Comparative analysis on microbial community associated with different gastrointestinal regions of wild northern snakehead Channa argus Cantor, 1842
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摘要
Microbial communities in different gastrointestinal regions(stomach, foregut, midgut, and hindgut) of the northern snakehead C hanna argus(Cantor, 1842) were compared by polymerase chain reaction and partial 16 S r DNA sequencing. A total of 194, 140, 212, and 122 OTUs were detected in the stomach, foregut, midgut, and hindgut, respectively. Significant dif ferences were found in the Sobs, ACE, Shannon, and Simpson indices among samples(P <0.05). The gastrointestinal microbial community of C. argus consisted predominantly of Proteobacteria with either H alomonas, Shewanella, Plesiomonas, or Sphingomonas. Fusobacteria, Firmicutes, and Bacteroidetes also existed in the gastrointestinal tracts. However, significant diff erences were found in the compositions of microbial community among the four regions( P <0.05). Cyanobacteria and Spirochetes were significantly higher in the midgut and hindgut( P <0.05). Fusobacteria and Firmicutes were dominant in the hindgut and foregut, respectively(P <0.05). Proteobacteria was the lowest in the hindgut( P <0.05). At genus level, C etobacterium and Plesiomonas were significantly higher in the hindgut than in the other three samples( P <0.05). Clostridium and Prevotella were the highest in the midgut(P <0.05). Halomonas, Shewanella, and S phingomonas were the highest in the foregut( P <0.05). Paracoccus and Vibrio were the highest in the stomach. Several genera were only detected in certain regions, as follows: stomach, P aracoccus and Vibrio; foregut, Halomonas, Shewanella, and Sphingomonas; midgut, Clostridium and Prevotella; and hindgut, C etobacterium and Plesiomonas( P <0.05). At the species level, A cinetobacter rhizosphaerae was only detected in the stomach. P revotella copri and Clostridium perfring were not detected in the foregut and midgut, respectively, whereas Prevotella copri and Faecalibacterium pra were not detected in the hindgut. These findings provide valuable information on the microbial community in each gastrointestinal region of C. argus. Moreover, this study indicated that microbial community was not only related to rearing environment but also to the physico-chemical characteristics of each gastrointestinal region.
Microbial communities in different gastrointestinal regions(stomach, foregut, midgut, and hindgut) of the northern snakehead C hanna argus(Cantor, 1842) were compared by polymerase chain reaction and partial 16 S r DNA sequencing. A total of 194, 140, 212, and 122 OTUs were detected in the stomach, foregut, midgut, and hindgut, respectively. Significant dif ferences were found in the Sobs, ACE, Shannon, and Simpson indices among samples(P <0.05). The gastrointestinal microbial community of C. argus consisted predominantly of Proteobacteria with either H alomonas, Shewanella, Plesiomonas, or Sphingomonas. Fusobacteria, Firmicutes, and Bacteroidetes also existed in the gastrointestinal tracts. However, significant diff erences were found in the compositions of microbial community among the four regions( P <0.05). Cyanobacteria and Spirochetes were significantly higher in the midgut and hindgut( P <0.05). Fusobacteria and Firmicutes were dominant in the hindgut and foregut, respectively(P <0.05). Proteobacteria was the lowest in the hindgut( P <0.05). At genus level, C etobacterium and Plesiomonas were significantly higher in the hindgut than in the other three samples( P <0.05). Clostridium and Prevotella were the highest in the midgut(P <0.05). Halomonas, Shewanella, and S phingomonas were the highest in the foregut( P <0.05). Paracoccus and Vibrio were the highest in the stomach. Several genera were only detected in certain regions, as follows: stomach, P aracoccus and Vibrio; foregut, Halomonas, Shewanella, and Sphingomonas; midgut, Clostridium and Prevotella; and hindgut, C etobacterium and Plesiomonas( P <0.05). At the species level, A cinetobacter rhizosphaerae was only detected in the stomach. P revotella copri and Clostridium perfring were not detected in the foregut and midgut, respectively, whereas Prevotella copri and Faecalibacterium pra were not detected in the hindgut. These findings provide valuable information on the microbial community in each gastrointestinal region of C. argus. Moreover, this study indicated that microbial community was not only related to rearing environment but also to the physico-chemical characteristics of each gastrointestinal region.
Microbial communities in different gastrointestinal regions(stomach, foregut, midgut, and hindgut) of the northern snakehead C hanna argus(Cantor, 1842) were compared by polymerase chain reaction and partial 16 S r DNA sequencing. A total of 194, 140, 212, and 122 OTUs were detected in the stomach, foregut, midgut, and hindgut, respectively. Significant dif ferences were found in the Sobs, ACE, Shannon, and Simpson indices among samples(P <0.05). The gastrointestinal microbial community of C. argus consisted predominantly of Proteobacteria with either H alomonas, Shewanella, Plesiomonas, or Sphingomonas. Fusobacteria, Firmicutes, and Bacteroidetes also existed in the gastrointestinal tracts. However, significant diff erences were found in the compositions of microbial community among the four regions( P <0.05). Cyanobacteria and Spirochetes were significantly higher in the midgut and hindgut( P <0.05). Fusobacteria and Firmicutes were dominant in the hindgut and foregut, respectively(P <0.05). Proteobacteria was the lowest in the hindgut( P <0.05). At genus level, C etobacterium and Plesiomonas were significantly higher in the hindgut than in the other three samples( P <0.05). Clostridium and Prevotella were the highest in the midgut(P <0.05). Halomonas, Shewanella, and S phingomonas were the highest in the foregut( P <0.05). Paracoccus and Vibrio were the highest in the stomach. Several genera were only detected in certain regions, as follows: stomach, P aracoccus and Vibrio; foregut, Halomonas, Shewanella, and Sphingomonas; midgut, Clostridium and Prevotella; and hindgut, C etobacterium and Plesiomonas( P <0.05). At the species level, A cinetobacter rhizosphaerae was only detected in the stomach. P revotella copri and Clostridium perfring were not detected in the foregut and midgut, respectively, whereas Prevotella copri and Faecalibacterium pra were not detected in the hindgut. These findings provide valuable information on the microbial community in each gastrointestinal region of C. argus. Moreover, this study indicated that microbial community was not only related to rearing environment but also to the physico-chemical characteristics of each gastrointestinal region.
引文
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Chen C H,Tanaka Y,Komiya Y,Itoi S,Sugita H.2013.Predominant intestinal bacteria of the puffer fish(Takifugu rubripes Temminck&Schlegel,1850)reared in an indoor tank as determined by the clone library analysis and culture method.J.Appl.Ichthyol.,29(6):1 374-1 377.
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Day S B,Salie K,Stander H B.2016.A growth comparison among three commercial tilapia species in a biofloc system.Aquacult.Int.,24(5):1 309-1 322.
Fan L M,Barry K,Hu G D,Meng S L,Song C,Wu W,Chen JZ,Xu P.2016.Bacterioplankton community analysis in tilapia ponds by Illumina high-throughput sequencing.World J.Microbiol.Biotechnol.,32(1):10.
Gao F,Tan J,Sun H L,Yan J P.2014.Bacterial diversity of gut content in sea cucumber(Apostichopus japonicus)and its habitat surface sediment.J.Ocean Univ.China,13(2):303-310.
Gatesoupe F,Huelvan C,Bayon N L,Delliou H L,Madec L,Mouchel O,Quazuguel P,Mazurais D,ZamboninoInfante J L.2016.The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass,dicentrarchus labrax,submitted to different nutritional histories.BMCMicrobiology,16:266.
Godoy-Vitorino F,Goldfarb K C,Karaoz U,Leal S,GarciaAmado M A,Hugenholtz P,Tringe S G,Brodie E L,Dominguez-Bello M G.2012.Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows.ISME J.,6(3):531-541.
Hada H S,West P A,Lee J V,Stemmler J,Colwell R R.1984.Vibrio tubiashii sp.nov.,a pathogen of bivalve mollusks.Int.J.Syst.Bacteriol.,34(1):1-4.
Hartviksen M,Bakke A M,Vecino J G,Ring?E,Krogdahl?.2014.Evaluation of the effect of commercially available plant and animal protein sources in diets for Atlantic salmon(Salmo salar L.):digestive and metabolic investigations.Fish Physiol.Biochem.,40(5):1 621-1 637.
Holben W E,Williams P,Saarinen M,S?rkilahti L K,Apajalahti J H A.2002.Phylogenetic analysis of intestinal microflora indicates a novel Mycoplasma phylotype in farmed and wild salmon.Microb.Ecol.,44(2):175-185.
Johnson C N,Barnes S,Ogle J,Grimes D J,Chang Y J,Peacock A D,Kline L.2008.Microbial community analysis of water,foregut,and hindgut during growth of pacific white shrimp,Litopenaeus vannamei in closedsystem aquaculture.J.World Aquacult.Soc.,39(2):251-258.
Krogdahl?,Sundby A,Holm H.2015.Characteristics of digestive processes in Atlantic salmon(Salmo salar).Enzyme p H optima,chyme p H,and enzyme activities.Aquaculture,449:27-36.
Kushmaro A,Banin E,Loya Y,Stackebrandt E,Rosenberg E.2001.Vibrio shiloi sp.nov.,the causative agent of bleaching of the coral Oculina patagonica.Int.J.Syst.Evol.Microbiol.,51(4):1 383-1 388.
Li X M,Yu Y H,Feng W S,Yan Q Y,Gong Y C.2012.Host species as a strong determinant of the intestinal microbiota of fish larvae.J.Microbiol.,50(1):29-37.
Li Y Y,Zhang T,Zhang C Y,Zhu Y,Ding J F,Ma Y X.2015.Bacterial diversity in the intestine of young farmed puffer fish Takifugu rubripes.Chin.J.Oceanol.Limnol.,33(4):913-918.
Ragauskas A J,Williams C K,Davison B H,Britovsek G,Cairney J,Eckert C A,Frederick W J Jr,Hallett J P,Leak D J,Liotta C L,Mielenz J R,Murphy R,Templer R,Tschaplinski T.2006.The path forward for biofuels and biomaterials.Science,311(5760):484-489.
Ramirez R F,Dixon B A.2003.Enzyme production by obligate intestinal anaerobic bacteria isolated from oscars(Astronotus ocellatus),angelfish(Pterophyllum scalare)and southern flounder(Paralichthys lethostigma).Aquaculture,227(1-4):417-426.
Rico R M,Tejedor-Junco M T,Tapia-Paniagua S T,Alarcón FJ,Mancera J M,López-Figueroa F,Balebona M C,Abdala-Díaz R T,Mori?ig M A.2015.Influence of the dietary inclusion of Gracilaria cornea and Ulva rigida on the biodiversity of the intestinal microbiota of Sparus aurata juveniles.Aquacult.Int.,24(4):965-984.
Shakibazadeh S,Saad C R,Christianus A,Kamarudin M S,Sijam K,Shamsudin M N,Neela V K.2009.Bacteria flora associated with different body parts of hatchery reared juvenile Penaeus monodon,tanks water and sediment.Ann.Microbiol.,59(3):425-430.
Standen B T,Rodiles A,Peggs D L,Davies S J,Santos G A,Merrifield D L.2015.Modulation of the intestinal microbiota and morphology of tilapia,Oreochromis niloticus,following the application of a multi-species probiotic.Appl.Microbiol.Biotechnol.,99(20):8 403-8 417.
Stanley D,Hughes R J,Moore R J.2014.Microbiota of the chicken gastrointestinal tract:influence on health,productivity and disease.Appl.Microbiol.Biotechnol.,98(10):4 301-4 310.
Sugita H,Noguchi T,Hwang D F,Furuta M,Motokane T,Sonoda T,Hashimoto K,Deguchi Y.1997.Intestinal microflora of coastal puffer fishes.Nippon Suisan Gakk aishi,53(12):2 201-2 207.
Wan X L,Ruan R,Mc Laughlin R W,Hao Y J,Zheng J S,Wang D.2015.Fecal bacterial composition of the endangered Yangtze finless porpoises living under captive and semi-natural conditions.Curr.Microbiol.,72(3):306-314.
Wu S G,Gao T H,Zheng Y Z,Wang W W,Cheng Y Y,Wang T.2010.Microbial diversity of intestinal contents and mucus in yellow catfish(Pelteobagrus fulvidraco).Aquaculture,303(1-4):1-7.
Wu S G,Wang G T,Angert E R,Wang W W,Li W X,Zou H.2012.Composition,diversity,and origin of the bacterial community in grass carp intestine.PLo S One,7(2):e30440,https://doi.org/10.1371/journal.pone.0030440.
Xiong J B,Wang K,Wu J F,Qiuqian L L,Yang K J,Qian Y X,Zhang D M.2015.Changes in intestinal bacterial communities are closely associated with shrimp disease severity.Appl.Microbiol.Biotechnol.,99(16):6 911-6 919.
Yuan X C,Zhao W W.2016.China Fishery Statistical Yearbook2016.Chinese Agricultural Press,Beijing,China.p.31.(in Chinese)
Zarkasi K Z,Taylor R S,Abell G C J,Tamplin M L,Glencross B D,Bowman J P.2016.Atlantic salmon(Salmo salar L.)gastrointestinal microbial community dynamics in relation to digesta properties and diet.Microb.Ecol.,71(3):589-603.
Zhang P Y H,Himmel M E,Mielenz J R.2006.Outlook for cellulase improvement:screening and selection strategies.cellulase improvement:screening and selection strategies.Biotechnol.Adv.,24(5):452-481.
Chaiyapechara S,Rungrassamee W,Suriyachay I,Kuncharin Y,Klanchui A,Karoonuthaisiri N,Jiravanichpaisal P.2012.Bacterial community associated with the intestinal tract of P.monodon in commercial farms.Microb.Ecol.,63(4):938-953.
Chen C H,Tanaka Y,Komiya Y,Itoi S,Sugita H.2013.Predominant intestinal bacteria of the puffer fish(Takifugu rubripes Temminck&Schlegel,1850)reared in an indoor tank as determined by the clone library analysis and culture method.J.Appl.Ichthyol.,29(6):1 374-1 377.
da Cruz Ramos G F,Ramos P L,Passarini M R Z,Silveira MA V,Okamoto D N,de Oliveira L C G,Zezzo L V,Marem A,Rocha R C S,da Cruz J B,Juliano L,de Vasconcellos S P.2016.Cellulolytic and proteolytic ability of bacteria isolated from gastrointestinal tract and composting of a hippopotamus.AMB Express,6:17.
Day S B,Salie K,Stander H B.2016.A growth comparison among three commercial tilapia species in a biofloc system.Aquacult.Int.,24(5):1 309-1 322.
Fan L M,Barry K,Hu G D,Meng S L,Song C,Wu W,Chen JZ,Xu P.2016.Bacterioplankton community analysis in tilapia ponds by Illumina high-throughput sequencing.World J.Microbiol.Biotechnol.,32(1):10.
Gao F,Tan J,Sun H L,Yan J P.2014.Bacterial diversity of gut content in sea cucumber(Apostichopus japonicus)and its habitat surface sediment.J.Ocean Univ.China,13(2):303-310.
Gatesoupe F,Huelvan C,Bayon N L,Delliou H L,Madec L,Mouchel O,Quazuguel P,Mazurais D,ZamboninoInfante J L.2016.The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass,dicentrarchus labrax,submitted to different nutritional histories.BMCMicrobiology,16:266.
Godoy-Vitorino F,Goldfarb K C,Karaoz U,Leal S,GarciaAmado M A,Hugenholtz P,Tringe S G,Brodie E L,Dominguez-Bello M G.2012.Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows.ISME J.,6(3):531-541.
Hada H S,West P A,Lee J V,Stemmler J,Colwell R R.1984.Vibrio tubiashii sp.nov.,a pathogen of bivalve mollusks.Int.J.Syst.Bacteriol.,34(1):1-4.
Hartviksen M,Bakke A M,Vecino J G,Ring?E,Krogdahl?.2014.Evaluation of the effect of commercially available plant and animal protein sources in diets for Atlantic salmon(Salmo salar L.):digestive and metabolic investigations.Fish Physiol.Biochem.,40(5):1 621-1 637.
Holben W E,Williams P,Saarinen M,S?rkilahti L K,Apajalahti J H A.2002.Phylogenetic analysis of intestinal microflora indicates a novel Mycoplasma phylotype in farmed and wild salmon.Microb.Ecol.,44(2):175-185.
Johnson C N,Barnes S,Ogle J,Grimes D J,Chang Y J,Peacock A D,Kline L.2008.Microbial community analysis of water,foregut,and hindgut during growth of pacific white shrimp,Litopenaeus vannamei in closedsystem aquaculture.J.World Aquacult.Soc.,39(2):251-258.
Krogdahl?,Sundby A,Holm H.2015.Characteristics of digestive processes in Atlantic salmon(Salmo salar).Enzyme p H optima,chyme p H,and enzyme activities.Aquaculture,449:27-36.
Kushmaro A,Banin E,Loya Y,Stackebrandt E,Rosenberg E.2001.Vibrio shiloi sp.nov.,the causative agent of bleaching of the coral Oculina patagonica.Int.J.Syst.Evol.Microbiol.,51(4):1 383-1 388.
Li X M,Yu Y H,Feng W S,Yan Q Y,Gong Y C.2012.Host species as a strong determinant of the intestinal microbiota of fish larvae.J.Microbiol.,50(1):29-37.
Li Y Y,Zhang T,Zhang C Y,Zhu Y,Ding J F,Ma Y X.2015.Bacterial diversity in the intestine of young farmed puffer fish Takifugu rubripes.Chin.J.Oceanol.Limnol.,33(4):913-918.
Ragauskas A J,Williams C K,Davison B H,Britovsek G,Cairney J,Eckert C A,Frederick W J Jr,Hallett J P,Leak D J,Liotta C L,Mielenz J R,Murphy R,Templer R,Tschaplinski T.2006.The path forward for biofuels and biomaterials.Science,311(5760):484-489.
Ramirez R F,Dixon B A.2003.Enzyme production by obligate intestinal anaerobic bacteria isolated from oscars(Astronotus ocellatus),angelfish(Pterophyllum scalare)and southern flounder(Paralichthys lethostigma).Aquaculture,227(1-4):417-426.
Rico R M,Tejedor-Junco M T,Tapia-Paniagua S T,Alarcón FJ,Mancera J M,López-Figueroa F,Balebona M C,Abdala-Díaz R T,Mori?ig M A.2015.Influence of the dietary inclusion of Gracilaria cornea and Ulva rigida on the biodiversity of the intestinal microbiota of Sparus aurata juveniles.Aquacult.Int.,24(4):965-984.
Shakibazadeh S,Saad C R,Christianus A,Kamarudin M S,Sijam K,Shamsudin M N,Neela V K.2009.Bacteria flora associated with different body parts of hatchery reared juvenile Penaeus monodon,tanks water and sediment.Ann.Microbiol.,59(3):425-430.
Standen B T,Rodiles A,Peggs D L,Davies S J,Santos G A,Merrifield D L.2015.Modulation of the intestinal microbiota and morphology of tilapia,Oreochromis niloticus,following the application of a multi-species probiotic.Appl.Microbiol.Biotechnol.,99(20):8 403-8 417.
Stanley D,Hughes R J,Moore R J.2014.Microbiota of the chicken gastrointestinal tract:influence on health,productivity and disease.Appl.Microbiol.Biotechnol.,98(10):4 301-4 310.
Sugita H,Noguchi T,Hwang D F,Furuta M,Motokane T,Sonoda T,Hashimoto K,Deguchi Y.1997.Intestinal microflora of coastal puffer fishes.Nippon Suisan Gakk aishi,53(12):2 201-2 207.
Wan X L,Ruan R,Mc Laughlin R W,Hao Y J,Zheng J S,Wang D.2015.Fecal bacterial composition of the endangered Yangtze finless porpoises living under captive and semi-natural conditions.Curr.Microbiol.,72(3):306-314.
Wu S G,Gao T H,Zheng Y Z,Wang W W,Cheng Y Y,Wang T.2010.Microbial diversity of intestinal contents and mucus in yellow catfish(Pelteobagrus fulvidraco).Aquaculture,303(1-4):1-7.
Wu S G,Wang G T,Angert E R,Wang W W,Li W X,Zou H.2012.Composition,diversity,and origin of the bacterial community in grass carp intestine.PLo S One,7(2):e30440,https://doi.org/10.1371/journal.pone.0030440.
Xiong J B,Wang K,Wu J F,Qiuqian L L,Yang K J,Qian Y X,Zhang D M.2015.Changes in intestinal bacterial communities are closely associated with shrimp disease severity.Appl.Microbiol.Biotechnol.,99(16):6 911-6 919.
Yuan X C,Zhao W W.2016.China Fishery Statistical Yearbook2016.Chinese Agricultural Press,Beijing,China.p.31.(in Chinese)
Zarkasi K Z,Taylor R S,Abell G C J,Tamplin M L,Glencross B D,Bowman J P.2016.Atlantic salmon(Salmo salar L.)gastrointestinal microbial community dynamics in relation to digesta properties and diet.Microb.Ecol.,71(3):589-603.
Zhang P Y H,Himmel M E,Mielenz J R.2006.Outlook for cellulase improvement:screening and selection strategies.cellulase improvement:screening and selection strategies.Biotechnol.Adv.,24(5):452-481.