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Anaerococcus jeddahensis sp. nov., a New Bacterial Species Isolated From Healthy Nomadic Bedouin Woman From Saudi Arabia

  • Niokhor Dione
  • Sara Bellali
  • Muhammad Yasir
  • Esam I. Azhar
  • Fehmida Bibi
  • Mamadou Beye
  • Nicholas Armstrong
  • Frédéric Cadoret
  • Asif A. Jiman-Fatani
  • Nayel Helmy
  • Jaishriram Rathored
  • Noémie Labas
  • Pierre-Edouard Fournier
  • Didier Raoult
  • Jean-Christophe Lagier
Article

Abstract

An understanding of the microbial diversity of the human body has generated significant interest in recent years. With the advent of MALDI-TOF mass spectrometry, high-speed sequencing, and the rebirth of microbial culture, knowledge of human microbiota is growing. Using culturomics, a strategy to explore the microbial diversity of samples, coupled with a taxono-genomic strategy, we isolated a new bacterium named Anaerococcus jeddahensis sp. nov. strain SB3T. This strain was isolated from the stool sample of a healthy nomadic Bedouin woman from Saudi Arabia. Here, we describe the characteristics of this organism, and the complete genome sequence and annotation. Strain SB3T is a Gram-positive obligate anaerobic coccus which is non-motile and non-spore forming. Fatty acid analysis shows that the major fatty acid is by far hexadecanoic acid (C16:0; 52%). Its genome is 1,903,534 bp long and has 29.70 mol% of G+C content. It contains 1756 protein-coding genes and 53 RNA genes. These results show that strategy provides a better understanding of the microorganism and that is a good methodology for microbial identification and characterization.

Abbreviations

CSUR

Collection de souches de l’Unité des Rickettsies

DSM

Deutsche Sammlung von Mikroorganismen

FAME

Fatty acid methyl ester

GC/MS

Gas chromatography/mass spectrometry

MALDI-TOF MS

Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry

TE buffer

Tris–EDTA buffer

SDS

Sodium dodecyl sulfate

MEPHI

Microbes evolution phylogeny and infections MEPHI

AP-HM

Assistance Publique-Hôpitaux de Marseille

DPD

Digital protologue database

EMBL–EBI

European Molecular Biology Laboratory–European Bioinformatics Institute

Notes

Acknowledgements

The authors thank the Xegen Company (http://www.xegen.fr) for automating the genomic annotation process. This work has benefited from the French State support, managed by the ‘Agence Nationale pour la Recherche’ including the “Programme d’Investissement d’avenir” under the reference Méditerranée Infection 10-IAHU-03. This work was supported by Région Provence Alpes Côte d’Azur and European funding FEDER PRIMI. We thank Claudia Andrieu for her administrative assistance.

Compliance with Ethical Standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

284_2018_1538_MOESM1_ESM.docx (33 kb)
Supplementary material 1 (DOCX 32 KB)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Niokhor Dione
    • 1
  • Sara Bellali
    • 1
  • Muhammad Yasir
    • 2
  • Esam I. Azhar
    • 2
    • 3
  • Fehmida Bibi
    • 2
  • Mamadou Beye
    • 1
  • Nicholas Armstrong
    • 1
  • Frédéric Cadoret
    • 1
  • Asif A. Jiman-Fatani
    • 3
  • Nayel Helmy
    • 4
  • Jaishriram Rathored
    • 1
  • Noémie Labas
    • 1
  • Pierre-Edouard Fournier
    • 1
  • Didier Raoult
    • 1
    • 2
  • Jean-Christophe Lagier
    • 1
  1. 1.Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU Méditerranée InfectionMarseilleFrance
  2. 2.Special Infectious Agents Unit, King Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia
  3. 3.Departments of Medical Laboratory Technology and Medical Microbiology and ParasitologyKing Abdulaziz UniversityJeddahSaudi Arabia
  4. 4.Department of Obstetrics and GynecologySuliman Fageeh HospitalJeddahSaudi Arabia

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