The gut microbiota plays an important role in human development and health. Gut dysbiosis has been associated with many diseases, including diabetes and obesity. The incidence of both as well as gestational diabetes mellitus (GDM) is increasing especially in the developed countries. GDM is one of the important risk factors for the birth of an overweight baby, called macrosomia. The latter is associated with birth-related injuries of mother and child as well as increased risk of obesity and diabetes type 2 of the child. In the doctoral thesis, we investigated whether there were links between the gut microbiota of the GDM-women and the occurrence of macrosomia. The study included 47 GDM-women. We defined the main differences between the microbiota of GDM-women with macrosomic baby and the microbiota of GDM-women with non-macrosomic baby. 30 percent of GDM-women gave birth to a macrosomic baby. 18 metagenomes from feces, from the 2nd and 3rd trimesters (in total 36 metagenomes) were included in the NGS analyzes of 16S rRNA gene sequences. At the phyla level, the main differences between the groups were in the relative abundances of Firmicutes and Proteobacteria. We detected a lower percentage of Firmicutes and a higher percentage of Proteobacteria in the group of GDM-women with a macrosomic baby, due to a lower percentage of Clostridia and higher levels of Bilophila wadsworthia. However, we often find that NGS data do not always show clear correlations between microbiota composition and the studied host phenotype, due to microbiota interindividual diversity. In addition, due to genome plasticity of certain bacterial species, only particular strains, which cannot be identified by target sequencing, can be responsible for a particular phenotype. Therefore, we characterized bacteria Escherichia coli. GDM-women who gave birth to a macrosomal baby had different populations of E. coli in the faeces compared to GDM-women who gave birth to a normal weight baby. We have also shown that the structures of E. coli populations depend on several factors, including the body mass index before pregnancy and the consumption of iron supplements, and also that E. coli from B2 phylogroup is associated with microbiota with higher taxa richness. We paid special attention to genotoxins as the prevalence of E. coli strains from B2 group, that often carries genes for genotoxins, has increased significantly in developed countries. 42 percent of the isolates from B2 group had a gene for colibactin and gene was exclusively present in the B2 phylogenetic group. As many as 95,5 percent of B2 isolates had a gene for Usp and also 90 percent of isolates from F group. The genotoxin producer is protected against the action of its own toxin. Mechanisms to protect a producer from the action of their own toxin can act more broadly and can protect the bacteria from other toxins, presumably providing a selective advantage for bacterial strains encountering stressful conditions also within the host.