Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh
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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 outer-membrane 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.
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Metagenomic studies have been mainly conducted on single food types and on limited sample sizes, hindering inter-study integrative analyses currently available only for other environments such as the human gut.
“Nevertheless, metagenomic studies have been mainly conducted on single food types 18-24 and on limited sample sizes, 25,26 hindering inter-study integrative analyses currently available only for other environments such as the human gut. 27-31”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [22]
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- Authors
- Yulandi, A., Suwanto, A., Waturangi, D. E., & Wahyudi, A. T.
- Affiliations
- Atma Jaya Catholic University of Indonesia (ID)
- IPB University (ID)
- Corresponding author
- Suwanto, Antonius
- Venue
- BMC Research Notes
- Published
- 2020-12
- Volume
- 13
- Issue
- 1
- Pages
- 562-562
- ISSN
- 1756-0500 (ISSN-L)
- PMC
- PMC7731626
- OpenAlex
- W3112278034
- Cited by
- 27
- References
- 36
- Citations by year
- 2026: 8 · 2025: 5 · 2024: 6 · 2023: 3 · 2022: 4 · 2021: 1
- FWCI
- 1.30
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Research Notes (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Lembaga Pengelola Dana Pendidikan
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- tempeh, bacterial community composition, fermented food microbiota, metagenome-assembled genomes, Lactobacillus fermentum, Enterococcus cecorum, Escherichia coli, Klebsiella pneumoniae, Proteobacteria, paraprobiotics, functional profiling
- MeSH terms
- RNA, Ribosomal, 16S, Enterococcus, Soy Foods, Metagenome, Metagenomics
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