The Metagenomic Characterization of Bacterial Community in Aquacultured Shrimp Penaeus monodon

Dini Chandran C. S. *

CEPCI Research Centre, Govt. of India, Kollam, Kerala, India.

Rekha Sivadasan

CEPCI Research Centre, Govt. of India, Kollam, Kerala, India.

*Author to whom correspondence should be addressed.


Aquaculture has grown rapidly during the last few decades due to research and developmental activities but we are still unaware of the various microbial species thriving within the aquaculture systems and their specific roles for knowing that Mmetagenomics study required environmental sample to discover the unexplored microbial community. The aim of this present study is to characterize the gut microbiota of giant tiger shrimp, Penaeus monodon collected gut sample and16S rRNA gene-based high-throughput sequencing revealed distinct and diverse microbial communities. The results showed a high abundance of Betaproteobacteria, followed by Alphaproteobacteria, Clostridia, Actinobacteria, Gammaproteobacteria and Bacilli found in the gut sample Microbes that play essential roles in nutrient cycling and mineralization of organic compounds such as Bacteroidetes, Planctomycetes, Gammaproteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria could also be identified. Due to the strong influence of the gut microbiota on fish health, dominant bacterial species in the gut are strong candidates for probiotics. These findings provide valuable information on the microbial community and contribute to controlling the diseases in shrimp farms.

Keywords: Metagenomics, bacterial community, next generation sequencing, 16S rRNA

How to Cite

Dini Chandran C. S., & Sivadasan, R. (2023). The Metagenomic Characterization of Bacterial Community in Aquacultured Shrimp Penaeus monodon. Biotechnology Journal International, 27(5), 71–81.


Download data is not yet available.


FDA. Animal husbandry and disease control: Aquaculture. Silver Spring, MD: U. S. Food and Drug Administration; 2012.

Bacanu GM, Oprea L. Differences in the gut microbiota between wild and domestic Acipenser ruthenus evaluated by denaturing gradient gel electrophoresis. Rom Biotechnol Lett. 2013;18:8069- 8076.

Balcazar JL, de Blas I, Ruiz-Zarzuela I, Cunningham D, Vendrell D, Muzquiz JL. The role of probiotics in aquaculture. Vet Microbiol. 2006;114:173–186.

Bennett KW, Eley A. Fusobacteria – new taxonomy and related diseases. J Med Microbiol. 1993;39:246-254.

Bourgault AM, Lamothe F, Dolce P, SaintJean L. SaintAntoine P. Fusobacterium bacteremia: clinical experience with 40 cases; 1997.

Cipriano RC, Bullock GL, Pyle SW. Aeromonas hydrophila and Motile Aeromonad Septicemias of Fish. US Department of the Interior, US Fish and Wildlife Service, Divison of Fishery Research, Fish Disease Leaflet, Washington. 1984;68.

Clarke KR, Gorley RN. Primer v6: User manual/tutorial. Plymouth, UK: Primer-e; 2006.

Clements KD, Choat JH. Fermentation in tropical marine herbivorous fishes. Physiol Zool. 1995;68:355-378.

Clements KD, Gleeson VP, Slaytor M. Shortchain fatty-acid metabolism in temperate marine herbivorous fish. J Comp Physiol B. 1994;164:372-377.

Collinder E, Bjornhag G, Cardona M, Norin E, Rehbinder C, Midtvedt T. Gastrointestinal host-microbial interactions in mammals and fish: Comparative studies in man, mice, rats, pigs, horses, cows, elk, reindeer, salmon and cod. Microb Ecol Health Dis. 2003;15:66-78.

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72: 5069- 5072.

Di Maiuta N, Schwarzentruber P, Schenker M, Schoelkopf J. Microbial population dynamics in the faeces of wood-eating loricariid catfishes. Lett Appl Microbiol. 2013;56:401-407.

Donkeng NN, Maiwore J, Ngoune LT, Montet D. Mbofung CMF. Characterization of the bacterial flora of tilapia (Oreochoromis niloticus) harvested from four lakes in the north of Cameroon; 2011.

Bartels W, Kirschberger J, Duttingdorf S, HDMZ Busche R. Role of short-chain fatty acids in the hind gut. 1998;20:S52-S59.

Azim ME, Little DC. The biofloc technology (BFT) in indoor tanks: Water quality, biofloc composition, and growth and welfare of Nile tilapia (Oreochromis niloticus); 2008.

Glencross BD, Booth M, Allan GL. A feed is only as good as its ingredients–a review of ingredient evaluation strategies for aquaculture feeds. Aquac Nutr. 2007; 13(1):17-34. Available: 50.x

Troell M, Joyce A, Chopin T, Neori A, Buschmann AH, Fang JG. Ecological engineering in aquaculture-potential for integrated multi-trophic aquaculture (IMTA) in marine offshore systems. Aquaculture. 2009;297(1-4):1–9.


Caruso G. Microbes and their use as indicators of pollution. J Pollut Eff Cont. 2013;1:e102.

Available: .

FDA. Aquaculture Drugs. In fish and fishery products hazards and controls guide ed. u. s. department of health and human services. Washington, DC: FDA, Center for Food Safety and Applied Nutition, Office of Food Safety. 2011;183–207.

Finegold SM, Vaisanen ML, Molitoris DR, Tomzynski TJ, Song Y, Liu C, Collins MD, Lawson PA. Cetobacterium somerae sp. nov from human feces and emended description of the genus Cetobacterium. Syst Appl Microbiol. 2003;26:177-181.

Gao YL, Storebakken T, Shearer KD, Penn M, Overland M. Supplementation of fishmeal and plant protein-based diets for rainbow trout with a mixture of sodium formate and butyrate; 2011.

Griswold BL, Tubb RA. Food of yellow perch, white bass, freshwater drum, and channel catfish in Sandusky Bay, Lake Erie; 1977.

Hamer H, Jonkers D, Troost FJ, Bast A, Vanhoutvin S, Venema K, Brummer RJ. Butyrate modulates oxidative stress in the colonic mucosa of healthy humans. Gastroenterology. 2007;132:A79.

Hargreaves JE, Lucey DR. Life-threatening Edwardsiella tarda soft-tissue infection associated with catfish puncture wound. J Infect Dis. 1990;162: 1416–1417.

Harris NJ. Seasonal food habits of bluegills in Richmond Lake, South Dakota. Proc S Dak Acad Sci. 1999;78:79-85.

Heikkinen J, Vielma J, Kemilainen O, Tiirola M, Eskelinen P, Kiuru T, Navia-Paldanius D, von Wright A. Effects of soybean meal based diet on growth performance. gut histopathology and intestinal microbiota of juvenile rainbow trout (Oncorhynchus mykiss); 2006.