New Insights into the Composition of the Early-Life Gut Microbiome: A Metagenomic Analysis of Fecal Samples in Children Up to 18 Months of Age.

PURPOSE: To determine the gut microbiome composition and associated factors in infants. METHODS: Cross-sectional study was conducted in primary healthcare centers including healthy children up to 18 months of age. Parents of children answered a questionnaire and bring a fecal sample of their child. Fecal samples were analyzed using shotgun sequencing. The relative abundances of taxonomic profile were detected and compared with associated factors. RESULTS: In the study were included 91 children. The most abundant taxonomic units belonged to phyla: Bacillota, Bacteroidota, Actinobacteria. In contrast, the most abundant species were Bifidobacterium longum and Bifidobacterium breve, demonstrating an age-appropriate microbial composition. The viral fraction mainly consisted of bacteriophages, with the most abundant viral family being Tospoviridae. Nevertheless, more than 50 rather new taxonomic entities were observed to cause shifts in the taxonomic units of the infant gut microbiome in association with perinatal antibacterial therapy, type of delivery, feeding type in the first 6 months of life. Higher relative abundance of Kitasatospora spp. MMS16 BH015 was associated with C-section and antibacterial treatment during delivery. A total of 302 antimicrobial resistance genes were identified, the most frequently encountered genes were associated with glycopeptide antibiotic resistance: vanG, vanT, vanW, vanY and adeF. The distribution of ARGs did not differ among different age groups. CONCLUSION: Metagenomic sequencing provides broader insights into the composition of the gut microbiome, emphasizing the presence of unusual species associated with environmental and perinatal factors. Perinatal antibacterial treatment may have a greater impact on the infant microbiome than was previously estimated.