The gut mycobiota of rural and urban individuals is shaped by geography

BACKGROUND : Understanding the structure and drivers of gut microbiota remains a major ecological endeavour. Recent studies have shown that several factors including diet, lifestyle and geography may substantially shape the human gut microbiota. However, most of these studies have focused on the more abundant bacterial component and comparatively less is known regarding fungi in the human gut. This knowledge deficit is especially true for rural and urban African populations. Therefore, we assessed the structure and drivers of rural and urban gut mycobiota. RESULTS : Our participants (n = 100) were balanced by geography and sex. The mycobiota of these geographically separated cohorts was characterized using amplicon analysis of the Internal Transcribed Spacer (ITS) gene. We further assessed biomarker species specific to rural and urban cohorts. In addition to phyla which have been shown to be ubiquitous constituents of gut microbiota, Pichia were key constituents of the mycobiota. We found that geographic location was a major driver of gut mycobiota. Other factors such as smoking where also determined gut mycobiota albeit to a lower extent, as explained by the small proportion of total variation. Linear discriminant and the linear discriminant analysis effect size analysis revealed several distinct urban and rural biomarkers. CONCLUSIONS : Together, our analysis reveals distinct community structure in urban and rural South African individuals. Geography was shown to be a key driver of rural and urban gut mycobiota.Additional file 1. Questionnaire Details of the questionnaire provided to participants prior to enrolment in the study. The questionnaire details essential required information, clinical information, voluntary dietary information and questions regarding data sharing.Additional file 2. Results from the partition of variance analysis in RDAAdditional file 3: Fig. S1. Rarefaction plot showing sequencing coverage. The estimated average sequence coverage of high-quality paired end reads after quality control assessed using Nonpareil (in alignment mode).Additional file 4: Fig. S2. Venn diagram showing the unique and shared phylotypes for samples collected from urban and rural participants.Additional file 5: Fig. S3. Taxa abundance data was normalised to obtain the proportion of most abundant taxa per sample. The diameter of the points at the bottom of the plot corresponds to the magnitude of the LCBD value for a particular sample. The bars correspond to taxa that are most abundant with the top taxa sharing a bigger portion of the bar for each sample.The South African Medical Research Foundation (TPM), the National Research Foundation, the Fulbright program, the Microbiomes in Transition (MinT) initiative at the Pacific Northwest National Laboratory in Richland, WA, USA.https://bmcmicrobiol.biomedcentral.comam2020BiochemistryGeneticsMicrobiology and Plant Patholog