Gut metagenomics in ME/CFS vs healthy controls, Utah, USA
Case-control shotgun metagenomic study of 238 gut microbiome samples from adults (and some elderly) in Utah, USA, comparing short-term and long-term ME/CFS patients with healthy controls. machine-written summary
238 samples · 238 runs · US · Adult · 2023 · 2.33 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,142 sample values (age, collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 476 sample values (location locality, location site) · PMC10353054, PMC10764071 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 238 sample values (antibiotic exposure) · from Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 196 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 | 238 | 100% | ||||
| country | 238 | 100% | 238 | |||
| health_condition | 238 | 100% | 238 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 238 | 100% | 238 | |||
| antibiotic_exposure | 238 | 100% | 238 | |||
| collection_date | 238 | 100% | 238 | |||
| detailed_location | 238 | 100% | ||||
| health_condition_detail | 238 | 100% | 238 | |||
| latitude | 238 | 100% | 238 | |||
| location_locality | 238 | 100% | 238 | |||
| location_region | 238 | 100% | 238 | |||
| location_site | 238 | 100% | 238 | |||
| longitude | 238 | 100% | 238 | |||
| sex | 238 | 100% | 238 |
- Multi-'omics of gut microbiome-host interactions in short- and long-term myalgic encephalomyelitis/chronic fatigue syndrome patients. 2023 PMID 36758521 PMC10353054 own_data
- KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome. 2024 PMID 38160303 PMC10764071 own_data
Archive description
Here, we performed deep multi-omics (shotgun metagenomics of gut microbiota and plasma metabolomics) and clinical phenotyping of healthy controls (n=79) vs. two cohorts of ME/CFS patients - those with short-term disease (<4 years, n=75), and patients with long-term disease (>10y, n=79). Overall, ME/CFS was characterized by reduced gut microbiome diversity and richness with high heterogeneity, and depletion of sphingomyelins and short-chain fatty acids in the plasma. We found significant differences when stratifying by cohort short-term ME/CFS was associated with more microbial dysbiosis, but long-term ME/CFS was associated with markedly more severe phenotypic and metabolic abnormalities. We identified a reduction in the gene-coding capacity (and relative abundance of butyrate producers) of microbial butyrate biosynthesis together with a reduction in the plasma concentration of butyrate, especially in the short-term group.
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.description · “(shotgun metagenomics of gut microbiota and plasma”
- body site external_curation.infant_catalog · “body_site_call gut”
- body site study.description · “gut microbiota and plasma metabolomics) and clinical”
- 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 |
|---|---|---|---|---|---|---|
| SAMN35684996 | age_at_collection_days | 23376.0 | R1 | 0.70 | sample.attr.age | 64 |
| SAMN35684996 | antibiotic_exposure | no | R2 | 0.70 | external.meta2db source | antibiotics: FALSE |
| SAMN35684996 | collection_date | 2019-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2019-01-01 |
| SAMN35684996 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Utah |
| SAMN35684996 | health_condition | other_disease | R1 | 0.85 | biosample.attribute:illness_duration | illness_duration: Short |
| SAMN35684996 | health_condition_detail | Short | R1 | 0.85 | biosample.attribute:illness_duration | illness_duration: Short |
| SAMN35684996 | latitude | 39.3200 | R1 | 0.90 | biosample.attribute:lat_lon | 39.32 N 111.09 W |
| SAMN35684996 | location_locality | Salt Lake City | R3 | 0.70 | paper.fulltext.methods | Bateman Horne Center, Salt Lake City, UT |
| SAMN35684996 | location_region | Utah | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Utah |
| SAMN35684996 | location_site | Bateman Horne Center | R3 | 0.70 | paper.fulltext.methods | All subjects were recruited at Bateman Horne Center, Salt Lake City, UT |
| SAMN35684996 | longitude | -111.0900 | R1 | 0.90 | biosample.attribute:lat_lon | 39.32 N 111.09 W |
| SAMN35684996 | sex | female | R1 | 0.90 | sample.attr.gender | female |
Sequencing
238 runs over 238 samples · mean 3.49 Gbp per run (median 2.33 Gbp, total 829.85 Gbp; 238 runs with a base count) · layout PAIRED 238 · platform ILLUMINA 238 · models Illumina NovaSeq 6000 (154), Illumina HiSeq 2500 (84) · 82% of runs with a Sandpiper profile · first public 2023-06-21
Authors (10)
Xiong R first · Gunter C · Fleming E · Vernon SD · Bateman L · Unutmaz D · Oh J last · Sapoval N first · Tanevski M · Treangen TJ last
Downloads
PRJNA878603.csv.gz (7.6 KB) · parquet (80.4 KB) — all 238 samples, every field with route and confidence · PRJNA878603_determinations.csv.gz (19.8 KB) — 2,856 evidence rows