Infant gut microbiota and metal availability, USA cohort
81 samples from US infants and neonates, part of a longitudinal cohort study examining how metal availability (calprotectin, formula vs. breastfeeding) shapes early gut microbial community assembly and succession. machine-written summary
81 samples · 81 runs · US · Infant / toddler · 2024 · 1.78 Gbp / sample · cohort Benitez 2025 USA
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 324 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 132 sample values (age, location site) · PMC11558993, PMC12375414 |
| ○ 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 |
longitudinal
25 of 28 people sampled more than once (78 samples; median 2, up to 5 per person) · follow-up median 30 d (max 30 d) · median interval between samples 7 d (time from age at collection). Schedule stated by the source: “0-4 days, 1 week, 2 weeks, 3 weeks, 1 month” (time origin: birth); stated follow-up 30 d.
Each row is one person (25 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 63 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 | 78 | 96% | ||||
| country | 81 | 100% | 81 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 81 | 100% | 81 | |||
| collection_date | 81 | 100% | 81 | |||
| detailed_location | 81 | 100% | ||||
| location_site | 81 | 100% | 81 | |||
| timepoint_label | 81 | 100% | 81 | |||
| age_at_collection_days | 51 | 63% | 51 |
- Metal availability shapes early life microbial ecology and community succession. PMID 39440978 PMC11558993 curated
- Amino acid competition shapes Acinetobacter baumannii gut carriage. PMID 40763731 PMC12375414 curated
Archive description
The gut microbiota plays a critical role in human health and disease. Microbial community assembly and succession early in life are influenced by numerous factors. In turn, the microbial community is known to influence the host, including immune system development, and has been linked to outcomes later in life. To date, the role of host-mediated nutritional immunity and metal availability in shaping microbial community assembly and succession early in life has not been explored in depth. Using a human infant cohort, we show that the metal chelating protein calprotectin is highly abundant in infants. Taxa previously shown to be successful early colonizers of the infant gut, such as Enterococcus, Enterobacteriaceae, and Bacteroides, are highly resistant to experimental metal starvation in culture. Lactobacillus, meanwhile, is highly susceptible to metal restriction, pointing to a possible mechanism by which host-mediated metal limitation shapes fitness of early colonizing taxa in the infant gut. We further demonstrate that formula-fed infants harbor markedly higher levels of metals in their gastrointestinal tract compared to breastfed infants. Formula-fed infants with high levels of metals harbor distinct microbial community structures compared to breastfed infants, with enrichment in bacteria from the genera Enterococcus, Enterobacter, and Klebsiella, taxa which are relatively resistant to the toxic effect of high metal concentrations. These data highlight a new paradigm in microbial community assembly and suggest an unappreciated role for nutritional immunity and dietary metals in shaping the earliest colonization events in the microbiota.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “The gut microbiota plays a”
- 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 · “Metal availability shapes early life microbial ecology and”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN43048656 | age_at_collection_days | 30 | R3 | 0.40 | paper.fulltext.methods | through 1 month of age (week 4) |
| SAMN43048656 | collection_date | 2016 | R1 | 0.85 | biosample.attribute:collection_date | 2016 |
| SAMN43048656 | country | US | R1 | 0.90 | biosample_attr | USA |
| SAMN43048656 | location_site | Children's Hospital of Philadelphia | R3 | 0.60 | paper.fulltext.results | conducted at the Children's Hospital of Philadelphia |
| SAMN43048656 | subject_id | s607 | R1 | 0.85 | biosample_attr | s607 |
| SAMN43048656 | timepoint_label | 1M | R1 | 0.80 | biosample_attr | 1M |
Sequencing
81 runs over 81 samples · mean 1.55 Gbp per run (median 1.78 Gbp, total 125.20 Gbp; 81 runs with a base count) · layout PAIRED 81 · platform ILLUMINA 81 · models Illumina HiSeq 2500 (81) · 79% of runs with a Sandpiper profile · first public 2024-08-09 – 2024-08-25
Authors (26)
Soto Ocaña J first · Friedman ES · Keenan O · Bayard NU · Ford E · Tanes C · Munneke MJ · Beavers WN · Skaar EP · Bittinger K · Zemel BS · Wu GD · Zackular JP last · Ren X first · Clark RM · Bansah DA · Varner EN · Tiffany CR · Jaswal K · Geary JH · Todd OA · Winkelman JD · Jarrett RN · DePas WH · Behnsen J · Palmer LD last
Downloads
PRJNA1145027.csv.gz (3.4 KB) · parquet (74.0 KB) — all 81 samples, every field with route and confidence · PRJNA1145027_determinations.csv.gz (3.3 KB) — 456 evidence rows