Gut microbiota in biliary atresia, Beijing case-control
40 fecal samples from Beijing, China, comparing gut microbiota between patients with liver disease (biliary atresia, n=30) and healthy controls (n=10) in a case-control design involving surgical intervention. machine-written summary
40 samples · 40 runs · CN · Infant / toddler · 2021 · 6.35 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 156 sample values (collection date, country, health condition, health condition detail, intervention) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 80 sample values (location locality, location site) · PMC10269646, PMC8273867 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 28 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population liver_disease · Liver transplantation and prior Kasai surgery in biliary atresia
“samples were obtained again 6 months after LT” — abstract:34262484 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 34 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 | 40 | 100% | 40 | |||
| health_condition | 40 | 100% | 26 | 14 | ||
| subject_id | 0 | 0% | ||||
| collection_date | 40 | 100% | 40 | |||
| detailed_location | 40 | 100% | ||||
| health_condition_detail | 40 | 100% | 26 | 14 | ||
| location_locality | 40 | 100% | 40 | |||
| location_site | 40 | 100% | 40 | |||
| intervention | 24 | 60% | 24 |
- Characteristics of Gut Microbiota in Children With Biliary Atresia After Liver Transplantation. PMID 34262484 PMC8273867 curated
- Effects of Previous Kasai Surgery on Gut Microbiota and Bile Acid in Biliary Atresia With End-Stage Liver Disease. PMID 34646837 PMC8502819 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
Archive description
To investigate the gut microbiota in biliary atresia
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids 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 · “The composition of gut microbiota in biliary”
- body site study.description · “To investigate the gut microbiota in biliary”
- body site study.title · “gut microbiota in biliary atresia”
- body site study.description · “gut microbiota in biliary atresia”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN19237332 | collection_date | 2017 | R1 | 0.85 | biosample.attribute:collection_date | 2017 |
| SAMN19237332 | country | CN | R1 | 0.90 | biosample_attr | China:Beijing |
| SAMN19237332 | health_condition | liver_disease | R1 | 0.70 | sample.name_rule:library_names | BA1 |
| SAMN19312594 | health_condition | liver_disease | R2 | 0.75 | external.gmrepo source | phenotype: Biliary Atresia |
| SAMN19237332 | health_condition_detail | BA | R1 | 0.70 | sample.name_rule:library_names | BA1 |
| SAMN19312594 | health_condition_detail | Biliary Atresia | R2 | 0.75 | external.gmrepo source | phenotype: Biliary Atresia |
| SAMN19237348 | intervention | no_intervention | R1 | 0.70 | sample.name_rule:library_names | Con1 |
| SAMN19237332 | location_locality | Beijing | R3 | 0.70 | paper.fulltext.methods | Beijing Friendship Hospital, Capital Medical University |
| SAMN19237332 | location_site | Beijing Friendship Hospital, Capital Medical University | R3 | 0.70 | paper.fulltext.methods | Beijing Friendship Hospital, Capital Medical University |
Sequencing
40 runs over 40 samples · mean 6.72 Gbp per run (median 6.35 Gbp, total 268.98 Gbp; 40 runs with a base count) · layout PAIRED 40 · platform ILLUMINA 40 · models HiSeq X Ten (40) · 85% of runs with a Sandpiper profile · first public 2021-05-20 – 2021-05-24
Authors (20)
Song W first · Sun LY · Zhu ZJ · Wei L · Qu W · Zeng ZG · Yang YS last · Rizzo SM first · Alessandri G · Lugli GA · Fontana F · Tarracchini C · Mancabelli L · Viappiani A · Bianchi MG · Bussolati O · van Sinderen D · Ventura M · Turroni F last · Milani C last
Downloads
PRJNA730640.csv.gz (2.1 KB) · parquet (71.7 KB) — all 40 samples, every field with route and confidence · PRJNA730640_determinations.csv.gz (2.5 KB) — 264 evidence rows