Metagenomics is defined as the study of all microbiota genetic content within a sample. The term metagenomics still carries ambiguity since it can refer to both marker gene sequencing and whole-genome metagenomics. It has been recommended the usage of the term "Metataxonomics" to marker gene sequencing and metagenomics to the random "shotgun" sequencing of microbial DNA, without selecting any particular gene. Both metataxonomics and metagenomics can provide information on the species composition of a microbiome.
