Home › Studies › PRJNA1042925

PRJNA1042925 SRP475251

Gut microbiome in GI cancer immunotherapy response, Beijing

Fecal samples of microsatellite instability-high cancer patients Raw sequence reads

375 fecal samples from gastrointestinal cancer patients in Beijing, China, studied for links between gut microbiota (e.g., Lactobacillus salivarius) and anti-PD-1 immunotherapy response, in a case-control design. machine-written summary

375 samples · 375 runs · CN · Age unknown · 2025 · 12.09 Gbp / sample

ENA BioProject Sample sheet Registry Download Flag an issue

Sources

✓Sequence archive 1,500○Abstract / description✓Full text 1,500○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave

✓ Sequence archive	1,500 sample values (collection date, country, location locality, subject id)
○ Abstract / description	read; no usable statement
✓ Full text	1,500 sample values (antibiotic exposure, health condition, health condition detail, location site) · PMC10829783, PMC13589492
○ Supplementary tables	files read; no table could be matched to the samples
– External resources	not covered by the external resources we ingest
– User contribution	nothing uploaded yet
– Human verified	not yet checked by a person · I checked this project — verify it

Samples at a glance

1 country

Age

unknown375

Condition

other_cancer375

Country

CN375

Body site

primary375

Collected 2018–2022

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal

63 of 109 people sampled more than once (329 samples; median 3, up to 20 per person) · follow-up median 7 mo (max 2.6 y) · median interval between samples 34 d (time from collection dates). Schedule stated by the source: “Stool collected at baseline and every two weeks during treatment, continuing until disease progression (PD)”.

Each row is one person (36 shown of 63); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition

Phocaeicola 13.1%Bacteroides 11.5%Prevotella 6.8%Bifidobacterium 6.3%Faecalibacterium 4.5%Escherichia 4.2%Alistipes 3.0%Roseburia 2.8%Blautia_A 2.2%Ruminococcoides 1.9%Streptococcus 1.7%Mediterraneibacter 1.7%not assigned to a genus 2.8%other genera 37.4%

Genera, mean relative abundance over 363 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage

field	samples	coverage	R1	R3
age_category	0	0%
country	375	100%	375
health_condition	375	100%		375
subject_id	375	100%	375
antibiotic_exposure	375	100%		375
collection_date	375	100%	375
detailed_location	375	100%
health_condition_detail	375	100%		375
location_locality	375	100%	375
location_site	375	100%		375

Papers (2)

Multi-omics of the gut microbial ecosystem in patients with microsatellite-instability-high gastrointestinal cancer resistant to immunotherapy. 2024 PMID 38194971 PMC10829783 own_data
Lactobacillus salivarius potentiates gastrointestinal cancer immunotherapy through its metabolite chenodeoxycholic acid. 2026 PMID 42664954 PMC13589492 own_data

Details

Archive description

The gut microbial ecosystem in the immunotherapy resistance in microsatellite instability-high cancer patients

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.80. Assay shotgun_dna.

host run.host_tax_id · “9606”
body site run.scientific_name · “gut metagenome”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN38354324	antibiotic_exposure	no	R3	0.70	paper.fulltext.methods	received broad-spectrum antibiotics orally or intravenously within one month
SAMN38354324	collection_date	2019-06-25	R1	0.90	biosample.attribute:collection_date	2019-06-25
SAMN38354324	country	CN	R1	0.90	sample.attr.geo_loc_name	China:Beijing
SAMN38354324	health_condition	other_cancer	R3	0.60	paper.fulltext.results	advanced GI cancer with MSI-H/dMMR
SAMN38354324	health_condition_detail	Advanced gastric or colorectal cancer with MSI-H/dMMR	R3	0.60	paper.fulltext.results	advanced GI cancer with MSI-H/dMMR
SAMN38354324	location_locality	Beijing	R1	0.85	biosample.attribute:geo_loc_name	China:Beijing
SAMN38354324	location_site	Beijing Cancer Hospital	R3	0.60	paper.fulltext.results	enrolled at the Beijing Cancer Hospital
SAMN38354324	subject_id	1679347	R1	0.85	sample.attr.host_subject_id	1679347

Sequencing

375 runs over 375 samples · mean 12.57 Gbp per run (median 12.09 Gbp, total 4,712.38 Gbp; 375 runs with a base count) · layout PAIRED 375 · platform ILLUMINA 375 · models Illumina NovaSeq 6000 (375) · 97% of runs with a Sandpiper profile · first public 2025-05-12

Authors (27)

Cheng S first · Han Z · Dai D · Li F · Zhang X · Lu M · Lu Z · Wang X · Zhou J · Li J · Guo X · Song P · Qiu C · Shen W · Zhang Q · Zhu N · Tan Y · Kou Y · Yin X · Shen L · Peng Z last · Zhang B first · Zhang Y · Cai Y · Xie T · Feng Y · Wang Y

Downloads

PRJNA1042925.csv.gz (12.6 KB) · parquet (86.8 KB) — all 375 samples, every field with route and confidence · PRJNA1042925_determinations.csv.gz (19.0 KB) — 3,000 evidence rows

Samples (375 · every field this project has values for · hover a cell for its source)

Loading the sample table…