Gut metagenome in asthma: case-control study, USA
78 stool metagenome samples from a USA case-control study comparing healthy subjects and those with moderate-to-severe asthma, examining metabolic pathways and antibiotic resistance gene signatures. machine-written summary
78 samples · 78 runs · US · Mixed ages · 2024 · 3.12 Gbp / sample · cohort The gut metagenome harbors metabolic and antibioti
One study deposited as 2 BioProjects (173 catalog samples together): PRJEB56741 · PRJEB59709 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 234 sample values (collection date, country, subject id) |
| ✓ Abstract / description | 78 sample values (health condition detail) |
| ✓ Full text | 156 sample values (location locality, location region) · PMC10981462 |
| ✓ Supplementary tables | 247 sample values (antibiotic exposure, health condition, sex, smoking status) |
| – 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 69 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 | 0 | 0% | ||||
| country | 78 | 100% | 78 | |||
| health_condition | 78 | 100% | 78 | |||
| subject_id | 78 | 100% | 78 | |||
| antibiotic_exposure | 78 | 100% | 78 | |||
| collection_date | 78 | 100% | 78 | |||
| detailed_location | 78 | 100% | ||||
| health_condition_detail | 78 | 100% | 78 | |||
| location_locality | 78 | 100% | 78 | |||
| location_region | 78 | 100% | 78 | |||
| sex | 78 | 100% | 78 | |||
| smoking_status | 13 | 17% | 13 |
- The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma. 2024 PMID 38560624 PMC10981462 own_data
Archive description
Asthma is a common allergic airway disease that develops in association with the human microbiome early in life. Both the composition and function of the infant gut microbiota have been linked to asthma risk, but functional alterations in the gut microbiota of older patients with established asthma remain an important knowledge gap. Here, we performed whole metagenomic shotgun sequencing on 95 stool samples from 59 healthy and 36 subjects with moderate-to-severe asthma to characterize the metagenomes of gut microbiota in children and adults 6 years and older. Mapping of functional orthologs revealed that asthma contributes to 2.9% of the variation in metagenomic content even when accounting for other important clinical demographics. Differential abundance analysis showed an enrichment of long-chain fatty acid (LCFA) metabolism pathways which has been previously implicated in airway smooth muscle and immune responses in asthma. We also observed increased richness of antibiotic resistance genes in people with asthma accompanied by increased abundance of a macrolide resistance marker, ermF. ErmF significantly co-occurred with the Bacteroides fragilis toxin, suggesting a possible relationship between enterotoxigenic B. fragilis, antibiotic resistance, and asthma. Lastly, we found multiple virulence factors and antibiotic resistance gene pairs that co-occurred in both cohorts suggesting that virulence and antibiotic resistance traits are co-selected in the fecal microbiota of asthmatics. Overall, our results show functional alterations in LCFA biosynthesis and increases in antibiotic resistance in the gut microbiota of subjects with moderate-to-severe asthma and could have implications asthma management and treatment.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and adult by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “95 stool samples from 59 healthy”
- life stage study.description · “children and adults 6 years and older”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112253744 | antibiotic_exposure | yes | R2 | 0.80 | paper.supp.xtae010_supplemental_files.zip::Table S1.xlsx[Table S1!Antibiotics used in the past 12 months / ] | Subject=MARS0002; Antibiotics used in the past 12 months /=TRUE |
| SAMEA112253744 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMEA112253744 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA112253744 | health_condition | allergy_or_atopy | R2 | 0.80 | paper.supp.xtae010_supplemental_files.zip::Table S1.xlsx[Table S1!Asthma] | Subject=MARS0002; Asthma=Asthmatic |
| SAMEA112253744 | health_condition_detail | mixed_case_control: healthy controls vs moderate-to-severe asthma | R4 | 0.50 | study.description | 59 healthy and 36 subjects with moderate-to-severe asthma |
| SAMEA112253744 | location_locality | St. Louis | R3 | 0.70 | paper.body.methods_results | MARS participants were recruited from the St. Louis, Missouri area |
| SAMEA112253744 | location_region | Missouri | R3 | 0.70 | paper.body.methods_results | MARS participants were recruited from the St. Louis, Missouri area |
| SAMEA112253744 | sex | female | R2 | 0.80 | paper.supp.xtae010_supplemental_files.zip::Table S1.xlsx[Table S1!Sex] | Subject=MARS0002; Sex=Female |
| SAMEA112253745 | smoking_status | current | R2 | 0.80 | paper.supp.xtae010_supplemental_files.zip::Table S1.xlsx[Table S1!Tobacco Use] | Subject=MARS0003; Tobacco Use=TRUE |
| SAMEA112253744 | subject_id | MARS0002 | R1 | 0.80 | biosample.attribute:alias | alias: MARS0002 |
Sequencing
78 runs over 78 samples · mean 3.57 Gbp per run (median 3.12 Gbp, total 278.30 Gbp; 78 runs with a base count) · layout PAIRED 78 · platform ILLUMINA 78 · models Illumina NovaSeq 6000 (78) · 88% of runs with a Sandpiper profile · first public 2024-12-28
Authors (0)
No author record.
Downloads
PRJEB56741.csv.gz (3.1 KB) · parquet (74.1 KB) — all 78 samples, every field with route and confidence · PRJEB56741_determinations.csv.gz (6.8 KB) — 715 evidence rows