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Article

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.

Genome research - 2 May 2025

Smith Byron J, Zhao Chunyu, Dubinkina Veronika, Jin Xiaofan, Zahavi Liron, Shoer Saar, Moltzau-Anderson Jacqueline, Segal Eran, Pollard Katherine S

Abstract excerpt

Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional...

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PMID: 40210439
DOI: 10.1101/gr.279543.124
PMCID: PMC12047655

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