Recent advances in metagenomics and bioinformatics allow the robust analysis of the composition and abundance of microbial communities, functional genes, and their metabolic pathways. So far, there has been a variety of computational/statistical tools or software for analyzing microbiome, the common problems that occurred in its implementation are, however, the lack of synchronization and compatibility of output/input data formats between such software. To overcome these challenges, in this study context, we aim to apply the DADA2 pipeline (written in R programming language) instead of using a set of different bioinformatics tools to create our own workflow for microbial community analysis in a continuous and synchronous manner. For the first effort, we tried to investigate the composition and abundance of coral-associated bacteria using their 16S rRNA gene amplicon sequences. The workflow or framework includes the following steps: data processing, sequence clustering, taxonomic assignment, and data visualization. Moreover, we also like to catch readers’ attention to the information about bacterial communities living in the ocean as most marine microorganisms are unculturable, especially residing in coral reefs, namely, bacteria are associated with the coral Acropora tenuis in this case. The outcomes obtained in this study suggest that the DADA2 pipeline written in R programming language is one of the potential bioinformatics approaches in the context of microbiome analysis other than using various software. Besides, our modifications for the workflow execution help researchers to illustrate metagenomic data more easily and systematically, elucidate the composition, abundance, diversity, and relationship between microorganism communities as well as to develop other bioinformatic tools more effectively.
Coral reefs harbor the extraordinary biodiversity and not only provide livelihoods for coastal communities but also play a crucial role in economic development generally. Unfortunately, they are in decline in Vietnam and around the world because mass coral bleaching events have become more common worldwide. However, little is discovered, about viruses that infect corals and their symbionts. Herein, we present metagenomic analyses of the viral communities in coral mucus associated with healthy and bleached coral Acropora formosa which was collected at Con Dao Island, Vietnam. Interestingly, the number of viral species in bleached specimens are higher than those in healthy status. Viruses similar to those that infect humans and some marine animals also appeared in the coral viral assemblage. The results indicated that the proportion of shared viruses were quite small, and represented extremely abundance. Among the phage identified, vibriophage and cyanophage were only presented in healthy and bleached coral, respectively. Therefore, coral-associated viruses could prospectively infect all constituents of the holobiont - coral, microalgal and microbial. Thus, we expect viruses to be illustrated prominently in the preservation and breakdown of coral health.
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