An environmental study of multiple mycetoma pathogens: Metabarcoding analysis for soil DNA of the endemic area in Sudan

Mycetoma is a tropical disease caused by several fungi and bacteria present in the soil. Especially fungal mycetoma or eumycetoma is challenging to treat; therefore, prevention, early diagnosis, and ealy treatment are important, but it is necessary to grasp the geographic distribution of pathogenic fungi. In this study, we evaluated DNA metabarcoding methodology for identifying fungal species from soil samples. Soil sampling was implemented at seven villages in the endemic area of Sennar State in Sudan in 2019, and ten sampling sites were selected in each village according to land-use conditions. In total, 70 soil samples were collected from ground surfaces, and DNA in the soil was extracted with the combined method of alkaline DNA extraction and a commercial soil DNA extraction kit. The region of universal primers was selected to be the ribosomal internal transcribed spacer one region for metabarcoding. After the second PCR for DNA library preparation, the amplicon-based DNA analysis was performed using next-generation sequencing.