16S rRNA gene amplicon sequencing (short and long reads) from Oligo-MM12 mouse gut
16S rRNA amplicon sequencing is conventionally used to identify microbes and determine their composition in microbial communities. Deep amplicon sequencing of complex microbiomes is well established using short-read sequencing targeting variable regions of the 16S rRNA gene. Short reads enable the classification of bacteria until the genus level in the taxa hierarchy, whereas long reads provide better chances of identifying bacteria to specie and even strain levels. This study introduces a streamlined approach for analyzing simple microbial communities using full-length 16S rRNA amplicon nanopore long read sequencing. This approach surpasses Illumina sequencing in species accuracy, is cost-effective and time-efficient. Tailored for low-complexity microbiota, it facilitates studies in natural or synthetic communities, especially beneficial for smaller-scale projects with limited resources.