Judul: Shotgun Metagenomics Analysis of Gastrointestinal Microbiome of Bird of Paradise in Papua Northwest Lowland Region
Abstrak: Mikrobioma saluran pencernaan burung, termasuk burung cendrawasih, spesies endemis di Pulau Papua dan Maluku penting di pahami mekanismenya. Penelitian sebelumnya lebih banyak fokus pada aspek eksternal dan perilaku, sedangkan pemahaman tentang mikroorganisme yang hidup di dalam saluran pencernaan burung ini masih terbatas. Mikrobioma tersebut memiliki peran vital dalam kesehatan dan fisiologi burung cendrawasih. Penelitian ini menggunakan metode shotgun metagenomic untuk menganalisis DNA mikrobiota dalam feses burung, memberikan gambaran mendalam tentang keanekaragaman dan dinamika mikrobioma tersebut. Tujuan penelitian ini untuk mengidentifikasi dan menganalisis komposisi mikrobioma saluran pencernaan burung cendrawasih, mengkarakterisasi secara mendalam mikrobioma saluran pencernaan burung cendrawasih dalam habitat alaminya dan interaksi antara mikrobioma serta dampaknya terhadap kesehatan dan fisiologi burung. Sampel feses dikumpulkan dari Papua, Indonesia. Tahap awal yang dilakukan adalah ekstraksi DNA dengan menggunakan DNeasy PowerSoil Pro Kit. Selanjutnya, proses sekuensing metagenomik shotgun dari platform MGI DNBSEQ-G400 dilakukan untuk mendapatkan data sekuen DNA dari gen-gen yang ada di dalam sampel. Data sekuen DNA yang dihasilkan kemudian dianalisis menggunakan perangkat lunak MEGAN6 dengan menggunakan basis data SEED dan KEGG. Mikrobioma di saluran pencernaan burung cendrawasih didominasi oleh filum Proteobacter, Bacteroidetes, dan Firmicutes dengan spesies seperti Flavobacterium sp. dan Bacillus pumilus paling sering dikarakterisasi. Beberapa spesies baru yang ditemukan bisa menjadi standar analisis untuk burung cendrawasih yang akan dilepaskan kembali ke alam liar. Terdapat interaksi antara anotasi fungsional dengan kelimpahan mikrobiota secara menyeluruh tanpa didominasi oleh satu spesies dalam mikrobiom saluran pencernaan burung cendrawasih. Fungsi tertinggi adalah metabolisme asam amino dan turunannya; dan metabolisme karbohidrat.
Keyword: burung cendrawasih, interaksi mikrobioma, karakteristik mikrobiom, shotgun metagenomic

Judul: Identification and Characterization of Lactic Acid Bacteria from Feces of Birds of Paradise (Paradisaeidae sp.)
Abstrak: Bakteri asam laktat (BAL) diisolasi menggunakan metode streak pada media de Man, Rogosa and Sharpe Agar (MRSA). Media MRSA mendukung pertumbuhan bakteri asam laktat termasuk genus Lactobacillus. Identifikasi koloni bakteri dari 4 sampel feses burung cenderawasih secara makroskopis, mikroskopis, dan uji biokimia. Koloni teridentifikasi sebagai bakteri asam laktat dilakukan karakterisasi probiotik mencakup uji ketahanan garam NaCl (NaCl 2%, 4%, dan 6,5%), uji ketahanan pH (pH 2 dan pH 3), serta uji ketahanan garam empedu (MRS Bile Salt Broth 0,3% dan 3%). Hasil penelitian menunjukkan bahwa dari 8 isolat yang diidentifikasi, 7 isolat BAL diuji untuk karakterisasi sebagai kandidat probiotik. Hasil karakterisasi pada 7 isolat BAL menunjukkan 5 bakteri memiliki karakter sebagai kandidat probiotik yakni Aerococcus sp., Pediococcus sp., Streptococcus sp., Leuconostoc sp., dan Weisella sp. Penelitian ini memberikan informasi tentang bakteri asam laktat sebagai kandidat probiotik pada saluran pencernaan burung cenderawasih demi mengoptimalkan proses pencernaan, sehingga dapat meningkatkan kesehatan saluran pencernaan burung cenderawasih., Lactic acid bacteria (LAB) were isolated using the streak method on de Man, Rogosa and Sharpe Agar (MRSA) media. MRSA media supports the growth of lactic acid bacteria including the genus Lactobacillus. Identification of bacterial colonies from 4 bird of paradise feces samples using macroscopic, microscopic and biochemical tests. Colonies identified as lactic acid bacteria were subjected to probiotic characterization including a NaCl salt resistance test (2%, 4% and 6.5% NaCl), a pH resistance test (pH 2 and pH 3), and a bile salt resistance test (MRS Bile Salt Broth 0.3 % and 3%). The results showed that of the 8 isolates identified, 7 LAB isolates were tested for characterization as probiotic candidates. The characterization results of 7 LAB isolates showed that 5 bacteria had characteristics as probiotic candidates, namely Aerococcus sp., Pediococcus sp., Streptococcus sp., Leuconostoc sp., and Weisella sp. This research provides information about lactic acid bacteria as probiotic candidates in the digestive tract of birds of paradise in order to optimize the digestive process, thereby improving the health of the digestive tract of birds of paradise.
Keyword: bakteri asam laktat, burung cenderawasih, konservasi, pencernaan, probiotik, birds of paradise, conservation, digestion, lactic acid bacteria, probiotic

Judul: The Construction of Greedy SVP LLL Algorithm
Abstrak: A lattice is a set of all integer linear combination of a set of linearly independent vectors in ℝ𝑛���. The independent vectors are called bases of lattice. Any lattice can be generated from many bases, and these bases have the same cardinality. In the lattice, the most fundamental and renowned problem is the Shortest Vector Problem (SVP). SVP is a tracking problem of the shortest nonzero vector in a lattice with equivalent bases. In two dimensions, SVP problem has resolved exactly by Gauss’ algorithm. When the lattice dimension is higher than two, A.K. Lenstra, H.W. Lenstra and L. Lovasz gave a LLL algorithm to compute approximation of nonzero shortest vector in the lattice. Reduced bases solution obtained from LLL algorithm still be an approximation and has polynomial running time of arbitrary dimension which large enough. In 1994, Schnoor and Euchner modified this LLL algorithm as a new variant which later was named deep insertion LLL algorithm. This algorithm is a modified version of the LLL algorithm to the terms of the exchange step to improve the accuracy of output of LLL reduced bases and applying it to the subset sum problem. The purpose of this research are: (1) Reconstruct the LLL algorithm and deep insertion LLL algorithm using a geometric approach. (2) Construct a greedy SVP LLL algorithm. (3) Implement the three algorithms in a symbolic programming language, and evaluate them experimentally. A bases ℬ=[𝐛���1,𝐛���2,…,𝐛���𝑛���] in ℝ𝑚��� is called reduced LLL with parameter 𝛿��� if satisfies: (a) |𝜇���𝑗���𝑖���|≤12, for every integer 𝑖���,𝑗��� with 1≤𝑖���<𝑗���<𝑛���. (b)𝛿���‖𝜋���𝑗���(𝐛���𝑗���)‖2≤‖𝜋���𝑗���(𝐛���𝑗���+1)‖2, for 𝑗���=1,2,…,𝑛���−1,where 𝛿��� is a reduced parameter of real numbers with 14<𝛿���<1. The first requirement is the reduced basis 𝛿��� must “nearly orthogonal” and in its computation case, this requirement can be reached out by using the Gram-Schmidt’s orthogonalization. While the second requirement is called exchange step, or used to called as Lovasz condition. By using both of these requirements, then they establish the LLL algorithm. Then, Schnoor and Euchner modify the LLL algorithm based on the requirements of the exchange step called the deep insertion LLL algorithm, where the exchange step is based on the comparison of the projected vector in orthogonal complement [𝐛���1,𝐛���2,…,𝐛���𝑘���−1]⊥ after j-th reduction. To construct greedy SVP LLL algorithm, the requirements of the exchange step is based on purely by comparing norm of lattice 𝐛���𝑗��� with norm lattice 𝐛���𝑖��� for 𝑖���=1,2,3…,𝑗���−1. The process of insertion reduced vector after the exchange step also has done greedily. Then, we calculate the number of arithmetic operation in greedy SVP LLL algorithm for further analysis. The result of our exprimentation for three algorithms on the certain matrix size shows that the running time of the three algorithms increases propotional to the size of the matrix. The result also shows that by using 𝛿���=34 for the LLL algorithm and the deep insertion LLL algorithm, and the greedy SVP LLL algorithm which is a new variant made by using no parameter of 𝛿���, outperform of the other of two previous algorithm in terms of speed with the same output.
Keyword: LLL algorithm, LLL deep insertion algorithm, greedy SVP LLL algorithm