Shotgun Metagenomic Analysis Reveals New Insights on Bacterial Community Profiles in Tempeh

ObjectiveAmplicon sequencing targeted 16S ribosomal RNA (rRNA) has been widely used for the analysis profile of the microbial community from fermented food samples. Previous results of 16S rRNA analysis metagenome showed that Firmicutes was the dominant phylum in tempeh. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in the estimation of microbial community composition. An alternative approach known as shotgun metagenomic might be able to avoid this limitation. In this study, we employed total metagenomic DNA fragments sequenced directly for taxonomic dan functional profiling analysis. ResultTaxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from direct shotgun metagenomic analysis in all tempeh samples. In terms of composition, the shotgun metagenomic study revealed that Proteobacteria was the most relatively abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein (KEGG ID: K02014) was the most transcribed genes based on metagenome from tempeh samples.