Bacterial composition analysis on rank genus of the low-abundance members by using different taxonomic profiling tools.

<p>‘SmashCommunity RG’ depicts SmashCommunity reference genomes, ‘SmashCommunity 16S (1)’ depicts the SmashCommunity 16S rRNA gene-based method using the meta_rrna approach, ‘SmashCommunity 16S (2)’ depicts the SmashCommunity 16S rRNA gene-based method using the 16S rRNA gene sequence database approach.</p

Bacterial composition analysis on ranks class and order by using different taxonomic profiling tools.

<p>Classes within the orders <i>Bacilli</i> and <i>γ-Proteobacteria</i> are shown on the left y-axis; classes within the orders <i>Actinobacteria</i>, <i>α-Proteobacteria</i>, and others are shown on the right y-axis. ‘SmashCommunity RG’ depicts SmashCommunity reference genomes, ‘SmashCommunity 16S (1)’ depicts the SmashCommunity 16S rRNA gene-based method using the meta_rrna approach, ‘SmashCommunity 16S (2)’ depicts the SmashCommunity 16S rRNA gene-based method using the 16S rRNA gene sequence database approach.</p

Comparison of different community composition analysis methods on rank species.

*<p>Detected at 30 h.</p>**<p>No analysis performed at 30 h.</p>***<p>Only phylogenetic marker gene(s) sequences available in databases.</p><p>Species are only considered as present in the ecosystem if they could be detected by all five taxonomic profiling tools. The relative species abundances, predicted by the different classification tools, are expressed as a range that represent the lowest and highest values obtained. For the other methods, the presence of a species is denoted by “X”. <i>A.</i>: <i>Acetobacter</i>; <i>E.</i>: <i>Escherichia</i>; <i>En.</i>: <i>Enterobacter</i>; <i>Er.</i>: <i>Erwinia</i>; <i>G.</i>: <i>Gluconobacter</i>; <i>Ga.</i>: <i>Gluconacetobacter</i>; <i>K.</i>: <i>Klebsiella</i>; <i>L.</i>: <i>Lactobacillus</i>; <i>Leuc.</i>: <i>Leuconostoc</i>; <i>Lc.</i>: <i>Lactococcus</i>; <i>O.</i>: <i>Oenococcus</i>; <i>P.</i>: <i>Pediococcus</i>; <i>Pe.</i>: <i>Pectobacterium</i>; <i>S.</i>: <i>Salmonella</i>; <i>St.</i>: <i>Streptococcus</i>; <i>T.</i>: <i>Tatumella</i>.</p

Rarefaction analysis of the genera found with data sets A and B.

<p>The rarefaction curves represent an estimation of the number of genera associated with different sampling sizes. As the results of the two 16S rRNA gene-based methods of the SmashCommunity platform were similar, only one method (based on similarity with the 16S rRNA gene sequence database of the SmashCommunity platform) is shown. As the plateau phase of the SmashCommunity reference genomes platform and MEGAN was reached at 25,000 reads, the X-axis is limited to this number of reads.</p