An effect of filtration strategy on recovery of signals from different organisms from wastewaters
Filtration is one of the most widely used pre-processing steps in environmental microbiome characterization, yet its selective impact(s) on the recovery of distinct taxonomic groups via amplicon and shotgun sequencing of complex matrices like wastewater remains poorly quantified. To characterize some of these biases, we applied targeted amplicon, shotgun metagenomic, and metatranscriptomic sequencing wastewater samples processed across varying filter pore sizes (3.0 um, 0.45 um, and 0.22 um). Collectively, our results indicate that no single filtration workflow or sequencing strategy universally optimizes the recovery of all taxonomic groups, thus methodological selection must be explicitly tailored to the target organisms and specific biosurveillance objectives.