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PRJNA1169175 SRP536720

Gut microbiome in CRC patients on fluoropyrimidine chemo, SF

Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity

255 gut microbiome samples from adult colorectal cancer patients in San Francisco, USA, studying oral fluoropyrimidine chemotherapy (drug therapy intervention) and its effect on gut bacteria and drug toxicity. machine-written summary

255 samples · 255 runs · US · Adult · 2024 · 7.51 Gbp / sample

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Sources
✓Sequence archive 2,725○Abstract / description✓Full text 285○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 archive2,725 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude)
○ Abstract / descriptionread; no usable statement
✓ Full text285 sample values (health condition, health condition detail, location site) · PMC12087798
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention — arms not resolved

Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population colorectal_cancer · Oral fluoropyrimidine (5-FU) chemotherapy in CRC patients; mouse/ex vivo FMT & bacterial colonization

“longitudinal profiling of the human gut microbiome during colorectal cancer (CRC) treatment” — abstract:40238917 (study level; per-sample arms are in the intervention column below)

Samples at a glance
1 sampling locations · 1 country
Age
adult255
Condition
colorectal_cancer255
Country
US255
Body site
primary255
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 8 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 1 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 1 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 8 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 172 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 64 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)this project, 30–100 Gbp: 1 samplesall projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 7.51 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal

41 of 42 people sampled more than once (239 samples; median 6, up to 11 per person) · follow-up median 1 d (max 1 d) · median interval between samples 1 d (time from timepoint labels). Schedule stated by the source: “Stool collected at 7 timepoints spanning pre-treatment through Cycle 1, Cycle 2 Day 1, Cycle 3 Day 1, post-treatment” (time origin: intervention_start); stated follow-up 50 d.

1616: day 016: day 12424: day 024: day 10 d0 d0 d1 d1 d

Each row is one person (2 shown of 41); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition
Blautia_A 7.2%Roseburia 5.3%Bacteroides 5.1%Faecalibacterium 4.9%Phocaeicola 3.5%Ruminococcoides 3.4%Bifidobacterium 3.4%Mediterraneibacter 3.2%Escherichia 3.1%Prevotella 3.0%Streptococcus 2.3%Fusicatenibacter 2.1%not assigned to a genus 4.2%other genera 49.4%

Genera, mean relative abundance over 231 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category255 100%
country255 100%255
health_condition255 100%24015
subject_id240 94%240
collection_date255 100%255
detailed_location255 100%
health_condition_detail255 100%24015
latitude255 100%255
location_locality255 100%255
location_region255 100%255
location_site255 100%255
longitude255 100%255
medication240 94%240
timepoint_label235 92%235
Papers (1)
  • Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity. 2025 PMID 40238917 PMC12087798 own_data
Details
Archive description

Study of the impact of oral fluoropyrimidine chemotherapy on the gut microbiome in colorectal cancer patients, mice, humanized mice, and stool-derived in vitro communities. All experiments are described in the manuscript "Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity."

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site run.scientific_name · “human gut metagenome”
  • life stage study.description · “colorectal cancer patients”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN44102592collection_date2024R10.90biosample.attribute:collection_date2024
SAMN44102592countryUSR10.90sample.attr.geo_loc_nameUSA:San Francisco
SAMN44102592health_conditioncolorectal_cancerR10.70sample.name_rule:library_namesPa1Tx5FUPt19R2_S185
SAMN44106117health_conditioncolorectal_cancerR30.70paper.fulltext.methodsenrolling participants with colorectal adenocarcinoma expected to receive
SAMN44102592health_condition_detailPaR10.70sample.name_rule:library_namesPa1Tx5FUPt19R2_S185
SAMN44106117health_condition_detailColorectal adenocarcinoma patients receiving oral fluoropyrimidine chemotherapy, longitudinal stool collectionR30.70paper.fulltext.methodspatients were treated with oral fluoropyrimidines with longitudinal stool collection
SAMN44102592latitude37.7626R10.90biosample.attribute:lat_lon37.7626 N 122.4587 W
SAMN44102592location_localitySan FranciscoR10.85biosample.attribute:geo_loc_nameUSA:San Francisco
SAMN44102592location_regionCaliforniaR10.60biosample.attribute:lat_lon37.7626 N 122.4587 W
SAMN44102592location_siteUCSFR30.70paper.fulltext.methodsParticipants were recruited and sampled, without any compensation, at UCSF
SAMN44102592longitude-122.4587R10.90biosample.attribute:lat_lon37.7626 N 122.4587 W
SAMN44102592medicationchemotherapyR10.70sample.name_rule:library_namesPa1Tx5FUPt19R2_S185
SAMN44102592subject_id19R10.70sample.name_rule:library_namesPa1Tx5FUPt19R2_S185
SAMN44106271subject_idPt40R10.70sample.name_rule:aliasGO_Pt40_Baseline_S184_L003
SAMN44106124timepoint_labelBaselineR10.70sample.name_rule:library_namesGO_Pt1_Baseline_S46
SAMN44106273timepoint_labelC1D7R10.70sample.name_rule:TITLEGO_Pt40_C1D7_duplicate_S93_L002
Sequencing

255 runs over 255 samples · mean 8.04 Gbp per run (median 7.51 Gbp, total 2,050.36 Gbp; 255 runs with a base count) · layout PAIRED 255 · platform ILLUMINA 255 · models Illumina NovaSeq 6000 (255) · 91% of runs with a Sandpiper profile · first public 2024-12-01

Authors (19)

Trepka KR first · Kidder WA · Kyaw TS · Halsey T · Olson CA · Ortega EF · Noecker C · Upadhyay V · Stanfield D · Steiding P · Guthrie BGH · Spanogiannopoulos P · Dumlao D · Turnbaugh JA · Stachler MD · Van Blarigan EL · Venook AP · Atreya CE · Turnbaugh PJ last

Downloads

PRJNA1169175.csv.gz (7.5 KB) · parquet (80.2 KB) — all 255 samples, every field with route and confidence · PRJNA1169175_determinations.csv.gz (23.1 KB) — 3,010 evidence rows

Samples (255 · every field this project has values for · hover a cell for its source)
Loading the sample table…