ORIGINAL RESEARCH article
Front. Cell. Infect. Microbiol.
Sec. Parasite and Host
Volume 15 - 2025 | doi: 10.3389/fcimb.2025.1647377
This article is part of the Research TopicParasite-Induced Liver Diseases Volume IIView all 4 articles
Enterocytozoon bieneusi infection disrupts bile acid metabolism in the wild rodent gut microbiota: Adaptive shifts in microbial metabolism and community structure
Provisionally accepted
Kai-Meng Shang1,2,3
He Ma3Yong-Jie Wei3Ji-Xin Zhao3Ya Qin3,4Jian-Ming Li4Zi-Yu Zhao4
Hai-Long Yu3,4
Quan Zhao4Bei-Ni Chen2*
Hany M. Elsheikha5*
Xiao-Xuan Zhang3
Xing Yang1*- 1Dali University, Dali, China
- 2Changchun Sci-Tech University, Changchun, China
- 3Qingdao Agricultural University, Qingdao, China
- 4Jilin Agricultural University, Changchun, China
- 5University of Nottingham, Nottingham, United Kingdom
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In this study, we reconstructed 6,332 genomes from the gut microbiota of wild rodents to investigate the bile acid (BA) metabolic potential of their resident microorganisms. Of these, 5,208 genomes were found to participate in essential BA metabolic pathways, including deconjugation, oxidation, and dihydroxylation, with the majority belonging to the bacterial phyla Bacillota_A and Bacteroidota. Interestingly, members of the Bacteroidota phylum, particularly within the Muribaculaceae family and the CAG-485 lineage, encoded bile salt hydrolase (BSH), a key enzyme in BA metabolism. Comparative analysis across several host species, including humans, pigs, laboratory mice, and chickens, revealed a striking absence of 7β-hydroxysteroid dehydrogenase (7β-HSDH) in laboratory mice. This absence suggests that conventional laboratory mice may have limited utility as models for studying intestinal BA metabolism and highlights wild-type rodents as potentially more suitable models for such research. Functional profiling further showed that BSH-encoding genomes were significantly enriched in glycoside hydrolase families GH13 and GH16, suggesting a possible link between BA transformation and carbohydrate metabolism. Intriguingly, when the data on Enterocytozoon bieneusi infection were integrated, a marked increase in BA-associated microbial taxa was observed in infected wild rodents. This suggests a complex interplay between pathogenic infection and host BA metabolism. These findings reveal intricate interconnections between gut microbial functions, host metabolic processes, and pathogen interactions, opening new avenues for understanding microbiome-driven host adaptation and health.
Keywords: Gut Microbiota, microbial functional profiling, Bile acid metabolism, Enterocytozoon bieneusi, Rodentia
Received: 15 Jun 2025; Accepted: 05 Sep 2025.
Copyright: © 2025 Shang, Ma, Wei, Zhao, Qin, Li, Zhao, Yu, Zhao, Chen, Elsheikha, Zhang and Yang. 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:
Bei-Ni Chen, Changchun Sci-Tech University, Changchun, China
Hany M. Elsheikha, University of Nottingham, Nottingham, United Kingdom
Xing Yang, Dali University, Dali, China
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