The sequencing and studying of fungal biota of human microbiome is still progressing. Comprehensive study of the eukaryotic component of the human microbiome is just beginning and lags far behind our understanding of the bacterial communities.
As Sudeep said, the study of microbiome is in its first steps and actually it focuses on bacterium. This articles may help you. One of the authors mentions that yeast accounts for less that 0.01% of the microbiome