The two common species of house dust mites (HDMs), Dermatophagoides farinae and D. pteronyssinus, are major sources of allergens in human dwellings worldwide. Many allergens from HDMs have been described, but their extracts vary in immunogens. Mite strains may differ in their microbiomes, which affect mite allergen expression and contents of bacterial endotoxins. Some bacteria, such as the intracellular symbiont Cardinium, can affect both the sex ratio and biochemical pathways of mites, resulting in abundance variations of mite allergens/immunogens. Here, we investigated the bacterial microbiomes of D. farinae and D. pteronyssinus males and females using barcode 16S rDNA sequencing, qPCR, and genomic data analysis. We found a single species of Cardinium associated with D. farinae strains from the USA, China and Europe. Cardinium had high abundance relative to other bacterial taxa and represented 99% of all bacterial DNA reads from female mites from the USA. Cardinium was also abundant with respect to the number of host cells-we estimated 10.4-11.8 cells of Cardinium per single female mite cell. In a European D. farinae strain, Cardinium was more prevalent in females than in males (representing 92 and 67% of all bacterial taxa in females and males, respectively). In contrast, D. pteronyssinus lacked any Cardinium species, and the microbiomes of male and female mites were similar. We produced a Cardinium genome assembly (1.48 Mb; GenBank: PRJNA555788, GCA_007559345.1) associated with D. farinae. The ascertained ubiquity and abundance of Cardinium strongly suggest that this intracellular bacterium plays an important biological role in D. farinae.

Crop Research Institute Drnovska 507 73 161 06 Prague 6 Ruzyne Czechia Department of Biophysics 2nd Faculty of Medicine Charles University 150 00 Prague 5 Czechia Proteomics and Metabolomics Laboratory Crop Research Institute Drnovska 507 73 16106 Prague 6 Ruzyne Czechia

Crop Research Institute Drnovska 507 73 161 06 Prague 6 Ruzyne Czechia Department of Microbiology Nutrition and Dietetics Faculty of Agrobiology Food and Natural Resources Czech University of Life Sciences Kamycka 129 165 21 Prague 6 Suchdol Czechia

Crop Research Institute Drnovska 507 73 161 06 Prague 6 Ruzyne Czechia Department of Parasitology Faculty of Science Charles University Vinicna 7 128 44 Prague 2 Czechia

Department of Ecology and Evolutionary Biology University of Michigan 3600 Varsity Drive Ann Arbor MI 48109 USA Institute of Biology University of Tyumen Pirogova 3 Tyumen Russia 625043

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