Evaluating the information content of shallow shotgun metagenomics

Benjamin Hillmann, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Daryl M. Gohl, Kenneth B. Beckman, Rob Knight, Dan Knights

Research output: Contribution to journalArticlepeer-review

128 Scopus citations


Although microbial communities are associated with human, environmental, plant, and animal health, there exists no cost-effective method for precisely characterizing species and genes in such communities. While deep whole-metagenome shotgun (WMS) sequencing provides high taxonomic and functional resolution, it is often prohibitively expensive for large-scale studies. The prevailing alternative, 16S rRNA gene amplicon (16S) sequencing, often does not resolve taxonomy past the genus level and provides only moderately accurate predictions of the functional profile; thus, there is currently no widely accepted approach to affordable, high-resolution, taxonomic, and functional microbiome analysis. To address this technology gap, we evaluated the information content of shallow shotgun sequencing with as low as 0.5 million sequences per sample as an alternative to 16S sequencing for large human microbiome studies. We describe a library preparation protocol enabling shallow shotgun sequencing at approximately the same per-sample cost as 16S sequencing. We analyzed multiple real and simulated biological data sets, including two novel human stool samples with ultradeep sequencing of 2.5 billion sequences per sample, and found that shallow shotgun sequencing recovers more-accurate specieslevel taxonomic and functional profiles of the human microbiome than 16S sequencing. We discuss the inherent limitations of shallow shotgun sequencing and note that 16S sequencing remains a valuable and important method for taxonomic profiling of novel environments. Although deep WMS sequencing remains the gold standard for high-resolution microbiome analysis, we recommend that researchers consider shallow shotgun sequencing as a useful alternative to 16S sequencing for large-scale human microbiome research studies where WMS sequencing may be cost-prohibitive.

Original languageEnglish (US)
Article numbere00069
Issue number6
StatePublished - Nov 1 2018

Bibliographical note

Funding Information:
The research leading to these results has received funding from NIH grant R01AI121383 (to D.K.), grant P01DK078669, and in-kind support from Illumina (to R.K.).

Publisher Copyright:
© 2018 Hillmann et al.


  • Human microbiome
  • Metagenomics
  • Microbiome
  • Shotgun metagenomics


Dive into the research topics of 'Evaluating the information content of shallow shotgun metagenomics'. Together they form a unique fingerprint.

Cite this