Shifts in the human gut microbiome during cancer chemotherapy are diet-dependent

Trepka, K. R.; Van Blarigan, E. L.; Kyaw, T. S.; Olson, C. A.; Partipilo, G.; Ortega, E. F.; Noecker, C.; Upadhyay, V.; Zhang, C.; Gempis, D.; Steiding, P.; Stanfield, D.; Venook, A. P.; Atreya, C. E.; Kidder, W. A.; Turnbaugh, P. J.

doi:10.64898/2025.12.23.696294

bioRxiv · 10.64898/2025.12.23.696294

Shifts in the human gut microbiome during cancer chemotherapy are diet-dependent

Trepka, K. R.·Van Blarigan, E. L.·Kyaw, T. S.·Olson, C. A.·Partipilo, G.·Ortega, E. F.·Noecker, C.·Upadhyay, V.·Zhang, C.·Gempis, D.·Steiding, P.·Stanfield, D.·Venook, A. P.·Atreya, C. E.·Kidder, W. A.·Turnbaugh, P. J.

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Abstract

Numerous studies have implicated both dietary intake and the human gut microbiome in colorectal cancer (CRC) treatment outcomes. However, little is known about how patients adjust their dietary intake during cancer chemotherapy or if these dietary changes contribute to treatment-associated alterations in the gut microbiome. We performed paired longitudinal diet and microbiome analysis during CRC treatment with oral fluoropyrimidines (NCT04054908) and validated key associations using cell culture assays. At each timepoint, diet was measured by averaging up to 3 consecutive days of 24-hour dietary records (NCI ASA24; 35 patients; 2.5{+/-}1.1 timepoints per patient), while microbiome composition was measured from stool (16S rRNA gene sequencing, metagenomics, qPCR; 40 patients; 5.6{+/-}1.4 timepoints per patient). Diet quality significantly decreased during chemotherapy. Carbohydrate and refined grain intake increased, accompanied by decreased consumption of fats, nuts and seeds, and fat-soluble micronutrients. Multiple individual dietary components were strongly linked to the gut microbiome. Decreases in theobromine intake correlated with decreases in overall microbial diversity and more gastrointestinal toxicities. Diet shifts partly explained changes in bacterial abundance during chemotherapy, including more severe depletion of Faecalibacterium prausnitzii in patients with decreased vitamin K1 intake. Changes in diet were correlated with multiple bacterial gene families involved in micronutrient metabolism and drug sensitivity. Increased copper intake was linked to decreased Fusobacterium nucleatum in patients and inhibited F. nucleatum in cell assays. Together, these data suggest that changes in diet during chemotherapy contribute to changes in gut bacterial diversity, taxonomic composition, and gene abundance. Our approach may generalize to other cancer therapies and emphasizes the need for collecting more robust dietary data in clinical microbiome studies.

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Trepka, K. R., Van Blarigan, E. L., Kyaw, T. S., Olson, C. A., Partipilo, G., Ortega, E. F., Noecker, C., Upadhyay, V., Zhang, C., Gempis, D., Steiding, P., Stanfield, D., Venook, A. P., Atreya, C. E., Kidder, W. A., Turnbaugh, P. J.. 2025-12-24. Shifts in the human gut microbiome during cancer chemotherapy are diet-dependent. https://doi.org/10.64898/2025.12.23.696294

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