{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T17:02:34Z","timestamp":1789664554639,"version":"4.0.1"},"reference-count":39,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T00:00:00Z","timestamp":1762819200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"\n Background<\/jats:title>\n \n Enterocytozoon bieneusi<\/jats:italic>\n (\n E. bieneusi<\/jats:italic>\n ) is a pathogenic microsporidian that infects a variety of hosts, including wild mice, potentially influencing their gut microbiota. This study aims to explore how\n E. bieneusi<\/jats:italic>\n infection influences the gut microbiota composition and function in wild mice.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n Fecal samples were collected from 20 wild mice (\n Rattus flavipectus<\/jats:italic>\n ) in September 2023 in Yunnan Province, China. The PCR results showed that 10 were infected with\n E. bieneusi<\/jats:italic>\n and 10 were uninfected, with no samples testing positive for\n Cryptosporidium<\/jats:italic>\n spp.\n , Blastocystis, Giardia, Cyclospora or Balantioides coli.<\/jats:italic>\n DNA was extracted and subjected to metagenomic sequencing using Illumina HiSeq. Gut microbiota composition was assessed using MetaPhlAn4 for species-level annotation. The contigs were used to construct a gene catalog and perform functional annotation. Additionally, viral sequences were identified by analyzing the contigs with software, such as CheckV and Vibrant.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n The gut microbiota diversity showed no significant difference between mice infected with\n E. bieneusi<\/jats:italic>\n and the control group, with the dominant phyla being\n Firmicutes<\/jats:italic>\n and\n Bacteroidetes<\/jats:italic>\n . Virome analysis identified 18,192 high-quality viral sequences, with the\n E. bieneusi<\/jats:italic>\n group exhibiting higher viral species diversity. Furthermore, significant differences were observed in 178 viral operational taxonomic units (vOTUs) between the two groups, with 161 vOTUs enriched in the\n E. bieneusi<\/jats:italic>\n group. Functional analysis demonstrated significant enrichment of several metabolic pathways in the gut microbiota of wild mice infected with\n E. bieneusi<\/jats:italic>\n , particularly in the metabolism of terpenoids and polyketides, digestive system, biosynthesis of other secondary metabolites and metabolism of cofactors and vitamins. Notably, unique virus-bacteria correlations were observed in the\n E. bieneusi<\/jats:italic>\n group.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n \n E. bieneusi<\/jats:italic>\n infection significantly alters the gut virome in wild mice, affecting microbial composition and interactions. The infection appears to drive adaptive changes in microbial functions, especially in metabolic processes, suggesting a host response to infection-related stress.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fcimb.2025.1708266","type":"journal-article","created":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T06:31:59Z","timestamp":1762842719000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Metagenomic analysis of gut microbiota composition and function in wild mice (Rattus flavipectus) infected with Enterocytozoon bieneusi"],"prefix":"10.3389","volume":"15","author":[{"given":"Hai-Long","family":"Yu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hai-Tao","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qing-Yu","family":"Hou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya","family":"Qin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xing","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen-Qiu","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li-Hua","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quan","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"He","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,11,11]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1016\/j.chom.2021.01.003","article-title":"Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation","volume":"29","author":"Becattini","year":"2021","journal-title":"Cell Host Microbe"},{"key":"B2","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1186\/s40168-021-01017-w","article-title":"Thousands of previously unknown phages discovered in whole-community human gut metagenomes","volume":"9","author":"Benler","year":"2021","journal-title":"Microbiome"},{"key":"B3","doi-asserted-by":"publisher","first-page":"1633","DOI":"10.1038\/s41587-023-01688-w","article-title":"Extending and improving metagenomic taxonomic profiling with uncharacterized species using metaphlan 4","volume":"41","author":"Blanco-M\u00edguez","year":"2023","journal-title":"Nat. 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