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16s vs shotgun

16S versus Shotgun sequencing

In contrast to 16S, sequencing entire genomes (shotgun sequencing) provides a higher taxonomic resolution and the possibility to extract the functional gene content of each genome.   

   16S  Shotgun
 Costs  inexpensive  high sequencing & computational costs
 Taxonomic resolution
 resolution is limited at genus level
 → 16S tools
 high taxonomic resolution at species and strain level
 → Strain-level tools
 Gene/functional analysis
 assumptions based on known references
 exact estimation of present and absent genes/functions, novel gene detection
 not detectable
 at a certain level detectable, based on current databases and pipelines
 Computational tools  many well developed tool available
 high variation of tools available or under development
 Host contamination
 applicable to high host DNA contamination
 host DNA should be removed to avoid unnecessary sequencing costs