Neonatal gut microbiome and meconium metabolome cohort
191 samples from infants and neonates, including meconium from 88 newborns, profiled by shotgun metagenomics (plus proteome and metabolome) in a longitudinal cohort study of early gut bacterial colonization; no countries reported. machine-written summary
191 samples · 191 runs · US · Infant / toddler · 2019 · 0.78 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 264 sample values (age, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 397 sample values (country, location site, preterm status) · PMC10092070, PMC10175488, PMC10269646, PMC10769871, PMC11322291, PMC11494892, PMC8052915, PMC8518733, PMC9512645, PMC9622858 |
| ✓ Supplementary tables | 440 sample values (age, country, subject id) |
| – 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
88 of 88 people sampled more than once (176 samples; median 2, up to 2 per person) · follow-up median 29 d (max 29 d) · median interval between samples 29 d (time from age at collection). Schedule stated by the source: “Two visits per infant: V01 (~1.4 days after birth) and V02 (~1 month after birth), per library naming pattern” (time origin: birth); stated follow-up 30 d.
Each row is one person (36 shown of 88); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 115 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 | 191 | 100% | ||||
| country | 191 | 100% | 176 | 15 | ||
| health_condition | 0 | 0% | ||||
| subject_id | 176 | 92% | 176 | |||
| detailed_location | 191 | 100% | ||||
| location_site | 191 | 100% | 191 | |||
| preterm_status | 191 | 100% | 191 | |||
| age_at_collection_days | 176 | 92% | 88 | 88 | ||
| timepoint_label | 176 | 92% | 176 |
- Bacterial colonization reprograms the neonatal gut metabolome. PMID 32284564 PMC8052915 curated
- Investigating the infant gut microbiota in developing countries: worldwide metagenomic meta-analysis involving infants living in sub-urban areas of Côte d'Ivoire. PMID 34152069 PMC8518733 curated
- Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach. PMID 36123315 PMC10092070 curated
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium. PMID 36316342 PMC9622858 curated
5 more
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892
Archive description
Microbial colonization and succession in the gut of human infants are linked to health and disease later in life. Although the taxonomic and functional characteristics of the infant microbiome just after birth have been extensively investigated, we are just beginning to decipher its impact on the biochemical environment. To examine this, we characterized the microbiome, proteome, and metabolome of meconium samples from 88 newborn infants. Using shotgun metagenomic DNA sequencing, we found that human DNA accounted for >75% of sequence reads in 52 samples. High levels of human DNA were found preferentially in samples collected within 16 hours of birth. Quantification by 16S qPCR confirmed that absolute bacterial abundance was low in samples with high human DNA. Escherichia coli, Enterococcus faecalis, and Bacteroides vulgatus were the most commonly detected species, and they did not exhibit a strong phylogenetic or pan-genome signature unique to meconium. The number of strains increased with time after birth at a rate of 1.2 strains per day
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 · “reprograms the neonatal gut metabolome”
- body site study.description · “succession in the gut of human infants”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “gut of human infants are linked to”
- life stage study.title · “colonization reprograms the neonatal gut metabolome”
- life stage study.description · “and metabolome of meconium samples from 88”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN12418407 | age_at_collection_days | 30 | R1 | 0.85 | run.library_name | V02 |
| SAMN12418319 | age_at_collection_days | 1 | R2 | 0.75 | paper.supp.table | Age (days)=1.4 |
| SAMN12418319 | country | US | R2 | 0.75 | paper.supp.table | Geographic location=USA |
| SAMN12418495 | country | US | R3 | 0.40 | paper.fulltext.abstract | 88 African American newborns using fecal samples |
| SAMN12418319 | location_site | Children's Hospital of Philadelphia | R3 | 0.70 | paper.fulltext.methods | Children's Hospital of Philadelphia |
| SAMN12418319 | preterm_status | term | R3 | 0.80 | paper.fulltext.results | 88 healthy African-American term infants |
| SAMN12418319 | subject_id | PRJNA557731_s101 | R2 | 0.75 | paper.supp.table | Host ID=PRJNA557731_s101 |
| SAMN12418319 | timepoint_label | V01 | R1 | 0.70 | run.library_name | s101.STL.V01_1.4d |
Sequencing
191 runs over 191 samples · mean 0.94 Gbp per run (median 0.78 Gbp, total 179.15 Gbp; 191 runs with a base count) · layout PAIRED 191 · platform ILLUMINA 191 · models Illumina HiSeq 2500 (191) · 60% of runs with a Sandpiper profile · first public 2019-08-02
Authors (100)
Zhao C · Li Y · Ford E · Friedman ES · Ni J · Kulkarni CV · Cai J · Tian Y · Liu Q · Sarkar D · Chan SHJ · Maranas C · Saha-Shah A · Lund P · Garcia BA · Mattei LM · Gerber JS · Elovitz MA · Kelly A · DeRusso P · Kim D · Hofstaedter CE · Goulian M · Li H · Bushman FD · Fontana F first · Mancabelli L · Lugli GA · Taracchini C · Alessandri G · Longhi G · Anzalone R · Viappiani A · Famo R · Brognan M · Micondo KH · Turroni F · Ventura M · D'Alfonso R · Milani C last · Tarracchini C · Bianchi MG · Rizzo SM · Argentini C · Vergna LM · Taurino G · Chiu M · Bussolati O · van Sinderen D · Hall B first · Levy S · Dufault-Thompson K · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Jiang X last · Rimal B first · Collins SL · Tanes CE · Rocha ER · Granda MA · Solanki S · Hoque NJ · Gentry EC · Koo I · Reilly ER · Hao F · Paudel D · Singh V · Yan T · Kim MS · Bittinger K · Zackular JP · Krausz KW · Desai D · Amin S · Coleman JP · Shah YM · Bisanz JE · Gonzalez FJ · Vanden Heuvel JP · Wu GD · Zemel BS · Dorrestein PC · Weinert EE · Patterson AD last · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last
Downloads
PRJNA557731.csv.gz (6.3 KB) · parquet (78.2 KB) — all 191 samples, every field with route and confidence · PRJNA557731_determinations.csv.gz (9.6 KB) — 1,101 evidence rows