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Background:  The neonatal period is a critical period for the establishment of the intestinal microbial community. Antibiotics can change the composition of gut microbiota.   Methods:  Fecal samples were collected from 14 patients with pneumonia and 14 patients with meningitis before and after antibiotic treatment, and fecal samples from five healthy neonates at the 14th and 21st days after birth were collected as well. DNA of fecal samples was extracted, and PCR amplification was performed targeting the V3–V4 variable region of 16S rDNA. After detection by high-throughput sequencing, OTU (operational taxonomic unit) clustering, species annotation, and α diversity analysis were calculated and analyzed statistically.   Results:  In the healthy control group, the abundance of  Bifidobacterium  increased significantly from 16.75 to 40.42%, becoming the most dominant bacteria. The results of α diversity analysis suggested that the Sobs indexes of the gut microbiota in the pneumonia and meningitis groups were significantly lower than that in the healthy control group ( p  < 0.05). PCoA analysis showed that the gut microbiota of pneumonia and meningitis groups clustered distinctly with the control group (Adonis  p  = 0.001,  R  2  = 0.565), and there was no significant change in the diversity of gut microbiota before and after the use of antibiotics.   Conclusions:  The gut microbiota of neonates with infectious diseases were mainly related to the disease conditions. The initial state of neonatal gut microbiome determines its state after 1-week antibiotic treatment. Antibiotic application with 7 days had little effect on the community richness and some effect on the composition of gut microbiota of neonates with pneumonia or meningitis.

One-Week Effects of Antibiotic Treatment on Gut Microbiota of Late Neonates With Pneumonia or Meningitis