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Applied Microbiology
Volume 6
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10.3390/applmicrobiol6010017
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Review

Microbial Fermentation: A Sustainable Strategy for Producing High-Value Bioactive Compounds for Agriculture, Animal Feed, and Human Health

by
Victor Eduardo Zamudio-Sosa
1,†,
Luis Angel Cabanillas-Bojórquez
2,3,*,†,
Evangelina García-Armenta
4,
Marilyn Shomara Criollo-Mendoza
2,
José Andrés Medrano-Felix
5,
Alma Haydee Astorga-Gaxiola
3,6,
José Basilio Heredia
1,
Laura Aracely Contreras-Angulo
1 and
Erick Paul Gutiérrez-Grijalva
5,7,*
1
Centro de Investigación en Alimentación y Desarrollo, AC. Carretera a Eldorado Km 5.5, Col. Campo el Diez, Culiacán CP 80110, Sinaloa, Mexico
2
Posdoc SECIHTI-Centro de Investigación en Alimentación y Desarrollo, AC. Carretera a Eldorado Km 5.5, Col. Campo el Diez, Culiacán CP 80110, Sinaloa, Mexico
3
Tecnológico Nacional de México–Instituto Tecnológico de Culiacán, Juan de Dios Bátiz 310 pte, Colonia Guadalupe, Culiacán CP 80220, Sinaloa, Mexico
4
Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa, Culiacán CP 80013, Sinaloa, Mexico
5
5 Programa Investigadoras e investigadores SECIHTI-Centro de Investigación en Alimentación y Desarrollo, AC. Carretera a Eldorado Km 5.5, Col. Campo el Diez, Culiacán CP 80110, Sinaloa, Mexico
6
Facultad de Ciencias de la Nutrición y Gastronomía, Universidad Autónoma de Sinaloa, Culiacán CP 80019, Sinaloa, Mexico
7
Centro de Investigación y Docencia en Ciencias de la Salud, Universidad Autónoma de Sinaloa, Culiacán CP 80030, Sinaloa, Mexico
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Appl. Microbiol. 2026, 6(1), 17; https://doi.org/10.3390/applmicrobiol6010017 (registering DOI)
Submission received: 7 December 2025 / Revised: 16 January 2026 / Accepted: 16 January 2026 / Published: 18 January 2026
Versions Notes

Abstract

Microbial fermentation is a key biotechnological tool for producing bioactive metabolites such as alkaloids, carotenoids, essential oils, and phenolic compounds, among others, with applications in human health, agriculture, and food industries. This review comprehensively reviews recent information on the synthesis of valuable compounds and enzymes through fermentation processes. Here, we discuss the advantages of the different types of fermentation, such as submerged and solid-state fermentation, in optimizing metabolite production by bacteria, fungi, and yeast. The role of microbial metabolism, enzymatic activity, and fermentation conditions in enhancing the bioavailability and functionality of these compounds is discussed. Integrating fermentation with emerging biotechnologies, including metabolic engineering, further enhances yields and specificity. The potential of microbial-derived bioactive compounds in developing functional foods, pharmaceuticals, and eco-friendly agricultural solutions positions fermentation as a pivotal strategy for future biotechnological advancements. Therefore, microbial fermentation is a sustainable tool to obtain high-quality metabolites from different sources that can be used in agriculture, animal, and human health.
Keywords: fermentation; microorganism; bioactive compounds; one-health fermentation; microorganism; bioactive compounds; one-health

Share and Cite

MDPI and ACS Style

Zamudio-Sosa, V.E.; Cabanillas-Bojórquez, L.A.; García-Armenta, E.; Criollo-Mendoza, M.S.; Medrano-Felix, J.A.; Astorga-Gaxiola, A.H.; Heredia, J.B.; Contreras-Angulo, L.A.; Gutiérrez-Grijalva, E.P. Microbial Fermentation: A Sustainable Strategy for Producing High-Value Bioactive Compounds for Agriculture, Animal Feed, and Human Health. Appl. Microbiol. 2026, 6, 17. https://doi.org/10.3390/applmicrobiol6010017

AMA Style

Zamudio-Sosa VE, Cabanillas-Bojórquez LA, García-Armenta E, Criollo-Mendoza MS, Medrano-Felix JA, Astorga-Gaxiola AH, Heredia JB, Contreras-Angulo LA, Gutiérrez-Grijalva EP. Microbial Fermentation: A Sustainable Strategy for Producing High-Value Bioactive Compounds for Agriculture, Animal Feed, and Human Health. Applied Microbiology. 2026; 6(1):17. https://doi.org/10.3390/applmicrobiol6010017

Chicago/Turabian Style

Zamudio-Sosa, Victor Eduardo, Luis Angel Cabanillas-Bojórquez, Evangelina García-Armenta, Marilyn Shomara Criollo-Mendoza, José Andrés Medrano-Felix, Alma Haydee Astorga-Gaxiola, José Basilio Heredia, Laura Aracely Contreras-Angulo, and Erick Paul Gutiérrez-Grijalva. 2026. "Microbial Fermentation: A Sustainable Strategy for Producing High-Value Bioactive Compounds for Agriculture, Animal Feed, and Human Health" Applied Microbiology 6, no. 1: 17. https://doi.org/10.3390/applmicrobiol6010017

APA Style

Zamudio-Sosa, V. E., Cabanillas-Bojórquez, L. A., García-Armenta, E., Criollo-Mendoza, M. S., Medrano-Felix, J. A., Astorga-Gaxiola, A. H., Heredia, J. B., Contreras-Angulo, L. A., & Gutiérrez-Grijalva, E. P. (2026). Microbial Fermentation: A Sustainable Strategy for Producing High-Value Bioactive Compounds for Agriculture, Animal Feed, and Human Health. Applied Microbiology, 6(1), 17. https://doi.org/10.3390/applmicrobiol6010017

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