Penelitian untuk mengetahui keanekaragaman genetik bakteri dari usus ikan nila melalui teknik metagenom sequence-based telah dilakukan. Hasil amplifikasi gen 16S rRNA dari usus sebesar 1550 pb, kemudian dilakukan sequencing pada isolat dari Kolam Laboratorium PTPP, Serpong (L1, L2); Tambak Ikan Nila Salin, Karawang (Mu, Pu); dan KJA Waduk Cirata, Purwakarta (A1, C1). Identifikasi ke-6 isolat bakteri berdasarkan BLAST menunjukkan bahwa terdapat similaritas terhadap 4 spesies bakteri dengan nilai max identity tertinggi. Hasil analisis pohon filogenetik menggunakan metode neighbor-joining memperlihatkan bahwa isolat L1, L2 dan C1 diduga berkerabat dekat dengan bakteri Ochrobactrum anthropi, isolat A1 diduga berkerabat dekat dengan Lysinibacillus boronitolerans, isolat Pu diduga berkerabat dekat dengan Stenotrophomonas maltophilia, sementara isolat Mu diduga berkerabat dekat dengan Cetobacterium somerae. Berdasarkan hasil yang didapat, maka terbukti bahwa terdapat keanekaragaman gen 16S rRNA dari usus ikan nila yang dianalisis melalui teknik metagenom sequence-based.

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Research to know the genetic diversity of intestinal bacterias in Tilapia gut had been done using sequence-based metagenome. 16S rRNA gene amplification produced PCR fragment with 1550 bp length, then followed by sequencing of isolates from Outdoor Laboratory, Serpong (L1, L2); Saline Tilapia Ponds, Karawang (Mu, Pu); and Cirata Reservoir, Purwakarta (A1, C1). Identification six bacteria isolates based on BLAST showed that there are 4 different species of bacteria with the highest value of max identity.

Phylogenetic analysis using neighbor-joining method showed that L1, L2, and C1 isolates is close relatives to Orchrobacterum anthropi, while A1 isolates is close relative to Lysinibacillus boronitolerans, Pu isolate is having close relationship with Stenotrophomonas maltophilia, and Mu isolates with Cetobacterium somerae. Thus, based on the results, it is proven that there is 16S rRNA gene diversity from tilapia intestines using metagenome sequence-based method.