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PRJNA1291832 SRP601013

Gut metagenomes in melanoma patients on ICB, Melbourne

Shotgun metagenomics data of melanoma patients undergoing ICB

87 fecal shotgun metagenome samples from metastatic melanoma patients in Melbourne, Australia, undergoing immune checkpoint blockade therapy, collected longitudinally at baseline and Week 17. machine-written summary

87 samples · 87 runs · AU · Adult · 2025 · 7.33 Gbp / sample

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Sources

✓Sequence archive 1,044✓Abstract / description 174–Full text–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	1,044 sample values (age, collection date, country, intervention, intervention detail, latitude, location locality, location region)
✓ Abstract / description	174 sample values (health condition, health condition detail)
– Full text	no open-access full text linked
– Supplementary tables	no supplementary tables available (or none open access)
– 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 sampling locations · 1 country

Age

elderly54

adult33

Condition

other_cancer87

Sex

male51

female36

Country

AU87

Body site

primary87

Collected 2018–2022

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal

35 of 39 people sampled more than once (83 samples; median 2, up to 4 per person) · follow-up median 4 mo (max 2.5 y) · median interval between samples 4 mo (time from collection dates).

Each row is one person (35 shown); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition

Bacteroides 11.5%Phocaeicola 9.0%Prevotella 7.0%Alistipes 5.4%Faecalibacterium 4.6%Blautia_A 4.5%Roseburia 3.1%Ruminococcoides 2.1%Parabacteroides 1.7%Gemmiger 1.4%Vescimonas 1.3%Streptococcus 1.3%not assigned to a genus 4.4%other genera 42.8%

Genera, mean relative abundance over 86 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	R4
age_category	87	100%
country	87	100%	87
health_condition	87	100%		87
subject_id	87	100%	87
age_at_collection_days	87	100%	87
collection_date	87	100%	87
detailed_location	87	100%
health_condition_detail	87	100%		87
intervention	87	100%	87
intervention_detail	87	100%	87
latitude	87	100%	87
location_locality	87	100%	87
location_region	87	100%	87
longitude	87	100%	87
sex	87	100%	87
timepoint_label	87	100%	87

Details

Archive description

This project includes shotgun metagenomic sequencing of fecal samples from patients with metastatic melanoma that were undergoing immune checkpoint blockade (ICB) therapy. Samples were collected at baseline and Week 17 after treatment. Shotgun metagenomic libraries for all samples were prepared using the Nextera DNA Library Prep Kit and sequenced on the Illumina NovaSeq 6000 SP platform.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.85. Assay shotgun_dna.

host run.host_tax_id · “9606”
body site study.description · “fecal samples from patients with metastatic melanoma”
life stage study.description · “patients with metastatic melanoma”
life stage sample.attr.host_age · “71 (n=52/87)”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN49979959	age_at_collection_days	25190.0	R1	0.85	sample.attr.host_age	69
SAMN49979959	collection_date	2018-08-20	R1	0.90	biosample.attribute:collection_date	2018-08-20
SAMN49979959	country	AU	R1	0.90	sample.attr.geo_loc_name	Australia: Melbourne
SAMN49979959	health_condition	other_cancer	R4	0.50	study.description	patients with metastatic melanoma
SAMN49979959	health_condition_detail	Metastatic melanoma undergoing ICB therapy	R4	0.50	study.description	patients with metastatic melanoma
SAMN49979959	intervention	no_intervention	R1	0.90	biosample.attribute:sample_timepoint	sample_timepoint: Baseline
SAMN49979959	intervention_detail	pre-ICB baseline sample	R1	0.90	biosample.attribute:sample_timepoint	sample_timepoint: Baseline
SAMN49979959	latitude	-37.8100	R1	0.90	biosample.attribute:lat_lon	37.81 S 144.96 E
SAMN49979959	location_locality	Melbourne	R1	0.85	biosample.attribute:geo_loc_name	Australia: Melbourne
SAMN49979959	location_region	Victoria	R1	0.60	biosample.attribute:lat_lon	37.81 S 144.96 E
SAMN49979959	longitude	144.9600	R1	0.90	biosample.attribute:lat_lon	37.81 S 144.96 E
SAMN49979959	sex	male	R1	0.90	sample.attr.host_sex	male
SAMN49979959	subject_id	CHA003	R1	0.85	sample.attr.host_subject_id	CHA003
SAMN49979959	timepoint_label	Baseline	R1	0.85	sample.attr.sample_timepoint	Baseline

Sequencing

87 runs over 87 samples · mean 7.43 Gbp per run (median 7.33 Gbp, total 646.02 Gbp; 87 runs with a base count) · layout PAIRED 87 · platform ILLUMINA 87 · models Illumina NovaSeq 6000 (87) · 99% of runs with a Sandpiper profile · first public 2025-08-07

Authors (0)

No author record.

Downloads

PRJNA1291832.csv.gz (4.3 KB) · parquet (76.6 KB) — all 87 samples, every field with route and confidence · PRJNA1291832_determinations.csv.gz (9.3 KB) — 1,218 evidence rows

Samples (87 · every field this project has values for · hover a cell for its source)

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