Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes

Chenhong Zhang (1) , Muriel Derrien (2) , Florence Levenez (1) , Rémi Brazeilles (2) , Sonia A. Ballal (3) , Jason Kim (3) , Marie-Christine Degivry (2) , Gaëlle Quéré (2) , Peggy Garault (2) , Johan E. T. van Hylckama Vlieg (2) , Wendy S. Garrett (3) , Joël Dore (1) , Patrick Veiga (2, 3)

1 MetaGenoPolis
2 Life Science
3 Harvard T.H. Chan School of Public Health

Resident gut microbes co-exist with transient bacteria to form the gut microbiota. Despite increasing evidence suggesting a role for transient microbes on gut microbiota function, the interplay between resident and transient members of this microbial community is poorly defined. We aimed to determine the extent to which a host's autochthonous gut microbiota influences niche permissivity to transient bacteria using a fermented milk product (FMP) as a vehicle for five food-borne bacterial strains. Using conventional and gnotobiotic rats and gut microbiome analyses (16S rRNA genes pyrosequencing and reverse transcription qPCR), we demonstrated that the clearance kinetics of one FMP bacterium, Lactococcus lactis CNCM I-1631, were dependent on the structure of the resident gut microbiota. Susceptibility of the resident gut microbiota to modulation by FMP intervention correlated with increased persistence of L. lactis. We also observed gut microbiome configurations that were associated with altered stability upon exposure to transient bacteria. Our study supports the concept that allochthonous bacteria have transient and subject-specific effects on the gut microbiome that can be leveraged to re-engineer the gut microbiome and improve dysbiosis-related diseases.

Domaines: Sciences du Vivant [q-bio]

Chenhong Zhang, Muriel Derrien, Florence Levenez, Rémi Brazeilles, Sonia A. Ballal, et al.. Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes. The International Society of Microbiologial Ecology Journal, 2016, 10 (9), pp.2235-2245. ⟨10.1038/ismej.2016.13⟩. ⟨hal-01604968⟩