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

Accuracy of NRAD-based classification.

Accuracy of NRAD-based classification.</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

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

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

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

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

Diversity of the <i>V</i>_<i>H</i> region of BCRs.

<p>(A) The human genome contains sets of <i>V</i>_<i>H</i>, <i>D</i>_<i>H</i>, and <i>J</i>_<i>H</i> gene segments. (B) The “variable” <i>V</i>_<i>H</i> segments can be grouped into seven <i>V</i>_<i>H</i> families based on sequence similarity. (C) A genetically diverse pool of B cells is generated by V(D)J recombination. (D) Exposure to antigens induces an adaptation of the BCR repertoire, generating genetic variants and changing the usage pattern of <i>V</i>_<i>H</i> gene segments.</p

Rank abundance distributions of memory B cell receptors.

<p>Four different B cell receptor sub-classes from donors 1 (replicate samples A, B) and 2 (replicates C, D) are compared. Top left panel: Log-log plot of RADs prior to normalization. Top right: Log-log plot of corresponding NRADs. Legend for RADs and NRADs is given in bottom right panel. Bottom left: Hierarchical clustering tree based on all pairwise distances between the 16 NRADs.</p

A typical Rank Abundance Distribution (RAD).

<p>A RAD with species abundances plotted in decreasing order from the most abundant (rank 10⁰ = 1) on the left to the least abundant species sampled from the community on the right. Both axes are scaled logarithmically to reveal the global structure of the RAD. Quantities such as the number of sampled individuals or the richness of the sample can be easily retrieved from the RAD.</p