CoreBiome Founders Publish on the Efficacy of Shallow Shotgun Sequencing

The recent mSystems publication details how shallow-depth (0.5 million reads) and moderate-depth (1-2 million reads) shotgun sequencing provides species-level taxonomic and functional data for nearly the same cost as amplicon sequencing. Highlights of the publication include the finding that species-level biomarker discovery could be recovered down to a 0.05% relative abundance with as few as 0.5 million sequences per sample, and that when compared to ultra-deep-sequencing (2.5 billion reads per sample), shallow sequencing recovered 97% to 99% of the correlated species and functional profiles. The publication also details the higher precision and recall associated with exhaustive end-to-end gapped alignment in comparison to k-mer-based approaches, allowing for estimation of strain-level coverage in samples. Of note, Hillmann et al. also discuss that shallow shotgun sequencing is not always a viable replacement for 16S amplicon sequencing for samples types with high host-DNA contamination or for environments harboring bacteria whose genomes are not within reference databases. The full publication can be found here:

Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D. Evaluating the Information Content of Shallow Shotgun Metagenomics. mSystems. 2018;3(6):e00069-18. doi:10.1128/mSystems.00069-18