Abstract
We report the main characteristics of “Collinsella bouchesdurhonensis” strain Marseille-P3296, which was isolated from a stool sample of a healthy 50-year-old pygmy (Baka) woman.
Keywords: “Collinsella bouchesdurhonensis”, culturomics, emerging bacteria, gut microbiota, human microbiota
We obtained approval for the study from the ethics committee of the Institut Fédératif de Recherches 48 (no. 09-022) before we initiated the project. Samples were collected in Congo for analysis as part of the project describing the human microbiome by culturomics [1].
First, a stool sample from a 50-year-old pygmy (Baka) woman was diluted with 1 mL phosphate-buffered saline and incubated in a blood culture bottle containing an extra 5 mL of filtered rumen and sheep’s blood. The culture bottle was incubated at 37°C for 30 days under anaerobic conditions. At day 10, a “Collinsella bouchesdurhonensis” colony was isolated on 5% sheep’s blood–enriched Columbia agar (bioMérieux, Marcy l’Etoile, France). Strain Marseille-P3296 identification by matrix-assisted desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) using a Microflex spectrometer (Bruker Daltonics, Leipzig, Germany) failed [2]. Then, 16S rRNA gene sequencing was performed for further analysis using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France) with fD1-rP2 primers (Eurogentec, Seraing, Belgium) as previously described [3]. Strain Marseille-P3296 exhibited a 96.19% sequence identity with Collinsella aerofaciens type strain JCM 10188 (AB 011816), the phylogenetically closest species with standing in nomenclature (Fig. 1). Thus, strain Marseille-P3296 can be classified as a new species within Collinsella genus [4].
Fig. 1.
Phylogenetic tree showing branching of “Collinsella bouchesdurhonensis” strain Marseille-P3296 among other phylogenetically close neighbours. Sequence alignment was performed by CLUSTALW tool; then MEGA software was used for phylogenetic tree generation by neighbour-joining method. Five hundred bootstraps were performed; scores of at least 90% are shown on nodes. Scale bar indicates 2% nucleotide sequence divergence.
Because the 16S rRNA gene sequence of strain Marseille-P3296 diverges by more than 1.3% from the 16S rRNA gene sequence of its phylogenetically closest species with standing in nomenclature [5], we suggest the discovery of the new species “Collinsella bouchesdurhonensis” (bou.ches.du.rho.nen′sis, N.L. fem. adj. bouchesdurhonensis, pertaining to Bouches du Rhône, the name of the French territory where strain Marseille-P3296 was isolated). Strain Marseille-P3296 is the type strain of the new species “Collinsella bouchesdurhonensis.” Colonies were smooth with a mean diameter of 0.1 to 0.5 mm. Bacterial cells were Gram-positive bacilli, were catalase and oxidase negative and had a mean diameter of 2.6 μm.
MALDI-TOF MS spectrum accession number
The MALDI-TOF MS spectrum of “C. bouchesdurhonensis” is available online (http://www.mediterranee-infection.com/article.php?laref=256&titre=urms-database).
Nucleotide sequence accession number
The 16S rRNA gene sequence was deposited in GenBank under accession number LT623900.
Deposit in a culture collection
Strain Marseille-P3296 was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P3296.
Acknowledgement
This study was funded by the Fondation Méditerranée Infection.
Conflict of Interest
None declared.
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