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Clostridium culturomicium sp. nov. and Clostridium jeddahitimonense sp. nov., novel members of the Clostridium genus isolated from the stool of an obese Saudi Arabian

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Abstract

Taxono-genomics is an innovative concept coined for the description of new bacterial species. Phenotypic characteristics were combined with a genomic approach to describe two new species within the Clostridium senso stricto genus: Clostridium culturomicium strain CL-6T and Clostridium jeddahitimonense strain CL-2T, both isolated from the gut microbiota of an obese man from Saudi Arabia. Strains CL-6T and CL-2T shared a similarity of 98.4% with the 16S rRNA gene of Clostridium subterminale strain JCM 1417T (accession number NR113027) and 98% with that of Clostridium disporicum strain DS1T (accession number NR026491), respectively. The highest OrthoANI values were shared with Clostridium punense for strain CL-6T (70.8%) and with Clostridium disporicum for strain CL-2T (87.1%). Additionally, strain CL-6T and strain CL-2T shared a 16S rRNA similarity of 91.4%. Both strains were anaerobic, spore-forming and Gram-stain-positive non-motile bacilli. The genome of Clostridium culturomicium strain CL-6T is 4,325,182 bp long with 32.2% GC content. As for Clostridium jeddahitimonense strain CL-2T, the genome is 4,074,758 bp long with 29.2% GC content.

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Abbreviations

ANI:

Nucleotide identity

BMI:

Body mass index

COGs:

Cluster orthologous groups

COS:

Columbia agar with 5% sheep blood

dDDH:

DNA-DNA Hybridization

FAMEs:

Fatty acid methyl ester

GBDP:

Genome BLAST distance phylogeny approach

GC/MS:

Gaz 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

ORFs:

Open reading frames

PHAST:

PHAge search tool

RAST:

Rapid annotation using subsystem technology

TYGS:

Type (strain) genome server

UPGMA:

Unweighted pair group method with arithmetic

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Acknowledgements

The authors thank the Xegen Company (www.xegen.fr) for automating the genomic annotation process. The authors also thank Camille Valles and Sabrina Naud in the contribution of phylogenic tree and COG analysis.

Funding

This study was funded by the Méditerranée Infection Foundation and the Agence Nationale pour la Recherche (ANR), under the “Programme d’Investissement d’Avenir” reference Méditerranée Infection 10-IAHU-03.

Author information

Authors and Affiliations

  1. Aix Marseille University, RD, AP-HM, MEPHI, Marseille, France

    Hoang Thong Kieu, Jean-Christophe Lagier, Maryam Tidjani Alou & Didier Raoult

  2. IHU-Méditerranée Infection, Marseille, France

    Hoang Thong Kieu, Noémie Garrigou, Amael Fadlane, Ludivine Brechard, Nicholas Armstrong, Philippe Decloquement, Jean-Christophe Lagier & Didier Raoult

  3. Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia

    Esam Ibraheem Azhar

  4. Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia

    Muhammad Yasir & Esam Ibraheem Azhar

  5. Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia

    Saad B. Al-Masaudi

Authors
  1. Hoang Thong Kieu
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Contributions

Hoang Thong Kieu: Investigation (Lead); formal analysis (equal); writing – original draft (Lead). Noémie Garrigou: Investigation (equal). Esam Ibraheem Azhar, Fehmida Bibi and Amael Fadlane: Resources (equal). Ludivine Brechard, Nicholas Amstrong and Philippe Decloquement: Formal analysis (equal). Jean-Christophe Lagier: Supervision (equal), Validation (equal), Review & editing (support). Maryam Tidjani Alou: Supervision (equal), Validation (equal), Writing – original draft (support); review & editing (Lead). Didier Raoult: Conceptualization (Lead), Funding acquisition (Lead), Supervision (equal), Review & editing (support).

Corresponding author

Correspondence to Didier Raoult.

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An informed and written consent was obtained from the donor and the study was validated by the ethics commitee of the Institut Federatif de Recherche 48 under number 09-022.

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Kieu, H.T., Garrigou, N., Fadlane, A. et al. 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 (2021). https://doi.org/10.1007/s00284-021-02616-4

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