{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T11:14:56Z","timestamp":1780917296012,"version":"3.54.1"},"reference-count":41,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T00:00:00Z","timestamp":1780876800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Michinoku GAP Fund from the Michinoku Academia Startup Platform","award":["MASP2025_09"],"award-info":[{"award-number":["MASP2025_09"]}]},{"name":"Michinoku GAP Fund from the Michinoku Academia Startup Platform","award":["MASP2026_02"],"award-info":[{"award-number":["MASP2026_02"]}]},{"DOI":"10.13039\/501100002241","name":"JST SPRING","doi-asserted-by":"publisher","award":["JPMJSP2114"],"award-info":[{"award-number":["JPMJSP2114"]}],"id":[{"id":"10.13039\/501100002241","id-type":"DOI","asserted-by":"publisher"}]},{"name":"LPDP\u2013RIIM BRIN","award":["B-803\/II.7.5\/FR\/6\/2022"],"award-info":[{"award-number":["B-803\/II.7.5\/FR\/6\/2022"]}]},{"name":"LPDP\u2013RIIM BRIN","award":["B-1373\/III\/PR.03.08\/06\/2022"],"award-info":[{"award-number":["B-1373\/III\/PR.03.08\/06\/2022"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Dairy production in Indonesia relies on two contrasting calf-rearing systems: concentrate-driven commercial dairy systems (CDS) and smallholder farms (SH). As these systems differ in feeding practices, they may influence gut development in calves. This study examined how farm management affects the fecal microbiota and metabolites in healthy and diarrhea post-weaning calves. Fecal samples were collected from 11 and 14 calves from CDS and SH facilities, respectively. Gut bacterial communities were analyzed using 16S rRNA gene amplicon sequencing, and metabolites were characterized using untargeted gas chromatography\u2013mass spectrometry (GC-MS). Microbial diversity, metabolite profiles, and correlation networks were compared between the farm types and diarrhea status. Our results showed that farm management strongly shaped microbial community structure and metabolic outputs, but did not alter microbial richness. Although diarrhea is typically associated with reduced microbial richness, it did not affect the microbial community structure, suggesting that it primarily impacted microbial function, particularly the metabolic environment. Correlation network analysis revealed stronger linkages between microbes and metabolites in SH calves, especially under healthy conditions. Overall, these findings indicate that dietary structure is a key determinant of fermentation stability, with CDS calves showing greater metabolic instability. In contrast, SH calves maintain a more resilient, fiber-driven functional state.<\/jats:p>","DOI":"10.3390\/ani16121766","type":"journal-article","created":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T10:04:14Z","timestamp":1780913054000},"page":"1766","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Assessing the Effects of Farm Management Systems and Diarrhea on Gut Microbiota and Metabolites in Dairy Calves in Indonesia"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-5916-9337","authenticated-orcid":false,"given":"Andi","family":"Hiroyuki","sequence":"first","affiliation":[{"name":"International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"},{"name":"Laboratory of Animal Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jahidul","family":"Islam","sequence":"additional","affiliation":[{"name":"International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"},{"name":"Laboratory of Animal Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"},{"name":"Laboratory of Animal Mucosal Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"},{"name":"Laboratory of Animal Data Science & Innovation, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ainissya","family":"Fitri","sequence":"additional","affiliation":[{"name":"Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong 16911, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4831-4642","authenticated-orcid":false,"given":"Rusli","family":"Fidriyanto","sequence":"additional","affiliation":[{"name":"Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong 16911, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1772-0840","authenticated-orcid":false,"given":"Ki Ageng","family":"Sarwono","sequence":"additional","affiliation":[{"name":"Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong 16911, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andhika Yudha","family":"Prawira","sequence":"additional","affiliation":[{"name":"Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong 16911, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edy","family":"Sophian","sequence":"additional","affiliation":[{"name":"Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong 16911, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"family":"Rohmatussolihat","sequence":"additional","affiliation":[{"name":"Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong 16911, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wulansih Dwi","family":"Astuti","sequence":"additional","affiliation":[{"name":"Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong 16911, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"family":"Sukarman","sequence":"additional","affiliation":[{"name":"Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong 16911, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Delicia Yunita","family":"Rahman","sequence":"additional","affiliation":[{"name":"Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong 16911, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5005-3579","authenticated-orcid":false,"given":"Yantyati","family":"Widyastuti","sequence":"additional","affiliation":[{"name":"Research Center for Animal Husbandry, National Research and Innovation Agency (BRIN), Cibinong 16911, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natsuki","family":"Ohtani","sequence":"additional","affiliation":[{"name":"International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"},{"name":"Laboratory of Animal Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryota","family":"Hirakawa","sequence":"additional","affiliation":[{"name":"International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"},{"name":"Laboratory of Animal Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"},{"name":"Laboratory of Animal Mucosal Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mutsumi","family":"Furukawa","sequence":"additional","affiliation":[{"name":"International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"},{"name":"Laboratory of Animal Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"},{"name":"Laboratory of Animal Mucosal Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2386-662X","authenticated-orcid":false,"given":"Roni","family":"Ridwan","sequence":"additional","affiliation":[{"name":"Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong 16911, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1800-6972","authenticated-orcid":false,"given":"Tomonori","family":"Nochi","sequence":"additional","affiliation":[{"name":"International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"},{"name":"Laboratory of Animal Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"},{"name":"Laboratory of Animal Mucosal Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan"},{"name":"Division of Mucosal Vaccines, International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan"},{"name":"Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada"},{"name":"School of Nutrition and Health Sciences, Taipei Medical University, Taipei City 11031, Taiwan"},{"name":"Tohoku Center for Teaching and Learning, Institute for Excellence in Higher Education, Tohoku University, Sendai 980-8576, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5996","DOI":"10.3168\/jds.2016-12239","article-title":"Understanding the gut microbiome of dairy calves: Opportunities to improve early-life gut health","volume":"100","author":"Malmuthuge","year":"2017","journal-title":"J. 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