Culturable gut bacteria of Ikan Batak (Neolissochilus sumatranus Weber & de Beaufort, 1916) collected in Toba Samosir, Indonesia
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Abstract. Dinoto A, Handayani R, Setianingrum N, Julistiono H. 2020. Culturable gut bacteria of Ikan Batak (Neolissochilus sumatranus Weber & de Beaufort, 1916) collected in Toba Samosir, Indonesia. Biodiversitas 21: 4483-4488. Ikan Batak (Neolissochilus sumatranus Weber & de Beaufort, 1916) is one of the fish species that is rarely found in water and have the status of endangered species. In consequence, the loss of endemic fish may contribute to the loss of microorganisms that inhabits the fish as a host. The studies on microorganisms associated with N. sumatranus are very limited. Therefore, the purpose of this study was to isolate and identify the culturable bacteria isolated from the gut of N. sumatranus. Sampling of N. sumatranus was carried out in a river within Toba Samosir area which flows to Lake Toba. Fish gut content was collected for isolating microorganisms using three media, including MRS, 10X diluted MRS, and MRS supplemented with 1% bile salt. Thirteen isolates were successfully isolated and identified based on 16S rRNA. This study revealed various species of gut bacteria recovered from N. sumatranus based on BLAST analysis. The isolates showed closest relationship to species Bacillus subtilis (3 isolates), Bacillus tequilensis (2 isolates), Tumebacillus ginsengisoli (6 isolates), Klebsiella pneumoniae (1 isolate), and Lactobacillus pentosus (1 isolate) with the similarity ranging at 98.7 to 100%. All 16S rRNA gene nucleotides of isolates have been submitted to GenBank. This study also described the isolates that have a very close relationship with Bacillus tequilla and Bacillus subtilis. Further identification is challenged to obtain a big picture of the diversity of microorganisms and the functionality in the digestive ecosystem of N. sumatranus for their conservation and bioprospecting of microbial-based aquaculture.
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References
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Barati A, Ghaderpour A, Chew LL, Bong CW, Thong KL, Chong VC, Chai LC,. 2016. Isolation and characterization of aquatic-borne Klebsiella pneumoniae from tropical estuaries in Malaysia. Int J Environ Res Public Health 13:.
Barus TA, Wahyuningsih H, Ginting EM, Ph C,. 2014. Ecobiological review of Neolissochilus sumatranus (Ikan Batak) (Weber and de Beaufort, 1916) in Asahan River, North Sumatera. In: Proceeding of The First International Seminar on Trends in Science and Science Education 2014. pp. 39–45.
Birhanu BT, Lee JS, Lee SJ, Choi SH, Hossain MA, Park JY, Kim JC, Suh JW, Park SC,. 2016. Immunomodulation of Lactobacillus pentosus PL11 against Edwardsiella tarda infection in the head kidney cells of the Japanese eel (Anguilla japonica). Fish Shellfish Immunol 54: 466–472.
Carper DL, Schadt CW, Burdick LH, Kalluri UC, Pelletier A,. 2020. Draft genome sequence of Tumebacillus sp. strain BK434, Isolated from the roots of Eastern Cottonwood. Microbiol Resour Announc 9: 9:e00351-20.
Clements KD, Angert ER, Montgomery WL, Choat JH,. 2014. Intestinal microbiota in fishes: What’s known and what’s not. Mol Ecol 23: 1891–1898.
Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Bruce DC, Chain PS, Coyne SR, Frey KG, Jaissle J, Koroleva GI, Ladner JT, Lo CC, Meincke L, Munk AC, Palacios GF, Redden CL, Johnson SL,. 2014. Draft genome assembly of Klebsiella pneumoniae type strain ATCC 13883. Genome Announc 2: 4–5.
Das A, Acharya S, Behera BK, Paria P, Bhowmick S, Parida PK, Das BK,. 2018. Isolation, identification and characterization of Klebsiella pneumoniae from infected farmed Indian Major Carp Labeo rohita (Hamilton 1822) in West Bengal, India. Aquaculture 482: 111–116.
Dinoto A, Sulistiani S, Suswati S, Handayani R, Julistiono H,. 2018. Weissella paramesenteroides from intestine of Indonesian eel (Anguilla bicolor McClelland) and their potential antimicrobial property. In: AIP Conference Proceedings. p. 070001.
Gatson JW, Benz BF, Chandrasekaran C, Satomi M, Venkateswaran K, Hart ME,. 2006. Bacillus tequilensis sp. nov., isolated from a 2000-year-old Mexican shaft-tomb, is closely related to Bacillus subtilis. Int J Syst Evol Microbiol 56: 1475–1484.
Kayath CA, Ibala Zamba A, Goma-Tchimbakala J, Mamonékéné V, Mombo Makanga GM, Lebonguy AA, Nguimbi E,. 2019. Microbiota landscape of gut system of guppy fish (Poecilia reticulata) plays an outstanding role in adaptation mechanisms. Int J Microbiol 2019: 3590584.
Larsen AM, Mohammed HH, Arias CR,. 2014. Characterization of the gut microbiota of three commercially valuable warmwater fish species. J Appl Microbiol 116: 1396–1404.
Lee JS, Damte D, Lee SJ, Hossain MA, Belew S, Kim JY, Rhee MH, Kim JC, Park SC,. 2015. Evaluation and characterization of a novel probiotic Lactobacillus pentosus PL11 isolated from Japanese eel (Anguilla japonica) for its use in aquaculture. Aquac Nutr 21: 444–456.
Liu CH, Chiu CH, Wang SW, Cheng W,. 2012. Dietary administration of the probiotic, Bacillus subtilis E20, enhances the growth, innate immune responses, and disease resistance of the grouper, Epinephelus coioides. Fish Shellfish Immunol 33: 699–706.
Liu H, Guo X, Gooneratne R, Lai R, Zeng C, Zhan F, Wang W,. 2016. The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels. Sci Rep 6: 1–12.
Novita H, Rusmana I, Yuhana M, Pasaribu FH,. 2015. Karakterisasi bakteri anti quorum sensing (AQS) sebagai penghambat virulensi penyakit pada ikan lele dumbo (Clarias gariepinus). J Ris Akuakultur 10: 89.
Pan J, Huang T, Yao F, Huang Z, Powell CA, Qiu S, Guan X,. 2008. Expression and characterization of aiiA gene from Bacillus subtilis BS-1. Microbiol Res 163: 711–716.
Prasad R V., Bhumika V, Anil Kumar P, Srinivas NRT,. 2015. Tumebacillus lipolyticus sp. nov., isolated from river water. Int J Syst Evol Microbiol 65: 4363–4368.
Purba M, Barus TA, Ilyas S,. 2013. Hubungan antara kualitas air dengan kebiasaan makanan Ikan Batak (Neolissochilus sumatranus) di Sungai Asahan, Sumatera Utara. J Biosains 1: 21–28.
Ren X, Wu B, Zhao F, Qi L, Qiu X, Li R, Yang S, Liu F, Yi G, Ding X, Xia L, Sun Y,. 2019. Antagonistic activity and protective effect of a Bacillus subtilis isolate against fish pathogen Edwardsiella piscicida. Fish Sci 85: 1011–1018.
Reyes AT, Jorduela EL, Doctolero JS,. 2019. Bacillus tequilensis, a novel unionized ammonia-nitrogen degrading bacterium isolated from tilapia pond soil. Int J Fish Aquat Stud 7: 161–165.
Roesma ID, Chornelia A, Mursyid A,. 2019. Phenotype analysis of endemic mahseer fish (Neolissochilus sumatranus) from Batang Toru tributaries, North Sumatra, Indonesia. In: IOP Conference Series: Journal of Physics: Conference Series. p. 012099.
Romero J, Ringø E, Merrifield DL,. 2014. The gut microbiota of fish. In: Merrifield, D., Ringo, E. (Eds.), Aquaculture Nutrition: Gut Health, Probiotic and Prebiotics. John Wiley & Sons, Ltd., Chichester, pp. 75–100.
Sullam KE, Essinger SD, Lozupone CA, Connor MPO,. 2012. Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis. Mol Ecol 21: 3363–3378.
Sung H, Kim HS, Lee JY, Kang W, Kim PS, Hyun DW, Tak EJ, Jung MJ, Yun JH, Kim MS, Shin NR, Whon TW, Rho JR, Park SD, Shim HE, Bae JW,. 2018. Tumebacillus avium sp. nov., isolated from the gut of a cinereous vulture, Aegypius monachus. Int J Syst Evol Microbiol 68: 1659–1664.
Thakur AK, Shakya A, Mohammed G,. 2014. Gut-microbiota and mental health: current and future perspectives. J Pharmacol Clin Toxicol 2: 1016.
Wang Q, Xie N, Qin Y, Shen N, Zhu J, Mi H, Huang R,. 2013. Tumebacillus flagellatus sp. nov., an ?-amylase/ pullulanase-producing bacterium isolated from cassava wastewater. Int J Syst Evol Microbiol 63: 3138–3142.
Wong S, Rawls JF,. 2012. Intestinal microbiota composition in fishes is influenced by host ecology and environment. Mol Ecol 21: 3100–3102.
Xiong JB, Nie L, Chen J,. 2019. Current understanding on the roles of gut microbiota in fish disease and immunity. Zool Res 40: 70–76.
Zanoni P, Farrow JAE, Phillips BA, Collins MD,. 1987. Lactobacillus pentosus (Fred, Peterson, and Anderson) sp. nov., norn, rev. Int J Syst Bacteriol 37: 339–341.
Zokaeifar H, Balcázar JL, Saad CR, Kamarudin MS, Sijam K, Arshad A, Nejat N,. 2012. Effects of Bacillus subtilis on the growth performance, digestive enzymes, immune gene expression and disease resistance of white shrimp, Litopenaeus vannamei. Fish Shellfish Immunol 33: 683–689.
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