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We report the main characteristics of “Eggerthella timonensis” strain Marseille-P3135 which was isolated from a stool sample of a healthy 8-year-old pygmy (Baka) girl.
Ahead of the initiation of the study, ethical approval (09-022) was obtained from Institut Fédératif de Recherche IFR48. Samples were collected from Congo and stored at 4°C. “Eggerthella timonensis” strain Marseille-P3135 was isolated from a stool sample of a healthy 8-year-old pygmy (Baka) girl as part of the study aiming to describe the human gut microbiota using culturomics as a technique .
Samples were diluted with phosphate-buffered saline and incubated for 30 days in a blood culture bottle with 5 mL of sheep’s blood under anaerobic conditions at 37°C. Strain Marseille-P3135 was isolated after 10 days on 5% sheep’s blood–enriched Columbia agar (bioMérieux, Marcy l’Etoile, France). We failed to identify this bacteria using matrix-assisted desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) screening on a Microflex spectrometer (Bruker Daltonics, Bremen, Germany) .
The colonies of strain Marseille-P3135 were smooth with a mean diameter of 0.5 mm. Bacterial cells were Gram and catalase positive, oxidase negative and rod shaped with a diameter of 0.7 to 1.6 μm. The 16S rRNA gene sequencing was performed on 3130-XL sequencer (Applied Biosciences, Saint Aubin, France) using fD1-rP2 primer (Eurogentec, Seraing, Belgium) as previously described . Strain Marseille-P3135 exhibited a 97.62% sequence identity with Eggerthella sinensis strain HKU14 (NR_042840.1), the phylogenetically closest species with standing in nomenclature (Fig. 1). Thus, strain Marseille-P3135 can be classified as a member of the genus Eggerthella within the family Coriobacteriaceae and under the Actinobacteria phylum .
Because the 16S rRNA gene sequence of Marseille-P3135 and E. sinensis strain HKU14 diverge by more than 1.3% , we discovered a new species “Eggerthella timonensis” (ti.mo.nen′sis, N.L. masc. adj. timonensis, pertaining to Timone, the name of the main university hospital in Marseille, France, where strain Marseille-P3135 was isolated). Strain Marseille-P3135 is the type strain of the new species “Eggerthella timonensis.”
The MALDI-TOF MS spectrum of “Eggerthella timonensis” is available online (http://www.mediterranee-infection.com/article.php?laref=256&titre=urms-database).
The 16S rRNA gene sequence was deposited in GenBank under accession number LT598568.
Strain Marseille-P3135 was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P3135.
This study was funded by the Fondation Méditerranée Infection.