Preterm infant gut microbiome and atopic risk, San Diego
Longitudinal cohort of 90 samples from preterm neonates and infants in San Diego, CA, comparing gut/oral/milk microbiome patterns between those with allergy or atopy and healthy controls. machine-written summary
90 samples · 96 runs · US · Infant / toddler · 2022 · 0.29 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,438 sample values (age, antibiotic exposure, birth weight grams, country, delivery mode, family id, family role, feeding mode) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 270 sample values (collection date, location locality, location region) · PMC9018729 |
| ✓ Supplementary tables | 23 sample values (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 |
antibiotic exposure: two sequence archives disagree for 30 samples (e.g. no vs yes) — withheld.
The sources disagree on 30 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (30)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA13943173 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943174 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943180 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943181 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943183 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943184 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943185 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943186 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943190 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943191 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943193 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943194 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943195 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943196 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943198 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943199 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943200 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943201 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943203 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943204 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943205 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943206 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943208 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943209 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943210 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943211 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943238 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943239 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943240 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA13943241 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
longitudinalmother–infanttwins
18 of 18 people sampled more than once (54 samples; median 3, up to 3 per person) · follow-up median 38 d (max 44 d) · median interval between samples 15 d (time from age at collection). Schedule stated by the source: “Gut, oral and breast milk microbiome assessed over time in preterm infants, followed through 2 years of age” (time origin: birth); stated follow-up 2.0 y.
Each row is one person (18 shown); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
13 families: 16 preterm infants and 13 mothers (23 mother's-own breast-milk samples); 3 twin pairs; donor milk/formula samples excluded · 13 families with 29 sampled people (13 with a parent and a child), 6 twin sets.
motherchild · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 13 linked groups from explicit relations. 18 people in the project overall.
Families (13)
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 90 | 100% | ||||
| country | 90 | 100% | 90 | |||
| health_condition | 90 | 100% | 90 | |||
| subject_id | 90 | 100% | 67 | 23 | ||
| age_at_collection_days | 90 | 100% | 90 | |||
| birth_weight_grams | 90 | 100% | 90 | |||
| collection_date | 90 | 100% | 90 | |||
| delivery_mode | 90 | 100% | 90 | |||
| detailed_location | 90 | 100% | ||||
| gestational_age_weeks | 90 | 100% | 90 | |||
| health_condition_detail | 90 | 100% | 90 | |||
| location_locality | 90 | 100% | 90 | |||
| location_region | 90 | 100% | 90 | |||
| maternal_antibiotics | 90 | 100% | 90 | |||
| nec_status | 90 | 100% | 90 | |||
| preterm_status | 90 | 100% | 90 | |||
| sex | 90 | 100% | 90 | |||
| timepoint_label | 90 | 100% | 90 | |||
| feeding_mode | 89 | 99% | 89 | |||
| family_id | 71 | 79% | 71 | |||
| family_role | 71 | 79% | 71 | |||
| antibiotic_exposure | 60 | 67% | 60 |
- The impact of maternal asthma on the preterm infants' gut metabolome and microbiome (MAP study). PMID 35440708 PMC9018729 curated
Archive description
There is increasing recognition that the microbiome may be important in the development of allergic disease. Studies have shown that term infants who later developed asthma showed transient gut microbial dysbiosis during first 3 months of life that was different than healthy infants. Dysbiosis may occur in preterm infants due to their critical condition (i.e. feeding type, antibiotic use, sepsis etc.). However, the specific microbial pattern in allergy-prone preterm infants has not been studied. MAP Study aims to Assess if there is a specific pattern of gut, oral and/or breast milk microbiome over time that is affected by the type of nutrition a preterm baby receives (donor vs maternal vs formula), Assess whether there are patterns in the microbiome associated with the development of allergic sensitization patterns Determine if early patterns of the microbiome and allergic sensitization predict atopy (food allergies, allergic rhinitis, eczema, asthma) by 2 years of age.
How this project entered the registry
Classified as human human milk / gut / stool / oral cavity shotgun DNA metagenome of infant / toddler and neonate and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “The Association Between Milk Feedings in the”
- body site study.description · “gut, oral and/or breast milk microbiome over time”
- body site study.description · “asthma showed transient gut microbial dysbiosis during”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.description · “pattern of gut, oral and/or breast milk”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “shown that term infants who later developed”
- life stage study.title · “Feedings in the Preterm Population, the Microbiome”
- life stage study.description · “may occur in preterm infants due to”
- life stage study.description · “receives (donor vs maternal vs formula), Assess”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA13943167 | age_at_collection_days | 2 | R1 | 0.90 | biosample_attr | 2 |
| SAMEA13943167 | antibiotic_exposure | no | R1 | 0.85 | biosample_attr | no |
| SAMEA13943167 | birth_weight_grams | 1327 | R1 | 0.90 | biosample_attr | 1327 |
| SAMEA13943167 | collection_date | 2019-06/2020-09 | R3 | 0.70 | paper.fulltext.methods | NICUs in San Diego, California, USA from June 2019 to September 2020 |
| SAMEA13943167 | country | US | R1 | 0.90 | biosample_attr | USA:CA:San Diego |
| SAMEA13943167 | delivery_mode | c_section | R1 | 0.90 | biosample_attr | caesarean |
| SAMEA13943167 | family_id | J10 | R1 | 0.85 | biosample.attribute:host_subject_id | host_subject_id: J10 |
| SAMEA13943192 | family_id | twin_mother_2 | R1 | 0.85 | biosample.attribute:twin_mother_id | twin_mother_id: 2 |
| SAMEA13943167 | family_role | child | R1 | 0.85 | biosample.attribute:sample_type+twin_in_study+twin_id | sample_type: meconium; twin_in_study: FALSE; twin_id: not applicable |
| SAMEA13943168 | family_role | mother | R1 | 0.85 | biosample.attribute:sample_type+type_of_milk+type_milk_feed_in_sample | sample_type: breast milk; type_of_milk: Mothers; MBM |
| SAMEA13943167 | feeding_mode | mixed | R1 | 0.85 | biosample_attr | MBM + PE30 |
| SAMEA13943167 | gestational_age_weeks | 31.3 | R1 | 0.90 | biosample_attr | 31.3 |
| SAMEA13943167 | health_condition | allergy_or_atopy | R1 | 0.90 | sample.attr.diagnosis | diagnosis=Asthma |
| SAMEA13943168 | health_condition | allergy_or_atopy | R1 | 0.80 | biosample.attribute:diagnosis | diagnosis: Asthma |
| SAMEA13943167 | health_condition_detail | Asthma | R1 | 0.90 | biosample.attribute:diagnosis | diagnosis: Asthma |
| SAMEA13943167 | location_locality | San Diego | R3 | 0.70 | paper.fulltext.methods | two level III NICUs in San Diego, California, USA |
| SAMEA13943167 | location_region | California | R3 | 0.70 | paper.fulltext.methods | two level III NICUs in San Diego, California, USA |
| SAMEA13943167 | maternal_antibiotics | yes | R1 | 0.85 | biosample_attr | yes |
| SAMEA13943167 | nec_status | no | R1 | 0.85 | biosample_attr | no |
| SAMEA13943167 | preterm_status | preterm | R1 | 0.85 | biosample_attr | 31.3 |
| SAMEA13943167 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMEA13943167 | subject_id | J10 | R1 | 0.85 | biosample_attr | J10 |
| SAMEA13943168 | subject_id | J10_mother | R2 | 0.80 | archive | |
| SAMEA13943167 | timepoint_label | Timepoint 1 | R1 | 0.80 | biosample_attr | Timepoint 1 |
| SAMEA13943186 | timepoint_label | W4 | R1 | 0.70 | sample.name_rule:title | 13241.J14W4.S |
Sequencing
96 runs over 90 samples · mean 0.44 Gbp per run (median 0.29 Gbp, total 42.12 Gbp; 96 runs with a base count) · layout PAIRED 96 · platform ILLUMINA 96 · models Illumina NovaSeq 6000 (96) · 0% of runs with a Sandpiper profile · first public 2022-04-11 – 2022-07-20
Authors (15)
Bai-Tong SS first · Thoemmes MS · Weldon KC · Motazavi D · Kitsen J · Hansen S · Furst A · Geng B · Song SJ · Gilbert JA · Bode L · Dorrestein PC · Knight R · Leibel SA · Leibel SL last
Downloads
PRJEB52147.csv.gz (4.4 KB) · parquet (76.6 KB) — all 90 samples, every field with route and confidence · PRJEB52147_determinations.csv.gz (12.4 KB) — 1,731 evidence rows