Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 5

Description of subsp. subsp. nov., an anaerobic bacterium isolated from human faeces, and emended description of Open Access

Abstract

A recent metagenomic survey has revealed an unknown bacterial clade within the species to be significantly more prevalent in non-urbanized populations, compared to urbanized ones. We isolated and characterized a strain of this clade from the stool of a healthy adult volunteer. Strain CMD8551 is strictly anaerobic, appears as long chains of Gram-positive rods and produces acetate in the presence of glucose. The lipidomic profile showed a higher proportion of saturated lipid species amongst the detected phospholipids. The whole genome is 2,320,430 bp long and has a G+C content of 33.7 mol% with 2,239 CDSs. A phylogenetic analysis comparing the sequences of the strain CMD8551 with publicly available reference genomes from the genus revealed that the CMD8551 isolate, together with other isolate genomes, forms a distinct subspecies of and has an average nucleotide identity lower than 94% with respect to the previously described subsp. . Given the phenotypic, chemotaxonomic and phylogenetic characteristics of the newly isolated CMD8551 (=DSM 118469=LMG 33725=CIP 112509) that clearly differ from those of the subsp. type strain RCA14-39, we propose it as the type strain of a novel subspecies of , with the name subsp. subsp. nov.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): human gut microbiota , non-urbanized lifestyle and tridentinum subspecies
Funding
This study was supported by the:
  • Assessore Regionale dei Beni Culturali e dell'identità Siciliana, Regione Siciliana
    • Principal Award Recipient: NicolaSegata
  • Ministero della Salute (Award RF-2016-02364814)
    • Principal Award Recipient: NicolaSegata
  • H2020 Societal Challenges (Award 825410)
    • Principal Award Recipient: NicolaSegata
  • HORIZON EUROPE European Research Council (Award 716575)
    • Principal Award Recipient: NicolaSegata
  • HORIZON EUROPE European Research Council (Award 101045015)
    • Principal Award Recipient: NicolaSegata
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006798
2025-05-30
2026-04-15

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/ijsem/75/5/ijsem006798.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006798&mimeType=html&fmt=ahah

References

  1. Collins SL, Stine JG, Bisanz JE, Okafor CD, Patterson AD. Bile acids and the gut microbiota: metabolic interactions and impacts on disease. Nat Rev Microbiol 2023; 21:236–247 [View Article] [PubMed]
     [Google Scholar]
  2. Wang Q, Lin H, Shen C, Zhang M, Wang X et al. Gut microbiota regulates postprandial GLP-1 response via ileal bile acid-TGR5 signaling. Gut Microbes 2023; 15:2274124 [View Article] [PubMed]
     [Google Scholar]
  3. Marchesi JR, Adams DH, Fava F, Hermes GDA, Hirschfield GM et al. The gut microbiota and host health: a new clinical frontier. Gut 2016; 65:330–339 [View Article]
     [Google Scholar]
  4. Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 2019; 176:649–662 [View Article] [PubMed]
     [Google Scholar]
  5. Kageyama A, Benno Y. Catenibacterium mitsuokai gen. nov., sp. nov., a gram-positive anaerobic bacterium isolated from human faeces. Int J Syst Evol Microbiol 2000; 50 Pt 4:1595–1599 [View Article] [PubMed]
     [Google Scholar]
  6. Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol 2023; 41:1633–1644 [View Article] [PubMed]
     [Google Scholar]
  7. Valles-Colomer M, Blanco-Míguez A, Manghi P, Asnicar F, Dubois L et al. The person-to-person transmission landscape of the gut and oral microbiomes. Nature 2023; 614:125–135 [View Article] [PubMed]
     [Google Scholar]
  8. Ricci L, Selma-Royo M, Golzato D, Nabinejad A, Servais C et al. Draft genome sequence of a representative strain of the Catenibacterium genus isolated from human feces. Microbiol Resour Announc 2023; 12:e0032923 [View Article] [PubMed]
     [Google Scholar]
  9. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989; 17:7843–7853 [View Article] [PubMed]
     [Google Scholar]
  10. Stackebrandt E. Nucleic Acids and Classification. In Handbook of New Bacterial Systematics 1993;151–194
     [Google Scholar]
  11. Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A et al. BLAST: a more efficient report with usability improvements. Nucleic Acids Res 2013; 41:W29–33 [View Article] [PubMed]
     [Google Scholar]
  12. Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun 2020; 11:2500 [View Article] [PubMed]
     [Google Scholar]
  13. Shaw J, Yu YW. Fast and robust metagenomic sequence comparison through sparse chaining with skani. Nat Methods 2023; 20:1661–1665 [View Article] [PubMed]
     [Google Scholar]
  14. Segata N, Börnigen D, Morgan XC, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 2013; 4:2304 [View Article] [PubMed]
     [Google Scholar]
  15. Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 2007; 23:1282–1288 [View Article] [PubMed]
     [Google Scholar]
  16. Ruiz-Perez CA, Conrad RE, Konstantinidis KT. MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. BMC Bioinformatics 2021; 22:11 [View Article] [PubMed]
     [Google Scholar]
  17. Duncan SH, Hold GL, Harmsen HJM, Stewart CS, Flint HJ. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int J Syst Evol Microbiol 2002; 52:2141–2146 [View Article] [PubMed]
     [Google Scholar]
  18. Pedron R, Luchi E, Albiac MA, Di Cagno R, Catorci D et al. Mesorhizobium comanense sp. nov., isolated from groundwater. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  19. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M et al. Fiji: an open-source platform for biological-image analysis. Nat Methods 2012; 9:676–682 [View Article] [PubMed]
     [Google Scholar]
  20. Shields P, Cathcart L. Motility test medium protocol. American Society for Microbiology; n.d https://asm.org/ASM/media/Protocol-Images/Motility-Test-Medium-Protocol.pdf?ext=.pdf (2011
  21. Selma-Royo M, Ricci L, Golzato D, Servais C, Nabinejad A et al. Draft genome sequences of multiple bacterial strains isolated from human feces. Microbiol Resour Announc 2024; 13:e0030724 [View Article] [PubMed]
     [Google Scholar]
  22. Koransky JR, Allen SD, Dowell VR Jr. Use of ethanol for selective isolation of sporeforming microorganisms. Appl Environ Microbiol 1978; 35:762–765 [View Article]
     [Google Scholar]
  23. Matuschek E, Copsey-Mawer S, Petersson S, Åhman J, Morris TE et al. The European committee on antimicrobial susceptibility testing disc diffusion susceptibility testing method for frequently isolated anaerobic bacteria. Clin Microbiol Infect 2023; 29:795 [View Article] [PubMed]
     [Google Scholar]
  24. Neumann-Schaal M, Hofmann JD, Will SE, Schomburg D. Time-resolved amino acid uptake of Clostridium difficile 630Δerm and concomitant fermentation product and toxin formation. BMC Microbiol 2015; 15:281 [View Article] [PubMed]
     [Google Scholar]
  25. Garcia-Aloy M, Masuero D, Chitarrini G, Škrab D, Sivilotti P et al. Untargeted lipidomic profiling of grapes highlights the importance of modified lipid species beyond the traditional compound classes. Food Chem 2023; 410:135360 [View Article] [PubMed]
     [Google Scholar]
  26. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
/content/journal/ijsem/10.1099/ijsem.0.006798
Loading
Description of Catenibacterium mitsuokai subsp. tridentinum subsp. nov., an anaerobic bacterium isolated from human faeces, and emended description of C. mitsuokai
Int J Syst Evol Microbiol 75, 006798 (2025); https://doi.org/10.1099/ijsem.0.006798
/content/journal/ijsem/10.1099/ijsem.0.006798
/content/journal/ijsem/10.1099/ijsem.0.006798
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

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