{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T07:45:19Z","timestamp":1790667919566,"version":"4.1.0"},"reference-count":145,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,10,5]],"date-time":"2021-10-05T00:00:00Z","timestamp":1633392000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["652831"],"award-info":[{"award-number":["652831"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["773330"],"award-info":[{"award-number":["773330"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Ministerio de Ciencia e Innovaci\u00f3n","doi-asserted-by":"publisher","award":["RTI2018-094128-B-I00"],"award-info":[{"award-number":["RTI2018-094128-B-I00"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011033","name":"Agencia Estatal de Investigaci\u00f3n","doi-asserted-by":"publisher","award":["RYC2018-024049-I\/AEI\/10.13039\/501100011033"],"award-info":[{"award-number":["RYC2018-024049-I\/AEI\/10.13039\/501100011033"]}],"id":[{"id":"10.13039\/501100011033","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Physiol."],"abstract":"<jats:p>New types of fish feed based on processed animal proteins (PAPs), insect meal, yeast, and microbial biomasses have been used with success in gilthead sea bream. However, some drawback effects on feed conversion and inflammatory systemic markers were reported in different degrees with PAP- and non-PAP-based feed formulations. Here, we focused on the effects of control and two experimental diets on gut mucosal-adherent microbiota, and how it correlated with host transcriptomics at the local (intestine) and systemic (liver and head kidney) levels. The use of tissue-specific PCR-arrays of 93 genes in total rendered 13, 12, and 9 differentially expressed (DE) genes in the intestine, liver, and head kidney, respectively. Illumina sequencing of gut microbiota yielded a mean of 125,350 reads per sample, assigned to 1,281 operational taxonomic unit (OTUs). Bacterial richness and alpha diversity were lower in fish fed with the PAP diet, and discriminant analysis displayed 135 OTUs driving the separation between groups with 43 taxa correlating with 27 DE genes. The highest expression of intestinal <jats:italic>pcna<\/jats:italic> and <jats:italic>alpi<\/jats:italic> was achieved in PAP fish with intermediate values in non-PAP, being the pro-inflammatory action of <jats:italic>alpi<\/jats:italic> associated with the presence of <jats:italic>Psychrobacter piscatorii<\/jats:italic>. The intestinal <jats:italic>muc13<\/jats:italic> gene was down-regulated in non-PAP fish, with this gene being negatively correlated with anaerobic (Chloroflexi and <jats:italic>Anoxybacillus<\/jats:italic>) and metal-reducing (<jats:italic>Pelosinus<\/jats:italic> and <jats:italic>Psychrosinus<\/jats:italic>) bacteria. Other inflammatory markers (<jats:italic>igm, il8, tnf<\/jats:italic>\u03b1) were up-regulated in PAP fish, positively correlating the intestinal <jats:italic>igm<\/jats:italic> gene with the inflammasome activator <jats:italic>Escherichia\/Shigella<\/jats:italic>, whereas the systemic expression of <jats:italic>il8<\/jats:italic> and <jats:italic>tnf<\/jats:italic>\u03b1 was negatively correlated with the Bacilli class in PAP fish and positively correlated with <jats:italic>Paracoccus yeei<\/jats:italic> in non-PAP fish. Overall changes in the expression pattern of <jats:italic>il10<\/jats:italic>, galectins (<jats:italic>lgals1, lgals8<\/jats:italic>), and toll-like receptors (<jats:italic>tlr2, tlr5, tlr9<\/jats:italic>) reinforced the anti-inflammatory profile of fish fed with the non-PAP diet, with these gene markers being associated with a wide range of OTUs. A gut microbiota-liver axis was also established, linking the microbial generation of short chain fatty acids with the fueling of <jats:italic>scd1<\/jats:italic>- and <jats:italic>elovl6<\/jats:italic>-mediated lipogenesis. In summary, by correlating the microbiome with host gene expression, we offer new insights in the evaluation of fish diets promoting gut and metabolism homeostasis, and ultimately, the health of farmed fish.<\/jats:p>","DOI":"10.3389\/fphys.2021.748265","type":"journal-article","created":{"date-parts":[[2021,10,5]],"date-time":"2021-10-05T08:25:01Z","timestamp":1633422301000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":57,"title":["Cross-Talk Between Intestinal Microbiota and Host Gene Expression in Gilthead Sea Bream (Sparus aurata) Juveniles: Insights in Fish Feeds for Increased Circularity and Resource Utilization"],"prefix":"10.3389","volume":"12","author":[{"given":"Fernando","family":"Naya-Catal\u00e0","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriella","family":"do Vale Pereira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Carla","family":"Piazzon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Margarida","family":"Fernandes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josep Alvar","family":"Calduch-Giner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ariadna","family":"Sitj\u00e0-Bobadilla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis E. C.","family":"Concei\u00e7\u00e3o","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaume","family":"P\u00e9rez-S\u00e1nchez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2021,10,5]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B2","doi-asserted-by":"publisher","first-page":"444","DOI":"10.3389\/fcimb.2019.00444","article-title":"Age-related changes in the gut microbiota modify brain lipid composition","volume":"9","author":"Albouery","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.aquaculture.2015.11.018","article-title":"Hydrolysed wheat gluten as part of a diet based on animal and plant proteins supports good growth performance of Asian seabass (Lates calcarifer), without impairing intestinal morphology or microbiota","volume":"453","author":"Apper","year":"2016","journal-title":"Aquaculture"},{"key":"B5","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1111\/anu.13007","article-title":"Alternative formulations for gilthead seabream diets: towards a more sustainable production","volume":"26","author":"Arag\u00e3o","year":"2020","journal-title":"Aquac. Nutr."},{"key":"B6","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1023\/A:1007872929847","article-title":"Absorption of glucose, amino acids, and dipeptides by the intestines of Atlantic salmon (Salmo salar L.)","volume":"22","author":"Bakke-McKellep","year":"2000","journal-title":"Fish Physiol. Biochem."},{"key":"B7","doi-asserted-by":"publisher","first-page":"659567","DOI":"10.3389\/fphys.2021.659567","article-title":"The use of defatted Tenebrio molitor larvae meal as a main protein source is supported in European sea bass (Dicentrarchus labrax) by data on growth performance, lipid metabolism and flesh quality","volume":"12","author":"Basto","year":"2021","journal-title":"Front. Physiol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"e0166379","DOI":"10.1371\/journal.pone.0166379","article-title":"Ontogenetic characterization of the intestinal microbiota of channel catfish through 16S rRNA gene sequencing reveals insights on temporal shifts and the influence of environmental microbes","volume":"11","author":"Bledsoe","year":"2016","journal-title":"PLoS ONE"},{"key":"B9","doi-asserted-by":"publisher","first-page":"1195","DOI":"10.1016\/j.dci.2011.02.010","article-title":"PAMPs, PRRs and the genomics of gram negative bacterial recognition in fish","volume":"35","author":"Bolta\u00f1a","year":"2011","journal-title":"Dev. Comp. Immunol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1016\/j.aquaculture.2017.10.025","article-title":"Soybean meal-induced enteritis in Atlantic salmon (Salmo salar) and Chinook salmon (Oncorhynchus tshawytscha) but not in pink salmon (O. gorbuscha)","volume":"483","author":"Booman","year":"2018","journal-title":"Aquaculture"},{"key":"B11","doi-asserted-by":"publisher","first-page":"30046","DOI":"10.1038\/srep30046","article-title":"Probiotic modulation of the microbiota-gut-brain axis and behaviour in zebrafish","volume":"6","author":"Borrelli","year":"2016","journal-title":"Sci. Rep."},{"key":"B12","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1002\/path.2287","article-title":"TNF-mediated inflammatory disease","volume":"214","author":"Bradley","year":"2008","journal-title":"J. Pathol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"S25","DOI":"10.1097\/MCG.0000000000000391","article-title":"Role of gut microbiota in liver disease","volume":"49","author":"Brenner","year":"2015","journal-title":"J. Clin. Gastroenterol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1186\/1471-2164-14-178","article-title":"Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts","volume":"14","author":"Calduch-Giner","year":"2013","journal-title":"BMC Genomics"},{"key":"B15","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/j.fsi.2018.05.022","article-title":"Replacement of fishmeal by Spirulina Arthrospira platensis affects growth, immune related-gene expression in gibel carp (Carassius auratus gibelio var. CAS III), and its challenge against Aeromonas hydrophila infection","volume":"79","author":"Cao","year":"2018","journal-title":"Fish Shellfish Immunol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1093\/glycob\/cwu060","article-title":"Galectin-8 elicits pro-inflammatory activities in the endothelium","volume":"24","author":"Cattaneo","year":"2014","journal-title":"Glycobiology"},{"key":"B17","doi-asserted-by":"publisher","first-page":"1678","DOI":"10.3389\/fimmu.2017.01678","article-title":"Protective microbiota: from localized to long-reaching co-immunity","volume":"8","author":"Chiu","year":"2017","journal-title":"Front. Immunol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"10689","DOI":"10.1074\/jbc.274.16.10689","article-title":"Toll-like receptor-4 mediates lipopolysaccharide-induced signal transduction","volume":"274","author":"Chow","year":"1999","journal-title":"J. Biol. Chem."},{"key":"B19","doi-asserted-by":"publisher","first-page":"D633","DOI":"10.1093\/nar\/gkt1244","article-title":"Ribosomal database project: data and tools for high throughput rRNA analysis","volume":"42","author":"Cole","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"B20","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1007\/s10695-011-9592-y","article-title":"Dietary nitrogen and fish welfare","volume":"38","author":"Concei\u00e7\u00e3o","year":"2012","journal-title":"Fish Physiol. Biochem."},{"key":"B21","doi-asserted-by":"publisher","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":"B22","doi-asserted-by":"publisher","first-page":"13877","DOI":"10.1038\/s41598-017-13249-8","article-title":"Seawater transfer alters the intestinal microbiota profiles of Atlantic salmon (Salmo salar L.)","volume":"7","author":"Dehler","year":"2017","journal-title":"Sci. Rep."},{"key":"B23","doi-asserted-by":"publisher","first-page":"100031","DOI":"10.1016\/j.wroa.2019.100031","article-title":"Mixed culture purple phototrophic bacteria is an effective fishmeal replacement in aquaculture","volume":"4","author":"Delamare-Deboutteville","year":"2019","journal-title":"Water Res."},{"key":"B24","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1078\/0723-2020-00006","article-title":"Psychrobacter proteolyticus sp. nov., a psychrotrophic, halotolerant bacterium isolated from the Antarctic krill Euphausia superba Dana, excreting a cold-adapted metalloprotease","volume":"24","author":"Denner","year":"2001","journal-title":"Syst. Appl. Microbiol"},{"key":"B25","doi-asserted-by":"publisher","first-page":"1272","DOI":"10.1017\/S1751731107000596","article-title":"Reduced lipid intake leads to changes in digestive enzymes in the intestine but has minor effect on key enzymes of hepatic intermediary metabolism in rainbow trout (Oncorhynchus mykiss)","volume":"1","author":"Ducasse-Cabanot","year":"2007","journal-title":"Animal"},{"key":"B26","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1186\/s40168-020-00938-2","article-title":"Association of gut microbiota with metabolism in juvenile Atlantic salmon","volume":"8","author":"Dvergedal","year":"2020","journal-title":"Microbiome"},{"key":"B27","doi-asserted-by":"publisher","first-page":"4194","DOI":"10.1038\/s41598-020-60325-7","article-title":"Replacing fishmeal with plant protein in Atlantic salmon (Salmo salar) diets by supplementation with fish protein hydrolysate","volume":"10","author":"Egerton","year":"2020","journal-title":"Sci. Rep"},{"key":"B28","doi-asserted-by":"publisher","first-page":"238","DOI":"10.4103\/epj.epj_65_19","article-title":"Production and one-step purification of serratiopeptidase enzyme from Serratia marcescens with potent anti-inflammatory and antioxidant power","volume":"19","author":"El-Abd","year":"2020","journal-title":"Egypt Pharmaceut. J."},{"key":"B29","doi-asserted-by":"publisher","first-page":"e0166564","DOI":"10.1371\/journal.pone.0166564","article-title":"Dietary butyrate helps to restore the intestinal status of a marine teleost (Sparus aurata) fed extreme diets low in fish meal and fish oil","volume":"11","author":"Estensoro","year":"2016","journal-title":"PLoS ONE"},{"key":"B30","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1016\/j.fsi.2012.05.029","article-title":"Modulation of the IgM gene expression and IgM immunoreactive cell distribution by the nutritional background in gilthead sea bream (Sparus aurata) challenged with Enteromyxum leei (Myxozoa)","volume":"33","author":"Estensoro","year":"2012","journal-title":"Fish Shellfish Immunol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"e0136389","DOI":"10.1371\/journal.pone.0136389","article-title":"Impact of fishmeal replacement in diets for gilthead sea bream (Sparus aurata) on the gastrointestinal microbiota determined by pyrosequencing the 16S rRNA gene","volume":"10","author":"Estruch","year":"2015","journal-title":"PLoS ONE"},{"key":"B32","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1039\/c9mt00231f","article-title":"The role of metal ion binding in the antioxidant mechanisms of reduced and oxidized glutathione in metal-mediated oxidative DNA damage","volume":"12","author":"Eteshola","year":"2020","journal-title":"Metallomics"},{"key":"B33","first-page":"200","article-title":"Evaluation of growth performance, oxidative stress and immune response response in gilthead seabream fed novel feed formulations","author":"Fernandes","year":"2021","journal-title":"Proceedings of the Journal of Abstracts of the Aquaculture Europe 2020 Congress"},{"key":"B34","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1016\/j.jclepro.2019.05.012","article-title":"The use of insect meal as a sustainable feeding alternative in aquaculture: current situation, Spanish consumers' perceptions and willingness to pay","volume":"229","author":"Ferrer Llagostera","year":"2019","journal-title":"J. Clean. Prod."},{"key":"B35","doi-asserted-by":"publisher","first-page":"625297","DOI":"10.3389\/fimmu.2021.625297","article-title":"Diet, immunity, and microbiota interactions: an integrative analysis of the intestine transcriptional response and microbiota modulation in gilthead seabream (Sparus aurata) fed an essential oils-based functional diet","volume":"12","author":"Firmino","year":"2021","journal-title":"Front. Immunol."},{"key":"B36","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1038\/mi.2013.13","article-title":"The role of pattern recognition receptors in intestinal inflammation","volume":"6","author":"Fukata","year":"2013","journal-title":"Mucosal Immunol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"e02615","DOI":"10.1128\/AEM.02615-16","article-title":"Alternative protein sources in the diet modulate microbiota and functionality in the distal intestine of Atlantic salmon (Salmo salar)","volume":"83","author":"Gajardo","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1016\/j.aquaculture.2015.06.033","article-title":"A new view of the fish gut microbiome: advances from next-generation sequencing","volume":"448","author":"Ghanbari","year":"2015","journal-title":"Aquaculture"},{"key":"B39","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/j.micpath.2019.04.035","article-title":"Antioxidant, antibacterial, and antiadhesive activities of biosurfactants isolated from Bacillus strains","volume":"132","author":"Giri","year":"2019","journal-title":"Microb. Pathog."},{"key":"B40","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1017\/S0007114517000228","article-title":"Olive oil bioactive compounds increase body weight, and improve gut health and integrity in gilthead sea bream (Sparus aurata)","volume":"117","author":"Gisbert","year":"2017","journal-title":"Br. J. Nutr."},{"key":"B41","doi-asserted-by":"publisher","first-page":"564","DOI":"10.4049\/jimmunol.1601621","article-title":"Host-microbiota interactions shape local and systemic inflammatory diseases","volume":"198","author":"Grigg","year":"2017","journal-title":"J. Immunol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1385\/1-59259-766-1-491","article-title":"Microflora of the gastrointestinal tract: a review","volume":"268","author":"Hao","year":"2004","journal-title":"Methods Mol. Biol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/s12865-015-0083-2","article-title":"Systemic effects of gut microbiota and its relationship with disease and modulation","volume":"16","author":"Ho","year":"2015","journal-title":"BMC Immunol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1016\/j.oneear.2019.10.018","article-title":"The future of aquatic protein: implications for protein sources in aquaculture diets","volume":"1","author":"Hua","year":"2019","journal-title":"One Earth"},{"key":"B45","doi-asserted-by":"publisher","first-page":"e0166104","DOI":"10.1371\/journal.pone.0166104","article-title":"Piphillin: improved prediction of metagenomic content by direct inference from human microbiomes","volume":"11","author":"Iwai","year":"2016","journal-title":"PLoS ONE"},{"key":"B46","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.fm.2011.07.005","article-title":"Species diversity and metabolic impact of the microbiota are low in spontaneously acidified Belgian sausages with an added starter culture of Staphylococcus carnosus","volume":"29","author":"Janssens","year":"2012","journal-title":"Food Microbiol."},{"key":"B47","doi-asserted-by":"publisher","first-page":"461","DOI":"10.3389\/fimmu.2014.00461","article-title":"Toll-like receptor signaling pathways","volume":"5","author":"Kawasaki","year":"2014","journal-title":"Front. Immunol."},{"key":"B48","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1128\/IAI.01239-06","article-title":"Serratia marcescens serralysin induces inflammatory responses through protease-activated receptor 2","volume":"75","author":"Kida","year":"2007","journal-title":"Infect. Immun."},{"key":"B49","doi-asserted-by":"publisher","first-page":"F857","DOI":"10.1152\/ajprenal.00513.2015","article-title":"Resistant starch alters gut microbiome and metabolomic profiles concurrent with amelioration of chronic kidney disease in rats","volume":"310","author":"Kieffer","year":"2016","journal-title":"Am. J. Physiol. Renal Physiol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"3760","DOI":"10.1038\/s41467-018-05767-4","article-title":"The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice","volume":"9","author":"Kindt","year":"2018","journal-title":"Nat. Commun."},{"key":"B51","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/j.mimet.2017.01.016","article-title":"Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet","volume":"135","author":"Koo","year":"2017","journal-title":"J. Microbiol. Methods"},{"key":"B52","doi-asserted-by":"publisher","first-page":"3887","DOI":"10.1021\/jf506242t","article-title":"Soya saponins induce enteritis in Atlantic salmon (Salmo salar L.)","volume":"63","author":"Krogdahl","year":"2015","journal-title":"J. Agric. Food Chem."},{"key":"B53","doi-asserted-by":"publisher","first-page":"55","DOI":"10.3390\/metabo11010055","article-title":"Linking gut microbiome and lipid metabolism: moving beyond associations","volume":"11","author":"Lamichhane","year":"2021","journal-title":"Metabolites"},{"key":"B54","doi-asserted-by":"publisher","first-page":"16209","DOI":"10.1073\/pnas.0705984104","article-title":"Gel-forming mucins appeared earlyin metazoan evolution","volume":"104","author":"Lang","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B55","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1016\/j.cyto.2014.11.027","article-title":"The role of IL-10 in microbiome-associated immune modulation and disease tolerance","volume":"75","author":"Levast","year":"2015","journal-title":"Cytokine"},{"key":"B56","doi-asserted-by":"publisher","first-page":"8292","DOI":"10.1038\/ncomms9292","article-title":"The outer mucus layer hosts a distinct intestinal microbial niche","volume":"6","author":"Li","year":"2015","journal-title":"Nat. Commun."},{"key":"B57","doi-asserted-by":"publisher","first-page":"1087","DOI":"10.1016\/j.biocel.2012.03.017","article-title":"Metabolic responses to ethanol in Saccharomyces cerevisiae using a gas chromatography tandem mass spectrometry-based metabolomics approach","volume":"44","author":"Li","year":"2012","journal-title":"Int. J. Biochem. Cell Biol."},{"key":"B58","doi-asserted-by":"publisher","first-page":"114832","DOI":"10.1016\/j.envpol.2020.114832","article-title":"Dietary administration of probiotic Lactobacillus rhamnosus modulates the neurological toxicities of perfluorobutanesulfonate in zebrafish","volume":"265","author":"Liu","year":"2020","journal-title":"Environ. Pollut."},{"key":"B59","doi-asserted-by":"publisher","first-page":"5393","DOI":"10.3390\/ijms22105393","article-title":"Transcriptome and metabolomic analyses reveal regulatory networks controlling maize stomatal development in response to blue light","volume":"22","author":"Liu","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"B60","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2-\u0394\u0394CT method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"B61","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"B62","doi-asserted-by":"publisher","first-page":"R815","DOI":"10.1016\/j.cub.2014.06.068","article-title":"Epithelial homeostasis","volume":"24","author":"Macara","year":"2014","journal-title":"Curr. Biol."},{"key":"B63","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1016\/j.aquaculture.2017.04.021","article-title":"Black soldier fly (Hermetia illucens) pre-pupae meal as a fish meal replacement in diets for European seabass (Dicentrarchus labrax)","volume":"476","author":"Magalh\u00e3es","year":"2017","journal-title":"Aquaculture"},{"key":"B64","doi-asserted-by":"publisher","first-page":"897","DOI":"10.1242\/bio.024299","article-title":"Dietary supplementation of heat-treated Gracilaria and Ulva seaweeds enhanced acute hypoxia tolerance in gilthead sea bream (Sparus aurata)","volume":"6","author":"Magnoni","year":"2017","journal-title":"Biol. Open"},{"key":"B65","doi-asserted-by":"publisher","first-page":"G433","DOI":"10.1152\/ajpgi.00466.2002","article-title":"Rat enterocytes secrete SLPs containing alkaline phosphatase and cubilin in response to corn oil feeding","volume":"285","author":"Mahmood","year":"2003","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"735705","DOI":"10.1016\/j.aquaculture.2020.7357","article-title":"Replacement of fish oil by soybean oil and microalgal meals in diets for Totoaba macdonaldi (Gilbert, 1890) juveniles","volume":"529","author":"Maldonado-Oth\u00f3n","year":"2020","journal-title":"Aquaculture"},{"key":"B67","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1111\/2041-210X.13115","article-title":"Methods for normalizing microbiome data: an ecological perspective","volume":"10","author":"McKnight","year":"2019","journal-title":"Methods Ecol. Evol."},{"key":"B68","doi-asserted-by":"publisher","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":"B69","doi-asserted-by":"publisher","first-page":"e0197256","DOI":"10.1371\/journal.pone.0197256","article-title":"Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus)","volume":"13","author":"Mekuchi","year":"2018","journal-title":"PLoS ONE"},{"key":"B70","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1089\/jir.2019.0011","article-title":"Mechanisms by which the gut microbiota influences cytokine production and modulates host inflammatory responses","volume":"39","author":"Mendes","year":"2019","journal-title":"J. Interf. Cytok. Res."},{"key":"B71","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1007\/s11302-005-5435-6","article-title":"Alkaline Phosphatases: structure, substrate specificity and functional relatedness to other members of a large superfamily of enzymes","volume":"2","author":"Mill\u00e1n","year":"2006","journal-title":"Purinergic Signal."},{"key":"B72","doi-asserted-by":"publisher","first-page":"1334","DOI":"10.1111\/jam.13690","article-title":"Bacillus probiotics: an alternative to antibiotics for livestock production","volume":"124","author":"Mingmongkolchai","year":"2018","journal-title":"J. Appl. Microbiol."},{"key":"B73","doi-asserted-by":"publisher","first-page":"659519","DOI":"10.3389\/fmars.2021.659519","article-title":"Effects of nisin-producing Lactococcus lactis strain used as probiotic on gilthead sea bream (Sparus aurata) growth, gut microbiota, and transcriptional response","volume":"8","author":"Moroni","year":"2021","journal-title":"Front. Mar. Sci."},{"key":"B74","doi-asserted-by":"publisher","first-page":"25038","DOI":"10.1074\/jbc.M112.374041","article-title":"Lipolytic products activate peroxisome proliferator-activated receptor (PPAR) \u03b1 and \u03b4 in brown adipocytes to match fatty acid oxidation with supply","volume":"287","author":"Mottillo","year":"2012","journal-title":"J. Biol. Chem."},{"key":"B75","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1016\/j.fsi.2010.02.017","article-title":"Probiotics and immunity: a fish perspective","volume":"29","author":"Nayak","year":"2010","journal-title":"Fish Shellfish Immunol."},{"key":"B76","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1007\/s40071-017-0182-1","article-title":"Alteration in expression of atrogenes and IGF-1 induced by fasting in Nile tilapia Oreochromis niloticus juveniles","volume":"9","author":"Nebo","year":"2017","journal-title":"Int. Aquat. Res"},{"key":"B77","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1007\/s00439-020-02237-0","article-title":"The relationship between the gut microbiome and host gene expression: a review","volume":"140","author":"Nichols","year":"2021","journal-title":"Human Genet."},{"key":"B78","doi-asserted-by":"publisher","first-page":"92","DOI":"10.3390\/microorganisms6030092","article-title":"Gut bacterial communities in geographically distant populations of farmed sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax)","volume":"6","author":"Nikouli","year":"2018","journal-title":"Microorganisms"},{"key":"B79","doi-asserted-by":"publisher","first-page":"277","DOI":"10.3389\/fimmu.2019.00277","article-title":"Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases","volume":"10","author":"Parada Venegas","year":"2019","journal-title":"Front. Immunol."},{"key":"B80","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1016\/j.anifeedsci.2016.10.022","article-title":"Next-generation sequencing characterization of the gut bacterial community of gilthead sea bream (Sparus aurata, L.) fed low fishmeal based diets with increasing soybean meal levels","volume":"222","author":"Parma","year":"2016","journal-title":"Anim. Feed. Sci. Tech."},{"key":"B81","doi-asserted-by":"publisher","first-page":"720","DOI":"10.1016\/j.jhep.2014.10.039","article-title":"Molecular mechanism of PPAR\u03b1 action and its impact on lipid metabolism, inflammation and fibrosis in non-alcoholic fatty liver disease","volume":"62","author":"Pawlak","year":"2015","journal-title":"J. Hepatol."},{"key":"B82","doi-asserted-by":"publisher","first-page":"16134","DOI":"10.1038\/s41598-019-52693-6","article-title":"Protective effects of seaweed supplemented diet on antioxidant and immune responses in European seabass (Dicentrarchus labrax) subjected to bacterial infection","volume":"9","author":"Peixoto","year":"2019","journal-title":"Sci. Rep."},{"key":"B83","doi-asserted-by":"publisher","first-page":"664701","DOI":"10.3389\/fmars.2021.664701","article-title":"Interaction between dietary lipid level and seasonal temperature changes in gilthead sea bream Sparus aurata: effects on growth, fat deposition, plasma biochemistry, digestive enzyme activity, and gut bacterial community","volume":"8","author":"Pelusio","year":"2021","journal-title":"Front. Mar. Sci."},{"key":"B84","doi-asserted-by":"publisher","first-page":"101869","DOI":"10.1016\/j.algal.2020.101869","article-title":"Incorporation of defatted microalgal biomass (Tetraselmis sp. CTP4) at the expense of soybean meal as a feed ingredient for juvenile gilthead seabream (Sparus aurata)","volume":"47","author":"Pereira","year":"2020","journal-title":"Algal Res"},{"key":"B85","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1080\/15592294.2019.1699982","article-title":"Stearoyl-CoA desaturase (scd1a) is epigenetically regulated by broodstock nutrition in gilthead sea bream (Sparus aurata)","volume":"15","author":"Perera","year":"2020","journal-title":"Epigenetics"},{"key":"B86","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1016\/j.fsi.2014.01.022","article-title":"Interleukin gene expression is strongly modulated at the local levelin afisheparasite model","volume":"37","author":"P\u00e9rez-Cord\u00f3n","year":"2014","journal-title":"Fish Shell. Immunol."},{"key":"B87","doi-asserted-by":"publisher","first-page":"e65457","DOI":"10.1371\/journal.pone.0065457","article-title":"Mucins as diagnostic and prognostic biomarkers in a fish-parasite model: transcriptional and functional analysis","volume":"8","author":"P\u00e9rez-S\u00e1nchez","year":"2013","journal-title":"PLoS ONE"},{"key":"B88","doi-asserted-by":"publisher","first-page":"760","DOI":"10.3389\/fmars.2019.00760","article-title":"Genome sequencing and transcriptome analysis reveal recent species-specific gene duplications in the plastic gilthead sea bream (Sparus aurata)","volume":"6","author":"P\u00e9rez-S\u00e1nchez","year":"2019","journal-title":"Front. Mar. Sci."},{"key":"B89","doi-asserted-by":"publisher","first-page":"687","DOI":"10.3389\/fendo.2018.00687","article-title":"Somatotropic axis regulation unravels the differential effects of nutritional and environmental factors in growth performance of marine farmed fishes","volume":"9","author":"P\u00e9rez-S\u00e1nchez","year":"2018","journal-title":"Front. Endocrinol."},{"key":"B90","doi-asserted-by":"publisher","first-page":"637","DOI":"10.3389\/fimmu.2016.00637","article-title":"Differential Modulation of IgT and IgM upon parasitic, bacterial, viral and dietary challenges in a perciform fish","volume":"7","author":"Piazzon","year":"2016","journal-title":"Front. Immunol."},{"key":"B91","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1186\/s40168-017-0390-3","article-title":"Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets","volume":"5","author":"Piazzon","year":"2017","journal-title":"Microbiome"},{"key":"B92","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1186\/s40168-020-00922-w","article-title":"Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream","volume":"8","author":"Piazzon","year":"2020","journal-title":"Microbiome"},{"key":"B93","doi-asserted-by":"publisher","first-page":"2512","DOI":"10.3389\/fmicb.2019.02512","article-title":"Sex, age, and bacteria: How the intestinal microbiota is modulated in a protandrous hermaphrodite fish","volume":"10","author":"Piazzon","year":"2019","journal-title":"Front. Microbiol."},{"key":"B94","doi-asserted-by":"publisher","first-page":"187","DOI":"10.4049\/jimmunol.1402093","article-title":"Carp Il10 has anti-inflammatory activities on phagocytes, promotes proliferation of memory T cells, and regulates B cell differentiation and antibody secretion","volume":"194","author":"Piazzon","year":"2015","journal-title":"J. Immunol"},{"key":"B95","doi-asserted-by":"publisher","first-page":"2109","DOI":"10.1099\/00207713-50-6-2109","article-title":"Anoxybacillus pushchinensis gen. nov., sp. nov., a novel anaerobic, alkaliphilic, moderately thermophilic bacterium from manure, and description of Anoxybacillus flavitherms comb. nov","volume":"50","author":"Pikuta","year":"2000","journal-title":"Int. J. Syst. Evol. Microbiol"},{"key":"B96","first-page":"1163","article-title":"Dephosphorylation of endotoxin by alkaline phosphatase in vivo","volume":"151","author":"Poelstra","year":"1997","journal-title":"Am. J. Clin. Pathol."},{"key":"B97","doi-asserted-by":"publisher","first-page":"897","DOI":"10.3389\/fimmu.2017.00897","article-title":"Alkaline phosphatase, an unconventional immune protein","volume":"8","author":"Rader","year":"2017","journal-title":"Front. Immunol."},{"key":"B98","doi-asserted-by":"publisher","first-page":"1689","DOI":"10.3389\/fmicb.2018.01689","article-title":"Metal transformation by a novel Pelosinus isolate from a subsurface environment","volume":"9","author":"Ray","year":"2018","journal-title":"Front. Microbiol."},{"key":"B99","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1007\/s10811-021-02377-4","article-title":"Health status in gilthead seabream (Sparus aurata) juveniles fed diets devoid of fishmeal and supplemented with Phaeodactylum tricornutum","volume":"33","author":"Reis","year":"2021","journal-title":"J. App. Phycol."},{"key":"B100","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1016\/j.fsi.2014.11.002","article-title":"Humoral immune response and TLR9 gene expression in Pacific red snapper (Lutjanus peru) experimentally exposed to Aeromonas veronii","volume":"42","author":"Reyes-Becerril","year":"2015","journal-title":"Fish Shellfish Immunol."},{"key":"B101","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.fsi.2014.08.029","article-title":"Induction of anti-inflammatory cytokine expression by IPNV in persistent infection","volume":"41","author":"Reyes-Cerpa","year":"2014","journal-title":"Fish Shellfish Immunol."},{"key":"B102","doi-asserted-by":"publisher","first-page":"564","DOI":"10.3389\/fimmu.2019.00564","article-title":"Effect of Bacillus subtilis strains on intestinal barrier function and inflammatory response","volume":"10","author":"Rhayat","year":"2019","journal-title":"Front. Immunol"},{"key":"B103","doi-asserted-by":"publisher","first-page":"143","DOI":"10.3390\/ani9040143","article-title":"The effects of dietary insect meal from Hermetia illucens prepupae on autochthonous gut microbiota of rainbow trout (Oncorhynchus mykiss)","volume":"9","author":"Rimoldi","year":"2019","journal-title":"Animals"},{"key":"B104","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1186\/s12917-020-02335-1","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":"B105","doi-asserted-by":"publisher","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: A versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"B106","doi-asserted-by":"publisher","first-page":"1062","DOI":"10.1017\/S0007114512002899","article-title":"Prevention of soya-induced enteritis in Atlantic salmon (Salmo salar) by bacteria grown on natural gas is dose dependent and related to epithelial MHC II reactivity and CD8\u03b1+ intraepithelial lymphocytes","volume":"109","author":"Romarheim","year":"2013","journal-title":"Br. J. Nutr."},{"key":"B107","doi-asserted-by":"publisher","first-page":"994","DOI":"10.4315\/0362-028X.JFP-15-569","article-title":"Occurrence of Clostridium perfringens types A, E, and C in fresh fish and its public health significance","volume":"79","author":"Sabry","year":"2016","journal-title":"J. Food Prot."},{"key":"B108","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1254\/jjp.24.109","article-title":"Anti-inflammatory polysaccharide produced by Serratia piscatorum","volume":"24","author":"Saeki","year":"1974","journal-title":"Jpn. J. Pharmacol."},{"key":"B109","doi-asserted-by":"publisher","first-page":"943","DOI":"10.1111\/anu.12313","article-title":"Nutritional evaluation of Tenebrio molitor meal as fishmeal substitute for tilapia (Oreochromis niloticus) diet","volume":"22","author":"S\u00e1nchez-Muros","year":"2016","journal-title":"Aquac. Nutr."},{"key":"B110","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","article-title":"Quality control and preprocessing of metagenomic datasets","volume":"27","author":"Schmieder","year":"2011","journal-title":"Bioinformatics"},{"key":"B111","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1007\/s11154-019-09512-0","article-title":"Dietary lipids, gut microbiota and lipid metabolism","volume":"20","author":"Schoeler","year":"2019","journal-title":"Rev. Endocr. Metab. Disord."},{"key":"B112","doi-asserted-by":"publisher","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":"B113","doi-asserted-by":"publisher","first-page":"1349","DOI":"10.3389\/fmicb.2017.01349","article-title":"Walleye autochthonous bacteria as promising probiotic candidates against Flavobacterium columnare","volume":"8","author":"Seghouani","year":"2017","journal-title":"Front. Microbiol."},{"key":"B114","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1152\/physrev.00045.2009","article-title":"Gut microbiota in health and disease","volume":"90","author":"Sekirov","year":"2010","journal-title":"Physiol. Rev."},{"key":"B115","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2018\/8696543","article-title":"Galectin-1 as an emerging mediator of cardiovascular inflammation: mechanisms and therapeutic opportunities","volume":"8696543","author":"Seropian","year":"2018","journal-title":"Mediat. Inflamm."},{"key":"B116","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1111\/j.1574-6941.2011.01155.x","article-title":"Influence of the diet on the microbial diversity of faecal and gastrointestinal contents in gilthead sea bream (Sparus aurata) and intestinal contents in goldfish (Carassius auratus)","volume":"78","author":"Silva","year":"2011","journal-title":"FEMS Microbiol. Ecol."},{"key":"B117","doi-asserted-by":"publisher","first-page":"e4001","DOI":"10.7717\/peerj.4001","article-title":"Sodium salt medium-chain fatty acids and Bacillus-based probiotics strategies to improve growth and intestinal health of gilthead sea bream (Sparus aurata)","volume":"5","author":"Sim\u00f3-Mirabet","year":"2017","journal-title":"PeerJ"},{"key":"B118","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1016\/j.aquaculture.2018.11.052","article-title":"Microbial biomass (NovacqTM) stimulates feeding and improves the growth performance on extruded low to zero-fishmeal diets in tilapia (GIFT strain)","volume":"501","author":"Simon","year":"2019","journal-title":"Aquaculture"},{"key":"B119","doi-asserted-by":"publisher","first-page":"734679","DOI":"10.1016\/j.aquaculture.2019.734679","article-title":"Microbial biomass, marine invertebrate meals and feed restriction influence the biological and gut microbiota response of shrimp Penaeus monodon","volume":"520","author":"Simon","year":"2020","journal-title":"Aquaculture"},{"key":"B120","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1016\/j.cmet.2015.09.028","article-title":"Microbiota-dependent hepatic lipogenesis mediated by stearoyl CoA desaturase 1 (SCD1) promotes metabolic syndrome in TLR5-deficient mice","volume":"22","author":"Singh","year":"2015","journal-title":"Cell Metab."},{"key":"B121","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","article-title":"Cytoscape 2.8: new features for data integration and network visualization","volume":"27","author":"Smoot","year":"2011","journal-title":"Bioinformatics"},{"key":"B122","doi-asserted-by":"publisher","first-page":"705041","DOI":"10.3389\/fmars.2021.705041","article-title":"Reshaping of gut microbiota in gilthead sea bream fed microbial and processed animal proteins as the main dietary protein source","volume":"8","author":"Sol\u00e9-Jim\u00e9nez","year":"2021","journal-title":"Front. Mar. Sci."},{"key":"B123","doi-asserted-by":"publisher","first-page":"2015","DOI":"10.3389\/fmicb.2019.02015","article-title":"The phylogeny, biodiversity, and ecology of the chloroflexi in activated sludge","volume":"10","author":"Speirs","year":"2019","journal-title":"Front. Microbiol."},{"key":"B124","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.jare.2010.04.001","article-title":"Bacterial coldwater disease of fishes caused byFlavobacterium psychrophilum","volume":"2","author":"Starliper","year":"2011","journal-title":"J. Adv. Res."},{"key":"B125","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/23308249.2014.987209","article-title":"Feed matters: satisfying the feed demand of aquaculture","volume":"23","author":"Tacon","year":"2015","journal-title":"Trends Food Sci. Technol."},{"key":"B126","doi-asserted-by":"publisher","first-page":"1667","DOI":"10.1007\/s10695-012-9663-8","article-title":"Characterization, genomic organization, and expression profiles of MyD88, a key adaptor molecule in the TLR signaling pathways in miiuy croaker (Miichthys miiuy)","volume":"38","author":"Tang","year":"2012","journal-title":"Fish Physiol. Biochem."},{"key":"B127","doi-asserted-by":"publisher","first-page":"3322","DOI":"10.1021\/acs.jproteome.5b00354","article-title":"Analysis of the human adult urinary metabolome variations with age, body mass index, and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses","volume":"14","author":"Th\u00e9venot","year":"2015","journal-title":"J. Prot. Res."},{"key":"B128","doi-asserted-by":"publisher","first-page":"e9646","DOI":"10.7717\/peerj.9646","article-title":"Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance","volume":"8","author":"Uengwetwanit","year":"2020","journal-title":"PeerJ"},{"key":"B129","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1111\/j.1365-2761.2009.01049.x","article-title":"Time-related changes of the intestinal morphology of Atlantic salmon, Salmo salar L., at two different soybean meal inclusion levels","volume":"32","author":"Ur\u00e1n","year":"2009","journal-title":"J. Fish. Dis."},{"key":"B130","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1038\/nature22814.Trans-kingdom","article-title":"Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota","volume":"546","author":"Wang","year":"2017","journal-title":"Nat. Genet."},{"key":"B131","doi-asserted-by":"publisher","first-page":"1669","DOI":"10.1038\/ismej.2015.235","article-title":"Correlation detection strategies in microbial data sets vary widely in sensitivity and precision","volume":"10","author":"Weiss","year":"2016","journal-title":"ISME J."},{"key":"B132","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1111\/j.1749-7345.2006.00070.x","article-title":"Immune response and resistance to stress and Edwardsiella ictaluri challenge in channel catfish, Ictalurus punctatus, fed diets containing commercial whole-cell yeast or yeast subcomponents","volume":"38","author":"Welker","year":"2007","journal-title":"J. World Aquacult. Soc."},{"key":"B133","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1111\/1751-7915.13323","article-title":"Diet and diet-associated bacteria shape early microbiome development in Yellowtail Kingfish (Seriola lalandi)","volume":"12","author":"Wilkes Walburn","year":"2019","journal-title":"Microb. Biotechnol."},{"key":"B134","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/S0169-7439(01)00155-1","article-title":"PLS-regression: a basic tool of chemometrics","volume":"58","author":"Wold","year":"2001","journal-title":"Chemom. Intell. Lab. Syst."},{"key":"B135","doi-asserted-by":"publisher","first-page":"1085","DOI":"10.1111\/anu.12647","article-title":"Replacing fish meal with a blend of poultry by-product meal and feather meal in diets for giant croaker (Nibea japonica)","volume":"24","author":"Wu","year":"2018","journal-title":"Aquacult. Nutr."},{"key":"B136","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1186\/1471-2164-15-266","article-title":"The intestinal microbiome of fish under starvation","volume":"15","author":"Xia","year":"2014","journal-title":"BMC Genomics"},{"key":"B137","doi-asserted-by":"publisher","first-page":"e0230154","DOI":"10.1371\/journal.pone.0230154","article-title":"Integrated analysis of the transcriptome and metabolome of purple and green leaves of Tetrastigma hemsleyanum reveals gene expression patterns involved in anthocyanin biosynthesis","volume":"15","author":"Yan","year":"2020","journal-title":"PLoS ONE"},{"key":"B138","doi-asserted-by":"publisher","first-page":"001","DOI":"10.4172\/2155-9546.S1-001","article-title":"Probiotic Psychrobacter sp. improved the autochthonous microbial diversity along the gastrointestinal tract of grouper Epinephelus coioides","volume":"1","author":"Yang","year":"2011","journal-title":"J. Aquac. Res. Dev. S"},{"key":"B139","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1038\/s43018-020-0078-7","article-title":"Amending microbiota by targeting intestinal inflammation with TNF blockade attenuates development of colorectal cancer","volume":"1","author":"Yang","year":"2020","journal-title":"Nat. Cancer"},{"key":"B140","doi-asserted-by":"publisher","first-page":"1614","DOI":"10.1111\/jam.14059","article-title":"Intestinal microbiota lipid metabolism varies across rainbow trout (Oncorhynchus mykiss) phylogeographic divide","volume":"125","author":"Yildirimer","year":"2018","journal-title":"J. Appl. Microbiol."},{"key":"B141","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1016\/j.aquaculture.2015.06.023","article-title":"Utilisation of feed resources in production of Atlantic salmon (Salmo salar) in Norway","volume":"448","author":"Ytrest\u00f8yl","year":"2015","journal-title":"Aquaculture"},{"key":"B142","doi-asserted-by":"publisher","first-page":"1064","DOI":"10.1007\/s00343-016-4393-x","article-title":"Activation of macrophages by an exopolysaccharide isolated from Antarctic Psychrobactersp. B-3","volume":"34","author":"Yu","year":"2016","journal-title":"Chin. J. Ocean Limnol."},{"key":"B143","doi-asserted-by":"publisher","first-page":"617030","DOI":"10.3389\/fmicb.2020.617030","article-title":"Integrative metagenomics\u2013metabolomics for analyzing the relationship between microorganisms and non-volatile profiles of traditional Xiaoqu","volume":"11","author":"Zhao","year":"2021","journal-title":"Front. Microbiol."},{"key":"B144","doi-asserted-by":"publisher","first-page":"5951","DOI":"10.3390\/ijms22115951","article-title":"Serratia symbiotica enhances fatty acid metabolism of pea aphid to promote host development","volume":"22","author":"Zhou","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"B145","doi-asserted-by":"publisher","first-page":"454","DOI":"10.3390\/ani10030454","article-title":"Application of Bacillus coagulans in animal husbandry and its underlying mechanisms","volume":"10","author":"Zhou","year":"2020","journal-title":"Animals"}],"container-title":["Frontiers in Physiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fphys.2021.748265\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,5]],"date-time":"2021-10-05T08:25:12Z","timestamp":1633422312000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fphys.2021.748265\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,5]]},"references-count":145,"alternative-id":["10.3389\/fphys.2021.748265"],"URL":"https:\/\/doi.org\/10.3389\/fphys.2021.748265","relation":{},"ISSN":["1664-042X"],"issn-type":[{"value":"1664-042X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,10,5]]},"article-number":"748265"}}