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Da Silva Morais E, Grimaud GM, Warda A, Stanton C, Ross P. Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus. Sci Rep 2024; 14:10109. [PMID: 38698002 PMCID: PMC11066082 DOI: 10.1038/s41598-024-59148-7] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
Phocaeicola dorei and Phocaeicola vulgatus are very common and abundant members of the human gut microbiome and play an important role in the infant gut microbiome. These species are closely related and often confused for one another; yet, their genome comparison, interspecific diversity, and evolutionary relationships have not been studied in detail so far. Here, we perform phylogenetic analysis and comparative genomic analyses of these two Phocaeicola species. We report that P. dorei has a larger genome yet a smaller pan-genome than P. vulgatus. We found that this is likely because P. vulgatus is more plastic than P. dorei, with a larger repertoire of genetic mobile elements and fewer anti-phage defense systems. We also found that P. dorei directly descends from a clade of P. vulgatus¸ and experienced genome expansion through genetic drift and horizontal gene transfer. Overall, P. dorei and P. vulgatus have very different functional and carbohydrate utilisation profiles, hinting at different ecological strategies, yet they present similar antimicrobial resistance profiles.
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Affiliation(s)
- Emilene Da Silva Morais
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Microbiology Department, University College Cork, Co. Cork, Ireland
| | - Ghjuvan Micaelu Grimaud
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Alicja Warda
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Paul Ross
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland.
- Microbiology Department, University College Cork, Co. Cork, Ireland.
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Huber-Ruano I, Calvo E, Mayneris-Perxachs J, Rodríguez-Peña MM, Ceperuelo-Mallafré V, Cedó L, Núñez-Roa C, Miro-Blanch J, Arnoriaga-Rodríguez M, Balvay A, Maudet C, García-Roves P, Yanes O, Rabot S, Grimaud GM, De Prisco A, Amoruso A, Fernández-Real JM, Vendrell J, Fernández-Veledo S. Orally administered Odoribacter laneus improves glucose control and inflammatory profile in obese mice by depleting circulating succinate. Microbiome 2022; 10:135. [PMID: 36002880 PMCID: PMC9404562 DOI: 10.1186/s40168-022-01306-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/17/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Succinate is produced by both human cells and by gut bacteria and couples metabolism to inflammation as an extracellular signaling transducer. Circulating succinate is elevated in patients with obesity and type 2 diabetes and is linked to numerous complications, yet no studies have specifically addressed the contribution of gut microbiota to systemic succinate or explored the consequences of reducing intestinal succinate levels in this setting. RESULTS Using germ-free and microbiota-depleted mouse models, we show that the gut microbiota is a significant source of circulating succinate, which is elevated in obesity. We also show in vivo that therapeutic treatments with selected bacteria diminish the levels of circulating succinate in obese mice. Specifically, we demonstrate that Odoribacter laneus is a promising probiotic based on its ability to deplete succinate and improve glucose tolerance and the inflammatory profile in two independent models of obesity (db/db mice and diet-induced obese mice). Mechanistically, this is partly mediated by the succinate receptor 1. Supporting these preclinical findings, we demonstrate an inverse correlation between plasma and fecal levels of succinate in a cohort of patients with severe obesity. We also show that plasma succinate, which is associated with several components of metabolic syndrome including waist circumference, triglycerides, and uric acid, among others, is a primary determinant of insulin sensitivity evaluated by the euglycemic-hyperinsulinemic clamp. CONCLUSIONS Overall, our work uncovers O. laneus as a promising next-generation probiotic to deplete succinate and improve glucose tolerance and obesity-related inflammation. Video Abstract.
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Affiliation(s)
- Isabel Huber-Ruano
- Hospital Universitari de Tarragona Joan XXIII, Institut d’Investigació Sanitària Pere Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Enrique Calvo
- Hospital Universitari de Tarragona Joan XXIII, Institut d’Investigació Sanitària Pere Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Madrid, Spain
| | - M-Mar Rodríguez-Peña
- Hospital Universitari de Tarragona Joan XXIII, Institut d’Investigació Sanitària Pere Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | | | - Lídia Cedó
- Hospital Universitari de Tarragona Joan XXIII, Institut d’Investigació Sanitària Pere Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Catalina Núñez-Roa
- Hospital Universitari de Tarragona Joan XXIII, Institut d’Investigació Sanitària Pere Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Joan Miro-Blanch
- Hospital Universitari de Tarragona Joan XXIII, Institut d’Investigació Sanitària Pere Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Rovira i Virgili University, 43003 Tarragona, Spain
| | - María Arnoriaga-Rodríguez
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Madrid, Spain
| | - Aurélie Balvay
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Claire Maudet
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Pablo García-Roves
- Department of Physiological Sciences, School of Medicine and Health Sciences, Nutrition, Metabolism and Gene therapy Group Diabetes and Metabolism Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Oscar Yanes
- Hospital Universitari de Tarragona Joan XXIII, Institut d’Investigació Sanitària Pere Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Rovira i Virgili University, 43003 Tarragona, Spain
| | - Sylvie Rabot
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | | | - Angela Amoruso
- Probiotical Research S.r.l., Enrico Mattei, 3, -28100 Novara, Italy
| | - José Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Madrid, Spain
| | - Joan Vendrell
- Hospital Universitari de Tarragona Joan XXIII, Institut d’Investigació Sanitària Pere Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Rovira i Virgili University, 43003 Tarragona, Spain
| | - Sonia Fernández-Veledo
- Hospital Universitari de Tarragona Joan XXIII, Institut d’Investigació Sanitària Pere Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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