Integrated metatranscriptomics and metaproteomics for the characterization of bacterial microbiota in unfed Ixodes ricinus

Bacterial community of ticks (Acari: Ixodidae) and mammals from Arauca, Colombian Orinoquia

Ticks are obligate hematophagous ectoparasites of vertebrates and are relevant worldwide due to the number of bacterial and other pathogens they can transmit. To date, the knowledge about the microorganisms that ticks harbor and transmit to their hosts is incipient. In this study, 24 samples of mammals belonging to four taxonomic orders and ticks of the genera Amblyomma and Rhipicephalus from the Orinoco region of Colombia were analyzed to described and compare the bacterial microbiome. Genetic extraction was performed, and the V3-V4 region of the 16S rRNA gene was amplified by PCR. Libraries were created, and those samples with adequate quality indices were sequenced using Illumina MiSeq technology. Bacterial taxonomic assignment analyses were conducted through Amplicon Sequence Variants (ASVs) and Operational Taxonomic Units (OTUs). The results correspond to 16 samples that passed the quality filters, with 3218 OTUs (415 families). Although a considerable number of unknown bacteria was found, Enterobacteriaceae, Beijerinckiaceae, Moraxellaceae, and Burkholderiaceae are the most prevalent families, and the presence of the genera Coxiella, Escherichia-Shigella, Enterobacter, which can harbor pathogenic species was confirmed. In individuals of Amblyomma mixtum found actively feeding on Hydrochoerus hydrochaeris, bacteria of the genera Escherichia-Shigella and Enterobacter were documented. Similarly, Rhipicephalus microplus found actively feeding on Odocoileus virginianus cariacou shared Escherichia-Shigella. Ralstonia was shared among the blood samples of H. hydrochaeris, while Anaplasma and Eubacterium were shared in blood and liver samples of O. v. cariacou. Shared bacteria between A. mixtum and R. microplus included Bacillus, Coxiella, and Escherichia-Shigella. The results highlight the need of additional studies in other natural regions of Colombia and other American countries where tick-borne diseases have been detected. Likewise, the recorded data are the first at the level of bacterial communities in ticks of the family Ixodidae and provide valuable knowledge for the understanding host-tick and pathogen interactions.

Diversity of midgut microbiota in ticks collected from white-tailed deer (Odocoileus virginianus) from northern Mexico

Ticks host different pathogens as endosymbiont and nonpathogenic microorganisms and play an important role in reproductive fitness and nutrient provision. However, the bacterial microbiomes of white-tailed deer ticks have received minimal attention. This study aimed to examine the bacterial microbiome of ticks collected from Odocoileus virginianus on the Mexico-United States border to assess differences in microbiome diversity in ticks of different species, sexes, and localities. Five different tick species were collected: Rhipicephalus microplus, Dermacentor nitens, Otobius megnini, Amblyomma cajennense, and A. maculatum. The tick microbiomes were analyzed using next-generation sequencing. Among all tick species, the most predominant phylum was Proteobacteria, followed by Actinobacteria and Firmicutes. The ticks from Tamaulipas and Nuevo León presented the highest bacterial species diversity. Acinetobacter johnsonii and A. lwoffii were the common bacterial species in the microbiome of all ticks, Coxiella were present in R. microplus, and Dermacentor nitens also exhibited a Francisella-like endosymbiont. The microbiome of most females in D. nitens was less diverse than that of males, whereas R. microplus occurs in females, suggesting that microbiome diversity is influenced by sex. In the bacterial communities of A. maculatum and O. megnini, Candidatus Midichloria massiliensis, and Candidatus Endoecteinascidia fumentensis were the most predominant endosymbionts. These results constitute the initial report on these bacteria, and this is also the first study to characterize the microbiome of O. megnini.

Frankenbacteriosis targeting interactions between pathogen and symbiont to control infection in the tick vector

Tick microbiota can be targeted for the control of tick-borne diseases such as human granulocytic anaplasmosis (HGA) caused by model pathogen, Anaplasma phagocytophilum. Frankenbacteriosis is inspired by Frankenstein and defined here as paratransgenesis of tick symbiotic/commensal bacteria to mimic and compete with tick-borne pathogens. Interactions between A. phagocytophilum and symbiotic Sphingomonas identified by metaproteomics analysis in Ixodes scapularis midgut showed competition between both bacteria. Consequently, Sphingomonas was selected for frankenbacteriosis for the control of A. phagocytophilum infection and transmission. The results showed that Franken Sphingomonas producing A. phagocytophilum major surface protein 4 (MSP4) mimic pathogen and reduce infection in ticks by competition and interaction with cell receptor components of infection. Franken Sphingomonas-MSP4 transovarial and trans-stadial transmission suggests that tick larvae with genetically modified Franken Sphingomonas-MSP4 could be produced in the laboratory and released in the field to compete and replace the wildtype populations with associated reduction in pathogen infection/transmission and HGA disease risks.

Characterization of the bacterial microbiome of Swedish ticks through 16S rRNA amplicon sequencing of whole ticks and of individual tick organs

BACKGROUND

The composition of the microbial flora associated with ixodid ticks has been studied in several species, revealing the importance of geographical origin, developmental stage(s) and feeding status of the tick, as well as substantial differences between tissues and organs. Studying the microbiome in the correct context and scale is therefore necessary for understanding the interactions between tick-borne pathogens and other microorganisms as well as other aspects of tick biology.

METHODS

In the present study the microbial flora of whole Ixodes ricinus, I. persulcatus and I. trianguliceps ticks were analyzed with 16S rRNA amplicon sequencing. Additionally, tick organs (midguts, Malpighian tubules, ovaries, salivary glands) from flat and engorged I. ricinus female ticks were examined with the same methodology.

RESULTS

The most abundant bacteria belonged to the group of Proteobacteria (Cand. Midichloria mitochondrii and Cand. Lariskella). 16S amplicon sequencing of dissected tick organs provided more information on the diversity of I. ricinus-associated microbial flora, especially when organs were collected from engorged ticks. Bacterial genera significantly associated with tick feeding status as well as genera associated with the presence of tick-borne pathogens were identified.

CONCLUSIONS

These results contribute to the knowledge of microbial flora associated with ixodid ticks in their northernmost distribution limit in Europe and opens new perspectives for other investigations on the function of these bacteria, including those using other approaches like in vitro cultivation and in vitro models.

The Microbiota of Ixodes ricinus and Dermacentor reticulatus Ticks Collected from a Highly Populated City of Eastern Europe

Recent investigations have examined, through sequencing the V6 region of 16S rRNA gene, the microbiota of questing Ixodes ricinus and Dermacentor reticulatus ticks collected from rural areas of Central (Dnipropetrovs'k (region D) and Poltava (region P)) and Northeastern (Kharkiv (region K)) Ukraine. In addition to defining the bacterial microbiota of both tick species, the previous investigations also revealed a high degree of inter-sex and inter-regional variations in the tick microbiota. As a continuation of the two studies, the present investigation has analyzed individual microbiota of questing I. ricinus (n = 50) and D. reticulatus (n = 50) ticks originating from Kyiv, the largest city of Ukraine. The Kyiv tick microbiota were compared between males and females for each tick species. Additionally, a cross-regional analysis was performed to compare the microbiota of Kyiv ticks to those from regions D, K, and P. Numerous statistically significant inter-sex and inter-regional variations were detected when alpha diversity, beta diversity, the bacterial relative and differential abundances were assessed. The overall results demonstrated that the microbiota of Kyiv ticks were statistically different compared to the ticks of the other three regions. Besides existing climatic and geographical differences between the four regions, the authors hypothesize that various anthropogenic factors of the megapolis (e.g., animal species translocation, land management, ecology) could have contributed to the distinct microbiota of Kyiv ticks observed in this study.

Ecology and evolution of chlamydial symbionts of arthropods

The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae, which is predicted to be the largest and most diverse chlamydial family, with the few described members known to infect arthropod hosts. Using published 16 S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we used a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we added novel complete genome sequences of Rhabdochlamydia porcellionis infecting the woodlouse Porcellio scaber, and of 'Candidatus R. oedothoracis' associated with the linyphiid dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested distinct niches for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia, pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. This type of genome reduction has never been described before for any member of the phylum Chlamydiae. This study provides new insights into the molecular ecology, genomic diversity, and evolution of representatives of one of the most divergent chlamydial families.

Bacterial microbiota analysis demonstrates that ticks can acquire bacteria from habitat and host blood meal

Ticks have a diversity of habitats and host blood meals. Whether and how factors such as tick developmental stages, habitats and host blood meals affect tick bacterial microbiota is poorly elucidated. In the present study, we investigated the bacterial microbiotas of the hard tick Haemaphysalis longicornis, their blood meals and habitats using 16S rRNA gene high-throughput sequencing. The bacterial richness and diversity in ticks varied depending on the tick developmental stage and feeding status. Results showed that fed ticks present a higher bacterial richness suggesting that ticks may acquire bacteria from blood meals. The significant overlap of the bacteria of fed ticks and the host blood also supports this possibility. Another possibility is that blood meals can stimulate the proliferation of certain bacteria. However, most shared bacteria cannot transmit throughout the tick life cycle, as they were not present in tick eggs. The most shared bacteria between ticks and habitats are members of the genera Staphylococcus, Pseudomonas, Enterobacter, Acinetobacter and Stenotrophomonas, suggesting that these environmental bacteria cannot be completely washed away and can be acquired by ticks. The predominant proportion of Coxiella in fed females further demonstrates that this genus is involved in H. longicornis physiology, such as feeding activity and nutritional provision. These findings further reveal that the bacterial composition of ticks is influenced by a variety of factors and will help in subsequent studies of the function of these bacteria.

Current debates and advances in tick microbiome research

The main importance of ticks resides in their ability to harbor pathogens that can be transmitted to terrestrial vertebrates including humans. Recently, studies have focused on the taxonomic and functional composition of the tick microbiome, its microbial diversity and variation under different factors including tick species, sex, and environment among others. Of special interest are the interactions between the tick, the microbiome and pathogens since tick microbiome can influence pathogen colonization within the tick vector, and potentially, transmission to the vertebrate host. In this review, we tackled a synthesis on the growing field of tick microbiomes. We focus on the current state of tick microbiome research, addressing controversial and hotly debated topics and advances in the precise manipulation of tick microbiome. Furthermore, we discuss the innovative anti-tick microbiota vaccines as a possible tool for microbiome modulation and thus, control of tick-borne diseases. Deciphering tick-microbiome pathogen interactions can spur new strategies to control tick-borne diseases via modulation of tick microbiome.

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Whether the diversity observed in tick microbiomes concerns the biology or the methodology remains an open question.

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Tick immunity must play a major role in selecting ‘who stays and who leaves’ the microbiome.

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Anti-tick microbiota vaccines can target specific bacteria and subsequently modulate tick microbiome.

Advances in the Study of the Tick Cattle Microbiota and the Influence on Vectorial Capacity

The information from the tick cattle microbiota suggests that the microbial populations may modulate a successful infection process of the tick-borne pathogens. Therefore, there is a need to know the microbial population and their interactions. In this mini-review, we present several examples of how microbiota regulates the survival of pathogens inside the tick and contributes to fitness, adaptation, and tick immunity, among others. The communication between the tick microbiota and the host microbiota is vital to understanding the pathogen transmission process. As part of the tick microbiota, the pathogen interacts with different microbial populations, including the microorganisms of the host microbiota. These interactions comprise a microsystem that regulates the vectorial capacity involved in tick-borne diseases. The knowledge we have about the vectorial capacity contributes to a better understanding of tick-borne pathogens. Additionally, using approaches based on multi-omics strategies applied to studying the microbiota and its microbiome allows the development of strategies to control ticks. The results derived from those studies reveal the dynamics of the microbiota and potential targets for anti-tick vaccine development. In this context, the anti-microbiota vaccines have emerged as an alternative with a good prognosis. Some strategies developed to control other arthropods vectors, such as paratransgenesis, could control ticks and tick-borne diseases.

Presence of Human Pathogens of the Borrelia burgdorferi sensu lato Complex Shifts the Sequence Read Abundances of Tick Microbiomes in Two German Locations

The distribution of human Lyme borreliosis (LB) is assumed random in Germany, indicating that the human pathogenic species of the Borrelia burgdorferi sensu lato complex (Bb) are similarly distributed as part of the tick microbiome. The aim of this study was to differentiate if the presence of Bb occurs with a defined tick microbiome composition. Furthermore, the effect of location on tick microbiome composition was addressed for two German locations. Therefore, nucleic acid extracts from 82 Borrelia-positive and 118 Borrelia-negative Ixodes ricinus ticks sampled from human hosts in both districts were selected. Nucleic acid extracts were used for human pathogenic Bb species diagnostics based on qPCR and multilocus sequence typing (MLST) and bacterial 16S rRNA gene amplicon sequencing followed by network analyses. As a result, the presence of Bb shifted the sequence read abundances of Candidatus Midichloria, Rickettsia, Pseudomonas, Staphylococcus, and Candidatus Neoehrlichia and their topological roles in the tick microbiome. Moreover, the location was less important in the tick microbiome composition but shifted significantly sequence read abundances of Pseudomonas and Wolbachia as well as the topological role of microbial members. Since the presence of human pathogenic Bb species with other tick-associated pathogens varies regionally, we suggest that a bacterial 16S rRNA gene-based microbiome survey should be implemented in the routine diagnostics for both tick and host if human pathogenic species of Bb were detected. This diagnostic extension will help to optimize therapeutic approaches against Bb infection and co-occurring pathogens.

Grappling with the tick microbiome

Ixodes scapularis and Ixodes pacificus are the predominant vectors of multiple human pathogens, including Borrelia burgdorferi, one of the causative agents of Lyme disease in North America. Differences in the habitats and host preferences of these closely related tick species present an opportunity to examine key aspects of the tick microbiome. While advances in sequencing technologies have accelerated a descriptive understanding of the tick microbiome, molecular and mechanistic insights into the tick microbiome are only beginning to emerge. Progress is stymied by technical difficulties in manipulating the microbiome and by biological variables related to the life cycle of Ixodid ticks. This review highlights these challenges and examines avenues to understand the significance of the tick microbiome in tick biology.

Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions

BACKGROUND

Ticks transmit pathogens of medical and veterinary importance and are an increasing threat to human and animal health. Assessing disease risk and developing new control strategies requires identifying members of the tick-borne microbiota as well as their temporal dynamics and interactions.

METHODS

Using high-throughput sequencing, we studied the Ixodes ricinus microbiota and its temporal dynamics. 371 nymphs were monthly collected during three consecutive years in a peri-urban forest. After a Poisson lognormal model was adjusted to our data set, a principal component analysis, sparse network reconstruction, and differential analysis allowed us to assess seasonal and monthly variability of I. ricinus microbiota and interactions within this community.

RESULTS

Around 75% of the detected sequences belonged to five genera known to be maternally inherited bacteria in arthropods and to potentially circulate in ticks: Candidatus Midichloria, Rickettsia, Spiroplasma, Arsenophonus and Wolbachia. The structure of the I. ricinus microbiota varied over time with interannual recurrence and seemed to be mainly driven by OTUs commonly found in the environment. Total network analysis revealed a majority of positive partial correlations. We identified strong relationships between OTUs belonging to Wolbachia and Arsenophonus, evidence for the presence of the parasitoid wasp Ixodiphagus hookeri in ticks. Other associations were observed between the tick symbiont Candidatus Midichloria and pathogens belonging to Rickettsia. Finally, more specific network analyses were performed on TBP-infected samples and suggested that the presence of pathogens belonging to the genera Borrelia, Anaplasma and Rickettsia may disrupt microbial interactions in I. ricinus.

CONCLUSIONS

We identified the I. ricinus microbiota and documented marked shifts in tick microbiota dynamics over time. Statistically, we showed strong relationships between the presence of specific pathogens and the structure of the I. ricinus microbiota. We detected close links between some tick symbionts and the potential presence of either pathogenic Rickettsia or a parasitoid in ticks. These new findings pave the way for the development of new strategies for the control of ticks and tick-borne diseases. Video abstract.

Conservation genomics reveals pesticide and pathogen exposure in the declining bumble bee Bombus terricola

In recent years, many pollinators have experienced large population declines, which threaten food security and the stability of natural ecosystems. Bumble bees are particularly important because their ability to “buzz” pollinate and tolerate cooler conditions make them critical pollinators for certain plants and regions. Here, we apply a conservation genomics approach to study the vulnerable Bombus terricola. We sequenced RNA from 30 worker abdomens, 18 of which were collected from agricultural sites and 12 of which were collected from nonagricultural sites. We found transcriptional signatures associated with exposure to insecticides, with gene expression patterns suggesting that bumble bees were exposed to neonicotinoids and/or fipronil—two compounds known to negatively impact bees. We also found transcriptional signatures associated with pathogen infections. In addition to the transcriptomic analysis, we carried out a metatranscriptomic analysis and detected five pathogens in the abdomens of workers, three of which are common in managed honey bee and bumble bee colonies. Our conservation genomics study provides functional support for the role of pesticides and pathogen spillover in the decline of B. terricola. We demonstrate that conservation genomics is an invaluable tool which allows researchers to quantify the effects of multiple stressors that impact pollinator populations in the wild.

Metagenomic analysis of individually analyzed ticks from Eastern Europe demonstrates regional and sex-dependent differences in the microbiota of Ixodes ricinus

Understanding the microbial ecology of disease vectors may be useful for development of novel strategies aimed at preventing transmission of vector-borne pathogens. Although Ixodes ricinus is one of the most important tick vectors, the microbiota of this tick has been examined for only limited parts of the globe. To date, the microbiota of I. ricinus ticks collected from Eastern Europe has not been defined. The objective of this study was to compare microbiota of I. ricinus ticks within (males vs. females) and between collection sites that represented three administrative regions of Ukraine, Dnipropetrovs'k (D), Kharkiv (K), and Poltava (P). A total of 89 questing I. ricinus adults were collected from region D (number of ticks, n = 29; 14 males and 15 females), region K (n = 30; 15 males and 15 females) and region P (n = 30; 15 males and 15 females). Each tick was subjected to metagenomic analysis by targeting the V6 region of 16S rRNA gene through the Illumina 4000 Hiseq sequencing. The alpha diversity analysis demonstrated that, regardless of tick sex, patterns of bacterial diversity in ticks from regions K and P were similar, whereas the microbiota of region D ticks was quite distinct. A number of inter-regional differences were detected by most beta diversity metrics for both males and females. The inter-regional variations were also supported by the principal coordinate analysis based on the unweighted UniFrac metrics with three region-specific clusters of female ticks and one distinct cluster of region D males. Lastly, numerous region- and sex-specific differences were also identified in the relative abundance of various bacterial taxa. Collectively, the present findings demonstrate that the microbiota of the I. ricinus tick can exhibit a high degree of variation between tick sexes and geographical regions.

Molecular characterization of bacterial communities of two neotropical tick species (Amblyomma aureolatum and Ornithodoros brasiliensis) using rDNA 16S sequencing

Ticks are one of the main vectors of pathogens for humans and animals worldwide. However, they harbor non-pathogenic microorganisms that are important for their survival, facilitating both their nutrition and immunity. We investigated the bacterial communities associated with two neotropical tick species of human and veterinary potential health importance from Brazil: Amblyomma aureolatum and Ornithodoros brasiliensis. In A. aureolatum (adult ticks collected from wild canids from Southern Brazil), the predominant bacterial phyla were Proteobacteria (98.68%), Tenericutes (0.70%), Bacteroidetes (0.14%), Actinobacteria (0.13%), and Acidobacteria (0.05%). The predominant genera were Francisella (97.01%), Spiroplasma (0.70%), Wolbachia (0.51%), Candidatus Midichloria (0.25%), and Alkanindiges (0.13%). The predominant phyla in O. brasiliensis (adults, fed and unfed nymphs collected at the environment from Southern Brazil) were Proteobacteria (90.27%), Actinobacteria (7.38%), Firmicutes (0.77%), Bacteroidetes (0.44%), and Planctomycetes (0.22%). The predominant bacterial genera were Coxiella (87.71%), Nocardioides (1.73%), Saccharopolyspora (0.54%), Marmoricola (0.42%), and Staphylococcus (0.40%). Considering the genera with potential importance for human and animal health which can be transmitted by ticks, Coxiella sp. was found in all stages of O. brasiliensis, Francisella sp. in all stages of A. aureolatum and in unfed nymphs of O. brasiliensis, and Rickettsia sp. in females of A. aureolatum from Banhado dos Pachecos (BP) in Viamão municipality, Brazil, and in females and unfed nymphs of O. brasiliensis. These results deepen our understanding of the tick-microbiota relationship in Ixodidae and Argasidae, driving new studies with the focus on the manipulation of tick microbiota to prevent outbreaks of tick-borne diseases in South America.

When bacteria meet mitochondria: The strange case of the tick symbiont Midichloria mitochondrii†

Mitochondria are key eukaryotic organelles that perform several essential functions. Not surprisingly, many intracellular bacteria directly or indirectly target mitochondria, interfering with innate immunity, energy production or apoptosis, to make the host cell a more hospitable niche for bacterial replication. The alphaproteobacterium Midichloria mitochondrii has taken mitochondrial targeting to another level by physically colonising mitochondria, as shown by transmission electron micrographs of bacteria residing in the mitochondrial intermembrane space. This unique localization provokes a number of questions around the mechanisms allowing, and reasons driving intramitochondrial tropism. We suggest possible scenarios that could lead to this peculiar localization and hypothesize potential costs and benefits of mitochondrial colonisation for the bacterium and its host.

The bacterial community of the lone star tick (Amblyomma americanum)

BACKGROUND

The lone star tick (Amblyomma americanum), an important vector of a wide range of human and animal pathogens, is very common throughout the East and Midwest of the USA. Ticks are known to carry non-pathogenic bacteria that may play a role in their vector competence for pathogens. Several previous studies using the high throughput sequencing (HTS) technologies reported the commensal bacteria in a tick midgut as abundant and diverse. In contrast, in our preliminary survey of the field collected adult lone star ticks, we found the number of culturable/viable bacteria very low.

METHODS

We aimed to analyze the bacterial community of A. americanum by a parallel culture-dependent and a culture-independent approach applied to individual ticks.

RESULTS

We analyzed 94 adult females collected in eastern Kansas and found that 60.8% of ticks had no culturable bacteria and the remaining ticks carried only 67.7 ± 42.8 colony-forming units (CFUs)/tick representing 26 genera. HTS of the 16S rRNA gene resulted in a total of 32 operational taxonomic units (OTUs) with the dominant endosymbiotic genera Coxiella and Rickettsia (> 95%). Remaining OTUs with very low abundance were typical soil bacterial taxa indicating their environmental origin.

CONCLUSIONS

No correlation was found between the CFU abundance and the relative abundance from the culture-independent approach. This suggests that many culturable taxa detected by HTS but not by culture-dependent method were not viable or were not in their culturable state. Overall, our HTS results show that the midgut bacterial community of A. americanum is very poor without a core microbiome and the majority of bacteria are endosymbiotic.

Interactions Between Ticks and Lyme Disease Spirochetes

Borrelia burgdorferi sensu lato causes Lyme borreliosis in a variety of animals and humans. These atypical bacterial pathogens are maintained in a complex enzootic life cycle that primarily involves a vertebrate host and Ixodes spp. ticks. In the Northeastern United States, I. scapularis is the main vector, while wild rodents serve as the mammalian reservoir host. As B. burgdorferi is transmitted only by I. scapularis and closely related ticks, the spirochete-tick interactions are thought to be highly specific. Various borrelial and arthropod proteins that directly or indirectly contribute to the natural cycle of B. burgdorferi infection have been identified. Discrete molecular interactions between spirochetes and tick components also have been discovered, which often play critical roles in pathogen persistence and transmission by the arthropod vector. This review will focus on the past discoveries and future challenges that are relevant to our understanding of the molecular interactions between B. burgdorferi and Ixodes ticks. This information will not only impact scientific advancements in the research of tick- transmitted infections but will also contribute to the development of novel preventive measures that interfere with the B. burgdorferi life cycle.

Metagenomics for taxonomy profiling: tools and approaches

The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.

Characterization of Microbial Communities in Ixodes persulcatus (Ixodida: Ixodidae), a Veterinary and Medical Important Tick Species in Northeastern China

The importance of ticks in veterinary and medical science has received much attention. The dominant tick species in northeastern China, Ixodes persulcatus tick can transmit various pathogens to humans and animals and there are some studies on the microbiome composition of this tick. Our study characterized the bacterial communities in I. persulcatus by 16S amplicon pyrosequencing and described the differences of microorganisms in male and female tick and assessed the variation of microorganisms in the development stages in northeastern China. We mainly found the following bacteria genera: Pseudomonas (Pseudomonadales: Pseudomonadaceae), Citrobacter (Enterobacteriales: Enterobacteriaceae), and Rickettsia (Rickettsiales: Rickettsiaceae). Rickettsia is common and harmful pathogen transmitted by ticks. Meanwhile, we found there were differences between male and female tick of microbiomes, and the diversity of microbiome increased from engorged female ticks to eggs, but decreased when the eggs were molting into larvae. Our data showed that male ticks exhibited greater microbial diversity than female I. persulcatus tick and larvae presented with a different bacterial community compared to engorged female tick and hatched eggs. These findings may be useful for further understanding the interaction between I. persulcatus and microbiome biology.

Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host

Metaproteomics of gut microbiomes from animal hosts lacking a reference genome is challenging. Here we describe a strategy combining high-resolution metaproteomics and host RNA sequencing (RNA-seq) with generalist database searching to survey the digestive tract of Gammarus fossarum, a small crustacean used as a sentinel species in ecotoxicology. This approach provides a deep insight into the full range of biomasses and metabolic activities of the holobiont components, and differentiates between the intestine and hepatopancreatic caecum.

Effects from diet-induced gut microbiota dysbiosis and obesity can be ameliorated by fecal microbiota transplantation: A multiomics approach

Obesity and its comorbidities are currently considered an epidemic, and the involved pathophysiology is well studied. Hypercaloric diets are tightly related to the obesity etiology and also cause alterations in gut microbiota functionality. Diet and antibiotics are known to play crucial roles in changes in the microbiota ecosystem and the disruption of its balance; therefore, the manipulation of gut microbiota may represent an accurate strategy to understand its relationship with obesity caused by diet. Fecal microbiota transplantation, during which fecal microbiota from a healthy donor is transplanted to an obese subject, has aroused interest as an effective approach for the treatment of obesity. To determine its success, a multiomics approach was used that combined metagenomics and metaproteomics to study microbiota composition and function. To do this, a study was performed in rats that evaluated the effect of a hypercaloric diet on the gut microbiota, and this was combined with antibiotic treatment to deplete the microbiota before fecal microbiota transplantation to verify its effects on gut microbiota-host homeostasis. Our results showed that a high-fat diet induces changes in microbiota biodiversity and alters its function in the host. Moreover, we found that antibiotics depleted the microbiota enough to reduce its bacterial content. Finally, we assessed the use of fecal microbiota transplantation as a complementary obesity therapy, and we found that it reversed the effects of antibiotics and reestablished the microbiota balance, which restored normal functioning and alleviated microbiota disruption. This new approach could be implemented to support the dietary and healthy habits recommended as a first option to maintain the homeostasis of the microbiota.

Comparison of metaproteomics workflows for deciphering the functions of gut microbiota in an animal model of obesity

Metaproteomics has emerged as a new, revolutionary approach to study gut microbiota functionality, but the lack of consistent studies in this field due to the great complexity of samples has prompted to search new strategies to achieve better metaproteome characterization. Some steps in sample preparation and data analysis procedures are critical for obtaining accurate results, therefore protein extraction buffers, digestion procedures and fractionation steps were tested here. Initially, two lysis buffers were used to improve protein extraction, two common digestion protocols were compared, and fractionation processes were employed at both the peptide and protein levels. The combination of these procedures resulted in five different methodologies; SDS buffer, in-gel digestion and fractionation at the peptide level provided the best results. Finally, the metaproteomics workflow was tested in a real case study with obese rats, in which a metagenomics study was previously performed. Important differences in protein levels were observed between groups that were potentially related to the taxonomical family, indicating that functional processes are modulated by the microbiota. Therefore, in addition to the necessity of combining different metaomics approaches, an optimized metaproteomics workflow such as the presented in this study is required to obtain a better understanding of the microbiota function. SIGNIFICANCE: Gut microbiota has emerged as an important factor with affects the health balance in host. To study its function new methodologies are necessary and the most appropriate one seems to be metaproteomics. The lack of studies in this field requires a deeply research in the most accurate workflow to better comprehend such complex samples. In this paper, five different methodologies have been compared, mainly in the most critical steps in classical proteomics and the methodology chosen was validated in a real case study in obese animals.

Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778)

The poultry red mite (PRM), Dermanyssus gallinae (De Geer, 1778), is a worldwide distributed ectoparasite and considered a major pest affecting the laying hen industry in Europe. Based on available information in other ectoparasites, the mite microbiome might participate in several biological processes and the acquisition, maintenance and transmission of pathogens. However, little is known about the role of PRM as a mechanical carrier or a biological vector in the transmission of pathogenic bacteria. Herein, we used a metaproteomics approach to characterize the alphaproteobacteria in the microbiota of PRM, and variations in its profile with ectoparasite development (nymphs vs. adults) and feeding (unfed vs. fed). The results showed that the bacterial community associated with D. gallinae was mainly composed of environmental and commensal bacteria. Putative symbiotic bacteria of the genera Wolbachia, C. Tokpelaia and Sphingomonas were identified, together with potential pathogenic bacteria of the genera Inquilinus, Neorickettsia and Roseomonas. Significant differences in the composition of alphaproteobacterial microbiota were associated with mite development and feeding, suggesting that bacteria have functional implications in metabolic pathways associated with blood feeding. These results support the use of metaproteomics for the characterization of alphaproteobacteria associated with the D. gallinae microbiota that could provide relevant information for the understanding of mite-host interactions and the development of potential control interventions. Research highlights Metaproteomics is a valid approach for microbiome characterization in ectoparasites. Alphaproteobacteria putative bacterial symbionts were identified in D. gallinae. Mite development and feeding were related to variations in bacterial community. Potentially pathogenic bacteria were identified in mite microbiota.

The bacterial microbiome of field-collected Dermacentor marginatus and Dermacentor reticulatus from Slovakia

Background

The important roles of microbial flora in tick biology and ecology have received much attention. Dermacentor marginatus and Dermacentor reticulatus are known vectors of various pathogens across Europe, including Slovakia. However, their bacterial microbiomes are poorly explored.

Methods

In this study, bacterial microbiomes of field-collected D. marginatus and D. reticulatus from Slovakia were characterized using 16S rRNA high-throughput sequencing.

Results

Different analyses demonstrated that the D. marginatus and D. reticulatus microbiomes differ in their diversity and taxonomic structures. Furthermore, species- and sex-specific bacteria were detected in the two species. A possible bacterial pathogen “Candidatus Rhabdochlamydia sp.” was detected from D. marginatus males. Among the observed bacteria, Rickettsia showed high abundance in the two species. Several maternally inherited bacteria such as Coxiella, Arsenophonus, Spiroplasma, Francisella and Rickettsiella, were abundant, and their relative abundance varied depending on tick species and sex, suggesting their biological roles in the two species.

Conclusions

The bacterial microbiomes of field-collected D. marginatus and D. reticulatus were shaped by tick phylogeny and sex. Maternally inherited bacteria were abundant in the two species. These findings are valuable for understanding tick-bacteria interactions, biology and vector competence of ticks.

Electronic supplementary material

The online version of this article (10.1186/s13071-019-3582-9) contains supplementary material, which is available to authorized users.

A metaproteomics approach reveals changes in mandibular lymph node microbiota of wild boar naturally exposed to an increasing trend of Mycobacterium tuberculosis complex infection

Constraints in the characterization of microbiota community that circulates in the host have limited the extent of co-infection studies in natural populations. In this study, we used a metaproteomics approach to characterize the mandibular lymph nodes microbiota of wild boar (Sus scrofa) naturally exposed to an increasing trend of Mycobacterium tuberculosis complex (MTC) infection. Our results showed a reduction in microbiota diversity and changes in the composition, structure and functionality of the microbiota community associated with an increase in tuberculosis prevalence, from 45% in 2002/06 to 83% in 2009/12. These temporal changes were accompanied by an increase in the relative abundance of Babesia, Theileria and Pestivirus genera and a decrease in the Ascogregarina and Chlorella. A positive association was also evidenced between the prevalence of tuberculosis and the presence of microbial proteins responsible for carbohydrate transport and metabolism. Our findings suggest MTC-host-microbiota interactions at the population level, which may occur in order to ensure sufficient metabolic resources for MTC survival, growth and transmission. We strongly recommend the use of metaproteomics when studying microbiota communities in wildlife populations, for which traditional diagnostic techniques are limited and in which new organisms with a pathogenic potential for domestic animals and humans may appear.

Biotic and abiotic factors shape the microbiota of wild-caught populations of the arbovirus vector Culicoides imicola

Biting midges of the genus Culicoides are known vectors of arboviruses affecting human and animal health. However, little is known about Culicoides imicola microbiota and its influence on this insect's biology. In this study, the impact of biotic and abiotic factors on C. imicola microbiota was characterized using shotgun-metagenomic sequencing of whole-body DNA samples. Wild-caught C. imicola adult nulliparous females were sampled in two locations from Sicily, Italy. The climatic variables of temperature and soil moisture from both localities were recorded together with potential host bloodmeal sources. Shared core microbiome among C. imicola populations included Pseudomonas, Escherichia, Halomonas, Candidatus Zinderia, Propionibacterium, and Schizosaccharomyces. Specific and unique taxa were also found in C. imicola from each location, highlighting similarities and differences in microbiome composition between the two populations. DNA and protein identification showed differences in host preferences between the two populations, with Homo sapiens and Canis lupus familiaris L. being the preferred bloodmeal source in both locations. A principal component analysis showed that the combined effect of host preferences (H. sapiens) and local soil moisture factors shape the microbiome composition of wild-caught populations of C. imicola. These results contribute to characterizing the role of the microbiome in insect adaptation and its utility in predicting geographic expansion of Culicoides species with potential implications for the control of vector-borne diseases.

Characterization of the bacterial microbiota in wild-caught Ixodes ventalloi

Exploring the microbial diversity of ticks is crucial to understand geographical dispersion and pathogen transmission. Tick microbes participate in many biological processes implicated in the acquisition, maintenance, and transmission of pathogens, and actively promote host phenotypic changes, and adaptation to new environments. The microbial community of Ixodes ventalloi still remains unexplored. In this study, the bacterial microbiota of wild-caught I. ventalloi was characterized using shotgun-metagenomic sequencing in samples from unfed adults collected during December 2013-January 2014 in two locations from Sicily, Italy. The microbiota identified in I. ventalloi was mainly composed of symbiotic, commensal, and environmental bacteria. Interestingly, we identified the genera Anaplasma and Borrelia as members of the microbiota of I. ventalloi. These results advance our information on I. ventalloi microbiota composition, with potential implications in tick-host adaptation, geographic expansion, and vector competence.