Preterm infant fecal microbiome & early-onset sepsis risk
361 fecal samples from preterm (VLBW) infants in the USA, comparing low-risk vs non-low-risk for early-onset sepsis groups, in a longitudinal cohort study of early microbiome assembly. machine-written summary
361 samples · 361 runs · US · Infant / toddler · 2022 · 0.56 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,971 sample values (age, antibiotic exposure, birth weight grams, collection date, country, gestational age weeks, maternal antibiotics, preterm status) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12677589, PMC9733690 |
| ✓ Supplementary tables | 350 sample values (delivery mode) |
| – 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 (361 samples; median 7, up to 12 per person) · follow-up median 38 d (max 49 d) · median interval between samples 7 d (time from age at collection). Schedule stated by the source: “serial fecal samples, days of life recorded (DOL values including 3,4,5,6,7,8,...,33)” (time origin: birth).
Each row is one person (36 shown of 48); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 288 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 | 361 | 100% | ||||
| country | 361 | 100% | 361 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 361 | 100% | 361 | |||
| age_at_collection_days | 361 | 100% | 361 | |||
| antibiotic_exposure | 361 | 100% | 361 | |||
| birth_weight_grams | 361 | 100% | 361 | |||
| collection_date | 361 | 100% | 361 | |||
| gestational_age_weeks | 361 | 100% | 361 | |||
| maternal_antibiotics | 361 | 100% | 361 | |||
| preterm_status | 361 | 100% | 361 | |||
| sex | 361 | 100% | 361 | |||
| timepoint_label | 361 | 100% | 361 | |||
| delivery_mode | 350 | 97% | 350 |
- Preterm infants at low risk for early-onset sepsis differ in early fecal microbiome assembly. PMID 36474348 PMC9733690 curated
- The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset. PMID 41025564 PMC12677589 curated
Archive description
Antibiotics are administered near-universally to very low birth weight (VLBW) infants after birth for suspected early-onset sepsis (EOS). We previously identified a phenotypic group of VLBW infants whose risk of EOS is low enough to avoid routine antibiotic initiation. In this cohort study we compared 18 infants at low-risk for EOS (LRE), with 30 infants categorized as non-LRE to determine if the lower risk of pathogen transmission at birth is accompanied by differences in microbiome acquisition and development. We did shotgun metagenomic sequencing of 361 fecal samples obtained serially. LRE infants had a higher human-to-bacterial DNA ratio than non-LRE infants in fecal samples on days 1-3 after birth, confirming lower bacterial acquisition among LRE infants. The microbial diversity and composition in samples from days 4-7 differed between the groups with a predominance of Staphylococcus epidermidis in LRE infants and Enterobacteriaceae sp. in non-LRE infants. Compositional differences were congruent with the distribution of virulence factors and antibiotic resistant genes. After the first week, the overall composition was similar, but changes with age in relative abundance for several taxa differed between groups. Late-onset bacteremia occurred predominantly in non-LRE infants (8/9 episodes). Species isolated from the blood culture was detected in the pre-antibiotic fecal samples of the infant for all episodes, though these species were also found in infants without bacteremia. In conclusion, LRE infants present a distinct pattern of microbiome development that is aligned with their low risk for EOS, and warrant further investigation to determine the impact of these difference on later outcomes.
How this project entered the registry
Classified as human gut / stool / skin / blood / tissue / internal fluids 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 · “differ in early fecal microbiome assembly”
- body site study.description · “sequencing of 361 fecal samples obtained serially.”
- body site study.description · “predominance of Staphylococcus epidermidis in LRE infants”
- body site study.description · “isolated from the blood culture was detected”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Preterm infants at low risk”
- life stage study.title · “Preterm infants at low”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN30466095 | age_at_collection_days | 3 | R1 | 0.90 | biosample_attr | 3 |
| SAMN30466095 | antibiotic_exposure | no | R1 | 0.85 | biosample_attr | 0 |
| SAMN30466095 | birth_weight_grams | 1195 | R1 | 0.90 | biosample_attr | 1195 |
| SAMN30466095 | collection_date | 2019 | R1 | 0.85 | biosample.attribute:collection_date | 2019 |
| SAMN30466095 | country | US | R1 | 0.90 | biosample_attr | USA |
| SAMN30466095 | delivery_mode | c_section | R2 | 0.70 | paper.supp.table | Delivery mode=CS |
| SAMN30466095 | gestational_age_weeks | 28.0 | R1 | 0.90 | biosample_attr | 28 |
| SAMN30466095 | maternal_antibiotics | no | R1 | 0.85 | biosample_attr | 0 |
| SAMN30466095 | preterm_status | preterm | R1 | 0.85 | biosample_attr | 28 |
| SAMN30466095 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMN30466095 | subject_id | inf124 | R1 | 0.85 | biosample_attr | inf124 |
| SAMN30466095 | timepoint_label | T1 | R1 | 0.80 | biosample_attr | T1 |
Sequencing
361 runs over 361 samples · mean 0.79 Gbp per run (median 0.56 Gbp, total 286.41 Gbp; 361 runs with a base count) · layout PAIRED 361 · platform ILLUMINA 361 · models Illumina HiSeq 2500 (361) · 80% of runs with a Sandpiper profile · first public 2022-12-06
Authors (33)
Mukhopadhyay S first · Lee JJ · Hartman E · Woodford E · Dhudasia MB · Mattei LM · Daniel SG · Wade KC · Underwood MA · Bittinger K last · Zeng S first · Wang H · Zhang L · Li S · Yuan Y · Tian M · Qu Y · Ying J · Zhou M · Hu Y · Huang J · Zou R · Zhao F · Su X · Liu Q · He Y · Feng J · Huang W · Luo Y · Zhou Z · Shen W · Mu D · Wang S last
Downloads
PRJNA872399.csv.gz (12.1 KB) · parquet (85.8 KB) — all 361 samples, every field with route and confidence · PRJNA872399_determinations.csv.gz (21.0 KB) — 4,321 evidence rows