The bioBakery help forum

Trouble downloading data


The integrated portal ( gives us an error message when trying to download the IBDMBD 16S abundance matrices from stool (.tsv files). Can you please assist us in how to proceed?


Hi @jessicabaker ,

Apologies for the delay. Can you redirect this issue to the NIH Human Microbiome Project - Feedback page please?
If you want to proceed with HMP2 data, you can refer to the page here: Results | IBDMDB.


Hi @sagunmaharjann,

Thank you for the response. We have redirected our data portal issue to the link provided above.

In terms of the HMP2 data, we are interested in16S from stool, bacterial metabolomics and clinical outcomes (e.g., flares). We downloaded the 16S stool data (HMP2_Pilot) and the clinical data (HMP2 Metadata). However, we were only able to identify around 11-12 patients with 16S stool data and clinical outcomes (i.e., SES-CD score, CRP, etc). This seems low compared to previous reports (i.e., Lloyd-Price et al. Nature 2019)? The ‘HMP2’ 16S file appears to only have 16S from biopsies. Are there more patients with stool 16S and clinical outcomes?