Gut microbiota alterations are linked to COVID-19 severity in North African and European populations

NPJ Biofilms Microbiomes. 2025 juin 13;11(1):106

ABSTRACT:

Although COVID-19 primarily affects the respiratory system, many patients experience gastrointestinal symptoms, suggesting a role for the gut microbiota in disease pathogenesis. To explore this, we performed shotgun metagenomic sequencing on stool samples from 200 COVID-19 patients and 102 healthy controls in Morocco and France. Despite geographic differences in microbiota composition, patients with COVID-19 in both continents exhibited significant gut microbiota alterations, which were more pronounced in severe cases, with similar features compared with controls. Functional pathways, including L-Tryptophan biosynthesis, were disrupted, particularly in patients with severe disease. Machine learning models accurately predicted disease severity based on gut microbial profiles in the Moroccan cohort, though not in the French cohort. These results highlight consistent microbiota changes associated with COVID-19 and support a potential link between gut dysbiosis and disease severity.

Conflict of interest statement

Competing interests: H.S. report lecture fee, board membership, or consultancy from Amgen, Fresenius, IPSEN, Actial, Astellas, Danone, THAC, Biose, BiomX, Eligo, Immusmol, Adare, Nestle, Ferring, MSD, Bledina, Pfizer, Biocodex, BMS, Bromatech, Gilead, Janssen, Mayoli, Roche, Sanofi, Servier, Takeda, Abbvie, has stocks from Enterome bioscience and is co-founder of Exeliom Biosciences. The other authors declare that they have no competing interests. Ethics approval: The Moroccan part of the study was approved by the Local Ethics Committee of Cheikh Zaid Hospital (CEFCZ/PR/2020-PR04), Rabat, Morocco, and complies with the Declaration of Helsinki. The French part of the study was approved by a research ethics committee (CPP Ile de France XI, advice N°20026-80727) and authorized by the French agency for data security (Commission Nationale Informatique et Liberté: CNIL, authorization N°920123). The healthy subjects were recruited in the framework of the Suivitheque study (Comité de Protection des Personnes Ile-de-France IV, IRB 00003835, registration number 2012/05NICB).