Skip to main content
NCBI home page
New Microbes and New Infections logoLink to New Microbes and New Infections
. 2016 Jun 6;13:54–55. doi: 10.1016/j.nmni.2016.06.002

‘Mediterranea massiliensis’ gen. nov., sp. nov., a new human-associated bacterium isolated from the right and left colon lavage of a 58-year-old patient

M Mailhe 1, D Ricaboni 1,2, A Benezech 3, S Khelaifia 1, P-E Fournier 1, D Raoult 1,∗
PMCID: PMC4932483  PMID: 27408745

Abstract

We report here the main characteristics of ‘Mediterranea massiliensis’ strain Marseille-P2645T (CSURP2645) that was isolated from stored samples of gut.

Keywords: Culturomics, genomics, Mediterranea massiliensis, taxonogenomics, taxonomy

In the context of a human microbiome study using culturomics [1], [2], in April 2016, we isolated a strain from a right and left colon lavage [3] of a 58-year-old women without medical history, who underwent a colonoscopy due to a positive screening test for a colorectal cancer. This bacterial strain could not be identified by our systematic matrix-assisted laser desorption-ionization time-of-flight screening on a Microflex spectrometer (MALDI-TOF MS) (Bruker Daltonics, Bremen, Germany) [4]. Signed and informed consent was collected from the patient and the study obtained approval from the ethics committee of the Institut Fédératif de Recherche IFR48 under number 09-022.

Samples were transported in an antioxidant-enriched liquid medium (unpublished data) before being seeded on a solid medium composed of 5% sheep blood-enriched Columbia agar (bioMérieux, Marcy l'Etoile, France). The initial growth was obtained after 1 day of culture at 37°C in anaerobic conditions (anaeroGEN, Oxoid Ltd, Dardilly, France). Colonies grown on 5% sheep blood-enriched Columbia agar medium were translucent and slightly haemolytic, with a diameter of 0.5 mm. Bacterial cells were Gram-negative bacilli, 1 μm in length and 0.6 μm in diameter. Strain Marseille-P2645' catalase and oxidase reactions were negative.

The 16S rRNA gene sequence was obtained using fD1-rP2 primers as previously described [5], using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France). Strain Marseille-P2645 exhibited a 92.9% sequence identity [6] with Bacteroides helcogenes strain P36-108T (GenBank Accession no. CP002352), which is the phylogenetically closest species with standing in nomenclature (Fig. 1). Bacteroides helcogenes strain P36-108T is an obligately anaerobic and a Gram-negative bacterium that was identified for the first time from abscesses and faeces of pigs in 1983 [7]. Bacteroides coprophilus strain CB42T (AB260026) was also a close validated species of strain Marseille-P2645; this strain is a Gram-negative anaerobic bacterium isolated from human faeces in 2007 [8].

Fig. 1.

Fig. 1

Open in a new tab

Phylogenetic tree showing the position of ‘Mediterranea massiliensis’ strain Marseille-P2645T relative to other phylogenetically close members of the family Bacteroidaceae. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences were obtained using the maximum likelihood method within the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Only the bootstraps score ≥95% were retained. The scale bar indicates a 2% nucleotide sequence divergence.

Because of a 16S rRNA gene sequence divergence >5% from its phylogenetically closest species with standing in nomenclature [9], we suggest the creation of the new genus Mediterranea gen. nov. (me.di.ter.ra.nea' N. L. fem. n., from Mare ‘Mediterraneum’, the Latin name of the Mediterranean sea) as this strain was first isolated in Marseille, located by the Mediterranean sea. ‘Mediterranea massiliensis’ gen. nov., sp. nov. (ma.si.li.en'sis. L. fem. adj., from massiliensis, of Massilia, the Latin name of Marseille where the strain was first cultivated) is classified as a member of the family Bacteroidaceae in the phylum Bacteroidetes.

Strain Marseille-P2645T is the type strain of the new species ‘Mediterranea massiliensis’ gen. nov., sp. nov.

MALDI-TOF Spectrum

The MALDI-TOF spectrum of ‘Mediterranea massiliensis’ strain Marseille-P2645T is available at http://www.mediterranee-infection.com/article.php?laref=256&titre=urms-database.

Nucleotide Sequence Accession Number

The 16Sr RNA gene sequence was deposited in GenBank under Accession number LT558847.

Deposit in a Culture Collection

Strain Marseille-P2645T was deposited in the collection de Souches de l'Unités des Rickettsies (CSUR, WDCM 875) under number P2645.

Funding

This work was funded by Mediterranée-Infection Foundation.

Conflict of Interest

The authors have no conflicts of interest to declare.

References

  • 1.Lagier J.C., Armougom F., Million M., Hugon P., Pagnier I., Robert C. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect. 2012;18:1185–1193. doi: 10.1111/1469-0691.12023. [DOI] [PubMed] [Google Scholar]
  • 2.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]
  • 3.Raoult D., Henrissat B. Are stool samples suitable for studying the link between gut microbiota and obesity? Eur J Epidemiol. 2014;29:307–309. doi: 10.1007/s10654-014-9905-4. [DOI] [PubMed] [Google Scholar]
  • 4.Seng P., Drancourt M., Gouriet F., La Scola B., Fournier P.-E., Rolain J.M. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis. 2009;49:543–551. doi: 10.1086/600885. [DOI] [PubMed] [Google Scholar]
  • 5.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]
  • 6.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]
  • 7.Benno Y., Watabe J., Mitsuoka T. Bacteroides pyogenes sp. nov., Bacteroides suis sp. nov., and Bacteroides helcogenes sp. nov., new species from abscesses and feces of pigs. Syst Appl Microbiol. 1983;4:396–407. doi: 10.1016/S0723-2020(83)80024-1. [DOI] [PubMed] [Google Scholar]
  • 8.Hayashi H., Shibata K., Abdul Bakir M., Sakamoto M., Tomita S., Benno Y. Bacteroides coprophilus sp. nov., isolated from human faeces. Int J Syst Evol Microbiol. 2007;57:1323–1326. doi: 10.1099/ijs.0.64979-0. [DOI] [PubMed] [Google Scholar]
  • 9.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]

Articles from New Microbes and New Infections are provided here courtesy of Elsevier

RESOURCES