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Antonius Suwanto
Bogor Agricultural University
Corresponding Author
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Objective: Amplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used for the profile analysis 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 that were sequenced directly for taxonomic dan functional profiling analysis.
Results: Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from the direct 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 genes based in this metagenomic analysis. 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
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CURRENT STATUS: Published
View the published article at BMC Research Notes.
No community comments so far
Submission checks complete
On 27 Nov, 2020
Editorial decision: Accept
On 25 Nov, 2020
No comments provided
Reviewer #2 agreed
On 12 Nov, 2020
Review #1 received
Received 11 Nov, 2020
Reviewers invited
Invitations sent on 11 Nov, 2020
Reviewer #1 agreed
On 11 Nov, 2020
Editor assigned
On 04 Nov, 2020
Submission checks complete
On 04 Nov, 2020
Editor invited
On 04 Nov, 2020
Version 1
Posted 16 Jul, 2020
No comments provided
Editorial decision: Major revision
On 13 Oct, 2020
Review #2 received
Received 06 Aug, 2020
Reviewer #2 agreed
On 30 Jul, 2020
Review #1 received
Received 30 Jul, 2020
Reviewer #1 agreed
On 27 Jul, 2020
Editor assigned
On 25 Jul, 2020
Reviewers invited
Invitations sent on 25 Jul, 2020
Submission checks complete
On 15 Jul, 2020
Editor invited
On 15 Jul, 2020
First submitted
On 13 Jul, 2020
Metrics
Comments: 0
PDF Downloads: ...
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A new preprint design is coming!
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See the published version of this preprint at BMC Research Notes.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research note
Antonius Suwanto
Bogor Agricultural University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Research Notes.
No community comments so far
Submission checks complete
On 27 Nov, 2020
Editorial decision: Accept
On 25 Nov, 2020
No comments provided
Reviewer #2 agreed
On 12 Nov, 2020
Review #1 received
Received 11 Nov, 2020
Reviewers invited
Invitations sent on 11 Nov, 2020
Reviewer #1 agreed
On 11 Nov, 2020
Editor assigned
On 04 Nov, 2020
Submission checks complete
On 04 Nov, 2020
Editor invited
On 04 Nov, 2020
Version 1
Posted 16 Jul, 2020
No comments provided
Editorial decision: Major revision
On 13 Oct, 2020
Review #2 received
Received 06 Aug, 2020
Reviewer #2 agreed
On 30 Jul, 2020
Review #1 received
Received 30 Jul, 2020
Reviewer #1 agreed
On 27 Jul, 2020
Editor assigned
On 25 Jul, 2020
Reviewers invited
Invitations sent on 25 Jul, 2020
Submission checks complete
On 15 Jul, 2020
Editor invited
On 15 Jul, 2020
First submitted
On 13 Jul, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Research Notes.
Objective: Amplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used for the profile analysis 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 that were sequenced directly for taxonomic dan functional profiling analysis.
Results: Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from the direct 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 genes based in this metagenomic analysis. The binning pipeline could reveal almost complete whole genome sequence of Lactobacillus fermentum, Enterococcus cecorum, Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii.
Figure 1
Figure 2
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