Increase in sampling depth in recent years

Shotgun metagenomic sequencing - human gut 

Average sample size of whole-genome sequencing (WGS) samples of human gut metagenomes deposited at the NCBI short read archive. Median run size of each study was chosen to avoid dominating the results by larger studies.

How deep is enough for metagenomic shotgun sequencing?

It's a balance between sampling depth and number of samples (for a given budget).

• Increasing sampling depth
  led to increased detection of bacterial species and strains at lower abundance level.


• Higher number of samples
  will increase the statistical power to proof that our experimental findings are correct.
  

See also:

 → Coverage depth of a genome

Ni et al., 2013. Scientific Reports
How much metagenomic sequencing is enough to achieve a given goal?

Statistical sample sizes and power calculations
https://www.ncbi.nlm.nih.gov/pubmed/23284876
https://www.ncbi.nlm.nih.gov/pubmed/25819674