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

• Identifying the gene content and functional potential of new strains of a species (strain diversity). Accessory genes, present only in some strains, can encode important functions required for specific environments.
  → 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
  → microbial strain level in Forensic Science
  

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

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

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Read more

Diversity within species: interpreting strains in microbiomes
Thea Van Rossum, Pamela Ferretti, Oleksandr M. Maistrenko & Peer Bork
Nature Reviews Microbiology (2020)