Microbiome in autoimmune/inflammatory disease
49 stool metagenome samples (24 adult, 19 elderly, 6 unknown age) from individuals with autoimmune/inflammatory conditions, part of a cross-sectional study contributing to a multi-study gut microbiome health index analysis. machine-written summary
49 samples · 49 runs · Age unknown · 2020 · 6.09 Gbp / sample · cohort Gut microbial determinants of clinically important
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 184 sample values (age, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC7492273, PMC8439035 |
| ○ 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 |
Genera, mean relative abundance over 43 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 | 43 | 88% | ||||
| country | 0 | 0% | ||||
| health_condition | 49 | 100% | 49 | |||
| subject_id | 0 | 0% | ||||
| health_condition_detail | 49 | 100% | 49 | |||
| age_at_collection_days | 43 | 88% | 43 | |||
| sex | 43 | 88% | 43 |
- A predictive index for health status using species-level gut microbiome profiling. 2020 PMID 32934239 PMC7492273 own_data
- Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis. 2021 PMID 34517888 PMC8439035 unsure
Archive description
Providing insight into ones health status from a gut microbiome sample is an important clinical goal in current human microbiome research. Herein, we introduce Gut Microbiome Health Index (GMHI), a biologically-interpretable mathematical formula for predicting the likelihood of disease irrespective of the diagnosis. GMHI is formulated upon 50 microbial species associated with healthy gut ecosystems. These species are identified through a multi-study, integrative analysis on 4,347 human stool metagenomes from 34 published studies across healthy and 12 different non-healthy conditions, i.e., disease or abnormal bodyweight. When demonstrated on our population-scale meta-dataset, GMHI is the most robust and consistent predictor of disease presence (or absence) compared to alpha-diversity indices. Validation on 679 samples from 9 additional studies results in a balanced accuracy of 73.7% in distinguishing healthy from non-healthy groups. Our findings suggest that gut taxonomic signatures can predict health status, and highlight how data sharing efforts can provide broadly-applicable discoveries.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly and adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host study.title · “Health Status Using Species-level Gut”
- body site study.description · “human stool metagenomes from 34 published studies”
- life stage sample.attr.age · “62 (n=29/49)”
- life stage sample.attr.age · “61 (n=14/49)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN13705424 | age_at_collection_days | 20088.8 | R1 | 0.70 | sample.attr.age | 55 |
| SAMN13705424 | health_condition | autoimmune_inflammatory | R1 | 0.90 | biosample_attr | Rheumatoid arthritis |
| SAMN13705424 | health_condition_detail | Rheumatoid arthritis | R1 | 0.90 | sample.attr.disease | Rheumatoid arthritis |
| SAMN13705424 | sex | female | R1 | 0.90 | sample.attr.sex | female |
Sequencing
49 runs over 49 samples · mean 6.24 Gbp per run (median 6.09 Gbp, total 305.72 Gbp; 49 runs with a base count) · layout PAIRED 49 · platform ILLUMINA 49 · models Illumina HiSeq 4000 (49) · 88% of runs with a Sandpiper profile · first public 2020-08-07
Authors (21)
Gupta VK first · Kim M · Bakshi U · Cunningham KY · Davis JM · Lazaridis KN · Nelson H · Chia N · Sung J last · Hur B · Huang H · Warrington KJ · Taneja V · Myasoedova E · Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last
Downloads
PRJNA598446.csv.gz (2.3 KB) · parquet (70.9 KB) — all 49 samples, every field with route and confidence · PRJNA598446_determinations.csv.gz (1.5 KB) — 184 evidence rows