Strain-level metagenomics

Identifying and characterizing bacterial strains in metagenomic samples (shotgun sequencing)

What is a bacterial strain?

Family - Genus - Species - Strain

A strain is a low-level taxonomic rank describing genetic variants or subtypes of a species. Theoretically, a strain lineage refers to genetically identical genomes, but practically also closely related variants are considered as the same strain. With an increasing number of mutations or acquisition of new genes (HGT) a strain can evolve in an order to be considered as a different strain.

Tools (shotgun sequencing)

→ PanPhlAn

identifies the gene set of bacterial strains which enables users to functionally characterize the strains present in metagenomic samples.

→ StrainPhlAn

distinquishes strains by identifying sequence variations in hundreds of marker genes per species.

→ MetaMLST

identifies sequence variations in genes traditionally used in web-lab multilocus sequence typing (MLST) in order to place new strains in the context of thousands of well-characterized MLST strain profiles.

→ ConStrains

attemps to identify multiple strains of the same species in the same sample using MetaPhlAn2 marker genes profiles

→ MetaSNV

identifies single nucleotide variants (SNVs) in sequenced samples compared to reference genomes to explore the variation of microbial populations


is a co-assembly and binning approach applied across multiple samples to identifies haplotypes and the corresponding strains

Read more

Diversity within species: interpreting strains in microbiomes

Thea Van Rossum, Pamela Ferretti, Oleksandr M. Maistrenko & Peer Bork

Nature Reviews Microbiology (2020)