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The composition of the vaginal microbiome may lead to adverse pregnancy outcomes. Normal pregnancy is associated with changes in the vaginal bacterial community composition, which tend to be more enriched with one or two <i>Lactobacillus</i> species promoting a healthy vagina and favorable birth outcomes. The aim of the current study was to determine compositional changes in the healthy vaginal microbiome composition during the three trimesters of pregnancy in Ismailia, Egypt using Illumina MiSeq sequencing of the V3–V4 region of the 16S rRNA. The phylum <i>Firmicutes</i> and the genus <i>Lactobacillus</i> dominated across the three trimesters of pregnancy. <i>L. iners</i> was the most abundant species. However, <i>L. coleohominis</i> and <i>L. reuteri</i> represented the least dominant vaginal lactobacilli. Core microbiome analyses showed the <i>Lactobacillus</i> genus and <i>L. iners</i> species to have the highest prevalence in all the samples of our study groups. The phylum <i>Firmicutes</i> was found to be negatively correlated with almost all other vaginal phyla during pregnancy. Likewise, a negative correlation between <i>Lactobacillus</i> and almost all other genera was detected, including significant negative correlations with <i>Dialister</i> and <i>Prevotella.</i> Furthermore, negative correlations of <i>L. iners</i> were detected with almost all other species, including a significant negative correlation with <i>L. helveticus, G. vaginalis, S. anginosus</i>, and <i>S. agalactiae.</i>