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Many multicellular organisms symbiotically host a wide variety of prokaryotic species, described collectively as the microbiome. The total amount of unique genetic sequence in the human microbiome is likely many times that in the human genome, and can vary widely from individual-to-individual. Because the microbiome plays important roles regulating a number of systems, identifying and estimating the relative abundance of different species is a critical first step in understanding its function. Abundances of microorganisms can be estimated by one of the following techniques.

Shotgun metagenomic sequencing
Shotgun sequencing of the metagenomic DNA is performed and the assembled contigs are used to determine relative abundances of microogransism. This technique can allow one to probe not only taxonomic but genotypic diversity of the metagenome, as it is possible to detect the presence of a variety of different genes. This additional coverage requires additional sequencing depth and thus is more costly than amplicon approaches.
Amplicon sequencing (16s rRNA)
This technique employs an initial step to selectively amplify a particular gene/region from the metagenomic DNA. This technique requires less sequencing depth, as it targets are particular region, however typically only reports taxonomic diversity of the sample as only one gene/region is sequenced. The DNAS facility at UIC has developed a flexible and robust workflow that allows different regions to be targeted for amplicon sequencing, e.g. 16S rRNA or ITS. For microbiomes, the 16S rRNA region typically selected for the most universal coverage of bacterial and archaeal microorganisms while fungal communities can be studied using the ITS region.
These experiments can provide insight into changes in the active processes within the microbiome.