Metagenomic Analysis of Suansun, a Traditional Chinese Unsalted Fermented Food
Abstract
:1. Introduction
2. Materials and Methods
2.1. Preparation of Suansun and Sampling
2.2. DNA Extraction and Illumina MiSeq Sequencing
2.3. Amplicon Sequence Processing and Analysis
2.4. Analysis of Alpha Diversity in Microbial Community
2.5. Analysis of Beta Diversity in Microbial Community
3. Results and Discussion
3.1. Statistics of Sequencing Data
3.2. Microbial Diversity in Suansun
3.3. Main Active Microorganisms in Suansun
3.4. Functional Annotation and Analysis of Microbial Gene of Suansun
3.5. Metabolic Pathways of Nutrients and Flavor Substances in Suansun
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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Samples | Original Reads (M) | Effective Reads (M) | Original Bases (G) | Effective Bases (G) | Average Length (bp) |
---|---|---|---|---|---|
GL | 71.92 | 66.82 | 10.78 | 9.54 | 143.6 |
LZ | 67.06 | 62.05 | 10.06 | 8.91 | 143.7 |
LB | 78.58 | 69.78 | 11.37 | 10.04 | 143.8 |
BS | 84.85 | 76.03 | 12.72 | 10.56 | 139.4 |
NN | 77.59 | 70.72 | 11.63 | 9.79 | 138.2 |
GG | 73.30 | 67.21 | 10.99 | 9.32 | 138.2 |
Average | 75.10 | 68.75 | 11.27 | 9.70 | 141.2 |
Sampling Location | Number of Microbial Species | Evenness | Shannon Index |
---|---|---|---|
GL | 9.67 ± 1.06 d | 0.72 ± 0.06 a | 1.64 ± 0.15 a |
LZ | 16.33 ± 1.53 c | 0.26 ± 0.00 c | 0.73 ± 0.01 b |
LB | 25.33 ± 1.53 b | 0.27 ± 0.04 c | 0.88 ± 0.13 b |
BS | 17.00 ± 4.36 c | 0.39 ± 0.06 b | 1.10 ± 0.09 b |
NN | 9.00 ± 1.00 d | 0.69 ± 0.04 a | 1.52 ± 0.17 a |
GG | 77.00 ± 0.90 a | 0.38 ± 0.12 bc | 1.65 ± 0.55 a |
Major Strains | Function |
---|---|
Lactiplantibacillus fermentum | Antibacterial activity, cholesterol-lowering ability, immune activity [22]. |
Lactiplantibacillus plantarum | Immunomodulating effect, inhibit pathogenic bacteria, lower serum cholesterol [23]. |
Lactiplantibacillus buchneri | Produces mannitol, bacteriocins, de-cholesterolization, antioxidant capacity [24]. |
Lactiplantibacillus brevis | High acid production capacity and detoxification, antibacterial, improve the immunity of the body, and other functional characteristics [25]. |
Lactiplantibacillus casei paracasei | Regulates the abundance and proportion of gut flora, protects the liver, and prevents liver damage. [26]. |
Lactiplantibacillus pentosus | Synthesis of extracellular polysaccharides, antitumor, anti-ulcer, immunomodulation, and cholesterol-lowering [27]. |
Lactococcus lactis | Limit intestinal damage and protect the intestinal mucosal barrier [28]. |
Weissella cibaria | Antioxidant activity, inhibition of bacteria [29]. |
Leuconostoc citreum | Production of bacteriocins with broad-spectrum antibacterial action [30]. |
Acinetobacter johnsonii | Improve obesity, lower body fat, and reduce cholesterol [31]. |
Functional Database | Number of Unigenes | Percentage |
---|---|---|
NR | 39,294 | 72.21% |
eggNOG | 37,746 | 69.37% |
KEGG | 19,051 | 35.01% |
KEGG pathway | 12,751 | 23.43% |
KO | 14,075 | 25.87% |
GO | 29,889 | 54.93% |
Total number of genes | 53,265 | 97.88% |
Total number of unigenes | 54,415 | 100% |
Ko Number | KEGG Pathway | Gene Number | Major Microorganisms Annotated to KEGG Pathway |
---|---|---|---|
ko00250 | Alanine, aspartate, and glutamate metabolism | 320 | Lactiplantibacillus plantarum, Lactiplantibacillus pentosus, Pediococcus pentosaceus, Lactiplantibacillus, Lactococcus Lactis, Lactiplantibacillus buchneri |
ko00270 | Cysteine and methionine metabolism | 230 | Lactiplantibacillus plantarum, Lactiplantibacillus parafarraginis, Lactiplantibacillus fermentum, Lactiplantibacillus mucosae, Acinetobacter |
ko00260 | Glycine, serine, and threonine metabolism | 220 | Lactiplantibacillus amylolyticus, Lactiplantibacillus casei, Lactiplantibacillus buchneri, Lactiplantibacillus plantarum, Lactiplantibacillus fermentum, Lactiplantibacillus vaginalis |
ko00300 | Lysine biosynthesis | 212 | Lactiplantibacillus amylolyticus, Lactiplantibacillus casei, Lactiplantibacillus buchneri, Lactiplantibacillus plantarum, Lactiplantibacillus fermentum, Lactiplantibacillus vaginalis, Acinetobacter, Flavobacterium, Acinetobacter johnsonii |
ko00400 | Phenylalanine, tyrosine, and tryptophan biosynthesis | 139 | Lactiplantibacillus buchneri, Lactiplantibacillus amylolyticus, Lactiplantibacillus plantarum, Lactiplantibacillus pentosus, Acinetobacter guillouia, Lactiplantibacillus mucosae |
ko00350 | Tyrosine metabolism | 110 | Lactiplantibacillus buchneri, Lactiplantibacillus amylolyticus, Lactiplantibacillus plantarum, Lactiplantibacillus pentosus, Lactiplantibacillus mucosae, Lactiplantibacillus hilgardii, |
ko00340 | Histidine metabolism | 93 | Lactiplantibacillus buchneri, Lactiplantibacillus plantarum, Lactiplantibacillus parafarraginis, Lactiplantibacillus fermentum, Lactiplantibacillus mucosae, Acinetobacter |
ko00330 | Arginine and proline metabolism | 77 | Pediococcus pentosaceus, Lactiplantibacillus plantarum, Lactiplantibacillus brevis, Lactococcus lactis |
ko00280 | Valine, leucine, and isoleucine degradation | 70 | Lactiplantibacillus pentosus, Lactiplantibacillus casei, Lactiplantibacillus buchneri, Lactiplantibacillus plantarum |
ko00471 | D-glutamine and D-glutamine metabolism | 55 | Lactococcus lactis, Lactiplantibacillus buchneri, Acinetobacter parvus, Lactiplantibacillus plantarum, Lactiplantibacillus pentosus |
ko00473 | D-alanine metabolism | 51 | Lactococcus weissella, Lactiplantibacillus, Lactiplantibacillus fermentum, Lactococcus lactis, Lactiplantibacillus plantarum, Lactiplantibacillus pentosus |
ko00380 | Tryptophan metabolism | 45 | Lactiplantibacillus buchneri, Lactiplantibacillus amylolyticus, Lactiplantibacillus plantarum, Lactiplantibacillus pentosus, Acinetobacter guillouia, Lactiplantibacillus mucosae |
ko00290 | Valine, leucine, and isoleucine biosynthesis | 38 | Lactiplantibacillus buchneri, Lactiplantibacillus amylolyticus, Lactiplantibacillus plantarum, Lactiplantibacillus pentosus |
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Hu, Y.; Chen, X.; Zhou, J.; Jing, W.; Guo, Q. Metagenomic Analysis of Suansun, a Traditional Chinese Unsalted Fermented Food. Processes 2021, 9, 1669. https://0-doi-org.brum.beds.ac.uk/10.3390/pr9091669
Hu Y, Chen X, Zhou J, Jing W, Guo Q. Metagenomic Analysis of Suansun, a Traditional Chinese Unsalted Fermented Food. Processes. 2021; 9(9):1669. https://0-doi-org.brum.beds.ac.uk/10.3390/pr9091669
Chicago/Turabian StyleHu, Yaping, Xiaodong Chen, Jie Zhou, Wenxuan Jing, and Qirong Guo. 2021. "Metagenomic Analysis of Suansun, a Traditional Chinese Unsalted Fermented Food" Processes 9, no. 9: 1669. https://0-doi-org.brum.beds.ac.uk/10.3390/pr9091669