Gut microbiome in ASD vs neurotypical children, Hong Kong
Case-control shotgun metagenomics study of 128 stool samples from Hong Kong, comparing gut microbiome composition between children with a neurological/psychiatric condition (ASD) and healthy controls (64 each) to identify fecal bacterial markers. machine-written summary
128 samples · 128 runs · Infant / toddler · 2021 · 20.32 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 512 sample values (collection date, health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12769767 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
country: sequence archive and GMrepo disagree for 128 samples (e.g. HK vs CN) — withheld.
The sources disagree on 128 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 128)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN17126019 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126020 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126021 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126022 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126023 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126024 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126025 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126026 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126027 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126028 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126029 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126030 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126031 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126032 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126033 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126034 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126035 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126036 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126037 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126038 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126039 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126040 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126041 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126042 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126043 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126044 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126045 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126046 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126047 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126048 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126049 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126050 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126051 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126052 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126053 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126054 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126055 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126056 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126057 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMN17126058 | country | HK (sequence archive) | CN (GMrepo) | withheld: neither value published |
Genera, mean relative abundance over 118 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 | 0 | 0% | ||||
| health_condition | 128 | 100% | 128 | |||
| subject_id | 128 | 100% | 128 | |||
| collection_date | 128 | 100% | 128 | |||
| health_condition_detail | 128 | 100% | 128 |
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767 curated
Archive description
Comparison of gut microbiome between ASD children and neurotypical children. We characterized compositional alterations in gut microbiome in ASD and identified novel fecal bacterial markers for ASD.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “data from human stool microorganism Raw sequence”
- body site study.description · “Comparison of gut microbiome between ASD”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “microbiome between ASD children and neurotypical children.”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17126019 | collection_date | 2017-11-03 | R1 | 0.85 | biosample.attribute:collection_date | 2017-11-03 |
| SAMN17126019 | health_condition | neurological_psychiatric | R1 | 0.70 | sample.name_rule:isolate | a001 |
| SAMN17126019 | health_condition_detail | ASD (autism spectrum disorder) case-group sample, per project title/description 'Comparison of gut microbiome between ASD children and neurotypical children' and systematic 'a0xx' isolate/library nami | R1 | 0.70 | sample.name_rule:isolate | a001 |
| SAMN17126019 | subject_id | a001 | R1 | 0.50 | biosample_attr | a001 |
Sequencing
128 runs over 128 samples · mean 20.18 Gbp per run (median 20.32 Gbp, total 2,583.11 Gbp; 128 runs with a base count) · layout PAIRED 128 · platform ILLUMINA 128 · models Illumina NovaSeq 6000 (128) · 92% of runs with a Sandpiper profile · first public 2021-08-30
Authors (14)
Tarracchini C first · Longhi G · Gennaioli E · Muscò A · Rizzo SM · Viappiani A · Vitale SG · Mancabelli L · Lugli GA · Angioni S · Turroni F · van Sinderen D · Milani C · Ventura M last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, country. Share metadata
Downloads
PRJNA686821.csv.gz (5.3 KB) · parquet (77.0 KB) — all 128 samples, every field with route and confidence · PRJNA686821_determinations.csv.gz (6.7 KB) — 512 evidence rows