Infant fecal metagenome in eczema, case-control, Singapore
Case-control study of 12 infant fecal samples from Singapore (9 with location recorded), comparing stool microbiota gene composition between 6 samples from healthy controls and 6 from infants with allergy or atopy, in relation to eczema development. machine-written summary
12 samples · 28 runs · SG · Infant / toddler · 2015 · 19.24 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 56 sample values (age, collection date, country, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10092070, PMC10175488, PMC5648123 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 1 sample values (country) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
country: supplementary table and GMrepo disagree for 7 samples (e.g. MY vs SG) — withheld.
The sources disagree on 7 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 (7)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN03281006 | country | MY (supplementary table) | SG (GMrepo) | withheld: neither value published |
| SAMN03281007 | country | MY (supplementary table) | SG (GMrepo) | withheld: neither value published |
| SAMN03281009 | country | IO (supplementary table) | SG (GMrepo) | withheld: neither value published |
| SAMN03281010 | country | MY (supplementary table) | SG (GMrepo) | withheld: neither value published |
| SAMN03281016 | country | MY (supplementary table) | SG (GMrepo) | withheld: neither value published |
| SAMN03281018 | country | MY (supplementary table) | SG (GMrepo) | withheld: neither value published |
| SAMN03281021 | country | MY (supplementary table) | SG (GMrepo) | withheld: neither value published |
Genera, mean relative abundance over 12 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 | 12 | 100% | ||||
| country | 5 | 42% | 4 | 1 | ||
| health_condition | 12 | 100% | 12 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 12 | 100% | 12 | |||
| health_condition_detail | 12 | 100% | 12 | |||
| sex | 12 | 100% | 12 | |||
| collection_date | 4 | 33% | 4 |
- Immune-modulatory genomic properties differentiate gut microbiota of infants with and without eczema. PMID 29049378 PMC5648123 curated
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082 curated
- Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach. PMID 36123315 PMC10092070 curated
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488 curated
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated
6 more
- Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut. PMID 37259063 PMC10230729
- A metagenomic catalog of the early-life human gut virome. PMID 38424077 PMC10904392
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
Archive description
Eczema is common chronic inflammatory skin disorder with significant impact on child health, and its prevalence is increasing worldwide. It is known that the interaction between gut microbes and the host immune system influences early life development of the immune system. We and others have shown that the composition of the stool microbiota signatures differ between eczema and healthy controls in infancy. The scope of work will include the identification of functional and structural gene composition present in the stools of infants with and without eczema by comparative metagenomics. The proposed study will provide the initial steps towards a comprehensive evaluation of the bacterial gene composition in stool microbiota in relation to development of eczema.
How this project entered the registry
Classified as human gut / stool / skin 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 · “Infant fecal microbiome related to”
- body site study.description · “the interaction between gut microbes and the”
- body site study.description · “common chronic inflammatory skin disorder with significant”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Infant fecal microbiome related”
- life stage study.description · “significant impact on child health, and its”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN03279760 | age_at_collection_days | 30 | R1 | 0.90 | biosample_attr | 1 month |
| SAMN03279760 | collection_date | 2005-09-16 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2005-09-16 |
| SAMN03279760 | country | SG | R1 | 0.90 | biosample_attr | Singapore |
| SAMN03281017 | country | SG | R2 | 0.75 | external.gmrepo source | country: Singapore |
| SAMN03279760 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:title | title: Fecal microbiome of healthy infant |
| SAMN03279760 | health_condition_detail | Fecal microbiome of healthy infant | R1 | 0.85 | biosample.attribute:title | title: Fecal microbiome of healthy infant |
| SAMN03279760 | sex | male | R1 | 0.90 | biosample_attr | male |
Sequencing
28 runs over 12 samples · mean 7.83 Gbp per run (median 6.34 Gbp, total 219.14 Gbp; 28 runs with a base count) · layout PAIRED 23, SINGLE 5 · platform ILLUMINA 23, LS454 5 · models Illumina HiSeq 2500 (12), Illumina MiSeq (11), 454 GS FLX+ (5) · 71% of runs with a Sandpiper profile · first public 2015-09-15
Authors (60)
Oh S first · Yap GC · Hong PY · Huang CH · Aw MM · Shek LP · Liu WT · Lee BW last · Zeng S first · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Stanton C · Wang S last · Fontana F first · Alessandri G · Tarracchini C · Bianchi MG · Rizzo SM · Mancabelli L · Lugli GA · Argentini C · Vergna LM · Anzalone R · Longhi G · Viappiani A · Taurino G · Chiu M · Turroni F · Bussolati O · van Sinderen D · Milani C · Ventura M last · Ormaasen I first · Rudi K · Diep DB · Snipen L last · Li S · Ying J · Wang H · Qu Y · Niu X · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Gennaioli E · Muscò A · Vitale SG · Angioni S
Downloads
PRJNA272371.csv.gz (1.3 KB) · parquet (70.1 KB) — all 12 samples, every field with route and confidence · PRJNA272371_determinations.csv.gz (1.1 KB) — 57 evidence rows