Cardinium bacteria are well known as endosymbionts that infect a wide range of arthropods and can manipulate host reproduction to promote their vertical transmission. As intracellular bacteria, Cardinium species undergo dramatic genome evolution, especially their chromosomal genome reduction. Although Cardinium plasmids have been reported to harbor important genes, the role of these plasmids in the genome evolution is yet to be fully understood. In this study, 2 genomes of Cardinium endosymbiont bacteria in astigmatic mites were de novo assembled, including the complete circular chromosomal genome of Cardinium sp. DF that was constructed in high quality using high-coverage long-read sequencing data. Intriguingly, 2 circular plasmids were assembled in Cardinium sp. DF and were identified to be endogenous for over 10 homologous genes shared with the chromosomal genome. Comparative genomics analysis illustrated an outline of the genome evolution of Cardinium bacteria, and the in-depth analysis of Cardinium sp. DF shed light on the multiple roles of endogenous plasmids in the molecular process of the chromosomal genome reduction. The endogenous plasmids of Cardinium sp. DF not only harbor massive homologous sequences that enable homologous recombination with the chromosome, but also can provide necessary functional proteins when the coding genes decayed in the chromosomal genome. IMPORTANCE As bacterial endosymbionts, Cardinium typically undergoes genome reduction, but the molecular process is still unclear, such as how plasmids get involved in chromosome reduction. Here, we de novo assembled 2 genomes of Cardinium in astigmatic mites, especially the chromosome of Cardinium sp. DF was assembled in a complete circular DNA using high-coverage long-read sequencing data. In the genome assembly of Cardinium sp. DF, 2 circular endogenous plasmids were identified to share at least 10 homologous genes with the chromosomal genome. In the comparative analysis, we identified a range of genes decayed in the chromosomal genome of Cardinium sp. DF but preserved in the 2 plasmids. Taken together with in-depth analyses, our results unveil that the endogenous plasmids harbor homologous sequences of chromosomal genome and can provide a structural basis of homologous recombination. Overall, this study reveals that endogenous plasmids participate in the ongoing chromosomal genome reduction of Cardinium sp. DF.
- Klíčová slova
- Cardinium endosymbiont, chromosomal genome reduction, endogenous plasmid, host-associated bacteria,
- MeSH
- Bacteria MeSH
- Bacteroidetes * genetika MeSH
- chromozomy MeSH
- Dermatophagoides farinae * MeSH
- genom bakteriální MeSH
- plazmidy genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
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.
- Klíčová slova
- Acaridida, Allergen production, Astigmata, Cardinium, Dermatophagoides pteronyssinus, Microbiome,
- MeSH
- Bacteroidetes izolace a purifikace MeSH
- Dermatophagoides farinae mikrobiologie MeSH
- Dermatophagoides pteronyssinus mikrobiologie MeSH
- genom bakteriální * MeSH
- mikrobiota MeSH
- sekvenování celého genomu MeSH
- symbióza MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Čína MeSH
- Evropa MeSH
- Spojené státy americké MeSH
The allergen repertoire of the house dust mite, Dermatophagoides farinae, is incomplete despite most mite allergens having been described in this species. Using proteogenomics, we aimed to compare proteins and allergens between sexes and provide a foundation for the identification of novel allergens. Overall, 6297 protein hits were identified, and 2899 and 886 were male- and female-specific, respectively. Removal of trace results narrowed the dataset to 3478 hits, including 275 and 157 male- and female-specific hits, respectively. All 34 WHO/IUIS-approved D. farinae allergens (omitting Der f 17) were identified, and we also identified homologs of the yet undescribed Der f 9 and 38. Der f 27/serpin exhibited the largest sex-dependent difference and was dominant in females. Using official protein sequences, Der f 11, 14, 23, 28 and 30 were identified with low success. However, identification success of Der f 11 and 14 was greatly increased by using longer/complete sequences. Der f 30 is characterized by the same tryptic digests as the more abundant Der f 30 (isoform) identified here. Der f 23 appears to be of low abundance in mite bodies. Der f 28.0101 and Der f 28.0201 were detected at low abundance and in trace amounts, respectively. SIGNIFICANCE: In this work, we performed a proteogenomic annotation of the house dust mite, Dermatophagoides farinae, which is the most important source of house dust allergens. The proteogenomic analysis performed here provides a foundation for not only understanding the biology of the mite but also the identification of novel allergens. This study generated a robust proteomic dataset for D. farinae and reviewed existing and candidate allergens in this species. We stress some pitfalls of high-throughput analyses, especially that improper headers of allergen protein records provided in databases can lead to confusion. Using partial sequences in proteomic identification and quantification can lead to low identification success (low signal intensity or MS/MS counts). Thus, we individually curated the protein sequences for proper identification and quantification. The discovered sex differences can be one factor affecting allergen/immunogen variations in mite extracts. Overall, this work provides a benchmark for accurate identification of mite immunogenic proteins using proteomics.
- Klíčová slova
- Der f 28, Der f 38, Der f 9, Ferritin Der f 30, Label-free proteomics, Serpin Der f 27,
- MeSH
- alergeny genetika imunologie metabolismus MeSH
- Dermatophagoides farinae genetika imunologie metabolismus MeSH
- proteiny členovců genetika imunologie metabolismus MeSH
- proteogenomika metody MeSH
- proteom metabolismus MeSH
- Pyroglyphidae genetika imunologie metabolismus MeSH
- sekvence aminokyselin MeSH
- sekvenční homologie MeSH
- sexuální faktory MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
- Názvy látek
- alergeny MeSH
- proteiny členovců MeSH
- proteom MeSH
- Klíčová slova
- Bartonella, Blattabacterium, Wolbachia, house dust mite, intracellular symbionts, stored product mite,
- MeSH
- Acaridae genetika imunologie MeSH
- alergeny genetika imunologie MeSH
- exprese genu * MeSH
- mikrobiota * MeSH
- stanovení celkové genové exprese MeSH
- transkriptom MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- dopisy MeSH
- práce podpořená grantem MeSH
- Názvy látek
- alergeny MeSH
The variation in house dust mite microbial communities is important because various microorganisms modulate the production of allergens by their mite hosts and/or contaminate immunotherapeutic extracts. Temporal changes in mite microbiomes and the mite culture environment occurring at different stages of mite culture development are particularly understudied in this system. Here, we analyzed the dynamics of microbial communities during the culture growth of Dermatophagoides farinae. Changes in microbiomes were related to three key variables: the mite population density, microbial microcosm respiration and concentration of guanine (the mite nitrogenous waste metabolite). Mite populations exhibited the following phases: exponential growth, plateau and exponential decline. The intracellular bacterium Cardinium and the yeast Saccharomyces cerevisiae prevailed in the internal mite microbiomes, and the bacterium Lactobacillus fermentum was prevalent in the mite diet. The reduction in the mite population size during the late phases of culture development was related to the changes in their microbial profiles: the intracellular bacterium Cardinium was replaced by Staphylococcus, Oceanobacillus and Virgibacillus, and S. cerevisiae was replaced by the antagonistic fungi Aspergillus penicillioides and Candida. Increases in the guanine content were positively correlated with increases in the Staphylococcus and A. penicillioides profiles in the culture environment. Our results show that the mite microbiome exhibits strong, dynamic alterations in its profiles across different mite culture growth stages.
- Klíčová slova
- Dermatophagoides farinae, allergens, bacteria, guanine, microbiome, mite culture, yeasts,
- MeSH
- alergeny MeSH
- Bacteroidetes izolace a purifikace MeSH
- Dermatophagoides farinae růst a vývoj mikrobiologie MeSH
- Limosilactobacillus fermentum izolace a purifikace MeSH
- mikrobiota * MeSH
- Saccharomyces cerevisiae izolace a purifikace MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- alergeny MeSH
Interactions with microorganisms might enable house dust mites (HDMs) to derive nutrients from difficult-to-digest structural proteins and to flourish in human houses. We tested this hypothesis by investigating the effects of changes in the mite culture growth and population of two HDM species on HDM microbiome composition and fitness. Growing cultures of laboratory and industrial allergen-producing populations of Dermatophagoides farinae (DFL and DFT, respectively) and Dermatophagoides pteronyssinus (DPL and DPT, respectively) were sampled at four time points. The symbiotic microorganisms of the mites were characterized by DNA barcode sequencing and quantified by qPCR using universal/specific primers. The population growth of mites and nutrient contents of mite bodies were measured and correlated with the changes in bacteria in the HDM microbiome. The results showed that both the population and culture age significantly influenced the microbiome profiles. Cardinium formed 93% and 32% of the total sequences of the DFL and DFT bacterial microbiomes, respectively, but this bacterial species was less abundant in the DPL and DPT microbiomes. Staphylococcus abundance was positively correlated with increased glycogen contents in the bodies of mites, and increased abundances of Aspergillus, Candida, and Kocuria were correlated with increased lipid contents in the bodies of mites. The xerophilic fungus Wallemia accounted for 39% of the fungal sequences in the DPL microbiome, but its abundance was low in the DPT, DFL, and DFT microbiomes. With respect to the mite culture age, we made three important observations: the mite population growth from young cultures was 5-8-fold higher than that from old cultures; specimens from old cultures had greater abundances of fungi and bacteria in their bodies; and yeasts predominated in the gut contents of specimens from young cultures, whereas filamentous mycelium prevailed in specimens from old cultures. Our results are consistent with the hypothesis that mites derive nutrients through associations with microorganisms.
- Klíčová slova
- Bacteria, Dermatophagoides farinae, Dermatophagoides pteronyssinus, Diet, Fungi, Gut, Nutrition, Symbiosis, Yeasts,
- MeSH
- Bacteria * klasifikace MeSH
- bakteriální RNA analýza MeSH
- druhová specificita MeSH
- fungální RNA analýza MeSH
- houby * klasifikace MeSH
- kvantitativní polymerázová řetězová reakce MeSH
- mikrobiota * MeSH
- populační dynamika MeSH
- Pyroglyphidae mikrobiologie fyziologie MeSH
- RNA ribozomální 16S analýza MeSH
- RNA ribozomální 18S analýza MeSH
- taxonomické DNA čárové kódování MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- bakteriální RNA MeSH
- fungální RNA MeSH
- RNA ribozomální 16S MeSH
- RNA ribozomální 18S MeSH
Background: Tyrophagus putrescentiae is a ubiquitous mite species in soil, stored products and house dust and infests food and causes allergies in people. T. putrescentiae populations harbor different bacterial communities, including intracellular symbionts and gut bacteria. The spread of microorganisms via the fecal pellets of T. putrescentiae is a possibility that has not been studied in detail but may be an important means by which gut bacteria colonize subsequent generations of mites. Feces in soil may be a vector for the spread of microorganisms. Methods: Extracts from used mite culture medium (i.e., residual food, mite feces, and dead mite bodies) were used as a source of feces-inhabiting microorganisms as food for the mites. Two T. putrescentiae populations (L and P) were used for experiments, and they hosted the intracellular bacteria Cardinium and Wolbachia, respectively. The effects of the fecal fraction on respiration in a mite microcosm, mite nutrient contents, population growth and microbiome composition were evaluated. Results: Feces from the P population comprised more than 90% Bartonella-like sequences. Feces from the L population feces hosted Staphylococcus, Virgibacillus, Brevibacterium, Enterobacteriaceae, and Bacillus. The mites from the P population, but not the L population, exhibited increased bacterial respiration in the microcosms in comparison to no-mite controls. Both L- and P-feces extracts had an inhibitory effect on the respiration of the microcosms, indicating antagonistic interactions within feces-associated bacteria. The mite microbiomes were resistant to the acquisition of new bacterial species from the feces, but their bacterial profiles were affected. Feeding of P mites on P-feces-enriched diets resulted in an increase in Bartonella abundance from 6 to 20% of the total bacterial sequences and a decrease in Bacillus abundance. The population growth was fivefold accelerated on P-feces extracts in comparison to the control. Conclusion: The mite microbiome, to a certain extent, resists the acquisition of new bacteria when mites are fed on feces of the same species. However, a Bartonella-like bacteria-feces-enriched diet seems to be beneficial for mite populations with symbiotic Bartonella-like bacteria. Coprophagy on the feces of its own population may be a mechanism of bacterial acquisition in T. putrescentiae.
- Klíčová slova
- Bartonella, bacteria, diets, feces, feeding, fungi, soil, transmission,
- Publikační typ
- časopisecké články MeSH
Mites of the genus Tyrophagus (Acari: Acaridae) are among the most widespread and common mites, inhabiting diverse natural and anthropogenic habitats. Some species are pests of agricultural products and stored food and/or live in house dust, causing allergies to humans. We sequenced 1.2 kb of the mitochondrial COI gene for 38 individuals belonging to seven species of Tyrophagus, including T. curvipenis, T. putrescentiae, T. fanetzhangorum, T. longior, T. perniciosus, and T. cf. similis. Molecular phylogenetic analyses (1) recovered two major clades corresponding to the presence or absence of eyespots, and (2) separated all included morphological species. Tyrophagus curvipenis and T. putrescentiae had the lowest between-species genetic distances (range, mean ± SD): 14.20-16.30, 15.17 ± 0.40 (K2P). The highest within-species variation was found in T. putrescentiae 0.00-4.33, 1.78 ± 1.44 (K2P). In this species, we recovered two distinct groups; however, no geographical or ecological dissimilarities were observed between them. Based on our analyses, we document important morphological differences between T. curvipenis and T. putrescentiae. For the first time, we record the occurrence of T. curvipenis in the New World and suggest that it may be an emerging pest as it is currently spreading in agricultural produce.
- Klíčová slova
- COI, DNA barcode, Genetic distances, Tyrophagus curvipenis, Tyrophagus phylogeny,
- MeSH
- Acaridae anatomie a histologie klasifikace enzymologie genetika MeSH
- biologická evoluce * MeSH
- fylogeneze * MeSH
- mitochondriální proteiny genetika MeSH
- proteiny členovců genetika MeSH
- respirační komplex IV genetika MeSH
- rozšíření zvířat MeSH
- sekvenční analýza DNA MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- mitochondriální proteiny MeSH
- proteiny členovců MeSH
- respirační komplex IV MeSH
