Figure 2

Stability testing of gut and saliva microbiota time series. (A-C) Pairwise Jensen Shannon Distances between samples from Subject A’s gut (A), Subject B’s gut (B), and Subject A’s saliva (C). Dark green regions indicate date ranges with similar microbiota. To quantify how stable individual microbial taxa were across the labeled date ranges, we performed the Augmented Dickey Fuller (ADF) test, which evaluated the null hypothesis that a given OTU is non-stationary (that is, the OTU tends to return to an equilibrium value). The majority of tested OTUs were stationary according to the ADF test (88%, 85%, 84%, 79%, and 94% for date ranges I-V, P <0.05). (D-F) Phylogeny of stationary and non-stationary OTUs. Inner rings denote phyla (the Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Tenericutes are colored purple, blue, green, yellow, and red, respectively). Outer rings are white for stationary OTUs and red for non-stationary ones. Non-stationary taxa clustered phylogenetically for date ranges II (D), III (E), and V (F) (P <0.05, P-test), supporting the hypothesis that closely-related taxa are more likely to be in competition. (G-I) Time series of closely-related, non-stationary OTUs (Greengenes prokMSA ids given in boxes). An artificial abundance floor of 1e-5 was added to improve visibility. Shown are members of the genus Lachnospira over date range II (G), the genus Akkermansia over date range III (H), and the genus Leptotrichia over date range V (I). The summed abundances of the selected Lachnospira and Leptotrichia are stationary over the given date ranges (P <0.05, ADF test).