ArticleNature microbiology2019
Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.
Article in Nature microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 134 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
134 citing papers in PubMed, 1 synthesis or guideline pooled it, 237 citations in OpenAlex.
- Pooled it
- An Extensively Hydrolyzed Formula Supplemented with Two Human Milk Oligosaccharides Modifies the Fecal Microbiome and Metabolome in Infants with Cow's Milk Protein Allergy.International journal of molecular sciences · 2023Trial
- Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial.Frontiers in cellular and infection microbiology · 2021Trial
- LGTM: Gaussian process modulated neural topic modeling for longitudinal microbiome.Gut microbes · 2026Article
- MetaStrainer: accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.Bioinformatics (Oxford, England) · 2026Article
- Maternal Preconception Antibiotic Exposure Disrupts Microbial Succession: A Transgenerational Risk for Offspring Gut Mucosal Immaturity and Colitis Susceptibility.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Early life bacteria and sibling exposure associate with restoration of the infant gut microbiome after cesarean section.Nature communications · 2026Article
- Article
- Two Vibrio species co-colonize a morphologically complex symbiotic light organ.The ISME journal · 2026Article
- Changes in Healthy Infant Gut Microbiota over the Past Decades.Neonatology · 2026Article
- Characteristics and longitudinal stability of Gut Microbiota in healthy individuals across different age groups.Current research in microbial sciences · 2026Article
- Early-life microbiome trajectories as biomarkers to predict health outcomes.Microbiome research reports · 2026Review
- From Womb to World: Unravelling the Microbiota's Impact on Health and Disease.International journal of microbiology · 2026Review
- Infant gut microbiome reprogramming following introduction of solid foods (weaning).Gut microbes · 2025Review
- Microbiome-derived bile acid signatures in early life and their association with islet autoimmunity.Nature communications · 2025Article
- Assessing live microbial therapeutic transmission.Gut microbes · 2025Review
- Identification of strain-specific cues that regulate biofilm formation inMicrobiology spectrum · 2025Article
- Comparative Genomics and Adaptive Evolution ofFoods (Basel, Switzerland) · 2025Article
- Impact of Parabacteroides distasonis colonization on host microbiome, metabolome, immunity, and diabetes onset.Journal of molecular endocrinology · 2025Article
- Gut microbiome evolution from infancy to 8 years of age.Nature medicine · 2025Article
74 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
28 authors at 11 institutions in 6 countries.
Funding
Abstract
The human gut microbiome matures towards the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on gut microbiome development using integrated early childhood data sets collected in the DIABIMMUNE study in Finland, Estonia and Russian Karelia. We show that gut microbial diversity is associated with household location and linear growth of children. Single nucleotide polymorphism- and metagenomic assembly-based strain tracking revealed large and highly dynamic microbial pangenomes, especially in the genus Bacteroides, in which we identified evidence of variability deriving from Bacteroides-targeting bacteriophages. Our analyses revealed functional consequences of strain diversity; only 10% of Finnish infants harboured Bifidobacterium longum subsp. infantis, a subspecies specialized in human milk metabolism, whereas Russian infants commonly maintained a probiotic Bifidobacterium bifidum strain in infancy. Groups of bacteria contributing to diverse, characterized metabolic pathways converged to highly subject-specific configurations over the first two years of life. This longitudinal study extends the current view of early gut microbial community assembly based on strain-level genomic variation.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.