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. 2016 Jul 29;14:21–23. doi: 10.1016/j.nmni.2016.07.008

“Ihuprevotella massiliensis” gen. nov., sp. nov., isolated from human gut

D Ricaboni 1,3, M Mailhe 1, A Benezech 2, PE Fournier 1, D Raoult 1, S Khelaifia 1,∗
PMCID: PMC5008045  PMID: 27621825

Abstract

We report here the main characteristics of “Ihuprevotella massiliensis” strain Marseille-P2826T (CSURP 2826) that was isolated from a human right colon lavage sample.

Keywords: Culturomics, genomics, human, “Ihuprevotella massiliensis”, taxonomy

n recent years, scientific interest in the role played by endogenous gut microflora in human health has undergone a great expansion, but our knowledge remains far from exhaustive [1]. During an ongoing study aimed at analysing the gut microflora by culturomics [2], we grew by pure culture a bacterial strain that escaped matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification using a MicroFlex spectrometer (Bruker Daltonics, Bremen, Germany) [3]. Strain Marseille-P2826 was isolated from a right colon lavage sample of a 58-year-old man who underwent upper and lower endoscopy examination to investigate sideropenic anemia. Signed informed consent was obtained, and the agreement of the ethics committee of the IFR48 (Faculty of Medicine, Marseille, France) was obtained under number 09-022. Growth of strain Marseille-P2826 was obtained on 5% sheep's blood–enriched Columbia agar (bioMérieux, Marcy l'Etoile, France) incubated in an anaerobic atmosphere (anaeroGEN, Oxoid, Dardilly, France) after a 15-day enrichment step of the fresh right colon sample in an anaerobic blood culture bottle (Becton Dickinson, Pont de Claix, France) enriched with sheep’s blood and 0.2 μm filtered rumen at 37°C. Bacterial cells were Gram negative, rod shaped and polymorphic but did not form spores and were not motile. Strain Marseille-P2826 exhibited no catalase and no oxidase activities. After 48 hours of anaerobic incubation, colonies varied from 0.6 to 1.2 mm in diameter and were circular, convex, smooth, opaque, whitish and not haemolytic.

The 16S rRNA gene sequence was obtained using the fD1-rP2 primers as previously described using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France) [4]. Strain Marseille-P2826 exhibited a 90% sequence similarity with Alloprevotella rava (NR 118334.1), the closest species with standing in nomenclature (Fig. 1), which putatively classifies it as a member of a new genus within the family Prevotellaceae in the Bacteroidetes phylum [5]. The family Prevotellaceae is composed of four genera with validly published names, including Prevotella, Alloprevotella, Hallella and Paraprevotella [6]. Xylanibacter oryzae, the only representative of a fifth genus within the Prevotellaceae family, has been relocated among the Prevotella genus on the basis of the hsp60 sequence analysis [7], although it is still not clear if Hallella constitutes a distinct genus or if it should be part of the Prevotella genus [8]. The Alloprevotella genus was created in 2013 after the isolation of Alloprevotella rava from the human oral cavity and comprises only two species [9]. Species belonging to the genus Alloprevotella are Gram negative, obligately anaerobic, nonmotile bacilli that are usually isolated from the human oral cavity [9].

Fig. 1.

Fig. 1

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Phylogenetic tree showing position of “Ihuprevotella massiliensis” strain P2826T (in red) relative to other phylogenetically close members of family Prevotellaceae. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences were obtained using maximum-likelihood method within MEGA software. Numbers at nodes are percentages of bootstrap values obtained by repeating analysis 500 times to generate majority consensus tree. Only values >95% are displayed. Scale bar indicates 2% nucleotide sequence divergence.

On the basis of the 16S rRNA gene sequence divergence of strain Marseille-P2826 (>5%) with the phylogenetically closest species [10] we propose the creation of the new genus Ihuprevotella (ihu.pre.vo.tel'la, with IHU from Institut Hospitalier Universitaire, the institution in Marseille where the strain was first described; N.L. fem. n. Prevotella, a bacterial generic name; N.L. fem. n. Ihuprevotella, organism related to the family Prevotellaceae isolated at IHU). Strain Marseille-P2826 is the type strain of Ihuprevotella massiliensis gen. nov., sp. nov. (mas.si.li.en'sis, N.L. fem. adj., massiliensis, “of Massilia,” the Roman name of Marseille, where strain Marseille-P2826 was isolated).

Nucleotide sequence accession number

The 16S rRNA gene sequence was deposited in GenBank under accession number LT576392. The MALDI-TOF MS spectrum of “Ihuprevotella massiliensis” strain Marseille-P2826 T is available at http://www.mediterranee-infection.com/article.php?laref=256&titre=urms-database.

Deposit in a culture collection

Strain Marseille-P2826T was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number Marseille-P2826.

Conflict of Interest

None declared.

References

  • 1.Eckburg P.B., Bik E.M., Bernstein C.N., Purdom E., Dethlefsen L., Sargent M. Diversity of the human intestinal microbial flora. Science. 2005;308:1635–1638. doi: 10.1126/science.1110591. [DOI] [PMC free article] [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., 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]
  • 4.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]
  • 5.Euzeby J. Validation list no. 143. Int J Syst Evol Microbiol. 2012;62:1–4. [Google Scholar]
  • 6.Rosenberg E. The family Prevotellaceae. In: Rosenberg E., DeLong E.F., Lory S., Stackebrandt E., Thompson F., editors. The prokaryotes. 4th ed. Springer; New York: 2014. pp. 825–827. [Google Scholar]
  • 7.Sakamoto M., Ohkuma M. Reclassification of Xylanibacter oryzae Ueki et al. 2006 as Prevotella oryzae comb. nov., with an emended description of the genus Prevotella. Int J Syst Evol Microbiol. 2012;62(Pt 11):2637–2642. doi: 10.1099/ijs.0.038638-0. [DOI] [PubMed] [Google Scholar]
  • 8.Shah H.N., Collins D.M. Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides. Int J Syst Bacteriol. 1990;40:205–208. doi: 10.1099/00207713-40-2-205. [DOI] [PubMed] [Google Scholar]
  • 9.Downes J., Dewhirst F.E., Tanner A.C.R., Wade W.G. Description of Alloprevotella rava gen. nov., sp. nov., isolated from the human oral cavity, and reclassification of Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov. Int J Syst Evol Microbiol. 2013;63:1214–1218. doi: 10.1099/ijs.0.041376-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Angly F.E., Willner D., Prieto-Davó A., Edwards R.A., Schmieder R., Vega-Thurber R. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol. 2009;5:e1000593. doi: 10.1371/journal.pcbi.1000593. [DOI] [PMC free article] [PubMed] [Google Scholar]

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