{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,29]],"date-time":"2026-01-29T04:30:13Z","timestamp":1769661013227,"version":"3.49.0"},"reference-count":65,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T00:00:00Z","timestamp":1769558400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Foundation for Science and Technology (FCT), Portugal","doi-asserted-by":"publisher","award":["UI\/BD\/150902\/2021"],"award-info":[{"award-number":["UI\/BD\/150902\/2021"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The gut plays a central role in fish nutrition, immunity, and overall health, making it key in aquaculture research. The microbiota, crucial to gut function, is increasingly studied as an indicator of health and nutritional status. This study characterized the gut microbiota of juvenile meagre (Argyrosomus regius) (initial weight 4.6 \u00b1 0.4 g) fed for seven weeks on diets in which fishmeal (FM) and fish oil (FO) were replaced by increased proportions of plant-based ingredients, with the aim of identifying microbial profiles associated with nutritional challenge. Fish were fed a FM\/FO control diet (CTRL; 55.1% FM, 11.3% FO), a low FM\/FO diet (CD; 15% FM, 7% FO), or a very low FM\/FO diet (ED; 5% FM, 5% FO). Next-generation sequencing analysis of gut mucosa and digesta revealed no significant differences in alpha or beta diversity among different dietary groups. Firmicutes dominated all samples, particularly Bacilli, Mycoplasmatales, Mycoplasmataceae, and Mycoplasma. Significant differences were only observed in low-abundance taxa (&lt;1%), with higher abundance of Thermoactinomycetales (p = 7.71 \u00d7 10\u22124), Thermoactinomycetaceae (p = 7.71 \u00d7 10\u22124), Kroppenstedtia (p = 1.70 \u00d7 10\u22123), and Pseudogracilibacillus (p = 0.039) in challenged groups. This study highlights the potential of low-abundance microbial groups as targets to establish gut health biomarkers in fish.<\/jats:p>","DOI":"10.3390\/ani16030407","type":"journal-article","created":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T15:56:12Z","timestamp":1769615772000},"page":"407","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Gut Microbiota Response in Meagre (Argyrosomus regius) Subjected to a Plant-Based Nutritional Challenge"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7885-0262","authenticated-orcid":false,"given":"Joana","family":"Oliveira","sequence":"first","affiliation":[{"name":"FCUP\u2014Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal"},{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-208 Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6965-0958","authenticated-orcid":false,"given":"Marisa","family":"Barata","sequence":"additional","affiliation":[{"name":"IPMA\u2014EPPO\u2014Portuguese Institute for Sea and Atmosphere\u2014Aquaculture Research Station, 8700-194 Olh\u00e3o, Portugal"},{"name":"S2AQUA\u2014Collaborative Laboratory, Association for a Sustainable and Smart Aquaculture, 8700-194 Olh\u00e3o, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5747-4248","authenticated-orcid":false,"given":"Rafaela","family":"Santos","sequence":"additional","affiliation":[{"name":"FCUP\u2014Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal"},{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-208 Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9852-2426","authenticated-orcid":false,"given":"Cl\u00e1udia","family":"Serra","sequence":"additional","affiliation":[{"name":"FCUP\u2014Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal"},{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-208 Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6075-2472","authenticated-orcid":false,"given":"Florbela","family":"Soares","sequence":"additional","affiliation":[{"name":"IPMA\u2014EPPO\u2014Portuguese Institute for Sea and Atmosphere\u2014Aquaculture Research Station, 8700-194 Olh\u00e3o, Portugal"},{"name":"S2AQUA\u2014Collaborative Laboratory, Association for a Sustainable and Smart Aquaculture, 8700-194 Olh\u00e3o, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6746-764X","authenticated-orcid":false,"given":"Pedro","family":"Pous\u00e3o-Ferreira","sequence":"additional","affiliation":[{"name":"IPMA\u2014EPPO\u2014Portuguese Institute for Sea and Atmosphere\u2014Aquaculture Research Station, 8700-194 Olh\u00e3o, Portugal"},{"name":"S2AQUA\u2014Collaborative Laboratory, Association for a Sustainable and Smart Aquaculture, 8700-194 Olh\u00e3o, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5730-836X","authenticated-orcid":false,"given":"Aires","family":"Oliva-Teles","sequence":"additional","affiliation":[{"name":"FCUP\u2014Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal"},{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-208 Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1664-3556","authenticated-orcid":false,"given":"Ana","family":"Couto","sequence":"additional","affiliation":[{"name":"FCUP\u2014Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal"},{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-208 Matosinhos, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,28]]},"reference":[{"key":"ref_1","unstructured":"Kim, S.-K. 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