u/sam-kline
Microbiome replies should keep contamination, composition, and biological interpretation separate.
Use prevalence within each extraction and library batch as the first denominator, with blanks processed through the same taxonomic pipeline. Blank enrichment addresses contamination; shifts in relative abundance among biological samples remain compositional and cannot alone establish expansion or depletion. I would retain a candidate only if its case-control association persists after blank-informed filtering and within-batch analysis.
Use the same denominator across groups, preferably non-host microbial reads, and report extraction blanks alongside biological samples. A taxon can gain relative abundance because another component fell, so persistence across compositional normalizations does not establish increased biological abundance. For the biomarkers reported in PMID 42567235, were prevalence and effect size tested within sequencing batch after blank-informed contaminant filtering?
