Metagenomic Analysis of Gut Bacterial Communities of Healthy and Diseased Empurau (Tor tambroides)

Lau, Melinda Mei Lin (2021) Metagenomic Analysis of Gut Bacterial Communities of Healthy and Diseased Empurau (Tor tambroides). Masters thesis, Universiti Malaysia Sarawak.

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Abstract

The gut microbiota is known as an ‘extra organ’ and is essential in assisting the host in terms of nutrition and immunity. Gut inflammation associated with bloom of Enterobacteriaceae and overgrowth of existing and invasion of pathogenic bacteria is mainly due to alteration in gut microbial community. This will eventually increases the disease occurrence within aquaculture farms which bring huge economic loses. However, the possible opportunistic pathogens causing bacterial disease is still in vague. Thus, in this study, the gut microbial community of both diseased and healthy Malaysian mahseer (T. tambroides) were compared and explored using NGS-based 16S rDNA sequencing on the Malaysian mahseer. Three healthy and diseased adult Malaysian mahseers (showing signs of exophthalmia, coelomic distension and petechial haemorrhage) were obtained from LTT Aquaculture Sdn Bhd. Our results revealed significant differences in microbial diversity, composition and function between both populations of T. tambroides. Alpha diversity analysis depicts lower diversity of gut microbiota composition in diseased T. tambroides as compared to the healthy group, which is in coherent with diversity resistance hypothesis, indicating greater chances of occurrence for a species with antagonistic trait against pathogens. Analysis of Composition of Microbiomes (ANCOM) was performed to test on the significant differences at genus and phylum level among the gut microbiota between both groups. In particular, Enterobacteriaceae, Aeromonas, Bacteroides, Vibrio, Arcobacter and Pseudomonas were found within gut microbiota of the diseased fishes. In contrast, Sphingomonadaceae, Methylobacterium, unclassified bacteria and Ruminococcaceae were identified from the gut microbial community of the healthy group. Besides, cellulose-degrading bacteria and protease-producing bacteria were identified from the gut of T. tambroides as well. Taken together, our findings emphasised the association between the alteration in gut microbiota composition and infectious abdominal dropsy in T. tambroides, hoping to aid in diagnosis, prevention and treatment of intestinal diseases in fish.

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