Metax enables accurate cross-domain taxonomic profiling of metagenomes.

Metax improves cross-domain, species-level taxonomic profiling across >600 metagenome samples, delivering on average 55% higher F1 scores and 45% lower Bray-Curtis dissimilarity than other methods.

• Why it matters: Species-level accuracy is hard in complex communities spanning bacteria, viruses, eukaryotes, and archaea, especially in low-biomass, host-dominated samples where artifacts are common.
• What they did: Metax integrates coverage-based probabilistic modeling with an expectation-maximization framework to separate true microbial signals from artifacts, evaluated across host-associated, environmental, wastewater, and low-biomass clinical settings.
• The result: In peri-implantitis oral microbiomes, Metax resolves bacterial and viral signatures, and in plasma-cell-free DNA it reveals signals suggestive of reagent-borne contaminants and reference misassemblies.

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