. Author manuscript; available in PMC: 2019 Jul 1.

Published in final edited form as: Biol Blood Marrow Transplant. 2018 Feb 19;24(7):1322–1340. doi: 10.1016/j.bbmt.2018.02.009

Table 4.

Sequencing technologies used in microbiome research

Method	Definition	References
Metagenomics	The study of genes and non-coding genetic information in a mixed population of organisms in order to infer functional potential and taxonomic structure of the population and its individual organisms	Marchesi, 2015³²
16S ribosomal RNA/DNA sequencing	PCR amplification of bacterial RNA/DNA from the variable regions of the 16S ribosomal RNA gene for taxonomic profiling (the region selected is usually determined by the niche that is being investigated; e.g. V4 for stool, V1-3 for skin)	Weisburg, 1991³³
Shotgun next-generation metagenomic sequencing	High-throughput DNA sequence generation and analysis from any organism or group of organisms via fragmentation, tagging, amplification, and massively parallel or deep sequencing. Allows for taxonomic identification in addition to generating information about gene presence, genetic bioregulation and potential metabolic pathways	Loman, 2012³⁴
Metatranscriptomics	High-throughput RNA sequence generation and analysis from any organism or group of organisms via reverse transcription, tagging, amplification, and massively parallel or deep sequencing. Provides a snapshot of which genes are being transcribed	Marchesi, 2015³²
Metabolomics	Characterization of the collection of metabolites produced by an organism or a single tissue. The term has been used to described characterization of the collection of metabolites produced by a collection of organisms (i.e. the microbiota), although some prefer the term “metabonomics” for that definition	Marchesi, 2015³²
Metaproteomics	Characterization of all proteins within a clinical or environmental sample	Marchesi, 2015³²