Infant gut microbiota and probiotic intake in Davis, CA
60 stool samples from healthy, exclusively breastfed term infants (vaginal or C-section delivery) in Davis, CA, studying a 21-day probiotic supplementation using a nonrandomized intervention design. machine-written summary
60 samples · 60 runs · US · Infant / toddler · 2018 · 3.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 180 sample values (age, country, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 240 sample values (intervention, location locality, location region, preterm status) · PMC13391359, PMC5717325, PMC6168692, PMC6693174 |
| ✓ Supplementary tables | 120 sample values (feeding mode, probiotic exposure) |
| ✓ External resources | 120 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
Probiotic (live microorganisms; single strain or mixture) design non_randomized_controlled · population healthy_control · Bifidobacterium infantis EVC001 fed daily day 7-28 of life vs no probiotic
“fed B. infantis EVC001 to their infants from day 7 to day” — abstract:29242832 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 53 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 | 60 | 100% | ||||
| country | 60 | 100% | 60 | |||
| health_condition | 60 | 100% | 60 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 60 | 100% | 60 | |||
| detailed_location | 60 | 100% | ||||
| feeding_mode | 60 | 100% | 60 | |||
| health_condition_detail | 60 | 100% | 60 | |||
| intervention | 60 | 100% | 60 | |||
| location_locality | 60 | 100% | 60 | |||
| location_region | 60 | 100% | 60 | |||
| preterm_status | 60 | 100% | 60 | |||
| probiotic_exposure | 60 | 100% | 60 | |||
| timepoint_label | 60 | 100% | 60 |
- Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants. PMID 29242832 PMC5717325 curated
- Reduced colonic mucin degradation in breastfed infants colonized by Bifidobacterium longum subsp. infantis EVC001. PMID 30338216 PMC6168692 curated
- Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria. PMID 31423298 PMC6693174 curated
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082 curated
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488 curated
4 more
- A metagenomic catalog of the early-life human gut virome. PMID 38424077 PMC10904392
- Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life. PMID 38882494 PMC11170968
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291
- Commensal-derived acetylcholine enhances mucosal immune education. PMID 42236946 PMC13391359
Archive description
The purpose of this study is to determine if supplementing healthy term infants delivered by C-section or vaginal delivery who only consume breastmilk with a probiotic for 21 consecutive days increases levels of bacteria in infants' stool.
How this project entered the registry
Classified as human gut / stool / vaginal / urogenital / human milk 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 · “bacteria in infants' stool .”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.description · “by C-section or vaginal delivery who only”
- body site study.description · “who only consume breastmilk with a probiotic”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Infant Microbiota and Probiotic”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07247352 | age_at_collection_days | 60.0 | R1 | 0.85 | biosample.attribute:target_collection_day | 60 |
| SAMN07247352 | country | US | R1 | 0.90 | biosample_attr | USA:Davis,CA |
| SAMN07247352 | feeding_mode | exclusive_breast | R2 | 0.75 | paper.supp.table | Nutrition=breast-fed |
| SAMN07247352 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07247352 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07247352 | intervention | probiotic | R3 | 0.85 | paper.body.Table 1[Supplementation with B. infantis EVC001] | EBGC2P: Yes |
| SAMN07247352 | location_locality | Davis and Sacramento | R3 | 0.70 | paper.fulltext.methods | Davis and Sacramento metropolitan region of Northern California |
| SAMN07247352 | location_region | Northern California | R3 | 0.70 | paper.fulltext.methods | Davis and Sacramento metropolitan region of Northern California |
| SAMN07247352 | preterm_status | term | R3 | 0.70 | paper.fulltext.abstract | healthy term infants delivered by C-section or vaginal |
| SAMN07247352 | probiotic_exposure | yes | R2 | 0.75 | paper.supp.table | Treatment=Probiotic |
| SAMN07247352 | timepoint_label | 60 | R1 | 0.80 | biosample_attr | 60 |
Sequencing
60 runs over 60 samples · mean 3.72 Gbp per run (median 3.39 Gbp, total 222.99 Gbp; 60 runs with a base count) · layout PAIRED 60 · platform ILLUMINA 60 · models Illumina HiSeq 4000 (60) · 88% of runs with a Sandpiper profile · first public 2018-12-07
Authors (79)
Frese SA first · Hutton AA · Contreras LN · Shaw CA · Palumbo MC · Casaburi G · Xu G · Davis JCC · Lebrilla CB · Henrick BM · Freeman SL · Barile D · German JB · Mills DA · Smilowitz JT · Underwood MA last · Karav S first · Duar RM · Vance DP · Mitchell R · Contreras L · Zeng S first · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Stanton C · Wang S last · Lugli GA first · Mancabelli L · Milani C · Fontana F · Tarracchini C · Alessandri G · van Sinderen D · Turroni F · Ventura M last · Li S · Ying J · Wang H · Qu Y · Niu X · Xu X first · Feng Q · Zhang T · Gao Y · Cheng Q · Zhang W · Wu Q · Xu K · Li Y · Nguyen N · Taft DH · Lemay DG · Zhu W · Mao S · Zhang A · Liu J last · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Song D first · Duncan-Lowey B · Khetrapal V · Hamchand R · Deng T · Brown H · Wu A · Martin AL · Bauer KM · Zhao Y · Nguyen MT · Sonnert ND · Leopold SR · Crawford JM · Palm NW last
Downloads
PRJNA390646.csv.gz (2.9 KB) · parquet (72.9 KB) — all 60 samples, every field with route and confidence · PRJNA390646_determinations.csv.gz (6.0 KB) — 660 evidence rows