Fig. 2

Principal Coordinate Analysis (PCoA). Each BAL sample is represented by a dot and the distances between dots represent the weighted UniFrac distance between samples. During PCoA, samples were scaled down to two unit-free dimensions (coordinates) for visualization. a Tropheryma-dominant vs high diversity monkeys. Red dots correspond to time points at which Tropheryma whipplei was the predominant organism in the BAL sample of any monkey; circles highlight the earliest time point for each monkey (weeks −13 or −10). b Monkeys color-coded by colony from which the monkey originated. Yellow and blue dots separate the samples collected at all time points from monkeys originating from each of the two colonies. Colony origin does not predict microbial composition, as seen by the lack of separation of the samples based on colony