Gut metagenomes in extremely preterm infants, Vienna
64 samples from extremely premature infants in Vienna, Austria, examining gut microbial features linked to perinatal white-matter brain injury, using a case-control/longitudinal cohort design. machine-written summary
64 samples · 132 runs · AT · Infant / toddler · 2026 · 5.38 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 765 sample values (age, birth weight grams, collection date, country, family id, family role, gestational age weeks, health condition) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 128 sample values (location site, probiotic exposure) · PMC11459832 |
| ○ 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 |
health condition: two sequence archives disagree for 7 samples (e.g. healthy_control vs sepsis_or_infection) — 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 |
|---|---|---|---|---|
| SAMN18325546 | health condition | healthy_control (sequence archive) | sepsis_or_infection (sequence archive) | withheld: neither value published |
| SAMN18325648 | health condition | healthy_control (sequence archive) | sepsis_or_infection (sequence archive) | withheld: neither value published |
| SAMN18325657 | health condition | healthy_control (sequence archive) | sepsis_or_infection (sequence archive) | withheld: neither value published |
| SAMN18325675 | health condition | healthy_control (sequence archive) | sepsis_or_infection (sequence archive) | withheld: neither value published |
| SAMN18325929 | health condition | healthy_control (sequence archive) | sepsis_or_infection (sequence archive) | withheld: neither value published |
| SAMN18325931 | health condition | healthy_control (sequence archive) | sepsis_or_infection (sequence archive) | withheld: neither value published |
| SAMN18325939 | health condition | healthy_control (sequence archive) | sepsis_or_infection (sequence archive) | withheld: neither value published |
longitudinaltwins
15 of 32 people sampled more than once (47 samples; median 3, up to 6 per person) · follow-up median 42 d (max 51 d) · median interval between samples 14 d (time from age at collection). Schedule stated by the source: “No fixed protocol stated; 64 stool samples from 32 infants (~2 per infant) collected at varying Days_of_life values (e.g., 11, 14, 15, 27, 29, 55, 56, 57)” (time origin: birth).
Each row is one person (15 shown); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
5 dichorionic/diamniotic twin pairs among 32 extremely premature infants (Twins attribute) · 2 families with 4 sampled people, 7 twin sets.
twin · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 5 linked groups from explicit relations. 32 people in the project overall.
Families (2)
| family | members | samples |
|---|---|---|
| PB34+PB35 | twin×2 | SAMN18325621 · SAMN18325671 · SAMN18325687 · SAMN18325688 · SAMN18325695 · SAMN18325708 · SAMN18325710 · SAMN18325716 |
| PB05+PB06 | twin×2 | SAMN18325929 · SAMN18325931 · SAMN18325939 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 64 | 100% | ||||
| country | 64 | 100% | 64 | |||
| health_condition | 57 | 89% | 57 | |||
| subject_id | 64 | 100% | 64 | |||
| age_at_collection_days | 64 | 100% | 64 | |||
| birth_weight_grams | 64 | 100% | 64 | |||
| collection_date | 64 | 100% | 64 | |||
| detailed_location | 64 | 100% | ||||
| gestational_age_weeks | 64 | 100% | 64 | |||
| health_condition_detail | 64 | 100% | 64 | |||
| location_site | 64 | 100% | 64 | |||
| nec_status | 64 | 100% | 64 | |||
| preterm_status | 64 | 100% | 64 | |||
| probiotic_exposure | 64 | 100% | 64 | |||
| sex | 64 | 100% | 64 | |||
| maternal_antibiotics | 34 | 53% | 34 | |||
| family_id | 17 | 27% | 17 | |||
| family_role | 17 | 27% | 17 |
- Gut microbiota genome features associated with brain injury in extremely premature infants. PMID 39679616 PMC11459832 curated
Archive description
Nanopore sequencing reveals microbial features that are linked to the pathology of perinatal white-matter injury in extremely premature infants. Sequencing was performed at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna under the project ID JMF-2103-08.
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 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 · “Metagenomic signatures of early life brain damage”
- life stage study.description · “injury in extremely premature infants. Sequencing was”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18325440 | age_at_collection_days | 45 | R1 | 0.90 | biosample_attr | 45 |
| SAMN18325440 | birth_weight_grams | 680 | R1 | 0.90 | biosample_attr | 680 |
| SAMN18325440 | collection_date | 2017 | R1 | 0.85 | biosample.attribute:collection_date | 2017 |
| SAMN18325440 | country | AT | R1 | 0.90 | biosample_attr | Austria: Vienna |
| SAMN18325520 | family_id | PB50+PB51 | R1 | 0.85 | biosample.attribute:Twins | Twins: PB50+PB51 |
| SAMN18325520 | family_role | twin | R1 | 0.85 | biosample.attribute:Twins | Twins: PB50+PB51; Type_of_twin: dc/da gemini |
| SAMN18325440 | gestational_age_weeks | 24.57 | R1 | 0.90 | biosample_attr | 24+4 |
| SAMN18325440 | health_condition | other_disease | R1 | 0.60 | sample.attr.is_healthy | is_healthy=no |
| SAMN18325440 | health_condition_detail | connatal infection: yes | R1 | 0.85 | biosample.attribute:connatal_infection | connatal_infection: yes |
| SAMN18325448 | health_condition_detail | is healthy: no | R1 | 0.85 | biosample.attribute:is_healthy | is_healthy: no |
| SAMN18325440 | location_site | General Hospital of Vienna/Medical University of Vienna | R3 | 0.70 | paper.fulltext.methods | General Hospital of Vienna/Medical University of Vienna as part of the PreMiBraIn |
| SAMN18325440 | maternal_antibiotics | yes | R1 | 0.85 | biosample_attr | Standacillin |
| SAMN18325440 | nec_status | no | R1 | 0.85 | biosample_attr | 0 |
| SAMN18325440 | preterm_status | preterm | R1 | 0.85 | biosample_attr | 24+4 |
| SAMN18325440 | probiotic_exposure | yes | R3 | 0.80 | paper.fulltext.methods | every infant received the probiotic preparation Infloran |
| SAMN18325440 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN18325440 | subject_id | PB40 | R1 | 0.85 | biosample_attr | PB40 |
Sequencing
132 runs over 64 samples · mean 3.02 Gbp per run (median 2.22 Gbp, total 399.07 Gbp; 132 runs with a base count) · layout PAIRED 66, SINGLE 66 · platform ILLUMINA 66, OXFORD_NANOPORE 66 · models Illumina NovaSeq 6000 (66), PromethION (66) · 0% of runs with a Sandpiper profile · first public 2026-06-25
Authors (10)
Seki D first · Kirkegaard R · Osvatic J · Hausmann B · Séneca J · Pjevac P · Berger A · J Hall L · Wisgrill L · Berry D last
Downloads
PRJNA1112760.csv.gz (3.5 KB) · parquet (75.2 KB) — all 64 samples, every field with route and confidence · PRJNA1112760_determinations.csv.gz (7.7 KB) — 893 evidence rows