NICU infant feeding tube microbiota, USA (Davis)
18 samples from feeding tube segments, residual feeding tube contents, and feces of infants/neonates in a NICU in Davis, USA; case series design, with 16S rRNA sequencing and metagenomic sequencing on a small subset. machine-written summary
18 samples · 18 runs · US · Infant / toddler · 2019 · 3.33 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 54 sample values (age, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10269646 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 6 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 | 18 | 100% | ||||
| country | 18 | 100% | 18 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 18 | 100% | 18 | |||
| age_at_collection_days | 18 | 100% | 18 |
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767 curated
Archive description
16S rRNA sequences of feeding tube segments, residual feeding tube contents, and fecal samples. A small subset of samples also have whole metagenomic sequencing data.
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.description · “tube contents, and fecal samples. A small”
- 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 · “Diversity of NICU Infant Feeding Tubes”
- life stage study.title · “Microbial Diversity of NICU Infant Feeding Tubes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09985562 | age_at_collection_days | 14 | R1 | 0.90 | biosample_attr | 14 Days |
| SAMN09985562 | country | US | R1 | 0.90 | biosample_attr | USA: Davis |
| SAMN09985562 | subject_id | 35 | R1 | 0.85 | biosample_attr | 35 |
Sequencing
18 runs over 18 samples · mean 3.26 Gbp per run (median 3.33 Gbp, total 58.75 Gbp; 18 runs with a base count) · layout PAIRED 18 · platform ILLUMINA 18 · models Illumina HiSeq 4000 (18) · 94% of runs with a Sandpiper profile · first public 2019-06-15
Authors (18)
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 · Longhi G · Gennaioli E · Muscò A · Vitale SG · Angioni S · Milani C
Downloads
PRJNA489693.csv.gz (1.4 KB) · parquet (69.5 KB) — all 18 samples, every field with route and confidence · PRJNA489693_determinations.csv.gz (627 B) — 54 evidence rows