Cite this paper:
ZHAO Ye, WANG Qing, LIU Hui, LI Bingjun, ZHANG Hongxia. High-throughput sequencing of 16S rRNA amplicons characterizes gut microbiota shift of juvenile sea cucumber Apostichopus japonicus feeding with three antibiotics[J]. HaiyangYuHuZhao, 2019, 37(5): 1714-1725

High-throughput sequencing of 16S rRNA amplicons characterizes gut microbiota shift of juvenile sea cucumber Apostichopus japonicus feeding with three antibiotics

ZHAO Ye1, WANG Qing2, LIU Hui2, LI Bingjun1, ZHANG Hongxia2
1 Ocean School, Yantai University, Yantai 264005, China;
2 Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
Sea cucumber Apostichopus japonicus is an important marine economic species in Asian countries due to its profound nutritional and medicinal value. So far, with the rapid development of intensified artificial aquaculture of sea cucumbers, the use of antibiotics is still an inexpensive and dispensable way to treat pathogenic infections, especially during the nursery phase. However, there is little information on the effects of antibiotics on the intestinal microbiota of sea cucumber. Therefore an Illumina based sequencing method was used to examine the intestinal bacterial composition of juvenile A. japonicas following diets with three typical antibiotics (tetracycline, erythromycin, and norfloxacin) under 15, 30, and 45 d. The findings reveal that different antibiotics have distinct effects on the growth performance of juvenile sea cucumbers. However, the richness and diversity of microbiota were barely affected by antibiotics but the community composition alterations indicated that the three antibiotics exhibited their respective patterns of reshaping the intestinal bacteria of juvenile sea cucumbers. In common, the abundance of some sensitive genera with helpful functions, such as Thalassotalea, Shewanella, Sulfitobacter, and Halomonas decreased significantly with exposure to antibiotics and the abundance of multiple potential pathogenic- and suspected antibiotic-resistant microorganisms like Arcobacter, Leucothrix, and Clostridium_sensu_stricto_1 was found increased significantly in the antibiotic groups. These results suggest that low doses of antibiotics could affect the composition of the intestinal microbiota of sea cucumbers and might increase the risk of infection of the hosts. This study could help us to explore how antibacterial compounds modify the gut microbiota of sea cucumbers and provide theoretical guidance in hatchery management by scientific antibiotic use in sea cucumber mariculture.
Key words:    gut microbiota|sea cucumber|antibiotic|16S rRNA gene|illumina sequencing   
Received: 2018-10-22   Revised: 2018-12-07
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Angelakis E, Merhej V, Raoult D. 2013. Related actions of probiotics and antibiotics on gut microbiota and weight modification. The Lancet Infectious Diseases, 13(10):889-899,
Austin B, Al-Zahrani A J. 1988. The effect of antimicrobial compounds on the gastrointestinal microflora of rainbow trout, Salmo gairdneri Richardson. Journal of Fish Biology, 33(1):1-14,
Becattini S, Taur Y, Pamer E G. 2016. Antibiotic-induced changes in the intestinal microbiota and disease. Trends in Molecular Medicine, 22(6):458-478,
Becker P T, Egea E, Eeckhaut I. 2008. Characterization of the bacterial communities associated with the bald sea urchin disease of the echinoid Paracentrotus lividus. Journal of Invertebrate Pathology, 98(2):136-147,
Caporaso J G, Kuczynski J, Stombaugh J, Bittinger K, Bushman F D, Costello E K, Fierer N, Peña A G, Goodrich J K, Gordon J I, Huttley G A, Kelley S T, Knights D, Koenig J E, Ley R E, Lozupone C A, McDonald D, Muegge B D, Pirrung M, Reeder J, Sevinsky J R, Turnbaugh P J, Walters W A, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QⅡME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5):335-336,
Carding S, Verbeke K, Vipond D T, Corfe B M, Owen L J. 2015. Dysbiosis of the gut microbiota in disease.Microbial Ecology in Health and Disease, 26:26 191.
Carlson J M, Leonard, A B, Hyde E R, Petrosino J F, Primm T P. 2017. Microbiome disruption and recovery in the fish Gambusia affinis following exposure to broad-spectrum antibiotic. Infection & Drug Resistance, 10:143-154,
Carvalho I T, Santos L. 2016. Antibiotics in the aquatic environments:a review of the European scenario.Environment International, 94:736-757,
Chen Q L, An X L, Li H, Su J Q, Ma Y B, Zhu Y G. 2016.Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil.Environment International, 92-93:1-10,
Collado L, Figueras M J. 2011. Taxonomy, epidemiology, and clinical relevance of the genus Arcobacter. Clinical Microbiology Reviews, 24(1):174-192,
Deng H, He C B, Zhou Z C, Liu C, Tan K F, Wang N B, Jiang B, Gao X G, Liu W D. 2009. Isolation and pathogenicity of pathogens from skin ulceration disease and viscera ejection syndrome of the sea cucumber Apostichopus japonicus. Aquaculture, 287(1-2):18-27,
DiBaise J K, Zhang H S, Crowell M D, Krajmalnik-Brown R, Decker G A, Rittmann B E. 2008. Gut microbiota and its possible relationship with obesity. Mayo Clinic Proceedings, 83(4):460-469,
Edgar R C, Haas B J, Clemente J C, Quince C, Knight R. 2011.UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16):2 194-2 200,
Flint H J, Scott K P, Louis P, Duncan S H. 2012. The role of the gut microbiota in nutrition and health. Nature Reviews Gastroenterology & Hepatology, 9(10):577-589,
Gao F, Li F H, Tan J, Yan J P, Sun H L. 2014. Bacterial community composition in the gut content and ambient sediment of sea cucumber Apostichopus japonicus revealed by 16S rRNA gene pyrosequencing. PLoS One, 9(6):e100092,
Gutiérrez-Salazar G J, Molina-Garza Z J, Hernández-Acosta M, García-Salas J A, Mercado-Hernández R, GalavizSilva L. 2011. Pathogens in pacific white shrimp(Litopenaeus vannamei Boone, 1931) and their relationship with physicochemical parameters in three different culture systems in Tamaulipas, Mexico.Aquaculture, 321(1-2):34-40,
Han B, Sivaramakrishnan P, Lin C C J, Neve I A A, He J Q, Tay L W R, Sowa J N, Sizovs A, Du G W, Wang J, Herman C, Wang M C. 2017. Microbial genetic composition tunes host longevity. Cell, 169(7):1 249-1 262.e13,
Jakobsson H E, Jernberg C, Andersson A F, Sjölund-Karlsson M, Jansson J K, Engstrand L. 2010. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One, 5(3):e9836,
Jiang H F, Liu X L, Chang Y Q, Liu M T, Wang G X. 2013.Effects of dietary supplementation of probiotic Shewanella colwelliana WA64, Shewanella olleyana WA65 on the innate immunity and disease resistance of abalone, Haliotis discus hannai Ino. Fish & Shellfish Immunology, 35(1):86-91,
Li W H, Gao L H, Shi Y L, Liu J M, Cai Y Q. 2015. Occurrence, distribution and risks of antibiotics in urban surface water in Beijing, China. Environmental Science:Processes & Impacts, 17(9):1 611-1 619,
Liao Y L. 1997. Fauna Sinica:Phylum Enchinodermata Class Holothuroidea. Science Press, Beijing. p.148-150. (in Chinese)
Liu H D, Wang L, Liu M, Wang B J, Jiang K Y, Ma S S, Li Q F. 2011. The intestinal microbial diversity in Chinese shrimp(Fenneropenaeus chinensis) as determined by PCR-DGGE and clone library analyses. Aquaculture, 317(1-4):32-36,
Loo V G, Bourgault A M, Poirier L, Lamothe F, Michaud S, Turgeon N, Toye B, Beaudoin A, Frost E H, Gilca R, Brassard P, Dendukuri N, Béliveau C, Oughton M, Brukner I, Dascal A. 2011. Host and pathogen factors for Clostridium difficile infection and colonization. The New England Journal of Medicine, 365(18):1 693-1 703,
Magoč T, Salzberg S L. 2011. FLASH:fast length adjustment of short reads to improve genome assemblies.Bioinformatics, 27(21):2 957-2 963,
Navarrete P, Mardones P, Opazo R, Espejo R, Romero J. 2008.Oxytetracycline treatment reduces bacterial diversity of intestinal microbiota of Atlantic salmon. Journal of Aquatic Animal Health, 20(3):177-183,
Panda S, El Khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F, Manichanh C. 2014. Short-term effect of antibiotics on human gut microbiota. PLoS One, 9(4):e95476,
Sanchez-Martínez J G, Pérez-Castañeda R, Rábago-Castro J L, Aguirre-Guzmán G, Vázquez-Sauceda M L. 2008. A preliminary study on the effects on growth, condition, and feeding indexes in channel catfish, Ictalurus punctatus, after the prophylactic use of potassium permanganate and oxytetracycline. Journal of the World Aquaculture Society, 39(5):664-670,
Schmitt S, Tsai P, Bell J, Fromont J, Ilan M, Lindquist N, Perez T, Rodrigo A, Schupp P J, Vacelet J, Webster N, Hentschel U, Taylor M W. 2012. Assessing the complex sponge microbiota:core, variable and species-specific bacterial communities in marine sponges. ISME Journal, 6(3):564-576,
Schuijt T J, Lankelma J M, Scicluna B P, Melo F D S E, Roelofs J J T H, de Boer J D, Hoogendijk A J, de Beer R, de Vos A, Belzer C, de Vos W M, van de Poll T, Wiersinga W J. 2016.
The gut microbiota plays a protective role in the host defence against Pneumococcal pneumonia. Gut, 65(4):575-583,
Sha Y J, Liu M, Wang B J, Jiang K Y, Sun G Q, Wang L. 2016.Gut bacterial diversity of farmed sea cucumbers Apostichopus japonicus with different growth rates.Microbiology, 85(1):109-115,
Sharifah E N, Eguchi M. 2012. Benefits of live phytoplankton, Chlorella vulgaris, as a biocontrol agent against fish pathogen Vibrio anguillarum. Fisheries Science, 78(2):367-373,
Snieszko S F, Wood E M. 1955. The effect of some sulfonamides on the growth of brook trout, brown trout, and rainbow trout. Transactions of the American Fisheries Society, 84(1):86-92,[86:TEOSSO]2.0.CO;2.
Stiemsma L T, Turvey S E. 2017. Asthma and the microbiome:defining the critical window in early life. Allergy, Asthma & Clinical Immunology, 13:3,
Topping D L, Clifton P M. 2001. Short-chain fatty acids and human colonic function:roles of resistant starch and nonstarch polysaccharides. Physiological Reviews, 81(3):1 031-1 064,
Toprak E, Veres A, Michel J B, Chait R, Hartl D L, Kishony R. 2012. Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nature Genetics, 44(1):101-105,
Tremaroli V, Bäckhed F. 2012. Functional interactions between the gut microbiota and host metabolism. Nature, 489(7415):242-249,
Uyaguari M, Key P, Moore J, Jackson K, Scott G. 2009. Acute effects of the antibiotic oxytetracycline on the bacterial community of the grass shrimp, Palaemonetes pugio.Environmental Toxicology & Chemistry, 28(12):2 715-2 724,
Van Boeckel T P, Gandra S, Ashok A, Caudron Q, Grenfell B T, Levin S A, Laxminarayan R. 2014. Global antibiotic consumption 2000 to 2010:an analysis of national pharmaceutical sales data. The Lancet Infectious Diseases, 14(8):742-750,
Verner-Jeffreys D W, Shields R J, Bricknell I R, Birkbeck T H. 2004. Effects of different water treatment methods and antibiotic addition on larval survival and gut microflora development in Atlantic halibut (Hippoglossushippoglossus L.) yolk-sac larvae. Aquaculture, 232(1-4):129-143,
Vijay-Kumar M, Aitken J D, Carvalho F A, Cullender T C, Mwangi S, Srinivasan S, Sitaraman S V, Knight R, Ley R E, Gewirtz A T. 2010. Metabolic syndrome and altered gut microbiota in mice lacking toll-like receptor 5.Science, 328(5975):228-231,
Wang J, Huang Y J, Xu K H, Zhang X Y, Sun H Y, Fan L F, Yan M T. 2019. White spot syndrome virus (WSSV) infection impacts intestinal microbiota composition and function in Litopenaeus vannamei. Fish & Shellfish Immunology, 84:130-137,
Wang L, Zhao X W, Xu H C, Bao X Y, Liu X J, Chang Y Q, Ding J. 2018. Characterization of the bacterial community in different parts of the gut of sea cucumber (Apostichopus japonicus) and its variation during gut regeneration.Aquaculture Research, 49(5):1 987-1 996,
Wang P H, Chang Y Q, Yu J H, Li C Y, Xu G R. 2007. Acute peristome edema disease in juvenile and adult sea cucumbers Apostichopus japonicus (Selenka) reared in North China. Journal of Invertebrate Pathology, 96(1):11-17,
Yamazaki Y, Meirelles P M, Mino S, Suda W, Oshima K, Hattori M, Thompson F L, Sakai Y, Sawabe T, Sawabe T. 2016. Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps. Scientific Reports, 6:21 631,
Zhang D Y, Ji H F, Liu H, Wang S X, Wang J, Wang Y M. 2016a. Changes in the diversity and composition of gut microbiota of weaned piglets after oral administration of Lactobacillus or an antibiotic. Applied Microbiology and Biotechnology, 100(23):10 081-10 093,
Zhang M L, Sun Y H, Liu Y K, Qiao F, Chen L Q, Liu W T, Du Z Y, Li E C. 2016b. Response of gut microbiota to salinity change in two euryhaline aquatic animals with reverse salinity preference. Aquaculture, 454:72-80,
Zhang Q Q, Ying G G, Pan C G, Liu Y S, Zhao J L. 2015.Comprehensive evaluation of antibiotics emission and fate in the river basins of China:source analysis, multimedia modeling, and linkage to bacterial resistance.Environmental Science & Technology, 49(11):6 772-6 782,
Zhang X C, Nakahara T, Murase S, Nakata H, Inoue T, Kudo T. 2013. Physiological characterization of aerobic culturable bacteria in the intestine of the sea cucumber Apostichopus japonicus. Journal of General and Applied Microbiology, 59(1):1-10,
Zhang Z, Xing R, Lv Z, Shao Y, Zhang W, Zhao X, Li C. 2018.Analysis of gut microbiota revealed Lactococcus garviaeae could be an indicative of skin ulceration syndrome in farmed sea cucumber Apostichopus japonicas. Fish & Shellfish Immunology, 80:148-154,
Zhao Y, Liu H, Wang Q, Li B J. 2019. The influence of three antibiotics on the growth, intestinal enzyme activities, and immune response of the juvenile sea cucumber Apostichopus japonicus Selenka. Fish & Shellfish Immunology, 84:434-440,
Zhou L, Limbu S M, Shen M L, Zhai W Y, Qiao F, He A Y, Du Z Y, Zhang M L. 2018. Environmental concentrations of antibiotics impair zebrafish gut health. Environmental Pollution, 235:245-254,