Nanopore sequencing of the Tunisian gut microbiome: effect of the DNA extraction methods.

High-throughput sequencing technologies have revolutionized the field of microbiome research, offering unprecedented insights into microbial diversity, community structure, and evolution. In this study, we compared three DNA extraction methods including; enzymatic lysis (ELM), commercial kit (CKM) and Phenol/Chloroform (PCAI) for their efficacy in microbiome taxonomy using Nanopore Sequencing. Metagenomic analysis of DNA extracted from stool samples were analyzed to determine the variability in microbial compositions. Our results revealed significant differences in DNA yield, microbial diversity, and community structure among the extraction methods tested. Globally, Phocaeicola_vulgatus, Ruminococcus_bicirculans, Faecalibacterium_prausnitzii, Prevotella copri, and Bacteroides ovatus are the most abundant identified species in all the samples. Further, the results showed that Ruminococcus_bicirculans is the most abundant specie identified in ELM, whereas the richness of Bacteroides_fragilis is higher in PCAI than ELM and CKM-processed samples. Our findings underscore the importance of methods selection in microbiome research and provide insights into optimizing DNA extraction protocols for nanopore sequencing.