2.5. Decontamination pipeline
Contaminant species were detected and removed using the decontam R
package.19 We used the most stringent hyperparameter
value (P * = 0.5) for both frequency-based and prevalence-based
contaminant identification of the isContaminant function. DNA
concentrations for the frequency method were measured by qPCR and were
obtained during library preparation. The scores from the frequency and
prevalence methods were combined using the “minimum” approach. We
performed decontamination in batches and the species identified as
contaminants in any batch were removed. The species not identified as
contaminants with decontam were further excluded if they met one of the
following criteria: (1) The relative abundance of a species show an
inverse correlation with DNA concentration20 (ρ
< -0.2, P < 0.05, Spearman’s correlation);
(2) The relative abundance of a species > 0.01% in at
least one negative blank control.