Othman, Nursyuhada (2023) Metabarcoding of mitochondrial and chloroplast DNA on selected endangered mammals in Malaysia by using next generation sequencing. Doctoral thesis, Universiti Tun Hussein Onn Malaysia.

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Abstract

The introduction of Next Generation Sequencing (NGS) has revolutionized the field of wildlife conservation, offering a powerful tool for dietary assessment and gut health analysis in mammals. Previously, most of study focus on the usage of the conventional methods in monitoring of wildlife which require attention from the researches due to the lack of study. Thus, the objectives of the study are to evaluate the diversity of gut microbiomes between wild and captive population of Asian elephant (Elephas maximus) using 16S rRNA, characterized the plant consumed by Siamang (Symphalangus syndactylus) using trnL marker and characterized the dietary composition between two species of otter, Asian small-clawed otter (Aonyx cinereus) and smooth-coated otter (Lutrogale perspicillata) using Cytochrome b gene. All the outcomes of the research were used as the guideline and reference in developing a framework for next-generation wildlife monitoring in Malaysia based on NGS methods. Our results successfully revealed the identification of 34 phyla, 260 families, and 514 genera in the gut microbiomes of E. maximus, with Bacteroidetes (26.8%), Firmicutes (24.2%), and Proteobacteria (23.8%) being the predominant phyla. No significance differences of gut microbiomes was shown in the age and sex of Asian elephant. For diet analysis of Siamang, the sequences were indicated to 97 families and 426 genera where the dominant plant consumed was genus Ficus (26.4%). While for otter, the analysis was successfully assigned to four families and 11 species of food consumed by both species. These findings provide important insights into the health status of the Asian elephant, as the gut microbiota is found to be affected by the environmental factors. Additionally, the identification and conservation of plant species consumed by Siamang and food eaten by otter can be easier and more efficient without the need for extensive field observation data. Our study highlights the need for long-term monitoring using fresh faecal samples with NGS, which can complement traditional monitoring methods and enhance biomonitoring efficiency for wildlife especially mammals conservation in Malaysia

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