Fig. 2: Microbiome alpha and beta diversity showed opposing patterns of variation across dietary regimes.
From: Diet and gut microbiome enterotype are associated at the population level in African buffalo
a Diversity metrics in panel a are colored by feed regime (green indicating green vegetation, yellow indicating hay, and red indicating restricted feed). For each box plot, the lower and upper hinges correspond to the first and third quartiles. The upper and lower whiskers extend from the hinges to the largest and smallest values no more than 1.5 IQR from the hinge. Outliers beyond these points are plotted individually. Gamma diversity did not significantly change across the three dietary regimes (Kruskal–Wallace p = 0.076, n = 15 time points), whereas alpha diversity was significantly reduced in the restricted regime compared with hay (p = 7.12e−7) and green vegetation (p = 0.00136) regimes (generalized linear mixed model, n = 426 samples). Beta diversity for each time point was greater in the restricted regime than either the hay (permuted p-value = 0.001) or green vegetation (permuted p-value = 0.002) regimes (permutation test for homogeneity of multivariate dispersion, n = 426 samples). A single individual with near-complete longitudinal sampling (Buffalo #45) was selected to demonstrate temporal shifts at the individual level, with time points connected chronologically by dashed lines. Individual shifts in microbiome composition aligned with population-level shifts in dietary availability. b Temporal patterns in alpha and beta diversity appeared to oppose each other, while gamma diversity remained stable over time. Source data are provided as a Source Data file.
