A review of common methods used in the analysis of human microbiome sequencing data

The past two decades have seen a rapid rise in the development and use of sequencing technologies. The advent of high-throughput sequencing (HTS) has allowed scientists sequence the genomic content of entire microbial communities rapidly and affordably. Methods for data management, visualization, and analysis of this microbiome sequencing data are now widespread in open and closed source software tools. In this review, we identify common analysis methods used in microbiome sequencing studies, including methods for normalisation of abundance table data, visualization of high-dimensional microbiome data and the analysis of longitudinal microbiome sequencing data. In particular we find that a very small proportion of metagenomic studies made use of compositional data analysis methods and none that made use of compositional methods for longitudinal microbiome data.