Role of the Gut Microbiome in Nutrient Absorption, Immune Defense and Animal Health

Authors

  • OLUWAFEMI ABEL AGBETUYI Federal University Oye Ekiti, Ekiti State.
  • EMMANUEL KEHINDE ASANIYAN Department of Animal Production and Health, Olusegun Agagu University of Science and Technology, Okiti Pupa, Nigeria
  • ADEMIJU ADEOLU AGANGA Department of Animal Production and Health, Federal University, Oye Ekiti, Nigeria
  • ADETUNMBI TELLA Department of Animal Production and Health, Federal University, Oye Ekiti, Nigeria
  • TOMILOLA AYO ARILEKOLASI Department of Animal Production and Health, Federal University, Oye Ekiti, Nigeria
  • KEHINDE LUKE AKINSOLA Department of Animal Production and Health, Federal University, Oye Ekiti, Nigeria

DOI:

https://doi.org/10.57038/usjas.v9i02.7742

Abstract

The gut microbiome, a complex network of microorganisms that flourish in the gastrointestinal tract, is crucial for immune defense, nutrient absorption, and preservation of physiological balance in animals. This influences the development and function of the immune system, which aids in the synthesis of essential vitamins and complex carbohydrates conversion with a focus on how microbial ecosystems aid in the digestion, absorption, and metabolism of nutrients. This study highlights the complex interactions among gut microbiomes, their metabolic products (metabolomics), and the animals. More information was given about how this microbiome affects immune responses, particularly inflammation regulation and pathogenic resistance. A balanced gut microbiome is necessary because any disruption to this ecosystem can result in a number of health problems. New evidence suggests that the gut microbiome must be balanced to maintain homeostasis and prevent various diseases. Understanding of intricate microorganism colonies can be utilized to improve animal well-being and productivity using microbiome-based techniques.

References

Agbetuyi, O. A., Ekeocha, A. H., Aganga, A. A., & Oloruntola, O. D. (2024a). Moringa oleifera

and Allium sativum in broiler nutrition: carcass traits, biochemical characterization, and economic analysis. Discover Food, 4(1), 86. https://doi.org/10.1007/s44187-024-00155-y

Agbetuyi, O. A., Ekeocha, A. H., & Aganga, A. A. (2024b). Assessing the impact of moringa and garlic supplementation on egg production and quality in laying hens. Dysona-Applied Science, 5(2), 41-51. http://dx.doi.org/10.30493/DAS.2024.451601

Arshad, M. A., Hassan, F., Rehman, M. S., Huws, S. A., Cheng, Y., & Din, A. U. (2021). Gut

microbiome colonization and development in neonatal ruminants: strategies, prospects, and opportunities. Animal Nutrition, 7, 883–895.

Bamias, G., Kitsou, K., & Rivera-Nieves, J. (2023). The underappreciated role of secretory IgA

in IBD free. Inflammatory Bowel Diseases, 29(8), 1327-1341. https://doi.org/10.1093/ibd/izad024

Bickhart, D. M., McClure, J. C., Schnabel, R. D., Rosen, B. D., Medrano, J. F., & Smith, T. P. L.

(2020). Symposium review: advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection. Journal of Dairy Science, 103, 5278–5290.

Barone, M. D., Amico, F., Brigidi, P., & Turroni, S. (2022). Gut microbiome-micronutrient

interaction: the key to controlling the bioavailability of minerals and vitamins? Biofactors, 48(2), 307-314. https://doi.org/10.1002/biof.1835.

Chaitman, J., Ziese, A. L., Pilla, R., Minamoto, Y., Blake, A. B., Guard, B. C., Isaiah, A., Lidbury,

J. A., Steiner, J. M., & Unterer, S. (2020). Fecal microbial and metabolic profiles in dogs with acute diarrhea receiving either fecal microbiota transplantation or oral metronidazole. Frontiers in Veterinary Science, 7, 192. https://doi.org/10.3389/fvets.2020.00192

Chen, S., Xiang, H., Zhang, H., Zhu, X., Wang, D., Wang, J., Yin, T., Liu, L., Kong, M., & Li, H.

(2019). Rearing system causes changes of behavior, microbiome, and gene expression of chickens. Poultry Science, 98, 3365–3376.

Chenbo, Y., Chuanq, C., Jianxi, Z., Ha, Z., Wei, C., & Qixiao, Z. (2022). Dietary strategies to

promote the abundance of intestinal Akkermansia muciniphila, a focus on the effect of plant extracts. Journal of Functional Foods, 93, 105093. https://doi.org/10.1016/j.jff.2022.10509

Cronkite, D. A., & Strutt, T. M. (2018). The regulation of inflammation by innate and adaptive

lymphocytes. Journal of Immunological Research, 2018, 1467538.

Gebrayel, P., Nicco, C., Al Khodor, S., Bilinski, J., Caselli, E., Comelli, E. M., Egert, M.,

Giaroni, C., Karpinski, T. M., Loniewski, I., Mulak, A., Reygner, J., Samczuk, P., Serino, M., Sikora, M., Terranegra, A., Ufnal, M., Villeger, R., Pichon, C., Konturek, P., & Edeas, M. (2022). Microbiota medicine: towards clinical revolution. Journal of Translational Medicine, 20(1), 111. https://doi.org/10.1186/s12967-022-03296-9.

Ghosh, S., & Ray, R. R. (2025). Use of alternative sources (AMP, Nanomaterials,

Phytocompounds) for handling biofilm-associated infections in livestock. In: Lahiri, D., Nag, M., Bhattacharya, D., Ray, R.R. (eds) biofilm associated livestock diseases and their management. Livestock Diseases and Management. Springer, Singapore. https://doi.org/10.1007/978-981-96-1885-9_13

Guo, S., Ma, T., Kwok, L., Quan, K., Li, B., & Wang, H. (2024). Effects of postbiotics on chronic

diarrhea in young adults: a randomized, double-blind, placebo-controlled crossover trial assessing clinical symptoms, gut microbiota, and metabolite profiles. Gut Microbes, 16, 1

https://doi.org/10.1080/19490976.2024.2395092

Hick, E., Suarez, M., Rey, A., Mantecón, L., Fernandez, N., Solis, G., Gueimonde, M., &

Arboleya, S. (2024). Personalized nutrition with banked human milk for early gut microbiota development: in pursuit of the perfect match. Nutrients, 16, 1976.

Jager, R., Zaragoza, J., Purpura, M., Iametti, S., Marengo, M., Tinsley, G. M., Anzalone, A. J.,

Oliver, J. M., Fiore, W., Biffi, A., Urbina, S., & Taylor, L. (2020). Probiotic administration increases amino acid absorption from plant protein: a placebo-controlled, randomized, double-blind, multicenter, crossover study. Probiotics and Antimicrobial Proteins, 12(4), 1330-1339. https://doi.org/10.1007/s12602-020-09656-5.

Kumar, S., Mukherjee, R., Gaur, P., Leal, E., Lyu, X., Ahmad, S., Puri, P., Chang, C., Raj, V. S.

& Pandey, R. P. (2025). Unveiling roles of beneficial gut bacteria and optimal diets for health. Frontiers in Microbiology, 16, 1527755. https://doi.org/10.3389/fmicb.2025.1527755

Lam, N., Lee, Y., & Farber, D. L. (2024). A guide to adaptive immune memory. Nature Reviews

Immunology, 24, 810-829.

Lavelle, A., & Sokol, H. (2020). Gut microbiota-derived metabolites as key actors in

inflammatory bowel disease. Nature Reviews Gastroenterology and Hepatology, 17, 223-237. https://doi.org/10.1038/s41575-019-0258-z

Lee, J., Gonzalez-Vega, J. C., Htoo, J. K., & Nyachoti, C. M. (2024). Effects of dietary crude

protein content and resistant starch supplementation on growth performance, intestinal histomorphology and microbial metabolites in weaned pigs. Archives of Animal Nutrition, 78(2), 191-206. https://doi.org/10.1080/1745039X.2024.2376093

Li, D., Li, C., Liu, N., Liu, H., Yu, Z., Liu, Q., Shu, G., Lin, J., Zhang, W., Peng, G., Zhao, L.,

Tang, H., Li, H., Xu, F., & Fu, H. (2025). Integrated metabolomics and intestinal microbiota analysis to reveal anti-post-weaning diarrhea mechanisms of Modified Yupingfeng Granule in Rex rabbits. Frontiers in Microbiology, 16. https://doi.org/10.3389/fmicb.2025.1470731

Li, Q., Larouche-Lebel, E., Loughran, K. A., Huh, T. P., Suchodolski, J. S., & Oyama, M. A.

(2021). Gut dysbiosis and its associations with gut microbiota-derived metabolites in dogs with myxomatous mitral valve disease. MSystems, 6(2), e00111-e00121. https://doi.org/10.1128/msystems. 00111-21

Lin, Y. C., Wu, C. C., Li, Y. E., Chen, C. L, Lin, C. R., & Ni, Y. H. (2025). Full-length 16S rRNA

Sequencing Reveals Gut Microbiome Signatures Predictive of MASLD in children with obesity. BMC Microbiology, 25, 146. https://doi.org/10.1186/s12866-025-03849-0

Lin, Y., Zhou, B., & Zhu, W. (2021). Pathogenic Escherichia coli-specific bacteriophages and

polyvalent bacteriophages in piglet guts with increasing coliphage numbers after weaning. Applied and Environmental Microbiology, 87, e00966-21.

Liu, M. J., Yang, J. Y., Yan, Z. H., Hu, S., Li, J. Q., & Xu, Z. X. (2022). Recent findings in

Akkermansia muciniphila-regulated metabolism and its role in intestinal diseases. Clinical Nutrition, 41, 2333-2344. https://doi.org/10.1016/j.clnu.2022.08.029

Ma, Y., Ma, S., Chang, L., Wang, H., Ga, Q., Ma, L., Bai, Z., Shen, Y., & Ge, R. L. (2019). Gut

microbiota adaptation to high altitude in indigenous animals. Biochemical and Biophysical Research Communications, 516, 120-126.

Mann, E. R., Lam, Y. K., & Uhlig, H. H. (2024). Short-chain fatty acids: Linking diet, the

microbiome and immunity. Nature Reviews Immunology, 24, 577-595.

Magalhaes, M. I., Azevedo, M. J., Castro, F., Oliveira, M. J., Costa, A. M., & Sampaio Maia, B.

(2024). The link between obesity and the gut microbiota and immune system in early-life. Critical Reviews in Microbiology, 51(2), 264-284. https://doi.org/10.1080/1040841X.2024.2342427

Manus, J., Millette, M., Uscanga, B. R. A., Salmieri, S., Maherani, B., & Lacroix, M. (2021). In

vitro protein digestibility and physico-chemical properties of lactic acid bacteria fermented beverages enriched with plant proteins. Journal of Food Sciences, 86(9), 4172-4182. https://doi.org/10.1111/1750-3841.15859

Markowiak, P., & Slizewska, K. (2017). Effects of probiotics, prebiotics, and Synbiotics on

human health. Nutrients, 9, 1021. https://doi.org/10.3390/nu9091021

Matsuoka, M., Soria, S. A., Pires, J. R., Sant’Ana, A. C. P., & Freire, M. (2025). Natural and

induced immune responses in oral cavity and saliva. BMC Immunology, 26(34) https://doi.org/10.1186/s12865-025-00713-8

McCallum, G., & Tropini, C. (2024). The gut microbiota and its biogeography. Nature Reviews

Microbiology, 22, 105–118.

Paul, J. (2024). Gastrointestinal tract infections. in: disease causing microbes. Springer,

Cham. 149-215.

Reuben, R. C., Sarkar, S. L., Roy, P. C., Anwar, A., Hossain, M. A., & Jahid, I. K. (2021).

Prebiotics, probiotics and postbiotics for sustainable poultry production. World’s Poultry Science Journal, 77(4), 825-882. https://doi.org/10.1080/00439339.2021.1960234

Riegelman, E., Xue, K. S., Wang, J. S., & Tang, L. (2024). Gut-brain axis in focus: polyphenols,

microbiota, and their influence on ?-synuclein in parkinson’s disease. Nutrients, 16, 2041.

Rindels, J. E., & Loman, B. R. (2024). Gut microbiome – the key to our pets’ health and

happiness? Animal Frontiers, 14 (3), 46-53. https://doi.org/10.1093/af/vfae015

Roy, S., & Singh, S. (2025). Metabolomics approaches for microbiome analysis. In: Kesheri, M.,

Kanchan, S., Hader, DP., Sinha, R.P. (eds) Multi-Omics in Biomedical Sciences and Environmental Sustainability. Springer, Singapore. https://doi.org/10.1007/978-981-96-7067-3_9

Satam, H., Joshi, K., Mangrolia, U., Waghoo, S., Zaidi, G., Rawool, S., Thakare, R. P., Banday,

S., Mishra, A. K., & Das, G. (2023). Next-generation sequencing technology: current trends and advancements. Biology, 12, 997.

Shkoporov, A. N., & Hill, C. (2019). Bacteriophages of the human gut: the “known unknown” of

the microbiome. Cell Host Microbe, 25, 195–209.

Shoaib, M., Gul, S., Majeed, S., He, Z., Hao, B., Tang, M., Zhang, X., Wu, Z., Wang, S., Pu, W.

(2025). Pathogenomic characterization of multidrug-resistant Escherichia coli strains carrying wide efflux-associated and virulence genes from the dairy farm environment in Xinjiang, China, Antibiotics, 14(5), 511. https://doi.org/10.3390/antibiotics14050511

Stavroulaki, E. M., Suchodolski, J. S., Pilla, R., Fosgate, G. T., Sung, C. H., Lidbury, J. A.,

Steiner, J. M., & Xenoulis, P. G. (2021). Short- and long-term effects of amoxicillin/clavulanic acid or doxycycline on the gastrointestinal microbiome of growing cats. PLoS One. 16(12), e0253031. https://doi.org/10.1371/ journal.pone.0253031

Stephens, R. W., Arhire, L., & Covasa, M. (2018). Gut microbiota: From microorganisms to

metabolic organ influencing obesity. Obesity, 26, 801-809.

Sun, W., Zhang, Y., Guo, R., Sha, S., Chen, C., Ullah, H., Zhang, Y., Ma, J., You, W., Meng, J.,

Lv, Q., Cheng, L., Fan, S., Li, R., Mu, X., Li, S., & Yan, Q. (2024). A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases. npj Biofilms Microbiomes, 10, 96. https://doi.org/10.1038/s41522-024-00567-9

Sultan, S., El-Mowafy, M., Elgaml, A., Ahmed, T., Hassan, H., & Mottawea, W. (2021).

Metabolic influences of gut microbiota dysbiosis on inflammatory bowel disease. Frontiers in Physiology, 12, 715506. https://doi.org/10.3389/fphys.2021.715506

Tardiolo, G., La Fauci, D., Riggio, V., Daghio, M., Di Salvo, E., Zumbo, A., & Sutera, A. M.

(2025). Gut microbiota of ruminants and monogastric livestock: an overview. Animals, 15(5), 758. https://doi.org/10.3390/ani15050758

Tugnoli, B., Giovagnoni, G., Piva, A., & Grilli, E. (2020). From acidifiers to intestinal health

enhancers: how organic acids can improve growth efficiency of Pigs. Animals, 10, 134.

Uebanso, T., Shimohata, T., Mawatari, K., & Takahashi, A. (2020). Functional roles of

B-vitamins in the gut and gut microbiome. Molecular Nutrition & Food Research, 64, e2000426. https://doi.org/10.1002/mnfr.202000426

Verma, M., Randhawa, S., Bathla, M., Tejiab, N., & Acharya, A. (2025). Strategic use of

nanomaterials as double-edged therapeutics to control carcinogenesis via regulation of dysbiosis and bacterial infection: current status and future prospects. Journal of Materials Chemistry B, 16.

Walden, K. E., Hagele, A. M., Orr, L. S., Gross, K. N., Krieger, J. M., Jager, R., & Kerksick,

C. M. (2022). Probiotic BC30 improves amino acid absorption from plant protein concentrate in older women. Probiotics and Antimicrobia Proteins. https://doi.org/10.1007/s12602-022-10028-4

Wang, X. Y., Ding, Z. L., Xu, Y. X., Yang, D. Z, Yang, S., & Fei, H. (2025). Effect of

supplementing exogenous glucanase or/and mannanase to diets containing Torula yeast on growth performance, biochemical indices, liver and intestinal morphology, and intestinal microbiota and metabolism of largemouth bass (Micropterus salmoides). Probiotics and Antimicrobial Proteins, 1-15. https://doi.org/10.1007/s12602-025-10560-z

Yi, S., Lee, H. G., Kim, E., Jung, Y., Bok, E., Cho, A., Jung Do, Y., Hur, T., & Oh, S. (2023). Raw

potato starch diet supplement in weaned pigs could reduce Salmonella Typhimurium infection by altering microbiome composition and improving immune status. Frontiers in Veterinary Science, 10. https://doi.org/10.3389/fvets.2023.1183400

Yu, J., Liu, C., Wang, D., Wan, P., Cheng, L., & Yan, X. (2025). Integrated microbiome and

metabolome analysis reveals altered gut microbial communities and metabolite profiles in dairy cows with subclinical mastitis. BMC Microbiology, 25, 115. https://doi.org/10.1186/s12866-025-03810-1

Zakrzewska, Z., Zawartka, A., Schab, M., Martyniak, A., Skoczen, S., Tomasik, P. J.,

W?drychowicz, A. (2022). Prebiotics, probiotics, and postbiotics in the prevention and treatment of anemia. Microorganisms, 10(7), 1330. https://doi.org/10.3390/microorganisms10071330

Zhang, D., & Frenette, P. S. (2019). Cross talk between neutrophils and the microbiota. Blood,

, 2168-2177.

Zheng, D., Liwinski, T., & Elinav, E. (2020). Interaction between microbiota and immunity in

health and disease. Cell Research, 30, 492–506.

Zhou, G., Liang, X., He, X., Li, J., Tian, G., Liu, Y., Wang, X., Chen, Y., & Yang, Y. (2023).

Compound enzyme preparation supplementation improves the production performance of goats by regulating rumen microbiota. Applied Microbiology and Biotechnology, 107, 7287-7299.

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Published

2025-12-30