Gut microbiome and Long COVID in US outpatients
944 longitudinal stool samples from USA outpatients tested for SARS-CoV-2 (380 positive, 419 negative), collected at acute and post-acute time points to assess whether gut microbiome composition predicts Long COVID. machine-written summary
944 samples · 944 runs · US · Adult · 2026 · 2.56 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 8,976 sample values (age, collection date, country, health condition, health condition detail, latitude, longitude, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 944 sample values (location site) · PMC13502034 |
| ○ 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 |
longitudinal
145 of 799 people sampled more than once (290 samples; median 2, up to 2 per person) · follow-up median 22 d (max 9 mo) · median interval between samples 22 d (time from collection dates). Schedule stated by the source: “Two stool samples per subject, at week 0-2 and week 3-5 after initial SARS-CoV-2 test; T1 within 31 d of index date, T2 after.” (time origin: initial SARS-CoV-2 test date (index date)).
Each row is one person (36 shown of 145); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 935 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 | 944 | 100% | ||||
| country | 944 | 100% | 944 | |||
| health_condition | 480 | 51% | 480 | |||
| subject_id | 944 | 100% | 944 | |||
| age_at_collection_days | 944 | 100% | 944 | |||
| collection_date | 944 | 100% | 944 | |||
| detailed_location | 944 | 100% | ||||
| health_condition_detail | 944 | 100% | 944 | |||
| latitude | 944 | 100% | 944 | |||
| location_site | 944 | 100% | 944 | |||
| longitude | 944 | 100% | 944 | |||
| sex | 944 | 100% | 944 | |||
| timepoint_label | 944 | 100% | 944 |
- Gut microbiome signatures during acute infection are associated with long COVID. 2026 PMID 42615987 PMC13502034 own_data
Archive description
Longitudinal metagenomic sampling of an outpatient cohort who underwent SARS-CoV-2 respiratory testing prior to enrollment.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.55. Assay shotgun_dna.
- host study.title · “Gut Microbiome Signatures Predict Long COVID”
- body site study.title · “Gut Microbiome Signatures Predict Long COVID”
- life stage study.description · “outpatient cohort who underwent SARS-CoV-2”
- life stage sample.attr.age · “67 (n=337/944)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN44000795 | age_at_collection_days | 19711.0 | R1 | 0.85 | sample.attr.age | 54 |
| SAMN44000795 | collection_date | 2021-09-23 | R1 | 0.90 | biosample.attribute:collection_date | 2021-09-23 |
| SAMN44000795 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN44000795 | health_condition | other_infection | R1 | 0.90 | biosample_attr | Positive |
| SAMN44000795 | health_condition_detail | Positive | R1 | 0.90 | sample.attr.sars_cov2_status | Positive |
| SAMN44000795 | latitude | 38.8000 | R1 | 0.90 | biosample.attribute:lat_lon | 38.80 N 106.53 W |
| SAMN44000795 | location_site | Mayo Clinic multi-site health system | R3 | 0.70 | paper.fulltext.methods | underwent SARS-CoV-2 respiratory testing at Mayo Clinic's multi-site health system |
| SAMN44000795 | longitude | -106.5300 | R1 | 0.90 | biosample.attribute:lat_lon | 38.80 N 106.53 W |
| SAMN44000795 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN44000795 | subject_id | Subject_828 | R1 | 0.85 | sample.attr.subject_id | Subject_828 |
| SAMN44000795 | timepoint_label | T1 | R1 | 0.85 | sample.attr.time_point | T1 |
Sequencing
944 runs over 944 samples · mean 2.58 Gbp per run (median 2.56 Gbp, total 2,436.42 Gbp; 944 runs with a base count) · layout PAIRED 944 · platform ILLUMINA 944 · models Illumina NovaSeq 6000 (944) · 99% of runs with a Sandpiper profile · first public 2026-01-01
Authors (18)
Comba IY first · Mars RAT · Yang L · Dumais M · Chen J · Van Gorp TM · Harrington JJ · Sinnwell JP · Johnson S · Holland LA · Khan AK · Lim ES · Aakre C · Athreya AP · Gerber GK · O'Horo JC · Lazaridis KN · Kashyap PC last
Downloads
PRJNA1167328.csv.gz (30.8 KB) · parquet (114.0 KB) — all 944 samples, every field with route and confidence · PRJNA1167328_determinations.csv.gz (63.7 KB) — 9,920 evidence rows