Abstract
The intestinal microbiota plays crucial roles in host health. The Pacific white shrimp is one of the most profitable aquaculture species in the world. Antibiotic supplement in feed is an optional practice to treat shrimp bacterial diseases. However, little is known about antibiotic effects on intestinal microbiota in pacific white shrimp. Here, shrimps were given feed supplemented with ciprofloxacin (Cip) (40 and 80 mg kg−1) and sulfonamide (Sul) (200 and 400 mg kg−1) to investigate the microbial community by targeting the V4 region of 16S rRNA genes. Within 4 days after feeding with normal feed and with antibiotics, antibiotic concentrations of Cip and Sul groups in the intestine dropped sharply. Significantly, increased abundance of antibiotic resistance genes (ARGs) of ciprofloxacin (qnrB, qnrD, and qnrS) and sulfonamide (sul1, sul2, and sul3) was observed in Cip and Sul groups (P < 0.05). A total of 3191 operational taxonomic units (OTUs) were obtained and 41 phyla were identified from 63 samples in shrimp intestine. The numbers of OTUs and Shannon index decreased rapidly at day 1 (the first day after feeding with antibiotics) and increased at day 3 (the third day after feeding with antibiotics). The relative abundance of dominant phyla and genera in Cip and Sul groups were significantly different from that in the control group (Ctrl). Furthermore, functional potentials that were related to amino acid metabolism, carbohydrate metabolism, and cellular processes and signaling varied significantly in Cip and Sul groups. These results point to an antibiotic-induced shift in shrimp intestinal microbiota, which highlights the importance of considering the microbiota in shrimp health management.
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Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methe B, Schloss PD, Gevers D, Mitreva M, Huttenhower C (2012) Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 8(6):e1002358. https://doi.org/10.1371/journal.pcbi.1002358
Akinbowale OL, Peng H, Barton MD (2007) Diversity of tetracycline resistance genes in bacteria from aquaculture sources in Australia. J Appl Microbiol 103(5):2016–2025. https://doi.org/10.1111/j.1365-2672.2007.03445.x
Albuquerque Costa R, Araujo RL, Souza OV, Vieira RH (2015) Antibiotic-resistant vibrios in farmed shrimp. Biomed Res Int 2015:505914. https://doi.org/10.1155/2015/505914
Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5(5):908–917. https://doi.org/10.1038/ismej.2010.171
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336. https://doi.org/10.1038/nmeth.f.303
DeLorenzo ME, Brooker J, Chung KW, Kelly M, Martinez J, Moore JG, Thomas M (2016) Exposure of the grass shrimp, Palaemonetes pugio, to antimicrobial compounds affects associated Vibrio bacterial density and development of antibiotic resistance. Environ Toxicol 31(4):469–477. https://doi.org/10.1002/tox.22060
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72(7):5069–5072. https://doi.org/10.1128/AEM.03006-05
Dethlefsen L, Relman DA (2011) Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 108(Suppl 1):4554–4561. https://doi.org/10.1073/pnas.1000087107
Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6(11):e280. https://doi.org/10.1371/journal.pbio.0060280
Donskey CJ, Hujer AM, Das SM, Pultz NJ, Bonomo RA, Rice LB (2003) Use of denaturing gradient gel electrophoresis for analysis of the stool microbiota of hospitalized patients. J Microbiol Methods 54(2):249–256. https://doi.org/10.1016/s0167-7012(03)00059-9
Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10(10):996–998. https://doi.org/10.1038/nmeth.2604
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27(16):2194–2200. https://doi.org/10.1093/bioinformatics/btr381
FAO (2018) Global aquaculture production. http://www.fao.org/fishery/statistics/collections/en. Accessed July 2018
Flores-Miranda BM, Espinosa-Plascencia A, Gomez-Jimenez S, Lopez-Zavala AA, Gonzalez-Carrillo HH, Bermudez-Almada Mdel C (2012) Accumulation and elimination of enrofloxacin and ciprofloxacin in tissues of shrimp Litopenaeus vannamei under laboratory and farm conditions. ISRN Pharm 2012:374212. https://doi.org/10.5402/2012/374212
Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C (2015) Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling. Nat Rev Microbiol 13(6):360–372. https://doi.org/10.1038/nrmicro3451
Gao P, Mao D, Luo Y, Wang L, Xu B, Xu L (2012) Occurrence of sulfonamide and tetracycline-resistant bacteria and resistance genes in aquaculture environment. Water Res 46(7):2355–2364. https://doi.org/10.1016/j.watres.2012.02.004
He S, Wang Q, Li S, Ran C, Guo X, Zhang Z, Zhou Z (2017) Antibiotic growth promoter olaquindox increases pathogen susceptibility in fish by inducing gut microbiota dysbiosis. Sci China Life Sci 60(11):1260–1270. https://doi.org/10.1007/s11427-016-9072-6
Heirali AA, Workentine ML, Acosta N, Poonja A, Storey DG, Somayaji R, Rabin HR, Whelan FJ, Surette MG, Parkins MD (2017) The effects of inhaled aztreonam on the cystic fibrosis lung microbiome. Microbiome 5(1):51. https://doi.org/10.1186/s40168-017-0265-7
Hollister EB, Riehle K, Luna RA, Weidler EM, Rubio-Gonzales M, Mistretta T-A, Raza S, Doddapaneni HV, Metcalf GA, Muzny DM, Gibbs RA, Petrosino JF, Shulman RJ, Versalovic J (2015) Structure and function of the healthy pre-adolescent pediatric gut microbiome. Microbiome 3:36. https://doi.org/10.1186/s40168-015-0101-x
Hou D, Huang Z, Zeng S, Liu J, Wei D, Deng X, Weng S, Yan Q, He J (2018) Intestinal bacterial signatures of white feces syndrome in shrimp. Appl Microbiol Biotechnol 102(8):3701–3709. https://doi.org/10.1007/s00253-018-8855-2
Huang Z, Chen Y, Weng S, Lu X, Zhong L, Fan W, Chen X, Zhang H, He J (2016) Multiple bacteria species were involved in hepatopancreas necrosis syndrome (HPNS) of Litopenaeus vannamei. Acta Sci Natur Univ SunYatseni 55(1):1–11. https://doi.org/10.13471/j.cnki.acta.snus
Huang F, Pan L, Song M, Tian C, Gao S (2018) Microbiota assemblages of water, sediment, and intestine and their associations with environmental factors and shrimp physiological health. Appl Microbiol Biotechnol 101(6):2493–2505. https://doi.org/10.1007/s00253-018-9229-5
Jernberg C, Lofmark S, Edlund C, Jansson JK (2007) Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1(1):56–66. https://doi.org/10.1038/ismej.2007.3
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40(Database issue):D109–D114. https://doi.org/10.1093/nar/gkr988
Lane AN, Fan TW (2015) Regulation of mammalian nucleotide metabolism and biosynthesis. Nucleic Acids Res 43(4):2466–2485. https://doi.org/10.1093/nar/gkv047
Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31(9):814–821. https://doi.org/10.1038/nbt.2676
Lankelma JM, Cranendonk DR, Belzer C, de Vos AF, de Vos WM, van der Poll T, Wiersinga WJ (2016) Antibiotic-induced gut microbiota disruption during human endotoxemia: a randomised controlled study. Gut 66(9):1623–1630. https://doi.org/10.1136/gutjnl-2016-312132
LeBlanc JG, Chain F, Martin R, Bermudez-Humaran LG, Courau S, Langella P (2017) Beneficial effects on host energy metabolism of short-chain fatty acids and vitamins produced by commensal and probiotic bacteria. Microb Cell Factories 16(1):79. https://doi.org/10.1186/s12934-017-0691-z
Lee C-T, Chen IT, Yang Y-T, Ko T-P, Huang Y-T, Huang J-Y, Huang M-F, Lin S-J, Chen C-Y, Lin S-S, Lightner DV, Wang H-C, Wang AHJ, Wang H-C, Hor L-I, Lo C-F (2015) The opportunistic marine pathogen Vibrio parahaemolyticus becomes virulent by acquiring a plasmid that expresses a deadly toxin. Proc Natl Acad Sci U S A 112(34):10798–10803. https://doi.org/10.1073/pnas.1503129112
Magoc T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21):2957–2963. https://doi.org/10.1093/bioinformatics/btr507
Mu C, Yang Y, Su Y, Zoetendal EG, Zhu W (2017) Differences in microbiota membership along the gastrointestinal tract of piglets and their differential alterations following an early-life antibiotic intervention. Front Microbiol 8:797. https://doi.org/10.3389/fmicb.2017.00797
Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, Chung J, Sohn J, Barber CM, Goldfarb DS, Raju K, Abubucker S, Zhou Y, Ruiz VE, Li H, Mitreva M, Alekseyenko AV, Weinstock GM, Sodergren E, Blaser MJ (2015) Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nat Commun 6:7486. https://doi.org/10.1038/ncomms8486
Perez-Cobas AE, Artacho A, Knecht H, Ferrus ML, Friedrichs A, Ott SJ, Moya A, Latorre A, Gosalbes MJ (2013) Differential effects of antibiotic therapy on the structure and function of human gut microbiota. PLoS One 8(11):e80201. https://doi.org/10.1371/journal.pone.0080201
Pham DK, Chu J, Do NT, Brose F, Degand G, Delahaut P, De Pauw E, Douny C, Nguyen KV, Vu TD, Scippo ML, Wertheim HF (2015) Monitoring antibiotic use and residue in freshwater aquaculture for domestic use in Vietnam. Ecohealth 12(3):480–489. https://doi.org/10.1007/s10393-014-1006-z
Puhl NJ, Uwiera RR, Yanke LJ, Selinger LB, Inglis GD (2012) Antibiotics conspicuously affect community profiles and richness, but not the density of bacterial cells associated with mucosa in the large and small intestines of mice. Anaerobe 18(1):67–75. https://doi.org/10.1016/j.anaerobe.2011.12.007
Rashid MU, Zaura E, Buijs MJ, Keijser BJ, Crielaard W, Nord CE, Weintraub A (2015) Determining the long-term effect of antibiotic administration on the human normal intestinal microbiota using culture and pyrosequencing methods. Clin Infect Dis 60(Suppl 2):S77–S84. https://doi.org/10.1093/cid/civ137
Raymann K, Shaffer Z, Moran NA (2017) Antibiotic exposure perturbs the gut microbiota and elevates mortality in honeybees. PLoS Biol 15(3):e2001861. https://doi.org/10.1371/journal.pbio.2001861
Reed LA, Siewicki TC, Shah JC (2006) The biopharmaceutics and oral bioavailability of two forms of oxytetracycline to the white shrimp, Litopenaeus setiferus. Aquaculture 258(1–4):42–54. https://doi.org/10.1016/j.aquaculture.2006.03.029
Schmidt V, Gomez-Chiarri M, Roy C, Smith K, Amaral-Zettler L (2017) Subtle microbiome manipulation using probiotics reduces antibiotic-associated mortality in fish. mSystems 2(6):e00133–e00117. https://doi.org/10.1128/mSystems.00133-17
Schweinitzer T, Josenhans C (2010) Bacterial energy taxis: a global strategy? Arch Microbiol 192(7):507–520. https://doi.org/10.1007/s00203-010-0575-7
Stalin N, Srinivasan P (2016) Molecular characterization of antibiotic resistant Vibrio harveyi isolated from shrimp aquaculture environment in the south east coast of India. Microb Pathog 97:110–118. https://doi.org/10.1016/j.micpath.2016.05.021
Stocker R, Seymour JR (2012) Ecology and physics of bacterial chemotaxis in the ocean. Microbiol Mol Biol Rev 76(4):792–812. https://doi.org/10.1128/MMBR.00029-12
Tetzner NF, Maniero MG, Rodrigues-Silva C, Rath S (2016) On-line solid phase extraction-ultra high performance liquid chromatography-tandem mass spectrometry as a powerful technique for the determination of sulfonamide residues in soils. J Chromatogr A 1452:89–97. https://doi.org/10.1016/j.chroma.2016.05.034
Wilkinson N, Hughes RJ, Aspden WJ, Chapman J, Moore RJ, Stanley D (2016) The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica. Appl Microbiol Biotechnol 100(9):4201–4209. https://doi.org/10.1007/s00253-015-7280-z
Willing BP, Russell SL, Finlay BB (2011) Shifting the balance: antibiotic effects on host-microbiota mutualism. Nat Rev Microbiol 9(4):233–243. https://doi.org/10.1038/nrmicro2536
Wu H, Shi Y, Guo X, Zhao S, Du J, Jia H, He L, Du L (2016) Determination and removal of sulfonamides and quinolones from environmental water samples using magnetic adsorbents. J Sep Sci 39(22):4398–4407. https://doi.org/10.1002/jssc.201600631
Xiong J (2018) Progress in the gut microbiota in exploring shrimp disease pathogenesis and incidence. Appl Microbiol Biotechnol 102(17):7343–7350. https://doi.org/10.1007/s00253-018-9199-7
Xiong J, Dai W, Qiu Q, Zhu J, Yang W, Li C (2018) Response of host–bacterial colonization in shrimp to developmental stage, environment and disease. Mol Ecol 27(18):3686–3699. https://doi.org/10.1111/mec.14822
Xu W, Zhu X, Wang X, Deng L, Zhang G (2006) Residues of enrofloxacin, furazolidone and their metabolites in Nile tilapia (Oreochromis niloticus). Aquaculture 254(1-4):1–8. https://doi.org/10.1016/j.aquaculture.2005.10.030
Zeng S, Huang Z, Hou D, Liu J, Weng S, He J (2017) Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages. PeerJ 5:e3986. https://doi.org/10.7717/peerj.3986
Zhang C, Yu M, Yang Y, Mu C, Su Y, Zhu W (2017) Differential effect of early antibiotic intervention on bacterial fermentation patterns and mucosal gene expression in the colon of pigs under diets with different protein levels. Appl Microbiol Biotechnol 101(6):2493–2505. https://doi.org/10.1007/s00253-016-7985-7
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This work was financially supported by the China Agriculture Research System (CARS-48), the Guangzhou Science Technology and Innovation Commission Project (201510010071), and the Guangdong Ocean and Fishery Bureau Project (20164200042090023).
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Zeng, S., Hou, D., Liu, J. et al. Antibiotic supplement in feed can perturb the intestinal microbial composition and function in Pacific white shrimp. Appl Microbiol Biotechnol 103, 3111–3122 (2019). https://doi.org/10.1007/s00253-019-09671-9
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DOI: https://doi.org/10.1007/s00253-019-09671-9