Microbiome in school-age children, Oregon, cross-sectional
40 gut metagenome samples from early school-aged children in Oregon, USA, examining how psychosocial environment and caregiving relate to the child gut microbiome and behavioral dysregulation symptoms; cross-sectional design. machine-written summary
40 samples · 40 runs · US · Child · 2018 · 2.63 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 239 sample values (age, antibiotic exposure, collection date, country, location region, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 40 sample values (subject id) · PMC12867399, PMC6974564, PMC7445748 |
| ✓ Supplementary tables | 40 sample values (medication) |
| – 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 33 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 | 40 | 100% | ||||
| country | 40 | 100% | 40 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 40 | 100% | 40 | |||
| antibiotic_exposure | 40 | 100% | 40 | |||
| collection_date | 40 | 100% | 40 | |||
| detailed_location | 40 | 100% | ||||
| location_region | 40 | 100% | 40 | |||
| medication | 40 | 100% | 40 | |||
| sex | 40 | 100% | 40 | |||
| age_at_collection_days | 39 | 98% | 39 |
- Gut Feelings Begin in Childhood: the Gut Metagenome Correlates with Early Environment, Caregiving, and Behavior. 2020 PMID 31964729 PMC6974564 own_data
- Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA. 2020 PMID 32839473 PMC7445748 own_data
- Socioeconomic position and the gut microbiota: a narrative synthesis of the association and recommendations. 2026 PMID 41620643 PMC12867399 unsure
Archive description
Childhood is a formative period of behavioral and biological development, which can be modified for better or for worse, by the psychosocial environment. Not only do our own genes and the external environment influence such developmental trajectories, but the community of microbes living in, on, and around our bodies–the microbiome–plays an important role as well. By surveying the gut microbiomes of a cohort of early school-aged children with a range of psychosocial environments and subclinical mental health symptoms, we demonstrated that caregiving behaviors modified the child gut microbiome’s relationship to socioeconomic risk and child behavioral dysregulation symptoms.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site study.title · “human gut metagenome Metagenome”
- body site study.description · “By surveying the gut microbiomes of a”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.description · “Childhood is a formative”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10438914 | age_at_collection_days | 2192.0 | R1 | 0.85 | sample.attr.host_age | 6 |
| SAMN10438914 | antibiotic_exposure | yes | R1 | 0.90 | biosample_attr | 1 |
| SAMN10438914 | collection_date | 2016-04 | R1 | 0.90 | biosample.attribute:collection_date | 2016-04 |
| SAMN10438914 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Oregon |
| SAMN10438914 | location_region | Oregon | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Oregon |
| SAMN10438914 | medication | none_reported | R2 | 0.85 | paper.supp.mBio.02780-19-st001.xlsx[metadata!gut_probiotics7days] | 0 |
| SAMN10438914 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN10438914 | subject_id | SAMN10438914 | R3 | 0.75 | design.one_sample_per_subject:fulltext | we collected stool from 40 children ... This study was cross-sectional |
Sequencing
40 runs over 40 samples · mean 2.78 Gbp per run (median 2.63 Gbp, total 111.08 Gbp; 40 runs with a base count) · layout PAIRED 40 · platform ILLUMINA 40 · models Illumina HiSeq 4000 (40) · 82% of runs with a Sandpiper profile · first public 2018-11-19
Authors (30)
Flannery JE first · Stagaman K · Burns AR · Hickey RJ · Roos LE · Giuliano RJ · Fisher PA · Sharpton TJ last · Duranti S first · Ruiz L · Lugli GA · Tames H · Milani C · Mancabelli L · Mancino W · Longhi G · Carnevali L · Sgoifo A · Margolles A · Ventura M · Ruas-Madiedo P · Turroni F last · Ormaasen I first · Rudi K · Diep DB · Snipen L last · Ratcliff JS first · Kumari M · Varga-Weisz P · O'Gorman R last
Downloads
PRJNA496479.csv.gz (2.1 KB) · parquet (71.6 KB) — all 40 samples, every field with route and confidence · PRJNA496479_determinations.csv.gz (2.6 KB) — 319 evidence rows