Gut microbiome in autistic children vs siblings
194 stool samples from autistic children (ages 2-7) and their typically developing siblings, profiled by 16S rRNA, shotgun metagenomics/metatranscriptomics, and LC-MS metabolomics, in a case-control design. machine-written summary
194 samples · 194 runs · US, CA, FR · Child · 2023 · 1.53 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,459 sample values (age, country, diet, diet detail, family id, health condition, health condition detail, medication) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 164 sample values (country) · PMC10345091, PMC8527694, PMC9554176, PMC9723651 |
| ✓ Supplementary tables | 76 sample values (health condition) |
| – 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 |
age: two sequence archives disagree for 90 samples (e.g. 2343.7 vs 28102.5) — withheld.
The sources disagree on 90 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 90)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN31514442 | age | 2343.7 (sequence archive) | 28102.5 (sequence archive) | withheld: neither value published |
| SAMN31514443 | age | 1643.6 (sequence archive) | 19711.0 (sequence archive) | withheld: neither value published |
| SAMN31514445 | age | 2587.2 (sequence archive) | 31018.0 (sequence archive) | withheld: neither value published |
| SAMN31514451 | age | 2343.7 (sequence archive) | 28102.5 (sequence archive) | withheld: neither value published |
| SAMN31514460 | age | 2100.2 (sequence archive) | 25169.2 (sequence archive) | withheld: neither value published |
| SAMN31514461 | age | 1400.1 (sequence archive) | 16791.8 (sequence archive) | withheld: neither value published |
| SAMN31514466 | age | 791.4 (sequence archive) | 9496.5 (sequence archive) | withheld: neither value published |
| SAMN31514475 | age | 1826.2 (sequence archive) | 21915.0 (sequence archive) | withheld: neither value published |
| SAMN31514478 | age | 1308.8 (sequence archive) | 15704.0 (sequence archive) | withheld: neither value published |
| SAMN31514479 | age | 730.5 (sequence archive) | 8766.0 (sequence archive) | withheld: neither value published |
| SAMN31514480 | age | 2587.2 (sequence archive) | 31018.0 (sequence archive) | withheld: neither value published |
| SAMN31514493 | age | 2100.2 (sequence archive) | 25169.2 (sequence archive) | withheld: neither value published |
| SAMN31514496 | age | 1765.4 (sequence archive) | 21165.0 (sequence archive) | withheld: neither value published |
| SAMN31514499 | age | 2739.4 (sequence archive) | 32868.0 (sequence archive) | withheld: neither value published |
| SAMN31514505 | age | 2100.2 (sequence archive) | 25169.2 (sequence archive) | withheld: neither value published |
| SAMN31514506 | age | 2100.2 (sequence archive) | 25169.2 (sequence archive) | withheld: neither value published |
| SAMN31514518 | age | 2252.4 (sequence archive) | 27004.0 (sequence archive) | withheld: neither value published |
| SAMN31514525 | age | 1552.3 (sequence archive) | 18614.0 (sequence archive) | withheld: neither value published |
| SAMN31514526 | age | 913.1 (sequence archive) | 10957.0 (sequence archive) | withheld: neither value published |
| SAMN31514530 | age | 1095.8 (sequence archive) | 13149.0 (sequence archive) | withheld: neither value published |
| SAMN31514546 | age | 2556.8 (sequence archive) | 30660.0 (sequence archive) | withheld: neither value published |
| SAMN31514560 | age | 730.5 (sequence archive) | 8766.0 (sequence archive) | withheld: neither value published |
| SAMN31514565 | age | 2252.4 (sequence archive) | 27004.0 (sequence archive) | withheld: neither value published |
| SAMN31514566 | age | 2252.4 (sequence archive) | 27004.0 (sequence archive) | withheld: neither value published |
| SAMN31514571 | age | 1521.9 (sequence archive) | 18262.0 (sequence archive) | withheld: neither value published |
| SAMN31514577 | age | 1765.4 (sequence archive) | 21165.0 (sequence archive) | withheld: neither value published |
| SAMN31514578 | age | 1126.2 (sequence archive) | 13504.0 (sequence archive) | withheld: neither value published |
| SAMN31514584 | age | 3287.2 (sequence archive) | 39447.0 (sequence archive) | withheld: neither value published |
| SAMN31514586 | age | 882.7 (sequence archive) | 10584.0 (sequence archive) | withheld: neither value published |
| SAMN31514587 | age | 2739.4 (sequence archive) | 32868.0 (sequence archive) | withheld: neither value published |
| SAMN31514588 | age | 3469.9 (sequence archive) | 41608.0 (sequence archive) | withheld: neither value published |
| SAMN31514589 | age | 1491.4 (sequence archive) | 17872.0 (sequence archive) | withheld: neither value published |
| SAMN31514591 | age | 2161.1 (sequence archive) | 25922.0 (sequence archive) | withheld: neither value published |
| SAMN31514609 | age | 1308.8 (sequence archive) | 15704.0 (sequence archive) | withheld: neither value published |
| SAMN31514610 | age | 2008.9 (sequence archive) | 24090.0 (sequence archive) | withheld: neither value published |
| SAMN31514611 | age | 1217.5 (sequence archive) | 14610.0 (sequence archive) | withheld: neither value published |
| SAMN31514612 | age | 1217.5 (sequence archive) | 14610.0 (sequence archive) | withheld: neither value published |
| SAMN31514613 | age | 2100.2 (sequence archive) | 25169.2 (sequence archive) | withheld: neither value published |
| SAMN31514623 | age | 1217.5 (sequence archive) | 14610.0 (sequence archive) | withheld: neither value published |
| SAMN31514624 | age | 1826.2 (sequence archive) | 21915.0 (sequence archive) | withheld: neither value published |
longitudinal — not resolvedsiblings
7 of 187 people sampled more than once (14 samples; median 2, up to 2 per person).
~96 sibling-pair families (autistic child + typically developing sibling); family_group_id links dyads. · 89 families with 178 sampled people.
member · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 24 of 89 families (one per family structure, then more). 187 people in the project overall.
Families (25 of 89)
Genera, mean relative abundance over 182 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 | 194 | 100% | ||||
| country | 194 | 100% | 30 | 164 | ||
| health_condition | 176 | 91% | 100 | 76 | ||
| subject_id | 194 | 100% | 194 | |||
| diet | 194 | 100% | 194 | |||
| diet_detail | 194 | 100% | 194 | |||
| health_condition_detail | 194 | 100% | 194 | |||
| sex | 194 | 100% | 194 | |||
| family_id | 183 | 94% | 183 | |||
| age_at_collection_days | 104 | 54% | 104 | |||
| medication | 36 | 19% | 36 | |||
| medication_detail | 36 | 19% | 36 |
- Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism. 2023 PMID 37443184 PMC10345091 own_data
- Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups 2022 PMID 36220843 PMC9554176 own_data
- Longitudinal study of stool-associated microbial taxa in sibling pairs with and without autism spectrum disorder 2021 PMID 37938270 PMC9723651 own_data
- Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism 2022 own_data
- Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers 2021 PMID 34666677 PMC8527694 own_data
Archive description
16s rRNA amplicon, shotgun metagenomic, shotgun metatranscriptomic, and LCMS metabolomic profiling of stool samples from autistic children (ages 2-7) and their typically developing siblings.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and adult and elderly 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 · “Multi-omic gut microbiomes of autistic”
- body site study.description · “metabolomic profiling of stool samples from autistic”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “microbiomes of autistic children and their typically”
- life stage sample.attr.age · “63 (n=110/194)”
- life stage sample.attr.age · “69 (n=83/194)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN31514444 | age_at_collection_days | 2130.6 | R1 | 0.90 | sample.attr.age | 70 |
| SAMN31514480 | country | GB | R1 | 0.90 | sample.attr.travel_to_country_biospecimen | United Kingdom of Great Britain and Northern Ireland |
| SAMN31514442 | country | US | R3 | 0.70 | paper.fulltext.methods | from all over the United States |
| SAMN31514442 | diet | omnivore | R1 | 0.90 | biosample.attribute:dietary_regime_biospecimen | Omnivorous diet |
| SAMN31514450 | diet | gluten_free | R1 | 0.90 | biosample.attribute:dietary_restrictions_details_m3_biospecimen | Gluten free, casein free, soy free |
| SAMN31514442 | diet_detail | Omnivorous diet | R1 | 0.90 | biosample.attribute:dietary_regime_biospecimen | Omnivorous diet |
| SAMN31514450 | diet_detail | Gluten free, casein free, soy free | R1 | 0.90 | biosample.attribute:dietary_restrictions_details_m3_biospecimen | Gluten free, casein free, soy free |
| SAMN31514442 | family_id | 62 | R1 | 0.85 | biosample.attribute:Family.group.ID..Biospecimen. | 62 |
| SAMN31514443 | health_condition | healthy_control | R1 | 0.70 | biosample_attr | Control (disease status) |
| SAMN31514442 | health_condition | neurological_psychiatric | R2 | 0.80 | paper.supp.43705_2021_80_MOESM3_ESM.xlsx[quesstionaire_Supplementary_Fil!Host.disease.status] | B18012207: Case (disease status) |
| SAMN31514442 | health_condition_detail | Case (disease status) | R1 | 0.90 | sample.attr.host_disease_status_biospecimen | Case (disease status) |
| SAMN31514443 | medication | other_medication | R1 | 0.85 | biosample.attribute:vitamin_b_complex_supplement_consumption_frequency_biospecimen | vitamin_b_complex_supplement_consumption_frequency_biospecimen: Several times weekly |
| SAMN31514443 | medication_detail | vitamin_b_complex_supplement_consumption_frequency_biospecimen: Several times weekly | R1 | 0.85 | biosample.attribute:vitamin_b_complex_supplement_consumption_frequency_biospecimen | vitamin_b_complex_supplement_consumption_frequency_biospecimen: Several times weekly |
| SAMN31514442 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN31514442 | subject_id | 9413 | R1 | 0.85 | sample.attr.host_id | 9413 |
Sequencing
194 runs over 194 samples · mean 1.51 Gbp per run (median 1.53 Gbp, total 292.13 Gbp; 194 runs with a base count) · layout PAIRED 194 · platform ILLUMINA 194 · models NextSeq 500 (194) · 94% of runs with a Sandpiper profile · first public 2023-07-02
Authors (31)
Chrisman BS first · Paskov KM · Stockham N · Jung JY · Varma M · Washington PY · Tataru C · Iwai S · DeSantis TZ · David M · Wall DP last · West KA first · Yin X · Rutherford EM · Wee B · Choi J · Dunlap KL · Hannibal RL · Hartono W · Lin M · Raack E · Sabino K · Wu Y · David MM · Dabbagh K · Peras M · Rutherford E · Dunlap K · Martin A · Deitzler GE · Phillips A
Downloads
PRJNA895487.csv.gz (7.6 KB) · parquet (81.0 KB) — all 194 samples, every field with route and confidence · PRJNA895487_determinations.csv.gz (15.3 KB) — 1,699 evidence rows