Abstract
Dietary faba bean enhances fish muscle quality but concurrently reduces growth performance. The gut microbiota critically modulates muscle growth and quality. However, the specific microbial taxa, metabolites, and regulatory mechanisms responsible remain to be elucidated. This study established a differential gut microbiota model in faba-bean-fed Yellow River carp (Cyprinus carpio), used whole-intestinal microbiota transplantation (WIMT) to directly test its effect on muscle quality, and supplemented the key bacterium and its metabolite to confirm their contribution. After a 6-week faba bean diet, growth performance declined, whereas muscle texture improved (P < 0.05). This improvement was concomitant with a higher abundance of the genera Aeromonas and Cetobacterium in the gut. Following 8 weeks of daily WIMT from faba-bean-fed donors, Yellow River carp maintained normal growth performance (P > 0.05) and simultaneously showed improved muscle texture, characterized by more small-diameter fibers, lower fat content, and higher collagen levels (P < 0.05), recapitulating the donor’s key muscle phenotype. Meanwhile, WIMT reshaped the gut microbiome composition and its metabolic profile, and the marker species Cetobacterium somerae and its metabolite acetic acid showed associations with improvements in muscle quality. Further in vivo validation indicated that C. somerae reduced fat deposition and improved muscle texture, an effect possibly linked to activation of the AMPK-PGC-1α-FoxO pathway, and its metabolite acetic acid mirrored these changes. This study reveals the direct impact of gut microbiota on muscle quality through WIMT in Yellow River carp, provides novel evidence of the fish gut-muscle axis, and offers a scientific basis for improving muscle quality.
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Data availability
The “Gut microbiome sequencing data (fed with faba beans for 6 weeks)” are available in the NCBI SRA repository with the accession ID https://www.ncbi.nlm.nih.gov/search/all/?term=PRJNA1311008, reference number PRJNA1311008. The “Gut microbiome sequencing data (antibiotic treatment)” can be accessed in the NCBI SRA repository with the accession ID https://www.ncbi.nlm.nih.gov/search/all/?term=PRJNA1310288, reference number PRJNA1310288. The “Gut microbiome sequencing data (WIMT)” are deposited in the NCBI SRA repository and can be found using the accession ID https://www.ncbi.nlm.nih.gov/search/all/?term=PRJNA1310847, reference number PRJNA1310847. The “Muscle tissue transcriptome sequencing data” are stored in the NCBI SRA repository and are accessible via the accession ID https://www.ncbi.nlm.nih.gov/sra/PRJNA1344608, reference number PRJNA1344608. The “SCFAs data from intestinal contents” are available in the NGDC OMIX repository with the accession ID https://ngdc.cncb.ac.cn/omix/release/OMIX012256, reference number OMIX012256. The “SCFAs data from CS-CS” can be accessed in the NGDC OMIX repository using the accession ID https://ngdc.cncb.ac.cn/omix/release/OMIX012255, reference number OMIX012255. The “Non-targeted metabolomics data of intestinal contents” are deposited in the MetaboLights repository and can be found using the accession ID https://www.ebi.ac.uk/metabolights/MTBLS13128, reference number MTBLS13128.
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Acknowledgements
This work was supported by the National Natural Science Foundation of China (grant numbers U22A20532, 32473180); and the Special Fund for Henan Agriculture Research System (grant numbers HARS-22-16-S). The authors acknowledge the participants’ contributions to this research, and we are grateful to Professor Xiaolin Meng, Doctor Qingyang Su, and Master Yuan Liu (College of Fisheries, Henan Normal University, Xinxiang, China) for isolating and culturing the Cetobacterium somerae CFH_001 strain.
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All authors, L.J.C., Y.J.L., Y.J.Z., C.B.Q., L.P.Y., X.Y., and G.X.N. contributed to the conceptualizations, methodology, and experimentations of the manuscript. L.J.C., Y.J.L., and Y.J.Z.: investigation, animal husbandry, sample collection, measurement of experimental parameters, analysis, and interpretation of data. L.J.C.: visualization and writing the original draft. L.J.C., Y.J.L., and Y.J.Z.: writing, reviewing, and editing. L.J.C., Y.J.L., C.B.Q., L.P.Y., and X.Y.: validation, analysis, and interpretation of data, reviewing and editing the manuscript. G.X.N.: supervision, project administratio,n and funding acquisition. All the authors reviewed and approved the final manuscript.
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Cheng, L., Li, Y., Zhang, Y. et al. Cetobacterium somerae as a microbial correlate of improved muscle quality after intestinal microbiota transplantation in Yellow River carp (Cyprinus carpio). npj Biofilms Microbiomes (2026). https://doi.org/10.1038/s41522-026-00955-3
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DOI: https://doi.org/10.1038/s41522-026-00955-3
