Abundance dynamics of gut microbiomes of three individuals under treatment with antibiotic Ciprofloxacin (Cp).

(A) NRADs before (green), during (red), and after (blue) treatment. Bold lines are mean NRADs, shaded regions are 90% confidence intervals of the means. (B) MDS of NRADs with one point per NRAD using the same color code as in panel A. For each of the three individuals, arrows connect points corresponding to the last measurement before treatment, measurements during treatment, and the first measurement after treatment. The two coordinates of the MDS plot explain 89% of the NRAD distances.</p

Optimal parameters for the model of gut microbiome NRAD entropy as function of age.

Optimal parameters for the model of gut microbiome NRAD entropy as function of age.</p

Accuracy of NRAD-based classification.

Accuracy of NRAD-based classification.</p

Country of origin and age as determinants of gut microbiomes NRADs.

<p>(A) MDS-ordination of NRADs of those 489 gut microbiomes from Malawi/Venezuela (MV) and United States (US) with age information. Small symbols represent individual NRADs, large symbols are averages. Error bars are 90% confidence intervals of the averages. The two coordinates of the MDS plot explain 83% of the NRAD distances. (B) Importance of each of the 4105 NRAD ranks for the random forest classification according to country of origin (MV vs. US). The two peaks around ranks 20 and 200 are the NRAD regions that carry most information about the country of origin.</p

Broken stick distribution (solid line) and NRADs of <i>IgG</i>⁺<i>CD</i>27⁺ fractions (points).

<p>Inset: section of hierarchical clustering dendrogram where broken stick distribution appears. This plot adopts the usual presentation of the broken stick distribution in the literature with linear horizontal axis and logarithmic vertical axis. Therefore the boomerang shapes of the log-log <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005362#pcbi.1005362.g004" target="_blank">Fig 4</a> appear horizontally stretched.</p

GlobalPatterns dataset.

<p>(A) Hierarchical clustering dendrogram based on distances between NRADs. (B) NRADs of three samples of similar origin that form a cluster. (C) Microbiome of human palm of human individual 1 clusters closely with sediments 2 and 3, but is more distant to tongue microbiome of individual 1. (D) Three differently shaped NRADs with same entropy.</p

General process employed in this work.

<p>Flowchart of procedure from original species/abundances or sequence/reads data (top box) to original RADs, then to NRADs, and analyses based on NRADs.</p

Averaged NRADs of gut microbiome data in six age groups.

<p>The number of NRADs per group from youngest to oldest were 9, 18, 55, 64, 34, and 309, respectively. Solid lines are mean NRADs, shaded areas are 90% confidence intervals for the means.</p

Dependence of NRAD distances <i>d</i>_<i>R</i> on MaxRank <i>R</i>.

Co-ordinates are distances dR between all 26 ⋅ (26 − 1)/2 = 325 NRAD pairs of the 26 GlobalPatterns samples at three different values of R. If the distance of an NRAD pair is the same for both R, the point lies on the diagonal. (A) MaxRank normalization; (B) cutoff normalization.</p

Development of gut microbiome entropy <i>H</i>_<i>R</i> with age <i>t</i>.

<p>(A) Entropies (with <i>R</i> = 4105) in nats for 181 samples from Malawi and Venezuela (MV, blue dots), and 308 samples from the United States (US, orange dots). Log-scaled horizontal axis is age in years. Superimposed are models for (blue line) and (orange line) according to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005362#pcbi.1005362.e023" target="_blank">Eq (6)</a>. Areas around the model lines shaded in blue and orange are the corresponding 90% confidence intervals of the respective models. (B) and (C) Comparison of mean entropies of measured data (red points) and their corresponding 90% confidence intervals (error bars), with the model (solid gray lines) and its 90% confidence interval (shaded areas), for MV (panel B) and US (panel C). Model lines and shaded areas are the same as in panel A.</p