Additional file 1: of GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly

Algorithm for constructing extension links and BLASTP alignments between selected P. acnes proteins and their predicted homologous contigs. The file contains detailed algorithm and pseudo-code for linear construction of extension links. The file also contains NCBI BLASTP alignments of two P. acnes proteins, whose homologous reads were not identified by PSI-BLAST from DS2 but were identified by GRASPx. (PDF 813 kb

Diversity indices computed on all genera-based taxonomic units.

<p>Diversity indices computed on all genera-based taxonomic units.</p

Low abundance, high ubiquity taxa.

<p>This figure helps the observer to comprehend the relationship between abundance and ubiquity when defining a core microbiome. As one would expect, increasing the abundance threshold for defining whether a sample contains a particular taxon would reduce the percentage of samples (ubiquity) that would contain it. The lines that are presented refer to all taxa in the stool samples that are in more than 97.5% of the samples with an abundance cutoff of 0.05%. The taxon <i>Bacteroides</i> (red) is both relatively highly abundant and highly ubiquitous, so its fall off is less steep than the Clostridales shown.</p

Diversity indices computed on “common” genera-based taxonomic units.

<p>Diversity indices computed on “common” genera-based taxonomic units.</p

Comparison of diversity indices for median versus pooled taxonomic profiles.

<p>Simple regression lines were drawn in solid black for each median individual versus pooled samples scatterplot. The dashed blue lines (slope  = 1, y-intercept  = 0) represent where a hypothetical (median  =  pooled) relationship would exist if all individuals had identical taxonomic profiles. Both the OTU-based and genera-based comparisons using the Shannon diversity index indicate only a slight and almost constant elevation of the diversity between the median individual and pooled samples. However, τ is able to capture the lengthening tail attributed to the low abundant taxa that are exclusive to certain individuals. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032118#pone.0032118.s004" target="_blank">Table S2</a> for a mapping of abbreviations to habitat names. Green, red, black and blue points represent vaginal, skin, oral, and stool body regions, respectively.</p

Diversity indices computed on all OTU-based taxonomic units.

<p>Diversity indices computed on all OTU-based taxonomic units.</p

Comparison of all and “common” taxonomic units and their effect on the Shannon and τ statistics.

<p>For both genera-based and OTU-based taxonomic units, the Shannon diversity index and τ were compared against the median estimated S_max on all (blue) and common (green) taxonomic units. Each point in the scatterplot represents one of the 18 body habitats. There is a closer relationship between τ and S_max than for the Shannon diversity index, for both genera and OTU based profiles. The red line represents a simple regression line across all points.</p

Relationship between the Tail statistic, τ, and Standard Deviation, σ.

<p>τ is the standard deviation of the rank abundance curve after reflection around the most dominant taxonomic unit, <i>i</i>  = 1. The blue bars represent the rank abundance curve. Above each bar, the probability, Pr[<i>i</i>], of the <i>i</i>^th most dominant taxonomic unit has been labelled in italics. The natural numbers labelled in bold above the blue bars represent the rank, <i>i</i>, of each taxonomic unit. The name of each taxonomic unit is labelled along the x-axis. The grey bars represent the mirror image of the rank abundance curve. Treating <i>i</i>  = 1of the symmetric distribution as μ  = 1, the standard deviation, σ, is then 3.764, which also represents τ for this rank abundance curve and sample.</p

Diversity indices computed on “common” OTU-based taxonomic units.

<p>Diversity indices computed on “common” OTU-based taxonomic units.</p

Contribution of taxa to diversity.

<p>A theoretical rank abundance curve (a PDF) is overlayed with its CDF (black) as a “Pareto chart”. The overlaid colored lines represent each diversity index as lower abundant taxonomic units are included. For example at “c”, the height of each curve represents the relative value of the index if the sample were only composed of a, b, and c. The more quickly an index curve reaches it maximum normalized value of 1.0, the less the index is capable of resolving low abundance taxonomic units. From the graph, it can be observed that the Shannon and Simpson diversity indices approach their saturation point more quickly than the Tail statistic or a Renyi entropy with a fractional alpha.</p