Judul: Identification of Bacterial Community in Vannamei Shrimp (Litopenaeus vannamei) from Two Different Market Locations Using Metagenomic Technology
Abstrak: Udang merupakan komoditas hasil perairan yang mudah mengalami proses kemunduran mutu, salah satunya disebabkan oleh aktivitas bakteri. Penggunaan media kultur dalam proses identifikasi komunitas bakteri menjadi kurang optimal, karena proses kultivasi tidak dapat menumbuhkan semua jenis bakteri. Penelitian ini bertujuan untuk mengidentifikasi komunitas bakteri yang terdapat pada komoditas udang segar dengan teknik metagenomik. Proses identifikasi bakteri dilakukan melalui tahap pengusapan permukaan udang, kemudian isolasi DNA bakteri menggunakan Wizard Genomic DNA Purification Kit dan amplifikasi menggunakan primer universal 16S rRNA dengan wilayah V3-V4. Proses sekuensing dilakukan menggunakan teknik Next Generation Sequencing. Komunitas bakteri yang teridentifikasi didominasi oleh filum Bacteroidota, Patescibacteria, Firmicutes, Fusobacteriota, Campilobacteriota, Actinobacteriota, dan Proteobacteria. Potensi kelompok bakteri patogen dan pembusuk pada udang teridentifikasi berasal dari genus Myroides, Flavobacterium, Pseudomonas, Aeromonas, Escherichia, Shigella dan Shewanella, Shrimp is an aquatic product that is prone to deterioration in quality, one of which is caused by bacterial activity. The use of culture media in the identification process of bacterial communities is less than optimal because the cultivation process cannot grow all types of bacteria. This study aims to identify the bacterial community found in fresh shrimp commodities with a metagenomic approach. The bacterial identification process was carried out by swabbing the surface of the shrimp, then isolating bacterial DNA using the Wizard Genomic DNA Purification Kit and amplification using a universal 16S rRNA primer with a V3-V4 region. The sequencing process was carried out using Next Generation Sequencing. The identified bacterial community was dominated by the phyla Bacteroidota, Patescibacteria, Firmicutes, Fusobacteriota, Campilobacteriota, Actinobacteriota, and Proteobacteria. Potential groups of pathogenic and spoilage bacteria in shrimp were identified from the genera Myroides, Flavobacterium, Pseudomonas, Aeromonas, Escherichia, Shigella, and Shewanella
Keyword: amplicon sequence variants, bakteri, DNA, udang

Judul: Identification of Bacterial Communities in Eastern Little Tuna (Euthynnus affinis) from Traditional and Modern Market Locations with Metagenomic Analysis
Abstrak: Penanganan pasca panen dengan penerapan rantai dingin dan higiene yang baik merupakan tahapan penting untuk dapat menjaga kualitas ikan dan keamanan pangan. Perbedaan tingkat higiene yang diterapkan pada pasar tradisional dan modern akan mempengaruhi komunitas bakteri pada ikan tongkol. Penelitian ini bertujuan mengisolasi DNA bakteri dan mengidentifikasi komunitas bakteri dengan analisis metagenomik. Tahapan penelitian terdiri dari pengumpulan sampel, inkubasi bakteri, isolasi DNA bakteri dengan kit komersial, permurnian isolat DNA, Next Generation Sequencing dengan target gen 16S rRNA wilayah variabel V3-V4, dan analisis data dengan program bioinformatika. Kelimpahan sekuens bakteri pada ikan tongkol yang berasal dari pasar tradisional sebanyak 42.829 sekuen sedangkan dari pasar modern sebanyak 30.989 sekuen. Filum bakteri yang mendominasi pada kedua sampel tersebut yaitu Fusobakteriota, Bakteroidota, dan Patescibakteria. Komunitas bakteri pada ikan tongkol pasar tradisional memiliki kelimpahan relatif tertinggi pada genus Myroides (42,3%) sedangkan dari pasar modern pada genus Cetobacterium (80,2%)., Post-harvest handling, which includes the use of cold chain and proper hygiene, is a critical in maintaining fish quality and food safety. The bacterial community in eastern little tuna will be affected by differences in the level of hygiene used in traditional and modern markets. This study aims to isolate bacterial DNA and identify bacterial communities by metagenomic analysis. The research stages consisted of sample collection, bacterial incubation, isolation of bacterial DNA with commercial kits, purification of DNA isolates, NGS with the target gene for 16S rRNA V3-V4 variable region, and data analysis using bioinformatics programs. The sequence abundance of bacteria in eastern little tuna from traditional markets was 42.829 sequences while those from modern markets were 30.989 sequences. Fusobakteriota, Bacteroidota, and Patescibakteria were the most predominant bacterial phyla in both samples. Traditional market eastern little tuna had the highest relative abundance in the genus Myroides (42,3%), while the modern had the highest relative abundance in the genus Cetobacterium (80,2%).
Keyword: 16S rRNA, Next Generation Sequencing, Bacterial communities, Eastern Little Tuna, Hygiene

Judul: Hamiltonian formulation for linear waves motion in two layers fluid
Abstrak: The surface wave could be considered as a wave that separates two fluids, namely water and air. Based on this assumption, it is introduced the interfacial wave, a wave between two layers of fluid with different density. The formulation of interfacial waves motion begins with deriving the base equation of irrotational ideal fluid. Furthermore, according to irrotational fluid assumption, the base equation can be stated in velocity potential. In this derivation, the fluids domain is assumed to be restricted by rigid lid boundary conditions, both at the upper and lower limit. Therefore, the interfacial waves motion can be explained in a hamiltonian formulation. In the hamiltonian formulation, total energy is defined as the sum of kinetic and potential energy. The hamiltonian system is obtained from reduction of kinetic energy by using the Dirichlet Neumann Operator. The resulted kinetic energy equation is nonlinear. Therefore, this form is linearized by first part of the Taylor expansion. This linearization gives a dispersion relation of linear wave. Based on this dispersion relation, the phase speed of the linear wave depends on the density ratio of the two layers fluid.
Keyword: