Neonatal Jaundice and Gut Microbiome in Xinjiang, China
16 fecal samples from term neonates in Xinjiang, China (11 with pathologic jaundice, 5 matched healthy controls), collected within 48 hours of birth and profiled by shotgun metagenomics in a case-control study. machine-written summary
16 samples · 21 runs · CN · Infant / toddler · 2026 · 9.98 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 64 sample values (collection date, country, health condition, health condition detail) |
| ✓ Abstract / description | 16 sample values (subject id) |
| ✓ Full text | 48 sample values (age, location region, preterm status) · PMC12980891 |
| ○ 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 |
Genera, mean relative abundance over 5 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 | 16 | 100% | ||||
| country | 16 | 100% | 16 | |||
| health_condition | 16 | 100% | 16 | |||
| subject_id | 16 | 100% | 16 | |||
| age_at_collection_days | 16 | 100% | 16 | |||
| collection_date | 16 | 100% | 16 | |||
| detailed_location | 16 | 100% | ||||
| health_condition_detail | 16 | 100% | 16 | |||
| location_region | 16 | 100% | 16 | |||
| preterm_status | 16 | 100% | 16 |
- Neonatal jaundice and the infant gut microbiome: an integrated shotgun metagenomics and bidirectional Mendelian randomization study in Xinjiang. PMID 41834868 PMC12980891 curated
Archive description
We conducted a case–control study in Xinjiang to characterize the neonatal gut microbiome in relation to pathologic neonatal jaundice. Fecal samples were collected non-invasively from term neonates within 48 hours after birth and stored at −80 °C. The cohort included 11 neonates with pathologic jaundice and 5 matched healthy controls. Shotgun metagenomic sequencing was performed on the Illumina NovaSeq 6000 platform using a paired-end 150 bp strategy, generating approximately 8.2–11.6 Gb of raw data per sample. Sequencing reads were quality filtered, and host-derived reads were removed by aligning clean reads to the human reference genome (GRCh38) using Bowtie2 non-host reads were retained for downstream analyses. The resulting dataset enables taxonomic and functional profiling of the early-life gut microbiome, including pathway- and enzyme-family–level comparisons between jaundiced and control neonates, and supports integrative analyses alongside genetic causal inference approaches used in the associated study.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and neonate by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “and the Infant Gut Microbiome: An Integrated”
- body site study.description · “characterize the neonatal gut microbiome in relation”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Jaundice and the Infant Gut Microbiome: An”
- life stage study.title · “Neonatal Jaundice and the”
- life stage study.description · “to characterize the neonatal gut microbiome in”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA121309851 | age_at_collection_days | 2 | R3 | 0.40 | paper.fulltext.methods | collected non-invasively using sterile containers within 48 h |
| SAMEA121309851 | collection_date | 2025-01 | R1 | 0.85 | biosample.attribute:collection date | 2025-01 |
| SAMEA121309851 | country | CN | R1 | 0.90 | biosample_attr | China |
| SAMEA121309851 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:sample_alias | CG.01 |
| SAMEA121309851 | health_condition_detail | CG.01 | R1 | 0.70 | sample.name_rule:sample_alias | CG.01 |
| SAMEA121309851 | location_region | Xinjiang | R3 | 0.70 | paper.fulltext.methods | This study included neonates from the Xinjiang region |
| SAMEA121309851 | preterm_status | term | R3 | 0.80 | paper.fulltext.abstract | case–control study of term infants with pathologic jaundice |
| SAMEA121309851 | subject_id | SAMEA121309851 | R4 | 0.60 | design.one_sample_per_subject:description | The cohort included 11 neonates with pathologic jaundice and 5 matched healthy controls. |
Sequencing
21 runs over 16 samples · mean 9.26 Gbp per run (median 9.22 Gbp, total 194.47 Gbp; 21 runs with a base count) · layout PAIRED 21 · platform ILLUMINA 21 · models Illumina NovaSeq 6000 (21) · 24% of runs with a Sandpiper profile · first public 2026-02-11 – 2026-03-03
Authors (10)
Niu M first · Pan J · Guo Y · Zhang F · Guan H · Yang X · Li H · Xiong H · Zhang Y · Chen Y last
Downloads
PRJEB108038.csv.gz (1.4 KB) · parquet (70.6 KB) — all 16 samples, every field with route and confidence · PRJEB108038_determinations.csv.gz (2.0 KB) — 128 evidence rows