Fig. 3

Non-metric multidimensional scaling (nMDS) plot of the oropharyngeal microbiota based on Bray-Curtis dissimilarity metric. Each data point depicts the oropharyngeal bacterial communities of one patient. Data points and population standard deviation of data points (ellipses) are colored based on vicinity to poultry farm (dark gray, <1 km; light gray, ≥1 km). The stress-value indicates that the multi-dimensional structure of the data is well captured by the nMDS visualization. The figure suggests an association between living close to a poultry farm and the abundance of S. pneumoniae, which was verified by both supervised and unsupervised learning methods