Metagenomes in autism spectrum disorder children
60 fecal metagenome samples from children, 30 with autism spectrum disorder and 30 healthy controls, compared in a case-control design examining gut bacteriome and phageome differences. machine-written summary
60 samples · 60 runs · CN · Child · 2020 · 8.30 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 120 sample values (health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 120 sample values (collection date, subject id) · PMC10403902, PMC11334437, PMC11954268, PMC12866134, PMC13151442, PMC7524265, PMC7808426 |
| ✓ Supplementary tables | 120 sample values (age, sex) |
| ✓ External resources | 120 sample values (antibiotic exposure, country) · from BugSigDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 54 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 | 60 | 100% | ||||
| country | 60 | 100% | 60 | |||
| health_condition | 60 | 100% | 60 | |||
| subject_id | 60 | 100% | 60 | |||
| age_at_collection_days | 60 | 100% | 60 | |||
| antibiotic_exposure | 60 | 100% | 60 | |||
| collection_date | 60 | 100% | 60 | |||
| health_condition_detail | 60 | 100% | 60 | |||
| sex | 60 | 100% | 60 |
- Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder. 2020 PMID 32312186 PMC7524265 own_data
- Gene variations in autism spectrum disorder are associated with alteration of gut microbiota, metabolites and cytokines. 2021 PMID 33412999 PMC7808426 own_data
- Metagenomics revealed a correlation of gut phageome with autism spectrum disorder. 2023 PMID 37542330 PMC10403902 own_data
- Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. 2024 PMID 39078158 PMC11334437 unsure
- Modeling microbiome-trait associations with taxonomy-adaptive neural networks. 2025 PMID 40158141 PMC11954268 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
Here we report metagenomic sequencing data in gut microbiota of autism spectrum disorders (ASD) compared with healthy volunteers (30 for ASD children and 30 for healthy controls, respectively). The genes changed in autistic subjects involved 1,312,364 analytes that compare to 1,335,835 analytes in healthy controls. The number of taxa in autistic subjects were significantly increased as compared to the healthy controls based on the phylum and genus level (P = 0.001). However, the number of species were significantly decreased in autistic subjects (P = 0.001). Overall design: Microbial DNA from fecal samples [healthy control (n=30), ASD patients (n=30)] were collected. A total amount of 1μg DNA per sample was used as input material for the DNA sample preparations. The DNA sample was fragmented by sonication to a size of 350 bp, then end-polished, A-tailed, and ligated with the full-length adaptor for Illumina sequencing with further PCR amplification. Subject IDs (e.g. A3) in this study represent the same individual with identical id in GSE113690.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “feces metagenome”
- body site study.description · “Microbial DNA from fecal samples”
- life stage study.description · “ASD children and 30 for healthy controls”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08971317 | age_at_collection_days | 1826 | R2 | 0.85 | paper.supp.13099_2023_561_MOESM1_ESM.rar::Additional file 1 (ASD and TD samples).xlsx[sample details!Age] | 5 |
| SAMN08971317 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 3 months |
| SAMN08971317 | collection_date | 2016-05/2017-08 | R3 | 0.70 | paper.fulltext.methods | cohort study from May 2016 to August 2017 |
| SAMN08971317 | country | CN | R2 | 0.60 | external.bugsigdb source | Location of subjects: China |
| SAMN08971317 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | healthy control |
| SAMN08971317 | health_condition_detail | healthy control | R1 | 0.90 | sample.attr.diagnosis | healthy control |
| SAMN08971317 | sex | male | R2 | 0.85 | paper.supp.13099_2023_561_MOESM1_ESM.rar::Additional file 1 (ASD and TD samples).xlsx[sample details!Gender] | Male |
| SAMN08971317 | subject_id | SAMN08971317 | R3 | 0.70 | design.one_sample_per_subject:fulltext | only 30 ASD (3–13 years old, 27 male and 3 female, 30 constipated symptoms) and 30 aged-matched TD |
Sequencing
60 runs over 60 samples · mean 8.46 Gbp per run (median 8.30 Gbp, total 507.45 Gbp; 60 runs with a base count) · layout PAIRED 60 · platform ILLUMINA 60 · models HiSeq X Ten (60) · 90% of runs with a Sandpiper profile · first public 2020-10-03
Authors (51)
Dan Z first · Mao X · Liu Q · Guo M · Zhuang Y · Liu Z · Chen K · Chen J · Xu R · Tang J · Qin L · Gu B · Liu K · Su C · Zhang F · Xia Y · Hu Z · Liu X last · Pei Y · Shahin K first · Soleimani-Delfan A · He Z · Sansonetti P · Collard JM 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
PRJNA451479.csv.gz (2.6 KB) · parquet (72.4 KB) — all 60 samples, every field with route and confidence · PRJNA451479_determinations.csv.gz (3.9 KB) — 480 evidence rows