High Throughput Sequencing and Network Analysis Disentangle the Microbial Communities of Ticks and Hosts Within and Between Ecosystems

Exploring the microbiomes of camel ticks to infer vector competence: insights from tissue-level symbiont-pathogen relationships

Ticks are blood-feeding ectoparasites that harbor diverse pathogens and endosymbionts. Their microbial communities vary based on tick species, stage, sex, geographical location, surrounding environment, and tissue type. Understanding tick microbiota at the tissue level is crucial for unraveling how microbiomes are distributed in tick tissues and influence pathogen transmission. We used V1-V2 16 S rRNA gene sequencing to analyze tissue-specific bacterial compositions (hemolymph, saliva, salivary glands, and midgut) of Amblyomma gemma, Rhipicephalus pulchellus, Hyalomma dromedarii, and Hyalomma rufipes ticks collected from camels in Marsabit County, northern Kenya. The V1-V2 region of the 16 S rRNA gene effectively differentiated 43 Rickettsia africae and 16 Rickettsia aeschlimannii tick samples from other rickettsial species, as well as Coxiella endosymbionts from Coxiella burnetii. In contrast, the V3-V4 region sequences of these species could not be clearly distinguished. Coxiella endosymbionts were most common in Am. gemma and Rh. pulchellus, while Francisella endosymbionts predominated in Hyalomma ticks; both were primarily localized in the salivary glands. High abundances of Coxiella endosymbionts, as well as Pseudomonas, were associated with the absence or low abundance of Rickettsia pathogens in both Am. gemma and Rh. pulchellus, suggesting competitive interactions between these microbes. Additionally, Proteus mirabilis, an opportunistic pathogen of the urinary tract in humans, was found predominantly in Hyalomma ticks, except for the salivary glands, which were most abundant with Francisella endosymbionts. Furthermore, we detected the Acinetobacter, Pseudomonas, and Corynebacterium genera in all the tick tissues, supporting the hypothesis that these bacteria might circulate between camel blood and ticks. Saliva and hemolymph generally harbored more extracellular bacteria than the salivary glands and midgut. This study provides a new approach to unravel tick-endosymbiont-pathogen interactions by examining the tissue localization of tick-borne pathogens and symbionts in Am. gemma, Rh. pulchellus, Hy. dromedarii, and Hy. rufipes from camels in northern Kenya. Our findings establish a baseline for developing an understanding of the functional capacities of symbionts and for designing symbiont-based control strategies.

Microbial community variations in adult Hyalomma dromedarii ticks from single locations in Saudi Arabia and Tunisia

Introduction

The camel-infesting tick, Hyalomma dromedarii, is a prominent ectoparasite in the Middle East and North Africa (MENA) region, critically impacting camel health and acting as a vector for tick-borne pathogens. Despite prior studies on its microbiota, the effects of geographic origin and sex on microbial community structure and functional stability remain poorly understood.

Methods

To address this, we characterized the bacterial microbiota of H. dromedarii ticks collected from camels in Tunisia (TUN) and Saudi Arabia (SA) using 16S rRNA gene sequencing, microbial network analysis, and metabolic pathway prediction.

Results

Our findings indicate a dominant presence of Francisella endosymbionts in Tunisian ticks, suggesting adaptive roles of H. dromedarii ticks in arid ecosystems. Keystone taxa, particularly Staphylococcus and Corynebacterium, were identified as central to microbial network structure and resilience. Moreover, network robustness analyses demonstrated enhanced ecological stability in the Tunisian tick microbiota under perturbation, indicative of higher resilience to environmental fluctuations compared to Saudi Arabian ticks. Additionally, functional pathway predictions further revealed geographically distinct metabolic profiles between both groups (Tunisia vs. Saudi Arabia and males vs. females), underscoring environmental and biological influences on H. dromedarii microbiota assembly.

Discussion

These results highlight region-specific and sex-specific microbial adaptations in H. dromedarii, with potential implications for pathogen transmission dynamics and vector resilience. Understanding these microbial interactions may contribute to improved strategies for tick control and tick-borne disease prevention.

Microbiota profile in organs of the horseflies (Diptera: Tabanidae) in Northeastern China

Tabanids, commonly known as horseflies and belonging to the family Tabanidae, are blood-feeding arthropods (BFA) found worldwide. They are known for their ability to mechanically and biologically transmit various animal pathogens. Tabanids are potential vectors for diseases such as Francisella tularensis, Anaplasma marginale, Theileria spp., and contributors to lumpy skin diseases. Despite their involvement in common BFA studies, tabanids have not been extensively explored in microbiome research. In this study, the microbiota structure and composition in various organs of four distinct genera of tabanids: Atylotus, Haematopota, Tabanus, and Hybomitra were examined. High-throughput sequencing of the bacterial 16S rRNA gene was performed to gain insights into the microbial communities associated with the different tabanid species. Result display that microbiota composition and diversity, including Firmicutes, Proteobacteria, and Bacteroidetes, varied significantly among the different organs, with the ovaries exhibiting significantly higher diversity. Apart from the Haematopota genus, Tenericutes were enriched in the midgut of other tabanid species, whereas the Malpighian tubules exhibited a higher abundance of Bacteroides. Notably, the ovarian microbiota structure was conserved among the four tabanid species, indicating its potential association with reproductive development. Evaluation of the potential pathogen risk revealed putative pathogens in over 100 genera associated with these tabanid commensal organisms. Twenty genera were annotated as zoonotic agents with a high abundance of Citrobacter and Brucella, highlighting the presence of this important group of zoonotic pathogens. Functional predictions of vector-microbiota interactions indicate that microbiota significantly affects vector biological traits and can influence pathogen transmission via direct interactions or by regulating host immunity and nutrition. For the first time, the distribution characteristics and functions of four genera of horsefly microbiota were analyzed, revealing the presence of multiple potential pathogenic microorganisms. These findings provide valuable insights for future research and the development of symbiotic-based strategies to control insect-borne diseases among tabanids.

Retrospective Analysis of Potential Lyme Disease Clinical Cases in Argentina

Lyme disease, a multisystemic infectious disorder caused by pathogenic spirochetes of the genus Borrelia transmitted by the bite of ticks, typically from the family Ixodidae, pose a significant public health issue worldwide. The Borrelia burgdorferi sensu lato (s.l.) group encompasses the Borrelia Lyme Group (LG), Borrelia Echidna-Reptile Group (REPG), and Borrelia Relapsing Fever Group (RFG), with some species remaining unclassified due to culturing challenges. Research into B. burgdorferi s.l. infection (Lyme Group) has intensified, focusing on its epidemiology, diagnosis, and treatment. Originally identified in North America and Europe, Lyme disease has now become a global concern, with Latin American countries reporting the microorganism, the disease, and/or its vectors. In Argentina, the presence of B. burgdorferi and Lyme disease has sparked significant scientific and medical debate. Ecological changes due to climate and habitat shifts have expanded the geographical distribution of these ticks. Argentina, with its diverse geography and climate, hosts various tick species that could potentially act as Lyme disease vectors, raising important public health questions. The confirmed presence of B. burgdorferi s.l. and Lyme disease in Argentina remains contentious but relevant, necessitating thorough scientific and medical examination. This work aims to enhance understanding and discussion of Lyme disease in Argentina by presenting clinical cases and their laboratory analyses, highlighting the disease's presence and implications in the country. Through documenting suspected clinical cases and analyzing available data on B. burgdorferi and Lyme disease in Argentina, this study seeks to contribute to the understanding of the disease's current status and inform future research, prevention, and control strategies in the region. The goal is to provide a basis for addressing Lyme disease's public health impact in Argentina and promote further investigation into this evolving issue.

Metatranscriptomic investigation of single Ixodes pacificus ticks reveals diverse microbes, viruses, and novel mRNA-like endogenous viral elements

Ticks are increasingly important vectors of human and agricultural diseases. While many studies have focused on tick-borne bacteria, far less is known about tick-associated viruses and their roles in public health or tick physiology. To address this, we investigated patterns of bacterial and viral communities across two field populations of western black-legged ticks (Ixodes pacificus). Through metatranscriptomic analysis of 100 individual ticks, we quantified taxon prevalence, abundance, and co-occurrence with other members of the tick microbiome. In addition to commonly found tick-associated microbes, we assembled 11 novel RNA virus genomes from Rhabdoviridae, Chuviridae, Picornaviridae, Phenuiviridae, Reoviridae, Solemovidiae, Narnaviridae and two highly divergent RNA virus genomes lacking sequence similarity to any known viral families. We experimentally verified the presence of these in I. pacificus ticks across several life stages. We also unexpectedly identified numerous virus-like transcripts that are likely encoded by tick genomic DNA, and which are distinct from known endogenous viral element-mediated immunity pathways in invertebrates. Taken together, our work reveals that I. pacificus ticks carry a greater diversity of viruses than previously appreciated, in some cases resulting in evolutionarily acquired virus-like transcripts. Our findings highlight how pervasive and intimate tick-virus interactions are, with major implications for both the fundamental biology and vectorial capacity of I. pacificus ticks.

IMPORTANCE

Ticks are increasingly important vectors of disease, particularly in the United States where expanding tick ranges and intrusion into previously wild areas has resulted in increasing human exposure to ticks. Emerging human pathogens have been identified in ticks at an increasing rate, and yet little is known about the full community of microbes circulating in various tick species, a crucial first step to understanding how they interact with each and their tick host, as well as their ability to cause disease in humans. We investigated the bacterial and viral communities of the Western blacklegged tick in California and found 11 previously uncharacterized viruses circulating in this population.

The microbiome dynamics and interaction of endosymbiotic Symbiodiniaceae and fungi are associated with thermal bleaching susceptibility of coral holobionts

The thermal bleaching percentage of coral holobionts shows interspecific differences under heat-stress conditions, which are closely related to the coral-associated microbiome. However, the ecological effects of community dynamics and interactions between Symbiodiniaceae and fungi on coral thermal bleaching susceptibility remain unclear. In this study, we analyzed the diversity, community structure, functions, and potential interaction of Symbiodiniaceae and fungi among 18 coral species from a high thermal bleaching risk atoll using next-generation sequencing. The results showed that heat-tolerant C3u sub-clade and Durusdinium dominated the Symbiodiniaceae community of corals and that there were no core amplicon sequence variants in the coral-associated fungal community. Fungal richness and the abundance of confirmed functional animal-plant pathogens were significantly positively correlated with the coral thermal bleaching percentage. Fungal indicators, including Didymellaceae, Chaetomiaceae, Schizophyllum, and Colletotrichum, were identified in corals. Each coral species had a complex Symbiodiniaceae-fungi interaction network (SFIN), which was driven by the dominant Symbiodiniaceae sub-clades. The SFINs of coral holobionts with low thermal bleaching susceptibility exhibited low complexity and high betweenness centrality. These results indicate that the extra heat tolerance of coral in Huangyan Island may be linked to the high abundance of heat-tolerant Symbiodiniaceae. Fungal communities have high interspecific flexibility, and the increase of fungal diversity and pathogen abundance was correlated with higher thermal bleaching susceptibility of corals. Moreover, fungal indicators were associated with the degrees of coral thermal bleaching susceptibility, including both high and intermediate levels. The topological properties of SFINs suggest that heat-tolerant coral have limited fungal parasitism and strong microbial network resilience.IMPORTANCEGlobal warming and enhanced marine heatwaves have led to a rapid decline in coral reef ecosystems worldwide. Several studies have focused on the impact of coral-associated microbiomes on thermal bleaching susceptibility in corals; however, the ecological functions and interactions between Symbiodiniaceae and fungi remain unclear. We investigated the microbiome dynamics and potential interactions of Symbiodiniaceae and fungi among 18 coral species in Huangyan Island. Our study found that the Symbiodiniaceae community of corals was mainly composed of heat-tolerant C3u sub-clade and Durusdinium. The increase in fungal diversity and pathogen abundance has close associations with higher coral thermal bleaching susceptibility. We first constructed an interaction network between Symbiodiniaceae and fungi in corals, which indicated that restricting fungal parasitism and strong interaction network resilience would promote heat acclimatization of corals. Accordingly, this study provides insights into the role of microorganisms and their interaction as drivers of interspecific differences in coral thermal bleaching.

Evolutionary radiation and microbial community dynamics shape the thermal tolerance of Fungiidae in the southern South China Sea

Fungiidae have shown increased thermal adaptability in coral reef ecosystems under global warming. This study analyzes the evolutionary divergence and microbial communities of Fungiidae in the Sanjiao Reef of the southern South China Sea and explores the impact of coral evolution radiation and microbial dynamics on the heat tolerance of Fungiidae. The results found that Cycloseris was an ancient branch of Fungiidae, dating back approximately 147.8953 Mya, and Fungiidae differentiated into two ancestral clades (clades I and II) before 107.0312 Ma. Fungiidae exhibited specific symbioses with the Cladocopium C27 sub-clade. Notably, the Cladocopium C1 sub-clade has a high relative abundance in clade I, whereas the heat-tolerant Cladocopium C40 and C3u sub-clades subdominante in clade II. Regarding bacterial communities, Cycloseris costulata, the earliest divergent species, had higher bacterial β-diversity, while the latest divergent species, Lithophyllon scabra, displayed lower bacterial α-diversity and higher community stability. Beneficial bacteria dominante Fungiidae's bacterial community (54%). The co-occurrence network revealed that microbial networks in clade II exhibited lower complexity and greater resilience than those in clade I. Our study highlights that host evolutionary radiation and microbial communities shaped Fungiidae's thermal tolerance. The variability in subdominant Symbiodiniaceae populations may contribute to interspecific differences in thermal tolerance along the evolutionary branches of Fungiidae. The presence of abundant beneficial bacteria may further enhance the thermal ability of the Fungiidae. Furthermore, the later divergent species of Fungiidae have stronger heat tolerance, possibly driven by the increased regulation ability of the host on the bacterial community, greater microbial community stability, and interaction network resistance.IMPORTANCECoral reefs are facing significant threats due to global warming. The heat tolerance of coral holobionts depends on both the coral host and its microbiome. However, the association between coral evolutionary radiation and interspecific differences in microbial communities remains unclear. In this study, we investigated the role of evolutionary radiation and microbial community dynamics in shaping the thermal acclimation potential of Fungiidae in the Sanjiao Reef of the southern South China Sea. The study's results suggest that evolutionary radiation enhances the thermal tolerance of Fungiidae. Fungiidae species that have diverged more recently have exhibited a higher presence of heat-tolerant Symbiodiniaceae taxa, more stable bacterial communities, and a robust and resilient microbial interaction network, improving the thermal adaptability of Fungiidae. In summary, this study provides new insights into the thermal adaptation patterns of corals under global warming conditions.

Ixodes ricinus tick bacteriome alterations based on a climatically representative survey in Hungary

IMPORTANCE

Climate-sensitive disease vectors, such as ticks, respond to the environment with changes in their microbiome. These changes can affect the emergence or re-emergence of various vector-borne pathogens, such as the causative agent of Lyme borreliosis (LB) or tick-borne encephalitis. This aspect is particularly emphasized in light of climate change. The climatically representative assessment of microbiome differences in various developmental stages of the most common Central European tick species, Ixodes ricinus, deepens our understanding of the potential climatic factors behind microbial relative abundance and interaction changes. This knowledge can support the development of novel disease vector control strategies.

Cross-alteration of murine skin and tick microbiome concomitant with pathogen transmission after Ixodes ricinus bite

BACKGROUND

Ticks are major vectors of diseases affecting humans such as Lyme disease or domestic animals such as anaplasmosis. Cross-alteration of the vertebrate host skin microbiome and the tick microbiome may be essential during the process of tick feeding and for the mechanism of pathogen transmission. However, it has been poorly investigated.

METHODS

We used mice bitten by field-collected ticks (nymphs and adult ticks) in different experimental conditions to investigate, by 16S rRNA gene metabarcoding, the impact of blood feeding on both the mouse skin microbiome and the tick microbiome. We also investigated by PCR and 16S rRNA gene metabarcoding, the diversity of microorganisms transmitted to the host during the process of tick bite at the skin interface and the dissemination of the pathogen in host tissues (blood, heart, and spleen).

RESULTS

Most of the commensal bacteria present in the skin of control mice were replaced during the blood-feeding process by bacteria originating from the ticks. The microbiome of the ticks was also impacted by the blood feeding. Several pathogens including tick-borne pathogens (Borrelia/Borreliella, Anaplasma, Neoehrlichia, Rickettsia) and opportunistic bacteria (Williamsia) were transmitted to the skin microbiome and some of them disseminated to the blood or spleen of the mice. In the different experiments of this study, skin microbiome alteration and Borrelia/Borreliella transmission were different depending on the tick stages (nymphs or adult female ticks).

CONCLUSIONS

Host skin microbiome at the bite site was deeply impacted by the tick bite, to an extent which suggests a role in the tick feeding, in the pathogen transmission, and a potentially important impact on the skin physiopathology. The diversified taxonomic profiles of the tick microbiome were also modified by the blood feeding. Video Abstract.

Comparative Microbiome Analysis of Three Epidemiologically Important Tick Species in Latvia

(1) Background: Amplicon-based 16S rRNA profiling is widely used to study whole communities of prokaryotes in many niches. Here, we comparatively examined the microbial composition of three tick species, Ixodes ricinus, Ixodes persulcatus and Dermacentor reticulatus, which were field-collected in Latvia. (2) Methods: Tick DNA samples were used for microbiome analysis targeting bacterial 16S rDNA using next-generation sequencing (NGS). (3) Results: The results showed significant differences in microbial species diversity and composition by tick species and life stage. A close similarity between microbiomes of I. ricinus and I. persulcatus ticks was observed, while the D. reticulatus microbiome composition appeared to be more distinct. Significant differences in alpha and beta microbial diversity were observed between Ixodes tick life stages and sexes, with lower taxa richness indexes obtained for female ticks. The Francisella genus was closely associated with D. reticulatus ticks, while endosymbionts Candidatus Midichlorii and Candidatus Lariskella were associated with I. ricinus and I. persulcatus females, respectively. In I. ricinus females, the endosymbiont load negatively correlated with the presence of the Rickettsia genus. (4) Conclusions: The results of this study revealed important associations between ticks and their microbial community and highlighted the microbiome features of three tick species in Latvia.

Characterization of bacterial communities in ticks parasitizing cattle in a touristic location in southwestern China

The purpose of this study was to investigate tick species around Mount Fanjing and analyze bacterial communities in two species - Rhipicephalus microplus and Haemaphysalis longicornis - parasitizing cattle in Tongren, Guizhou province, Southwest China, using high-throughput sequencing methods. In April 2019, ticks were collected from five sites in Jiangkou County, Yinjiang County, and Songtao County. In total, 296 ticks were collected, comprising two genera and three species: H. longicornis, Haemaphysalis flava, and R. microplus. Rhipicephalus microplus was the most representative species (57.4%) within the collected group, being the dominant species in Tongren City, followed by H. longicornis (39.5%) and H. flava (3.0%). Beta-diversity analysis revealed differences in bacterial community composition among the tick species. The bacterial community structure of R. microplus collected in the three counties was highly similar. Chlorella and Bacillus were highly abundant in H. longicornis. Rickettsia was detected at high relative abundance in R. microplus but in low relative abundance in H. longicornis, suggesting that Rickettsia is more associated with R. microplus than with H. longicornis. More in-depth investigations are needed to determine the pathogenic risk of Rickettsia and its relationship with the host. This is the first survey on tick-borne bacterial communities in this area, which is of great significance for the prevention and control of tick-borne diseases locally.

Comparison of salivary gland and midgut microbiome in the soft ticks Ornithodoros erraticus and Ornithodoros moubata

Introduction

Ornithodoros erraticus and Ornithodoros moubata are the main vectors of African swine fever virus (ASFV) and the human relapsing fever spirochetes Borrelia hispanica and Borrelia crocidurae in the Mediterranean region and Borrelia duttoni in continental Africa. Manipulation of the tick microbiome has been shown to reduce vector fitness and competence in tick vectors, suggesting that the identification of key microbial players associated with tick tissues can inform interventions such as anti-microbiota vaccines to block pathogen development in the midgut and/or salivary glands.

Methods

In this study, we analyzed and compared the microbiome of the salivary glands and midgut of O. erraticus and O. moubata. For the taxonomic and functional characterization of the tissue-specific microbiome, we used 16S rRNA amplicon sequencing and prediction of metabolic profiles using PICRUSt2. Co-occurrence networks were built to characterize the community assembly and identify keystone taxa in each tick species.

Results

Our results revealed differences in the composition, diversity, and assembly of the bacterial microbiome of salivary glands and midgut within each tick species, but differences were more noticeable in O. moubata. Differences were also found in the microbiome of each tissue, salivary gland and midgut, between species. However, the 'Core Association Networks (CAN)' analysis revealed conserved patterns of interacting taxa in tissues within and between tick species. Different keystone taxa were identified in O. erraticus and O. moubata tissues, but Muribaculaceae and Alistipes were found as keystone taxa in the salivary glands of both tick species which justifies their use as anti-microbiota vaccine candidates to alter the microbiome and reduce tick fitness and/or block pathogen transmission. The high similarity of predicted metabolic pathways profiles between tissues of the two tick species suggests that taxonomic variability of the microbiome is not associated with significant changes in microbial functional profiles.

Conclusion

We conclude that the taxonomic structure of the microbiome in O. erraticus and O. moubata is tissue-specific, suggesting niche partitioning of bacterial communities associated to these soft ticks. However, shared keystone taxa and conserved patterns of interacting taxa between tissues and tick species suggest the presence of key microbial players that could be used as anti-microbiota vaccine candidates to affect tick physiology and/or pathogen colonization.

What do we know about the microbiome of I. ricinus?

I. ricinus is an obligate hematophagous parasitic arthropod that is responsible for the transmission of a wide range of zoonotic pathogens including spirochetes of the genus Borrelia, Rickettsia spp., C. burnetii, Anaplasma phagocytophilum and Francisella tularensis, which are part the tick´s microbiome. Most of the studies focus on "pathogens" and only very few elucidate the role of "non-pathogenic" symbiotic microorganisms in I. ricinus. While most of the members of the microbiome are leading an intracellular lifestyle, they are able to complement tick´s nutrition and stress response having a great impact on tick´s survival and transmission of pathogens. The composition of the tick´s microbiome is not consistent and can be tied to the environment, tick species, developmental stage, or specific organ or tissue. Ovarian tissue harbors a stable microbiome consisting mainly but not exclusively of endosymbiotic bacteria, while the microbiome of the digestive system is rather unstable, and together with salivary glands, is mostly comprised of pathogens. The most prevalent endosymbionts found in ticks are Rickettsia spp., Ricketsiella spp., Coxiella-like and Francisella-like endosymbionts, Spiroplasma spp. and Candidatus Midichloria spp. Since microorganisms can modify ticks' behavior, such as mobility, feeding or saliva production, which results in increased survival rates, we aimed to elucidate the potential, tight relationship, and interaction between bacteria of the I. ricinus microbiome. Here we show that endosymbionts including Coxiella-like spp., can provide I. ricinus with different types of vitamin B (B2, B6, B7, B9) essential for eukaryotic organisms. Furthermore, we hypothesize that survival of Wolbachia spp., or the bacterial pathogen A. phagocytophilum can be supported by the tick itself since coinfection with symbiotic Spiroplasma ixodetis provides I. ricinus with complete metabolic pathway of folate biosynthesis necessary for DNA synthesis and cell division. Manipulation of tick´s endosymbiotic microbiome could present a perspective way of I. ricinus control and regulation of spread of emerging bacterial pathogens.

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.

Influence of tick sex and geographic region on the microbiome of Dermacentor variabilis collected from dogs and cats across the United States

As tick-borne diseases continue to increase across North America, current research strives to understand how the tick microbiome may affect pathogen acquisition, maintenance, and transmission. Prior high throughput amplicon-based microbial diversity surveys of the widespread tick Dermacentor variabilis have suggested that life stage, sex, and geographic region may influence the composition of the tick microbiome. Here, adult D. variabilis ticks (n = 145) were collected from dogs and cats from 32 states with specimens originating from all four regions of the United States (West, Midwest, South, and Northeast), and the tick microbiome was examined via V4-16S rRNA gene amplification and Illumina sequencing. A total of 481,246 bacterial sequences were obtained (median 2924 per sample, range 399-11,990). Fifty genera represented the majority (>80%) of the sequences detected, with the genera Allofrancisella and Francisella being the most abundant. Further, 97%, 23%, and 5.5% of the ticks contained sequences belonging to Francisella spp., Rickettsia spp., and Coxiella spp., respectively. No Ehrlichia spp. or Anaplasma spp. were identified. Co-occurrence analysis, by way of correlation coefficients, between the top 50 most abundant genera demonstrated five strong positive and no strong negative correlation relationships. Geographic region had a consistent effect on species richness with ticks from the Northeast having a significantly greater level of richness. Alpha diversity patterns were dependent on tick sex, with males exhibiting higher levels of diversity, and geographical region, with higher level of diversity observed in ticks obtained from the Northeast, but not on tick host. Community structure, or beta diversity, of tick microbiome was impacted by tick sex and geographic location, with microbiomes of ticks from the western US exhibiting a distinct community structure when compared to those from the other three regions (Northeast, South, and Midwest). In total, LEfSe (Linear discriminant analysis Effect Size) identified 18 specific genera driving these observed patterns of diversity and community structure. Collectively, these findings highlight the differences in bacterial diversity of D. variabilis across the US and supports the interpretation that tick sex and geographic region affects microbiome composition across a broad sampling distribution.

MicNet toolbox: Visualizing and unraveling a microbial network

Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorporates the use of UMAP, a dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density; on the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple the resulting networks with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) we validate the improvements of our new version of SparCC. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data. This easy-to-use implementation is aimed to microbial ecologists with little to no experience in programming, while the most experienced bioinformatics will also be able to manipulate the source code's functions with ease.

Assessing Temporal Changes in Microbial Communities in Hyalomma dromedarii Collected From Camels in the UAE Using High-Throughput Sequencing

Ticks (Acari) are ectoparasites of animals that harbor communities of microbes of importance to animal and human health. Microbial communities associated with ticks exhibit temporal patterns of variation in their composition, with different genera dominating at different times of the year. In this study, molecular tools were used to assess the composition of the microbial communities associated with Hyalomma dromdarii. Adult ticks were collected every month for 1 year from 25 camels in the UAE. A total of 12 DNA pools were prepared (one pool for each month). We monitored the microbiota of ticks using high-throughput sequencing of the V3–V4 region of the bacterial 16S rRNA gene. A total of 614 operational taxonomic units were produced through de novo clustering and belonged to 17 phyla, 30 classes, 46 orders, 118 families, and 222 genera. Fifteen bacterial families were found to be the most abundant. The dominant bacterial communities associated with H. dromedarii belonged to the genera Staphylococcus, Bacillus, Francisella, and Corynebacterium, which were reported with high relative abundance from all months. No significant correlation occurred between the abundance of microbial families or genera in H. dromedarii ticks and the ambient temperature. Our findings revealed, for the first time in the UAE, temporal fluctuations of microbial communities in H. dromedarii ticks and provided key insights on the interaction between different microbial groups. Moreover, our results contribute to the current understanding of disease development and allow more investigations for potentially pathogenic microbiota.

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.

The Isolation of Culturable Bacteria in Ixodes ricinus Ticks of a Belgian Peri-Urban Forest Uncovers Opportunistic Bacteria Potentially Important for Public Health

Most bacteria found in ticks are not pathogenic to humans but coexist as endosymbionts and may have effects on tick fitness and pathogen transmission. In this study, we cultured and isolated 78 bacteria from 954 Ixodes ricinus ticks collected in 7 sites of a Belgian peri-urban forest. Most isolated species were non-pathogenic environmental microorganisms, and were from the Firmicutes (69.23%), Actinobacteria (17.95%) and Proteobacteria (3.84%) phyla. One bacterium isolate was particularly noteworthy, Cedecea davisae, a rare opportunistic bacterium, naturally resistant to various antibiotics. It has never been isolated from ticks before and this isolated strain was resistant to ampicillin, cefoxitin and colistin. Although cultivable bacteria do not represent the complete tick microbiota, the sites presented variable bacterial compositions and diversities. This study is a first attempt to describe the culturable microbiota of ticks collected in Belgium. Further collections and analyses of ticks of different species, from various areas and using other bacterial identification methods would strengthen these results. However, they highlight the importance of ticks as potential sentinel for opportunistic bacteria of public health importance.

Reconstruction of mitochondrial genomes from raw sequencing data provides insights on the phylogeny of Ixodes ticks and cautions for species misidentification

High-throughput sequencing (HTS) technology has profoundly been involved in sequencing whole genomes of several organisms in a fast and cost-effective manner. Although HTS provides an alternative biomonitoring method to the time-consuming and taxonomy-expertise dependent morphological approach, still we cannot rule out the possibility of the impediment and misidentification biases. In this article we aim to retrieve whole mitochondrial genome (mitogenome) sequences from publicly available raw sequencing data for phylogenetic comparison of Ixodes persulcatus. For this comparison, we sequenced whole mitogenomes of four I. persulcatus ticks from Japan and constructed mitogenomes from raw sequencing data of 74 I. persulcatus ticks from China. Bayesian phylogenetic trees were inferred by the concatenated fifteen mitochondrial genes. We further tested our results by the phylogenetic analysis of cytochrome c oxidase subunit 1 (cox1) gene and internal transcribed spacer 2 (ITS2) sequences. Our findings showed that 70 constructed mitogenomes from China were clustered with the sequenced four mitogenomes of I. persulcatus from Japan. We also revealed that mitogenome sequences retrieved from two data sets CRR142297 and CRR142298 were clustered with Ixodes nipponensis. Moreover, other two mitogenome sequences from CRR142310 and CRR142311 formed a clade with Ixodes pavlovskyi. The phylogenetic analysis of cox1 gene and ITS2 sequences confirmed the identification errors of these four samples. The overall phylogenetics in our study concluded that accurate morphological identification is necessary before implementing HTS to avoid any misidentification biases.

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.

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.

Resistance to Ticks and the Path to Anti-Tick and Transmission Blocking Vaccines

The medical and veterinary public health importance of ticks and tick-borne pathogens is increasing due to the expansion of the geographic ranges of both ticks and pathogens, increasing tick populations, growing incidence of tick-borne diseases, emerging tick transmitted pathogens, and continued challenges of achieving effective and sustained tick control. The past decades show an increasing interest in the immune-mediated control of tick infestations and pathogen transmission through the use of vaccines. Bovine tick resistance induced by repeated infestations was reported over a century ago. This review addresses the phenomena and immunological underpinning of resistance to tick infestation by livestock and laboratory animals; the scope of tick countermeasures to host immune defenses; and the impact of genomics, functional genomics, and proteomics on dissecting complex tick-host-pathogen interactions. From early studies utilizing tick tissue extracts to salivary gland derived molecules and components of physiologically important pathways in tick gut and other tissues, an increased understanding of these relationships, over time, impacted the evolution of anti-tick vaccine antigen selection. Novel antigens continue to emerge, including increased interest in the tick microbiome. Anti-tick and transmission blocking vaccines targeting pathogen reservoirs have the potential to disrupt enzootic cycles and reduce human, companion, domestic animal, and wildlife exposure to infected ticks.

Extensive sex-specific and regional variations observed in the microbiome of Dermacentor reticulatus

Recent progress in DNA sequencing technologies and advanced bioinformatic tools have enabled researchers to rapidly decipher the tick microbiome. To date, however, a number of microbiome studies performed on Dermacentor reticulatus ticks is still quite limited. Despite the importance of this ixodid tick for veterinary and human medicine, only two investigations have examined its microbiome. Moreover, these studies analyzed only a limited number of ticks/tick pools. Given the scarcity of microbiome data for D. reticulatus in general and the lack of microbiome studies on tick species from Eastern Europe in particular, the objective of the current investigation was to analyze the microbiome of D. reticulatus ticks collected from three geographical regions of Ukraine. A total of 88 individual tick microbiomes were analyzed by sequencing the V6 region of 16S rRNA. As a result, numerous significant differences in the bacterial relative abundance were detected between males and females of D. reticulatus for each region. The alpha diversity measures indicate that microbiomes were significantly different between females of D. reticulatus inter-regionally. In contrast, the collective results for male ticks are more suggestive of inter-regional microbiome homogeneity. The overall findings indicate that the composition and diversity of the D. reticulatus microbiome can be impacted by geographical and sex-related factors.

Changes in Bacterial Diversity, Composition and Interactions During the Development of the Seabird Tick Ornithodoros maritimus (Argasidae)

Characterising within-host microbial interactions is essential to understand the drivers that shape these interactions and their consequences for host ecology and evolution. Here, we examined the bacterial microbiota hosted by the seabird soft tick Ornithodoros maritimus (Argasidae) in order to uncover bacterial interactions within ticks and how these interactions change over tick development. Bacterial communities were characterised through next-generation sequencing of the V3-V4 hypervariable region of the bacterial 16S ribosomal RNA gene. Bacterial co-occurrence and co-exclusion were determined by analysing networks generated from the metagenomic data obtained at each life stage. Overall, the microbiota of O. maritimus was dominated by four bacterial genera, namely Coxiella, Rickettsia, Brevibacterium and Arsenophonus, representing almost 60% of the reads. Bacterial diversity increased over tick development, and adult male ticks showed higher diversity than did adult female ticks. Bacterial networks showed that co-occurrence was more frequent than co-exclusion and highlighted substantial shifts across tick life stages; interaction networks changed from one stage to the next with a steady increase in the number of interactions through development. Although many bacterial interactions appeared unstable across life stages, some were maintained throughout development and were found in both sexes, such as Coxiella and Arsenophonus. Our data support the existence of a few stable interactions in O. maritimus ticks, on top of which bacterial taxa accumulate from hosts and/or the environment during development. We propose that stable associations delineate core microbial interactions, which are likely to be responsible for key biological functions.

Tick Microbiomes in Neotropical Forest Fragments Are Best Explained by Tick-Associated and Environmental Factors Rather than Host Blood Source

The composition of tick microbiomes varies both within and among tick species. Whether this variation is intrinsic (related to tick characteristics) or extrinsic (related to vertebrate host and habitat) is poorly understood but important, as microbiota can influence the reproductive success and vector competence of ticks. We aimed to uncover what intrinsic and extrinsic factors best explain the microbial composition and taxon richness of 11 species of neotropical ticks collected from eight species of small mammals in 18 forest fragments across central Panama. Microbial richness varied among tick species, life stages, and collection sites but was not related to host blood source. Microbiome composition was best explained by tick life stage, with bacterial assemblages of larvae being a subset of those of nymphs. Collection site explained most of the bacterial taxa with differential abundance across intrinsic and extrinsic factors. Francisella and Rickettsia were highly prevalent, but their proportional abundance differed greatly among tick species, and we found both positive and negative cooccurrence between members of these two genera. Other tick endosymbionts (e.g., Coxiella and Rickettsiella) were associated with specific tick species. In addition, we detected Anaplasma and Bartonella in several tick species. Our results indicate that the microbial composition and richness of neotropical ticks are principally related to intrinsic factors (tick species and life stage) and collection site. Taken together, our analysis informs how tick microbiomes are structured and can help anchor our understanding of tick microbiomes from tropical environments more broadly.IMPORTANCE Blood-feeding arthropod microbiomes often play important roles in disease transmission, yet the factors that structure tick microbial communities in the Neotropics are unknown. Utilizing ticks collected from live animals in neotropical forest fragments, this study teases apart the contributions of intrinsic and extrinsic tick-associated factors on tick microbial composition as well as which specific microbes contribute to differences across tick species, tick life stages, the mammals they fed on, and the locations from where they were sampled. Furthermore, this study provides revelations of how notable tick-associated bacterial genera are interacting with other tick-associated microbes as well as the forest animals they encounter.

What do we still need to know about Ixodes ricinus?

In spite of many decades of intensive research on Ixodes ricinus, the castor bean tick of Europe, several important aspects of its basic biology remain elusive, such as the factors determining seasonal development, tick abundance and host specificity, and the importance of water management. Additionally, there are more recent questions about the geographical diversity of tick genotypes and phenotypes, the role of migratory birds in the ecoepidemiology of I. ricinus, the importance of protective immune responses against I. ricinus, particularly in the context of vaccination, and the role of the microbiome in pathogen transmission. Without more detailed knowledge of these issues, it is difficult to assess the likely effects of changes in climate and biodiversity on tick distribution and activity, to predict potential risks arising from new and established tick populations and I. ricinus-borne pathogens, and to improve prevention and control measures. This review aims to discuss the most important outstanding questions against the backdrop of the current state of knowledge of this important tick species.

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.

Update on the intricate tango between tick microbiomes and tick-borne pathogens

The recent development of high-throughput NGS technologies, (ie, next-generation sequencing) has highlighted the complexity of tick microbial communities-which include pathogens, symbionts, and commensals-and also their dynamic variability. Symbionts and commensals can confer crucial and diverse benefits to their hosts, playing nutritional roles or affecting fitness, development, nutrition, reproduction, defence against environmental stress and immunity. Nonpathogenic tick bacteria may also play a role in modifying tick-borne pathogen colonization and transmission, as relationships between microorganisms existing together in one environment can be competitive, exclusive, facilitating or absent, with many potential implications for both human and animal health. Consequently, ticks represent a compelling yet challenging system in which to investigate the composition and both the functional and ecological implications of tick bacterial communities, and thus merits greater attention. Ultimately, deciphering the relationships between microorganisms carried by ticks as well as symbiont-tick interactions will garner invaluable information, which may aid in some future arthropod-pest and vector-borne pathogen transmission control strategies. This review outlines recent research on tick microbiome composition and dynamics, highlights elements favouring the reciprocal influence of the tick microbiome and tick-borne agents and finally discusses how ticks and tick-borne diseases might potentially be controlled through tick microbiome manipulation in the future.

Microbial community of Hyalomma lusitanicum is dominated by Francisella-like endosymbiont

Exploring tick associations with complex microbial communities and single-microbial partners, especially intracellular symbionts, has become crucial to understand tick biology. Of particular interest are the underlying interactions with biological consequences i.e. tick fitness, vector competence. In this study, we first sequenced the 16S rRNA bacterial phylogenetic marker in adult male ticks of Hyalomma lusitanicum collected from 5 locations in the province of Cáceres to explore the composition of its microbial community. Overall, 16S rRNA sequencing results demonstrated that the microbial community of H. lusitanicum is mostly dominated by Francisella-like endosymbionts (FLEs) (ranging from 52% to 99% of relative abundance) suggesting it is a key taxon within the microbial community and likely a primary endosymbiont. However, further research is required to explore the mechanisms underlying the interaction between FLEs and H. lusitanicum.

Behind Taxonomic Variability: The Functional Redundancy in the Tick Microbiome

The taxonomic composition and diversity of tick midgut microbiota have been extensively studied in different species of the genera Rhipicephalus, Ixodes, Amblyomma, Haemaphysalis, Hyalomma, Dermacentor, Argas and Ornithodoros, while the functional significance of bacterial diversity has been proportionally less explored. In this study, we used previously published 16S amplicon sequence data sets from three Ixodes scapularis cohorts, two of uninfected nymphs, and one of larvae experimentally infected with Borrelia burgdorferi, to test the functional redundancy of the tick microbiome. We predicted the metabolic profiling of each sample using the state-of-the-art metagenomics tool PICRUSt2. The results showed that the microbiomes of all I. scapularis samples share only 80 taxa (24.6%, total 324), while out of the 342 metabolic pathways predicted, 82.7%, were shared by all the ticks. Borrelia-infected larvae lack 15.4% of pathways found in the microbiome of uninfected nymphs. Taxa contribution analysis showed that the functional microbiome of uninfected ticks was highly redundant, with, in some cases, up to 198 bacterial taxa contributing to a single pathway. However, Borrelia-infected larvae had a smaller redundancy with 6.7% of pathways provided by more than 100 genera, while 15.7-19.2% of pathways were provided by more than 100 genera in the two cohorts of uninfected ticks. In addition, we compared the functional profiles of three microbial communities from each data set, identified through a network-based approach, and we observed functional similarity between them. Based on the functional redundancy and functional similarity of the microbiome of ticks in different developmental stages and infection status, we concluded that the tick gut microbiota is a self-regulating community of very diverse bacteria contributing to a defined set of metabolic pathways and functions with yet unexplored relevance for tick fitness and/or bacterial community stability. We propose a change of focus in which the tick microbiome must be analyzed in all dimensions, highlighting their functional traits, instead of the conventional taxonomic profiling.

Evaluation of a novel multiplex PCR amplicon sequencing assay for detection of human pathogens in Ixodes ticks

Tickborne diseases are an increasing public health concern in the United States, where the majority of notifiable cases are caused by pathogens vectored by Ixodes ticks. To better monitor changes in acarological risk of human encounters with these ticks and their associated pathogens, the Centers for Disease Control and Prevention (CDC) recently established a national tick and tickborne pathogen surveillance program. Here, we describe and evaluate a new Multiplex PCR Amplicon Sequencing (MPAS) assay for potential use in surveillance programs targeting two common human-biting vector ticks, Ixodes scapularis and Ixodes pacificus. The ability of the MPAS assay to detect five Ixodes-associated human pathogens (Borrelia burgdorferi sensu stricto, Borrelia mayonii, Borrelia miyamotoi, Anaplasma phagocytophilum and Babesia microti) was compared to that of a previously published and routinely used probe-based (TaqMan) PCR testing algorithm for pathogen detection in Ixodes ticks. Assay performance comparisons included a set of 175 host-seeking Ixodes nymphs collected in Connecticut as well as DNA from our pathogen reference collection. The MPAS assay and the CDC standard TaqMan PCR pathogen testing algorithm were found to have equivalent detection sensitivity for Ixodes-associated human pathogens. However, the MPAS assay was able to detect a broader range of tick-associated microorganisms, more effectively detected co-infections of multiple pathogens in a single tick (including different species within the Borrelia burgdorferi sensu lato complex), and required a smaller volume of test sample (thus preserving more sample for future testing).

Taxon Appearance From Extraction and Amplification Steps Demonstrates the Value of Multiple Controls in Tick Microbiota Analysis

Background

The development of high-throughput sequencing technologies has substantially improved analysis of bacterial community diversity, composition, and functions. Over the last decade, high-throughput sequencing has been used extensively to identify the diversity and composition of tick microbial communities. However, a growing number of studies are warning about the impact of contamination brought along the different steps of the analytical process, from DNA extraction to amplification. In low biomass samples, e.g., individual tick samples, these contaminants may represent a large part of the obtained sequences, and thus generate considerable errors in downstream analyses and in the interpretation of results. Most studies of tick microbiota either do not mention the inclusion of controls during the DNA extraction or amplification steps, or consider the lack of an electrophoresis signal as an absence of contamination. In this context, we aimed to assess the proportion of contaminant sequences resulting from these steps. We analyzed the microbiota of individual Ixodes ricinus ticks by including several categories of controls throughout the analytical process: homogenization, DNA extraction, and DNA amplification.

Results

Controls yielded a significant number of sequences (1,126-13,198 mean sequences, depending on the control category). Some operational taxonomic units (OTUs) detected in these controls belong to genera reported in previous tick microbiota studies. In this study, these OTUs accounted for 50.9% of the total number of sequences in our samples, and were considered contaminants. Contamination levels (i.e., the percentage of sequences belonging to OTUs identified as contaminants) varied with tick instar and sex: 76.3% of nymphs and 75% of males demonstrated contamination over 50%, while most females (65.7%) had rates lower than 20%. Contamination mainly corresponded to OTUs detected in homogenization and extraction reagent controls, highlighting the importance of carefully controlling these steps.

Conclusion

Here, we showed that contaminant OTUs from sample laboratory processing steps can represent more than half the total sequence yield in sequencing runs, and lead to unreliable results when characterizing tick microbial communities. We thus strongly advise the routine use of negative controls in tick microbiota studies, and more generally in studies involving low biomass samples.

Biotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw Gradient

Plant-associated microbiomes are structured by environmental conditions and plant associates, both of which are being altered by climate change. The future structure of plant microbiomes will depend on the, largely unknown, relative importance of each. This uncertainty is particularly relevant for arctic peatlands, which are undergoing large shifts in plant communities and soil microbiomes as permafrost thaws, and are potentially appreciable sources of climate change feedbacks due to their soil carbon (C) storage. We characterized phyllosphere and rhizosphere microbiomes of six plant species, and bulk peat, across a permafrost thaw progression (from intact permafrost, to partially- and fully-thawed stages) via 16S rRNA gene amplicon sequencing. We tested the hypothesis that the relative influence of biotic versus environmental filtering (the role of plant species versus thaw-defined habitat) in structuring microbial communities would differ among phyllosphere, rhizosphere, and bulk peat. Using both abundance- and phylogenetic-based approaches, we found that phyllosphere microbial composition was more strongly explained by plant associate, with little influence of habitat, whereas in the rhizosphere, plant and habitat had similar influence. Network-based community analyses showed that keystone taxa exhibited similar patterns with stronger responses to drivers. However, plant associates appeared to have a larger influence on organisms belonging to families associated with methane-cycling than the bulk community. Putative methanogens were more strongly influenced by plant than habitat in the rhizosphere, and in the phyllosphere putative methanotrophs were more strongly influenced by plant than was the community at large. We conclude that biotic effects can be stronger than environmental filtering, but their relative importance varies among microbial groups. For most microbes in this system, biotic filtering was stronger aboveground than belowground. However, for putative methane-cyclers, plant associations have a stronger influence on community composition than environment despite major hydrological changes with thaw. This suggests that plant successional dynamics may be as important as hydrological changes in determining microbial relevance to C-cycling climate feedbacks. By partitioning the degree that plant versus environmental filtering drives microbiome composition and function we can improve our ability to predict the consequences of warming for C-cycling in other arctic areas undergoing similar permafrost thaw transitions.

Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network

Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver.IMPORTANCE Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.

The scale affects our view on the identification and distribution of microbial communities in ticks

Ticks transmit the highest variety of pathogens impacting human and animal health worldwide. It is now well established that ticks also harbour a microbial complex of coexisting symbionts, commensals and pathogens. With the development of high throughput sequencing technologies, studies dealing with such diverse bacterial composition in tick considerably increased in the past years and revealed an unexpected microbial diversity. These data on diversity and composition of the tick microbes are increasingly available, giving crucial details on microbial communities in ticks and improving our knowledge on the tick microbial community. However, consensus is currently lacking as to which scales (tick organs, individual specimens or species, communities of ticks, populations adapted to particular environmental conditions, spatial and temporal scales) best facilitate characterizing microbial community composition of ticks and understanding the diverse relationships among tick-borne bacteria. Temporal or spatial scales have a clear influence on how we conduct ecological studies, interpret results, and understand interactions between organisms that build the microbiome. We consider that patterns apparent at one scale can collapse into noise when viewed from other scales, indicating that processes shaping tick microbiome have a continuum of variability that has not yet been captured. Based on available reports, this review demonstrates how much the concept of scale is crucial to be considered in tick microbial community studies to improve our knowledge on tick microbe ecology and pathogen/microbiota interactions.

Bacterial microbiota composition of Ixodes ricinus ticks: the role of environmental variation, tick characteristics and microbial interactions

Ecological factors, host characteristics and/or interactions among microbes may all shape the occurrence of microbes and the structure of microbial communities within organisms. In the past, disentangling these factors and determining their relative importance in shaping within-host microbiota communities has been hampered by analytical limitations to account for (dis)similar environmental preferences ('environmental filtering'). Here we used a joint species distribution modelling (JSDM) approach to characterize the bacterial microbiota of one of the most important disease vectors in Europe, the sheep tick Ixodes ricinus, along ecological gradients in the Swiss Alps. Although our study captured extensive environmental variation along elevational clines, the explanatory power of such large-scale ecological factors was comparably weak, suggesting that tick-specific traits and behaviours, microhabitat and -climate experienced by ticks, and interactions among microbes play an important role in shaping tick microbial communities. Indeed, when accounting for shared environmental preferences, evidence for significant patterns of positive or negative co-occurrence among microbes was found, which is indicative of competition or facilitation processes. Signals of facilitation were observed primarily among human pathogens, leading to co-infection within ticks, whereas signals of competition were observed between the tick endosymbiont Spiroplasma and human pathogens. These findings highlight the important role of small-scale ecological variation and microbe-microbe interactions in shaping tick microbial communities and the dynamics of tick-borne disease.

Bacterial communities in Haemaphysalis, Dermacentor and Amblyomma ticks collected from wild boar of an Orang Asli Community in Malaysia

Ticks are hematophagous vectors of arthropod-borne disease agents globally. In Malaysia, despite seroprevalence studies indicating the presence of tick-borne diseases among the indigenous people, the etiological agents of these diseases are still unclear. These indigenous people, also known as the Orang Asli, still live in forested areas with frequent contact with wildlife. Wild boar are ubiquitously found in the forested areas where the Orang Asli communities are located and are commonly hunted as a food supplement. In this study, we aim to determine the tick species parasitizing wild boar from an Orang Asli community, and explore the tick-associated bacterial communities using 16 s rRNA amplicon sequencing on the Ion Torrent PGM™ platform. A total of 72 ticks were collected from three wild boar and were morphologically identified as Haemaphysalis hystricis (n = 32), Dermacentor compactus (n = 15), Amblyomma testudinarium (n = 13), Dermacentor steini (n = 10) and Dermacentor atrosignatus (n = 2). Across all tick samples, 910 bacterial taxa were identified. Although the bacterial communities were not significantly distinct between tick species in beta-diversity analyses, Coxiella, Rickettsia and Francisella were detected at high relative abundance in H. hystricis, D. compactus and D. steini respectively. Many other bacterial genera, including those that have been described in many different tick species, were also identified, including Pseudomonas, Acinetobacter, Staphylococcus and Corynebacterium. Beta-diversity analyses also showed that the bacterial communities were separated based on the animal host from which the ticks were collected from, suggesting that the bacterial communities here may be influenced by the animal skin microflora, host blood or the environment. PCR screening confirmed the presence of Rickettsia sp. related to spotted fever group Rickettsia in some of the ticks. This study provides baseline knowledge of the microbiome of H. hystricis, D. atrosignatus, D. compactus, D. steini and A. testudinarium parasitizing wild boar in this region. The information gained in this study provides the basis to target our efforts in H. hystricis, D. compactus and D. steini for the future investigation of vector competence and the zoonotic potential for the Coxiella, Rickettsia and Francisella detected here, as well as their implications for the risks of tick-borne diseases among the Orang Asli communities.

Sex-Specific Linkages Between Taxonomic and Functional Profiles of Tick Gut Microbiomes

Ticks transmit the most diverse array of disease agents and harbor one of the most diverse microbial communities. Major progress has been made in the characterization of the taxonomic profiles of tick microbiota. However, the functional profiles of tick microbiome have been comparatively less studied. In this proof of concept we used state-of-the-art functional metagenomics analytical tools to explore previously reported datasets of bacteria found in male and female Ixodes ovatus, Ixodes persulcatus, and Amblyomma variegatum. Results showed that both taxonomic and functional profiles have differences between sexes of the same species. KEGG pathway analysis revealed that male and female of the same species had major differences in the abundance of genes involved in different metabolic pathways including vitamin B, amino acids, carbohydrates, nucleotides, and antibiotics among others. Partial reconstruction of metabolic pathways using KEGG enzymes suggests that tick microbiome form a complex metabolic network that may increase microbial community resilience and adaptability. Linkage analysis between taxonomic and functional profiles showed that among the KEGG enzymes with differential abundance in male and female ticks only 12% were present in single bacterial genera. The rest of these enzymes were found in more than two bacterial genera, and 27% of them were found in five up to ten bacterial genera. Comparison of bacterial genera contributing to the differences in the taxonomic and functional profiles of males and females revealed that while a small group of bacteria has a dual-role, most of the bacteria contribute only to functional or taxonomic differentiation between sexes. Results suggest that the different life styles of male and female ticks exert sex-specific evolutionary pressures that act independently on the phenomes (set of phenotypes) and genomes of bacteria in tick gut microbiota. We conclude that functional redundancy is a fundamental property of male and female tick microbiota and propose that functional metagenomics should be combined with taxonomic profiling of microbiota because both analyses are complementary.

Evolutionary Insights into the Tick Hologenome

Recently, our knowledge of the composition and complexity of tick microbial communities has increased and supports microbial impact on tick biology. Results support a phylogenetic association between ticks and their microbiota across evolution; this is known as phylosymbiosis. Herein, using published datasets, we confirm the existence of phylosymbiosis between Ixodes ticks and their microbial communities. The strong phylosymbiotic signal and the phylogenetic structure of microbial communities associated with Ixodid ticks revealed that phylosymbiosis may be a widespread phenomenon in tick-microbiota evolution. This finding supports the existence of a species-specific tick hologenome with a largely unexplored influence on tick biology and pathogen transmission. These results may provide potential targets for the construction of paratransgenic ticks to control tick infestations and tick-borne diseases.

Drivers and patterns of microbial community assembly in a Lyme disease vector

Vector-borne diseases constitute a major global health burden and are increasing in geographic range and prevalence. Mounting evidence has demonstrated that the vector microbiome can impact pathogen dynamics, making the microbiome a focal point in vector-borne disease ecology. However, efforts to generalize preliminary findings across studies and systems and translate these findings into disease control strategies are hindered by a lack of fundamental understanding of the processes shaping the vector microbiome and the interactions therein. Here, we use 16S rRNA sequencing and apply a community ecology framework to analyze microbiome community assembly and interactions in Ixodes pacificus, the Lyme disease vector in the western United States. We find that vertical transmission routes drive population-level patterns in I. pacificus microbial diversity and composition, but that microbial function and overall abundance do not vary over time or between clutches. Further, we find that the I. pacificus microbiome is not strongly structured based on competition but assembles nonrandomly, potentially due to vector-specific filtering processes which largely eliminate all but the dominant endosymbiont, Rickettsia. At the scale of the individual I. pacificus, we find support for a highly limited internal microbial community, and hypothesize that the tick endosymbiont may be the most important component of the vector microbiome in influencing pathogen dynamics.

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.

Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis

OBJECTIVE

The aim of this study was to characterize the bacterial microbiome of hard ticks with affinity to bite humans in La Rioja (North of Spain).

METHODS

A total of 88 adult ticks (22 Rhipicephalus sanguineus sensu lato, 27 Haemaphysalis punctata, 30 Dermacentor marginatus and 9 Ixodes ricinus) and 120 I. ricinus nymphs (CRETAV collection, La Rioja, Spain), representing the main anthropophilic species in our environment, were subjected to a metagenomic analysis of the V3-V4 region of the 16S rRNA gene using an Illumina MiSeq platform. Data obtained with Greengenes database were refined with BLAST. Four groups of samples were defined, according to the four tick species.

RESULTS

Proteobacteria was the predominant phylum observed in all groups. Gammaproteobacteria was the most abundant class, followed by Alphaproteobacteria for R. sanguineus, H. punctata and D. marginatus but the relative abundance of reads for these classes was reversed for I. ricinus. This tick species showed more than 46% reads corresponding to 'not assigned' OTUs (Greengenes), and >97% of them corresponded to 'Candidatus Midichloriaceae' using BLAST. Within Rickettsiales, 'Candidatus Midichloria', Rickettsia, Ehrlichia, 'Candidatus Neoehrlichia' and Wolbachia were detected. I. ricinus was the most alpha-diverse species. Regarding beta-diversity, I. ricinus and H. punctata samples grouped according to their tick species but microbial communities of some R. sanguineus and D. marginatus specimens clustered together.

CONCLUSIONS

The metagenomics approach seems useful to discover the spectrum of tick-related bacteria. More studies are needed to identify and differentiate bacterial species, and to improve the knowledge of tick-borne diseases in Spain.