Fecal microbiota in early life and effects of early life antibiotics, annotated shotgun sequencing data

We performed a randomised controlled study in 147 infants requiring broad-spectrum antibiotic treatment for suspected early onset neonatal sepsis in their first week of life. Infants were randomly allocated to either treatment with penicillin + gentamicin, co-amoxiclav + gentamicin or amoxicillin + cefotaxime. Healthy infants not receiving antibiotics in their first week of life served as controls (subset of samples from BioProject ID PRJNA481243). Microbiota of faecal samples and rectal swabs were characterised by 16S rRNA-based sequencing (BioProject ID PRJNA612836). The microbiota of a subset of 20 samples were additionally characterised by whole genome shotgun sequencing.