2024-09-19
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21061165
SRA accession
spire_mag_01222133
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
megahit 1.2.9
assembly software
default
binning parameters
metabat 2.12.1
binning software
human digestive system
broad-scale environmental context
EBI-EMG
broker name
2015
collection date
50.85
%
completeness score
checkm2 0.1.3
completeness software
0.1
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run ERR2162212 of study ERP104610.
description
stool
environmental medium
USA
geographic location (country and/or sea)
missing: third party data
DD
geographic location (latitude)
missing: third party data
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
human gut metagenome
isolation_source
human gut
local environmental context
human gut metagenome
metagenomic source
Phocaeicola vulgatus
organism
Pre-clinical mouse models have suggested that the gut microbiome modulates tumor response to checkpoint blockade immunotherapy, however this has not been well-characterized in human cancer patients. Here we examined the oral and gut microbiome of melanoma patients undergoing PD-1 blockade immunotherapy (n=112). Significant differences were observed in the diversity and composition of the patient gut microbiome of responders (R) versus non-responders (NR). Analysis of patient fecal microbiome samples (n=43, 30R, 13NR) showed significantly higher alpha diversity (p<0.01) and relative abundance of Ruminococcaceae bacteria (p<0.01) in R. Metagenomic studies revealed functional differences in gut bacteria in R including enrichment of anabolic pathways. Immune profiling found enhanced systemic and anti-tumor immunity in responding patients with a favorable gut microbiome, as well as in germ-free mice receiving fecal transplants from responding patients. Together, these data have important implications for treatment with immune checkpoint blockade in melanoma.
project name
SAMEA104335953
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 2000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_01222133
title