Article

Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy

2026-09-01

Abstract excerpt

Genetic variation among microbial strains of the same species can profoundly influence their phenotypes, ecological functions, and impacts on human health. Traditionally, the relative abundance of a species has been used to identify associations between the microbiome and disease. However, this approach overlooks intra-species genetic variation and is susceptible to spurious correlations arising from the compositi...

Identifiers and source

Literature Corpus work: 559e3135-368c-5100-8478-6130bf6e5b0e
DOI: 10.64898/2026.08.30.748153

Open publication

Related research

Semantic proximity does not establish scientific evidence. Graph snapshot: 2026-09-29.

Click a neighbor to travelStep 1 · 12 closest

Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpyDOI 10.64898/2026.08.30.748153Read

Quantifying Metagenomic Strain Associations from Microbiomes with AnpanSemantic proximity Read

ZipStrain Enables Rapid and Precise Strain-Resolved MetagenomicsSemantic proximity Read

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGCSemantic proximity Read

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

StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communitiesSemantic proximity Read

Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s diseaseSemantic proximity Read

Intraspecies associations from strain-rich metagenome samplesSemantic proximity Read

Strain-Level Genetic Heterogeneity and Colonization Dynamics Drive Microbiome Therapeutic EfficacySemantic proximity Read

Bacterial strains in the human gut associate with host physiologySemantic proximity Read

Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatmentSemantic proximity Read

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains.Semantic proximity Read

Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases.Semantic proximity Read