Gut microbiome in infants at risk of celiac disease
Longitudinal cohort study of 199 fecal samples, mostly from infants, collected in Italy and the USA, examining environmental factors influencing gut microbiome development in infants at risk of celiac disease. machine-written summary
199 samples · 199 runs · IT, US · Infant / toddler · 2024 · 6.10 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,086 sample values (age, collection date, country, health condition, health condition detail, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC7488762, PMC8307711 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
48 of 48 people sampled more than once (199 samples; median 3, up to 9 per person) · follow-up median 18 mo (max 18 mo) · median interval between samples 3 mo (time from age at collection). Schedule stated by the source: “archive time labels: 6_Month, 3_Month, Enroll, 12_Month, 15_Month, 18_Month, 9_Month, 24_Month” (time origin: enrolment).
Each row is one person (20 shown of 48); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 185 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 | 171 | 86% | ||||
| country | 199 | 100% | 199 | |||
| health_condition | 61 | 31% | 61 | |||
| subject_id | 199 | 100% | 199 | |||
| collection_date | 199 | 100% | 199 | |||
| timepoint_label | 199 | 100% | 199 | |||
| age_at_collection_days | 168 | 84% | 168 | |||
| health_condition_detail | 61 | 31% | 61 |
- Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease. PMID 32917289 PMC7488762 curated
- Microbiome signatures of progression toward celiac disease onset in at-risk children in a longitudinal prospective cohort study. PMID 34253606 PMC8307711 curated
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892 curated
1 more
- Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy. PMID 39428758 PMC11497992
Archive description
Environmental factors on development of microbial community in infants at-risk of celiac disease
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “and development of gut microbiome composition and”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “metabolomics profiles in infants at-risk of celiac”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN44425542 | age_at_collection_days | 274 | R1 | 0.85 | sample.title | 9_Month |
| SAMN44425542 | collection_date | 2016 | R1 | 0.85 | biosample.attribute:collection_date | 2016 |
| SAMN44425542 | country | IT | R1 | 0.90 | biosample_attr | Italy |
| SAMN44425599 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:title | Control_1_18_Month |
| SAMN44425599 | health_condition_detail | Control | R1 | 0.70 | sample.name_rule:title | Control_1_18_Month |
| SAMN44425542 | subject_id | Case_1 | R1 | 0.70 | sample.name_rule:run.library_name | Case_1_9_Month |
| SAMN44425666 | subject_id | subject_11 | R1 | 0.70 | sample.name_rule:title | subject_11_3_Month |
| SAMN44425542 | timepoint_label | 9_Month | R1 | 0.70 | sample.title | Case_1_9_Month |
| SAMN44425660 | timepoint_label | Enroll | R1 | 0.70 | sample.name_rule:title | subject_1_Enroll |
Sequencing
199 runs over 199 samples · mean 6.13 Gbp per run (median 6.10 Gbp, total 1,218.90 Gbp; 199 runs with a base count) · layout SINGLE 199 · platform ILLUMINA 199 · models Illumina HiSeq 2500 (199) · 93% of runs with a Sandpiper profile · first public 2024-12-01
Authors (47)
Leonard MM first · Karathia H · Pujolassos M · Troisi J · Valitutti F · Subramanian P · Camhi S · Kenyon V · Colucci A · Serena G · Cucchiara S · Montuori M · Malamisura B · Francavilla R · Elli L · Fanelli B · Colwell R · Hasan N · Zomorrodi AR · Fasano A · CD-GEMM Team last · Trovato CM · Hasan NA · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Rizzo SM first · Viappiani A · Bianchi MG · Bussolati O · van Sinderen D · Minot SS first · Mayer-Blackwell K · Fiore-Gartland A · Johnson A · Self S · Bhatti P · Yao L · Liu L · Sun X · Jinfa Y · Kublin J last
Downloads
PRJNA486782.csv.gz (7.2 KB) · parquet (79.0 KB) — all 199 samples, every field with route and confidence · PRJNA486782_determinations.csv.gz (10.7 KB) — 1,086 evidence rows