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ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Systems Microbiology
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1557285
FACdb: a comprehensive resource for genes, gut Microbiota, and metabolites in farm animals
Provisionally accepted
Ze Zhang 1
Yang Li 1
Di Zhang 1
Shuai CHEN 1* Sien Lu 1 Kang Wang 1 Miao Zhou 2 Zehe Song 2 Qingcui Li 1*
Jie YIN 2*
Xiaoping Liu 1*- 1 Hangzhou Institute for Advanced Study, University of Chinese Academy of Science, Hangzhou, China
- 2 College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan Province, China
Farm animals, including livestock and poultry, play essential economic, social, and cultural roles and are indispensable in human welfare. Farm Animal Connectome database (FACdb) is a comprehensive resource that includes the association networks among gene expression, gut microbiota, and metabolites in farm animals. Although some databases present the relationship between gut microbes, metabolites, and gene expression, these databases are limited to human and mouse species, with limited data for farm animals. In this database, we calculate the associations and summarize the connections among gene expression, gut microbiota, and metabolites in farm animals using six correlation or distance calculation (including Pearson, Spearman, Cosine, Euclidean, Bray-Curtis, and Mahalanobis). FACdb contains over 55 million potential interactions of 73571 genes, 11046 gut microbiota, and 4540 metabolites. It provides an easy-to-use interface for browsing and searching the association information.Additionally, FACdb offers interactive visualization tools to effectively investigate the relationship among the genes, gut microbiota, and metabolites in farm animals. Overall, FACdb is a valuable resource for understanding interactions among gut microbiota, metabolites, and gene expression. It contributes to the further utilization of microbes in animal products and welfare promotion. Compared to mice, pigs or other farm animals share more similarities with humans in molecular, cellular, and organ-level responses, indicating that our database may offer new insights into the relationship among gut microbiota, metabolites, and gene expression in humans.
Keywords: Farm animal, Connectome database, Gene Expression, Gut Microbiota, Metabolites, Association networks
Received: 08 Jan 2025; Accepted: 28 Feb 2025.
Copyright: © 2025 Zhang, Li, Zhang, CHEN, Lu, Wang, Zhou, Song, Li, YIN and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Shuai CHEN, Hangzhou Institute for Advanced Study, University of Chinese Academy of Science, Hangzhou, China
Qingcui Li, Hangzhou Institute for Advanced Study, University of Chinese Academy of Science, Hangzhou, China
Jie YIN, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan Province, China
Xiaoping Liu, Hangzhou Institute for Advanced Study, University of Chinese Academy of Science, Hangzhou, China
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.