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Draft genome and description of Negativicoccus massiliensis strain Marseille-P2082, a new species isolated from the gut microbiota of an obese patient

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Abstract

Strain Marseille-P2082, an anaerobic, non-motile, asporogenous, Gram-negative, coccoid bacterium was isolated from the faeces of a 33 year-old obese French woman before bariatric surgery. The isolate exhibits 98.65% 16S rRNA gene nucleotide sequence similarity with Negativicoccus succinicivorans strain ADV 07/08/06-B-1388T, its current closest phylogenetic neighbour with standing in nomenclature. However, the dDDH relatedness between the new isolate and N. succinicivorans type strain ADV 07/08/06-B-1388T is 52.5 ± 2.7%. Strain Marseille-P2082 has a genome of 1,360,589 bp with a 51.1% G+C content. Its major fatty acids were identified as C18:1n9, C18:0 and C16:0. Based on its phenotypic, genomic and phylogenetic characteristics, strain Marseille-P2082T [= CSURP2082 (Collection de Souches de l’Unité des Rickettsies) = DSM 100853] is proposed as the type strain of the novel species Negativicoccus massiliensis sp. nov. The 16S rRNA gene sequence and whole-genome shotgun sequence have been deposited in EMBL-EBI under accession numbers LN876651 and LT700188, respectively.

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Data deposit

The whole-genome shotgun sequence of N. succinicivorans strain ADV 07/08/06-B-1388T has been deposited in NCBI under accession number PRJEB34910.

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Acknowledgements

The authors thank the Xegen Company (www.xegen.fr) for automating the genomic annotation process. The authors also thank Noémie Labas for the genome sequencing. We are grateful to Professor Hélène Marchandin for providing the Negativicoccus succinicivorans strain ADV 07/08/06-B-1388T.

Funding

This work was supported by the French Government under the « Investissements d’avenir » (Investments for the Future) program managed by the Agence Nationale de la Recherche (ANR, fr: National Agency for Research) under the number IHU Méditerranée Infection 10-IAHU-03.

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Authors and Affiliations

  1. IRD198, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France

    Amadou Hamidou Togo, Mamadou Lamine Tall, Matthieu Million, Saber Khelaifia, Didier Raoult & Grégory Dubourg

  2. IHU Méditerranée Infection, Marseille, France

    Amadou Hamidou Togo, Mamadou Lamine Tall, Matthieu Million, Saber Khelaifia, Didier Raoult, Pierre-Edouard Fournier & Grégory Dubourg

  3. IRD, SSA, VITROME, IHU-Méditerranée Infection, Aix Marseille Univ, Marseille, France

    Awa Diop & Pierre-Edouard Fournier

  4. NORT “Nutrition, Obesity and Risk of Thrombosis”, INSERM1062, INRA1260, Aix Marseille Université, Marseille, France

    Marie Maraninchi

Authors
  1. Amadou Hamidou Togo
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  2. Awa Diop
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  9. Grégory Dubourg
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Contributions

AHT isolated for the first time the strain Marseille-P2082, performed its phenotypic characterization and wrote the manuscript; AD and MLD actively participated to genome analysis; SK actively participated in the laboratory project in which the strain was isolated; MM and MM actively participated to the specimen collection and the study design; DR designed and directed the project; PEF corrected the manuscript, verified the accuracy of the Latin name of the strain; GD corrected the manuscript and acted as the corresponding author.

Corresponding author

Correspondence to Grégory Dubourg.

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Supplementary Fig. 1

Transmission electron microscopy of strain Marseille-P2082T using a Tecnai G20 (FEI company) at an operating voltage of 60 kV. The scale bar represents 200 µm (PDF 5423 kb)

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Togo, A.H., Diop, A., Tall, M.L. et al. Draft genome and description of Negativicoccus massiliensis strain Marseille-P2082, a new species isolated from the gut microbiota of an obese patient. Antonie van Leeuwenhoek 113, 997–1008 (2020). https://doi.org/10.1007/s10482-020-01414-5

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