Infant gut microbiome, 5-HMO formula vs control vs breastfed
1,110 stool samples from neonates and infants in Spain, Germany, and Italy, from a randomized trial comparing 5-HMO-supplemented formula, control formula, and breastfeeding. machine-written summary
1,110 samples · 1,110 runs · ES, DE, IT · Infant / toddler · 2023 · 5.44 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 11,841 sample values (age, collection date, country, delivery mode, feeding mode, health condition, health condition detail, hmo supplementation) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10383262 |
| ○ 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 |
intervention — arms not resolved
Prebiotic / dietary fibre supplement design randomized_controlled_trial · population healthy_control · 5HMO-mix supplemented formula vs control formula vs breastfed
“infant formula supplemented with five different HMOs” — abstract:37513505 (study level; per-sample arms are in the intervention column below)
longitudinal
222 of 246 people sampled more than once (1,086 samples; median 5, up to 7 per person) · follow-up median 3 mo (max 6 mo) · median interval between samples 28 d (time from age at collection). Schedule stated by the source: “Week 1, Week 2, Week 4, Week 8, Week 12, Week 16 (and 6 months)”.
Each row is one person (36 shown of 222); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 1,011 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 | 1,110 | 100% | ||||
| country | 1,110 | 100% | 1,110 | |||
| health_condition | 1,110 | 100% | 1,110 | |||
| subject_id | 1,110 | 100% | 1,110 | |||
| age_at_collection_days | 1,110 | 100% | 1,110 | |||
| delivery_mode | 1,110 | 100% | 1,110 | |||
| feeding_mode | 1,110 | 100% | 1,110 | |||
| health_condition_detail | 1,110 | 100% | 1,110 | |||
| hmo_supplementation | 1,110 | 100% | 1,110 | |||
| timepoint_label | 1,110 | 100% | 1,110 | |||
| collection_date | 1,108 | 100% | 1,108 | |||
| intervention | 743 | 67% | 743 |
- Infant Formula Supplemented with Five Human Milk Oligosaccharides Shifts the Fecal Microbiome of Formula-Fed Infants Closer to That of Breastfed Infants. PMID 37513505 PMC10383262 curated
Archive description
Breastfeeding is the optimal source of infant nutrition and confers established health benefits to the infant. Some of these benefits are associated with human milk oligosaccharides (HMOs), a unique group of carbohydrates that comprises the third most abundant solid component of human milk. We previously conducted the first clinical study with five different HMOs (5HMO-mix), namely 2’FL, 3FL, LNT, 3’SL and 6’SL, at the natural concentration of 5.75 g/L, in infant formula and now present the microbial findings of the study. We analyzed infant fecal samples by shotgun metagenomic sequencing and found that 5HMO-mix supplementation changed the microbial composition already at Week 1 and that the changes were persistent at Week 16 into supplementation. The microbiota of the 5HMO-mix supplemented infants were relatively increased in bifidobacteria and specifically bifidobacteria able to produce aromatic lactic acids when compared to infants receiving control formula. We further analyzed the functional potential of the microbiome with gut metabolic modules (GMM) and found shared features between 5HMO-mix and breastfed infants such as relative enrichment in mucus degradation and a relative decrease in proteolytic GMMs related to amino acid degradation. In conclusion, supplementation with 5HMO-mix supports the infant fecal microbiome in the direction towards that of breastfed infants.
How this project entered the registry
Classified as human gut / stool / 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.title · “Infant stool , 5-HMO supplemented”
- body site study.description · “We analyzed infant fecal samples by shotgun”
- body site study.description · “are associated with human milk oligosaccharides (HMOs), a”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Infant stool, 5-HMO supplemented”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA113561840 | age_at_collection_days | 84 | R1 | 0.85 | sample.title | Week 12 |
| SAMEA113561840 | collection_date | 2019-06-07 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2019-06-07 |
| SAMEA113561840 | country | IT | R1 | 0.90 | biosample_attr | Italy |
| SAMEA113561840 | delivery_mode | vaginal | R1 | 0.90 | biosample_attr | Vaginal |
| SAMEA113561840 | feeding_mode | exclusive_breast | R1 | 0.85 | biosample_attr | Breast milk |
| SAMEA113561840 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:formula | formula: Breast milk |
| SAMEA113561840 | health_condition_detail | Breast milk | R1 | 0.85 | biosample.attribute:formula | formula: Breast milk |
| SAMEA113561840 | hmo_supplementation | no | R1 | 0.85 | biosample_attr | Breast milk |
| SAMEA113561840 | intervention | no_intervention | R1 | 0.85 | biosample.attribute:formula | formula: Breast milk |
| SAMEA113561840 | subject_id | 09-004 | R1 | 0.85 | biosample_attr | 09-004 |
| SAMEA113561840 | timepoint_label | Week 12 | R1 | 0.70 | sample.title | 09-004 - Week 12 - chrhmo_10_10 |
Sequencing
1,110 runs over 1,110 samples · mean 5.48 Gbp per run (median 5.44 Gbp, total 6,086.81 Gbp; 1,110 runs with a base count) · layout PAIRED 1,110 · platform ILLUMINA 1,110 · models Illumina HiSeq 2000 (1,110) · 91% of runs with a Sandpiper profile · first public 2023-07-11
Authors (8)
Holst AQ first · Myers P · Rodríguez-García P · Hermes GDA · Melsaether C · Baker A · Jensen SR · Parschat K last
Downloads
PRJEB62690.csv.gz (39.2 KB) · parquet (119.9 KB) — all 1,110 samples, every field with route and confidence · PRJEB62690_determinations.csv.gz (95.1 KB) — 11,841 evidence rows