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Metagenomic screening of microbiomes identifies pathogen-enriched environments

Li, Xiaofang
Environmental sciences Europe 2019 v.31 no.1 pp. 37
Firmicutes, Nitrospirae, Proteobacteria, RNA, animal pathogens, bioinformatics, correspondence analysis, databases, feces, freshwater, metagenomics, microbiome, ornithine carbamoyltransferase, rapid methods, risk, screening, seawater, soil, toxins, wastewater, water pollution
BACKGROUND: Human pathogens are widespread in the environment, and examination of pathogen-enriched environments in a rapid and high-throughput fashion is important for development of pathogen-risk precautionary measures. In this study, a Local BLASTP procedure for metagenomic screening of pathogens in the environment was developed using a toxin-centered database. A total of 69 microbiomes derived from ocean water, freshwater, soils, feces, and wastewater were screened using the Local BLASTP procedure. Bioinformatic analysis and Canonical Correspondence Analysis were conducted to examine whether the toxins included in the database were taxonomically associated. RESULTS: The specificity of the Local BLASTP method was tested with known and unknown toxin sequences. Bioinformatic analysis indicated that most toxins were phylum-specific but not genus-specific. Canonical Correspondence Analysis implied that almost all of the toxins were associated with the phyla of Proteobacteria, Nitrospirae and Firmicutes. Local BLASTP screening of the global microbiomes showed that pore-forming RTX toxin, ornithine carbamoyltransferase ArgK, and RNA interferase Rel were most prevalent globally in terms of relative abundance, while polluted water and feces samples were the most pathogen-enriched. CONCLUSIONS: The Local BLASTP procedure was applied for rapid detection of toxins in environmental samples using a toxin-centered database built in this study. Screening of global microbiomes in this study provided a quantitative estimate of the most prevalent toxins and most pathogen-enriched environments. Feces-contaminated environments are of particular concern for pathogen risks.