Quality control for OTU sequences
Contamint species can be introduced into your samples at every stage in the experimental protocol from sample collection to sequencing (e.g., residue on the flow-cell).
Detecting contaminants is difficult / impossible except in control samples e.g., distilled water, or a mock community. Control samples can be used to detect contaminants introduced in the stages from library preparation to sequencing. Note that cross-talk can also cause unexpected sequences in a control sample.