Metagenomic Characterization of Resistance Genes in Deception Island and Their Association with Mobile Genetic Elements
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Site Description
2.2. DNA Extraction and Sequencing
2.3. Bioinformatic Data Analysis
2.3.1. Metagenomic Assembly
2.3.2. Resistance Genes Identification
- (a)
- Antibiotic resistance genes: Identification of clinical ARGs within the metagenomes was carried out with the Deeparg v2.0 Tool [20] using a concatenated database including the CARD [21] and ARBD databases [22] which are validated databases for ARGs. An identity cutoff of 60% was used to filter annotations and conduct further analyses. In this study, we have calculated the relative abundances of ARGs as the total number of ARGs per sample divided by the total number of Prodigal predicted genes as described by Van Goethem et al., 2018 [3].
- (b)
- Environmental resistance genes: Identification of ERGs in the metagenomes was done using a custom pipeline. Briefly, a gene prediction was carried out using Prodigal v2.6.3.8 [23]. Subsequently, Hmmscan v3.3 was used to identify the ERG-Like genes in coding regions using the SargFam v2.0 database. Afterward, Diamond v0.9.14 [24] was used for ERGs annotation using the BacMet v2.0 database [25]. An identity cutoff of 60% was used to filter annotations and carry out further analyses. Finally, plots and ARGs and ERGs diversity analyses were made using the MicrobiomeAnalyst tool [26]. In this study, we have calculated the relative abundances of ERGs as the total number of ERGs per sample divided by the total number of Prodigal predicted genes as described by Van Goethem et al., 2018 [3].
2.3.3. Taxonomy of Resistance Genes
2.3.4. Identification of Mobile Genetic Elements and Their Association with ARGs and ERGs
2.3.5. Co-Occurrence Gene Analysis
3. Results
3.1. Sample Collection and Description
3.2. Resistance Genes Identification
3.3. Taxonomy and Resistance Genes Associations
3.4. Contribution of Mobile Elements to de Dissemination of ARGs and ERGs
4. Discussion
4.1. Sample Collection and Description
4.2. ARGs Found in Deception Island
4.3. Resistance Mechanisms in Deception Island
4.4. ERGs Found in Deception Island
4.5. Taxonomy and Resistance Genes Associations
4.6. Co-Occurrence of ARGs and ERGs
4.7. Contribution of Mobile Elements to de Dissemination of ARGs and ERGs
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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Sample | Latitude S | Latitude W | pH | %N | %C |
---|---|---|---|---|---|
1ANT | 62°59′0.35″ S | 60°32′47.66″ W | 6.1 | 0.48 | 3.4 |
2ANT | 62°58′57.53″ S | 60°33′1.81″ W | 6.9 | 0.1 | 0.53 |
3ANT | 62°58′57.53″ S | 60°33′1.81″ W | 7.1 | 0.77 | 0.17 |
4ANT | 62°59′15.39″ S | 60°33′9.25″ W | 7.3 | 0.13 | 0.08 |
5ANT | 62°59′10.30″ S | 60°33′3.06″ W | 6.8 | 0.01 | 0.01 |
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Santos, A.; Burgos, F.; Martinez-Urtaza, J.; Barrientos, L. Metagenomic Characterization of Resistance Genes in Deception Island and Their Association with Mobile Genetic Elements. Microorganisms 2022, 10, 1432. https://doi.org/10.3390/microorganisms10071432
Santos A, Burgos F, Martinez-Urtaza J, Barrientos L. Metagenomic Characterization of Resistance Genes in Deception Island and Their Association with Mobile Genetic Elements. Microorganisms. 2022; 10(7):1432. https://doi.org/10.3390/microorganisms10071432
Chicago/Turabian StyleSantos, Andrés, Felipe Burgos, Jaime Martinez-Urtaza, and Leticia Barrientos. 2022. "Metagenomic Characterization of Resistance Genes in Deception Island and Their Association with Mobile Genetic Elements" Microorganisms 10, no. 7: 1432. https://doi.org/10.3390/microorganisms10071432
APA StyleSantos, A., Burgos, F., Martinez-Urtaza, J., & Barrientos, L. (2022). Metagenomic Characterization of Resistance Genes in Deception Island and Their Association with Mobile Genetic Elements. Microorganisms, 10(7), 1432. https://doi.org/10.3390/microorganisms10071432