Dietary fiber selectively regulates intestinal persistence of probiotic bifidobacteria

Choi, G.; Chatterjee, S.; Shah, U.; Won, T. H.; Skouris, A.; Kim, J.; Mujib, W.; Sun, H.; Fontaine, M. A.; Messyasz, A.; Lemenze, A.; Meyerholz, D.; Dominguez-Bello, M. G.; Schroeder, F.; van Sinderen, D.; Wong, L. Y. R.; BESSMAN, N.

doi:10.64898/2026.06.06.730603

bioRxiv · 10.64898/2026.06.06.730603

Dietary fiber selectively regulates intestinal persistence of probiotic bifidobacteria

Choi, G.·Chatterjee, S.·Shah, U.·Won, T. H.·Skouris, A.·Kim, J.·Mujib, W.·Sun, H.·Fontaine, M. A.·Messyasz, A.·Lemenze, A.·Meyerholz, D.·Dominguez-Bello, M. G.·Schroeder, F.·van Sinderen, D.·Wong, L. Y. R.·BESSMAN, N.

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Abstract

Bifidobacteria dominate the gut microbiota of breast-fed infants, and are strongly associated with human health, including immune regulation, colonization resistance, and protection against inflammation. However, bifidobacteria persist at high abundance after weaning in only a subset of individuals, and the factors that regulate intestinal persistence of bifidobacteria are poorly understood. Using gnotobiotic mouse models, we identified a common dietary fiber, raffinose, as a critical determinant of bifidobacterial persistence during microbial transitions associated with weaning. Bifidobacterial persistence depends on an intact raffinose utilization operon and is associated with disease resistance and restrained inflammation in adult mice. Specific dietary fiber recommendations commencing at weaning are a potential strategy to maintain bifidobacteria persistence beyond infancy, with potential long-term benefits for host resilience and reduced risk of inflammatory disease.

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Choi, G., Chatterjee, S., Shah, U., Won, T. H., Skouris, A., Kim, J., Mujib, W., Sun, H., Fontaine, M. A., Messyasz, A., Lemenze, A., Meyerholz, D., Dominguez-Bello, M. G., Schroeder, F., van Sinderen, D., Wong, L. Y. R., BESSMAN, N.. 2026-06-08. Dietary fiber selectively regulates intestinal persistence of probiotic bifidobacteria. https://doi.org/10.64898/2026.06.06.730603

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