Integrating eukaryotic and prokaryotic data, as well as urbanisation gradients

OBJECTIVE: Integrating eukaryotic and prokaryotic data, as well as urbanisation gradients into microbiome research METHODS: The Malagasy samples were collected within the SCHISDIMA study, cross-sectional study performed in Andina, Tsiroanomandidy, and Ankazomborona. As we were interested in spanning an urbanisation gradient, we complemented the samples with fecal samples from Kiel, Germany. For microbiota analysis of the gut, all provided stool samples underwent 16S rDNA sequencing as well as 18S rDNA sequencing and subsequent bioinformatic analyses. RESULTS: Malagasy cohorts showed a higher prevalence of helminths and protozoa. Notably, the diversity of particularly food-associated fungi increased with urbanisation, peaking in the industrialized German samples. Prokaryotic 16S amplicon sequencing confirmed and extended known geographical differences, showing a dominance of Bacteroides in Germany versus Prevotella and Firmicutes in Madagascar.