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Phoenicibacter congonensis gen. nov., sp. nov., a new genus isolated from the human gut and its description using a taxonogenomic approach

  • Melhem Bilen
  • Maxime Descartes Mbogning Fonkou
  • Aurélia Caputo
  • Thi-Thien Nguyen
  • Fabrizio Di Pinto
  • Fadi Bittar
  • Ziad Daoud
  • Anthony Levasseur
  • Pierre Edouard Fournier
  • Didier Raoult
  • Frédéric CadoretEmail author
Original Paper

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.

Keywords

Culturomics Taxonogenomics Pygmy Phoenicibacter congonensis Gut microbiota 

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

Notes

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).

Author’s contribution

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.

Conflict of interest

All authors declare that they have no conflict of interest.

Supplementary material

10482_2018_1211_MOESM1_ESM.tiff (9.9 mb)
Online resource 1 Gram staining of P. congonensis strain Marseille-P3241T (TIFF 10136 kb)
10482_2018_1211_MOESM2_ESM.tif (4.1 mb)
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_MOESM3_ESM.docx (18 kb)
Online resource 3 Nucleotide content and gene count levels (DOCX 17 kb)
10482_2018_1211_MOESM4_ESM.docx (15 kb)
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 (425 kb)
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_MOESM6_ESM.docx (15 kb)
Online resource 6 Total genes related to the 25 general COG functional categories (DOCX 15 kb)
10482_2018_1211_MOESM7_ESM.docx (16 kb)
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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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Melhem Bilen
    • 1
    • 2
  • Maxime Descartes Mbogning Fonkou
    • 1
  • Aurélia Caputo
    • 1
  • Thi-Thien Nguyen
    • 1
  • Fabrizio Di Pinto
    • 1
  • Fadi Bittar
    • 1
  • Ziad Daoud
    • 2
  • Anthony Levasseur
    • 1
  • Pierre Edouard Fournier
    • 1
  • Didier Raoult
    • 1
    • 3
  • Frédéric Cadoret
    • 4
    Email author
  1. 1.IRD, APHM, MEPHI, IHU Méditerranée InfectionAix-Marseille UniversitéMarseilleFrance
  2. 2.Clinical Microbiology Department, Faculty of Medicine and Medical SciencesUniversity of BalamandAmiounLebanon
  3. 3.Special Infectious Agents Unit, King Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia
  4. 4.Assistance Publique Hôpitaux de Marseille, BIOSTIC Service Biostatistique et Technologies de l’Information et de la CommunicationHôpital de la TimoneMarseilleFrance

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