Analisis Motif Imunoregulator DNA CpG, Gen Plantarisin, dan Gen Resistensi Mupirocin pada Genom Lactiplantibacillus plantarum SU-KC1a = Analysis of Immunoregulatory CpG DNA Motifs, Plantaricin Genes, and Mupirocin Resistance Genes in Lactiplantibacillus plantarum SU-KC1a

Timotius, Vania Austine Callista (2021) Analisis Motif Imunoregulator DNA CpG, Gen Plantarisin, dan Gen Resistensi Mupirocin pada Genom Lactiplantibacillus plantarum SU-KC1a = Analysis of Immunoregulatory CpG DNA Motifs, Plantaricin Genes, and Mupirocin Resistance Genes in Lactiplantibacillus plantarum SU-KC1a. Bachelor thesis, Universitas Pelita Harapan.

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Abstract

Lactobacillus dikenal baik dalam penggunaannya pada makanan sebagai probiotik. Diketahui pada ASI, terdapat banyak bakteri jenis Lactobacillus yang dapat mempengaruhi kesehatan bayi yang mengonsumsinya, terutama pada sistem imun dalam melawan patogen. Penelitian ini bertujuan untuk menganalisis isolat SU-KC1a yang diperoleh dari ASI. Melalui hasil Whole Genome Sequencing (WGS), dapat dilakukan identifikasi dan analisis motif DNA CpG yang berperan sebagai imunoregulator; kemudian motif CpG SU-KC1a dibandingkan dengan spesies atau genus lainnya; serta gen-gen plantarisin dan gen resistensi terhadap antibiotik Mupirocin dapat dianalisis. Metode yang dilakukan adalah mengkarakterisasi isolat SU-KC1a; data hasil sekuensing 16S-rRNA dari isolat SU-KC1a diperoleh dengan ekstraksi DNA dan PCR, kemudian dianalisa dengan BLAST; data WGS dari isolat SU-KC1a diperoleh dengan ekstraksi DNA kemudian dilakukan sekuensing dengan alat GridION sequencer; data hasil WGS dilakukan perakitan (assembly) genom dengan program Flye; hasil perakitan dipoles dengan program Medaka; contig disusun (contigs reordering) dengan program Mauve; motif CpG pada genom SU-KC1a dilakukan identifikasi dan analisis dengan program Fuzznuc; anotasi genom dilakukan untuk mencari keberadaan gen bakteriosin dengan program RAST; serta gen resistensi terhadap Mupirocin dengan program CARD. Hasil yang diperoleh, isolat SU-KC1a tergolong bakteri Gram positif yang berbentuk batang. Identifikasi molekular dengan 16S-rRNA dan WGS menunjukkan isolat SU-KC1a identik dengan Lactiplantibacillus plantarum. Panjang genom L. plantarum SU-KC1a adalah 3.211.037 bp dengan persentase GC 44,66%, serta jumlah total motif CpG tipe satu dan tipe dua masing-masing sebanyak 13.779 dan 8.960. Selanjutnya ditemukan gen pengkode berbagai protein untuk biosintesis plantarisin dan juga gen resistensi terhadap Mupirocin. Dari hasil penelitian, menunjukkan bahwa L. plantarum SU-KC1a berpotensi sebagai probiotik, tetapi perlu dilakukan penelitian dan pembuktian lebih lanjut. / Lactobacillus is well known for its use as a probiotic in food. It is also known that in human breast milk, there are many species of Lactobacillus that can affect the health of the babies who consume it, especially on the baby’s immune system against pathogen. This study aims to analyse the SU-KC1a isolate that obtained from human breast milk. Using result from Whole Genome Sequencing, identification and analysis of CpG DNA motifs that act as immunoregulators was carried out; the CpG motifs were then compared with other species and genera; plantaricin genes as well as Mupirocin resistance genes were also to be analyzed. The method used involved characterizing the SU-KC1a isolate; result data from SU-KC1a isolate 16S-rRNA sequencing were obtained by DNA extraction and PCR, then the result data was analysed by BLAST; genome assembly of the result data from WGS was carried out using Flye program; the assembly result was polished using Medaka program; contigs were reordered using Mauve program; CpG motifs in SU-KC1a genome were identified and analyzed using Fuzznuc program; genome annotation was performed using RAST program to search for the bacteriocin gene; Mupirocin resistance genes were also sought using CARD program. The result obtained showed that SU-KC1a isolate classified as being made up of Gram-positive rod-shaped bacteria. Molecular identification with 16S-rRNA and WGS showed that SU-KC1a identical to Lactiplantibacillus plantarum. The genome length was shown to be 3,211,037 bp with GC% 44.66%, and the total number of type 1 and type 2 CpG motifs were shown to be13,779 and 8,960 respectively. Genes that encode various proteins for plantaricin biosynthesis and Mupirocin resistance genes were found in the genome. The result showed that L. plantarum SU-KC1a has potential to be used as a probiotic, but further research need to be done.

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