Functional feeds marginally alter immune expression and microbiota of Atlantic salmon (Salmo salar) gut, gill, and skin mucosa though evidence of tissue-specific signatures and host–microbe coadaptation remain

Animal Microbiome
Jacob W. Bledsoe1, Michael Pietrak2, Gary S. Burr2, Brian Peterson2, Brian C. Small1
1Hagerman Fish Culture Experiment Station, Aquaculture Research Institute, University of Idaho, 3059-F National Fish Hatchery Rd., Hagerman, ID, 83332, USA
2Agricultural Research Service, National Cold Water Marine Aquaculture Center, United States Department of Agriculture, 25 Salmon Farm Road, Franklin, ME, 04634, USA

Tóm tắt

Abstract Background Mucosal surfaces of fish provide cardinal defense against environmental pathogens and toxins, yet these external mucosae are also responsible for maintaining and regulating beneficial microbiota. To better our understanding of interactions between host, diet, and microbiota in finfish and how those interactions may vary across mucosal tissue, we used an integrative approach to characterize and compare immune biomarkers and microbiota across three mucosal tissues (skin, gill, and gut) in Atlantic salmon receiving a control diet or diets supplemented with mannan-oligosaccharides, coconut oil, or both. Dietary impacts on mucosal immunity were further evaluated by experimental ectoparasitic sea lice (Lepeophtheirus salmonis) challenge. Results Fish grew to a final size of 646.5 g ± 35.8 during the 12-week trial, with no dietary effects on growth or sea lice resistance. Bacterial richness differed among the three tissues with the highest richness detected in the gill, followed by skin, then gut, although dietary effects on richness were only detected within skin and gill. Shannon diversity was reduced in the gut compared to skin and gill but was not influenced by diet. Microbiota communities clustered separately by tissue, with dietary impacts on phylogenetic composition only detected in the skin, although skin and gill communities showed greater overlap compared to the gut according to overall composition, differential abundance, and covariance networks. Inferred metagenomic functions revealed preliminary evidence for tissue-specific host–microbiota coadaptation, as putative microbiota functions showed ties to the physiology of each tissue. Immune gene expression profiles displayed tissue-specific signatures, yet dietary effects were also detected within each tissue and peripheral blood leukocytes. Procrustes analysis comparing sample-matched multivariate variation in microbiota composition to that of immune expression profiles indicated a highly significant correlation between datasets. Conclusions Diets supplemented with functional ingredients, namely mannan-oligosaccharide, coconut oil, or a both, resulted in no difference in Atlantic salmon growth or resistance to sea lice infection. However, at the molecular level, functional ingredients caused physiologically relevant changes to mucosal microbiota and host immune expression. Putative tissue-specific metagenomic functions and the high correlation between expression profiles and microbiota composition suggest host and microbiota are interdependent and coadapted in a tissue-specific manner.

Từ khóa


Tài liệu tham khảo

Adams A. Progress, challenges and opportunities in fish vaccine development. Fish Shellfish Immunol. 2019;90:210–4.

Ángeles Esteban M. An overview of the immunological defenses in fish skin. ISRN Immunol 2012.

Ashtiani M, Mirzaie M, Jafari M. CINNA: an R/CRAN package to decipher central informative nodes in network analysis. Bioinformatics. 2019;35:1436–7.

Attia YA, Al-Harthi MA, Abo El-Maaty HM. The effects of different oil sources on performance, digestive enzymes, carcass traits, biochemical, immunological, antioxidant, and morphometric responses of broiler chicks. Front Vet Sci. 2020;7:181.

Austbø L, Aas IB, König M, Weli SC, Syed M, Falk K, Koppang EO. Transcriptional response of immune genes in gills and the interbranchial lymphoid tissue of Atlantic salmon challenged with infectious salmon anemia virus. Dev Comp Immunol. 2014;45:107–14.

Bjørndal T, Tusvik A. Economic analysis of on-growing of salmon post-smolts. Aquac Econ Manag 2020;1–32.

Blaufuss PC, Bledsoe JW, Gaylord TG, Sealey WM, Overturf KE, Powell MS. Selectionon a plant-based diet reveals changes in oral tolerance, microbiota and growth in rainbow trout (Oncorhynchusmykiss) when fed a high soy diet. Aquaculture. 2020;525: https://doi.org/10.1016/j.aquaculture.2020.735287.

Bledsoe JW, Peterson BC, Swanson KS, Small BC. 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. PLoS ONE. 2016;11:e0166379.

Butt RL, Volkoff H. Gut microbiota and energy homeostasis in fish. Front Endocrinol. 2019;10:9.

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high- resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformat. 2009;10(1):1–9. https://doi.org/10.1186/1471-2105-10-421.

Cheaib B, Yang P, Kazlauskaite R, Lindsay E, Heys C, Dwyer T, DeNoa M, Shaal P, Sloan W, Ijaz UZ, Llewellyn MS. Genome erosion and evidence for an intracellular niche-exploring the biology of mycoplasmas in Atlantic salmon. Aquaculture. 2021;541:736772.

Chiarello M, Auguet J-C, Bettarel Y, Bouvier C, Claverie T, Graham NA, Rieuvilleneuve F, Sucré E, Bouvier T, Villéger S. Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet. Microbiome. 2018;6:1–14.

Choteau L, Parny M, Francois N, Bertin B, Fumery M, Dubuquoy L, Takahashi K, Colombel J-F, Jouault T, Poulain D. Role of mannose-binding lectin in intestinal homeostasis and fungal elimination. Mucosal Immunol. 2016;9:767–76.

Crippen TL, Bootland LM, Leong J-AC, Fitzpatrick MS, Schreck CB, Vella AT. Analysis of salmonid leukocytes purified by hypotonic lysis of erythrocytes. J Aquat Anim Health. 2001;13:234–45.

De Schryver P, Vadstein O. Ecological theory as a foundation to control pathogenic invasion in aquaculture. ISME J. 2014;8:2360–8.

Dehler CE, Secombes CJ, Martin SA. Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.). Aquaculture. 2017;467:149–57. https://doi.org/10.1016/j.aquaculture.2016.07.017.

Dimitroglou A, Merrifield DL, Spring P, Sweetman J, Moate R, Davies SJ. Effects of mannan oligosaccharide (MOS) supplementation on growth performance, feed utilization, intestinal histology and gut microbiota of gilthead sea bream (Sparus aurata). Aquaculture. 2010;300:182–8.

Dimitroglou A, Merrifield DL, Moate R, Davies SJ, Spring P, Sweetman J, Bradley G. Dietary mannan oligosaccharide supplementation modulates intestinal microbial ecology and improves gut morphology of rainbow trout, Oncorhynchus mykiss (Walbaum)1. J Anim Sci. 2009;87:3226–34.

Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MG. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol. 2020;1:5.

Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J. An improved dual- indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome. 2014;2:6.

Fast MD, Sims DE, Burka JF, Mustafa A, Ross NW. Skin morphology and humoral non-specific defense parameters of mucus and plasma in rainbow trout, coho and Atlantic salmon. Comp Biochem Physiol A Mol Integr Physiol. 2002;3:645–57.

Frederick C, Brady DC, Bricknell I. Landing strips: model development for estimating body surface area of farmed Atlantic salmon (Salmo salar). Aquaculture. 2017;473:299–302.

Friberg IM, Taylor JD, Jackson JA. Diet in the driving seat: natural diet-immunity-microbiome interactions in wild fish. Front Immunol. 2019;10:243.

Frøslev TG, Kjøller R, Bruun HH, Ejrnæs R, Brunbjerg AK, Pietroni C, Hansen AJ. Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nat Commun. 2017;8(1):1–11.

Gajardo K, Jaramillo-Torres A, Kortner TM, Merrifield DL, Tinsley J, Bakke AM, Krogdahl Å. Alternative protein sources in the diet modulate microbiota and functionality in the distal intestine of Atlantic salmon (Salmo salar). Appl Environ Microbiol. 2017;83:e02615.

Gjerde B, Ødegård J, Thorland I. Estimates of genetic variation in the susceptibility of Atlantic salmon (Salmo salar) to the salmon louse Lepeophtheirus salmonis. Aquaculture. 2011;314:66–72.

Gomez D, Sunyer JO, Salinas I. The mucosal immune system of fish: the evolution of tolerating commensals while fighting pathogens. Fish Shellfish Immunol. 2013;35:1729–39.

Gonçalves A, Gallardo-Escárate C. Microbiome dynamic modulation through functional diets based on pre-and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss). J Appl Microbiol. 2017;122:1333–47.

Guerreiro I, Oliva-Teles A, Enes P. Prebiotics as functional ingredients: focus on Mediterranean fish aquaculture. Rev Aquac. 2018;10:800–32.

Hervé M, Hervé MM. Package ‘RVAideMemoire’ 2020. See https://CRAN.R-project.RVAideMemoire.

Hirazawa N, Oshima SI, Hara T, Mitsuboshi T, Hata K. Antiparasitic effect of medium-chain fatty acids against the ciliate Cryptocaryon irritans infestation in the red sea bream Pagrus major. Aquaculture. 2001;198(3–4):219–28. https://doi.org/10.1016/S0044-8486(01)00503-8.

Hu Y, Maisey K, Subramani PA, Liu F, Flores-Kossack C, Imarai M, Secombes CJ, Wang T. Characterization of rainbow trout peripheral blood leucocytes prepared by hypotonic lysis of erythrocytes, and analysis of their phagocytic activity, proliferation and response to PAMPs and proinflammatory cytokines. Dev Comp Immunol. 2018;88:104–13.

Huang Q, Sha RC, Deng Y, Mao Y, Wang C, Zhang T, Leung KMY. Diversity of gut microbiomes in marine fishes is shaped by host-related factors. Mol Ecol. 2020;29(24):5019–34.

Huang CB, Alimova Y, Myers TM, Ebersole JL. Short-and medium-chain fatty acids exhibit antimicrobial activity for oral microorganisms. Arch Oral Biol. 2011;56:650–4.

Johnston CE, Horney BS, Deluca S, MacKenzie A, Eales JG, Angus R. Changes in alkaline phosphatase isoenzyme activity in tissues and plasma of Atlantic salmon (Salmo salar) before and during smoltification and gonadal maturation. Fish Physiol Biochem. 1994;12(6):485–97.

Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1–e1.

Kononova SV, Zinchenko DV, Muranova TA, Belova NA, Miroshnikov AI. Intestinal microbiota of salmonids and its changes upon introduction of soy proteins to fish feed. Aquacult Int. 2019;27:475–96.

Koppang EO, Kvellestad A, Fischer U. Fish mucosal immunity: gill, Mucosal Health in Aquaculture. Elsevier 2015;93–133.

Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput Biol. 2015;11:e1004226.

Lallès JP. Intestinal alkaline phosphatase in the gastrointestinal tract of fish: biology, ontogeny, and environmental and nutritional modulation. Rev Aquac. 2020;12:555–81.

Leary SL, Underwood W, Anthony R, Cartner S, Corey D, Grandin T, Greenacre C, Gwaltney-Brant S, McCrackin M, Meyer R. AVMA guidelines for the euthanasia of animals: 2013 edition. American Veterinary Medical Association Schaumburg, IL 2013.

Leclercq E, Pontefract N, Rawling M, Valdenegro V, Aasum E, Andujar LV, Migaud H, Castex M, Merrifield D. Dietary supplementation with a specific mannan-rich yeast parietal fraction enhances the gut and skin mucosal barriers of Atlantic salmon (Salmo salar) and reduces its susceptibility to sea lice (Lepeophtheirus salmonis). Aquaculture. 2020;529:735701.

Legrand TP, Wynne JW, Weyrich LS, Oxley AP. A microbial sea of possibilities: current knowledge and prospects for an improved understanding of the fish microbiome. Rev Aquac. 2020;12:1101–34.

Legrand TP, Catalano SR, Wos-Oxley ML, Stephens F, Landos M, Bansemer MS, Stone DA, Qin JG, Oxley A. The inner workings of the outer surface: skin and gill microbiota as indicators of changing gut health in yellowtail kingfish. Front Microbiol. 2018;8:2664.

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.

Løvoll M, Johnsen H, Boshra H, Bøgwald J, Sunyer JO, Dalmo RA. The ontogeny and extrahepatic expression of complement factor C3 in Atlantic salmon (Salmo salar). Fish Shellfish Immunol. 2007;23(3):542–52.

Luo L, Xue M, Vachot C, Geurden I, Kaushik S. Dietary medium chain fatty acids from coconut oil have little effects on postprandial plasma metabolite profiles in rainbow trout (Oncorhynchus mykiss). Aquaculture. 2014;420:24–31.

Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 2015;26:27663.

Martin SA, Król E. Nutrigenomics and immune function in fish: new insights from omics technologies. Dev Comp Immunol. 2017;75:86–98.

Matz MV, Wright RM, Scott JG. No control genes required: Bayesian analysis of qRT-PCR data. PLoS ONE. 2013;8:e71448.

McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.

Micallef G, Cash P, Fernandes JM, Rajan B, Tinsley JW, Bickerdike R, Martin SA, Bowman AS. Dietary yeast cell wall extract alters the proteome of the skin mucous barrier in Atlantic Salmon (Salmo salar): increased abundance and expression of a calreticulin-like protein. PLoS ONE. 2017;12:e0169075.

Minich JJ, Sanders JG, Amir A, Humphrey G, Gilbert JA, Knight R. Quantifying and understanding well-to-well contamination in microbiome research. mSystems. 2019;4(4):e00186-19.

Minich JJ, Poore GD, Jantawongsri K, Johnston C, Bowie K, Bowman J, Knight R, Nowak B, Allen EE. Microbial ecology of Atlantic salmon (Salmo salar) hatcheries: impacts of the built environment on fish mucosal microbiota. Appl Environ Microbiol. 2020;86:e00411-20.

Mutoloki S, Cooper GA, Marjara IS, Koop BF, Evensen Ø. High gene expression of inflammatory markers and IL-17A correlates with severity of injection site reactions of Atlantic salmon vaccinated with oil-adjuvanted vaccines. BMC Genom. 2010;11:336.

Naylor RL, Hardy RW, Bureau DP, Chiu A, Elliott M, Farrell AP, Forster I, Gatlin DM, Goldburg RJ, Hua K. Feeding aquaculture in an era of finite resources. PNAS. 2009;106:15103–10.

Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’hara R, Simpson GL, Solymos P, Stevens MHH, Wagner H. Package ‘vegan’. Community ecology package, version. 2, 2013:1–295.

Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics. 2014;30:3123–4.

Perry WB, Lindsay E, Payne CJ, Brodie C, Kazlauskaite R. The role of the gut microbiome in sustainable teleost aquaculture. Proc R Soc B. 2020;287:20200184.

Peterson BC, Peatman E, Ourth D, Waldbieser G. Effects of a phytogenic feed additive on growth performance, susceptibility of channel catfish to Edwardsiella ictaluri and levels of mannose binding lectin. Fish Shellfish Immunol. 2015;44:21–5.

Peterson BC, Burr GS, Pietrak MR, Proestou DA. Genetic Improvement of North American Atlantic Salmon and the Eastern Oyster Crassostrea virginica at the US Department of Agriculture-Agricultural Research Service National Cold Water Marine Aquaculture Center. N Am J Aquac. 2020;82(3):321–30.

Priya S, Burns MB, Ward T, Mars RA, Adamowicz B, Lock EF, Kashyap PC, Knights D, Blekhman R. Shared and disease-specific host gene-microbiome interactions across human diseases. BioRxiv. 2021. https://doi.org/10.1101/2021.03.29.437589.

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41:D590–6.

Rasmussen JA, Villumsen KR, Ernst M, Hansen M, Forberg T, Gopalakrishnan S, Gilbert MTP, Boejesen AM, Kristiansen K, Limborg MT. A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss). Microbiome. 2022;10:21.

Rasmussen JA, Villumsen KR, Duchêne DA, Puetz LC, Delmont TO, Sveier H, von Gersdorff Jøregensen L, Præbel K, Martin MD, Bojesen AM, Gilbert MTP. Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts. Commun Biol. 2021;4(1):1–10.

Refstie S, Baeverfjord G, Seim RR, Elvebø O. Effects of dietary yeast cell wall β-glucans and MOS on performance, gut health, and salmon lice resistance in Atlantic salmon (Salmo salar) fed sunflower and soybean meal. Aquaculture. 2010;305:109–16.

Rodriguez-Estrada U, Satoh S, Haga Y, Fushimi H, Sweetman J. Effects of inactivated Enterococcus faecalis and mannan oligosaccharide and their combination on growth, immunity, and disease protection in rainbow trout. N Am J Aquac. 2013;75:416–28.

Rombout JH, Yang G, Kiron V. Adaptive immune responses at mucosal surfaces of teleost fish. Fish Shellfish Immunol. 2014;40(2):634–43. https://doi.org/10.1016/j.fsi.2014.08.020.

Sahlmann C, Sutherland BJ, Kortner TM, Koop BF, Krogdahl Å, Bakke AM. Early response of gene expression in the distal intestine of Atlantic salmon (Salmo salar L.) during the development of soybean meal induced enteritis. Fish Shellfish Immunol. 2013;34:599–609.

Salinas I, Zhang Y-A, Sunyer JO. Mucosal immunoglobulins and B cells of teleost fish. Dev Comp Immunol. 2011;35:1346–65.

Schliep KP. phangorn: phylogenetic analysis in R. Bioinformatics. 2011;27:592–3.

Skugor S, Glover KA, Nilsen F, Krasnov A. Local and systemic gene expression responses of Atlantic salmon (Salmo salar L.) to infection with the salmon louse (Lepeophtheirus salmonis). BMC Genom. 2008;9:498.

Tadiso TM, Krasnov A, Skugor S, Afanasyev S, Hordvik I, Nilsen F. Gene expression analyses of immune responses in Atlantic salmon during early stages of infection by salmon louse (Lepeophtheirus salmonis) revealed bi-phasic responses coinciding with the copepod-chalimus transition. BMC Genom. 2011;12:141.

Tocher DR. Metabolism and functions of lipids and fatty acids in teleost fish. Rev Fish Sci. 2003;11:107–84.

Torrecillas S, Montero D, Izquierdo M. Improved health and growth of fish fed mannan oligosaccharides: potential mode of action. Fish Shellfish Immunol. 2014;36:525–44.

Torrecillas S, Montero D, Caballero MJ, Pittman KA, Custódio M, Campo A, Sweetman J, Izquierdo M. Dietary Mannan Oligosaccharides: Counteracting the Side Effects of Soybean Meal Oil Inclusion on European Sea Bass (Dicentrarchus labrax) Gut Health and Skin Mucosa Mucus Production? Front Immunol. 2015;6:397.

Torrecillas S, Rivero-Ramírez F, Izquierdo M, Caballero M, Makol A, Suarez-Bregua P, Fernández- Montero A, Rotllant J, Montero D. Feeding European Sea bass (Dicentrarchus labrax) juveniles with a functional synbiotic additive (mannan oligosaccharides and Pediococcus acidilactici): An effective tool to reduce low fishmeal and fish oil gut health effects? Fish Shellfish Immunol. 2018;81:10–20.

van Veelen HPJ, Falcão Salles J, Matson KD, van der Velde M, Tieleman BI. Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata. Animal Microbiome. 2020;2:1–17.

Wright ES. Using DECIPHER v2. 0 to analyze big biological sequence data in R. R Journal 2016:8.

Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinf. 2012;13:134.

Zhang Y-A, Salinas I, Li J, Parra D, Bjork S, Xu Z, LaPatra SE, Bartholomew J, Sunyer JO. IgT, a primitive immunoglobulin class specialized in mucosal immunity. Nat Immunol. 2010;11:827–35.

Zhang Z, Chi H, Niu C, Bøgwald J, Dalmo RA. Molecular cloning and characterization of Foxp3 in Atlantic salmon (Salmo salar). Fish Shellfish Immunol. 2011;30:902–9.

Zhao H, Li C, Beck BH, Zhang R, Thongda W, Davis DA, Peatman E. Impact of feed additives on surface mucosal health and columnaris susceptibility in channel catfish fingerlings, Ictalurus punctatus. Fish & Shellfish Immunol. 2015;46:624–37.

Zhu A, Ibrahim JG, Love MI. Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics. 2019;35:2084–92.

Zhu Q, Gao R, Zhang Y, Pan D, Zhu Y, Zhang X, Yang R, Jiang R, Xu Y, Qin H. Dysbiosis signatures of gut microbiota in coronary artery disease. Physiol Genom. 2018;50:893–903.

Thông tin
Thông tin xuất bản

Animal Microbiome

Thông tin tác giả