Evolution of gut microbiome in early childhood: a cross-sectional study of Chinese children

Temporal development of the human gut microbiome over early childhood is driven by a variety of factors. We surveyed the fecal microbiome of 729 Chinese children aged 0–36 months, aiming to identify the age-specific patterns of microbiota succession, and evaluate the impact of birth mode, gender, geographical location and gastrointestinal tract symptoms on shaping the gut microbiota. We demonstrated that phylogenetic diversity of the gut microbiome increased gradually over time, which was accompanied by an increase in Bacteroidetes and a reduction in Proteobacteria. At the community level, the succession from aerobic bacteria and anaerobic bacteria to facultative anaerobes, and from Gram-negative to Gram-positive species were found over the gut microbiota assembly. The metabolic functions of gut microbiome shifted tremendously alongside the physiological development, including an increase in alanine aspartate and glutamate metabolism, and reduction in glutathione metabolism, fatty acid metabolism and tyrosine metabolism. During the first year of life, the Bacteroidetes phylum was less abundant in children born by caesarean section compared to those delivered virginally; the Enterococcaceae family, a group of facultative anaerobic microorganisms with pathogenic potential was predominant in preterm infants. No measurable effects of maternal antibiotics exposure over the gut microbiota development were found in the first three years. The relative abundances of Coriobacteriaceae and Streptococcaceae families, and Megasphaera genus were found higher in girls than boys. Among the three first-tier Chinese cities, children born and fed in Beijing had a higher abundance of Enterococcaceae and Lachnospiraceae families, and Shenzhen children had a higher abundance of Fusobacteriaceae. The families Alcaligenaceae, Bacteroidaceae and Porphyromonadaceae were more abundant in children with constipation, whereas the relative abundance of Clostridium genus was higher in those with diarrhea.