• Identifying the gene content of new strains of a species (strain diversity)
  → explore region specific variations of strain in marine bacterial species
  
  
• In-vivo transcriptional activity of individual strains
  → strain-level transcriptomics in infant gut samples
  
  
• tracking of bacterial strain over different samples
  → transmission from mothers to infants
  → exploring strain replacement and persistent after fecal microbiota transplantation
  

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
→ PanPhlAn