Metagenomic Analysis of Microbial Contamination in the U.S. Portion of the Tijuana River Watershed
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection, E. coli and Coliform Measurements
2.2. DNA Extraction, Purification, and Sequencing
2.3. Processing and Taxonomic Classification
2.4. OTU Table Creation and Modification
2.5. Disease-Causing Microbe and Virus Identification
2.6. Breadth of Coverage
2.7. Diversity Analyses
2.8. Fecal Contamination Analysis
2.9. Antibiotic Resistance Genes (ARGs)
2.10. Scripts and Data
3. Results
3.1. DNA Concentration and Sequence Quality
3.2. Metagenomic Results with Disease-Causing Microbes and Viruses
3.3. Breadth of Coverage
3.4. Diversity Analysis
3.5. Alpha Diversity
3.6. Fecal Contamination Analysis
3.7. Antibiotic Resistance Genes (ARGs)
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Average Number of Hits * |
---|---|
Arcobacter cryaerophilus | 140,491.1 |
Pseudoarcobacter acticola | 98,044.3 |
Simplicispira metamorpha | 76,102.6 |
Bacteroides graminisolvens | 59,197.3 |
Tolumonas auensis | 57,818.1 |
Arcobacter suis | 50,397.2 |
Acinetobacter johnsonii | 39,478.1 |
Aeromonas media | 36,381.4 |
Arcobacter butzleri | 32,238.7 |
Rheinheimera sp. LHK132 | 32,046.6 |
Bacterial Species | Average Hits * | Eukaryotic Species | Average Hits |
---|---|---|---|
Salmonella enterica | 1890.4 | Trichomonas vaginalis | 97.8 |
Vibrio parahaemolyticus | 1602.4 | Plasmodium ovale | 36.2 |
Streptococcus pneumoniae | 1009.0 | Plasmodium vivax | 29.1 |
Vibrio alginolyticus | 462.8 | Cyclospora cayetanensis | 25.2 |
Bordetella pertussis | 459.6 | Plasmodium falciparum | 23.8 |
Francisella tularensis | 360.3 | Plasmodium yoelii | 21.7 |
Vibrio vulnificus | 340.5 | Entamoeba histolytica | 18.4 |
Neisseria meningitidis | 312.0 | Viruses | Average Hits |
Yersinia enterocolitica | 273.5 | HIV-1 | 14.2 |
Mycobacterium tuberculosis | 268.0 | Hepatitis C | 6.1 |
Listeria monocytogenes | 101.0 | Hepatitis B | 3.7 |
Species | Sample 1 2/12/20 | Sample 8 11/22/19 | Sample 14 12/6/19 | Sample 20 2/24/20 |
---|---|---|---|---|
S. enterica 45157 | 2.12% | 9.77% | 6.21% | 3.48% |
S. enterica DA34827 | 2.62% | 10.09% | 6.77% | 3.31% |
S. enterica FDAARGOS 94 | 2.50% | 10.14% | 6.71% | 3.72% |
S. enterica FDAARGOS 878 | 2.47% | 10.00% | 6.59% | 3.63% |
S. enterica LT2 | 2.48% | 10.01% | 6.63% | 3.66% |
S. enterica SA20021456 | 1.85% | 8.06% | 5.27% | 2.88% |
S. enterica SA20100201 | 1.97% | 8.79% | 5.68% | 3.15% |
Escherichia coli | 11.87% | 78.56% | 55.51% | 26.03% |
Arcobacter cryaerophilus | 91.27% | 79.60% | 94.81% | 94.20% |
HIV-1 | 0% | 0% | 0% | 0% |
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Allsing, N.; Kelley, S.T.; Fox, A.N.; Sant, K.E. Metagenomic Analysis of Microbial Contamination in the U.S. Portion of the Tijuana River Watershed. Int. J. Environ. Res. Public Health 2023, 20, 600. https://doi.org/10.3390/ijerph20010600
Allsing N, Kelley ST, Fox AN, Sant KE. Metagenomic Analysis of Microbial Contamination in the U.S. Portion of the Tijuana River Watershed. International Journal of Environmental Research and Public Health. 2023; 20(1):600. https://doi.org/10.3390/ijerph20010600
Chicago/Turabian StyleAllsing, Nicholas, Scott T. Kelley, Alexandra N. Fox, and Karilyn E. Sant. 2023. "Metagenomic Analysis of Microbial Contamination in the U.S. Portion of the Tijuana River Watershed" International Journal of Environmental Research and Public Health 20, no. 1: 600. https://doi.org/10.3390/ijerph20010600