Acknowledgements
We thank M. Meier, J. Serugo, S. Deng, K. Ahsan, J. Hoisington-Lopez and M. Crosby for technical assistance; members of the Genome Technology Access Center at Washington University School of Medicine for Illumina NovaSeq-based generation of faecal DNA shotgun sequencing and microbial RNA-seq datasets; and E. Martin and B. Koebbe for high-performance computing support. This work was supported by the Bill & Melinda Gates Foundation, the National Institutes of Health (DK30292) and the Washington University-Centene Personalized Medicine Initiative. J.I.G. is the recipient of an Agilent Thought Leader Award.