BACKGROUND: Gut microbes have been suggested as the possible targets in the management of allergic diseases. However, the way in which these microbes influence allergic diseases remain unclear. Forty-seven full-term newborns were selected from a 1000-infant birth cohort. Among them were 23 allergic infants, whereas 24 infants were healthy without allergic symptoms at 1 year of age. Two hundred and sixty-four fecal samples were collected at 7 time points following their birth. These fecal samples were microbiologically analyzed using 16S rRNA gene sequencing. The dynamic processes involved in gut microbiota diversity and composition in the tested infants were constructed. RESULTS: Healthy infants demonstrated more statistical differences in longitudinal changes in the alpha diversity of their microbiota at the time points compared with day 0 (meconium) than did allergic infants. Analysis of beta diversity showed that the fecal microbiota of days 0 and 2 comprised different communities in healthy infants, and that there were three separate communities in the fecal microbiota of day 0 of the healthy infants, those of day 2 of the healthy infants, and those of days 0-2 of the allergic infants. The relative abundance of dominant gut microbiota at phylum level varied at different time points in the healthy and diseased groups. Bifidobacterium, Escherichia-Shigella, Streptococcus, Clostridium_sensu_stricto_1, Akkermansia and Erysipelatoclostridium were significantly different between the healthy and diseased groups at a different time points. CONCLUSION: The dynamic construction processes of gut microbiota during early life might be associated with the occurrence of long-term allergic diseases, with the first month following birth potentially being the most critical.