A step-by-step procedure for analysing the 16S rRNA-based microbiome diversity using QIIME 2 and comprehensive PICRUSt2 illustration for functional prediction

Abstract

Short-read sequencing technology has emerged as a preferred tool to analyse the bacterial composition of a niche by targeting hypervariable regions of the 16S rRNA gene. It targets the short hypervariable regions of the 16S rRNA gene and uncovers the taxonomic profile and their associated pathways. QIIME 2 is preferred and ready-to-use pipelines that perform stepwise analysis of massive short reads of 16S rRNA genes. This wrapper comprises several tools that include quality checking, denoising, taxonomic classification, alignment, and diversity analysis. However, it demands huge bioinformatic analysis practices which are quite challenging to many microbiologists working in the field of traditional microbiology. This paper, therefore, aims to make microbiologists familiar with the steps of computational analysis for processing 16S rRNA-based sequences. Here, we are presenting stepwise processing of NGS sequences using the QIIME 2 platform along with their analyses, which include installing QIIME 2, importing and processing data, quality checks, taxonomy assignments, and diversity analysis. Besides, the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) has also been illustrated to understand the correlation between metabolic and physiological footprints of the different species observed during microbiome analysis. Therefore, this paper can be used as a handy toolkit for those researchers who are less familiar with its associated bioinformatic analysis.