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New Microbes New Infect. 2017 May; 17: 41–42.
Published online 2016 November 15. doi:  10.1016/j.nmni.2016.11.001
PMCID: PMC5328910

“Eggerthella timonensis” gen. nov. isolated from a human stool sample

Abstract

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.

Keywords: Culturomics, Eggerthella timonensis, emerging bacteria, gut microbiota, human microbiota

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 [1].

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) [2].

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 [3]. 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 [4].

Fig. 1
Phylogenetic tree representing position of “Eggerthella timonensis” strain Marseille-P3135 among its neighbours. Sequences of strains utilized in this tree were aligned using CLUSTALW. Additionally, by means of MEGA software, and using ...

Because the 16S rRNA gene sequence of Marseille-P3135 and E. sinensis strain HKU14 diverge by more than 1.3% [5], 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.”

MALDI-TOF MS spectrum

The MALDI-TOF MS spectrum of “Eggerthella timonensis” 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 LT598568.

Deposit in a culture collection

Strain Marseille-P3135 was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P3135.

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. [PubMed]
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. [PubMed]
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. [PubMed]
4. Lau S.K.P., Woo P.C.Y., Woo G.K.S., Fung A.M.Y., Wong M.K.M., Chan K.M. Eggerthella hongkongensis sp. nov. and Eggerthella sinensis sp. nov., two novel Eggerthella species, account for half of the cases of Eggerthella bacteremia. Diagn Microbiol Infect Dis. 2004;49:255–263. [PubMed]
5. 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. [PubMed]

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