Abstract
The microbiome is a complex yet defined set of microbial species in a given habitat. The mining of the human microbiome is pursued in several research projects globally. The microbiota of other vertebrate animals also needs to be studied. Fish represent a diverse group of vertebrates and are the primary source of animal protein. The fish gut microbiota plays a crucial role in the host’s metabolism and can be manipulated to maximize production. Similar to humans, the fish microbiota is studied using culture-dependent and culture-independent techniques, including next-generation sequencing, bioinformatics analysis, and omics. Various fish organs have been examined for their dominant and distinctive microbiota species, including the gills, skin, gut, kidney, liver, and spleen. Under various environmental, dietary, and other physiological situations, the gut microbiota is explored. Gnotobiotic zebrafish represent a valuable model for studying microbe–microbe and microbe–host interactions. Microbe–microbe interactions can be modulated by pre-, pro, and synbiotics, influencing the development of the fish immune system, which will eventually reduce the need for antibiotics. This chapter highlights the necessity of research to advance knowledge of fish health, immune system, metabolism, probiotic research, etc., and to extract novel biomolecules with functional features for creating new medications and pharmaceuticals.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Aleshina E, Miroshnikova E, Sizova E (2020) Transformation of microbiota of fish intestines and gills against the background of molybdenum oxide nanoparticles in environment. Int J Environ Sci Technol 17(2):721–732. https://doi.org/10.1007/s13762-019-02509-x
Austin B (2006) The bacterial microflora of fish, revised. Sci World J 6:931–945. https://doi.org/10.1100/tsw.2006.181
Baldo L, Santos ME, Salzburger W (2011) Comparative transcriptomics of eastern African cichlid fishes shows signs of positive selection and a large contribution of untranslated regions to genetic diversity. Genome Biol Evol 3:443–455. https://doi.org/10.1093/gbe/evr047
Behera BK, Dehury B, Rout AK, Patra B, Mantri N, Chakraborty HJ, Sarkar DJ, Kaushik NK, Bansal V, Singh I, Das BK, Rao AR, Rai A (2021) Metagenomics study in aquatic resource management: recent trends, applied methodologies and future needs. Gene Rep 25:101372. https://doi.org/10.1016/j.genrep.2021.101372
Berg G, Rybakova D, Fischer D, Cernava T, Vergès MC, Charles T, Chen X, Cocolin L, Eversole K, Corral GH, Kazou M, Kinkel L, Lange L, Lima N, Loy A, Macklin JA, Maguin E, Mauchline T, McClure R, Mitter B, Schloter M (2020) Microbiome definition re-visited: old concepts and new challenges. Microbiome 8(1):103. https://doi.org/10.1186/s40168-020-00875-0
Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R, Caporaso JG, Svanbäck R (2014) Individuals’ diet diversity influences gut microbial diversity in two freshwater fish (three spine stickleback and Eurasian perch). Ecol Lett 17(8):979–987. https://doi.org/10.1111/ele.12301
Busti S, Rossi B, Volpe E, Ciulli S, Piva A, D'Amico F, Soverini M, Candela M, Gatta PP, Bonaldo A, Grilli E, Parma L (2020) Effects of dietary organic acids and nature identical compounds on growth, immune parameters and gut microbiota of European sea bass. Sci Rep 10(1):21321. https://doi.org/10.1038/s41598-020-78441-9
Caipang CMA, Suharman I, Avillanosa AL, Bargoyo VT (2020) Host-derived probiotics for finfish aquaculture. In: IOP conference series: earth and environmental science, vol 430. IOP Publishing, Bristol, p 012026. https://doi.org/10.1088/1755-1315/430/1/012026
Cantas L, Sørby JR, Aleström P, Sørum H (2012) Culturable gut microbiota diversity in zebrafish. Zebrafish 9(1):26–37. https://doi.org/10.1089/zeb.2011.0712
Carda-Diéguez M, Mira A, Fouz B (2014) Pyrosequencing survey of intestinal microbiota diversity in cultured sea bass (Dicentrarchus labrax) fed functional diets. FEMS Microbiol Ecol 87(2):451–459. https://doi.org/10.1111/1574-6941.12236
Catalán N, Villasante A, Wacyk J, Ramírez C, Romero J (2018) Fermented soybean meal increases lactic acid bacteria in gut microbiota of Atlantic salmon (Salmo salar). Probiotics Antimicrob Proteins 10(3):566–576. https://doi.org/10.1007/s12602-017-9366-7
Cheesman SE, Neal JT, Mittge E, Seredick BM, Guillemin K (2011) Epithelial cell proliferation in the developing zebrafish intestine is regulated by the Wnt pathway and microbial signaling via Myd88. Proc Natl Acad Sci 108(supplement_1):4570–4577. https://doi.org/10.1073/pnas.1000072107
Chen P, Huang J, Rao L, Zhu W, Yu Y, Xiao F, Yu H, Wu Y, Hu R, Liu X, He Z, Yan Q (2022) Environmental effects of nanoparticles on the ecological succession of gut microbiota across zebrafish development. Sci Total Environ 806(Pt 4):150963. https://doi.org/10.1016/j.scitotenv.2021.150963
Chupani L, Barta J, Zuskova E (2019) Effects of food-borne ZnO nanoparticles on intestinal microbiota of common carp (Cyprinus carpio L.). Environ Sci Pollut Res Int 26(25):25869–25873. https://doi.org/10.1007/s11356-019-05616-x
Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, McCoy SJ, Zhang Y, Anderson MZ, Alvarez-Ponce D, Smirnova E, Karstens L, Dorrestein PC, Li H, Sen Gupta A, Cheung K, Powers JG, Zhao Z, Rosen GL (2020) Emerging priorities for microbiome research. Front Microbiol 11:136. https://doi.org/10.3389/fmicb.2020.00136
de Borba Gurpilhares D, Cinelli LP, Simas NK, Pessoa A Jr, Sette LD (2019) Marine prebiotics: polysaccharides and oligosaccharides obtained by using microbial enzymes. Food Chem 280:175–186. https://doi.org/10.1016/j.foodchem.2018.12.023
de Souza FP, de Lima ECS, Pandolfi VCF, Leite NG, Furlan-Murari PJ, Leal CNS, Mainardi RM, Suphoronski SA, Favero LM, Koch JFA, Pauda UDP, Lopera-Barrero NM (2020) Effect of β-glucan in water on growth performance, blood status and intestinal microbiota in tilapia under hypoxia. Aquac Rep 17:100369. https://doi.org/10.1016/j.aqrep.2020.100369
Degregori S, Casey JM, Barber PH (2021) Nutrient pollution alters the gut microbiome of a territorial reef fish. Mar Pollut Bull 169:112522. https://doi.org/10.1016/j.marpolbul.2021.112522
Desai AR, Links MG, Collins SA, Mansfield GS, Drew MD, Van Kessel AG, Hill JE (2012) Effects of plant-based diets on the distal gut microbiome of rainbow trout (Oncorhynchus mykiss). Aquaculture 350:134–142. https://doi.org/10.1016/j.aquaculture.2012.04.005
Dierckens K, Rekecki A, Laureau S, Sorgeloos P, Boon N, Van den Broeck W, Bossier P (2009) Development of a bacterial challenge test for gnotobiotic sea bass (Dicentrarchus labrax) larvae. Environ Microbiol 11(2):526–533. https://doi.org/10.1111/j.1462-2920.2008.01794.x
Diwan AD, Harke SN, Gopalkrishna, Panche AN (2022) Aquaculture industry prospective from gut microbiome of fish and shellfish: an overview. J Anim Physiol Anim Nutr 106(2):441–469. https://doi.org/10.1111/jpn.13619
Eddy SD, Jones SH (2002) Microbiology of summer flounder Paralichthys dentatus fingerling production at a marine fish hatchery. Aquaculture 211(1–4):9–28. https://doi.org/10.1016/S0044-8486(01)00882-1
Egerton S, Culloty S, Whooley J, Stanton C, Ross RP (2018) The gut microbiota of marine fish. Front Microbiol 9:873. https://doi.org/10.3389/fmicb.2018.00873
FAO (2018). https://www.fao.org/3/I9553EN/i9553en.pdf
Foysal MJ, Fotedar R, Siddik M, Tay A (2020) Lactobacillus acidophilus and L. plantarum improve health status, modulate gut microbiota and innate immune response of marron (Cherax cainii). Sci Rep 10(1):5916. https://doi.org/10.1038/s41598-020-62655-y
Galindo-Villegas J, García-Moreno D, de Oliveira S, Meseguer J, Mulero V (2012) Regulation of immunity and disease resistance by commensal microbes and chromatin modifications during zebrafish development. Proc Natl Acad Sci U S A 109(39):E2605–E2614. https://doi.org/10.1073/pnas.1209920109
Ganguly S, Prasad A (2012) Microflora in fish digestive tract plays significant role in digestion and metabolism. Rev Fish Biol Fish 22(1):11–16. https://doi.org/10.1007/s11160-011-9214-x
Geraylou Z, Souffreau C, Rurangwa E, Maes GE, Spanier KI, Courtin CM, Delcour JA, Buyse J, Ollevier F (2013) Pre-biotic effects of arabinoxylan oligosaccharides on juvenile Siberian sturgeon (Acipenser baerii) with emphasis on the modulation of the gut microbiota using 454 pyrosequencing. FEMS Microbiol Ecol 86(2):357–371. https://doi.org/10.1111/1574-6941.12169
Ghanbari M, Kneifel W, Domig KJ (2015) A new view of the fish gut microbiome: advances from next-generation sequencing. Aquaculture 448:464–475. https://doi.org/10.1016/j.aquaculture.2015.06.033
Ghosh K, Mukherjee A, Dutta D, Banerjee S, Breines EM, Hareide E, Ringø E (2021) Endosymbiotic pathogen-inhibitory gut bacteria in three Indian major carps under polyculture system: a step toward making a probiotics consortium. Aquac Fish 6(2):192–204. https://doi.org/10.1016/j.aaf.2020.03.009
Gómez GD, Balcázar JL (2008) A review on the interactions between gut microbiota and innate immunity of fish. FEMS Immunol Med Microbiol 52(2):145–154. https://doi.org/10.1111/j.1574-695X.2007.00343.x
Green TJ, Smullen R, Barnes AC (2013) Dietary soybean protein concentrate-induced intestinal disorder in marine farmed Atlantic salmon, Salmo salar is associated with alterations in gut microbiota. Vet Microbiol 166(1–2):286–292. https://doi.org/10.1016/j.vetmic.2013.05.009
Han S, Liu Y, Zhou Z, He S, Cao Y, Shi P, Yao B, Ringø E (2010) Analysis of bacterial diversity in the intestine of grass carp (Ctenopharyngodon idellus) based on 16S rDNA gene sequences. Aquac Res 42(1):47–56. https://doi.org/10.1111/j.1365-2109.2010.02543.x
Hansen GH, Olafsen JA (1989) Bacterial colonization of cod (Gadus morhua L.) and halibut (Hippoglossus hippoglossus) eggs in marine aquaculture. Appl Environ Microbiol 55(6):1435–1446. https://doi.org/10.1128/aem.55.6.1435-1446.1989
He S, Wu Z, Liu Y, Wu N, Tao Y, Xu L, Zhou Z, Yao B, Ringø E (2013) Effects of dietary 60 g kg− 1 dried distiller's grains in least-cost practical diets on production and gut allochthonous bacterial composition of cage-cultured fish: comparison among fish species with different natural food habits. Aquac Nutr 19(5):765–772. https://doi.org/10.1111/anu.12023
Higuera-Llantén S, Vásquez-Ponce F, Barrientos-Espinoza B, Mardones FO, Marshall SH, Olivares-Pacheco J (2018) Extended antibiotic treatment in salmon farms select multiresistant gut bacteria with a high prevalence of antibiotic resistance genes. PLoS One 13(9):e0203641. https://doi.org/10.1371/journal.pone.0203641
Horsley R (1977) A review of the bacterial flora of teleosts and elasmobranchs, including methods for its analysis. J Fish Biol 10:529–553. https://doi.org/10.1111/j.1095-8649.1977.tb04086.x
Hoseinifar SH, Esteban MÁ, Cuesta A, Sun YZ (2015) Prebiotics and fish immune response: a review of current knowledge and future perspectives. Rev Fish Sci Aquac 23(4):315–328. https://doi.org/10.1080/23308249.2015.1052365
Hoseinifar SH, Doan HV, Dadar M, Ringø E, Harikrishnan R (2019) Feed additives, gut microbiota, and health in finfish aquaculture. In: Microbial communities in aquaculture ecosystems. Springer, Cham, pp 121–142. https://doi.org/10.1007/978-3-030-16190-3_6
Hovda MB, Lunestad BT, Fontanillas R, Rosnes JT (2007) Molecular characterisation of the intestinal microbiota of farmed Atlantic salmon (Salmo salar L.). Aquaculture 272(1–4):581–588. https://doi.org/10.1016/j.aquaculture.2007.08.045
Hua K, Cobcroft JM, Cole A, Condon K, Jerry DR, Mangott A, Praeger C, Vucko MJ, Zeng C, Zenger K, Strugnell JM (2019) The future of aquatic protein: implications for protein sources in aquaculture diets. One Earth 1(3):316–329. https://doi.org/10.1016/j.oneear.2019.10.018
Ingerslev HC, Strube ML, von Gersdorff Jørgensen L, Dalsgaard I, Boye M, Madsen L (2014) Diet type dictates the gut microbiota and the immune response against Yersinia ruckeri in rainbow trout (Oncorhynchus mykiss). Fish Shellfish Immunol 40(2):624–633. https://doi.org/10.1016/j.fsi.2014.08.021
Kanther M, Sun X, Mühlbauer M, Mackey LC, Flynn EJ, Bagnat M, Jobin C, Rawls JF (2011) Microbial colonization induces dynamic temporal and spatial patterns of NF-κB activation in the zebrafish digestive tract. Gastroenterology 141(1):197–207. https://doi.org/10.1053/j.gastro.2011.03.042
Keating C, Bolton-Warberg M, Hinchcliffe J, Davies R, Whelan S, Wan A, Fitzgerald RD, Davies SJ, Ijaz UZ, Smith CJ (2021) Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae. Anim Microbiome 3(1):7. https://doi.org/10.1186/s42523-020-00065-1
Kim DH, Brunt J, Austin B (2007) Microbial diversity of intestinal contents and mucus in rainbow trout (Oncorhynchus mykiss). J Appl Microbiol 102(6):1654–1664. https://doi.org/10.1111/j.1365-2672.2006.03185.x
Kuang T, He A, Lin Y, Huang X, Liu L, Zhou L (2020) Comparative analysis of microbial communities associated with the gill, gut, and habitat of two filter-feeding fish. Aquac Rep 18:100501. https://doi.org/10.1016/j.aqrep.2020.100501
Kühlwein H, Emery MJ, Rawling MD, Harper GM, Merrifield DL, Davies SJ (2013) Effects of a dietary β-(1,3)(1,6)-D-glucan supplementation on intestinal microbial communities and intestinal ultrastructure of mirror carp (Cyprinus carpio L.). J Appl Microbiol 115(5):1091–1106. https://doi.org/10.1111/jam.12313
Larsen AM, Mohammed HH, Arias CR (2014) Characterization of the gut microbiota of three commercially valuable warm water fish species. J Appl Microbiol 116(6):1396–1404. https://doi.org/10.1111/jam.12475
Lee PT, Yamamoto FY, Low CF, Loh JY, Chong CM (2021) Gut immune system and the implications of oral-administered immunoprophylaxis in finfish aquaculture. Front Immunol 12:773193. https://doi.org/10.3389/fimmu.2021.773193
Legrand T, Wynne JW, Weyrich LS, Oxley A (2020) Investigating both mucosal immunity and microbiota in response to gut enteritis in yellowtail kingfish. Microorganisms 8(9):1267. https://doi.org/10.3390/microorganisms8091267
Li X, Yan Q, Xie S, Hu W, Yu Y, Hu Z (2013) Gut microbiota contributes to the growth of fast-growing transgenic common carp (Cyprinus carpio L.). PLoS One 8(5):e64577. https://doi.org/10.1371/journal.pone.0064577
Lindsay GJH, Gooday GW (1985) Chitinolytic enzymes and the bacterial microflora in the digestive tract of cod, Gadus morhua. J Fish Biol 26(3):255–265. https://doi.org/10.1111/j.1095-8649.1985.tb04264.x
Llewellyn MS, Boutin S, Hoseinifar SH, Derome N (2014) Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Front Microbiol 5:207. https://doi.org/10.3389/fmicb.2014.00207
Luna GM, Quero GM, Kokou F, Kormas K (2022) Time to integrate biotechnological approaches into fish gut microbiome research. Curr Opin Biotechnol 73:121–127. https://doi.org/10.1016/j.copbio.2021.07.018
MacDonald N, Stark J, Austin B (1986) Bacterial microflora in the gastrointestinal tract of Dover sole (Solea solea L.), with emphasis on the possible role of bacteria in the nutrition of the host. FEMS Microbiol Lett 35:107–111. https://doi.org/10.1111/j.1574-6968.1986.tb01508.x
Mansfield GS, Desai AR, Nilson SA, Van Kessel AG, Drew MD, Hill JE (2010) Characterization of rainbow trout (Oncorhynchus mykiss) intestinal microbiota and inflammatory marker gene expression in a recirculating aquaculture system. Aquaculture 307(1–2):95–104. https://doi.org/10.1016/j.aquaculture.2010.07.014
McMurtrie J, Alathari S, Chaput DL, Bass D, Ghambi C, Nagoli J, Deboitteville JD, Mohan CD, Cable J, Temperton B, Tyler CR (2022) Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi. Aquaculture 558:738367. https://doi.org/10.1101/2021.12.06.470702
Merrifield DL, Rodiles A (2015) The fish microbiome and its interactions with mucosal tissues. In: Mucosal health in aquaculture. Academic, Cambridge, MA, pp 273–295. https://doi.org/10.1016/B978-0-12-417186-2.00010-8
Navarrete P, Espejo RT, Romero J (2009) Molecular analysis of microbiota along the digestive tract of juvenile Atlantic salmon (Salmo salar L.). Microb Ecol 57(3):550–561. https://doi.org/10.1007/s00248-008-9448-x
Navarrete P, Magne F, Araneda C, Fuentes P, Barros L, Opazo R, Espejo R, Romero J (2012) PCR-TTGE analysis of 16S rRNA from rainbow trout (Oncorhynchus mykiss) gut microbiota reveals host-specific communities of active bacteria. PLoS One 7(2):e31335. https://doi.org/10.1371/journal.pone.0031335
Nayak SK (2010) Role of gastrointestinal microbiota in fish. Aquacult Res 41:1553–1573. https://doi.org/10.1111/j.1365-2109.2010.02546.x
Nissa MU, Pinto N, Parkar H, Goswami M, Srivastava S (2021) Proteomics in fisheries and aquaculture: an approach for food security. Food Control 127:108125. https://doi.org/10.1016/j.foodcont.2021.108125
Parata L, Mazumder D, Sammut J, Egan S (2020) Diet type influences the gut microbiome and nutrient assimilation of genetically improved farmed tilapia (Oreochromis niloticus). PLoS One 15(8):e0237775. https://doi.org/10.1371/journal.pone.0237775
Parma L, Candela M, Soverini M, Turroni S, Consolandi C, Brigidi P, Mandrioli L, Sirri R, Fontanillas R, Gatta PP, Bonaldo A (2016) 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. Anim Feed Sci Technol 222:204–216. https://doi.org/10.1016/j.anifeedsci.2016.10.022
Pérez T, Balcázar JL, Ruiz-Zarzuela I, Halaihel N, Vendrell D, De Blas I, Múzquiz JL (2010) Host–microbiota interactions within the fish intestinal ecosystem. Mucosal Immunol 3(4):355–360
Pérez-Pascual D, Estellé J, Dutto G, Rodde C, Bernardet JF, Marchand Y, Duchaud E, Przybyla C, Ghigo JM (2020) Growth performance and adaptability of European sea bass (Dicentrarchus labrax) gut microbiota to alternative diets free of fish products. Microorganisms 8(9):1346. https://doi.org/10.3390/microorganisms8091346
Perry WB, Lindsay E, Payne CJ, Brodie C, Kazlauskaite R (2020) The role of the gut microbiome in sustainable teleost aquaculture. Proc R Soc B 287(1926):20200184. https://doi.org/10.1098/rspb.2020.0184
Pham LN, Kanther M, Semova I, Rawls JF (2008) Methods for generating and colonizing gnotobiotic zebrafish. Nat Protoc 3(12):1862–1875. https://doi.org/10.1038/nprot.2008.186
Pond MJ, Stone DM, Alderman DJ (2006) Comparison of conventional and molecular techniques to investigate the intestinal microflora of rainbow trout (Oncorhynchus mykiss). Aquaculture 261(1):194–203. https://doi.org/10.1016/j.aquaculture.2006.06.037
Porter D, Peggs D, McGurk C, Martin S (2022) Immune responses to prebiotics in farmed salmonid fish: how transcriptomic approaches help interpret responses. Fish Shellfish Immunol 127:35–47. https://doi.org/10.1016/j.fsi.2022.05.055
Rangel F, Enes P, Gasco L, Gai F, Hausmann B, Berry D, Oliva-Teles A, Serra CR, Pereira FC (2022) Differential modulation of the european sea bass gut microbiota by distinct insect meals. Front Microbiol 13:831034. https://doi.org/10.3389/fmicb.2022.831034
Rawls JF, Samuel BS, Gordon JI (2004) Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci U S A 101(13):4596–4601. https://doi.org/10.1073/pnas.0400706101
Rawls JF, Mahowald MA, Goodman AL, Trent CM, Gordon JI (2007) In vivo imaging and genetic analysis link bacterial motility and symbiosis in the zebrafish gut. Proc Natl Acad Sci U S A 104(18):7622–7627. https://doi.org/10.1073/pnas.0702386104
Reid HI, Treasurer JW, Adam B, Birkbeck TH (2009) Analysis of bacterial populations in the gut of developing cod larvae and identification of vibrio logei, vibrio anguillarum and Vibrio splendidus as pathogens of cod larvae. Aquaculture 288(1–2):36–43. https://doi.org/10.1016/j.aquaculture.2008.11.022
Rendueles O, Ferrières L, Frétaud M, Bégaud E, Herbomel P, Levraud JP, Ghigo JM (2012) A new zebrafish model of oro-intestinal pathogen colonization reveals a key role for adhesion in protection by probiotic bacteria. PLoS Pathog 8(7):e1002815. https://doi.org/10.1371/journal.ppat.1002815
Rieu A, Aoudia N, Jego G, Chluba J, Yousfi N, Briandet R, Deschamps J, Gasquet B, Monedero V, Garrido C, Guzzo J (2014) The biofilm mode of life boosts the anti-inflammatory properties of lactobacillus. Cell Microbiol 16(12):1836–1853. https://doi.org/10.1111/cmi.12331
Rimoldi S, Terova G, Ascione C, Giannico R, Brambilla F (2018) Next generation sequencing for gut microbiome characterization in rainbow trout (Oncorhynchus mykiss) fed animal by-product meals as an alternative to fishmeal protein sources. PLoS One 13(3):e0193652. https://doi.org/10.1371/journal.pone.0193652
Ringø E, Sperstad S, Myklebust R, Refstie S, Krogdahl Å (2006) Characterisation of the microbiota associated with intestine of Atlantic cod (Gadus morhua L.): the effect of fish meal, standard soybean meal and a bioprocessed soybean meal. Aquaculture 261(3):829–841. https://doi.org/10.1016/j.aquaculture.2006.06.030
Ringø E, Sperstad S, Kraugerud OF, Krogdahl Å (2008) Use of 16S rRNA gene sequencing analysis to characterize culturable intestinal bacteria in Atlantic salmon (Salmo salar) fed diets with cellulose or non-starch polysaccharides from soy. Aquac Res 39(10):1087–1100. https://doi.org/10.1111/j.1365-2109.2008.01972.x
Ringø E, Hoseinifar SH, Ghosh K, Doan HV, Beck BR, Song SK (2018) Lactic acid bacteria in finfish—an update. Front Microbiol 9:1818. https://doi.org/10.3389/fmicb.2018.01818
Russo P, Iturria I, Mohedano ML, Caggianiello G, Rainieri S, Fiocco D, Angel Pardo M, López P, Spano G (2015) Zebrafish gut colonization by mCherry-labelled lactic acid bacteria. Appl Microbiol Biotechnol 99(8):3479–3490. https://doi.org/10.1007/s00253-014-6351-x
Saggese I, Sarà G, Dondero F (2016) Silver nanoparticles affect functional bioenergetic traits in the invasive red sea mussel Brachidontes pharaonis. Biomed Res Int 2016:1872351. https://doi.org/10.1155/2016/1872351
Salam MA, Rahman MA, Paul SI, Islam F, Barman AK, Rahman Z, Shaha DC, Rahman MM, Islam T (2021) Dietary chitosan promotes the growth, biochemical composition, gut microbiota, hematological parameters and internal organ morphology of juvenile Barbonymus gonionotus. PLoS One 16(11):e0260192. https://doi.org/10.1371/journal.pone.0260192
Semova I, Carten JD, Stombaugh J, Mackey LC, Knight R, Farber SA, Rawls JF (2012) Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Cell Host Microbe 12(3):277–288. https://doi.org/10.1016/j.chom.2012.08.003
Shehata HR, Mitterboeck TF, Hanner R (2020) Characterization of the microbiota of commercially traded finfish fillets. Food Res Int 137:109373. https://doi.org/10.1016/j.foodres.2020.109373
Sherif, AH, El-Sharawy, MES, El-Samannoudy, SI, Adel Seida, A, Sabry, NM, Eldawoudy, M, Abdelsalam, M, Younis, NA (2021). The deleterious impacts of dietary titanium dioxide nanoparticles on the intestinal microbiota, antioxidant enzymes, diseases resistances and immune response of Nile tilapia. Aquaculture Research, 52(12): pp.6699–6707
Skrodenyte-Arbaciauskiene V, Sruoga A, Butkauskas D (2006) Assessment of microbial diversity in the river trout Salmo trutta fario L. intestinal tract identified by partial 16S rRNA gene sequence analysis. Fish Sci 72:597–602. https://doi.org/10.1111/j.1444-2906.2006.01189.x
Skrodenytė-Arbačiauskienė V, Sruoga A, Butkauskas D, Skrupskelis K (2008) Phylogenetic analysis of intestinal bacteria of freshwater salmon Salmo salar and sea trout Salmo trutta trutta and diet. Fish Sci 74(6):1307–1314. https://doi.org/10.1111/j.1444-2906.2008.01656.x
Smriga S, Sandin SA, Azam F (2010) Abundance, diversity, and activity of microbial assemblages associated with coral reef fish guts and feces. FEMS Microbiol Ecol 73(1):31–42. https://doi.org/10.1111/j.1574-6941.2010.00879.x
Star B, Haverkamp TH, Jentoft S, Jakobsen KS (2013) Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location. BMC Microbiol 13:248. https://doi.org/10.1186/1471-2180-13-248
Sullam KE, Dalton CM, Russell JA, Kilham SS, El-Sabaawi R, German DP, Flecker AS (2015) Changes in digestive traits and body nutritional composition accommodate a trophic niche shift in Trinidadian guppies. Oecologia 177(1):245–257. https://doi.org/10.1007/s00442-014-3158-5
Sun Y, Yang H, Ling Z, Chang J, Ye J (2009) Gut microbiota of fast and slow growing grouper Epinephelus coioides. Afr J Microbiol Res 3(11):637–640
Terova G, Rimoldi S, Ascione C, Gini E, Ceccotti C, Gasco L (2019) Rainbow trout (Oncorhynchus mykiss) gut microbiota is modulated by insect meal from Hermetia illucens prepupae in the diet. Rev Fish Biol Fish 29(2):465–486. https://doi.org/10.1007/s11160-019-09558-y
Thomas A, Konteles SJ, Ouzounis S, Papatheodorou S, Tsakni A, Houhoula D, Tsironi T (2021) Bacterial community in response to packaging conditions in farmed gilthead seabream. Aquac Fish 8:410. https://doi.org/10.1016/j.aaf.2021.09.002
Ting CH, Pan CY, Chen YC, Lin YC, Chen TY, Rajanbabu V, Chen JY (2019) Impact of tilapia hepcidin 2-3 dietary supplementation on the gut microbiota profile and immunomodulation in the grouper (Epinephelus lanceolatus). Sci Rep 9(1):19047. https://doi.org/10.1038/s41598-019-55509-9
Toh MC, Goodyear M, Daigneault M, Allen-Vercoe E, Van Raay TJ (2013) Colonizing the embryonic zebrafish gut with anaerobic bacteria derived from the human gastrointestinal tract. Zebrafish 10(2):194–198. https://doi.org/10.1089/zeb.2012.0814
Tsuchiya C, Sakata T, Sugita H (2008) Novel ecological niche of Cetobacterium somerae, an anaerobic bacterium in the intestinal tracts of freshwater fish. Lett Appl Microbiol 46(1):43–48. https://doi.org/10.1111/j.1472-765X.2007.02258.x
Villasante A, Ramírez C, Catalán N, Opazo R, Dantagnan P, Romero J (2019) Effect of dietary carbohydrate-to-protein ratio on gut microbiota in Atlantic salmon (Salmo salar). Animals 9(3):89. https://doi.org/10.3390/ani9030089
Villasante A, Ramírez C, Rodríguez H, Dantagnan P, Hernández A, Figueroa E, Romero J (2022) Dietary carbohydrate-to-protein ratio influences growth performance, hepatic health and dynamic of gut microbiota in Atlantic salmon (Salmo salar). Anim Nutr 10:261–279. https://doi.org/10.1016/j.aninu.2022.04.003
Wang AR, Ran C, Ringø E, Zhou ZG (2018) Progress in fish gastrointestinal microbiota research. Rev Aquac 10(3):626–640. https://doi.org/10.1111/raq.12191
Wang SX, Zhang JY, Du XK, Liu DJ, Liu LX, Shen XH (2022) Comparative analysis of the intestinal microbiota in goldfish and crucian carps between different aquaponics and traditional farming. Aquac Rep 25:101240. https://doi.org/10.3389/fmicb.2021.760266
Ward NL, Steven B, Penn K, Methé BA, Detrich WH 3rd (2009) Characterization of the intestinal microbiota of two Antarctic notothenioid fish species. Extremophiles 13(4):679–685. https://doi.org/10.1007/s00792-009-0252-4
Webster TMU, Consuegra S, Hitchings M, de Leaniz CG (2018) Interpopulation variation in the Atlantic salmon microbiome reflects environmental and genetic diversity. Appl Environ Microbiol 84(16):e00691. https://doi.org/10.1128/AEM.00691-18
Xia JH, Lin G, Fu GH, Wan ZY, Lee M, Wang L, Liu XJ, Yue GH (2014) The intestinal microbiome of fish under starvation. BMC Genomics 15:266. https://doi.org/10.1186/1471-2164-15-266
Xiong JB, Nie L, Chen J (2019) Current understanding on the roles of gut microbiota in fish disease and immunity. Zool Res 40(2):70–76. https://doi.org/10.24272/j.issn.2095-8137.2018.069
Ye L, Amberg J, Chapman D, Gaikowski M, Liu WT (2014) Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish. ISME J 8(3):541–551. https://doi.org/10.1038/ismej.2013.181
Zarkasi KZ, Abell GC, Taylor RS, Neuman C, Hatje E, Tamplin ML, Katouli M, Bowman JP (2014) Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salar L.) within a commercial mariculture system. J Appl Microbiol 117(1):18–27. https://doi.org/10.1111/jam.12514
Zhang QL, Yan Y, Shen JY, Hao GJ, Shi CY, Wang QT, Liu H, Huang J (2013) Development of a reverse transcription loop-mediated isothermal amplification assay for rapid detection of grass carp reovirus. J Virol Methods 187(2):384–389. https://doi.org/10.1016/j.jviromet.2012.11.005
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Rajwade, J.M., Kulkarni, S.S., Vanjari, J. (2023). Introduction to Finfish Microbiome and Its Importance. In: Diwan, A., Harke, S.N., Panche, A. (eds) Microbiome of Finfish and Shellfish. Springer, Singapore. https://doi.org/10.1007/978-981-99-0852-3_1
Download citation
DOI: https://doi.org/10.1007/978-981-99-0852-3_1
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-99-0851-6
Online ISBN: 978-981-99-0852-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)