Metagenomes in children with autism, Moscow, case-control
78 gut metagenome samples from children in Moscow, Russia, comparing those with autism spectrum disorder (55) to healthy controls (23), focusing on CRISPR-Cas system features, in a case-control design. machine-written summary
78 samples · 78 runs · RU · Child · 2019 · 7.97 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 514 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12866134, PMC13151442, PMC7809157, PMC7924848, PMC8955288, PMC9405825, PMC9958793 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 319 sample values (age, antibiotic exposure, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: curatedMetagenomicData and GMrepo disagree for 3 samples (e.g. 730.5 vs 1095.75) — withheld; sex: curatedMetagenomicData and GMrepo disagree for 1 sample (e.g. female vs male) — withheld.
The sources disagree on 4 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 (4)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN13013054 | age | 730.5 (curatedMetagenomicData) | 1095.75 (GMrepo) | withheld: neither value published |
| SAMN13013071 | age | 1095.75 (curatedMetagenomicData) | 1461.0 (GMrepo) | withheld: neither value published |
| SAMN13013073 | age | 1095.75 (curatedMetagenomicData) | 1461.0 (GMrepo) | withheld: neither value published |
| SAMN13013076 | sex | female (curatedMetagenomicData) | male (GMrepo) | withheld: neither value published |
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 | 78 | 100% | ||||
| country | 78 | 100% | 78 | |||
| health_condition | 78 | 100% | 23 | 55 | ||
| subject_id | 0 | 0% | ||||
| collection_date | 78 | 100% | 78 | |||
| detailed_location | 78 | 100% | ||||
| health_condition_detail | 78 | 100% | 23 | 55 | ||
| latitude | 78 | 100% | 78 | |||
| location_locality | 78 | 100% | 78 | |||
| location_region | 78 | 100% | 78 | |||
| longitude | 78 | 100% | 78 | |||
| sex | 77 | 99% | 77 | |||
| age_at_collection_days | 75 | 96% | 75 | |||
| antibiotic_exposure | 57 | 73% | 57 |
- Gut Microbiome-Based Analysis of Lipid A Biosynthesis in Individuals with Autism Spectrum Disorder: An In Silico Evaluation. 2021 PMID 33669978 PMC7924848 own_data
- CRISPR-Cas Systems in Gut Microbiome of Children with Autism Spectrum Disorders. 2022 PMID 35330117 PMC8955288 own_data
- Machine Learning Data Analysis Highlights the Role of Parasutterella and Alloprevotella in Autism Spectrum Disorders. 2022 PMID 36009575 PMC9405825 own_data
- Virulence factor-related gut microbiota genes and immunoglobulin A levels as novel markers for machine learning-based classification of autism spectrum disorder. 2021 PMID 33510860 PMC7809157 unsure
- Gut Microbiota Analysis and In Silico Biomarker Detection of Children with Autism Spectrum Disorder across Cohorts. 2023 PMID 36838256 PMC9958793 unsure
2 more
- Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder. 2026 PMID 41421350 PMC12866134
- Bacterial genomic structural variations in children with autism serve as diagnostic biomarkers. 2026 PMID 41748159 PMC13151442
Archive description
Gut metagenomes were isolated from children with autism spectrum disorder (ASD) and control group. This work was supported by the Russian Science Foundation, project no. 17-15-01488
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.description · “Gut metagenomes were isolated”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “enteric microbiota in children with autism spectrum”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10781783 | age_at_collection_days | 730.5 | R2 | 0.75 | external.cmd source | age: 2; age_unit: Year; age_group: Child |
| SAMN10781783 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN10781783 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN10781783 | country | RU | R1 | 0.90 | sample.attr.geo_loc_name | Russia: Moscow |
| SAMN10781832 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:title | HC_6 |
| SAMN10781783 | health_condition | neurological_psychiatric | R2 | 0.75 | external.cmd source | disease: Autism Spectrum Disorder |
| SAMN10781832 | health_condition_detail | HC | R1 | 0.70 | sample.name_rule:title | HC_6 |
| SAMN10781783 | health_condition_detail | Autism Spectrum Disorder | R2 | 0.75 | external.cmd source | disease: Autism Spectrum Disorder |
| SAMN10781783 | latitude | 55.4500 | R1 | 0.90 | biosample.attribute:lat_lon | 55.45 N 37.37 E |
| SAMN10781783 | location_locality | Moscow | R1 | 0.85 | biosample.attribute:geo_loc_name | Russia: Moscow |
| SAMN10781783 | location_region | Moscow | R1 | 0.85 | biosample.attribute:geo_loc_name | Russia: Moscow |
| SAMN10781783 | longitude | 37.3700 | R1 | 0.90 | biosample.attribute:lat_lon | 55.45 N 37.37 E |
| SAMN10781783 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
Sequencing
78 runs over 78 samples · mean 8.10 Gbp per run (median 7.97 Gbp, total 632.18 Gbp; 78 runs with a base count) · layout PAIRED 78 · platform ILLUMINA 78 · models Illumina HiSeq 4000 (30), Illumina NovaSeq 6000 (28), Illumina HiSeq 2500 (20) · 88% of runs with a Sandpiper profile · first public 2019-01-27 – 2019-10-26
Authors (45)
Wang M first · Doenyas C · Wan J · Zeng S · Cai C · Zhou J · Liu Y · Yin Z · Zhou W last · Zakharevich NV first · Nikitin MS · Kovtun AS · Malov VO · Averina OV · Danilenko VN · Artamonova II last · Wang W first · Fu P last · Chen W first · Wang X · Zhu R · Gao W · Tao L · Yang R · Wei Q · Zhang Y · Gong Y · Zhong H · Huang L · Zhu X · Yang Y · Zhang L · Wan L · Yang G · Li Y · Jiao N · Wang J · Qin H · Zhu L last · Liu W first · Lu Y · Ng SC · Chan FK · Sung JJ · Yu J last
Downloads
PRJNA516054.csv.gz (3.0 KB) · parquet (74.0 KB) — all 78 samples, every field with route and confidence · PRJNA516054_determinations.csv.gz (7.6 KB) — 833 evidence rows