Simulation of CRADs of gut microbiomes in antibiotic-treated mice.

<p>The red and blue lines represent the CRADs of samples from two mice treated with antibiotics. Black boxplots represent the CRADs in the simulation with <i>p</i> = 1, where the growth rate of 197 of the 200 species was set to half that of the other 3 species. Lattice size in the following simulations was (<i>x</i>, <i>y</i>, <i>z</i>) = (40, 40, 2000). The simulation results are obtained from the average of 100 repetitions.</p

Simulation of CRADs of infant and adult gut microbiomes.

<p>Red and blue boxes represent the CRADs of the gut microbiomes of the 13 infants and the 104 Japanese adults, respectively. The solid line and the dashed line represent the simulation results for <i>p</i> = 1.0 with 100 initial species and <i>p</i> = 0.999 with 200 initial species, respectively. Lattice size in the following simulations was (<i>x</i>, <i>y</i>, <i>z</i>) = (40, 40, 2000). The simulation results are obtained from the average of 100 repetitions.</p

CRADs of the human infant gut microbiome.

<p>A: Clustering of the 13 human infant samples at the genus level. Hierarchal clustering is performed at the genus-level abundance of the human infant samples. Each genus is shown in a different color. B: Individual CRADs of gut microbiomes of 13 human infants based on the OTU-level composition. The CRADs of the gut microbiomes of the 13 infants (red) and the 104 healthy Japanese adults (black) are shown. C: Median CRADs of the same samples as those in (B). The CRADs of the gut microbiomes of the 13 infants (red) and the 104 healthy Japanese adults (black) are shown in the boxplot.</p

Concept of the mathematical model.

<p>To determine the species in the blue-shaded lattice (top), a species in the black shaded area (underneath) is randomly selected with probability <i>p</i>. A new additional species joins with probability 1-<i>p</i>.</p

Simulation of CRADs of mice microbiomes.

<p>The boxplot shows the observed CRADs of the combined samples, small and large intestine and cecum. Red and blue lines represent the average CRADs in the simulation with <i>p</i> = 1.0 and <i>p</i> = 0.9975, respectively, with 200 initial species. Lattice size in the following simulations was (<i>x</i>, <i>y</i>, <i>z</i>) = (40, 40, 2000). The simulation results are obtained from the average of 100 repetitions.</p

CRADs of murine gut microbiomes.

<p>A: Clustering of the bacterial composition at the OTU level in mice. Hierarchal clustering is performed at the OTU-level abundance of the samples. Each OTU is shown in a different color. B: Individual CRADs of murine gut microbiomes based on the OTU-level composition. C: Median CRADs of the same samples as those in (B).</p

CRADs of the dissected mouse gut contents.

<p>S1-S4, C, and L indicate the contents of the small intestine, the cecum, and the large intestine, respectively.</p