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Despite being a modest fraction, the fungal community, also referred to as mycobiota, represents a critical component of the gut microbiota. Emerging evidence suggests that fungi act as early colonizers of the intestine, exerting a lasting influence on gut development. Meanwhile, the composition of the mycobiota is influenced by multiple factors, with diet, nutrition, drug use (e.g., antimicrobials), and physical condition standing as primary drivers. During its establishment, the mycobiota forms both antagonistic and synergistic relationships with bacterial communities within the host. For instance, intestinal fungi can inhibit bacterial colonization by producing alcohol, while certain bacterial pathogens exploit fungal iron carriers to enhance their growth. However, the regulatory mechanisms governing these complex interactions remain poorly understood. In this review, we first introduce the methodologies for studying the microbiota, then address the significance of the mycobiota in the mammalian intestine, especially during weaning when all \u2018primary drivers\u2019 change, and, finally, discuss interactions between fungi and bacteria under various influencing factors. Our review aims to shed light on the complex inter-kingdom dynamics between fungi and bacteria in gut homeostasis and provide insights into how they can be better understood and managed to improve host health and disease outcomes.<\/jats:p>","DOI":"10.3390\/microorganisms13010070","type":"journal-article","created":{"date-parts":[[2025,1,2]],"date-time":"2025-01-02T10:32:26Z","timestamp":1735813946000},"page":"70","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Fungi in the Gut Microbiota: Interactions, Homeostasis, and Host Physiology"],"prefix":"10.3390","volume":"13","author":[{"given":"Hao-Yu","family":"Liu","sequence":"first","affiliation":[{"name":"College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China"},{"name":"Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, Yangzhou University, Yangzhou 225009, China"},{"name":"Joint International Research Laboratory of Agricultural & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shicheng","family":"Li","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China"},{"name":"Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, Yangzhou University, Yangzhou 225009, China"},{"name":"Joint International Research Laboratory of Agricultural & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kennedy Jerry","family":"Ogamune","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China"},{"name":"Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, Yangzhou University, Yangzhou 225009, China"},{"name":"Joint International Research Laboratory of Agricultural & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4015-2845","authenticated-orcid":false,"given":"Abdelkareem A.","family":"Ahmed","sequence":"additional","affiliation":[{"name":"Department of Veterinary Science, Botswana University of Agriculture and Natural Resources, Private Bag 0027, Gaborone P.O. Box 100, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6652-2504","authenticated-orcid":false,"given":"In Ho","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Animal Resource & Science, Dankook University, 119 Dandero, Donnamgu Cheonan, Cheonan-si 31116, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunzeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0500-5292","authenticated-orcid":false,"given":"Demin","family":"Cai","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China"},{"name":"Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, Yangzhou University, Yangzhou 225009, China"},{"name":"Joint International Research Laboratory of Agricultural & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,1,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1016\/j.immuni.2019.05.023","article-title":"Gut Mycobiota in Immunity and Inflammatory Disease","volume":"50","author":"Li","year":"2019","journal-title":"Immunity"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/nri.2016.42","article-title":"Gut microbiota, metabolites and host immunity","volume":"16","author":"Rooks","year":"2016","journal-title":"Nat. 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