Micro-Cm: restrictase-free microbiome-wide chromosome conformation profiling

Metax enables accurate cross-domain taxonomic profiling of metagenomes.

Taxonomic profiling is fundamental to microbiome research, yet achieving high species-level accuracy remains challenging for complex communities that span bacteria, viruses, eukaryotes, and archaea, and these limitations are exacerbated in low-biomass, host-dominated samples. We introduce Metax, a cross-domain taxonomi...

Mobile genetic elements are active and responsive to community context in model microbial consortium

Insertion and excision of genomic islands (GIs), chromosomally-integrated mobile genetic elements (MGEs), are major sources of microbial genome plasticity and can impact gene expression and phenotype of the host organism. GI mobilization also influences microbial communities beyond the host organism as GI excision gene...

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

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...

Plasmid-Resolved Metagenomics for Tracking Horizontal Transfer of Antimicrobial Resistance Determinants Across Microbial Communities

A critical assessment of the long-read assemblers such as hifiasm-meta, metaMDBG, metaFlye, HiCanu, and myloasm are carried out, finding that plasmids carrying AMR have a much wider range of phylogenetic host species than those that do not carry resistance, and thus form well-connected transmission networks across the...

Promises and pitfalls of long-read sequencing for resolving microbial complexity

This review elucidates the impact of LRS across isolate genomics, metagenomics, and multi-omics domains and indicates that LRS is increasingly becoming the method of choice for isolate genomics and metagenomics.

Enriching Microbial Cell-Free DNA in Clinical Metagenomics Using Epigenetic Filters.