ABSTRACT
The gut microbiome, the collective community of microorganisms residing in the gastrointestinal tract, plays important roles in host nutrition and the development of the host immune system and disease. The advent of next-generation sequencing technologies and the rapid development of computational tools and reference databases have revolutionized microbiome studies. The aggregate genetic material and environmental interactions in a specific environment have been the focus of intensive studies using marker gene–based approaches. In the past few years, numerous algorithms and computational resources have been developed to address unique characteristics of the count data, such as compositionality, sparseness, and high dimensionality, derived from the most widely used marker genes, small subunits of the ribosomal RNA gene. In this chapter, we summarize recent advances in the development of computational tools and methods, and discussed their practical implications in microbiology ecology and microbiome analyses.
