Profiling the Resistome of Microbial Communities from Unexplored Karst Forest Soils from Guiuan, Samar Province

Abstract

Karst forests comprise 11.7% of the total land surface of the Philippines. Limited research has been conducted to study this ecosystem since local research is chiefly focused on its economic value, and not on the public health threats these unexplored forests may impose. The possible relationship between resistomes and the soil microbial communities (SMCs) of these landscapes are still poorly understood. As of the writing of the current study, none of the karst forest soils have had their resistomes profiled. This objective of the study is to provide a resistome profile of the metagenomic datasets from unexplored karst forest soils in Guiuan, Samar. This includes the identification and quantification of resistome types and gene groups in relation to SMCs. An efficient and novel resistome pipeline, DugesiaAMR, was used for the descriptive and quantitative analysis of putative resistome types and gene groups found within existing metagenomic datasets. The datasets used were received from the Project 3 Team of CON-Kaigangan, a program dedicated to the assessment and conservation of the karst landscapes found in selected municipalities of Samar. Three resistome types were identified: drugs, metals, and multi-compound. There were 26 resistome gene groups under drugs, 3 under metals, and 2 under multi-compound. The findings showed the prevalence of drug resistance, namely Macrolide-Lincosamide-Streptogramin (MLS), Aminoglycoside, and Oxazolidinone resistance. DugesiaAMR was able to complete analysis of the datasets (average of 168 million reads each) in 27 minutes on the 88-core high-performance computing (HPC) machine and 81 minutes on the 4-core home computer, owing to the high scalability of the programs used in the pipeline. The resistome types identified by DugesiaAMR can spearhead further research on the resistome and SMCs of the environmental samples and can subsequently enhance resistome surveillance in the country.