Species Level Count matrix and Sample Data

Published: 3 November 2021| Version 1 | DOI: 10.17632/rwsvgmpr7y.1
Arun Jose


This was a pilot study to evaluate the gut microbial signature in PAH. This is data from 28 pairs of patients (PAH and non-PAH control) who underwent shotgun metagenomics microbiome sequencing. We identified a significant relative deficiency of Lachnospiracea in PAH as compared to non-PAH control patients. This dataset contains species count matrix and sample metadata.


Steps to reproduce

Metagenomic taxonomic and functional profiles were generated using the bioBakery3 metagenomic workflow for quality control and functional profiling, and using Kraken2 and Bracken for taxonomic profiling. Kneaddata was used to remove reads mapping to the human genome, trim reads where the average of the past four consecutive reads drops below 20, and filter reads <90bp in length. Functional profiling was performed via HUMAnN3 using default settings. Uniref90 gene families were aggregated to MetaCyc and Enzyme Commission pathways via HUMAnN3. Taxonomic profiling was performed by assigning sequence reads to the lowest common ancestor using Kraken2. The confidence interval was set to 0.1, and reads mapped to a custom database built from all complete genomes for bacteria, archaea, viruses, fungi, and the GRCh38.p13 human reference genome available in the RefSeq database as of 7/25/20. Relative abundances were obtained using Bracken with the threshold for species-level classification set to t-10.


University of Cincinnati


Microbiome, Pulmonary Hypertension