Longitudinal gut microbiota development from infancy to toddlerhood: a systematic review and platform-stratified...

Gut-microbiota development during early life is associated with immune, metabolic, and neurodevelopmental maturation, but longitudinal findings differ across sampling schedules and sequencing platforms.

PubMed/MEDLINE, Web of Science Core Collection, Embase.com, and Scopus were searched from inception through 21 July 2026. Two authors independently screened records and full reports. Reports were linked to their underlying studies/cohorts, and the full evidence set was mapped at cohort level. Hedges-corrected standardized mean changes were synthesized with REML random-effects models and modified Hartung-Knapp intervals only within compatible developmental windows, sequencing platforms, and taxonomic levels.

The searches identified 10,337 records; 5,640 duplicates were removed and 4,697 unique records were screened. Of 344 reports sought, 11 were not retrieved, 333 were assessed, and 173 reports representing 95 studies/cohorts were included. Seven reports contributed to the primary quantitative panels. In primary 16S syntheses, Shannon diversity was higher at approximately 12 months (Hedges g 1.62, 95% CI 0.85-2.39; I² = 83.0%; k = 4), as was Chao1 richness (g 2.14, 95% CI 1.69-2.60; I² = 0%; k = 3). Exact-paired-only sensitivity estimates remained positive but were imprecise for Shannon (g 1.93, 95% CI -1.00-4.85; k = 2) and Chao1 (g 2.07, 95% CI -1.73-5.88; k = 2). Primary taxon syntheses contained two 16S estimates per outcome and were exploratory.

The evidence suggests that alpha diversity generally increases during the first year of life, although the magnitude and between-cohort consistency remain uncertain. Certainty ranged from low to very low, and taxon-specific findings require platform- and age-window-specific interpretation.