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PRJNA1060349 SRP550663

Infant gut microbiome strain dynamics across weaning, St. Louis

Weaning accelerates and transforms within-host adaptation in the infant gut microbiome

Longitudinal cohort of 1,197 stool samples from twin infants and mothers in St. Louis, USA, tracking strain colonization, persistence, and evolution in the gut microbiome from birth through weaning to age 8. machine-written summary

1,197 samples · 1,197 runs · US · Infant / toddler · 2024 · 0.62 Gbp / sample

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Sources

✓Sequence archive 3,695○Abstract / description✓Full text 2,394–Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave

✓ Sequence archive	3,695 sample values (collection date, country, subject id, timepoint)
○ Abstract / description	read; no usable statement
✓ Full text	2,394 sample values (location locality, location region) · PMC12302008
– Supplementary tables	no supplementary tables available (or none open access)
– External resources	not covered by the external resources we ingest
– User contribution	nothing uploaded yet · share metadata
– Human verified	not yet checked by a person · I checked this project — verify it

Samples at a glance

1 country

Age

unknown1,197

Country

US1,197

Body site

primary1,197

Collected 2010–2019

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinalfamilies — not resolvedmother–infant — not resolvedtwins — not resolved

78 of 78 people sampled more than once (1,197 samples; median 16, up to 28 per person) · follow-up median 5.5 y (max 8.3 y) · median interval between samples 3 mo (time from collection dates). Schedule stated by the source: “Dense longitudinal sampling from childbirth through weaning to 8 years post-birth; 28 distinct timepoint labels (e.g. M00, M06, M07...M67)”.

Each row is one person (36 shown of 78); dots are samples at days since that person's first sample.

26 twin pairs (52 infants) plus their mothers = 78 subjects; strains shared within families (twins & mother-infant).

How longitudinal and relatedness information is derived

Community composition

Bifidobacterium 9.5%Blautia_A 8.7%Bacteroides 6.7%Roseburia 6.6%Faecalibacterium 4.7%Mediterraneibacter 4.0%Ruminococcoides 3.9%Phocaeicola 3.8%Prevotella 2.7%Anaerostipes 2.6%Fusicatenibacter 2.2%Alistipes 1.5%not assigned to a genus 7.9%other genera 35.3%

Genera, mean relative abundance over 253 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage

field	samples	coverage	R1	R3
age_category	0	0%
country	1,197	100%	1,197
health_condition	0	0%
subject_id	1,197	100%	1,197
collection_date	1,197	100%	1,197
detailed_location	1,197	100%
location_locality	1,197	100%		1,197
location_region	1,197	100%		1,197
timepoint_label	104	9%	104

Papers (1)

Gut microbiome evolution from infancy to 8 years of age. PMID 40175737 PMC12302008 curated

Details

Archive description

The human gut microbiome is most dynamic in early life. While sweeping changes in taxonomic architecture are well described, it remains unknown how, and to what extent, individual strains colonize and persist, and how selective pressures define their genomic architecture. Here, we combine shotgun sequencing of 1,203 stools from 26 densely-sampled twins (52 infants) and their mothers from childbirth to 8 years post-birth, with culture-enhanced, deep short-read, and long-read sequencing of stools from a subset of 10 twins (20 infants), to define transmission, persistence, and evolutionary trajectories of gut species from infancy to middle childhood. We construct 3,995 strain-resolved metagenome-assembled genomes across 399 taxa, and find that 27.4% persist within individuals. We identify 726 strains shared within families, with Bacteroidales, Oscillospiraceae, and Lachnospiraceae, but not Bifidobacteriaceae, vertically transferred. Lastly, we identify weaning as a critical inflection point that accelerates bacterial mutation rates and separates functional profiles of genes accruing mutations.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child 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 · “in the infant gut microbiome”
body site study.description · “The human gut microbiome is most”
life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
life stage study.title · “adaptation in the infant gut microbiome”
life stage study.description · “infancy to middle childhood . We construct”
life stage study.description · “infants) and their mothers from childbirth to”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN45576141	collection_date	2010-02-05	R1	0.85	biosample.attribute:collection_date	collection_date: 2010-02-05
SAMN45576141	country	US	R1	0.90	biosample_attr	USA: Saint Louis
SAMN45576141	location_locality	St. Louis	R3	0.70	paper.fulltext.methods	in St. Louis, Missouri, USA, were longitudinally collected
SAMN45576141	location_region	Missouri	R3	0.70	paper.fulltext.methods	in St. Louis, Missouri, USA, were longitudinally collected
SAMN45576141	subject_id	06-1	R1	0.85	biosample_attr	06-1
SAMN45579054	timepoint_label	M07	R1	0.70	run.library_name	C006-M07_reads

Sequencing

1,197 runs over 1,197 samples · mean 1.48 Gbp per run (median 0.62 Gbp, total 1,777.21 Gbp; 1,197 runs with a base count) · layout PAIRED 1,197 · platform ILLUMINA 1,197 · models NextSeq 500 (1,197) · 21% of runs with a Sandpiper profile · first public 2024-12-12

Authors (9)

Sawhney SS first · Thänert R · Thänert A · Hall-Moore C · Ndao IM · Mahmud B · Warner BB · Tarr PI · Dantas G last

Help complete this project

2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata

Downloads

PRJNA1060349.csv.gz (37.4 KB) · parquet (123.9 KB) — all 1,197 samples, every field with route and confidence · PRJNA1060349_determinations.csv.gz (39.1 KB) — 6,089 evidence rows

Samples (1,197 · every field this project has values for · hover a cell for its source)

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