|
|
|
| Structural Characteristics of Intestinal Microbiota in Black Rockfish Sebastes schlegelii during Early Life Stage |
| JIANG Yan1, CAO Yanan2, LIU Xuezhou1, XU Yongjiang1, LI Dejun3, SHI Bao1, WANG Bin1 |
1.Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries and Food Production Processes, Pilot National Laboratory for Marine Science andTechnology (Qingdao), Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
2.Yantai Marine Economic Research Institute, Yantai 264000, China;
3.Huangdao Fishery Technology PromotionStation, Qingdao 266400, China |
|
|
|
|
Abstract V3 and V4 variable regions of 16S rDNA of intestinal microbiota were sequenced in black rockfish Sebastes schlegelii larvae and juveniles with 1, 9, 20, 54 and 95 day after hatching (DAH) using Illumina MiSeq PE300 system. A total of 1039 operational taxonomic units (OTU) and 667 genera were obtained. At the genus level, there were higher microbial abundance and mean value (higher than 1%) (86%) in intestinal microbiota in wild fish than that in juvenile stage (73.5%), with the most abundances dominant genus of Acinetobacter (26.2%—45.3%), and followed by genus Brevibacillus. Meantime, the combined analysis of shared microflora revealed that there were 11 core microbiota. With growth of the larvae and juveniles, successional abundances for Bacillus, Brevibacillus, Acinetobacter and Rhizobium, belong to the core microbiota, were increased firstly and then declined rapidly, the maximal abundances of these four genera were all appeared on 54 DAH. However, Vibrio as one of the core microbiota, with abundances of 0.37%—12.41%, showed the opposite trend during the early life stage, with the minimal value on 54 DAH. There were only 14 shared genera in intestines between larvae and juveniles and wild ones, the minimum abundance of Brevibacillus and Massilia in intestine of larvae and juveniles being 9 times and 32 times as the maximum value of these two genera in wild fish, showing the obvious difference. The findings will provide the theoretical reference for the regulation of intestinal physiological health during the life stage.
|
|
Received: 17 October 2018
|
|
|
|
|
|
[1]Dwivedi M, Ansarullah, Radichev I, et al. Alteration of immune-mechanisms by human microbiota and development and prevention of human diseases[J]. Journal of Immunology Research,2017,2017:6985256.
[2]Wonnop V, Soottawat B, Wanchern P, et al. Accelerated proteolysis of soy proteins during fermentation of thua-nao-inoculated with Bacillus subtilis[J]. Journal of Food Biochemistry,2005,29(4):349-366.
[3]Pérez T, Balcázar J L, Ruiz-Zarzuela I, et al. Host-microbiota interactions within the fish intestinal ecosystem[J]. Mucosal Immunology,2010,3(4):355-360.
[4]Karasov W H, Martínez del Rio C, Caviedes-Vidal E. Ecological physiology of diet and digestive systems[J]. Annual Review of Physiology,2011,73(1):69-93.
[5]Ray A K, Ghosh K, Ringø E. Enzyme-producing bacteria isolated from fish gut:a review[J]. Aquaculture Nutrition,2012,18(5):465-492.
[6]Forsythe P, Bienenstock J. Immunomodulation by commensal and probiotic bacteria[J]. Immunological Investigations,2013,39(4/5):429-448.
[7]Gallo R L, Nakatsuji T. Microbial symbiosis with the innate immune defense system of the skin[J]. Journal of Investigative Dermatology,2011,131(10):1974-1980.
[8]Kim Y R, Kim E Y, Choi S Y, et al. Effect of a probiotic strain, Enterococcus faecium, on the immune responses of olive flounder (Paralichthys olivaceus) [J]. Journal of Microbiology and Biotechnology,2013,22(4):526-529.
[9]Ye L, Amberg J, Chapman D, et al. Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish[J]. The ISME Journal,2014,8(3):541-551.
[10]Gacias M, Gaspari S, Santos P M G, et al. Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior[J]. Elife,2016,5:e13442.
[11]Ntranos A, Casaccia P. The microbiome-gut-behavior axis: crosstalk between the gut microbiome and oligodendrocytes modulates behavioral responses[J]. Neurotherapeutics,2017,15(1):31-35.
[12]尹军霞,陈瑛,孟丽丽.益生菌剂对鲫鱼肠道菌群影响的初步研究[J].水产科学,2007,26(11):610-612.
[13]Zhou A, Liu Y, Shi P, et al. Molecular characterization of the autochthonous microbiota in the gastrointestinal tract of adult yellow grouper (Epinephelus awoara) cultured in cages[J]. Aquaculture,2009,286(3):184-189.
[14]Bakke I, Skjermo J, Vo T A, et al. Live feed is not a major determinant of the microbiota associated with cod larvae (Gadus morhua)[J]. Environmental Microbiology Reports,2013,5(4):537-548.
[15]李存玉. 池塘养殖牙鲆肠道菌群结构及其与益生菌调控的关系[D]. 上海:上海海洋大学,2015:11-24.
[16]Stephens W Z, Burns A R, Stagaman K, et al. The composition of the zebrafish intestinal microbial community varies across development[J]. The ISME Journal,2016,10(3):644-654.
[17]Turnbaugh P J, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins[J]. Nature,2009,457(7228):480-484.
[18]Hopkins M J, Sharp R, Macfarlane G T. Variation in human intestinal microbiota with age[J]. Digestive and Liver Disease,2002,34(Suppl.2):12-18.
[19]Tanaka S, Kobayashi T, Songjinda P, et al. Influence of antibiotic exposure in the early postnatal period on the development of intestinal microbiota[J]. FEMS Immunology and Medical Microbiology,2009,56(1):80-87.
[20]刁菁,李乐,叶海斌,等. 一种中草药复方和11种单方的体外抑菌效果及对大菱鲆肠道菌群的影响[J]. 水产科学,2018,37(4):433-440.
[21]Kelly P. Gut function:effects on over- and under nutrition, intestinal defense and the microbiome[J]. The Proceedings of Nutrition Society,2010,69(2):261-268.
[22]李存玉,徐永江,柳学周,等. 池塘和工厂化养殖牙鲆肠道菌群结构的比较分析[J]. 水产学报,2015,39(2):245-255.
[23]史秀清,王印庚,张正,等.大菱鲆(Scophthalmus maximus)仔稚鱼发育期消化道可培养细菌的菌群特征分析[J]. 渔业科学进展,2015,36(4):73-82.
[24]刘增新,柳学周,史宝,等.牙鲆(Paralichthys olivaceus)仔稚鱼肠道菌群结构比较分析[J]. 渔业科学进展,2017,38(1):111-119.
[25]Amato K R, Sanders J G, Song S J, et al. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes[J]. The ISME Journal,2019,13(3):576-587.
[26]顾中华,傅志茹,钱红,等.天津地区许氏平鲉人工育苗研究[J].水产科学,2015,34(8):519-522.
[27]刘立明,姜海滨,王茂剑,等.黑鲪仔、稚、幼鱼生长、发育与成活率变化的研究[J].中国海洋大学学报:自然科学版,2013,43(3):25-31.
[28]郭浩宇,张秀梅,张宗航,等. 许氏平鲉仔、稚鱼的摄食特性及幼鱼胃排空率[J].水产学报,2017,41(2):285-296.
[29]Bolger A M, Lohse M, Usadel B. Trimmomatic:a flexible trimmer for Illumina sequence data[J]. Bioinformatics,2014,30(15):2114-2120.
[30]Reyon D, Tsai S Q, Khayter C, et al. FLASH Assembly of TALENs enables high-throughput genome editing[J]. Nature Biotechnology,2012,30(5):460-465.
[31]Edgar R C, Haas B J, Clemente J C, et al. UCHIME improves sensitivity and speed of chimera detection[J]. Bioinformatics,2011,27(16):2194-2200.
[32]Rognes T, Flouri T, Nichols B, et al. VSEARCH:a versatile open source tool for metagenomics[J]. Peer Journal,2016,4:e2584.
[33]Wang Q, Garrity G M, Tiedje J M, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy[J]. Applied & Environmental Microbiology,2007,73(16):5261-5267.
[34]Quast C, Pruesse E, Yilmaz P, et al.The SILVA ribosomal RNA gene database project:improved data processing and web-based tools[J]. Nucleic Acids Research,2013,41(Database issue):D590-D596.
[35]Jiang Y, Zhang Z, Wang Y, et al. Effects of probiotic on microfloral structure of live feed used in larval breeding of turbot Scophthalmus maximus[J]. Chinese Journal of Oceanology and Limnology,2018,36 (3):1002-1012.
[36]Banerjee G, Ray A K. Bacterial symbiosis in the fish gut and its role in health and metabolism[J]. Symbiosis,2017,72(1):1-11.
[37]De Schryver P, Sinha A K, Kunwar P S, et al. Poly-β-hydroxybutyrate (PHB) increases growth performance and intestinal bacterial range-weighted richness in juvenile European sea bass, Dicentrarchus labrax[J]. Applied Microbiology and Biotechnology,2010,86(5):1535-1541.
[38]Ringø E, Zhou Z, Olsen R E, et al. Use of chitin and krill in aquaculture—the effect on gut microbiota and the immune system:a review[J]. Aquaculture Nutrition,2012,18(2):117-131.
[39]Li Y, Yang P, Zhang Y, et al. Effects of dietary glycinin on the growth performance, digestion, intestinal morphology and bacterial community of juvenile turbot, Scophthalmus maximus L.[J]. Aquaculture,2017,479:125-133.
[40]Garcés M E, Sequeiros C, Olivera N L. Marine Lactobacillus pentosus H16 protects Artemia franciscana from Vibrio alginolyticus pathogenic effects[J]. Diseases of Aquatic Organisms,2015,113(1):41-50.
[41]Verner-Jeffreys D W, Shields R J, Bricknell I R, et al. Changes in the gut-associated microflora during the development of Atlantic halibut (Hippoglossus hippoglossus L.) larvae in three British hatcheries[J]. Aquaculture,2003,219(1/4):21-42.
[42]Zorrilla I, Arijo S, Chabrillon M, et al. Vibrio species isolated from diseased farmed sole, Solea senegalensis (Kaup), and evaluation of the potential virulence role of their extracellular products[J]. Journal of Fish Diseases,2003,26(2):103-108.
[43]Liu P C, Lin J Y, Hsiao P T, et al. Isolation and characterization of pathogenic Vibrio alginolyticus from diseased cobia Rachycentron canadum[J]. Journal of Basic Microbiology,2004,44(1):23-28.
[44]Austin B, Zhang X H. Vibrio harveyi:a significant pathogen of marine vertebrates and invertebrates[J]. Letters in Applied Microbiology,2006,43(2):119-124.
[45]Hansen G H, Olafsen J A. Bacterial interactions in early life stages of marine cold water fish[J]. Microbial Ecology,1999,38(1):1-26.
[46]Villamil L, Figueras A, Planas M, et al. Control of Vibrio alginolyticus in Artemia culture by treatment with bacterial probiotics[J]. Aquaculture,2003,219(1/4):43-56.
[47]Bjornsdottir R, Johannsdottir J, Coe J, et al. Survival and quality of halibut larvae (Hippoglossus hippoglossus L.) in intensive farming:possible impact of the intestinal bacterial community[J]. Aquaculture,2009,286(1/2):53-63.
[48]Wong D, Nielsen T B, Bonomo R A, et al. Clinical and pathophysiological overview of Acinetobacter infections:a century of challenges[J]. Clinical Microbiology Reviews,2017,30(1):409-447.
[49]Rd L J, Zhanel G G, Clark N M. Infections due to Acinetobacter baumannii in the ICU:treatment options[J]. Seminars in Respiratory & Critical Care Medicine,2017,38(3):311-325.
[50]Reddy M R K, Mastan S A. Emerging Acinetobacter schindleri in red eye infection of Pangasius sutchi[J].African Journal of Biotechnology,2013,12(50):6992-6996.
[51]Koziñska A, Pazdzior E, Pekala A, et al. Acinetobacter johnsonii and Acinetobacter lwoffii-the emerging fish pathogens[J]. Bulletin of the Veterinary Institute in Pulawy,2014,58(2):193-199.
[52]Urdaci M C, Bressollier P, Pinchuk I. Bacillus clausii probiotic strains:antimicrobial and immunomodulatory activities[J]. Journal of Clinical Gastroenterology,2004,38 (Suppl.2):86-90.
[53]Ziaei-Nejad S, Rezaei M H, Takami G A, et al. The effect of Bacillus spp. bacteria used as probiotics on digestive enzyme activity, survival and growth in the Indian white shrimp Fenneropenaeus indicus[J]. Aquaculture,2006,252(2):516-524.
[54]Chantharasophon K, Warong T, Mapatsa P, et al. High potential probiotic Bacillus species from gastro-intestinal tract of Nile tilapia (Oreochromis niloticus)[J]. Biotechnology,2011,10(6):498-505.
[55]Ahotupa M, Saxelin M, Korpela R. Probiotic properties of Brevibacillus brevis and its influence on sea bass (Dicentrarchus labrax) larval rearing[J].African Journal of Microbiology Research,2012,6(35):6487-6495. |
|
|
|
