Infant gut microbiome development in China, first 6 months
N=94 stool samples from infants in China, collected monthly during the first 6 months of life. Metagenomic analysis identified bacterial consortia associated with infant health and development using strain-level profiling. machine-written summary
94 samples · 94 runs · CN · Infant / toddler · 2025 · 6.53 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 376 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11497992 |
| ✓ Supplementary tables | 79 sample values (age) |
| – 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 — not resolved
15 of 15 people sampled more than once (94 samples; median 6, up to 7 per person). Schedule stated by the source: “Monthly stool samples over first 6 months of life (month 1-6) plus one maternal sample per infant; 94 samples from 15 infants.” (time origin: birth).
Genera, mean relative abundance over 92 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 | 79 | 84% | ||||
| country | 94 | 100% | 94 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 94 | 100% | 94 | |||
| collection_date | 94 | 100% | 94 | |||
| timepoint_label | 94 | 100% | 94 | |||
| age_at_collection_days | 79 | 84% | 79 |
- Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy. 2024 PMID 39428758 PMC11497992 own_data
- Strain-level characterization of health-associated bacterial consortia that colonize the human gut during infancy 2023 own_data
Archive description
The human gut microbiome develops rapidly during infancy, a key window of development coinciding with maturation of the adaptive immune system. However, little is known of the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n=94) from a cohort of infants (n=15) at monthly intervals in the first six months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants.</p><p>Strain-level de novo analysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a published cohort of infants with cystic fibrosis identified one such novel consortium of diverse Enterobacterales which was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual.</p><p>By augmenting published metagenomic datasets with data from a newly established cohort we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.
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.title · “colonize the human gut during infancy”
- body site study.description · “The human gut microbiome develops rapidly”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “human gut during infancy”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN43428198 | age_at_collection_days | 30.0 | R2 | 0.80 | paper.supp.Supplementary Table 1.xlsx[2022-07-07-detailed-sample-summ!term_days] | 605011002C01: 30 |
| SAMN43428198 | collection_date | 2018 | R1 | 0.85 | biosample.attribute:collection_date | 2018 |
| SAMN43428198 | country | CN | R1 | 0.90 | biosample_attr | China |
| SAMN43428198 | subject_id | PID_605011002 | R1 | 0.85 | biosample_attr | PID_605011002 |
| SAMN43428198 | timepoint_label | month 1 | R1 | 0.80 | biosample_attr | month 1 |
Sequencing
94 runs over 94 samples · mean 6.20 Gbp per run (median 6.53 Gbp, total 582.33 Gbp; 94 runs with a base count) · layout PAIRED 94 · platform ILLUMINA 94 · models Illumina HiSeq 2000 (94) · 98% of runs with a Sandpiper profile · first public 2025-03-30
Authors (0)
No author record.
Downloads
PRJNA1154644.csv.gz (3.5 KB) · parquet (73.5 KB) — all 94 samples, every field with route and confidence · PRJNA1154644_determinations.csv.gz (3.1 KB) — 455 evidence rows