A novel <i>Erwiniaceae</i> gut symbiont modulates gene expression of the intracellular bacterium <i>Cardinium</i> in the stored product mite <i>Tyrophagus putrescentiae</i>

We examined host and bacterial gene expression profiles in the stored product mite <i>Tyrophagus putrescentiae</i> co-infected with <i>Wolbachia</i> (wTPut) and <i>Cardinium</i> (cTPut) while varying the presence of the <i>Erwiniaceae</i> symbiont (SLS). SLS, a novel symbiont in the family <i>Erwiniaceae</i>, with a genome size of 1.7 Mb, is found in 16% of mite species in infected cultures. In addition, SLS was detected in mite feces but not in their eggs. Although <i>Wolbachia</i> expression remained unchanged, the presence or absence of SLS significantly affected <i>Cardinium</i> expression. It indicated that the effect of <i>Wolbachia</i> on SLS was neutral. In SLS-positive samples, <i>Cardinium</i> exhibited 29 upregulated and 48 downregulated genes compared to SLS-negative samples. Furthermore, <i>Cardinium</i> gene expression strongly correlated with mite KEGG gene expression in SLS-positive samples. Positive Spearman's correlations between <i>Cardinium</i> gene expression and mite KEGG immune and regulatory pathways were doubled in SLS-positive compared to SLS-negative samples. The diversity of expressed genes in the mite host decreased in the presence of SLS. <i>Cardinium</i> had more interacting genes to mite host in SLS-positive samples than without SLS. Transposases are the most affected <i>Cardinium</i> genes, showing upregulation in the presence of SLS. Correlation analyses revealed interactions between <i>Cardinium</i> and SLS via mite immune and regulatory pathways, including lysosome, ubiquitin-mediated proteolysis, PIK3_Akt, and cGMP-PKG. The results showed that <i>Cardinium</i> indirectly affects the gut symbionts of mites.IMPORTANCEThis study introduces a new model to analyze interactions between intracellular bacterial symbionts, gut bacterial symbionts, and their mite hosts. Using gene expression correlations, we investigated how the intracellular <i>Cardinium</i> responds to the novel <i>Erwiniaceae</i> gut symbiont in the mold mite <i>Tyrophagus putrescentiae</i>. The data showed that both mite and <i>Cardinium</i> gene expression are different in the samples with and without <i>Erwiniaceae</i> symbionts. In the presence of <i>Erwiniaceae</i> symbionts, <i>Cardinium</i> increased the interaction with the mite host in terms of changes in gene expression. The mite immune and regulatory pathway gene expression is differently correlated to <i>Cardinium</i> genes in relation to <i>Erwiniaceae</i> symbionts. As a well-known producer of allergens, <i>T. putrescentiae</i> physiology and thus its allergen production are influenced by both symbionts, potentially affecting the release of allergens into human environments.