{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T10:26:12Z","timestamp":1773829572364,"version":"3.50.1"},"reference-count":85,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2023,6,3]],"date-time":"2023-06-03T00:00:00Z","timestamp":1685750400000},"content-version":"vor","delay-in-days":153,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","award":["857251"],"award-info":[{"award-number":["857251"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The activity of the microbiome of fish mucosae provides functions related to immune response, digestion, or metabolism. Several biotic and abiotic factors help maintaining microbial homeostasis, with disruptions leading to dysbiosis. Diseases and antibiotic administration are known to cause dysbiosis in farmed fish. Pathogen infections greatly affect the production of gilthead seabream, and antibiotic treatment is still frequently required. Here, we employed a 16S rRNA high-throughput metataxonomics approach to characterize changes in the gut, skin, and gill microbiomes occurring due to infection with Photobacterium damselae subsp. piscicida and subsequent antibiotic treatment with oxytetracycline (OTC), as well as during recovery. Although microbiota response differed between studied tissues, overall changes in composition, diversity, structure, and predicted function were observed in all mucosae. The skin and gill microbiomes of diseased fish became largely dominated by taxa that have been frequently linked to secondary infections, whereas in the gut the genus Vibrio, known to include pathogenic bacteria, increased with OTC treatment. The study highlights the negative impacts of disease and antibiotic treatment on the microbiome of farmed fish. Our results also suggest that fish transportation operations may have profound effects on the fish microbiome, but further studies are needed to accurately evaluate their impact.<\/jats:p>","DOI":"10.1093\/femsmc\/xtad011","type":"journal-article","created":{"date-parts":[[2023,6,8]],"date-time":"2023-06-08T08:54:55Z","timestamp":1686214495000},"source":"Crossref","is-referenced-by-count":23,"title":["Disruption of the skin, gill, and gut mucosae microbiome of gilthead seabream fingerlings after bacterial infection and antibiotic treatment"],"prefix":"10.1093","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9312-3648","authenticated-orcid":false,"given":"Daniela","family":"Rosado","sequence":"first","affiliation":[{"name":"S2AQUA \u2013 Collaborative Laboratory, Association for a Sustainable and Smart Aquaculture , Avenida Parque Natural da Ria Formosa s\/n, 8700-194 Olh\u00e3o, Portugal"}]},{"given":"Paula","family":"Canada","sequence":"additional","affiliation":[{"name":"CIIMAR \u2013 Interdisciplinary Center of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros de Leix\u00f5es. Av. General Norton de Matos, 4450-208 Matosinhos, Portugal"},{"name":"CMC \u2013 Centro de Maricultura da Calheta, Direc\u00e7\u00e3o Regional do Mar , Av. D. Manuel I, n\u00ba 7, 9370-135 Calheta, Madeira, Portugal"}]},{"given":"Sofia","family":"Marques\u00a0Silva","sequence":"additional","affiliation":[{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO Laborat\u00f3rio Associado, Campus de Vair\u00e3o, Universidade do Porto , R. Padre Armando Quintas 7, 4485-661 Vair\u00e3o, Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vair\u00e3o , R. Padre Armando Quintas 7, 4485-661 Vair\u00e3o, Portugal"}]},{"given":"Nuno","family":"Ribeiro","sequence":"additional","affiliation":[{"name":"MVAQUA \u2013 Servi\u00e7os M\u00e9dico Veterin\u00e1rios dedicados a Aquacultura , Av. do Parque de Campismo Lote 24, Frac\u0327a\u0303o C, 3840-264 Gafanha da Boa Hora, Portugal"}]},{"given":"Pedro","family":"Diniz","sequence":"additional","affiliation":[{"name":"Marismar \u2013 Aquicultura Marinha, Lda , Rua do Cabrestante 28, 9000-105 Funchal, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8800-3924","authenticated-orcid":false,"given":"Raquel","family":"Xavier","sequence":"additional","affiliation":[{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO Laborat\u00f3rio Associado, Campus de Vair\u00e3o, Universidade do Porto , R. Padre Armando Quintas 7, 4485-661 Vair\u00e3o, Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vair\u00e3o , R. Padre Armando Quintas 7, 4485-661 Vair\u00e3o, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2023,6,2]]},"reference":[{"key":"2023062819293014500_bib1","doi-asserted-by":"crossref","first-page":"109771","DOI":"10.1016\/j.ecoenv.2019.109771","article-title":"The impact of antibiotic exposure in water and zebrafish gut microbiomes: a 16S rRNA gene-based metagenomic analysis","volume":"186","author":"Almeida","year":"2019","journal-title":"Ecotoxicol Environ Saf"},{"key":"2023062819293014500_bib2","doi-asserted-by":"crossref","first-page":"116371","DOI":"10.1016\/j.envpol.2020.116371","article-title":"Zebrafish and water microbiome recovery after oxytetracycline exposure","volume":"272","author":"Almeida","year":"2021","journal-title":"Environ Pollut"},{"key":"2023062819293014500_bib3","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/j.chemosphere.2019.01.147","article-title":"Long-term effects of oxytetracycline exposure in zebrafish: a multi-level perspective","volume":"222","author":"Almeida","year":"2019","journal-title":"Chemosphere"},{"key":"2023062819293014500_bib4","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2023062819293014500_bib5","doi-asserted-by":"crossref","first-page":"e84772","DOI":"10.1371\/journal.pone.0084772","article-title":"Network analysis highlights complex interactions between pathogen, host and commensal microbiota","volume":"8","author":"Boutin","year":"2013","journal-title":"PLoS ONE"},{"key":"2023062819293014500_bib6","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat Methods"},{"key":"2023062819293014500_bib7","doi-asserted-by":"crossref","first-page":"R50","DOI":"10.1186\/gb-2011-12-5-r50","article-title":"Moving pictures of the human microbiome","volume":"12","author":"Caporaso","year":"2011","journal-title":"Genome Biol"},{"key":"2023062819293014500_bib8","doi-asserted-by":"crossref","first-page":"143","DOI":"10.2147\/IDR.S129055","article-title":"Microbiome disruption and recovery in the fish Gambusia affinis following exposure to broad-spectrum antibiotic","volume":"10","author":"Carlson","year":"2017","journal-title":"Infect Drug Resist"},{"key":"2023062819293014500_bib9","doi-asserted-by":"crossref","first-page":"3404","DOI":"10.3390\/ani11123404","article-title":"Exposure to oxy-tetracycline changes gut bacterial community composition in rainbow trout: a preliminary study","volume":"11","author":"Choudhury","year":"2021","journal-title":"Anim"},{"key":"2023062819293014500_bib10","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1016\/j.fsi.2015.05.010","article-title":"Modulation of immunity and gut microbiota after dietary administration of alginate encapsulated Shewanella putrefaciens Pdp11 to gilthead seabream (Sparus aurata L.)","volume":"45","author":"Cordero","year":"2015","journal-title":"Fish Shellfish Immunol"},{"key":"2023062819293014500_bib11","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1007\/s10311-013-0404-8","article-title":"Tetracycline antibiotics in the environment: a review","volume":"11","author":"Daghrir","year":"2013","journal-title":"Environ Chem Lett"},{"key":"2023062819293014500_bib12","first-page":"161","article-title":"Exploring fish microbial communities to mitigate emerging diseases in aquaculture","volume":"94","author":"de\u00a0Bruijn","year":"2018","journal-title":"FEMS Microbiol Ecol"},{"key":"2023062819293014500_bib13","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/j.aquaculture.2010.01.015","article-title":"Effects of mannan oligosaccharide (MOS) supplementation on growth performance, feed utilisation, intestinal histology and gut microbiota of gilthead sea bream (Sparus aurata)","volume":"300","author":"Dimitroglou","year":"2010","journal-title":"Aquaculture"},{"key":"2023062819293014500_bib14","doi-asserted-by":"crossref","first-page":"2878","DOI":"10.3389\/fimmu.2019.02878","article-title":"Viral-infected change of the digestive tract microbiota associated with mucosal immunity in teleost fish","volume":"10","author":"Dong","year":"2019","journal-title":"Front Immunol"},{"issue":"6","key":"2023062819293014500_bib15","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1038\/s41587-020-0548-6","article-title":"PICRUSt2 for prediction of metagenome functions","volume":"38","author":"Douglas","year":"2020","journal-title":"Nature biotechnology"},{"key":"2023062819293014500_bib16","doi-asserted-by":"crossref","first-page":"2506","DOI":"10.3390\/app10072506","article-title":"Effect of salinity on the gut microbiome of Pike Fry (Esox lucius)","volume":"10","author":"Dulski","year":"2020","journal-title":"Appl Sci"},{"key":"2023062819293014500_bib17","volume-title":"The State of World Fisheries and Aquaculture 2018 \u2013 Meeting the Sustainable Development Goals","author":"FAO","year":"2018"},{"key":"2023062819293014500_bib18","doi-asserted-by":"crossref","first-page":"1446","DOI":"10.3389\/fphys.2019.01446","article-title":"Impact of ocean acidification on the intestinal microbiota of the marine sea bream (Sparus aurata L.)","volume":"10","author":"Fonseca","year":"2019","journal-title":"Front Physiol"},{"key":"2023062819293014500_bib19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00248-020-01648-w","article-title":"A slimy business: the future of fish skin microbiome studies","volume":"82","author":"Gomez","year":"2021","journal-title":"Microb Ecol"},{"key":"2023062819293014500_bib20","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.fsi.2017.04.014","article-title":"Effects of dietary supplementation with fenugreek seeds, alone or in combination with probiotics, on gilthead seabream (Sparus aurata L.) skin mucosal immunity","volume":"65","author":"Guardiola","year":"2017","journal-title":"Fish Shellfish Immunol"},{"key":"2023062819293014500_bib21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/srep10561","article-title":"Exposure of clownfish larvae to suspended sediment levels found on the Great Barrier Reef: impacts on gill structure and microbiome","volume":"5","author":"Hess","year":"2015","journal-title":"Sci Rep"},{"key":"2023062819293014500_bib22","doi-asserted-by":"crossref","first-page":"e8705","DOI":"10.7717\/peerj.8705","article-title":"Alternative dietary protein and water temperature influence the skin and gut microbial communities of yellowtail kingfish (Seriola lalandi)","volume":"2020","author":"Horlick","year":"2020","journal-title":"PeerJ"},{"key":"2023062819293014500_bib23","doi-asserted-by":"crossref","first-page":"2429","DOI":"10.3389\/fmicb.2018.02429","article-title":"Probiotics as means of diseases control in aquaculture, a review of current knowledge and future perspectives","volume":"9","author":"Hoseinifar","year":"2018","journal-title":"Front Microbiol"},{"key":"2023062819293014500_bib24","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/s10123-002-0051-6","article-title":"Photobacterium damselae subsp. Piscicida: an integrated view of a bacterial fish pathogen","volume":"5","author":"Jes\u00fas","year":"2002","journal-title":"Int Microbiol"},{"key":"2023062819293014500_bib25","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gky962","article-title":"New approach for understanding genome variations in KEGG","volume":"47","author":"Kanehisa","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023062819293014500_bib26","doi-asserted-by":"crossref","first-page":"116760","DOI":"10.1016\/j.envpol.2021.116760","article-title":"Environmental concentrations of antibiotics alter the zebrafish gut microbiome structure and potential functions","volume":"278","author":"Kayani\u00a0M\u00a0ur","year":"2021","journal-title":"Environ Pollut"},{"key":"2023062819293014500_bib27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fimmu.2017.00559","article-title":"Under pressure: interactions between commensal microbiota and the teleost immune system","volume":"8","author":"Kelly","year":"2017","journal-title":"Front Immunol"},{"key":"2023062819293014500_bib28","doi-asserted-by":"crossref","first-page":"734330","DOI":"10.1016\/j.aquaculture.2019.734330","article-title":"Administration of antibiotics can cause dysbiosis in fish gut","volume":"512","author":"Kim","year":"2019","journal-title":"Aquaculture"},{"key":"2023062819293014500_bib29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13567-016-0383-4","article-title":"The impact of co-infections on fish: a review","volume":"47","author":"Kotob","year":"2016","journal-title":"Vet Res"},{"key":"2023062819293014500_bib30","doi-asserted-by":"crossref","first-page":"5112","DOI":"10.1128\/AEM.01043-13","article-title":"Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform","volume":"79","author":"Kozich","year":"2013","journal-title":"Appl Environ Microbiol"},{"key":"2023062819293014500_bib31","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s40168-020-0784-5","article-title":"Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system","volume":"8","author":"Krotman","year":"2020","journal-title":"Microbiome"},{"key":"2023062819293014500_bib32","article-title":"Introduction to the microbiome R package","author":"Lahti","year":"2018"},{"key":"2023062819293014500_bib33","volume-title":"The Long Term Economic and Ecological Impact of Larger Sustainable Aquaculture","author":"Lane","year":"2014"},{"key":"2023062819293014500_bib36","first-page":"1","article-title":"Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection","volume":"3","author":"Le\u00a0Luyer","year":"2021","journal-title":"Anim Microbiome"},{"key":"2023062819293014500_bib34","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/j.copbio.2012.08.005","article-title":"Bacteria as vitamin suppliers to their host: a gut microbiota perspective","volume":"24","author":"LeBlanc","year":"2013","journal-title":"Curr Opin Biotechnol"},{"key":"2023062819293014500_bib35","doi-asserted-by":"crossref","first-page":"2664","DOI":"10.3389\/fmicb.2017.02664","article-title":"The inner workings of the outer surface: skin and gill microbiota as indicators of changing gut health in yellowtail kingfish","volume":"8","author":"Legrand","year":"2018","journal-title":"Front Microbiol"},{"key":"2023062819293014500_bib37","doi-asserted-by":"crossref","first-page":"335","DOI":"10.4236\/aim.2014.47040","article-title":"The skin microbiome of Gambusia affinis is defined and selective","volume":"7","author":"Leonard","year":"2014","journal-title":"Adv Microbiol"},{"key":"2023062819293014500_bib38","first-page":"1","article-title":"The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels","volume":"6","author":"Liu","year":"2016","journal-title":"Sci Rep"},{"key":"2023062819293014500_bib39","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/srep43465","article-title":"Parasitism perturbs the mucosal microbiome of Atlantic Salmon","volume":"7","author":"Llewellyn","year":"2017","journal-title":"Sci Rep"},{"key":"2023062819293014500_bib51","doi-asserted-by":"crossref","first-page":"2588","DOI":"10.3389\/fmicb.2018.02588","article-title":"Exposure to antibiotics affects saponin immersion-induced immune stimulation and shift in microbial composition in zebrafish larvae","volume":"9","author":"L\u00f3pez\u00a0Nadal","year":"2018","journal-title":"Front Microbiol"},{"key":"2023062819293014500_bib42","doi-asserted-by":"crossref","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLoS ONE"},{"key":"2023062819293014500_bib41","doi-asserted-by":"crossref","first-page":"e1003531","DOI":"10.1371\/journal.pcbi.1003531","article-title":"Waste not, want not: why rarefying microbiome data is inadmissible","volume":"10","author":"McMurdie","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"2023062819293014500_bib40","first-page":"93","article-title":"In vitro selection of bacteria and isolation of probionts from farmed Sparus aurata with potential for use as probiotics","volume":"1","author":"Mancuso","year":"2015","journal-title":"Int J Anim Biol"},{"key":"2023062819293014500_bib43","doi-asserted-by":"crossref","DOI":"10.1002\/9781118897263","volume-title":"Aquaculture Nutrition: Gut Health, Probiotics and Prebiotics","author":"Merrifield","year":"2014"},{"key":"2023062819293014500_bib44","doi-asserted-by":"crossref","first-page":"35","DOI":"10.3354\/dao02563","article-title":"\u2018Candidatus Branchiomonas cysticola\u2019 is a common agent of epitheliocysts in seawater-farmed Atlantic salmon Salmo salar in Norway and Ireland","volume":"103","author":"Mitchell","year":"2013","journal-title":"Dis Aquat Organ"},{"key":"2023062819293014500_bib45","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1007\/s10482-020-01391-9","article-title":"Insights into the microbiome of farmed Asian sea bass (Lates calcarifer) with symptoms of tenacibaculosis and description of Tenacibaculum singaporense sp. nov","volume":"113","author":"Miyake","year":"2020","journal-title":"Antonie Van Leeuwenhoek"},{"key":"2023062819293014500_bib46","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1577\/H07-043.1","article-title":"Oxytetracycline treatment reduces bacterial diversity of intestinal microbiota of Atlantic salmon","volume":"20","author":"Navarrete","year":"2008","journal-title":"J Aquat Anim Health"},{"key":"2023062819293014500_bib47","doi-asserted-by":"crossref","first-page":"129","DOI":"10.3390\/md14070129","article-title":"Spotlight on antimicrobial metabolites from the marine bacteria Pseudoalteromonas: chemodiversity and ecological significance","volume":"14","author":"Offret","year":"2016","journal-title":"Mar Drugs"},{"key":"2023062819293014500_bib48","article-title":"The vegan package: community ecology package, version 1.13-1","author":"Oksanen","year":"2008"},{"key":"2023062819293014500_bib49","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/j.ygcen.2010.07.017","article-title":"The endocrinology of stress in fish: an environmental perspective","volume":"170","author":"Pankhurst","year":"2011","journal-title":"Gen Comp Endocrinol"},{"key":"2023062819293014500_bib50","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.3390\/antibiotics10101213","article-title":"Investigating the effect of an oxytetracycline treatment on the gut microbiome and antimicrobial resistance gene dynamics in Nile Tilapia (Oreochromis niloticus)","volume":"10","author":"Payne","year":"2021","journal-title":"Antibiot"},{"key":"2023062819293014500_bib52","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1016\/j.fsi.2013.02.007","article-title":"High mortality of juvenile gilthead sea bream (Sparus aurata) from photobacteriosis is associated with alternative macrophage activation and anti-inflammatory response: results of gene expression profiling of early responses in the head kidney","volume":"34","author":"Pellizzari","year":"2013","journal-title":"Fish Shellfish Immunol"},{"key":"2023062819293014500_bib53","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.aquaculture.2007.06.015","article-title":"Occurrence and virulence of Pseudoalteromonas spp. in cultured gilthead sea bream (Sparus aurata L.) and European sea bass (Dicentrarchus labrax L.). Molecular and phenotypic characterisation of P. undina strain U58","volume":"271","author":"Pujalte","year":"2007","journal-title":"Aquaculture"},{"key":"2023062819293014500_bib54","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1016\/j.fsi.2017.09.043","article-title":"Ammonia exposure alters the expression of immune-related and antioxidant enzymes-related genes and the gut microbial community of crucian carp (Carassius auratus)","volume":"70","author":"Qi","year":"2017","journal-title":"Fish Shellfish Immunol"},{"key":"2023062819293014500_bib55","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023062819293014500_bib76","article-title":"R: a language and environment for statistical computing","author":"R Core Team","year":"2012"},{"key":"2023062819293014500_bib56","doi-asserted-by":"crossref","first-page":"e0172856","DOI":"10.1371\/journal.pone.0172856","article-title":"Salmonid alphavirus infection causes skin dysbiosis in Atlantic salmon (Salmo salar L.) post-smolts","volume":"12","author":"Reid","year":"2017","journal-title":"PLoS ONE"},{"key":"2023062819293014500_bib57","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1111\/raq.12523","article-title":"Best therapeutic practices for the use of antibacterial agents in finfish aquaculture: a particular view on European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata) in Mediterranean aquaculture","volume":"13","author":"Rigos","year":"2021","journal-title":"Rev Aquac"},{"key":"2023062819293014500_bib58","first-page":"1","article-title":"Effects of hydrolyzed fish protein and autolyzed yeast as substitutes of fishmeal in the gilthead sea bream (Sparus aurata) diet, on fish intestinal microbiome","volume":"16","author":"Rimoldi","year":"2020","journal-title":"BMC Vet Res"},{"key":"2023062819293014500_bib59","doi-asserted-by":"crossref","first-page":"e5355","DOI":"10.7717\/peerj.5355","article-title":"Effect of a specific composition of short- and medium-chain fatty acid 1-monoglycerides on growth performances and gut microbiota of gilthead sea bream (Sparus aurata)","volume":"2018","author":"Rimoldi","year":"2018","journal-title":"PeerJ"},{"key":"2023062819293014500_bib60","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.marpolbul.2016.02.001","article-title":"Multidrug-resistant Vibrio associated with an estuary affected by shrimp farming in northeastern Brazil","volume":"105","author":"Rocha","year":"2016","journal-title":"Mar Pollut Bull"},{"key":"2023062819293014500_bib61","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s42523-020-00072-2","article-title":"Effects of aging on the skin and gill microbiota of farmed seabass and seabream","volume":"3","author":"Rosado","year":"2021","journal-title":"Anim Microbiome"},{"key":"2023062819293014500_bib62","first-page":"1","article-title":"Monitoring infection and antibiotic treatment in the skin microbiota of farmed European seabass (Dicentrarchus labrax) fingerlings","volume":"83","author":"Rosado","year":"2021","journal-title":"Microb Ecol"},{"key":"2023062819293014500_bib63","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s43705-021-00019-x","article-title":"Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics","volume":"1","author":"Rosado","year":"2021","journal-title":"ISME Commun"},{"key":"2023062819293014500_bib64","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-55314-4","article-title":"Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax)","volume":"9","author":"Rosado","year":"2019","journal-title":"Sci Rep"},{"key":"2023062819293014500_bib65","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40168-019-0632-7","article-title":"Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus","volume":"7","author":"S\u00e1enz","year":"2019","journal-title":"Microbiome"},{"key":"2023062819293014500_bib66","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.dci.2017.02.010","article-title":"Omics in fish mucosal immunity","volume":"75","author":"Salinas","year":"2017","journal-title":"Dev Comp Immunol"},{"key":"2023062819293014500_bib67","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1111\/faf.12158","article-title":"An overview of stress physiology of fish transport: changes in water quality as a function of transport duration","volume":"17","author":"Sampaio","year":"2016","journal-title":"Fish Fish"},{"issue":"3","key":"2023062819293014500_bib68","doi-asserted-by":"crossref","first-page":"1062","DOI":"10.1111\/are.15648","article-title":"Effects of live feed manipulation with algal-derived antimicrobial metabolites on fish larvae microbiome assembly: a molecular-based assessment","volume":"53","author":"Sanches-Fernandes","year":"2021","journal-title":"Aquac Res"},{"key":"2023062819293014500_bib69","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.3390\/ijms23031561","article-title":"Short-term immune responses of Gilthead Seabream (Sparus aurata) juveniles against Photobacterium damselae subsp. Piscicida","volume":"23","author":"Santos","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2023062819293014500_bib70","doi-asserted-by":"crossref","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol"},{"key":"2023062819293014500_bib71","doi-asserted-by":"crossref","first-page":"358","DOI":"10.3389\/fmicb.2021.567408","article-title":"Microbiome composition and function in aquatic vertebrates: small organisms making big impacts on aquatic animal health","volume":"12","author":"Sehnal","year":"2021","journal-title":"Front Microbiol"},{"key":"2023062819293014500_bib72","doi-asserted-by":"crossref","first-page":"1791","DOI":"10.1038\/ismej.2015.223","article-title":"Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular \u03b2-proteobacteria","volume":"10","author":"Seth-Smith","year":"2016","journal-title":"ISME J"},{"key":"2023062819293014500_bib73","doi-asserted-by":"crossref","first-page":"987","DOI":"10.3390\/microorganisms9050987","article-title":"The effect of antimicrobial treatment upon the gill bacteriome of Atlantic salmon (Salmo salar L.) and progression of amoebic gill disease (AGD) in vivo","volume":"9","author":"Slinger","year":"2021","journal-title":"Microorg"},{"key":"2023062819293014500_bib74","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1111\/jfb.13377","article-title":"Stress and welfare in ornamental fishes: what can be learned from aquaculture?","volume":"91","author":"Stevens","year":"2017","journal-title":"J Fish Biol"},{"key":"2023062819293014500_bib75","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/srep32032","article-title":"PH drop impacts differentially skin and gut microbiota of the Amazonian fish tambaqui (Colossoma macropomum)","volume":"6","author":"Sylvain","year":"2016","journal-title":"Sci Rep"},{"key":"2023062819293014500_bib77","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1016\/j.dci.2011.07.002","article-title":"Stress and immune modulation in fish","volume":"35","author":"Tort","year":"2011","journal-title":"Dev Comp Immunol"},{"key":"2023062819293014500_bib78","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1007\/s00203-018-1615-y","article-title":"Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome","volume":"201","author":"Tyagi","year":"2019","journal-title":"Arch Microbiol"},{"key":"2023062819293014500_bib79","article-title":"Interpopulation variation in the Atlantic salmon microbiome reflects environmental and genetic diversity","volume":"84","author":"Uren\u00a0Webster","year":"2018","journal-title":"Appl Environ Microbiol"},{"key":"2023062819293014500_bib80","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.3389\/fmicb.2020.01621","article-title":"Cortisol-related signatures of stress in the fish microbiome","volume":"0","author":"Uren\u00a0Webster","year":"2020","journal-title":"Front Microbiol"},{"key":"2023062819293014500_bib81","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1080\/23308249.2019.1643288","article-title":"Host-associated probiotics: a key factor in sustainable aquaculture","volume":"28","author":"Van\u00a0Doan","year":"2019","journal-title":"Rev Fish Sci Aquac"},{"key":"2023062819293014500_bib82","doi-asserted-by":"crossref","first-page":"2098","DOI":"10.1093\/bioinformatics\/btn358","article-title":"Phylocom: software for the analysis of phylogenetic community structure and trait evolution","volume":"24","author":"Webb","year":"2008","journal-title":"Bioinforma Appl Note"},{"key":"2023062819293014500_bib83","doi-asserted-by":"crossref","first-page":"1562","DOI":"10.3389\/fmicb.2020.01562","article-title":"The beta-diversity of Siganus fuscescens-associated microbial communities from different habitats increases with body weight","volume":"11","author":"Wu","year":"2020","journal-title":"Front Microbiol"},{"key":"2023062819293014500_bib84","doi-asserted-by":"crossref","first-page":"2972","DOI":"10.3389\/fimmu.2018.02972","article-title":"The change of teleost skin commensal microbiota is associated with skin mucosal transcriptomic responses during parasitic infection by Ichthyophthirius multifillis","volume":"9","author":"Zhang","year":"2018","journal-title":"Front Immunol"},{"key":"2023062819293014500_bib85","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.envpol.2017.12.073","article-title":"Environmental concentrations of antibiotics impair zebrafish gut health","volume":"235","author":"Zhou","year":"2018","journal-title":"Environ Pollut"}],"container-title":["FEMS Microbes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/femsmicrobes\/advance-article-pdf\/doi\/10.1093\/femsmc\/xtad011\/50514386\/xtad011.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/femsmicrobes\/article-pdf\/doi\/10.1093\/femsmc\/xtad011\/50733813\/xtad011.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/femsmicrobes\/article-pdf\/doi\/10.1093\/femsmc\/xtad011\/50733813\/xtad011.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,28]],"date-time":"2023-06-28T21:28:31Z","timestamp":1687987711000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/femsmicrobes\/article\/doi\/10.1093\/femsmc\/xtad011\/7189861"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023]]},"references-count":85,"URL":"https:\/\/doi.org\/10.1093\/femsmc\/xtad011","relation":{},"ISSN":["2633-6685"],"issn-type":[{"value":"2633-6685","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023]]},"published":{"date-parts":[[2023]]},"article-number":"xtad011"}}