Gut metagenome in treatment-naive MS vs controls, USA
48 fecal samples (24 from treatment-naïve, steroid-free MS patients and 24 from matched healthy machine-written summary
48 samples · 192 runs · US · Adult · 2019 · 8.69 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 432 sample values (age, antibiotic exposure, collection date, country, health condition, health condition detail, intervention, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 48 sample values (location locality) · PMC13519030, PMC6841666, PMC9538590 |
| ○ 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 48 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 | 48 | 100% | ||||
| country | 48 | 100% | 48 | |||
| health_condition | 48 | 100% | 48 | |||
| subject_id | 48 | 100% | 48 | |||
| age_at_collection_days | 48 | 100% | 48 | |||
| antibiotic_exposure | 48 | 100% | 48 | |||
| collection_date | 48 | 100% | 48 | |||
| detailed_location | 48 | 100% | ||||
| health_condition_detail | 48 | 100% | 48 | |||
| intervention | 48 | 100% | 48 | |||
| location_locality | 48 | 100% | 48 | |||
| sex | 48 | 100% | 48 |
- Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course. 2019 PMID 31705027 PMC6841666 own_data
- Untangling the link between the human gut microbiota composition and the severity of the symptoms of the COVID-19 infection. 2022 PMID 36086955 PMC9538590 unsure
- Multikingdom microbiome-based machine learning enables multiple sclerosis diagnosis. 2026 PMID 42218218 PMC13519030 unsure
Archive description
Although the intestinal microbiome has been increasingly implicated in autoimmune diseases, much is unknown about its roles in Multiple Sclerosis (MS). Our aim was to compare the microbiome between treatment-naïve MS subjects early in their disease course and controls, and between Caucasian (CA), Hispanic (HA), and African American (AA) MS subjects. From fecal samples, we performed 16S rRNA V4 sequencing and analysis from 45 MS subjects (15 CA, 16 HA, 14 AA) and 44 matched healthy controls, and whole metagenomic shotgun sequencing from 24 MS subjects (all newly diagnosed, treatment naïve, and steroid-free) and 24 controls. In all three ethnic groups, there was an increased relative abundance of the same single genus, Clostridium, compared to ethnicity-matched controls. Analysis of microbiota networks showed significantly different characteristics between the combined MS cohorts and controls, suggesting global differences not restricted to individual taxa. Metagenomic analysis revealed significant enrichment of individual species within Clostridia as well as particular functional pathways in the MS subjects. The increased relative abundance of Clostridia in all three early MS cohorts compared to controls confirmed by metagenomic analyses provides candidate taxa for further study as biomarkers or agents in MS.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “From fecal samples, we performed”
- life stage study.title · “treatment-naïve MS patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA4888521 | age_at_collection_days | 16791.5 | R1 | 0.85 | sample.attr.host_age | 46 |
| SAMEA4888521 | antibiotic_exposure | no | R1 | 0.85 | biosample.attribute:host_disease_status | MS |
| SAMEA4888521 | collection_date | 2017-01-05 | R1 | 0.90 | biosample.attribute:collection_date | 2017-01-05 |
| SAMEA4888521 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA4888521 | health_condition | neurological_psychiatric | R1 | 0.90 | biosample_attr | MS |
| SAMEA4888521 | health_condition_detail | MS | R1 | 0.90 | sample.attr.host_disease_status | MS |
| SAMEA4888521 | intervention | no_intervention | R1 | 0.85 | biosample.attribute:host_disease_status | MS |
| SAMEA4888521 | location_locality | New York City | R3 | 0.70 | paper.fulltext.methods | All cases and controls were recruited in the same geographic region |
| SAMEA4888521 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMEA4888521 | subject_id | W01 | R1 | 0.85 | sample.attr.host_subject_id | W01 |
Sequencing
192 runs over 48 samples · mean 2.18 Gbp per run (median 2.19 Gbp, total 419.06 Gbp; 192 runs with a base count) · layout PAIRED 192 · platform ILLUMINA 192 · models Illumina HiSeq 4000 (192) · 94% of runs with a Sandpiper profile · first public 2019-12-01
Authors (21)
Ventura RE first · Iizumi T · Battaglia T · Liu M · Perez-Perez GI · Herbert J · Blaser MJ last · Mancabelli L first · Milani C · Fontana F · Lugli GA · Tarracchini C · Viappiani A · Ciociola T · Ticinesi A · Nouvenne A · Meschi T · Turroni F · Ventura M last · Zhu G first · Yang G last
Downloads
PRJEB28543.csv.gz (2.5 KB) · parquet (72.3 KB) — all 48 samples, every field with route and confidence · PRJEB28543_determinations.csv.gz (4.0 KB) — 480 evidence rows