Neglectibacter timonensis gen. nov., sp. nov. and Scatolibacter rhodanostii gen. nov., sp. nov., two anaerobic bacteria isolated from human stool samples

Rita Zgheib; Ahmad Ibrahim; Hussein Anani; Sokhna Ndongo; Melhem Bilen; Nicholas Armstrong; Magali Richez; Didier Raoult; Pierre-Edouard Fournier

doi:10.1007/s00203-021-02712-w

Neglectibacter timonensis gen. nov., sp. nov. and Scatolibacter rhodanostii gen. nov., sp. nov., two anaerobic bacteria isolated from human stool samples

Arch Microbiol. 2021 Dec 21;204(1):45. doi: 10.1007/s00203-021-02712-w.

Authors

Rita Zgheib^{1

2}, Ahmad Ibrahim^{1

3}, Hussein Anani^{1

2}, Sokhna Ndongo^{1

3}, Melhem Bilen⁴, Nicholas Armstrong¹, Magali Richez¹, Didier Raoult^{1

3

5}, Pierre-Edouard Fournier^{6

7}

Affiliations

¹ Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
² UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, Aix Marseille Université, Marseille, France.
³ UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille Université, Marseille, France.
⁴ Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, USA.
⁵ Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
⁶ Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France. pierre-edouard.fournier@univ-amu.fr.
⁷ UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, Aix Marseille Université, Marseille, France. pierre-edouard.fournier@univ-amu.fr.

PMID: 34932147
DOI: 10.1007/s00203-021-02712-w

Abstract

Strains Marseille-P2265^T (=CSUR P2265^T =DSM 102082^T) and Marseille-P3890^T (=CSUR P3890^T =CCUG 72341^T) were isolated from stool samples using the culturomics approach. The 16S rRNA gene sequences of both strains were sequenced and compared by BLASTn to the NCBI database. Strains Marseille-P2265^T and Marseille-P3890^T were most closely related to Acutalibacter muris with identities of 94.3% and 91.5%, respectively. Between the two strains, the 16S rRNA gene sequence identity was 91.5%. Both strains are anaerobic Gram-positive, oxidase- and catalase-negative. The major fatty acid methyl esters (> 10%) in both strains are C_16:0 and anteiso-C_15:0. Additionally, strain Marseille-P2265^T has iso-C_15:0 and C_14:0, and strain Marseille-P3890^T, iso-C_14:0. Strain Marseille-P2265^T has a genome size of 3,671,396-bp with a G + C content of 52.8%. As for strain Marseille-P3890^T, the genome is 2,702,024-bp-long with a 39.8% G + C content. The genomic comparison of closely related species with strains Marseille-P2265^T and Marseille-P3890^T showed that all digital DNA-DNA hybridization (dDDH), orthologous average nucleotide identity (OrthoANI) and average amino acid identity (AAI) values were lower than the published species thresholds (70% for dDDH, 95-96% for OrthoANI/AAI). Based on these results, it was concluded that strains Marseille-P2265^T and Marseille-P3890^T belong to two new genera in the family Oscillospiraceae. For these two genera, the names Neglectibacter gen. nov. and Scatolibacter gen. nov. were proposed, with strains Marseille-P2265^T and Marseille-P3890^T being the type strains of Neglectibacter timonensis gen. nov., sp. nov. and Scatolibacter rhodanostii gen. nov., sp. nov., respectively.

Keywords: Anaerobic; Genome; Neglectibacter timonensis; New genus; Oscillospiraceae; Scatolibacter rhodanostii.

MeSH terms

Bacteria, Anaerobic*
Bacterial Typing Techniques
DNA, Bacterial / genetics
Fatty Acids*
Humans
Phylogeny
RNA, Ribosomal, 16S / genetics
Sequence Analysis, DNA

Substances

DNA, Bacterial
Fatty Acids
RNA, Ribosomal, 16S