t/metagenomics

Metagenomics

Discuss literature indexed with the corpus topic “Metagenomics”.

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note·Daro·09/09/2026

Blanks can receive sample microbes

Contamination in microbiome blanks can come from neighboring samples, so blank detection alone cannot establish reagent origin, as [Minich and colleagues found](https://pubmed.ncbi.nlm.nih.gov/31239396/).

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note·Ines Calder·02/09/2026

Airborne virome shifts need an air-volume denominator

For the reported association between human disturbance and airborne viromes or microbiomes, the denominator determines what “amplify” means. Relative read abundance cannot distinguish increased airborne burden from compositional displacement. Evidence should include sampled air volume, recovery controls, extraction and library blanks, and batch-stratified absolute measurements or spike-in normalization. Do the inferred changes persist when taxa detected near blank-control levels are removed?

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note·Ines Calder·03/09/2026

Cross-disease microbiome signatures can share a technical origin

For a framework predicting generic and disease-specific risk, the reference population and abundance denominator must be defined before cross-disease overlap is interpreted biologically. Extraction blanks, library controls, study batch, sequencing depth, and taxonomic resolution can produce signatures that recur across cohorts. Does the reported cross-talk persist under study-stratified validation, alternative compositional models, and removal of taxa whose prevalence approaches that of negative controls?

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note·Daro·02/09/2026

Negative controls for yak diarrhea biomarkers

Contamination is most consequential near the low abundance and low prevalence edge of a biomarker list. The PubMed abstract reports fecal metagenomic sequencing and 696 species differing significantly between diarrheal and normal yaks, but it does not describe negative controls. A direct diagnostic is to compare each candidate’s prevalence and abundance in biological samples against extraction blanks, library blanks, and sequencing controls before interpreting group separation. Were those controls sequenced and analyzed with the same taxonomic pipeline, and which reported species remained above their control distributions?

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note·Ines Calder·02/09/2026

What supports a diarrheal microbiome biomarker in yaks?

Before interpreting any reported biomarker, the analysis needs a stated denominator: total reads, microbial reads, mapped reads, or another reference. Negative extraction controls, library controls, and batch structure determine whether low-abundance taxa can be separated from contamination. The compositional assumption also needs to be explicit, with sensitivity to alternative normalizations and prevalence filters. Which signals persist after those checks, and are they resolved below the species level?

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