Longitudinal gut metagenomics in ME/CFS adults
479 longitudinal gut metagenome samples from adult and elderly participants with ME/CFS (myalgic encephalomyelitis/chronic fatigue syndrome), profiling gut microbiome diversity and metabolic function alongside immune and clinical data. machine-written summary
479 samples · 479 runs · US · Adult · 2025 · 2.95 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,269 sample values (age, collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 479 sample values (location site) · PMC12416096 |
| ○ 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
156 of 239 people sampled more than once (396 samples; median 3, up to 4 per person) · follow-up median 2.0 y (max 4.0 y) · median interval between samples 12 mo (time from visit codes mapped to the stated schedule).
Each row is one person (36 shown of 156); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 461 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 | 479 | 100% | ||||
| country | 479 | 100% | 479 | |||
| health_condition | 479 | 100% | 479 | |||
| subject_id | 479 | 100% | 479 | |||
| age_at_collection_days | 479 | 100% | 479 | |||
| collection_date | 479 | 100% | 479 | |||
| detailed_location | 479 | 100% | ||||
| health_condition_detail | 479 | 100% | 479 | |||
| latitude | 479 | 100% | 479 | |||
| location_region | 479 | 100% | 479 | |||
| location_site | 479 | 100% | 479 | |||
| longitude | 479 | 100% | 479 | |||
| sex | 479 | 100% | 479 | |||
| timepoint_label | 479 | 100% | 479 |
- AI-driven multi-omics modeling of myalgic encephalomyelitis/chronic fatigue syndrome. 2025 PMID 40715814 PMC12416096 own_data
Archive description
Here, we performed deep longitudinal multi-omics clinical phenotyping of ME/CFS, which included shotgun metagenomics of gut microbiota. Overall, ME/CFS was characterized by reduced gut microbiome diversity and richness, with high heterogeneity, and depletion of microbial BCAA and short-chain fatty acid biosynthesis capacity, alongside increased tryptophan and benzoate metabolism. These microbiome changes drive host-microbiome interactions differently, particularly with mucosal and inflammational immune responses, and plasma lipids. For more details, please check our publication at [TBD].
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Longitudinal Gut Metagenomics profiling of”
- body site study.description · “shotgun metagenomics of gut microbiota. Overall, ME/CFS”
- body site study.description · “immune responses, and plasma lipids. For more”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN46385289 | age_at_collection_days | 23376.0 | R1 | 0.70 | sample.attr.age | 64 |
| SAMN46385289 | collection_date | 2019-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2019-01-01 |
| SAMN46385289 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Utah |
| SAMN46385289 | health_condition | neurological_psychiatric | R1 | 0.85 | biosample.attribute:study_ptorhc | MECFS |
| SAMN46385289 | health_condition_detail | MECFS | R1 | 0.85 | biosample.attribute:study_ptorhc | MECFS |
| SAMN46385289 | latitude | 39.3200 | R1 | 0.90 | biosample.attribute:lat_lon | 39.32 N 111.09 W |
| SAMN46385289 | location_region | Utah | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Utah |
| SAMN46385289 | location_site | Bateman Horne Center | R3 | 0.70 | paper.fulltext.methods | Healthy and patient blood samples were obtained from Bateman Horne Center |
| SAMN46385289 | longitude | -111.0900 | R1 | 0.90 | biosample.attribute:lat_lon | 39.32 N 111.09 W |
| SAMN46385289 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN46385289 | subject_id | SAM000201 | R1 | 0.85 | biosample.attribute:sample_id_tp1 | SAM000201 |
| SAMN46385289 | timepoint_label | tp1 | R1 | 0.85 | sample.attr.timepoints | tp1 |
Sequencing
479 runs over 479 samples · mean 3.55 Gbp per run (median 2.95 Gbp, total 1,702.04 Gbp; 479 runs with a base count) · layout PAIRED 479 · platform ILLUMINA 479 · models Illumina NovaSeq 6000 (479) · 96% of runs with a Sandpiper profile · first public 2025-05-08 – 2025-05-28
Authors (9)
Xiong R first · Aiken E · Caldwell R · Vernon SD · Kozhaya L · Gunter C · Bateman L · Unutmaz D · Oh J last
Downloads
PRJNA1125469.csv.gz (15.1 KB) · parquet (90.2 KB) — all 479 samples, every field with route and confidence · PRJNA1125469_determinations.csv.gz (35.9 KB) — 5,748 evidence rows