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PRJNA974858 SRP439118

Ciprofloxacin exposure, gut microbiota, San Francisco adults

Temporal shotgun sequencing of the gut microbiota of healthy adults taking ciprofloxacin

1040 stool samples from 60 healthy adult volunteers given a 5-day ciprofloxacin course and 5 unexposed controls, longitudinally self-collected over 20 weeks in San Francisco, USA, to study antibiotic-driven gut microbiota and resistance evolution. machine-written summary

1,040 samples · 1,040 runs · US · Adult · 2024 · 5.29 Gbp / sample

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Sources

✓Sequence archive 7,280○Abstract / description✓Full text 2,080○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	7,280 sample values (collection date, country, latitude, location locality, location region, longitude, subject id)
○ Abstract / description	read; no usable statement
✓ Full text	2,080 sample values (health condition, health condition detail) · PMC12168174
○ 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

Interventions

intervention — arms not resolved

Antibiotic given as the study intervention (incl. eradication therapy design non_randomized_controlled · population healthy_control · Ciprofloxacin 500mg twice daily for 5 days vs unexposed controls

“took a short course of ciprofloxacin” — bioproject.description (study level; per-sample arms are in the intervention column below)

Samples at a glance

1 sampling locations · 1 country

Age

adult1,040

Condition

healthy_control1,040

Country

US1,040

Body site

primary1,040

Collected 2014–2016

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal

65 of 65 people sampled more than once (1,040 samples; median 16, up to 16 per person) · follow-up median 5 mo (max 5 mo) · median interval between samples 1 d (time from collection dates). Schedule stated by the source: “16 stool samples over 20 weeks, with daily sampling before, during, and immediately after antibiotic exposure”; stated follow-up 5 mo.

Each row is one person (36 shown of 65); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition

Bacteroides 9.3%Roseburia 8.4%Faecalibacterium 8.0%Blautia_A 5.9%Phocaeicola 5.9%Prevotella 3.3%Bifidobacterium 3.2%Fusicatenibacter 2.6%Gemmiger 2.3%Alistipes 2.1%Collinsella 1.9%Lachnospira 1.8%not assigned to a genus 4.9%other genera 40.3%

Genera, mean relative abundance over 948 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	1,040	100%
country	1,040	100%	1,040
health_condition	1,040	100%		1,040
subject_id	1,040	100%	1,040
collection_date	1,040	100%	1,040
detailed_location	1,040	100%
health_condition_detail	1,040	100%		1,040
latitude	1,040	100%	1,040
location_locality	1,040	100%	1,040
location_region	1,040	100%	1,040
longitude	1,040	100%	1,040

Papers (1)

Brief antibiotic use drives human gut bacteria towards low-cost resistance. 2025 PMID 40269166 PMC12168174 own_data

Details

Archive description

Sixty healthy adult volunteers took a short course of ciprofloxacin (500mg, twice daily, for 5 days) and self-collected 16 stool samples over 20 weeks, including daily sampling before, during, and immediately after the antibiotic exposure (960 samples in total). Additionally, five control subjects, who were not exposed to antibiotics, were sampled in a comparable fashion. This project generated deeply sequenced stool-derived DNA libraries to investigate the impacts of antibiotic exposure. Additional metadata tables can be found on https://purl.stanford.edu/rh071jg3250.

How this project entered the registry

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

host run.host_tax_id · “9606”
body site run.scientific_name · “human gut metagenome”
life stage study.description · “Sixty healthy adult volunteers took a short course”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN35299184	collection_date	2014-11-17	R1	0.90	biosample.attribute:collection_date	2014-11-17
SAMN35299184	country	US	R1	0.90	sample.attr.geo_loc_name	USA: San Francisco
SAMN35299184	health_condition	healthy_control	R3	0.70	paper.fulltext.methods	60 heathy adults living in the U.S. took ciprofloxacin
SAMN35299184	health_condition_detail	heathy adults	R3	0.70	paper.fulltext.methods	60 heathy adults living in the U.S. took ciprofloxacin
SAMN35299184	latitude	37.7631	R1	0.90	biosample.attribute:lat_lon	37.7631 N 122.4575 W
SAMN35299184	location_locality	San Francisco	R1	0.85	biosample.attribute:geo_loc_name	USA: San Francisco
SAMN35299184	location_region	California	R1	0.60	biosample.attribute:lat_lon	37.7631 N 122.4575 W
SAMN35299184	longitude	-122.4575	R1	0.90	biosample.attribute:lat_lon	37.7631 N 122.4575 W
SAMN35299184	subject_id	AAK	R1	0.85	sample.attr.host_subject_id	AAK

Sequencing

1,040 runs over 1,040 samples · mean 6.59 Gbp per run (median 5.29 Gbp, total 6,856.14 Gbp; 1,040 runs with a base count) · layout PAIRED 1,040 · platform ILLUMINA 1,040 · models Illumina NovaSeq 6000 (1,040) · 91% of runs with a Sandpiper profile · first public 2024-12-13 – 2024-12-29

Authors (6)

Yaffe E first · Dethlefsen L · Patankar AV · Gui C · Holmes S · Relman DA last

Downloads

PRJNA974858.csv.gz (26.9 KB) · parquet (106.0 KB) — all 1,040 samples, every field with route and confidence · PRJNA974858_determinations.csv.gz (57.9 KB) — 9,360 evidence rows

Samples (1,040 · every field this project has values for · hover a cell for its source)

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