Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh
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BMC Research Notes Open Access
RESEARCH NOTE
Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh Adi Yulandi1,2, Antonius Suwanto1*, Diana Elizabeth Waturangi2 and Aris Tri Wahyudi1
Abstract Objective: Amplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used to profile the microbial community from fermented food samples. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in estimating microbial community composition. As potential paraprobiotics sources, a comprehensive profiling study of tempeh microbial ecology could contribute to tempeh product development. This study employed a shotgun metagenomic approach, where metagenome fragments from tempeh samples were sequenced directly for taxonomic and functional profiling analysis. Results: Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from the shotgun metagenomic analysis in all tempeh samples. In terms of composition, this shotgun metagenomic study revealed that Proteobacteria was the most abundant phylum. Functional profiling showed that iron complex outermembrane recepter protein (KEGG ID: K02014) was the most transcribed gene based on this metagenomic analysis. The metagenome-assembled genomes (MAGs) results from the binning pipeline could reveal almost complete whole genome sequence of Lactobacillus fermentum, Enterococcus cecorum, Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii. Keywords: Tempeh, Shotgun metagenomic, Proteobacteria, Firmicutes Introduction Tempeh is fermented food originated from Indonesia. The biochemical changes of soybean during microbial fermentation increased nutritional values and healthpromoting bioactive compounds in tempeh. Compared to other indigenous soybean-based fermented food such as nato, miso (Japan), kinema (Nepal), and douchi (China), which used Bacillus spp. as inoculum, tempeh used Rhizopus spp. in the production [1]. The nature of tempeh production processes creates consortia of *Correspondence: [email protected] 1 Department of Biology, Faculty of Mathematics and Natural Science, IPB University (Bogor Agricultural University), Gedung Biologi. Jalan Agatis Kampus IPB Dramaga, 16680 Bogor, Indonesia Full list of author information is available at the end of the article
microorganisms not only from tempeh inoculum but also from production materials and environment [2]. Over the past decade, useful tools of next-generation sequencing (NGS) such as metagenomics has been applied to study microbial consortia from fermented food microbial ecology [3]. Previous metagenomic studies of the microbial community during tempeh production were conducted by employing amplicon sequencing targeting the V4 region of the 16S rRNA gene. These studies focused on the dynamic taxonomic profile of the microbial community from tempeh metagenome samples and indicated that Firmicutes was the pre
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