Background

This report uses the Sunbeam pipeline to reproduce findings from the 2015 Lewis et al. paper entitled “Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease” (PMID: 26468751). A key finding of this paper was that individuals with Crohn’s disease form two distinct clusters by Multidimensional Scaling (MDS)–the dysbiotic cluster tended to have a high human DNA fraction. Here, we test whether we can reproduce this finding using the originial data submitted to the SRA, and compare three different read-based classification methods available in Sunbeam or as Sunbeam extensions: Kaiju, Kraken, and MetaPhlAn2.

This report was generated by the extension sbx_lewis2015; this link also includes instructions for re-running this analysis from the beginning. It depends on output from two other extensions: sbx_kaiju and sbx_metaphlan.

Results

Below are Nonmetric Multidimensional Scaling plots generated using the vegan package in R. Each point is colored by the cluster in which it was annotated in the Lewis et al metadata, to query whether our results match those published previously. Cluster 2 (red) is the dysbiotic cluster, while cluster 1 (blue) is the healthy-like cluster. Lewis et al used MetaPhlAn to classify reads in the original analysis.

Kraken results

Kaiju results

MetaPhlAn2 results

For these, a few samples came out of MetaPhlAn with 100% unclassified–they are omitted from this plot.

Conclusion

All three classification methods support the conclusions of the original paper.