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. 2019 May;8(5):e00735.
doi: 10.1002/mbo3.735. Epub 2018 Oct 2.

Miniphocibacter massiliensis gen. nov., sp. nov., a new species isolated from the human gut and its taxono-genomics description

Melhem Bilen  1   2 , Maxime D Mbogning Fonkou  1 , Thi T Nguyen  1 , Magali Richez  1 , Ziad Daoud  2 , Pierre E Fournier  1 , Didier Raoult  1   3 , Frédéric Cadoret  1
Affiliations

Miniphocibacter massiliensis gen. nov., sp. nov., a new species isolated from the human gut and its taxono-genomics description

Melhem Bilen et al. Microbiologyopen. 2019 May.

Abstract

With the aim of describing the human microbiota by the means of culture methods, culturomics was developed in order to target previously un-isolated bacterial species and describe it via the taxono-genomics approach. While performing a descriptive study of the human gut microbiota of the pygmy people, strain Marseille-P4678T has been isolated from a stool sample of a healthy 39-year-old pygmy male. Cells of this strain were Gram-positive cocci, spore-forming, non-motile, catalase-positive and oxidase-negative, and grow optimally at 37°C under anaerobic conditions. Its 16S rRNA gene sequence exhibited 89.69% of sequence similarity with Parvimonas micra strain 3119BT (NR 036934.1), its phylogenetically closest species with standing in nomenclature. The genome of strain Marseille-P4678T is 2,083,161 long with 28.26 mol% of G+C content. Based on its phenotypic, biochemical, genotypic and proteomic profile, this bacterium was classified as a new bacterial genus and species Miniphocibacter massiliensis gen. nov., sp. nov. with the type strain Marseille-P4678T .

Keywords: Miniphocibacter massiliensis; culturomics; gut microbiota; new species; pygmy; taxono-genomics.

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Conflict of interest statement

None to be declared.

Figures

Figure 1
Figure 1
Phylogenetic tree representing the position of strain Marseille‐P4678T relative to other closely related species
Figure 2
Figure 2
(a) Reference mass spectrum representing of strain Marseille‐P4678T obtained after comparing 12 spectra. (b) Gel view comparing mass spectra of strain Marseille‐P4678T to other species with the raw spectra on the left. The x‐axis represents the m/z value. The left y‐axis indicates the running spectrum number acquired from successive spectra loading. The intensity of the peaks is indicated with the different gray scale, and the y‐axis indicates the relation between the peak color and its intensity
Figure 3
Figure 3
Electron micrographs of strain Marseille‐P4678T
Figure 4
Figure 4
Phage like sequences distribution among the strain Marseille‐P4678T's genome as predict by PHAST tool
Figure 5
Figure 5
Circular representation of the strain Marseille‐P4678T genome. From outer to inner: coding DNA sequences on the forward strand, coding DNA sequences on the reverse strand, rRNA, tRNA, and G+C plot and skew
See this image and copyright information in PMC

References

    1. Aziz, R. K. , Bartels, D. , Best, A. A. , DeJongh, M. , Disz, T. , Edwards, R. A. , … Zagnitko, O. (2008). The RAST Server: Rapid annotations using subsystems technology. BMC Genomics, 9, 75 10.1186/1471-2164-9-75 - DOI - PMC - PubMed
    1. Bilen, M. , Cadoret, F. , Richez, M. , Tomei, E. , Daoud, Z. , Raoult, D. , & Fournier, P. E. (2018). Libanicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from human stool. New Microbes and New Infections, 21, 63–71. 10.1016/j.nmni.2017.11.001 - DOI - PMC - PubMed
    1. Brettin, T. , Davis, J. J. , Disz, T. , Edwards, R. A. , Gerdes, S. , Olsen, G. J. , … Xia, F. (2015). RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Scientific Reports, 5, 8365 10.1038/srep08365 - DOI - PMC - PubMed
    1. Chen, S. , & Dong, X. (2005). Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater. International Journal of Systematic and Evolutionary Microbiology, 55(Pt 6), 2257–2261. 10.1099/ijs.0.63807-0 - DOI - PubMed
    1. Citron, D. M. , Tyrrell, K. L. , & Goldstein, E. J. C. (2012). Peptoniphilus coxii sp. nov. and Peptoniphilus tyrrelliae sp. nov. isolated from human clinical infections. Anaerobe, 18(2), 244–248. 10.1016/j.anaerobe.2011.11.008 - DOI - PubMed

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