鱼类肠道菌群影响因子研究进展
|
摘要
肠道菌群在维持肠道健康、促进肠道发育、抵抗病原入侵、调节机体能量吸收和脂质代谢过程中均发挥重要作用。在鱼类学研究中,由于种类繁多、食性差异大、生存环境复杂多变,导致鱼类肠道菌群方面的研究面临巨大挑战。本文在总结常见鱼类肠道微生物组成的基础上,着重介绍了鱼类饵料组成、水环境因子、物种、基因型、发育阶段、养殖模式及投喂策略对鱼类肠道菌群影响的相关研究进展,并对目前研究中存在的问题进行了剖析,以期为鱼类肠道菌群研究提供一定的参考依据。
The microbiota plays a major role in the health and disease in animals, including maintaining health ofthe gut, promoting development of epithelium cells, resisting the intrusion of pathogenic bacteria, regulating theabsorption harvest of energy and metabolism of lipid. It is a great challenge to the fish gut microbiota research dueto the complicated factors, such as differences of fish species, feeding habits or survival environment. Based on theprevious related researches, the present article first reviewed the gut microbiota composition of different fishes.Also, the effects of different factors on the gut microbiota of fish were reviewed, such as feed component, waterchemical factors, fish species, genotype, developmental stages, aquaculture models and strategies of feeding.Finally, some present issues and future research directions about the fish microbiota were presented.
The microbiota plays a major role in the health and disease in animals, including maintaining health ofthe gut, promoting development of epithelium cells, resisting the intrusion of pathogenic bacteria, regulating theabsorption harvest of energy and metabolism of lipid. It is a great challenge to the fish gut microbiota research dueto the complicated factors, such as differences of fish species, feeding habits or survival environment. Based on theprevious related researches, the present article first reviewed the gut microbiota composition of different fishes.Also, the effects of different factors on the gut microbiota of fish were reviewed, such as feed component, waterchemical factors, fish species, genotype, developmental stages, aquaculture models and strategies of feeding.Finally, some present issues and future research directions about the fish microbiota were presented.
引文
[1]Bondia-Pons I,Hy?tyl?inen T,Ore?i?M.Role of microbiota in regulating host lipid metabolism and disease risk[M]//Kochhar S,Martin F P.Metabonomics and Gut Microbiota in Nutrition and Disease.London:Springer,2015:235-260.
[2]El Aidy S,Derrien M,Merrifield C A,et al.Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon[J].The ISME Journal,2012,7(4):743-755.
[3]Sonnenburg J L,Backhed F.Diet-microbiota interactions as moderators of human metabolism[J].Nature,2016,535(7610):56-64.
[4]Candela M,Biagi E,Maccaferri S,et al.Intestinal microbiota is a plastic factor responding to environmental changes[J].Trends in Microbiology,2012,20(8):385-391.
[5]Karl J P,Margolis L M,Madslien E H,et al.Changes in intestinal microbiota composition and metabolism coincide with increased intestinal permeability in young adults under prolonged physiological stress[J].American Journal of Physiology-Gastrointestinal and Liver Physiology,2017,312(6):G559-G571.
[6]Benson A K,Kelly S A,Legge R,et al.Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors[J].Proceedings of the National Academy of Sciences of the United States of America,2010,107(44):18933-18938.
[7]Llewellyn M S,Boutin S,Hoseinifar S H,et al.Teleost microbiomes:the state of the art in their characterization,manipulation and importance in aquaculture and fisheries[J].Frontiers in Microbiology,2014,5:207.
[8]Burr G,Gatlin III D,Ricke S.Microbial ecology of the gastrointestinal tract of fish and the potential application of prebiotics and probiotics in finfish aquaculture[J].Journal of the World Aquaculture Society,2005,36(4):425-436.
[9]Nayak S K.Role of gastrointestinal microbiota in fish[J].Aquaculture Research,2010,41(11):1553-1573.
[10]Wang A R,Ran C,Ring?E,et al.Progress in fish gastrointestinal microbiota research[J].Reviews in Aquaculture,2018,10(3):626-640.
[11]Talwar C,Nagar S,Lal R,et al.Fish gut microbiome:current approaches and future perspectives[J].Indian Journal of Microbiology,2018,58(4):397-414.
[12]Kim D H,Brunt J,Austin B.Microbial diversity of intestinal contents and mucus in rainbow trout(Oncorhynchus mykiss)[J].Journal of Applied Microbiology,2007,102(6):1654-1664.
[13]Merrifield D L,Burnard D,Bradley G,et al.Microbial community diversity associated with the intestinal mucosa of farmed rainbow trout(Oncoryhnchus mykiss Walbaum)[J].Aquaculture Research,2009,40(9):1064-1072.
[14]Liu H,Guo X W,Gooneratne R,et al.The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels[J].Scientific Reports,2016,6:24340.
[15]Han S F,Liu Y C,Zhou Z G,et al.Analysis of bacterial diversity in the intestine of grass carp(Ctenopharyngodon idellus)based on 16S rDNA gene sequences[J].Aquaculture Research,2010,42(1):47-56.
[16]Wu S G,Wang G T,Angert E R,et al.Composition,diversity,and origin of the bacterial community in grass carp intestine[J].PLoS One,2012,7(2):e30440.
[17]Ni J J,Yan Q Y,Yu Y H,et al.Factors influencing the grass carp gut microbiome and its effect on metaboli- sm[J].FEMS Microbiology Ecology,2014,87(3):704-714.
[18]Jiang Y,Xie C X,Yang G M,et al.Cellulase-producing bacteria of Aeromonas are dominant and indigenous in the gut of Ctenopharyngodon idellus(Valenciennes)[J].Aquaculture Research,2011,42(4):499-505.
[19]Van Kessel M A H J,Dutilh B E,Neveling K,et al.Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp(Cyprinus carpio L.)[J].AMB Express,2011,1:41.
[20]Meng X L,Li S,Qin C B,et al.Intestinal microbiota and lipid metabolism responses in the common carp(Cyprinus carpio L.)following copper exposure[J].Ecotoxicology and Environmental Safety,2018,160:257-264.
[21]Gajardo K,Rodiles A,Kortner T M,et al.A highresolution map of the gut microbiota in Atlantic salmon(Salmo salar):a basis for comparative gut microbial research[J].Scientific Reports,2016,6:30893.
[22]Ring?E,Sperstad S,Myklebust R,et al.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[J].Aquaculture,2006,261(3):829-841.
[23]邢孟欣,李贵阳,侯战辉,等.不同大菱鲆(Scophthalmus maximus)个体肠道菌群结构差异研究[J].现代生物医学进展,2014,14(20):3801-3805.Xing M X,Li G Y,Hou Z H,et al.Different taxonomic distribution of gastrointestinal tract microbiome of turbot(Scophthalmus maximus)individuals[J].Progress in Modern Biomedicine,2014,14(20):3801-3805(in Chinese).
[24]Mansfield G S,Desai A R,Nilson S A,et al.Characterization of rainbow trout(Oncorhynchus mykiss)intestinal microbiota and inflammatory marker gene expression in a recirculating aquaculture system[J].Aquaculture,2010,307(1-2):95-104.
[25]Ceppa F,Faccenda F,De Filippo C,et al.Influence of essential oils in diet and life-stage on gut microbiota and fillet quality of rainbow trout(Oncorhynchus mykiss)[J].International Journal of Food Sciences and Nutrition,2018,69(3):318-333.
[26]Bledsoe J W,Peterson B C,Swanson K S,et al.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[J].PLoS One,2016,11(11):e0166379.
[27]Larsen A M,Mohammed H H,Arias C R.Characterization of the gut microbiota of three commercially valuable warmwater fish species[J].Journal of Applied Microbiology,2014,116(6):1396-1404.
[28]Li X M,Yan Q Y,Xie S Q,et al.Gut microbiota contributes to the growth of fast-growing transgenic common carp(Cyprinus carpio L.)[J].PLoS One,2013,8(5):e64577.
[29]Liu W S,Yang Y O,Zhang J L,et al.Effects of dietary microencapsulated sodium butyrate on growth,intestinal mucosal morphology,immune response and adhesive bacteria in juvenile common carp(Cyprinus carpio)prefed with or without oxidised oil[J].British Journal of Nutrition,2014,112(1):15-29.
[30]Roeselers G,Mittge E K,Stephens W Z,et al.Evidence for a core gut microbiota in the zebrafish[J].The ISMEJournal,2011,5(10):1595-1608.
[31]Cantas L,S?rby J R T,Alestr?m P,et al.Culturable gut microbiota diversity in zebrafish[J].Zebrafish,2012,9(1):26-37.
[32]Falcinelli S,Picchietti S,Rodiles A,et al.Lactobacillus rhamnosus lowers zebrafish lipid content by changing gut microbiota and host transcription of genes involved in lipid metabolism[J].Scientific Reports,2015,5:9336.
[33]Hovda M B,Lunestad B T,Fontanillas R,et al.Molecular characterisation of the intestinal microbiota of farmed Atlantic salmon(Salmo salar L.)[J].Aquaculture,2007,272(1-4):581-588.
[34]Bagi A,Riiser E S,Molland H S,et al.Gastrointestinal microbial community changes in Atlantic cod(Gadus morhua)exposed to crude oil[J].BMC Microbiology,2018,18(1):25.
[35]Ring?E,Bendiksen H R,Gausen S J,et al.The effect of dietary fatty acids on lactic acid bacteria associated with the epithelial mucosa and from faecalia of Arctic charr,Salvelinus alpinus(L.)[J].Journal of Applied Microbiology,1988,85(5):855-864.
[36]Xing M X,Hou Z H,Yuan J B,et al.Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot(Scophthalmus maximus)[J].FEMS Microbiology Ecology,2013,86(3):432-443.
[37]杜震宇.养殖鱼类脂肪肝成因及相关思考[J].水产学报,2014,38(9):1628-1638.Du Z Y.Causes of fatty liver in farmed fish:a review and new perspectives[J].Journal of Fisheries of China,2014,38(9):1628-1638(in Chinese).
[38]Falcinelli S,Rodiles A,Hatef A,et al.Dietary lipid content reorganizes gut microbiota and probiotic L.rhamnosus attenuates obesity and enhances catabolic hormonal milieu in zebrafish[J].Scientific Reports,2017,7(1):5512.
[39]Wong S,Stephens W Z,Burns A R,et al.Ontogenetic differences in dietary fat influence microbiota assembly in the zebrafish gut[J].Microbiology,2015,6(5):e00687-15.
[40]Lésel R,De La Noüe J,Choubert G.Fecal bacterial flora of rainbow trout under antibiotic treatment:effect of the number of pyloric caeca and the lipid content of food[M]//De Pauw N E,Jaspers E,Ackefords H,et al.Aquaculture:A Biotechnology in Progress.Bredene,Belgium:European Aquaculture Society,1989:897-903.
[41]Semova I,Carten J D,Stombaugh J,et al.Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish[J].Cell Host&Microbe,2012,12(3):277-288.
[42]Ring?E,Zhou Z,Vecino J L G,et al.Effect of dietary components on the gut microbiota of aquatic animals.Anever‐ending story?[J].Aquaculture Nutrition,2016,22(2):219-282.
[43]Ring?E,L?demel J B,Myklebust R,et al.The effects of soybean,linseed and marine oils on aerobic gut microbiota of Arctic charr Salvelinus alpinus L.before and after challenge with Aeromonas salmonicida ssp.salmonicida[J].Aquaculture Research,2002,33(8):591-606.
[44]Hartviksen M,Vecino J L G,Ring?E,et al.Alternative dietary protein sources for Atlantic salmon(Salmo salar L.)effect on intestinal microbiota,intestinal and liver histology and growth[J].Aquaculture Nutrition,2014,20(4):381-398.
[45]Desai A R,Links M G,Collins S A,et al.Effects of plant-based diets on the distal gut microbiome of rainbow trout(Oncorhynchus mykiss)[J].Aquaculture,2012,350-353:134-142.
[46]Cai C F,Wang W J,Ye Y T,et al.Effect of soybean meal,raffinose and stachyose on the growth,body composition,intestinal morphology and intestinal microflora of juvenile allogynogenetic silver crucian carp(Carassius auratus gibelio♀×Cyprinus carpio♂)[J].Aquaculture Research,2012,43(1):128-138.
[47]姜雪姣,梁丹妮,刘文斌,等.团头鲂对8种非常规饲料原料中营养物质的表观消化率[J].水产学报,2011,35(6):932-939.Jiang X J,Liang D N,Liu W B,et al.Apparent digestibility of eight unconventional feed ingredients for Megalobrama amblycephala[J].Journal of Fisheries of China,2011,35(6):932-939(in Chinese).
[48]Magalh?es R,Sánchez-López A,Leal R S,et al.Black soldier fly(Hermetia illucens)pre-pupae meal as a fish meal replacement in diets for European seabass(Dicentrarchus labrax)[J].Aquaculture,2017,476:79-85.
[49]Zhang Y R,Qin C B,Yang L P,et al.A comparative genomics study of carbohydrate/glucose metabolic genes:from fish to mammals[J].BMC Genomics,2018,19(1):246.
[50]Mojsov S.Glucagon-like peptide-1(GLP-1)and the control of glucose metabolism in mammals and teleost fish[J].American Zoologist,2000,40(2):246-258.
[51]Gatesoupe F J,Huelvan C,Le Bayon N,et al.The effects of dietary carbohydrate sources and forms on metabolic response and intestinal microbiota in sea bass juveniles,Dicentrarchus labrax[J].Aquaculture,2014,422:47-53.
[52]Geurden I,Mennigen J,Plagnes-Juan E,et al.High or low dietary carbohydrate:protein ratios during firstfeeding affect glucose metabolism and intestinal microbiota in juvenile rainbow trout[J].The Journal of Experimental Biology,2014,217(19):3396-3406.
[53]Liu Y,Chi L,Feng L,et al.Effects of graded levels of dietary vitamin C on the growth,digestive capacity and intestinal microflora of juvenile Jian carp(Cyprinus carpio var.Jian)[J].Aquaculture Research,2011,42(4):534-548.
[54]Wen Z P,Feng L,Jiang J,et al.Immune response,disease resistance and intestinal microflora of juvenile Jian carp(Cyprinus carpio var.Jian)fed graded levels of pantothenic acid[J].Aquaculture Nutrition,2010,16(4):430-436.
[55]Zhao J,Feng L,Liu Y,et al.Effect of dietary isoleucine on the immunity,antioxidant status,tight junctions and microflora in the intestine of juvenile Jian carp(Cyprinus carpio var.Jian)[J].Fish&Shellfish Immunology,2014,41(2):663-673.
[56]Zhao S,Feng L,Liu Y,et al.Effects of dietary biotin supplement on growth,body composition,intestinal enzyme activities and microbiota of juvenile Jian carp(Cyprinus carpio var.Jian)[J].Aquaculture Nutrition,2012,18(4):400-410.
[57]Tang L,Wang G X,Jiang JJ,et al.Effect of methionine on intestinal enzymes activities,microflora and humoral immune of juvenile Jian carp(cyprinus carpio var.Jian)[J].Aquaculture Nutrition,2009,15(5):477-483.
[58]Xie N B,Feng L,Liu Y,et al.Growth,body composition,intestinal enzyme activities and microflora of juvenile Jian carp(Cyprinus carpio var.Jian)fed graded levels of dietary phosphorus[J].Aquaculture Nutrition,2011,17(6):645-656.
[59]Hu C H,Xu Y,Xia M S,et al.Effects of Cu2+-exchanged montmorillonite on growth performance,microbial ecology and intestinal morphology of Nile tilapia(Oreochromis niloticus)[J].Aquaculture,2007,270(1-4):200-206.
[60]Merrifield D L,Shaw B J,Harper G M,et al.Ingestion of metal-nanoparticle contaminated food disrupts endogenous microbiota in zebrafish(Danio rerio)[J].Environmental Pollution,2013,174:157-163.
[61]Merrifield D L,Carnevali O.Probiotic modulation of the gut microbiota of fish[M]//Merrifield D,Ring?E.Aquaculture Nutrition:Gut Health,Probiotics and Prebiotics.Oxford,UK:John Wiley&Sons,2014:185-222.
[62]Ahire J J,Mokashe N U,Chaudhari B L.Effect of dietary probiotic Lactobacillus helveticus on growth performance,antioxidant levels,and absorption of essential trace elements in goldfish(Carassius auratus)[J].Probiotics and Antimicrobial Proteins,2018.
[63]Adel M,El-Sayed A F M,Yeganeh S,et al.Effect of potential probiotic Lactococcus lactis subsp.lactis on growth performance,intestinal microbiota,digestive enzyme activities,and disease resistance of Litopenaeus vannamei[J].Probiotics and Antimicrobial Proteins,2017,9(2):150-156.
[64]Zhai Q X,Yu L L,Li T Q,et al.Effect of dietary probiotic supplementation on intestinal microbiota and physiological conditions of Nile tilapia(Oreochromis niloticus)under waterborne cadmium exposure[J]Antonie van Leeuwenhoek,2017,110(4):501-513.
[65]Dawood M A O,Koshio S,Ishikawa M,et al.Effects of dietary supplementation of Lactobacillus rhamnosus or/and Lactococcus lactis on the growth,gut microbiota and immune responses of red sea bream,Pagrus major[J].Fish&Shellfish Immunology,2016,49:275-285.
[66]Nyman A,Huyben D,Lundh T,et al.Effects of microbe-and mussel-based diets on the gut microbiota in Arctic charr(Salvelinus alpinus)[J].Aquaculture Reports,2017,5:34-40.
[67]Giorgia G,Elia C,Andrea P,et al.Effects of lactogen13,a new probiotic preparation,on gut microbiota and endocrine signals controlling growth and appetite of Oreochromis niloticus juveniles[J].Microbial Ecology2018,76(4):1063-1074.
[68]Adel M,Lazado C C,Safari R,et al.Aqualase?,a yeastbased in-feed probiotic,modulates intestinal microbiota immunity and growth of rainbow trout Oncorhynchus mykiss[J].Aquaculture Research,2017,48(4):1815-1826.
[69]Liu Z,Liu W S,Ran C,et al.Abrupt suspension of probiotics administration may increase host pathogen susceptibility by inducing gut dysbiosis[J].Scientific Reports,2016,6:23214.
[70]Guerreiro I,Serra C R,Oliva-Teles A,et al.Short communication:gut microbiota of European sea bass(Dicentrarchus labrax)is modulated by short-chain fructooligosaccharides and xylooligosaccharides[J]Aquaculture International,2018,26(1):279-288.
[71]Hoseinifar S H,Mirvaghefi A,Amoozegar M A,et al.In vitro selection of a synbiotic and in vivo evaluation on intestinal microbiota,performance and physiological response of rainbow trout(Oncorhynchus mykiss)fingerlings[J].Aquaculture Nutrition,2017,23(1):111-118.
[72]Alonso S,Gastro M C,Berdasco M,et al.Islation and partial characterization of lactic acid bacteria from the gut microbiota of marine fishes for potential application as probiotics in aquaculture[J].Probiotics and Antimicrobial Proteins,2018,1-11
[73]Xu J,Chen H B,Li S L.Understanding the molecular mechanisms of the interplay between herbal medicines and gut microbiota[J].Medicinal Research Reviews,2017,37(5):1140-1185.
[74]Xu J,Lian F M,Zhao L H,et al.Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula[J].The ISME Journal,2015,9(3):552-562.
[75]刘红柏,张颖,杨雨辉,等.5种中草药作为饲料添加剂对鲤肠内细菌及生长的影响[J].大连水产学院学报,2004,19(1):16-20.Liu H B,Zhang Y,Yang Y H,et al.Effects of five Chinese herb medicines as additive in feed on the growth and intestinal microflora in common carp(Cyprinus carpio)[J].Journal of Dalian Fisheries University,2004,19(1):16-20(in Chinese).
[76]Wu Z B,Gatesoupe F J,Li T T,et al.Significant improvement of intestinal microbiota of gibel carp(Carassius auratus gibelio)after traditional Chinese medicine feeding[J].Journal of Applied Microbiology,2018,124(3):829-841.
[77]Giannenas I,Triantafillou E,Stavrakakis S,et al.Assessment of dietary supplementation with carvacrol or thymol containing feed additives on performance,intestinal microbiota and antioxidant status of rainbow trout(Oncorhynchus mykiss)[J].Aquaculture,2012,350-353:26-32.
[78]Sylvain Fé,Cheaib B,Llewellyn M,et al.pH drop impacts differentially skin and gut microbiota of the Amazonian fish tambaqui(Colossoma macropomum)[J].Scientific Reports,2016,6:32032.
[79]Li X M,Yu Y H,Feng W S,et al.Host species as a strong determinant of the intestinal microbiota of fish larvae[J].The Journal of Microbiology,2012,50(1):29-37.
[80]Stephens W Z,Burns A R,Stagaman K,et al.The composition of the zebrafish intestinal microbial community varies across development[J].The ISMEJournal,2016,10(3):644-654.
[81]Wong S,Waldrop T,Summerfelt S,et al.Aquacultured rainbow trout(Oncorhynchus mykiss)possess a large core intestinal microbiota that is resistant to variation in diet and rearing density[J].Applied and Environmental Microbiology,2013,79(16):4974-4984.
[82]Ingerslev H C,Von Gersdorff J?rgensen L V,Strube ML,et al.The development of the gut microbiota in rainbow trout(Oncorhynchus mykiss)is affected by first feeding and diet type[J].Aquaculture,2014,424-425:24-34.
[83]Xia J H,Lin G,Fu G H,et al.The intestinal microbiome of fish under starvation[J].BMC Genomics,2014,15:266.
[84]Sha Y J,Liu M,Wang B J,et al.Bacterial population in intestines of Litopenaeus vannamei fed different probiotics or probiotic supernatant[J].Journal of Microbiology and Biotechnology,2016,26(10):1736-1745.
[85]Sha Y J,Wang L,Liu M,et al.Effects of lactic acid bacteria and the corresponding supernatant on the survival,growth performance,immune response and disease resistance of Litopenaeus vannamei[J].Aquaculture,2016,452:28-36.
[86]Rawls J F,Samuel B S,Gordon J I.Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota[J].Proceedings of the National Academy of Sciences of the United States of America,2004,101(13):4596-4601.
[87]Sheng Y,Ren H,Limbu S M,et al.The presence or absence of intestinal microbiota affects lipid deposition and related genes expression in zebrafish(Danio rerio)[J].Frontiers in Microbiology,2018,9:1124.
[88]Rawls J F,Mahowald M A,Ley R E,et al.Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection[J].Cell,2006,127(2):423-433.
[2]El Aidy S,Derrien M,Merrifield C A,et al.Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon[J].The ISME Journal,2012,7(4):743-755.
[3]Sonnenburg J L,Backhed F.Diet-microbiota interactions as moderators of human metabolism[J].Nature,2016,535(7610):56-64.
[4]Candela M,Biagi E,Maccaferri S,et al.Intestinal microbiota is a plastic factor responding to environmental changes[J].Trends in Microbiology,2012,20(8):385-391.
[5]Karl J P,Margolis L M,Madslien E H,et al.Changes in intestinal microbiota composition and metabolism coincide with increased intestinal permeability in young adults under prolonged physiological stress[J].American Journal of Physiology-Gastrointestinal and Liver Physiology,2017,312(6):G559-G571.
[6]Benson A K,Kelly S A,Legge R,et al.Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors[J].Proceedings of the National Academy of Sciences of the United States of America,2010,107(44):18933-18938.
[7]Llewellyn M S,Boutin S,Hoseinifar S H,et al.Teleost microbiomes:the state of the art in their characterization,manipulation and importance in aquaculture and fisheries[J].Frontiers in Microbiology,2014,5:207.
[8]Burr G,Gatlin III D,Ricke S.Microbial ecology of the gastrointestinal tract of fish and the potential application of prebiotics and probiotics in finfish aquaculture[J].Journal of the World Aquaculture Society,2005,36(4):425-436.
[9]Nayak S K.Role of gastrointestinal microbiota in fish[J].Aquaculture Research,2010,41(11):1553-1573.
[10]Wang A R,Ran C,Ring?E,et al.Progress in fish gastrointestinal microbiota research[J].Reviews in Aquaculture,2018,10(3):626-640.
[11]Talwar C,Nagar S,Lal R,et al.Fish gut microbiome:current approaches and future perspectives[J].Indian Journal of Microbiology,2018,58(4):397-414.
[12]Kim D H,Brunt J,Austin B.Microbial diversity of intestinal contents and mucus in rainbow trout(Oncorhynchus mykiss)[J].Journal of Applied Microbiology,2007,102(6):1654-1664.
[13]Merrifield D L,Burnard D,Bradley G,et al.Microbial community diversity associated with the intestinal mucosa of farmed rainbow trout(Oncoryhnchus mykiss Walbaum)[J].Aquaculture Research,2009,40(9):1064-1072.
[14]Liu H,Guo X W,Gooneratne R,et al.The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels[J].Scientific Reports,2016,6:24340.
[15]Han S F,Liu Y C,Zhou Z G,et al.Analysis of bacterial diversity in the intestine of grass carp(Ctenopharyngodon idellus)based on 16S rDNA gene sequences[J].Aquaculture Research,2010,42(1):47-56.
[16]Wu S G,Wang G T,Angert E R,et al.Composition,diversity,and origin of the bacterial community in grass carp intestine[J].PLoS One,2012,7(2):e30440.
[17]Ni J J,Yan Q Y,Yu Y H,et al.Factors influencing the grass carp gut microbiome and its effect on metaboli- sm[J].FEMS Microbiology Ecology,2014,87(3):704-714.
[18]Jiang Y,Xie C X,Yang G M,et al.Cellulase-producing bacteria of Aeromonas are dominant and indigenous in the gut of Ctenopharyngodon idellus(Valenciennes)[J].Aquaculture Research,2011,42(4):499-505.
[19]Van Kessel M A H J,Dutilh B E,Neveling K,et al.Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp(Cyprinus carpio L.)[J].AMB Express,2011,1:41.
[20]Meng X L,Li S,Qin C B,et al.Intestinal microbiota and lipid metabolism responses in the common carp(Cyprinus carpio L.)following copper exposure[J].Ecotoxicology and Environmental Safety,2018,160:257-264.
[21]Gajardo K,Rodiles A,Kortner T M,et al.A highresolution map of the gut microbiota in Atlantic salmon(Salmo salar):a basis for comparative gut microbial research[J].Scientific Reports,2016,6:30893.
[22]Ring?E,Sperstad S,Myklebust R,et al.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[J].Aquaculture,2006,261(3):829-841.
[23]邢孟欣,李贵阳,侯战辉,等.不同大菱鲆(Scophthalmus maximus)个体肠道菌群结构差异研究[J].现代生物医学进展,2014,14(20):3801-3805.Xing M X,Li G Y,Hou Z H,et al.Different taxonomic distribution of gastrointestinal tract microbiome of turbot(Scophthalmus maximus)individuals[J].Progress in Modern Biomedicine,2014,14(20):3801-3805(in Chinese).
[24]Mansfield G S,Desai A R,Nilson S A,et al.Characterization of rainbow trout(Oncorhynchus mykiss)intestinal microbiota and inflammatory marker gene expression in a recirculating aquaculture system[J].Aquaculture,2010,307(1-2):95-104.
[25]Ceppa F,Faccenda F,De Filippo C,et al.Influence of essential oils in diet and life-stage on gut microbiota and fillet quality of rainbow trout(Oncorhynchus mykiss)[J].International Journal of Food Sciences and Nutrition,2018,69(3):318-333.
[26]Bledsoe J W,Peterson B C,Swanson K S,et al.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[J].PLoS One,2016,11(11):e0166379.
[27]Larsen A M,Mohammed H H,Arias C R.Characterization of the gut microbiota of three commercially valuable warmwater fish species[J].Journal of Applied Microbiology,2014,116(6):1396-1404.
[28]Li X M,Yan Q Y,Xie S Q,et al.Gut microbiota contributes to the growth of fast-growing transgenic common carp(Cyprinus carpio L.)[J].PLoS One,2013,8(5):e64577.
[29]Liu W S,Yang Y O,Zhang J L,et al.Effects of dietary microencapsulated sodium butyrate on growth,intestinal mucosal morphology,immune response and adhesive bacteria in juvenile common carp(Cyprinus carpio)prefed with or without oxidised oil[J].British Journal of Nutrition,2014,112(1):15-29.
[30]Roeselers G,Mittge E K,Stephens W Z,et al.Evidence for a core gut microbiota in the zebrafish[J].The ISMEJournal,2011,5(10):1595-1608.
[31]Cantas L,S?rby J R T,Alestr?m P,et al.Culturable gut microbiota diversity in zebrafish[J].Zebrafish,2012,9(1):26-37.
[32]Falcinelli S,Picchietti S,Rodiles A,et al.Lactobacillus rhamnosus lowers zebrafish lipid content by changing gut microbiota and host transcription of genes involved in lipid metabolism[J].Scientific Reports,2015,5:9336.
[33]Hovda M B,Lunestad B T,Fontanillas R,et al.Molecular characterisation of the intestinal microbiota of farmed Atlantic salmon(Salmo salar L.)[J].Aquaculture,2007,272(1-4):581-588.
[34]Bagi A,Riiser E S,Molland H S,et al.Gastrointestinal microbial community changes in Atlantic cod(Gadus morhua)exposed to crude oil[J].BMC Microbiology,2018,18(1):25.
[35]Ring?E,Bendiksen H R,Gausen S J,et al.The effect of dietary fatty acids on lactic acid bacteria associated with the epithelial mucosa and from faecalia of Arctic charr,Salvelinus alpinus(L.)[J].Journal of Applied Microbiology,1988,85(5):855-864.
[36]Xing M X,Hou Z H,Yuan J B,et al.Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot(Scophthalmus maximus)[J].FEMS Microbiology Ecology,2013,86(3):432-443.
[37]杜震宇.养殖鱼类脂肪肝成因及相关思考[J].水产学报,2014,38(9):1628-1638.Du Z Y.Causes of fatty liver in farmed fish:a review and new perspectives[J].Journal of Fisheries of China,2014,38(9):1628-1638(in Chinese).
[38]Falcinelli S,Rodiles A,Hatef A,et al.Dietary lipid content reorganizes gut microbiota and probiotic L.rhamnosus attenuates obesity and enhances catabolic hormonal milieu in zebrafish[J].Scientific Reports,2017,7(1):5512.
[39]Wong S,Stephens W Z,Burns A R,et al.Ontogenetic differences in dietary fat influence microbiota assembly in the zebrafish gut[J].Microbiology,2015,6(5):e00687-15.
[40]Lésel R,De La Noüe J,Choubert G.Fecal bacterial flora of rainbow trout under antibiotic treatment:effect of the number of pyloric caeca and the lipid content of food[M]//De Pauw N E,Jaspers E,Ackefords H,et al.Aquaculture:A Biotechnology in Progress.Bredene,Belgium:European Aquaculture Society,1989:897-903.
[41]Semova I,Carten J D,Stombaugh J,et al.Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish[J].Cell Host&Microbe,2012,12(3):277-288.
[42]Ring?E,Zhou Z,Vecino J L G,et al.Effect of dietary components on the gut microbiota of aquatic animals.Anever‐ending story?[J].Aquaculture Nutrition,2016,22(2):219-282.
[43]Ring?E,L?demel J B,Myklebust R,et al.The effects of soybean,linseed and marine oils on aerobic gut microbiota of Arctic charr Salvelinus alpinus L.before and after challenge with Aeromonas salmonicida ssp.salmonicida[J].Aquaculture Research,2002,33(8):591-606.
[44]Hartviksen M,Vecino J L G,Ring?E,et al.Alternative dietary protein sources for Atlantic salmon(Salmo salar L.)effect on intestinal microbiota,intestinal and liver histology and growth[J].Aquaculture Nutrition,2014,20(4):381-398.
[45]Desai A R,Links M G,Collins S A,et al.Effects of plant-based diets on the distal gut microbiome of rainbow trout(Oncorhynchus mykiss)[J].Aquaculture,2012,350-353:134-142.
[46]Cai C F,Wang W J,Ye Y T,et al.Effect of soybean meal,raffinose and stachyose on the growth,body composition,intestinal morphology and intestinal microflora of juvenile allogynogenetic silver crucian carp(Carassius auratus gibelio♀×Cyprinus carpio♂)[J].Aquaculture Research,2012,43(1):128-138.
[47]姜雪姣,梁丹妮,刘文斌,等.团头鲂对8种非常规饲料原料中营养物质的表观消化率[J].水产学报,2011,35(6):932-939.Jiang X J,Liang D N,Liu W B,et al.Apparent digestibility of eight unconventional feed ingredients for Megalobrama amblycephala[J].Journal of Fisheries of China,2011,35(6):932-939(in Chinese).
[48]Magalh?es R,Sánchez-López A,Leal R S,et al.Black soldier fly(Hermetia illucens)pre-pupae meal as a fish meal replacement in diets for European seabass(Dicentrarchus labrax)[J].Aquaculture,2017,476:79-85.
[49]Zhang Y R,Qin C B,Yang L P,et al.A comparative genomics study of carbohydrate/glucose metabolic genes:from fish to mammals[J].BMC Genomics,2018,19(1):246.
[50]Mojsov S.Glucagon-like peptide-1(GLP-1)and the control of glucose metabolism in mammals and teleost fish[J].American Zoologist,2000,40(2):246-258.
[51]Gatesoupe F J,Huelvan C,Le Bayon N,et al.The effects of dietary carbohydrate sources and forms on metabolic response and intestinal microbiota in sea bass juveniles,Dicentrarchus labrax[J].Aquaculture,2014,422:47-53.
[52]Geurden I,Mennigen J,Plagnes-Juan E,et al.High or low dietary carbohydrate:protein ratios during firstfeeding affect glucose metabolism and intestinal microbiota in juvenile rainbow trout[J].The Journal of Experimental Biology,2014,217(19):3396-3406.
[53]Liu Y,Chi L,Feng L,et al.Effects of graded levels of dietary vitamin C on the growth,digestive capacity and intestinal microflora of juvenile Jian carp(Cyprinus carpio var.Jian)[J].Aquaculture Research,2011,42(4):534-548.
[54]Wen Z P,Feng L,Jiang J,et al.Immune response,disease resistance and intestinal microflora of juvenile Jian carp(Cyprinus carpio var.Jian)fed graded levels of pantothenic acid[J].Aquaculture Nutrition,2010,16(4):430-436.
[55]Zhao J,Feng L,Liu Y,et al.Effect of dietary isoleucine on the immunity,antioxidant status,tight junctions and microflora in the intestine of juvenile Jian carp(Cyprinus carpio var.Jian)[J].Fish&Shellfish Immunology,2014,41(2):663-673.
[56]Zhao S,Feng L,Liu Y,et al.Effects of dietary biotin supplement on growth,body composition,intestinal enzyme activities and microbiota of juvenile Jian carp(Cyprinus carpio var.Jian)[J].Aquaculture Nutrition,2012,18(4):400-410.
[57]Tang L,Wang G X,Jiang JJ,et al.Effect of methionine on intestinal enzymes activities,microflora and humoral immune of juvenile Jian carp(cyprinus carpio var.Jian)[J].Aquaculture Nutrition,2009,15(5):477-483.
[58]Xie N B,Feng L,Liu Y,et al.Growth,body composition,intestinal enzyme activities and microflora of juvenile Jian carp(Cyprinus carpio var.Jian)fed graded levels of dietary phosphorus[J].Aquaculture Nutrition,2011,17(6):645-656.
[59]Hu C H,Xu Y,Xia M S,et al.Effects of Cu2+-exchanged montmorillonite on growth performance,microbial ecology and intestinal morphology of Nile tilapia(Oreochromis niloticus)[J].Aquaculture,2007,270(1-4):200-206.
[60]Merrifield D L,Shaw B J,Harper G M,et al.Ingestion of metal-nanoparticle contaminated food disrupts endogenous microbiota in zebrafish(Danio rerio)[J].Environmental Pollution,2013,174:157-163.
[61]Merrifield D L,Carnevali O.Probiotic modulation of the gut microbiota of fish[M]//Merrifield D,Ring?E.Aquaculture Nutrition:Gut Health,Probiotics and Prebiotics.Oxford,UK:John Wiley&Sons,2014:185-222.
[62]Ahire J J,Mokashe N U,Chaudhari B L.Effect of dietary probiotic Lactobacillus helveticus on growth performance,antioxidant levels,and absorption of essential trace elements in goldfish(Carassius auratus)[J].Probiotics and Antimicrobial Proteins,2018.
[63]Adel M,El-Sayed A F M,Yeganeh S,et al.Effect of potential probiotic Lactococcus lactis subsp.lactis on growth performance,intestinal microbiota,digestive enzyme activities,and disease resistance of Litopenaeus vannamei[J].Probiotics and Antimicrobial Proteins,2017,9(2):150-156.
[64]Zhai Q X,Yu L L,Li T Q,et al.Effect of dietary probiotic supplementation on intestinal microbiota and physiological conditions of Nile tilapia(Oreochromis niloticus)under waterborne cadmium exposure[J]Antonie van Leeuwenhoek,2017,110(4):501-513.
[65]Dawood M A O,Koshio S,Ishikawa M,et al.Effects of dietary supplementation of Lactobacillus rhamnosus or/and Lactococcus lactis on the growth,gut microbiota and immune responses of red sea bream,Pagrus major[J].Fish&Shellfish Immunology,2016,49:275-285.
[66]Nyman A,Huyben D,Lundh T,et al.Effects of microbe-and mussel-based diets on the gut microbiota in Arctic charr(Salvelinus alpinus)[J].Aquaculture Reports,2017,5:34-40.
[67]Giorgia G,Elia C,Andrea P,et al.Effects of lactogen13,a new probiotic preparation,on gut microbiota and endocrine signals controlling growth and appetite of Oreochromis niloticus juveniles[J].Microbial Ecology2018,76(4):1063-1074.
[68]Adel M,Lazado C C,Safari R,et al.Aqualase?,a yeastbased in-feed probiotic,modulates intestinal microbiota immunity and growth of rainbow trout Oncorhynchus mykiss[J].Aquaculture Research,2017,48(4):1815-1826.
[69]Liu Z,Liu W S,Ran C,et al.Abrupt suspension of probiotics administration may increase host pathogen susceptibility by inducing gut dysbiosis[J].Scientific Reports,2016,6:23214.
[70]Guerreiro I,Serra C R,Oliva-Teles A,et al.Short communication:gut microbiota of European sea bass(Dicentrarchus labrax)is modulated by short-chain fructooligosaccharides and xylooligosaccharides[J]Aquaculture International,2018,26(1):279-288.
[71]Hoseinifar S H,Mirvaghefi A,Amoozegar M A,et al.In vitro selection of a synbiotic and in vivo evaluation on intestinal microbiota,performance and physiological response of rainbow trout(Oncorhynchus mykiss)fingerlings[J].Aquaculture Nutrition,2017,23(1):111-118.
[72]Alonso S,Gastro M C,Berdasco M,et al.Islation and partial characterization of lactic acid bacteria from the gut microbiota of marine fishes for potential application as probiotics in aquaculture[J].Probiotics and Antimicrobial Proteins,2018,1-11
[73]Xu J,Chen H B,Li S L.Understanding the molecular mechanisms of the interplay between herbal medicines and gut microbiota[J].Medicinal Research Reviews,2017,37(5):1140-1185.
[74]Xu J,Lian F M,Zhao L H,et al.Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula[J].The ISME Journal,2015,9(3):552-562.
[75]刘红柏,张颖,杨雨辉,等.5种中草药作为饲料添加剂对鲤肠内细菌及生长的影响[J].大连水产学院学报,2004,19(1):16-20.Liu H B,Zhang Y,Yang Y H,et al.Effects of five Chinese herb medicines as additive in feed on the growth and intestinal microflora in common carp(Cyprinus carpio)[J].Journal of Dalian Fisheries University,2004,19(1):16-20(in Chinese).
[76]Wu Z B,Gatesoupe F J,Li T T,et al.Significant improvement of intestinal microbiota of gibel carp(Carassius auratus gibelio)after traditional Chinese medicine feeding[J].Journal of Applied Microbiology,2018,124(3):829-841.
[77]Giannenas I,Triantafillou E,Stavrakakis S,et al.Assessment of dietary supplementation with carvacrol or thymol containing feed additives on performance,intestinal microbiota and antioxidant status of rainbow trout(Oncorhynchus mykiss)[J].Aquaculture,2012,350-353:26-32.
[78]Sylvain Fé,Cheaib B,Llewellyn M,et al.pH drop impacts differentially skin and gut microbiota of the Amazonian fish tambaqui(Colossoma macropomum)[J].Scientific Reports,2016,6:32032.
[79]Li X M,Yu Y H,Feng W S,et al.Host species as a strong determinant of the intestinal microbiota of fish larvae[J].The Journal of Microbiology,2012,50(1):29-37.
[80]Stephens W Z,Burns A R,Stagaman K,et al.The composition of the zebrafish intestinal microbial community varies across development[J].The ISMEJournal,2016,10(3):644-654.
[81]Wong S,Waldrop T,Summerfelt S,et al.Aquacultured rainbow trout(Oncorhynchus mykiss)possess a large core intestinal microbiota that is resistant to variation in diet and rearing density[J].Applied and Environmental Microbiology,2013,79(16):4974-4984.
[82]Ingerslev H C,Von Gersdorff J?rgensen L V,Strube ML,et al.The development of the gut microbiota in rainbow trout(Oncorhynchus mykiss)is affected by first feeding and diet type[J].Aquaculture,2014,424-425:24-34.
[83]Xia J H,Lin G,Fu G H,et al.The intestinal microbiome of fish under starvation[J].BMC Genomics,2014,15:266.
[84]Sha Y J,Liu M,Wang B J,et al.Bacterial population in intestines of Litopenaeus vannamei fed different probiotics or probiotic supernatant[J].Journal of Microbiology and Biotechnology,2016,26(10):1736-1745.
[85]Sha Y J,Wang L,Liu M,et al.Effects of lactic acid bacteria and the corresponding supernatant on the survival,growth performance,immune response and disease resistance of Litopenaeus vannamei[J].Aquaculture,2016,452:28-36.
[86]Rawls J F,Samuel B S,Gordon J I.Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota[J].Proceedings of the National Academy of Sciences of the United States of America,2004,101(13):4596-4601.
[87]Sheng Y,Ren H,Limbu S M,et al.The presence or absence of intestinal microbiota affects lipid deposition and related genes expression in zebrafish(Danio rerio)[J].Frontiers in Microbiology,2018,9:1124.
[88]Rawls J F,Mahowald M A,Ley R E,et al.Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection[J].Cell,2006,127(2):423-433.