Skip to main content
SpringerLink
Log in

Raoultibacter phocaeensis sp. nov., A New Bacterium Isolated from a Patient with Recurrent Clostridioides difficile Infection

  • Short Communication
  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

Strain Marseille-P8396T is a new species isolated from a patient with recurrent Clostridioides difficile infection. Its optimal growth condition was observed at pH of 7.5, at a temperature of 37 °C after 72 h of incubation on Columbia agar (BioMérieux, France) with 5% sheep blood, under an anaerobic atmosphere. Strain Marseille-P8396T cells are Gram-positive rods, nonspore‐forming, and nonmotile. 9-Octadecenoic acid (41.9%), hexadecanoic acid (22.5%), and 11-Octadecenoic acid (11.0%) represent the major fatty acid of strain Marseille-P8396T. The optimal growth condition of strain Marseille-P8396T was observed at 37 °C after 72 h of incubation under an anaerobic atmosphere, pH ranging from 6.5 to 8.5, and salinity of 0.5 to 7.5%. Its genome (Genbank Accession Number NZ_CABDUX000000000) size was 3.86 Mb with 59.4 mol% of G+C content, and 3,124 protein-coding genes. The 16S rRNA gene sequence (Genbank accession number NR_148574.1) of strain Marseille-P8396T shared a similarity of 98.71% with Raoultibacter timonensis strain Marseille-P3277T (Genbank accession number NR_148574.1), currently the most closely related species. However, the OrthoANI and digital DNA–DNA hybridization values with Raoultibacter timonensis strain Marseille-P3277T (Genbank accession number OEPT01000000) were 80.15% and 24.6 ± 4.8%, respectively. Taken together, these results clearly demonstrate that strain Marseille-P8396T represents a new species within the genus Raoultibacter described here as Raoultibacter phocaeensis sp. nov. (type strain: Marseille-P8396T=CSUR8396T=CECT 30202T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Abbreviations

ANI:

Nucleotide identity

CECT:

Colección Española de Cultivos Tipo

COGs:

Cluster orthologous groups

COS:

Columbia agar with 5% sheep blood

CSUR:

Collection des Souches de l’Unité des Rickettsies

dDDH:

DNA–DNA hybridization

EUCAST:

European Committee on Antibiotic Susceptibility Testing

FAMEs:

Fatty acid methyl ester

GBDP:

Genome BLAST distance phylogeny

GC/MS:

Gas chromatography/mass spectrometry

gDNA:

Genomic DNA

MALDI-TOF MS:

Matrix-assisted laser desorption ionization–time of flight mass spectrometry

MIC:

Minimum inhibitory concentration

OAT:

Orthologous ANI tool

TYGS:

Type (strain) genome server

References

  1. Jh K, Ma O, Er D (2015) The morbidity, mortality, and costs associated with Clostridium difficile infection. Infect Dis Clin N Am 29:123–134. https://doi.org/10.1016/j.idc.2014.11.003

    Article  Google Scholar 

  2. Cammarota G, Ianiro G, Tilg H et al (2017) European consensus conference on faecal microbiota transplantation in clinical practice. Gut 66:569–580. https://doi.org/10.1136/gutjnl-2016-313017

    Article  PubMed  Google Scholar 

  3. Lagier J-C, Armougom F, Million M et al (2012) Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect Off Publ Eur Soc Clin Microbiol Infect Dis 18:1185–1193. https://doi.org/10.1111/1469-0691.12023

    Article  CAS  Google Scholar 

  4. Lagier J-C, 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  CAS  PubMed  PubMed Central  Google Scholar 

  5. Lagier J-C, Khelaifia S, Alou MT et al (2016) Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol 1:16203. https://doi.org/10.1038/nmicrobiol.2016.203

    Article  CAS  PubMed  Google Scholar 

  6. Traore SI, Bilen M, Beye M et al (2019) Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut. Microbiol Open 8:e00758. https://doi.org/10.1002/mbo3.758

    Article  CAS  Google Scholar 

  7. Traore SI, Yasir M, Azhar EI et al (2016) “Raoultibacter massiliensis” gen. nov., sp. nov., a new bacterium isolated from the human gut of a Saudi Bedouin. New Microbes New Infect 14:1–3. https://doi.org/10.1016/j.nmni.2016.06.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Bilen M, Cadoret F, Dubourg G et al (2017) “Raoultibacter timonensis” gen. nov., sp. nov., a new bacterium isolated from the human gut of a Pygmy woman. New Microbes New Infect 16:45–46. https://doi.org/10.1016/j.nmni.2016.12.016

    Article  CAS  PubMed  Google Scholar 

  9. Seng P, Drancourt M, Gouriet F et al (2009) Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis Off Publ Infect Dis Soc Am 49:543–551. https://doi.org/10.1086/600885

    Article  CAS  Google Scholar 

  10. Kieu HT, Garrigou N, Fadlane A et al (2021) Clostridium culturomicium sp. nov. and Clostridium jeddahitimonense sp. nov., novel members of the Clostridium genus isolated from the stool of an obese Saudi Arabian. Curr Microbiol 78:3586–3595. https://doi.org/10.1007/s00284-021-02616-4

    Article  CAS  PubMed  Google Scholar 

  11. Mayrer A (1974) Methods in clinical bacteriology. A manual of tests and procedures. Yale J Biol Med 47:68–69

    PubMed Central  Google Scholar 

  12. Dione N, Sankar SA, Lagier J-C 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  CAS  PubMed  PubMed Central  Google Scholar 

  13. 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  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  Google Scholar 

  15. Luo R, Liu B, Xie Y et al (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. https://doi.org/10.1186/2047-217X-1-18

    Article  PubMed  PubMed Central  Google Scholar 

  16. Anani H, Khodor M, Raoult D, Fournier P-E (2019) Whole-genome sequence of French clinical Olivibacter jilunii strain P8502. Microbiol Resour Announc. https://doi.org/10.1128/MRA.00701-19

    Article  PubMed  PubMed Central  Google Scholar 

  17. Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153

    Article  CAS  PubMed  Google Scholar 

  18. Page AJ, Cummins CA, Hunt M et al (2015) Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31:3691–3693. https://doi.org/10.1093/bioinformatics/btv421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36. https://doi.org/10.1093/nar/28.1.33

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Tatusov RL, Natale DA, Garkavtsev IV et al (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29:22–28. https://doi.org/10.1093/nar/29.1.22

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Natale DA, Galperin MY, Tatusov RL, Koonin EV (2000) Using the COG database to improve gene recognition in complete genomes. Genetica 108:9–17. https://doi.org/10.1023/A:1004031323748

    Article  CAS  PubMed  Google Scholar 

  22. Auch AF, von Jan M, Klenk H-P, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134. https://doi.org/10.4056/sigs.531120

    Article  PubMed  PubMed Central  Google Scholar 

  23. Auch AF, Klenk H-P, Göker M (2010) Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2:142. https://doi.org/10.4056/sigs.541628

    Article  PubMed  PubMed Central  Google Scholar 

  24. Lee I, Ouk Kim Y, Park S-C, 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  CAS  PubMed  Google Scholar 

  25. Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    Article  CAS  Google Scholar 

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

    Google Scholar 

  27. Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299–306. https://doi.org/10.1093/bib/bbn017

    Article  CAS  PubMed  Google Scholar 

  28. Grin I, Linke D (2011) GCView: the genomic context viewer for protein homology searches. Nucleic Acids Res 39:W353–W356. https://doi.org/10.1093/nar/gkr364

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Lefort V, Desper R, Gascuel O (2015) FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 32:2798–2800. https://doi.org/10.1093/molbev/msv150

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Farris JS (1972) Estimating phylogenetic trees from distance matrices. Am Nat 106:645–668. https://doi.org/10.1086/282802

    Article  Google Scholar 

Download references

Acknowledgements

The authors thank Hitachi Corporation for providing the SU5000® Tabletop microscope. They also thank Aurelia Caputo from IHU-Méditerranée Infection, Marseille for submitting the genomic sequences to GenBank and Magali Richez from IHU-Méditerranée Infection, Marseille for Fatty acid methyl ester analysis.

Funding

This work was supported by the “IHU Méditerranée Infection” and by the French Government “Investissements d’avenir” program managed by the Agence Nationale de la Recherche, under reference: Méditerranée Infection 10-IAHU-03.

Author information

Authors and Affiliations

  1. Aix Marseille Univ, IRD, Microbes, Evolution, Phylogeny and Infection (MEPHI), AP-HM, Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France

    Abdourahamane Yacouba, Edmond Kuete Yimagou, Ornella La Fortune Tchoupou Saha, Didier Raoult, Jean-Christophe Lagier & Grégory Dubourg

  2. IHU Méditerranée Infection, Marseille, France

    Abdourahamane Yacouba, Edmond Kuete Yimagou, Cheikh Ibrahima Lo, Ornella La Fortune Tchoupou Saha, Stephane Alibar, Amael Fadlane, Anthony Fontanini, Ludivine Brechard, Didier Raoult, Jean-Christophe Lagier & Grégory Dubourg

  3. Faculté des Sciences de la Santé, Université Abdou Moumouni, Niamey, Niger

    Abdourahamane Yacouba

  4. Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France

    Cheikh Ibrahima Lo

Authors
  1. Abdourahamane Yacouba
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Edmond Kuete Yimagou
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Cheikh Ibrahima Lo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ornella La Fortune Tchoupou Saha
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Stephane Alibar
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Amael Fadlane
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Anthony Fontanini
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ludivine Brechard
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Didier Raoult
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Jean-Christophe Lagier
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Grégory Dubourg
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

AY: Investigation, formal analysis, writing—original draft. EKY: Investigation and formal analysis. SA, AF, AF, and LB: Formal analysis. DR, JCL, and GD: Conceptualization, funding acquisition, supervision, review and editing.

Corresponding author

Correspondence to Grégory Dubourg.

Ethics declarations

Conflict of interest

Didier Raoult was a consultant in microbiology for the Hitachi High-Tech Corporation. All the other authors have no relevant conflicts of interest to declare.

Ethical Approval

This study was validated by the ethics committee of “IHU Méditerranée Infection” under Agreement Number 2017-009.

Additional information

Publisher's Note

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

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 249 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yacouba, A., Kuete Yimagou, E., Lo, C.I. et al. Raoultibacter phocaeensis sp. nov., A New Bacterium Isolated from a Patient with Recurrent Clostridioides difficile Infection. Curr Microbiol 79, 263 (2022). https://doi.org/10.1007/s00284-022-02959-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00284-022-02959-6

Search

Navigation