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Pilliol V, Beye M, Terlier L, Balmelle J, Kacel I, Lan R, Aboudharam G, Grine G, Terrer E. Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis. Microorganisms 2024; 12:215. [PMID: 38276200 PMCID: PMC10819710 DOI: 10.3390/microorganisms12010215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Among oral microbiota methanogens, Methanobrevibacter massiliense (M. massiliense) has remained less studied than the well-characterised and cultivated methanogens Methanobrevibacter oralis and Methanobrevibacter smithii. M. massiliense has been associated with different oral pathologies and was co-isolated with the Synergistetes bacterium Pyramidobacter piscolens (P. piscolens) in one case of severe periodontitis. Here, reporting on two additional necrotic pulp cases yielded the opportunity to characterise two co-cultivated M. massiliense isolates, both with P. piscolens, as non-motile, 1-2-µm-long and 0.6-0.8-µm-wide Gram-positive coccobacilli which were autofluorescent at 420 nm. The two whole genome sequences featured a 31.3% GC content, gapless 1,834,388-base-pair chromosome exhibiting an 85.9% coding ratio, encoding a formate dehydrogenase promoting M. massiliense growth without hydrogen in GG medium. These data pave the way to understanding a symbiotic, transkingdom association with P. piscolens and its role in oral pathologies.
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Affiliation(s)
- Virginie Pilliol
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
| | - Mamadou Beye
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Laureline Terlier
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Julien Balmelle
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Idir Kacel
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Romain Lan
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
- CNRS, EFS, ADES, Aix-Marseille University, 13385 Marseille, France
| | - Gérard Aboudharam
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
| | - Ghiles Grine
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Elodie Terrer
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
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Ndiaye AJS, Beye M, Lo G, Kacel I, Sow A, Leye N, Padane A, Mboup A, Diop-Ndiaye H, Sokhna C, Kane CT, Colson P, Fenollar F, Mboup S, Fournier PE. Genomic Epidemiology of SARS-CoV-2 in Urban Settings in Senegal. Viruses 2023; 15:1233. [PMID: 37376533 DOI: 10.3390/v15061233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
We used whole genome sequencing to identify and analyze mutations in SARS-CoV-2 in urban settings during the deadliest wave of the COVID-19 epidemic-from March to April 2021-in Senegal. Nasopharyngeal samples testing positive for SARS-CoV-2 were sequenced on the Illumina NovaSeq 6000 sequencing system using the COVIDSeq protocol. A total of 291 genotypable consensus genome sequences were obtained. Phylogenetic analyses grouped the genomes into 16 distinct PANGOLIN lineages. The major lineage was B.1.1.420, despite circulation of the Alpha variant of concern (VOC). A total of 1125 different SNPs, identified relative to the Wuhan reference genome, were detected. These included 13 SNPs in non-coding regions. An average density of 37.2 SNPs per 1000 nucleotides was found, with the highest density occurring in ORF10. This analysis allowed, for the first time, the detection of a Senegalese SARS-CoV-2 strain belonging to the P.1.14 (GR/20J, Gamma V3) sublineage of the Brazilian P.1 lineage (or Gamma VOC). Overall, our results highlight substantial SARS-CoV-2 diversification in Senegal during the study period.
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Affiliation(s)
- Anna Julienne Selbé Ndiaye
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Mamadou Beye
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Gora Lo
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Idir Kacel
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Aissatou Sow
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Nafissatou Leye
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Abdou Padane
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Aminata Mboup
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Halimatou Diop-Ndiaye
- Laboratoire Bactériologie-Virologie, Hôpital Aristide Le Dantec, Dakar 3001, Senegal
| | - Cheikh Sokhna
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
- VITROME, Campus International IRD-UCAD de l'IRD, Dakar 1386, Senegal
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France
| | - Coumba Touré Kane
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Philippe Colson
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France
| | - Souleymane Mboup
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France
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