doi.org/10.5056/jnm.2011.17.3.252

    Article  PubMed  PubMed Central  Google Scholar 

  17. Lee I, Kim YO, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760

    Article  PubMed  CAS  Google Scholar 

  18. Lo CI, Sankar SA, Fall B et al (2016) High-quality draft genome sequence and description of Haemophilus massiliensis sp. nov. Stand Genomic Sci 11:1–9. https://doi.org/10.1186/s40793-016-0150-1

    Article  CAS  Google Scholar 

  19. Lowe TM, Chan PP (2016) tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44:W54–W57. https://doi.org/10.1093/nar/gkw413

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Luo R, Liu B, Xie Y et al (2015) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 4:1. https://doi.org/10.1186/s13742-015-0069-2

    Article  CAS  Google Scholar 

  21. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60

    Article  PubMed  PubMed Central  Google Scholar 

  22. Meier-Kolthoff JP, Klenk HP, Göker M (2014) Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352–356. https://doi.org/10.1099/ijs.0.056994-0

    Article  PubMed  CAS  Google Scholar 

  23. Nagai F, Watanabe Y, Morotomi M (2010) Slackia piriformis sp. nov. and Collinsella tanakaei sp. nov., new members of the family Coriobacteriaceae, isolated from human faeces. Int J Syst Evol Microbiol 60:2639–2646. https://doi.org/10.1099/ijs.0.017533-0

    Article  PubMed  CAS  Google Scholar 

  24. Padmanabhan R, Dubourg G, Lagier JC et al (2015) Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov. Stand Genomic Sci 9:1144–1158. https://doi.org/10.4056/sigs.5399696

    Article  Google Scholar 

  25. Ramasamy D, Mishra AK, Lagier JC et al (2014) A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 64:384–391. https://doi.org/10.1099/ijs.0.057091-0

    Article  PubMed  Google Scholar 

  26. Sasser M (2006) Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME). Newark NY Microb ID

  27. Stackebrandt E, Jonas E (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155

    Google Scholar 

  28. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703. https://doi.org/10.1128/jb.173.2.697-703.1991

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Wormser GP, Stratton C (2008) Manual of Clinical Microbiology, 9th Edition Edited by Patrick R. Murray, Ellen Jo Baron, James H. Jorgensen, Marie Louise Landry, and Michael A. Pfaller Washington, DC: ASM Press, 2007 2488 pp., illustrated. $209.95 (hardcover). Clin Infect Dis 46:153–153. https://doi.org/10.1086/524076

  30. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. https://doi.org/10.1101/gr.074492.107

    Article  PubMed  PubMed Central  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank Amael Fadlane for culturing the strain and Aurelia Caputo for submitting the genomic sequence to GenBank.

Funding

This study was supported by the Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, the National Research Agency under the program “Investissements d’avenir” reference ANR-10-IAHU-03, the Région Provence-Alpes-Côte d’Azur and European funding FEDER PRIMI.

Author information

Affiliations

Authors

Contributions

Conceptualization, F.F. and D.R.; methodology, P.E.F. and F.F.; validation, D.R., and F.F.; formal analysis, C.I.L., M.B.K., F.S.D., and G.D; investigation, M.B.K. and F.S.D.; Culture and keeping bacterial strain, SA; writing-original draft preparation, M.B.K and C.I.L; writing-review and editing, C.I.L; supervision, F.F. and C.I.L; funding acquisition, D.R. All authors have read and agreed to the published version of the manuscript.

Corresponding author

Correspondence to Florence Fenollar.

Ethics declarations

Conflict of interest

The authors declare that there are not conflicts of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Communicated by Erko Stackebrandt.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 151 KB)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ben Khedher, M., Diouf, F.S., Lo, C.I. et al. Collinsella ihumii sp. nov., a new anaerobic bacterium isolated from human stool. Arch Microbiol 203, 6315–6322 (2021). https://doi.org/10.1007/s00203-021-02562-6

Download citation

Keywords

  • Collinsella ihumii
  • Culturomics
  • Microbiota
  • Human gut
  • Taxono-genomics