Analisis komunitas bakteri dari usus ular kobra jawa (naja sputatrix) dengan metode metagenomik = Gut bacterial community analysis of javan spitting cobra (naja sputatrix) with metagenomics.

Putri, Kathleen (2020) Analisis komunitas bakteri dari usus ular kobra jawa (naja sputatrix) dengan metode metagenomik = Gut bacterial community analysis of javan spitting cobra (naja sputatrix) with metagenomics. Bachelor thesis, Universitas Pelita Harapan.

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Abstract

sekuens DNA secara menyeluruh dalam jumlah besar. Melalui metode metagenomik, dapat diketahui interaksi antara organisme dengan lingkungan, misalnya mikrobiota yang hidup dalam usus mahluk hidup lainnya (host species). Kondisi serta komposisi komunitas mikrobiota usus dapat dijadikan acuan untuk menggambarkan kondisi kesehatan host species serta signifikansi mikrobiota tersebut terhadap host species. Dalam penelitian ini, host species yang dipelajari adalah ular kobra jawa (Naja sputatrix), spesies ular berbisa endemik Indonesia yang umum ditemukan di pulau Jawa dan sekitarnya. Keunikan kobra jawa ialah ular ini mampu bertahan tanpa makan selama beberapa waktu serta dipercaya bagian tubuhnya memiliki khasiat kesehatan. Terbatasnya penelitian mengenai ular kobra jawa mengakibatkan banyak aspek dari ular kobra jawa yang belum diketahui. Terutama, peranan mikrobiota usus terhadap diet unik ular kobra jawa. Untuk mengetahui hal tersebut, dilakukan ekstraksi DNA genom yang diperoleh dari usus ular kobra jawa, kemudian dilakukan sequencing metagenomik, lalu didapatkan data bioinformatika berupa identifikasi spesies (OTU) dan kelimpahan spesies dalam sampel. Analisa dilakukan menggunakan Illumina system dengan empat tahapan utama, yaitu amplifikasi dan purifikasi genom, amplifikasi genom target, anotasi sekuens DNA, dan sequencing. Dari hasil sequencing sampel, diketahui terdapat 297 OTU dengan dominasi oleh filum Proteobacteria sebesar 73%, diikuti filum dominan lainnya, seperti Firmicutes, spirochetes, Tenericutes, Bacteroidetes, dan Chlamydiae. Pada taxa genus terdapat dominasi oleh genus Edwardsiella. Aeromonas, Bordetella, Brevinema, Mycoplasma, Salmonella, serta Shewanella. Sebagian besar mikrobiota tersebut merupakan Gram negatif serta diduga merupakan mikrobiota komensal. Analisis statistik alpha diversity index menunjukkan nilai shannon index, simpson index, chao1, Good’s coverage, dan PD whole tree secara berurutan yaitu, 3,967; 0,858; 315,370; 313,303; 1,000; dan 47,263. / Metagenomics is molecular-based analysis method which process DNA sequences as a meta data. Through metagenomic analysis, the mechanism of interaction between organism and its environment can be known, such as gut microbiota living in a specific host species. The over all condition and composition of microbiota in gut microbiota community can be roughly discern as health profilling and depicting the importance of gut microbiota to the host species. In this research, the studied host species was javan spitting cobra (Naja sputatrix), a venomous cobra species native to Indonesia which commonly found in Java Island. Javan spitting cobra are uniquely able to survive for more than a few days without food and widely believed to have therapeutic effects. There are few known things regarding javan spitting cobra as research are limited, thus javan spitting cobra are not entirely understood. Particularly, how gut microbiota contributes to the cobra’s unique diet. To investigate it, genomic DNA of javan spitting cobra’s gut were extracted and sequenced, then results are reported as bioinformatics data consists of species identification (OTU) and species abundances within the sample. Sample was analyzed with Illumina system, sequencing process involved four main steps; genomic amplification and purification, targeted genome amplification, DNA sequence annotation, and sequencing. There are 297 OTU reported in the sample, dominated by 73% Proteobacteria phylum, followed by another dominant specieses, such as Firmicutes, spirochetes, Tenericutes, Bacteroidetes, dan Chlamydiae. On genus level, microbiota community composition was dominated by Edwardsiella. Aeromonas, Bordetella, Brevinema, Mycoplasma, Salmonella, and Shewanella. There are high prevalence of Gram negative bacteria in the microbiota community, supposedly as commensalism relationship to the cobra itself. Alpha diversity index estimation based on statistics analysis shows various values for shannon index, simpson index, chao1, Good’s coverage, dan PD whole tree, sequentially 3,967; 0,858; 315,370; 313,303; 1,000; and 47,263.

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