<i>Drosophila</i> microbiota impacts midgut genes expression.

<p>(A) A schematic representation of the experimental set-up used for transcriptome analysis; GF: Germ-Free. (B) A volcano plot showing the absolute value of the computed statistics from the SAM analysis (d-stat) based on to the fold change in gene expression between the GF and poly-associated groups. The genes selected as differentially expressed by the SAM analysis are highlighted with a red circle around them. The selection was made using a value of Delta that corresponds to a FDR of 0.2. (C) Adult tissue enrichment classification of the 105 microbiota-regulated genes. (D) A bar graph representing the fold-enrichment of different microbiota-regulated transcripts in dissected midguts from GF vs poly-associated wild-type animals (the value of the relative ΔCt<i>^gene</i>/ΔCt<i>^rp49</i> ratio was calculated for every sample and relativized to the ratio in the GF condition which was anchored to 1 to indicate fold induction). Statistical significance of the result is represented (Student's t-test: ns≥0.05>*≥0.01>**≥0.001>***). Of note, <i>PGRP-SC1</i> mRNAs are detected to a 16 folds higher level than <i>PGRP-SC2</i> mRNA in young poly-associated animals (ΔCt<i>^PGRP-SC1</i>/ΔCt<i>^rp49</i> = 63 and ΔCt<i>^PGRP-SC2</i>/ΔCt<i>^rp49</i> = 4). (E) Relative percentage of Gene Ontology Terms: Biological processes in the list of microbiota-regulated gene (pie chart) and (F) Enrichment p-values (Benjamini-Hochberg corrected) for GO:Biological processes and GO:Molecular Functions in the list of microbiota-regulated genes.</p

IMD/Relish signaling controls microbiota mediated transcript enrichment in midguts.

<p>Bar graphs representing the fold enrichment of different microbiota-regulated transcripts in dissected midguts from GF vs poly-associated <i>Relish^E20</i> (A) or <i>Dredd^F64</i> (B) mutant animals (the values of the relative ΔCt<i>^gene</i>/ΔCt<i>^rp49</i> ratios were calculated for every sample and relativized to the ratio in the GF condition which was anchored to 1 to indicate fold induction). Statistical significance of the result is represented (Student's t-test: ns≥0.05>*≥0.01>**≥0.001>***). nd: not detected.</p

Microbiota-regulated genes.

<p>Microbiota-regulated genes are classified by Gene Ontology (GO):Biological function groups. Columns for each microbiota-regulated gene are designated as such: (1) Gene names from Flybase; (2) fold induction in microbiota associated animals vs GF; (3) information on gene function: lower hierarchy GO:Biological process or GO:Molecular function or insight on molecular function by mentioning an Interpro domain present in the protein; (4) Regulation by GATAe; (5) Gene deregulated upon sugar-only diet challenge; (6) Regulation by Sug; (7) Regulation by Myc; (8) Gene regulation in the midgut upon <i>Ecc15</i> infection (<i>Ecc15</i>) and (9) Relish dependence (Rel regulation) for gene expression in the midgut in basal condition (basal) or upon <i>Ecc15</i> infection (inf). For columns “GATAe” the data were collected from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094729#pone.0094729-Buchon3" target="_blank">[21]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094729#pone.0094729-Senger1" target="_blank">[27]</a>; columns “Sugar only” and “Sug” data are from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094729#pone.0094729-Zinke1" target="_blank">[29]</a>; column “Myc” data are from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094729#pone.0094729-Li1" target="_blank">[28]</a>; columns “<i>Ecc15</i>” and “Rel” data are from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094729#pone.0094729-Buchon4" target="_blank">[31]</a>.</p