geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.
Samuel Schwartz MinotKevin C BarryCaroline KasmanJonathan L GolobAmy D WillisPublished in: Genome biology (2021)
Researchers must be able to generate experimentally testable hypotheses from sequencing-based observational microbiome experiments to discover the mechanisms underlying the influence of gut microbes on human health. We describe geneshot, a novel bioinformatics tool for identifying testable hypotheses based on gene-level metagenomic analysis of WGS microbiome data. By applying geneshot to two independent previously published cohorts, we identify microbial genomic islands consistently associated with response to immune checkpoint inhibitor (ICI)-based cancer treatment in culturable type strains. The identified genomic islands are within operons involved in type II secretion, TonB-dependent transport, and bacteriophage growth.
Keyphrases
- copy number
- genome wide
- human health
- risk assessment
- dna methylation
- climate change
- escherichia coli
- microbial community
- genome wide identification
- single cell
- electronic health record
- gene expression
- big data
- cross sectional
- machine learning
- systematic review
- deep learning
- antibiotic resistance genes
- wastewater treatment
- data analysis