Metagenomics Reveals the Diversity and Taxonomy of Carbohydrate-Active Enzymes and Antibiotic Resistance Genes in Suancai Bacterial Communities
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Sequencing
2.2. Metagenome Assembly and Taxonomic Assignment
2.3. Functional Annotation
2.4. ARGs Identification
2.5. Statistical Analysis
3. Results and Discussion
3.1. Metagenomic Assembly Revealed CAZymes
3.2. Phylogenetic Distribution of CAZymes
3.3. Occurrence and Characteristics of ARGs during Suancai Fermentation
3.4. Correlation of ARGs and Their Potential Hosts
3.5. Resistance Mechanisms
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Items | ARG Type | Resistance Mechanism | Abundance in Sample A | Abundance in Sample B | Abundance in Sample C |
---|---|---|---|---|---|
lnuA | lincosamide | antibiotic inactivation× | 1.53 × 10−5 | 0.000109 | 3.41 × 10−5 |
adeF | Multidrug | antibiotic efflux | 6.55 × 10−5 | 7.86 × 10−5 | 7.56 × 10−5 |
OXA−141 | Multidrug | antibiotic inactivation | 5.00 × 10−5 | 5.67 × 10−5 | 5.74 × 10−5 |
arnA | peptide | antibiotic target alteration | 4.03 × 10−5 | 3.20 × 10−5 | 3.12 × 10−5 |
APH3-VIa | aminoglycoside | antibiotic inactivation | 3.80 × 10−5 | 2.05 × 10−5 | 2.26 × 10−5 |
Erm43 | Multidrug | antibiotic target alteration | 2.01 × 10−5 | 1.42 × 10−5 | 2.80 × 10−5 |
FosB | fosfomycin | antibiotic inactivation | 3.83 × 10−6 | 2.02 × 10−5 | 4.69 × 10−6 |
MexS | Multidrug | antibiotic efflux | 6.48 × 10−6 | 2.00 × 10−5 | 4.52 × 10−6 |
ErmD | Multidrug | antibiotic target alteration | 1.66 × 10−5 | 6.00 × 10−6 | 9.15 × 10−6 |
fusD | fusidic acid | antibiotic inactivation | 1.39 × 10−6 | 1.51 × 10−5 | 4.27 × 10−6 |
OXA-50 | Multidrug | antibiotic inactivation | 1.50 × 10−6 | 1.33 × 10−5 | 6.17 × 10−6 |
mdsC | Multidrug | antibiotic efflux | 2.09 × 10−6 | 1.30 × 10−5 | 7.23 × 10−6 |
MexB | Multidrug | antibiotic efflux | 3.21 × 10−6 | 1.29 × 10−5 | 2.87 × 10−6 |
OXA-388 | Multidrug | antibiotic inactivation | 1.28 × 10−5 | 1.16 × 10−5 | 1.00 × 10−5 |
OXA-351 | Multidrug | antibiotic inactivation | 3.55 × 10−6 | 1.11 × 10−5 | 9.50 × 10−7 |
MexW | Multidrug | resistance-nodulation-cell division (RND) antibiotic efflux pump | 4.24 × 10−6 | 9.82 × 10−6 | 6.88 × 10−07 |
lmrC | lincosamide | antibiotic efflux | 9.78 × 10−6 | 2.23 × 10−6 | 1.39 × 10−6 |
tetS | tetracycline | antibiotic target protection | 7.24 × 10−6 | 9.75 × 10−6 | 1.94 × 10−6 |
APH3-VI | aminoglycoside | antibiotic inactivation | 8.98 × 10−6 | 7.35 × 10−6 | 6.19 × 10−6 |
lmrD | lincosamide | antibiotic efflux | 8.87 × 10−6 | 1.96 × 10−6 | 1.27 × 10−6 |
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Song, Q.; Wang, B.; Han, Y.; Zhou, Z. Metagenomics Reveals the Diversity and Taxonomy of Carbohydrate-Active Enzymes and Antibiotic Resistance Genes in Suancai Bacterial Communities. Genes 2022, 13, 773. https://doi.org/10.3390/genes13050773
Song Q, Wang B, Han Y, Zhou Z. Metagenomics Reveals the Diversity and Taxonomy of Carbohydrate-Active Enzymes and Antibiotic Resistance Genes in Suancai Bacterial Communities. Genes. 2022; 13(5):773. https://doi.org/10.3390/genes13050773
Chicago/Turabian StyleSong, Qiaozhi, Binbin Wang, Ye Han, and Zhijiang Zhou. 2022. "Metagenomics Reveals the Diversity and Taxonomy of Carbohydrate-Active Enzymes and Antibiotic Resistance Genes in Suancai Bacterial Communities" Genes 13, no. 5: 773. https://doi.org/10.3390/genes13050773
APA StyleSong, Q., Wang, B., Han, Y., & Zhou, Z. (2022). Metagenomics Reveals the Diversity and Taxonomy of Carbohydrate-Active Enzymes and Antibiotic Resistance Genes in Suancai Bacterial Communities. Genes, 13(5), 773. https://doi.org/10.3390/genes13050773