Abstract
We present the main features of ‘Bacteroides ihuae’ sp. nov., strain Marseille-P2824T (CSUR P2824), isolated from the sputum of healthy Frenchwoman living in Marseille.
Keywords: ‘Bacteroides ihuae’, culturomics, genomics, taxonogenomics, taxonomy
We applied the culturomics strategy [1], [2] to a sputum sample from a healthy French woman living in Marseille. We obtained the participant’s oral consent as well as authorization from the ethics committee of the Institut Federatif de Recherche IFR48 under number 09-022. After day 10 of preincubation of the sample in an aerobic blood culture bottle (Becton Dickinson, Le Pont-de-Claix, France) supplemented with filter-sterilized rumen at 30°C, strain Marseille-P2824T was subcultured on 5% sheep’s blood–enriched Columbia agar (bioMérieux, Marcy l’Etoile, France) at 30°C in an anaerobic atmosphere with 5% CO2. Colonies appeared to be smooth with a diameter ranging from 1 to 3 mm. Bacterial cells were Gram-positive and rod shaped, with a diameter ranging from 0.5 to 0.64 μm and a length ranging from 1.0 to 1.6 μm. Strain Marseille-P2824T was negative for catalase and oxidase production.
Strain Marseille-P2824T was not identified by our systematic matrix-assisted desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) (http://mediterraner-infection.com/article.php?laref=256&titre=urms-database) on a Microflex spectrometer (Bruker Daltonics, Bremen, Germany) [3], [4]. Consequently, 16S rRNA gene sequencing was performed using fD1-rP2 primers as previously described [5], with a 3130-XL sequencer (Applied Biosciences, Saint-Aubin, France). Strain Marseille-P2824T was classified as a member of the genus Bacteroides within family Bacteroidaceae in the phylum Bacteroidetes because it shares a 96% sequence identity with Bacteroides graminisolvens strain JCM 15093 (GenBank accession no. NR_113069) [6], which is the phylogenetically closest species with standing in nomenclature (Fig. 1). Because this similarity value was lower than the 98.65% threshold recommended to define a new species [7] when DNA-DNA hybridization is not performed, we propose that strain Marseille-P2824T may be the representative strain of a new species named ‘Bacteroides ihuae’ (i.hum.i′i, N.L. gen. n. ihuae, based on the acronym IHUMI, the Institut Hospitalo-Universitaire Méditerranée-Infection in Marseille, France, where the type strain was isolated). Strain Marseille-P2824T is the type strain of the new species ‘Bacteroides ihuae.’
Fig. 1.
Positioning of ‘Bacteroides ihuae’ strain Marseille-P2824T relative to other phylogenetically close strains in phylogenetic tree. CLUSTALW was used to align sequences, and phylogenetic inferences were generated using MEGA software with maximum likelihood method. Scale bar indicates 2% nucleotide sequence divergence. Numbers at nodes are percentages of 500 bootstrap values obtained in order to generate consensus tree. Only bootstraps with minimum of 90% score were retained.
MALDI-TOF MS spectrum
The MALDI-TOF MS spectrum of ‘Bacteroides ihuae’ strain Marseille-P2824T is available online (http://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 LT576386.
Deposit in a culture collection
Strain Marseille-P2824T was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P2824.
Acknowledgements
This study was funded by the Fondation Méditerranée Infection.
Conflict of Interest
None declared.
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.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]
- 4.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]
- 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.Nishiyama T., Ueki A., Kaku N., Watanabe K., Ueki K. Bacteroides graminisolvens sp. nov., a xylanolytic anaerobe isolated from a methanogenic reactor treating cattle waste. Int J Syst Evol Microbiol. 2009;59:1901–1907. doi: 10.1099/ijs.0.008268-0. [DOI] [PubMed] [Google Scholar]
- 7.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]