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Background  The initialization of the neonatal gut microbiota (GM) is affected by diverse factors and is associated with infant development and health outcomes.    Methods  In this study, we collected 207 faecal samples from 41 infants at 6 time points (1, 3, and 7 days and 1, 3, and 6 months after birth). The infants were assigned to four groups according to delivery mode (caesarean section (CS) or vaginal delivery (VD)) and feeding pattern (breastfeeding or formula milk).    Results  The meconium bacterial diversity was slightly higher in CS than in VD. Three GM patterns were identified, including  Escherichia / Shigella - Streptococcus -dominated,  Bifidobacterium - Escherichia / Shigella -dominated and  Bifidobacterium -dominated patterns, and they gradually changed over time. In CS infants,  Bifidobacterium  was less abundant, and the delay in GM establishment could be partially restored by breastfeeding. The frequency of respiratory tract infection and diarrhoea consequently decreased.    Conclusion  This study fills some gaps in the understanding of the restoration of the GM in CS towards that in VD.

Breastfeeding restored the gut microbiota in caesarean section infants and lowered the infection risk in early life