Abstract
Culturomics has recently allowed the isolation and description of previously uncultured bacteria from the human microbiome at different body sites. As part of a project aiming to describe the human gut microbiota by culturomics, Phoenicibacter congonensis strain Marseille-P3241T was isolated from the gut of a 45 years old Pygmy female. In the present work, we aim to describe this strain via the taxonogenomics approach. The major phenotypic, genomic and biochemical characteristics of this strain were analysed. Strain Marseille-P3241T is an anaerobic, Gram-positive and motile coccobacillus that grows optimally at 37 °C. The genome of strain Marseille-P3241T is 1,447,956 bp long with 43.44% GC content and its 16S rRNA gene sequence exhibited 89% sequence similarity with that of Denitrobacterium detoxificans strain NPOH1T, the phylogenetically closest related species with current standing in nomenclature. After performing a phylogenetic and genomic analysis, we conclude that strain Marseille-P3241T (= CCUG 70681T = CSUR P3241T) represents the type species of a new genus, for which we propose the name Phoenicibacter congonensis gen. nov., sp. nov.
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Abbreviations
- CCUG:
-
Culture Collection University Gothenburg, SWEDEN
- COG:
-
Clusters of Orthologous Groups
- CSUR:
-
Collection de Souches de l’Unité des Rickettsies, FRANCE
- dDDH:
-
Digital DNA–DNA hybridization
- FAME:
-
Fatty acid methyl ester
- GC/MS:
-
Gas chromatography/mass spectrometry
- MALDI-TOF MS:
-
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
- ORF:
-
Open reading frame
- SCFA:
-
Short chain fatty acids
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Acknowledgements
The authors would like to thank Xegen Company (http://www.xegen.fr/) for the genomic analysis assistance. The study was funded by Agence Nationale de la Recherche (Grant No. 10-IAHU- 03), Conseil Régional Provence-Alpes-Côte d’Azur (Grant No. FEDER PRIMI).
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Contributions
MB: Isolated, described and wrote the manuscript; MF: helped in the taxonogenomics description; AC: helped in the genomic analysis; TN: helped in the genomic sequencing; FP: helped in the electron microscope imaging; FB: helped in the genomic analyses, ZD: writing an critical analysis of the manuscript; AL: helped in the genomic analyses; PF: helped in writing and critical analysis of the manuscript; DR: designed the project, helped in writing, reviewing and critical analysis; FC: study design, data analysis and writing the manuscript.
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10482_2018_1211_MOESM2_ESM.tif
Online resource 2 Electron micrographs of P. congonensis strain Marseille-P3241T using a Tecnai G20, at an operating voltage of 200 keV. Scale bar = 500 nm (TIFF 4232 kb)
10482_2018_1211_MOESM4_ESM.docx
Online resource 4 COG distribution and descriptions of genes predicted to be implicated in virulence and antimicrobial activity (DOCX 15 kb)
10482_2018_1211_MOESM5_ESM.tif
Online resource 5 Circular representation of the P. congonensis strain Marseille-P3241T genome. From the outside in: Contigs (red/grey), COG category of genes on the forward strand (three circles), genes on forward strand (blue circle), genes on the reverse strand (red circle), COG category on the reverse strand (three circles), G + C content (TIFF 424 kb)
10482_2018_1211_MOESM7_ESM.docx
Online resource 7 Digital DNA-DNA hybridization values (%) obtained by strain Marseille-P3241T with other closely-related species using the GGDC formula 2 software (DDH estimates based on identities/HSP length)*, upper right. *The confidence intervals indicate the inherent uncertainty in estimating DDH values from intergenomic distances based on models derived from empirical test data sets (which are always limited in size) (DOCX 16 kb)
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Bilen, M., Fonkou, M.D.M., Caputo, A. et al. Phoenicibacter congonensis gen. nov., sp. nov., a new genus isolated from the human gut and its description using a taxonogenomic approach. Antonie van Leeuwenhoek 112, 775–784 (2019). https://doi.org/10.1007/s10482-018-01211-1
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DOI: https://doi.org/10.1007/s10482-018-01211-1
Keywords
- Culturomics
- Taxonogenomics
- Pygmy
- Phoenicibacter congonensis
- Gut microbiota