FAO. The State of World Fisheries and Aquaculture 2018 – Meeting the sustainable development goals. Rome. Licence: CC BY-NC-SA 3.0 IGO. (2018).
Okocha, R. C., Olatoye, I. O. & Adedeji, O. B. Food safety impacts of antimicrobial use and their residues in aquaculture. Public Health Reviews 39, 21, https://doi.org/10.1186/s40985-018-0099-2 (2018).
Cabello, F. C. Heavy use of prophylactic antibiotics in aquaculture: a growing problem for human and animal health and for the environment. Environmental microbiology 8, 1137–1144 (2006).
Cabello, F. C. et al. Antimicrobial use in aquaculture re-examined: its relevance to antimicrobial resistance and to animal and human health. Environmental Microbiology 15, 1917–1942, https://doi.org/10.1111/1462-2920.12134 (2013).
Defoirdt, T., Sorgeloos, P. & Bossier, P. Alternatives to antibiotics for the control of bacterial disease in aquaculture. Current opinion in microbiology 14, 251–258 (2011).
Muziasari, W. I. et al. The resistome of farmed fish feces contributes to the enrichment of antibiotic resistance genes in sediments below Baltic Sea fish farms. Frontiers in microbiology 7, 2137 (2017).
Vollaard, E. & Clasener, H. Colonization resistance. Antimicrobial agents and chemotherapy 38, 409 (1994).
Wang, E. et al. Consumption of florfenicol-medicated feed alters the composition of the channel catfish intestinal microbiota including enriching the relative abundance of opportunistic pathogens. Aquaculture 501, 111–118, https://doi.org/10.1016/j.aquaculture.2018.11.019 (2019).
Looft, T. et al. Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations. The ISME journal 8, 1566 (2014).
Looft, T. et al. In-feed antibiotic effects on the swine intestinal microbiome. Proceedings of the National Academy of Sciences 109, 1691–1696, https://doi.org/10.1073/pnas.1120238109 (2012).
Liu, Y. et al. Gibel carp Carassius auratus gut microbiota after oral administration of trimethoprim/sulfamethoxazole. Diseases of aquatic organisms 99, 207–213 (2012).
Zhou, Z. et al. Gut microbial status induced by antibiotic growth promoter alters the prebiotic effects of dietary DVAQUA® on Aeromonas hydrophila-infected tilapia: Production, intestinal bacterial community and non-specific immunity. Veterinary microbiology 149, 399–405 (2011).
Ringø, E. et al. Effect of dietary components on the gut microbiota of aquatic animals. A never-ending story? Aquacult Nutr 22, https://doi.org/10.1111/anu.12346 (2016).
Gupta, S., Fernandes, J. & Kiron, V. Antibiotic-Induced Perturbations Are Manifested in the Dominant Intestinal Bacterial Phyla of Atlantic Salmon. Microorganisms 7, 233 (2019).
Almeida, A. R., Alves, M., Domingues, I. & Henriques, I. The impact of antibiotic exposure in water and zebrafish gut microbiomes: A 16S rRNA gene-based metagenomic analysis. Ecotoxicology and Environmental Safety 186, 109771, https://doi.org/10.1016/j.ecoenv.2019.109771 (2019).
Narrowe, A. B. et al. Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure. Microbiome 3, 6, https://doi.org/10.1186/s40168-015-0069-6 (2015).
Kotzamanis, Y., Gisbert, E., Gatesoupe, F., Infante, J. Z. & Cahu, C. Effects of different dietary levels of fish protein hydrolysates on growth, digestive enzymes, gut microbiota, and resistance to Vibrio anguillarum in European sea bass (Dicentrarchus labrax) larvae. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 147, 205–214 (2007).
Gatesoupe, F. J. et al. The effects of dietary carbohydrate sources and forms on metabolic response and intestinal microbiota in sea bass juveniles, Dicentrarchus labrax. Aquaculture 422, https://doi.org/10.1016/j.aquaculture.2013.11.011 (2014).
Sun, H., Jami, E., Harpaz, S. & Mizrahi, I. Involvement of dietary salt in shaping bacterial communities in European sea bass (Dicentrarchus labrax). Scientific reports 3, 1558 (2013).
Carda-Dieguez, M., Mira, A. & Fouz, B. Pyrosequencing survey of intestinal microbiota diversity in cultured sea bass (Dicentrarchus labrax) fed functional diets. FEMS Microbiol Ecol 87, https://doi.org/10.1111/1574-6941.12236 (2014).
Gatesoupe, F.-J. et al. The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories. BMC Microbiology 16, 266, https://doi.org/10.1186/s12866-016-0885-2 (2016).
Kokou, F. et al. Core gut microbial communities are maintained by beneficial interactions and strain variability in fish. Nature Microbiology, 1–10, https://doi.org/10.1038/s41564-019-0560-0 (2019).
Rosado, D. et al. Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax). Scientific Reports 9, 18946, https://doi.org/10.1038/s41598-019-55314-4 (2019).
Pimentel, T., Marcelino, J., Ricardo, F., Soares, A. M. V. M. & Calado, R. Bacterial communities 16S rDNA fingerprinting as a potential tracing tool for cultured seabass Dicentrarchus labrax. Scientific Reports 7, 11862, https://doi.org/10.1038/s41598-017-11552-y (2017).
Rigos, G. & Troisi, G. Antibacterial agents in Mediterranean finfish farming: a synopsis of drug pharmacokinetics in important euryhaline fish species and possible environmental implications. Reviews in Fish Biology and Fisheries 15, 53–73 (2005).
Rigos, G., Bitchava, K. & Nengas, I. Antibacterial drugs in products originating from aquaculture: assessing the risks to public welfare. Mediterranean marine science 11, 33–42 (2010).
Lulijwa, R., Rupia, E. J. & Alfaro, A. C. Antibiotic use in aquaculture, policies and regulation, health and environmental risks: a review of the top 15 major producers. Reviews in Aquaculture (2019).
Wilson, J. & Castro, L. 1-Morphological diversity of the gastrointestinal tract in fishes. Fish physiology 30, 1–55 (2010).
Nayak, S. K. Role of gastrointestinal microbiota in fish. Aquac Res 41, https://doi.org/10.1111/j.1365-2109.2010.02546.x (2010).
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 13, 581, https://doi.org/10.1038/nmeth.3869 https://www.nature.com/articles/nmeth.3869#supplementary-information (2016).
Kurtz, Z. D. et al. Sparse and Compositionally Robust Inference of Microbial Ecological Networks. PLOS Computational Biology 11, e1004226, https://doi.org/10.1371/journal.pcbi.1004226 (2015).
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biology 12, R60, https://doi.org/10.1186/gb-2011-12-6-r60 (2011).
Langille, M. G. I. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotech 31, 814–821, https://doi.org/10.1038/nbt.2676 http://www.nature.com/nbt/journal/v31/n9/abs/nbt.2676.html#supplementary-information (2013).
Tyagi, A., Singh, B., Thammegowda, N. K. B. & Singh, N. K. Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome. Archives of microbiology 201, 295–303 (2019).
Chen, B. et al. Complex pollution of antibiotic resistance genes due to beta-lactam and aminoglycoside use in aquaculture farming. Water Research 134, 200–208, https://doi.org/10.1016/j.watres.2018.02.003 (2018).
Done, H. Y., Venkatesan, A. K. & Halden, R. U. Does the recent growth of aquaculture create antibiotic resistance threats different from those associated with land animal production in agriculture? The. AAPS journal 17, 513–524 (2015).
Nathan, C. Antibiotics at the crossroads. Nature 431, 899 (2004).
Willing, B. P., Russell, S. L. & Finlay, B. B. Shifting the balance: antibiotic effects on host–microbiota mutualism. Nature Reviews Microbiology 9, 233 (2011).
Jakobsson, H. E. et al. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PloS one 5, e9836 (2010).
Navarrete, P., Mardones, P., Opazo, R., Espejo, R. & Romero, J. Oxytetracycline treatment reduces bacterial diversity of intestinal microbiota of Atlantic salmon. Journal of Aquatic Animal Health 20, 177–183 (2008).
López Nadal, A., Peggs, D., Wiegertjes, G. F. & Brugman, S. Exposure to antibiotics affects saponin immersion-induced immune stimulation and shift in microbial composition in zebrafish larvae. Frontiers in microbiology 9, 2588 (2018).
Sáenz, J. S. et al. Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus. Microbiome 7, 24, https://doi.org/10.1186/s40168-019-0632-7 (2019).
Carlson, J. M., Hyde, E. R., Petrosino, J. F., Manage, A. B. & Primm, T. P. The host effects of Gambusia affinis with an antibiotic-disrupted microbiome. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 178, 163–168 (2015).
Carlson, J. M., Leonard, A. B., Hyde, E. R., Petrosino, J. F. & Primm, T. P. Microbiome disruption and recovery in the fish Gambusia affinis following exposure to broad-spectrum antibiotic. Infection and drug resistance 10, 143 (2017).
Christensen, A. M., Ingerslev, F. & Baun, A. Ecotoxicity of mixtures of antibiotics used in aquacultures. Environmental Toxicology and Chemistry 25, 2208–2215, https://doi.org/10.1897/05-415r.1 (2006).
Austin, B. & Al-Zahrani, A. M. J. The effect of antimicrobial compounds on the gastrointestinal microflora of rainbow trout, Salmo gairdneri Richardson. Journal of Fish Biology 33, 1–14, https://doi.org/10.1111/j.1095-8649.1988.tb05444.x (1988).
Gajardo, K. et al. A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): A basis for comparative gut microbial research. Scientific Reports 6, 30893, https://doi.org/10.1038/srep30893 http://www.nature.com/articles/srep30893#supplementary-information (2016).
Hallali, E. et al. Dietary salt levels affect digestibility, intestinal gene expression, and the microbiome, in Nile tilapia (Oreochromis niloticus). PloS one 13, e0202351 (2018).
Høj, L. et al. Crown-of-thorns sea star, <em>Acanthaster</em> cf. <em>solaris</em>, have tissue-characteristic microbiomes with potential roles in health and reproduction. Applied and Environmental Microbiology, 10.1128/aem.00181-18 (2018).
Nikolopoulou, D. et al. Patterns of gastric evacuation, digesta characteristics and pH changes along the gastrointestinal tract of gilthead sea bream (Sparus aurata L.) and European sea bass (Dicentrarchus labrax L.). Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 158, 406–414 (2011).
Derrick, C. W. & Reilly, K. M. Erythromycin, Lincomycin, and Clindamycin. Pediatric Clinics of North America 30, 63–69, https://doi.org/10.1016/S0031-3955(16)34320-6 (1983).
Calduch-Giner, J. A., Sitjà-Bobadilla, A. & Pérez-Sánchez, J. Gene Expression Profiling Reveals Functional Specialization along the Intestinal Tract of a Carnivorous Teleostean Fish (Dicentrarchus labrax). Frontiers in Physiology 7, https://doi.org/10.3389/fphys.2016.00359 (2016).
Bakke, A. M., Glover, C. & Krogdahl, Å. In Fish physiology Vol. 30 57-110 (Elsevier, 2010).
Katayama, Y., Zhang, H.-Z., Hong, D. & Chambers, H. F. Jumping the barrier to β-lactam resistance in Staphylococcus aureus. Journal of Bacteriology 185, 5465–5472 (2003).
Li, T. et al. Alterations of the gut microbiome of largemouth bronze gudgeon (Coreius guichenoti) suffering from furunculosis. Scientific reports 6, 30606 (2016).
Wong, S. et al. Aquacultured rainbow trout (Oncorhynchus mykiss) possess a large core intestinal microbiota that is resistant to variation in diet and rearing density. Applied and environmental microbiology 79, 4974–4984 (2013).
Cochetière, D. L. M. F. et al. Resilience of the Dominant Human Fecal Microbiota upon Short-Course Antibiotic Challenge. Journal of Clinical Microbiology 43, 5588–5592, https://doi.org/10.1128/jcm.43.11.5588-5592.2005 (2005).
Nachin, L., Nannmark, U. & Nyström, T. Differential roles of the universal stress proteins of Escherichia coli in oxidative stress resistance, adhesion, and motility. Journal of bacteriology 187, 6265–6272 (2005).
Kokou, F. et al. Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature. eLife 7, e36398, https://doi.org/10.7554/eLife.36398 (2018).
Kokou, F. et al. Short- and long-term low-salinity acclimation effects on the branchial and intestinal gene expression in the European seabass (Dicentrarchus labrax). Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 231, 11–18, https://doi.org/10.1016/j.cbpa.2019.01.018 (2019).
Pfeiffer, T. J., Summerfelt, S. T. & Watten, B. J. Comparative performance of CO2 measuring methods: Marine aquaculture recirculation system application. Aquacultural Engineering 44, 1–9, https://doi.org/10.1016/j.aquaeng.2010.10.001 (2011).
Roeselers, G. et al. Evidence for a core gut microbiota in the zebrafish. ISME J 5, https://doi.org/10.1038/ismej.2011.38 (2011).
Fantini, E., Gianese, G., Giuliano, G. & Fiore, A. In Bacterial Pangenomics: Methods and Protocols (eds Alessio Mengoni, Marco Galardini, & Marco Fondi) 77–90 (Springer New York, 2015).
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and environmental microbiology 73, 5261–5267 (2007).
McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. The. ISME journal 6, 610–618 (2012).
Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences 108, 4516–4522, https://doi.org/10.1073/pnas.1000080107 (2011).
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org (2019).
Pinheiro, J., Bates, D., DebRoy, S. & Sarkar, D. Team. tRDC nlme: linear and nonlinear mixed effects models. R package version 3, 1–102 (2013).
Anderson, M. J. A new method for non‐parametric multivariate analysis of variance. Austral ecology 26, 32–46 (2001).
Love, M. I., Anders, S. & Huber, W. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq. 2. Genome biology 15, 550 (2014).