Skin/oral/stool metagenomes post-antibiotics, US adults
377 samples from healthy adult volunteers in the USA, collected from skin, oral, and stool sites before, during, and after treatment with doxycycline, cephalexin, or TMP/SMX in a randomized intervention study. machine-written summary
377 samples · 694 runs · US · Adult · 2022 · 1.70 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,638 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 754 sample values (antibiotic exposure, health condition) |
| ○ Full text | read; no usable statement or table · PMC10591041, PMC10609127, PMC11510655, PMC8878148 |
| ○ 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 |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design randomized_controlled_trial · population healthy_control · Doxycycline, cephalexin, or TMP/SMX given to healthy volunteers
“administered four antibiotic regimens [doxycycline” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
8 of 8 people sampled more than once (32 samples; median 4, up to 4 per person) · follow-up median 4 mo (max 5 mo) · median interval between samples 40 d (time from collection dates). Schedule stated by the source: “Skin, oral, and stool samples collected before, during, and up to 1 year after antibiotic treatment (day-labeled, e.g. D0, D14, D28, D56, D224, D336)” (time origin: intervention_start); stated follow-up 12 mo.
Each row is one person (8 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 32 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 377 | 100% | ||||
| country | 377 | 100% | 377 | |||
| health_condition | 377 | 100% | 377 | |||
| subject_id | 377 | 100% | 377 | |||
| antibiotic_exposure | 377 | 100% | 377 | |||
| collection_date | 377 | 100% | 377 | |||
| detailed_location | 377 | 100% | ||||
| latitude | 377 | 100% | 377 | |||
| location_region | 377 | 100% | 377 | |||
| longitude | 377 | 100% | 377 | |||
| timepoint_label | 376 | 100% | 376 |
- Alterations of human skin microbiome and expansion of antimicrobial resistance after systemic antibiotics. 2021 PMID 34936382 PMC8878148 own_data
- Expanded microbiome niches of RAG-deficient patients. 2023 PMID 37757827 PMC10591041 unsure
- A Pipeline for Constructing Reference Genomes for Large Cohort-Specific Metagenome Compression. 2023 PMID 37894218 PMC10609127 unsure
- Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis. 2024 PMID 39458395 PMC11510655 unsure
Archive description
Systemic antibiotics are widely prescribed for infectious as well as cutaneous etiologies, ranging from cellulitis, abscesses, and impetigo, to acne. However, the effects of antibiotics on skin microbial communities are not well understood. Here, we administered four antibiotic regimens [doxycycline (20mg or 100mg twice daily for 56 days), cephalexin (500mg three times daily for 14 days), or trimethoprim/sulfamethoxazole (TMP/SMX, 160/800 mg twice daily for 14 days), n=3-4 for each regimen], which are commonly used in dermatology, to healthy human volunteers. Swabs from multiple skin and oral sites and stool samples were collected before, during, and up to 1 year after antibiotic use, and shotgun metagenomic sequencing performed.
How this project entered the registry
Classified as human skin / oral cavity / gut / stool / vaginal / urogenital shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host study.title · “healthy human subjects”
- body site run.scientific_name · “human skin metagenome”
- body site run.scientific_name · “human oral metagenome”
- body site run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human vaginal metagenome”
- life stage study.description · “administered four antibiotic regimens”
- life stage study.description · “healthy human volunteers”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN21207431 | antibiotic_exposure | yes | R4 | 0.50 | study.description | administered four antibiotic regimens |
| SAMN21207431 | collection_date | 2012-10-02 | R1 | 0.90 | biosample.attribute:collection_date | 2012-10-02 |
| SAMN21207431 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN21207431 | health_condition | healthy_control | R4 | 0.50 | study.title | healthy human subjects |
| SAMN21207431 | latitude | 38.9847 | R1 | 0.90 | biosample.attribute:lat_lon | 38.984652 N 77.094709 W |
| SAMN21207431 | location_region | Maryland | R1 | 0.60 | biosample.attribute:lat_lon | 38.984652 N 77.094709 W |
| SAMN21207431 | longitude | -77.0947 | R1 | 0.90 | biosample.attribute:lat_lon | 38.984652 N 77.094709 W |
| SAMN21207431 | subject_id | Subject1 | R1 | 0.85 | sample.attr.host_subject_id | Subject1 |
| SAMN21207431 | timepoint_label | 0 | R1 | 0.70 | sample.name_rule:alias | Subject1_Ac_D0 |
Sequencing
694 runs over 377 samples · mean 1.30 Gbp per run (median 0.71 Gbp, total 903.93 Gbp; 694 runs with a base count) · layout PAIRED 694 · platform ILLUMINA 694 · models Illumina HiSeq 2500 (654), Illumina NovaSeq 6000 (40) · 79% of runs with a Sandpiper profile · first public 2022-01-13 – 2023-06-05
Authors (38)
Jo JH first · Harkins CP · Schwardt NH · Portillo JA · NISC Comparative Sequencing Program · Zimmerman MD · Carter CL · Hossen MA · Peer CJ · Polley EC · Dartois V · Figg WD · Moutsopoulos NM · Segre JA · Kong HH last · Blaustein RA first · Shen Z · Kashaf SS · Lee-Lin S · Conlan S · Bosticardo M · Delmonte OM · Holmes CJ · Taylor ME · Banania G · Nagao K · Dimitrova D · Kanakry JA · Su H · Holland SM · Bergerson JRE · Freeman AF · Notarangelo LD · Wang L first · Ding R · He S · Wang Q · Zhou Y last
Downloads
PRJNA604820.csv.gz (10.1 KB) · parquet (83.4 KB) — all 377 samples, every field with route and confidence · PRJNA604820_determinations.csv.gz (22.3 KB) — 3,392 evidence rows