Microbial Diversity of Skin and Liver of Diseased Grass Carp Evaluated by High-Throughput Sequencing of 16S rRNA Gene
SUN Kun1, WANG Xiaolei2, ZHANG Jie1, FU Longwei3, LIU Xuemei4, ZHANG Yanzhen3, SUI Zhihai1, LIU Yunguo1
1. College of Life Sciences, Linyi University, Linyi 276000, China; 2. College of Education, Linyi University, Linyi 276000, China; 3. College of Life Sciences and Technology, Xinjiang University, Urumqi 830046, China; 4. Agricultural Technology Extension Station of Hedong District, Linyi 276003, China
Abstract：Grass carp Ctenopharyngodon idella is an important freshwater aquaculture species, but infection diseases induced by the bacterial pathogens cause serious economic losses. We used high-throughput sequencing of the V4 region of 16S rRNA gene to quickly evaluate the bacterial communities of skin and liver of diseased grass carp from different ponds. The results showed that the number of OTUs in the skin and liver of grass carp was 611 and 875 in pond No.1, 376 and 644 in pond No.2, more in pond No.1 than that in pond No. 2. Alpha diversity analysis revealed that the abundance and diversity of bacteria of the liver from pond No.1 were the highest. The beta diversity analysis indicated that there were similar community structures in the skin of No.1, and the skin and liver of No.2, but the bacterial community structure of liver from pond No.1 was different from the other three samples, indicating that the infection status of grass carp in the pond No.1 was more complicated than that in pond No.2. In the bacterial community structure of the all samples, we found that the dominant phylum in the phylum classification level was mainly Bacteroidetes and Proeobacteria. The dominant genera in the genus classification level were mainly Flavobacterium and Shewanella, which was most likely to be the dominant pathogenic bacteria of this disease. The findings could provide the scientific basis for disease prevention and control in early stage, and also provide guidance to the isolation and identification of the bacteial pathogens in later stage.
孙坤, 王晓磊, 张洁, 付龙威, 刘学美, 张艳珍, 隋智海, 刘云国. 基于16S rRNA高通量测序评价患病草鱼体表及肝脏细菌多样性[J]. 水产科学, 2022, 41(2): 202-209.
SUN Kun, WANG Xiaolei, ZHANG Jie, FU Longwei, LIU Xuemei, ZHANG Yanzhen, SUI Zhihai, LIU Yunguo. Microbial Diversity of Skin and Liver of Diseased Grass Carp Evaluated by High-Throughput Sequencing of 16S rRNA Gene. Fisheries Science, 2022, 41(2): 202-209.
[1] HU W, CHEN J. Whole-genome sequencing opens a new era for molecular breeding of grass carp (Ctenopharyngodon idellus)[J].Science China Life Sciences,2015,58(6):619-620. [2] TANG M, LU Y, XIONG Z M, et al. The grass carp genomic visualization database (GCGVD):an informational platform for genome biology of grass carp[J].International Journal of Biological Sciences,2019,15(10):2119-2127. [3] SONG X H, ZHAO J, BO Y X, et al. Aeromonas hydrophila induces intestinal inflammation in grass carp (Ctenopharyngodon idella):an experimental model[J].Aquaculture,2014,434:171-178. [4] 唐毅.草鱼、白鲢几种细菌性疾病病原的分离及其特性研究[D].重庆:西南大学,2008. [5] 余利,舒天成,何艳艳,等.一例草鱼大量死亡案例的病原分析[J].当代水产,2019,44(5):92-93. [6] 李思泉,李娜,罗玉双,等.草鱼细菌性烂鳃病病原菌的分离及其特异性卵黄抗体的初步研究[J].贵州畜牧兽医,2019,43(3):37-42. [7] 任燕,高彩霞,曾伟伟,等.两株草鱼源维氏气单胞菌菌株的主要表型特征及致病力比较[J].中国预防兽医学报,2019,41(2):145-150. [8] 高彩霞,任燕,王庆,等.草鱼源致病性维氏气单胞菌的分离鉴定及药物敏感性分析[J].安徽农业大学学报,2018,45(3):409-415. [9] ZHANG Z Y, LIU G Y, MA R, et al. The immunoprotective effect of whole-cell lysed inactivated vaccine with SWCNT as a carrier against Aeromonas hydrophila infection in grass carp[J].Fish & Shellfish Immunology,2020,97:336-343. [10] 饶毅,付辉云,陈文静,等.草鱼肝胆综合症并发细菌疾病病原分离鉴定及药敏试验[J].中国农学通报,2020,36(5):138-143. [11] 叶明皓,胡秀彩,吕爱军,等.草鱼致病性腐败希瓦氏菌的分离鉴定及药敏特性研究[J].天津农学院学报,2018,25(4):52-57. [12] 李楠,郭慧芝,焦冉,等.草鱼的一种急性细菌性传染病病原的分离鉴定及致病性研究[J].水生生物学报,2011,35(6):980-987. [13] 胡钱东,林强,石存斌,等.草鱼致病性类志贺邻单胞菌的分离与鉴定[J].微生物学报,2014,54(2):229-235. [14] 张飘,胡安东,杨霞,等.一株草鱼维氏气单胞菌的分离鉴定及毒力基因分析[J].中国畜牧兽医,2020,47(3):848-855. [15] 贾伟.水体微生物检测技术研究与应用进展[J].绿色科技,2019(8):71-72. [16] 史亚千,高瑞芳,王颖,等.高通量测序技术在进境小麦病原微生物检测上的应用前景[J].植物检疫,2016,30(3):9-11. [17] 周本翔,赵良杰,彭新亮.构树叶投喂草鱼肠道真菌群落多样性研究[J].基因组学与应用生物学,2020,39(8):3453-3460. [18] 朱文根,李星浩,饶刘瑜,等.感染草鱼呼肠孤病毒对肠道菌群多样性的影响[J].水生生物学报,2019,43(1):109-116. [19] 曾学琴,柳陈坚,杨雪,等.高通量测序法检测奶牛乳房炎关联微生物群落结构及多样性[J].浙江农业学报,2019,31(9):1437-1445. [20] 张德锋,刘礼辉,李宁求,等.我国南方地区鱼源气单胞菌不同种类的流行特征[J].水产科学,2015,34(11):673-682. [21] 邹升,龚亮,李东杰,等.患病草鱼肠道病原菌的分离鉴定及毒力研究[J].水产科学,2019,38(2):152-162. [22] TRINGE S G, RUBIN E M. Metagenomics:DNA sequencing of environmental samples[J].Nature Reviews Genetics,2005,6(11):805-814. [23] 任迪,李颖,曾晶晶,等.高通量测序在脓毒症患者病原体检测中的应用[J].海南医学,2019,30(21):2808-2810. [24] 涂飞云,韩卫杰,黄挺,等.基于高通量测序的圈养豪猪脓肿脓汁细菌群落结构[J].经济动物学报,2021,25(2)91-94. [25] NEMATOLLAHI A, DECOSTERE A, PASMANS F, et al. Adhesion of high and low virulence Flavobacterium psychrophilum strains to isolated gill arches of rainbow trout Oncorhynchus mykiss[J].Diseases of Aquatic Organisms,2003,55(2):101-107. [26] LARSEN A, TAO Z, BULLARD S A, et al. Diversity of the skin microbiota of fishes:evidence for host species specificity[J].FEMS Microbiology Ecology,2013,85(3):483-494. [27] CHIARELLO M, VILLÉGERger S, BOUVIER C, et al. High diversity of skin-associated bacterial communities of marine fishes is promoted by their high variability among body parts, individuals and species[J].FEMS Microbiology Ecology,2015,91(7):fiv061. [28] MINNITI G, HAGEN L H, PORCELLATO D, et al. The skin-mucus microbial community of farmed Atlantic salmon (Salmo salar)[J].Frontiers in Microbiology,2017,8:2043. [29] ZHANG X T, DING L G, YU Y Y, et al. The change of teleost skin commensal microbiota is associated with skin mucosal transcriptomic responses during parasitic infection by Ichthyophthirius multifillis[J].Frontiers in Immunology,2018,9:2972. [30] VERMA D K, RATHORE G. New host record of five Flavobacterium species associated with tropical fresh water farmed fishes from North India[J].Brazilian Journal of Microbiology,2015,46(4):969-976. [31] SHOEMAKER C A, LAFRENTZ B R. Growth and survival of the fish pathogenic bacterium, Flavobacterium columnare, in tilapia mucus and porcine gastric mucin[J].FEMS Microbiology Letters,2015,362(4):1-5. [32] PEKALA A, KOZIŃSKA A, PAźDZÍOR E, et al. Phenotypical and genotypical characterization of Shewanella putrefaciens strains isolated from diseased freshwater fish[J].Journal of Fish Diseases,2015,38(3):283-293. [33] SARKER S, ABRABAM T J, PATRA A. Prevalence of diseases caused by Flavobacterium spp. and other opportunistic bacteria in carps of sewage-fed farms in West Bengal, India[J]. Journal of Fisheries,2019,7(1),663-670. [34] PAPADOPOULOU A, DALSGAARD I, LINDÉN A, et al. In vivo adherence of Flavobacterium psychrophilum to mucosal external surfaces of rainbow trout (Oncorhynchus mykiss) fry[J].Journal of Fish Diseases,2017,40(10):1309-1320. [35] GOLDSCHMIDT-CLERMONT E, WAHLI T, FREY J, et al. Identification of bacteria from the normal flora of perch, Perca fluviatilis L., and evaluation of their inhibitory potential towards Aeromonas species[J].Journal of Fish Diseases,2008,31(5):353-359. [36] JARAU M, DI NATALE A, HUBER P E, et al. Virulence of Flavobacterium psychrophilum isolates in rainbow trout Oncorhynchus mykiss (Walbaum)[J].Journal of Fish Diseases,2018,41(10):1505-1514. [37] WU Y C, CHU L S, CHENG C H, et al. The presence of substances of the Shewanella strain 0409, isolated from grouper intestine, gives antiviral activity against Betanodavirus in cell cultures and protection of fish[J].Aquaculture,2020,518:734862. [38] DUCHAUD E, ROCHAT T, HABIB C, et al. Genomic diversity and evolution of the fish pathogen Flavobacterium psychrophilum[J].Frontiers in Microbiology,2018,9:138.
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