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Description and genomic characterization of Massiliimalia massiliensis gen. nov., sp. nov., and Massiliimalia timonensis gen. nov., sp. nov., two new members of the family Ruminococcaceae isolated from the human gut

  • Pamela Afouda
  • Sory Ibrahima Traore
  • Niokhor Dione
  • Claudia Andrieu
  • Enora Tomei
  • Magali Richez
  • Fabrizio Di Pinto
  • Jean-Christophe Lagier
  • Grégory Dubourg
  • Didier Raoult
  • Pierre-Edouard FournierEmail author
Original Paper

Abstract

Using the culturomics approach, we isolated two strains, Marseille-P2963 and Marseille-P3753, from the intestinal microbiota of a 19-year-old healthy Saudi Arabian Bedouin male and from a 32-year-old healthy Senegalese male faecal transplant donor. Here, we studied their phenotypic, phylogenetic and genomic characteristics. Both strains were phylogenetically related, but different from Ruminococcus species. Bacterial cells were anaerobic, rod-shaped, non-spore-forming and not motile, with neither catalase nor oxidase activities. Their growth temperatures ranged from 28 to 45 °C, with an optimal growth at 37 °C. The genomes are 2,842,720 bp- and 2,707,061 bp-long respectively. The G + C contents are 47.18% and 46.90%, respectively. Based on these characteristics, we propose the creation of a new genus within the family Ruminococcaceae named Massiliimalia gen. nov., that contains the new species Massiliimalia massiliensis gen. nov., sp. nov., and Massiliimalia timonensis gen. nov., sp. nov. Strains Marseille-P2963T (= CSUR P2963 = DSM 106837) and Marseille-P3753T (= CSUR P3753 = CCUG 71632) are their type strains, respectively.

Keywords

Culturomics Gut Massiliimalia massiliensis Massiliimalia timonensis Taxono-genomics 

Abbreviations

AGIOS

Average of genomic identity of orthologous gene sequences

ANI

Average nucleotide identity

bp

Base pairs

CCUG

Culture Collection, University of Gothenburg

COG

Clusters of Orthologous Groups

CSUR

Collection de Souches de l’Unité des Rickettsies

DDH

DNA-DNA hybridization

DSMZ

Deutsche Sammlung von Mikroorganismen und Zellkulturen

FAME

Fatty acid methyl ester

GC/MS

Gas chromatography/mass spectrometry

GGDC

Genome-to-Genome Distance Calculator

HSP

High-scoring segment pairs

MALDI-TOF MS

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

Mbp

Mega base pairs

SCFA

Short chain fatty acid

Notes

Acknowledgements

The authors thank the Xegen Company (www.xegen.fr) for automating the genomic annotation process and Magdalen LARDIERE for English correction.

Authors contributions

PA isolated for the first time the strain Marseille-P3753, performed its phenotypic characterization and wrote the manuscript; SIT isolated for the first time the strain Marseille-P2963 and performed its phenotypic characterization; ND, JCL and GD have actively participated in the laboratory project in which both strains were isolated; CA have performed the first correction of the manuscript; ET performed the genomes sequencing of both strains; MR performed for both strains fatty acid methyl ester analysis and measurements of short chain fatty acids; FDP performed for both strains the necessary work in electron microscopy for have the electron micrographs; DR designed and directed the project; PEF corrected the manuscript, verified the accuracy of the Latin name “Massiliimalia” and acted as the corresponding author.

Funding

This study was supported by “Fondation Méditerranée Infection” and 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), (reference: Méditerranée Infection 10-IAHU-03). This work was also supported by Région Provence Alpes Côte d’Azur and European funding FEDER PRIMI.

Compliance with ethical standards

See Materials and Methods.

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

10482_2018_1223_MOESM1_ESM.tif (2.1 mb)
Supplementary Figure S1. Spectra of Massiliimalia massiliensis gen. nov., sp. nov., strain Marseille-P2963T (A) and Massiliimalia timonensis gen. nov., sp. nov., strain Marseille-P3753T (B) obtained on MALDI-TOF MS. Spectra from 12 individual colonies were compared and a reference spectrum was generated (TIFF 2120 kb)
10482_2018_1223_MOESM2_ESM.tif (4.2 mb)
Supplementary Figure S2. Gel View of the two Massiliimalia strains relative to other Firmicutes. The gel view displays the raw spectra of loaded spectrum files arranged in a pseudo-gel-like look. The x-axis records the m/z value. The left y-axis displays the running spectrum number originating from subsequent spectra loading. The peak intensity is expressed by a grayscale scheme code. The color bar and the right y-axis indicate the relation between the color with which a peak is displayed and the peak intensity in arbitrary units (TIFF 4309 kb)
10482_2018_1223_MOESM3_ESM.tif (19.1 mb)
Supplementary Figure S3. Gram staining of strain of Massiliimalia massiliensis gen. nov., sp. nov., strain Marseille-P2963T (A) and Massiliimalia timonensis gen. nov., sp. nov., strain Marseille-P3753T (B) (TIFF 19579 kb)
10482_2018_1223_MOESM4_ESM.tif (13.2 mb)
Supplementary Figure S4. Electron micrographs of Massiliimalia massiliensis gen. nov., sp. nov., strain Marseille-P2963T (A) and Massiliimalia timonensis gen. nov., sp. nov., strain Marseille-P3753T (B), were acquired with a Tecnai G20 Cryo (FEI) and a Morgagni 268D (Philips) transmission electron microscopes operated at 200 keV and 80 keV, respectively. The scale bar represents respectively 200 nm and 500 nm (TIFF 13502 kb)
10482_2018_1223_MOESM5_ESM.tif (16.6 mb)
Supplementary Figure S5. Graphical circular map of the genomes of Massiliimalia massiliensis gen. nov., sp. nov., strain Marseille-P2963T (A) and Massiliimalia timonensis gen. nov., sp. nov., strain Marseille-P3753T (B). From outside to the center: 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), GC content (TIFF 16960 kb)
10482_2018_1223_MOESM6_ESM.tif (1.7 mb)
Supplementary Figure S6. Distribution of functional classes of predicted genes on the chromosomes of the two Massiliimalia strains and related taxa, according to the clusters of orthologous groups of protein (TIFF 1711 kb)
10482_2018_1223_MOESM7_ESM.docx (42 kb)
Supplementary material 7 (DOCX 42 kb)

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Pamela Afouda
    • 1
  • Sory Ibrahima Traore
    • 1
  • Niokhor Dione
    • 1
    • 2
  • Claudia Andrieu
    • 1
  • Enora Tomei
    • 3
  • Magali Richez
    • 1
  • Fabrizio Di Pinto
    • 1
  • Jean-Christophe Lagier
    • 1
  • Grégory Dubourg
    • 1
  • Didier Raoult
    • 1
  • Pierre-Edouard Fournier
    • 3
    Email author
  1. 1.IRD, AP-HM, MEPHI, IHU-Méditerranée InfectionAix Marseille UniversityMarseilleFrance
  2. 2.Canada Excellence Research Chair Microbiome-Endocannabinoidome Axis in Metabolic Health (CERC-MEND)Université LavalQuebec CityCanada
  3. 3.IRD, AP-HM, SSA, VITROME, IHU-Méditerranée InfectionAix Marseille UniversityMarseille Cedex 05France

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