Table 1.
Host/environmental factors with sample distribution and PERMANOVA analysis.
A list of host and environmental factors, which were collected with questionnaire, with corresponding distribution of samples inside their respective factor category. To the right we show the results of the PERMANOVA test (1000 permutations, Bray-Curtis distances), presented with the value for explained variance (R2) for each factor in relation to the bacterial or fungal community. Host/environmental factors with a significant P value, after adjustment with Benjamini-Hochberg correction (FDR < 0.05), are highlighted in grey.
Fig 1.
Rarefaction curves for bacterial and fungal OTUs.
Rarefaction curves for bacterial (blue) and fungal (red) OTUs were calculated by rarefying both bacterial and fungal community to 950 reads/sample (only for this specific analysis we rarefied bacterial community to 950 reads/sample in order for the rarefaction curves to be comparable). Plotted data points represent the mean value of OTUs for the respective number of samples (1000 iterations) with a 95% confidence interval.
Fig 2.
Bacterial and fungal phyla relative abundance.
A box plot presentation of relative abundances of bacterial (A) and fungal (B) phyla. Only phyla with an overall relative abundance greater than 1% are shown.
Fig 3.
The core microbiome is shown as a percent of samples (%) that include the corresponding percent (%) of fungal (red) and bacterial (blue) OTUs. To the right is the list of bacterial (n = 9) and fungal (n = 1) OTUs, which meet the criteria for inclusion into the core community. We compared our observed core taxa with four other studies also reporting core communities (information on studied cohorts and core community inclusion criteria are included in Materials and Methods). The dot indicates that the core taxa identified in our cohort was also reported by respective study at genus or family taxonomic level.
Fig 4.
Age-associated changes in bacterial communities.
Graph shows bacterial community Shannon diversity index in relation to age. The linear regression indicates the increase of the Shannon diversity with age and is presented with a 95% confidence interval (A) (Pearson's r = 0.213, P = 0.003). The bar plot shows Pearson correlations of bacterial OTUs that significantly increase (blue) or decrease (red) in relative abundance with age (FDR < 0.05) (B).
Fig 5.
Gender-associated differences in bacterial communities.
A box plot presentation of Shannon diversity indices in females compared to males (Kruskal-Wallis test, P = 0.014) (A). The bar plot presents LEfSe results showing LDA values for OTUs, which were significantly increased in males (red) and females (blue).
Fig 6.
Changes in fungal microbiota associated with the reported rate of physical activity.
Box plots presenting the Shannon diversity indices (A) and S. cerevisiae abundance (B) according to the rate of reported physical activity. Physical activity was defined with four categories, i.e. PA_1—occasional exercise; PA_2—exercise approximately once a week; PA_3—exercise multiple times weekly; PA_4—active athlete.