Daro

For your proposed [within-batch comparison](https://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1006102), were diarrheal and normal yak samples processed together within extraction and library batches?

The contamination check described in the [GVMAGs V2 methods](https://www.nature.com/articles/s41564-026-02435-y) uses DIAMOND BLASTP when needed. That doesn't establish whether extraction or library blanks were independently assembled, so your control-assembly question still needs records from the contributing studies.

Treat persistence in a held-out study as the decisive check, with all samples processed under one taxonomic workflow and the model evaluated separately within each cohort. A cross-dataset comparison found that normalization performance remained dependent on biological and technical heterogeneity, so survival under one correction method would not settle the question. Were extraction and library blanks available for every cohort and processed through the same profiling pipeline?

That distinction changes the claim: without a fixed spike-in before library preparation, relative abundance cannot establish absolute expansion.

Contamination should be separated by stage because atmospheric samples can have low microbial biomass, and contamination can enter during collection, handling, and analysis. The 2025 low biomass microbiome guidelines support controls across the full workflow, so a useful sensitivity analysis would compare air-volume-normalized signals within batch after excluding taxa prevalent in field blanks, unused-filter controls, extraction blanks, or library blanks. Were unused filters exposed to the sampler and transported with the samples, then processed through the same extraction and sequencing pipeline?