Fecal Metabolite Biomarkers for Monitoring Gut Health and Enteric Diseases in Poultry: A Systematic Review

https://doi.org/10.47637/agrimals.v5i2.1982
Published: Nov 17, 2025

Abstract:

Monitoring gastrointestinal health is essential for maintaining productivity, improving disease resistance, and ensuring welfare in poultry production. Conventional diagnostic methods are often invasive, delayed, or lack sensitivity for detecting early-stage gut disorders. Fecal metabolite biomarkers offer a promising, non-invasive alternative for assessing gut health in real time. This systematic review evaluates the application of fecal metabolites in identifying enteric diseases and monitoring gut status in poultry, focusing on biomarker classes, disease links, and nutritional strategies. Relevant studies were retrieved from PubMed, Scopus, and Google Scholar, screened using PRISMA guidelines, and assessed with an adapted SYRCLE Risk of Bias tool. Ten studies met all eligibility criteria. Key metabolite groups short-chain fatty acids (particularly butyrate), histamine, amino acids, indole derivatives, and trehalose were associated with necrotic enteritis, coccidiosis, and gut dysbiosis. Nutritional interventions including inulin, resistant starch, Hermetia illucens meal, and citrus extract consistently improved metabolite profiles and intestinal integrity. Several biomarkers exhibited disease-specific patterns, suggesting diagnostic value. These findings highlight the potential of fecal metabolite biomarkers as practical tools for non-invasive gut health surveillance in poultry. Further research should focus on standardizing biomarker panels, establishing diagnostic thresholds, and integrating multi-omics approaches to enable their application in precision poultry health management.

Authors:
1 . Dita Novarina Gunawati
Universitas Islam Madani Indonesia
2 . Cindy Audina Damayanti
PGRI Kanjuruhan Malang University
https://orcid.org/0000-0003-4314-0903
3 . Cesaria Fitri Puspitasari
Madani Indoensia University
https://orcid.org/0009-0001-9337-7901
4 . Nining Haryuni
Madani Indonesia University
https://orcid.org/0000-0001-8388-2982
5 . Luky Amalta
Brawijaya Universiy
https://orcid.org/0009-0009-6299-5705
6 . Fitria Tridyana Putri
Madani Indonesia University
https://orcid.org/0009-0005-7437-2645
7 . Errythrina Vinifera Arnyke
Madani Indonesia University
https://orcid.org/0009-0004-9564-2782
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How to Cite
Gunawati, D. N., Damayanti, C. A., Puspitasari, C. F., Haryuni, N., Amalta, L., Putri, F. T., & Arnyke, E. V. (2025). Fecal Metabolite Biomarkers for Monitoring Gut Health and Enteric Diseases in Poultry: A Systematic Review. Journal of Agriculture and Animal Science, 5(2), 243–261. https://doi.org/10.47637/agrimals.v5i2.1982
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Issue & Section
Vol. 5 No. 2 (2025): Volume 5 Nomor 2 Tahun 2025
Articles
Author Biographies

Cindy Audina Damayanti, PGRI Kanjuruhan Malang University

Faculty of Animal Husbandry

Cesaria Fitri Puspitasari, Madani Indoensia University

Faculty of Animal Husbandry

Nining Haryuni, Madani Indonesia University

Faculty of Animal Husbandry

Luky Amalta, Brawijaya Universiy

Faculty of Animal Science

Fitria Tridyana Putri, Madani Indonesia University

Faculty of Animal Husbandry 

Errythrina Vinifera Arnyke, Madani Indonesia University

Faculty of Animal Husbandry 

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  1. Bai, H., Shi, L., Guo, Q., Zou, J., Jiao, H., Wang, Y., & Chang, G. (2023). Metagenomic insights into the relationship between gut microbiota and residual feed intake of small-sized meat ducks. Frontiers in Microbiology, 13, 1-11. https://doi.org/10.3389/fmicb.2022.1075610
  2. Bassols, A., Amigó, N., Pérez-Rodado, M., Tibau, J., & Martí, S. (2025). Metagenomic insights into the relationship between gut microbiota and residual feed intake of small-sized meat ducks. Frontiers in Microbiology, 13, 1-11. https://doi.org/10.3389/fmicb.2022.1075610
  3. Brugaletta, G., Zappaterra, M., Mattioli, S., Sirri, F., & Meluzzi, A. (2020). Effect of alternative administration programs of a synbiotic supplemenet, foot pad dermatitis, cecal microbiota, and blood metabolites. Animals, 10(3), 522. https://doi.org/10.3390/ani10030522
  4. Bucław, M. (2016). The use of inulin in poultry feeding: A review. Journal of Animal Physiology and Animal Nutrition, 100(6), 1015-1022. https://doi.org/10.1111/jpn.12484
  5. Chen, L., Ding, H., Zhu, Y., Hu, S., Wang, S., Wang, R., Liu, X., Jin, S., Chen, Q., & Zhang, T. (2023). Untargeted and targeted metabolomics identify metabolite biomarkers for Salmonella enteritidis in chicken meat. Food Chemistry, 429, Article 136834. https://doi.org/10.1016/j.foodchem.2022.135294
  6. Choi, S., & Kim, E. B. (2023). A comprehensive longitudinal study of gut microbiota dynamic changes in laying hens at four growth stages prior to egg production. Animal Bioscience, 36(4), 637–648. doi: 10.5713/ab.23.0271
  7. Cisse, S., Matuszewski, A., Bień, D., Konieczka, P., Kozłowski, K., Rawski, M., ... & Benarbia, M. E. A. (2025). A comprehensive longitudinal study of gut microbiota dynamic changes in laying hens at four growth stages prior to egg production. Animal Bioscience, 36(4), 637–648. https://doi.org/10.3390/ani15020127
  8. De Meyer, F., Eeckhaut, V., Ducatelle, R., Dhaenens, M., Daled, S., Dedeurwaerder, A., Van Denberghe, W., Deforce, D., & Van Immerseel, F. (2019). Host intestinal biomarker identification in a gut leakage model in broilers. Veterinary Research, 50, Article 46. https://doi.org/10.1186/s13567-019-0663-x
  9. de Souza, M., Cicero, C. E., Menck-Costa, M. F., Oliveira, M. L. A. G., Correia, R. T. P., & Bracarense, A. P. F. R. L. (2021). Histological evaluation of the intestine of broiler chickens: Comparison of three sampling methods. Semina: Ciências Agrárias, 42(3), 1391–1400. https://doi.org/10.5433/1679-0359.2021v42n6p3247
  10. Fathima, S., Al Hakeem, W. G., Shanmugasundaram, R., ... & Selvaraj, R. K. (2024). The effect of supplemental arginine on the gut microbial homeostasis of broilers during sub-clinical necrotic enteritis challenge. Frontiers in Physiology, 15, 1291836. https://doi.org/10.3389/fphys.2024.1291836
  11. Santanilla F., E. B., Betancourt López, L. L., Contreras Rodríguez, L. E., & Granados Falla, D. S. (2024). Resistant starch from a tuberous root from the Andes cordillera improves metabolic and immune parameters in broilers. Bioactive Carbohydrates and Dietary Fibre, 31, 100372. https://doi.org/10.1016/j.bcdf.2024.100420
  12. Gautam, H., Ahmad, S. N., Banaganapalli, B., Popowich, S., Chow-Lockerbie, B., Ayalew, L. E., Mandal, R., Wishart, D. S., Tikoo, S., & Gomis, S. (2025). Elevated butyric acid and histamine in feces and serum as an indicator of onset of necrotic enteritis in broiler chickens. Frontiers in Microbiology, 16, 1581309. https://doi.org/10.3389/fmicb.2025.1581309
  13. Hartinger, K., Fröschl, K., Ebbing, M. A., Bruschek-Pfleger, B., Schedle, K., Schwarz, C., & Gierus, M. (2022). Suitability of Hermetia illucens larvae meal and fat in broiler diets: Effects on animal performance, apparent ileal digestibility, gut histology, and microbial metabolites. Journal of Animal Science and Biotechnology, 13, 50. https://doi.org/10.1186/s40104-022-00701-7
  14. Karl, J. P., Armstrong, N. J., Player, R. A., McClung, H. L. (2022). The fecal metabolome links diet composition, food processing, and the gut microbiota to gastrointestinal health in a randomized trial of adults consuming a processed diet. Journal of Nutrition. https://doi.org/10.1093/jn/nxac161
  15. Kayal, A., Yu, S. J., Van, T. T. H., Moore, R. J., & Stanley, D. (2025). Effect of early gut microbiota intervention using pre-designed poultry microbiota substitute on broiler health and performance. Animal Production Science, 65(1), 11–22. https://doi.org/10.1071/an24354
  16. Khalili, L., & Amini, A. (2015). Resistant starch in food industry. In Polysaccharides: Bioactivity and Biotechnology, 2024-2056. Springer. DOI:10.1007/978-3-319-03751-6_42-1
  17. Kozłowska, I., Marć-Pieńkowska, J., & Bednarczyk, M. (2016). Beneficial aspects of inulin supplementation as a fructooligosaccharide prebiotic in monogastric animal nutrition - A review. Annals of Animal Science, 16(4), 935-962. DOI: 10.1515/aoas-2015-0090
  18. Liu, Y. S., Zhang, Y. Y., Li, J. L., Wang, T., & Gao, F. (2020). Growth performance, carcass traits and digestive function of broiler chickens fed diets with graded levels of corn resistant starch. British Poultry Science, 61(2), 146-155. https://doi.org/10.1080/00071668.2019.1694137
  19. Ma, N., Zhao, Y., Wang, J., Li, Z., Tian, X., Zhang, P., ... & Wang, J. (2023). Inulin supplementation restores intestinal microbiota and gut barrier in three breeds of laying hens. Poultry Science, 102(2). 102266
  20. Mon, K. K. Z., Zhu, Y., Chanthavixay, G., ... & Zhou, H. (2020). Integrative analysis of gut microbiome and metabolites revealed novel mechanisms of intestinal Salmonella carriage in chicken. Scientific Reports, 10, 10107. doi: 10.1038/s41598-020-60892-9
  21. Montes-Vergara, D. E., Cardona-Alvarez, J., & Pérez-Cordero, A. (2021). Prevalence of gastrointestinal parasites in three groups of domestic poultry managed under backyard system in the Savanna subregion, Department of Sucre, Colombia. Journal of Advanced Veterinary and Animal Research, 8(1), 32–38. http://doi.org/10.5455/javar.2021.h551
  22. Nam, S. L., Tarazona Carrillo, K., de la Mata, A. P., Harynuk, J. J. (2023). Untargeted metabolomic profiling of aqueous and lyophilized pooled human feces from two diet cohorts using two-dimensional gas chromatography coupled with time-of-flight mass spectrometry. Metabolites. https://doi.org/10.3390/metabo13070828
  23. Naumova, N. B., Alikina, T. Y., Zolotova, N. S., Konev, A. V., Pleshakova, V. I., Lescheva, N. A., & Kabilov, M. R. (2021). Bacillus-based probiotic treatment modified bacteriobiome diversity in duck feces. Agriculture, 11(5), 406. https://doi.org/10.3390/agriculture11050406
  24. Oluseyifunmi, A., Smith, O., Johnson, M., & Anderson, D. (2024). Role of resistant starch and dietary fiber in modulation of gut health biomarkers in broilers. Animal Nutrition, 10(1), 55–654.
  25. Philip, D., Hodgkiss, R., Radhakrishnan, S. K., Acharjee, A. (2025). Deciphering microbial and metabolic influences in gastrointestinal diseases-unveiling their roles in gastric cancer, colorectal cancer, and inflammatory bowel disease. Journal of Translational Medicine. https://doi.org/10.1186/s12967-025-06552-w
  26. Pires, P. G. D. S., Cardinal, K. M., Elnesr, S. S., Fraceto, L. F., de Castro, F. L. S., & Moraes, P. D. O. (2025). Non-invasive biomarkers for monitoring intestinal health in broilers – A systematic review. Research in Veterinary Science, 162, 209-223. https://doi.org/10.1016/j.rvsc.2025.105669
  27. Rath, N. C., Gupta, A., Liyanage, R., & Lay, J. O. (2019). Phorbol 12-Myristate 13-Acetate-Induced Changes in Chicken Enterocytes. Proteomics Insights, 10, 1178641819851392 https://doi.org/10.1177/1178641819851392
  28. Rysman, K., Eeckhaut, V., Ducatelle, R., & Van Immerseel, F. (2023). The fecal biomarker ovotransferrin associates with broiler performance under field conditions. Poultry Science, 102, Article 102585. DOI: 10.1016/j.psj.2023.103011
  29. Salahi, A., Abd El-Ghany, W. A., Attia, Y. A., ... & Tufarelli, V. (2025). Gut dysbiosis: Nutritional causes and risk prevention in poultry, with reference to other animals. South African Journal of Animal Science, 55(1), 8–20.
  30. Song, J., Li, Q., Everaert, N., Liu, R., Zheng, M., Zhao, G., ... & Wen, J. (2020). Dietary inulin supplementation modulates short-chain fatty acid levels and cecum microbiota composition and function in chickens infected with Salmonella. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.584380
  31. Susanti, R., Yuniastuti, A., & Fibriana, F. (2020). Metagenome analysis of gut microbial in both the caged and non-caged ducks. Journal of Physics: Conference Series, 1467, 012024.
  32. Taleuzzaman, M., Anupam, Verma, M., Choudhary, R. (2025). Gut microbial metabolites as diagnostic biomarkers. Gut Microbiota and their Impact on Disease Pathways and Interventions. DOI: 10.2174/9789815324549125010012
  33. Ul Saqib, N., Islam, Z., Sultan, A., Ahmad, S., Raziq, F., & Jan, A. U. (2025). Effect of dried orange (Citrus sinensis) pulp on growth performance, serum biochemical parameters, and nutrient digestibility in broiler chickens. Pakistan Journal of Zoology, 57(1), 123-132. DOI:10.17582/journal.pjz/20230803122156
  34. Wang, S., Chen, L., He, M., Shen, J., Yin, J., Lu, L., & Wang, Y. (2018). Different rearing conditions alter gut microbiota composition and host physiology in Shaoxing ducks. Scientific Reports, 8, 7387. DOI: 10.1038/s41598-018-25760-7
  35. Wang, Z., Shang, P., Song, X., Wu, M., Zhang, T., Zhao, Q., Zhu, S., Qiao, Y., Zhao, F., Zhang, R., Jinwen Wang, Yu, Y., Han, H., & Dong, H. (2024). Alterations in ileal microbiota and fecal metabolite profiles of chickens with immunity to Eimeria mitis. Animals, 14(23), 3515. https://doi.org/10.3390/ani14233515
  36. White, Z., Cabrera, I., Mei, L., ... & Sano, T. (2025). Gut inflammation promotes microbiota-specific CD4 T cell-mediated neuroinflammation. Nature.
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