Abstract
Phage DNA analysis gives opportunity to understand living ecosystem of the environment where the samples are taken. In the present study, we analyzed phage DNA obtained from wastewater sample of university hospital sewage. After filtration, long high-speed centrifugation was done to collect phages. DNA was extracted from pellet by phenol chloroform extraction and used for NGS sequencing. The host profile, taxonomic and functional analyses were performed using MG-RAST, and ResFinder program was used for resistance gene detection. High amounts of reads belong to bacteriophage groups (~ 95%) from our DNA sample were obtained and all bacteriophage reads were found belonging to Caudovirales order and Myoviridae (56%), Siphoviridae (43%), and Podoviridae (0.02%) families. The most common host genera were Escherichia (88.20%), Salmonella (5.49%) and Staphylococcus (5.19%). SEED subsystems hits were mostly structural parts and KEGG Orthology hits were nucleotide- and carbohydrate metabolism-related genes. No anti-microbial resistance genes were detected. Our bacteriophage DNA purification method is favorable for phage metagenomic studies. Dominance of coliphages may explain infrequent Podoviridae. Dominancy of structural genes and auxiliary genes is probably due to abundance of lytic phages in our sample. Absence of antibiotic resistance genes even in hospital environment phages indicates that phages are not important carrier of resistance genes.
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The authors, Hanife Salih and Melis Yalcin, are supported by YOK 100/2000 fellowship program during the PhD.
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HS: methodology, formal analysis, investigation, writing—original draft, visualization; AK: methodology, investigation, resources; MY: methodology, investigation; EO: resources, writing—review & editing; CH: formal analysis; GB: writing—review & editing, supervision; BB: conceptualization, writing—review & editing, visualization, supervision, project administration. All authors approved the final manuscript.
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Salih, H., Karaynir, A., Yalcin, M. et al. Metagenomic analysis of wastewater phageome from a University Hospital in Turkey. Arch Microbiol 204, 353 (2022). https://doi.org/10.1007/s00203-022-02962-2
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DOI: https://doi.org/10.1007/s00203-022-02962-2