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. 2016 Nov 28;17:27–29. doi: 10.1016/j.nmni.2016.11.023

‘Colidextribacter massiliensis’ gen. nov., sp. nov., isolated from human right colon

D Ricaboni 1,3, M Mailhe 1, F Cadoret 1, V Vitton 2, P-E Fournier 1, D Raoult 1,∗
PMCID: PMC5328710  PMID: 28275436

Abstract

We report here the main characteristics of ‘Colidextribacter massiliensis’ strain Marseille-P3083T (CSURP3083), which was isolated from a human right colon lavage sample.

Keywords: Colidextribacter massiliensis, Culturomics, human gut, microbiota, taxonogenomics

In 2016, as a part of culturomics study of the human microbiome [1], we isolated from the right colon of a 27-year-old obese patient a bacterial strain that could not be identified by our systematic matrix-assisted desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) screening on a Microflex spectrometer (Bruker Daltonics, Bremen, Germany) [2]. The patient provided signed informed consent, and the study was validated by the ethics committee of the Institut Fédératif de Recherche IFR48 under number 2016-010.

Strain Marseille-P3083T growth was obtained on 5% sheep’s blood–enriched Columbia agar medium (bioMérieux, Marcy l’Etoile, France) in anaerobic atmosphere (anaeroGEN, Oxoid, Dardilly, France) after a 30-day enrichment of the fresh right colon sample in an anaerobic haemoculture bottle (Becton Dickinson, Pont de Claix, France) added with 5 mL of sheep’s blood (bioMérieux) and 5 mL of 0.2 μm filtered (Thermo Fisher Scientific, Villebon-sur-Yvette, France) rumen at 37°C.

After 96 hours of anaerobic incubation on 5% sheep’s blood–enriched agar (bioMérieux) colonies were punctiform, approximately round and translucid, with a mean diameter of 0.1 to 0.3 mm. Bacterial cells were small Gram-negative cocci ranging in length from 0.4 to 0.6 μm. Strain Marseille-P3083T tested catalase and oxidase negative. Sporulation test (20 minutes at 80°C) was negative, and no growth was achieved under aerobic or microaerophilic (campyGEN, Oxoid) conditions. The 16S rRNA gene was sequenced using fD1-rP2 primers as previously described [3] using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France). Strain Marseille-P3083T exhibited a 93.57% sequence identity with Pseudoflavonifractor capillosus strain ATCC 29799T (GenBank accession no. AY136666), the phylogenetically closest species with standing in nomenclature (Fig. 1). This value putatively classifies strain Marseille-P3083T as a member of a new genus within the Clostridiales cluster IV in the phylum Firmicutes. Clostridiales cluster IV was created in 1994 and collects microorganisms that exhibit Clostridium and non-Clostridium-like characteristics [4], including Gram-negative microorganisms [5]. Intestinimonas butyriciproducens DSM 26588T (16S rRNA similarity of 93.42%) is another phylogenetically very close species (Fig. 1) that exhibits the peculiar characteristic of appearing as a Gram-negative rod while electron microscopy demonstrated Gram-positive cell wall characteristics [6].

Fig. 1.

Fig. 1

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Phylogenetic tree showing position of ‘Colidextribacter massiliensis’ strain Marseille-P3083T relative to other phylogenetically close neighbours. Sequences were aligned using CLUSTALW, and phylogenetic inferences were obtained using maximum-likelihood method within MEGA software. Numbers at nodes are percentages of bootstrap values obtained by repeating analysis 1000 times to generate majority consensus tree. Only bootstrap scores of at least 90% were retained.

On the basis of the morphologic differences (morphology and Gram stain) and the 16S rRNA sequence divergence of strain Marseille-P3083T with the phylogenetically closest species with standing in nomenclature [7], [8] we propose here the creation of the new genus Colidextribacter (Co.li.dex.tri.bac.ter, L. neut. n. colon or colum, ‘colon’; L. adj. dexter, ‘right’; N.L. masc. n. bacter, ‘a rod’; N.L. masc. n. Colidextribacter, ‘a rod from the right colon’); and a new species Colidextribacter massiliensis for which Marseille-P3083T (= CSUR P3083) is the type strain.

Strain Marseille-P3083T is the type strain of Colidextribacter massiliensis gen. nov., sp. nov. (mas.si.li.en′sis, L., masc. adj., massiliensis, for Massilia, the Roman name of Marseille).

MALDI-TOF MS spectrum

The MALDI-TOF MS spectrum of ‘Colidextribacter massiliensis’ strain Marseille-P23083 T is available online (http://www.mediterranee-infection.com/article.php?laref=256&titre=urms-database).

Nucleotide sequence accession number

The 16S r RNA gene sequence was deposited in GenBank under accession number LT598546.

Deposit in a culture collection

Strain Marseille-P3083T was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P3083.

Acknowledgement

This study was funded by the Fondation Méditerranée Infection.

Conflict of Interest

None declared.

References

  • 1.Lagier J.C., Hugon P., Khelaifia S., Fournier P.E., La Scola B., Raoult D. The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev. 2015;28:237–264. doi: 10.1128/CMR.00014-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Seng P., Abat C., Rolain J.M., Colson P., Lagier J.C., Gouriet F. Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization–time of flight mass spectrometry. J Clin Microbiol. 2013;51:2182–2194. doi: 10.1128/JCM.00492-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Drancourt M., Bollet C., Carlioz A., Martelin R., Gayral J.P., Raoult D. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol. 2000;38:3623–3630. doi: 10.1128/jcm.38.10.3623-3630.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Collins M.D., Lawson P.A., Willems A., Cordoba J.J., Fernandez-Garayzabal J., Garcia P. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol. 1994;44:812–826. doi: 10.1099/00207713-44-4-812. [DOI] [PubMed] [Google Scholar]
  • 5.Carlier J.P., Bedora-Faure M., K’ouas G., Alauzet C., Mory F. Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov. Int J Syst Evol Microbiol. 2010;60:585–590. doi: 10.1099/ijs.0.016725-0. [DOI] [PubMed] [Google Scholar]
  • 6.Kläring K., Hanske L., Bui N., Charrier C., Blaut M., Haller D. Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine. Int J Syst Evol Microbiol. 2013;63:4606–4612. doi: 10.1099/ijs.0.051441-0. [DOI] [PubMed] [Google Scholar]
  • 7.Huson D.H., Auch A.F., Qi J., Schuster S.C. MEGAN analysis of metagenomic data. Genome Res. 2007;17:377–386. doi: 10.1101/gr.5969107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Kim M., Oh H.S., Park S.C., Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014;64:346–351. doi: 10.1099/ijs.0.059774-0. [DOI] [PubMed] [Google Scholar]

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