This dataset consists of 82 data files of which 78 are zipped fastq files containing the raw sequence data with two files per sample: R1 and R2. The names of the zip files start with the sampleID. Summary: Vertebrates evolved in concert with bacteria and have developed essential mutualistic relationships. Gut bacteria are vital for postnatal development of most organs and the immune and metabolic systems, and may likewise play a role during prenatal development. Prenatal transfer of gut bacteria is shown in four mammalian species including humans. For the 92% of the vertebrates that are oviparous prenatal transfer is debated, but it has been demonstrated in domestic chicken. We hypothesize that also non-domestic birds can prenatally transmit gut bacteria. We show that the first faeces of 21 neonate rock pigeons (Columba livia), hatched in incubator, contained a microbiome (bacterial community) which composition resembled the cloacal microbiome of females sampled from the same population (N=5) as indicated by multiple shared phyla, orders, families and genera. Neonates and females shared 16.1% of the total number of OTUs present (2881), and neonates shared 45.5% of their core microbiome with females. In contrast, the five females shared only 0.3% of the 1030 female OTUs present. These findings suggest that prenatal gut bacterial transfer may occur in birds. Our results support the hypothesis that gut bacteria may be important for prenatal development, and present a heritability pathway of gut bacteria in vertebrates.