Amplicon sequencing	DNA sequencing targeted at ubiquitous genes that contain taxon-specific variation. Bacterial community (or microbiota) profiling by amplicon sequencing of the 16S rRNA gene is the most commonly used microbiomic method in otitis media studies. Important limitations of short-read amplicon sequencing (where only a portion of the 16S rRNA gene is sequenced) include low resolving power (i.e. may not identify bacteria to the species-level) and distortion of relative abundance profiles due to amplification biases.
Mycobiomics	An amplicon sequencing method that is used to characterise fungal communities.
Metagenomics	Shotgun sequencing of all DNA in a specimen. An advantage of metagenomic sequencing is that it can provide strain-level identification of bacteria, as well as the genomes of other microbes that may be present (e.g. viruses and fungi). Metagenomics will provide the most comprehensive assessment of the genetic potential of a microbial community; however, analysis of otitis media specimen types can be challenging due to a high proportion of reads (>90%) mapping to human DNA [63]. Methods to selectively exclude human DNA are available [154], but have not yet been validated for otitis media specimen types. Additionally, no RNA-based viruses can be identified with this method.
Transcriptomics	A RNA-based measure of all genes expressed in a sample. A small number of studies have used transcriptomics to study human gene expression in otitis media (e.g. [160]). Pathogen transcriptomes were reported by one study of nasopharyngeal aspirates [71].
Proteomics	A measure of all proteins in a specimen. One study has used proteomics to investigate innate immune responses in middle ear fluid from patients with chronic otitis media [63]. Assaying microbial proteomes directly from specimens may be challenging when a high proportion of the proteome is derived from host-produced molecules.
Metabolomics	A measure of all metabolites in a sample. Metabolomics is an emerging technology with potential respiratory diagnostic applications [161]. Metabolomic studies of otitis media specimens are emerging [153], but there are not yet any published data. As with other OMICs technologies, distinguishing microbial-specific signal may be difficult when high proportions of host-derived molecules are present.