16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

Venom-microbiomics of eight species of Neotropical spiders from the Theraphosidae family

AIM

Tarantulas are one of the largest predatory arthropods in tropical regions. Tarantulas though not lethal to humans, their venomous bite kills small animals and insect upon which they prey. To understand the abiotic and biotic components involved in Neotropical tarantula bites, we conducted a venom-microbiomics study in eight species from Costa Rica.

METHODS AND RESULTS

We determined that the toxin profiles of tarantula venom are highly diverse using shotgun proteomics; the most frequently encountered toxins were ω-Ap2 toxin, neprilysin-1, and several teraphotoxins. Through culture-independent and culture-dependent methods, we determined the microbiota present in the venom and excreta to evaluate the presence of pathogens that could contribute to primary infections in animals, including humans. The presence of opportunistic pathogens with hemolytic activity was observed, with a prominence of Stenotrophomonas in the venoms. Other bacteria found in venoms and excreta with hemolytic activity included members of the genera Serratia, Bacillus, Acinetobacter, Microbacterium, and Morganella.

CONCLUSIONS

Our data shed light on the venom- and gut-microbiome associated with Neotropical tarantulas. This information may be useful for treating bites from these arthropods in both humans and farm animals, while also providing insight into the toxins and biodiversity of this little-explored microenvironment.

Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota

Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.

Co-occurrence network analysis reveals the alterations of the skin microbiome and metabolome in adults with mild to moderate atopic dermatitis

Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for treatment by identifying microbial and molecular biomarkers. This study investigates the skin microbiome and metabolome of healthy adult subjects and lesion (ADL) and non-lesion (ADNL) of AD patients by 16S rRNA gene sequencing and mass spectrometry, respectively. Samples from AD patients showed alterations in the diversity and composition of the skin microbiome, with ADL skin having the greatest divergence. Staphylococcus species, especially S. aureus, were significantly increased in AD patients. Metabolomic profiles were also different between the groups. Dipeptide derivatives are more abundant in ADL, which may be related to skin inflammation. Co-occurrence network analysis of the microbiome and metabolomics data revealed higher co-occurrence of metabolites and bacteria in healthy ADNL compared to ADL. S. aureus co-occurred with dipeptide derivatives in ADL, while phytosphingosine-derived compounds showed co-occurrences with commensal bacteria, for example, Paracoccus sp., Pseudomonas sp., Prevotella bivia, Lactobacillus iners, Anaerococcus sp., Micrococcus sp., Corynebacterium ureicelerivorans, Corynebacterium massiliense, Streptococcus thermophilus, and Roseomonas mucosa, in healthy and ADNL groups. Therefore, these findings provide valuable insights into how AD affects the human skin metabolome and microbiome.IMPORTANCEThis study provides valuable insight into changes in the skin microbiome and associated metabolomic profiles in an adult population with mild to moderate atopic dermatitis. It also identifies new therapeutic targets that may be useful for developing personalized treatments for individuals with atopic dermatitis based on their unique skin microbiome and metabolic profiles.

Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii

BACKGROUND

Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains.

RESULTS

We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen.

CONCLUSIONS

Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.

Presence and identity of Babesia microti in Ireland

Babesia microti is a tick-transmitted protozoan parasite of wildlife that can also cause serious disease in humans. It is now well established that B. microti represents an assemblage of different strains or species, only some of which are important zoonotic pathogens. Therefore, in order to assess the potential public health risk associated with B. microti in any given location, it is important to determine the strains that are present. This is the first study on the presence and identity of B. microti in Ireland. Overall, 314 wood mice (Apodemus sylvaticus), 243 bank voles (Myodes glareolus) and 634 questing Ixodes ricinus nymphs collected in various locations across Ireland were screened for the presence of B. microti by metabarcoding and nested PCR, respectively. Overall 8 rodent spleen samples (1.4%) were positive for B. microti, while all tick samples tested negative. Rodent isolates were identified as the 'Munich' strain which rarely causes human disease and is chiefly transmitted by the mouse tick, Ixodes trianguliceps. Together with reports from the UK these results suggest that B. microti does not represent a significant public health risk in Britain or Ireland.

Decontamination protocols affect the internal microbiota of ticks

Studies on the microbiota of ticks have promoted hypotheses about the combined effects of the bacterial community, its functional contributions to the tick's physiology or probable competition effects with some tick-borne pathogens. However, knowledge on the origin of the microbiota of newly hatched larvae is missing. This study aimed to elucidate the source(s) of the microbiota in unfed tick larvae, addressing the composition of the "core microbiota" and the best ways to decontaminate eggs for microbiota studies. We applied laboratory degree bleach washes and/or ultraviolet light treatments on engorged Rhipicephalus australis females and/or their eggs. No significant effects of these treatments on the reproductive parameters of females and the hatching rates of eggs were observed. However, the different treatments did show striking effects on the composition of the microbiota. The results indicated that bleach washes disrupted the internal tick microbiota in females, implying that bleach may have entered the tick and subsequently affected the microbiota. Furthermore, the analyses of results demonstrated that the ovary is a main source of tick microbiota, while the contribution of Gené's organ (a part of the female reproductive system that secretes a protective wax coat onto tick eggs) or the male's spermatophore requires further investigation. Further studies are needed to identify best practice protocols for the decontamination of ticks for microbiota studies.

Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations

Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.

Increasing helminth infection burden depauperates the diversity of the gut microbiota and alters its composition in mice

The gut microbiota constitutes a diverse community of organisms with pervasive effects on host homeostasis. The diversity and composition of the gut microbiota depend on both intrinsic (host genetics) and extrinsic (environmental) factors. Here, we investigated the reaction norms of fecal microbiota diversity and composition in three strains of mice infected with increasing doses of the gastrointestinal nematode Heligmosomoides polygyrus. We found that α-diversity (bacterial taxonomic unit richness) declined along the gradient of infective doses, and β-diversity (dissimilarity between the composition of the microbiota of uninfected and infected mice) increased as the infective dose increased. We did not find evidence for genotype by environment (host strain by infective dose) interactions, except when focusing on the relative abundance of the commonest bacterial families. A simulation approach also showed that significant genotype by environment interactions would have been hardly found even with much larger sample size. These results show that increasing parasite burden progressively depauperates microbiota diversity and contributes to rapidly change its composition, independently from the host genetic background.

The bacterial biome of ticks and their wildlife hosts at the urban-wildland interface

Advances in sequencing technologies have revealed the complex and diverse microbial communities present in ticks (Ixodida). As obligate blood-feeding arthropods, ticks are responsible for a number of infectious diseases that can affect humans, livestock, domestic animals and wildlife. While cases of human tick-borne diseases continue to increase in the northern hemisphere, there has been relatively little recognition of zoonotic tick-borne pathogens in Australia. Over the past 5 years, studies using high-throughput sequencing technologies have shown that Australian ticks harbour unique and diverse bacterial communities. In the present study, free-ranging wildlife (n=203), representing ten mammal species, were sampled from urban and peri-urban areas in New South Wales (NSW), Queensland (QLD) and Western Australia (WA). Bacterial metabarcoding targeting the 16S rRNA locus was used to characterize the microbiomes of three sample types collected from wildlife: blood, ticks and tissue samples. Further sequence information was obtained for selected taxa of interest. Six tick species were identified from wildlife: Amblyomma triguttatum, Ixodes antechini, Ixodes australiensis, Ixodes holocyclus, Ixodes tasmani and Ixodes trichosuri. Bacterial 16S rRNA metabarcoding was performed on 536 samples and 65 controls, generating over 100 million sequences. Alpha diversity was significantly different between the three sample types, with tissue samples displaying the highest alpha diversity (P<0.001). Proteobacteria was the most abundant taxon identified across all sample types (37.3 %). Beta diversity analysis and ordination revealed little overlap between the three sample types (P<0.001). Taxa of interest included Anaplasmataceae, Bartonella, Borrelia, Coxiellaceae, Francisella, Midichloria, Mycoplasma and Rickettsia. Anaplasmataceae bacteria were detected in 17.7% (95/536) of samples and included Anaplasma, Ehrlichia and Neoehrlichia species. In samples from NSW, 'Ca. Neoehrlichia australis', 'Ca. Neoehrlichia arcana', Neoehrlichia sp. and Ehrlichia sp. were identified. A putative novel Ehrlichia sp. was identified from WA and Anaplasma platys was identified from QLD. Nine rodent tissue samples were positive for a novel Borrelia sp. that formed a phylogenetically distinct clade separate from the Lyme Borrelia and relapsing fever groups. This novel clade included recently identified rodent-associated Borrelia genotypes, which were described from Spain and North America. Bartonella was identified in 12.9% (69/536) of samples. Over half of these positive samples were obtained from black rats (Rattus rattus), and the dominant bacterial species identified were Bartonella coopersplainsensis and Bartonella queenslandensis. The results from the present study show the value of using unbiased high-throughput sequencing applied to samples collected from wildlife. In addition to understanding the sylvatic cycle of known vector-associated pathogens, surveillance work is important to ensure preparedness for potential zoonotic spillover events.

Polystyrene microplastics induce microbial dysbiosis and dysfunction in surrounding seawater

Microplastics are ubiquitously present in the environment, accumulate in aquaculture water, and cause toxicological effects on aquatic organisms. Besides, microplastics provide ecological niches for microorganisms in aquatic environments. However, the effects of microplastics on microbial balance and function in surrounding water are still unclear, especially for aquaculture water. Therefore, 16S rRNA gene sequencing was employed to uncover polystyrene microplastics (PS)-induced microbial dysbiosis in surrounding seawater cultivating marine medaka (Oryzias melastigmas) and to screen related potential bacterial biomarkers. We found that Proteobacteria and Bacteroidetes were the dominant phyla in each group, accounting for more than 95% of the total abundance, and that 26 bacterial taxa belonging to Proteobacteria and Bacteroidetes were significantly altered in surrounding seawater after 10- and 200-µm PS exposure. Functional analysis revelated that photosynthesis, carbon metabolism (such as carbon fixation, glycolysis, tricarboxylic acid cycle, and glycan biosynthesis and metabolism), amino acid metabolism, lipid synthesis, and nucleotide metabolism were decreased, while environmental stress responses, such as xenobiotics biodegradation and metabolism, glutathione metabolism, and taurine and hypotaurine metabolism, were increased in surrounding seawater microbiota after separate 10- and 200-µm PS exposure. Pathway analysis and correlation networks demonstrated that changes in relative abundances of bacterial taxa belonging to Proteobacteria and Bacteroidetes were highly correlated with those in the liver metabolism of marine medaka. Subsequently, 8 bacterial taxa were discovered to be able to be used separately as the potential biomarker for assessing the surrounding seawater microbial dysbiosis and metabolic responses of marine medaka, with a diagnostic accuracy of 100.0%. This study provides novel insights into toxicological effects of microplastics on microbial dysbiosis and function in surrounding water and ecosystems, and suggests potential roles of biomarkers involved in surrounding microbial dysbiosis in assessing microplastic ecotoxicology, microbial dysbiosis, and the health status of organisms at higher trophic levels.

The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya

BACKGROUND

There is a global increase in reports of emerging diseases, some of which have emerged as spillover events from wild animals. The spleen is a major phagocytic organ and can therefore be probed for systemic microbiome. This study assessed bacterial diversity in the spleen of wild caught small mammals so as to evaluate their utility as surveillance tools for monitoring bacteria in an ecosystem shared with humans.

METHODS

Fifty-four small mammals (rodents and shrews) were trapped from different sites in Marigat, Baringo County, Kenya. To characterize their bacteriome, DNA was extracted from their spleens and the V3-V4 regions of the 16S rRNA amplified and then sequenced on Illumina MiSeq. A non-target control sample was used to track laboratory contaminants. Sequence data was analyzed with Mothur v1.35, and taxomy determined using the SILVA database. The Shannon diversity index was used to estimate bacterial diversity in each animal and then aggregated to genus level before computing the means. Animal species within the rodents and shrews were identified by amplification of mitochondrial cytochrome b (cytb) gene followed by Sanger sequencing. CLC workbench was used to assemble the cytb gene sequences, after which their phylogenetic placements were determined by querying them against the GenBank nucleotide database.

RESULTS

cytb gene sequences were generated for 49/54 mammalian samples: 38 rodents (Rodentia) and 11 shrews (Eulipotyphyla). Within the order Rodentia, 21 Acomys, eight Mastomys, six Arvicanthis and three Rattus were identified. In the order Eulipotyphyla, 11 Crucidura were identified. Bacteria characterization revealed 17 phyla that grouped into 182 genera. Of the phyla, Proteobacteria was the most abundant (67.9%). Other phyla included Actinobacteria (16.5%), Firmicutes (5.5%), Chlamydiae (3.8%), Chloroflexi (2.6%) and Bacteroidetes (1.3%) among others. Of the potentially pathogenic bacteria, Bartonella was the most abundant (45.6%), followed by Anaplasma (8.0%), Methylobacterium (3.5%), Delftia (3.8%), Coxiella (2.6%), Bradyrhizobium (1.6%) and Acinetobacter (1.1%). Other less abundant (<1%) and potentially pathogenic included Ehrlichia, Rickettsia, Leptospira, Borrelia, Brucella, Chlamydia and Streptococcus. By Shannon diversity index, Acomys spleens carried more diverse bacteria (mean Shannon diversity index of 2.86, p = 0.008) compared to 1.77 for Crocidura, 1.44 for Rattus, 1.40 for Arvicathis and 0.60 for Mastomys.

CONCLUSION

This study examined systemic bacteria that are filtered by the spleen and the findings underscore the utility of 16S rRNA deep sequencing in characterizing complex microbiota that are potentially relevant to one health issues. An inherent problem with the V3-V4 region of 16S rRNA is the inability to classify bacteria reliably beyond the genera. Future studies should utilize the newer long read methods of 16S rRNA analysis that can delimit the species composition.

Feeding sites promoting wildlife-related tourism might highly expose the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) to parasite transmission

An increasing number of studies have found that the implementation of feeding sites for wildlife-related tourism can affect animal health, behaviour and reproduction. Feeding sites can favour high densities, home range overlap, greater sedentary behaviour and increased interspecific contacts, all of which might promote parasite transmission. In the Yunnan snub-nosed monkey (Rhinopithecus bieti), human interventions via provisioning monkeys at specific feeding sites have led to the sub-structuring of a group into genetically differentiated sub-groups. The fed subgroup is located near human hamlets and interacts with domesticated animals. Using high-throughput sequencing, we investigated Entamoeba species diversity in a local host assemblage strongly influenced by provisioning for wildlife-related tourism. We identified 13 Entamoeba species or lineages in faeces of Yunnan snub-nosed monkeys, humans and domesticated animals (including pigs, cattle, and domestic chicken). In Yunnan snub-nosed monkeys, Entamoeba prevalence and OTU richness were higher in the fed than in the wild subgroup. Entamoeba polecki was found in monkeys, pigs and humans, suggesting that this parasite might circulates between the wild and domestic components of this local social–ecological system. The highest proportion of faeces positive for Entamoeba in monkeys geographically coincided with the presence of livestock and humans. These elements suggest that feeding sites might indirectly play a role on parasite transmission in the Yunnan snub-nosed monkey. The implementation of such sites should carefully consider the risk of creating hotspots of disease transmission, which should be prevented by maintaining a buffer zone between monkeys and livestock/humans. Regular screenings for pathogens in fed subgroup are necessary to monitor transmission risk in order to balance the economic development of human communities dependent on wildlife-related tourism, and the conservation of the endangered Yunnan snub-nosed monkey.

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.

Maternal effects shape the seed mycobiome in Quercus petraea

The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of the present study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and confocal microscopy to analyze the fungal communities of seeds collected in the canopy and on the ground in four natural populations of sessile oak (Quercus petraea). Ecological processes shaping the seed mycobiome were inferred using joint species distribution models. Fungi were present in seed internal tissues, including the embryo. The seed mycobiome differed among oak populations and trees within the same population. Its composition was largely influenced by the mother, with weak significant environmental influences. The models also revealed several probable interactions among fungal pathogens and mycoparasites. Our results demonstrate that maternal effects, environmental filtering and biotic interactions all shape the seed mycobiome of sessile oak. They provide a starting point for future research aimed at understanding how maternal genes and environments interact to control the vertical transmission of fungal species that could then influence seed dispersal and germination, and seedling recruitment.

Leaf-associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems

Plants are colonized by diverse fungal and viral communities that influence their growth and survival as well as ecosystem functioning. Viruses interact with both plants and the fungi they host. Our understanding of plant-fungi-virus interactions is very limited, especially in wild plants. Combining metagenomic and culturomic approaches, we assessed the richness, diversity, and composition of leaf-associated fungal and viral communities from pools of herbaceous wild plants representative of four sites corresponding to cultivated or natural ecosystems. We identified 161 fungal families and 18 viral families comprising 249 RNA-dependent RNA polymerase-based operational taxonomic units (RdRp OTUs) from leaves. Fungal culturomics captured 12.3% of the fungal diversity recovered with metagenomic approaches and, unexpectedly, retrieved viral OTUs that were almost entirely different from those recovered by leaf metagenomics. Ecosystem management had a significant influence on both leaf mycobiome and virome, with a higher fungal community richness in natural ecosystems and a higher viral family richness in cultivated ecosystems, suggesting that leaf-associated fungal and viral communities are under the influence of different ecological drivers. Both the leaf-associated fungal and viral community compositions showed a strong site-specificity. Further research is needed to confirm these trends and unravel the factors structuring plant-fungi-virus interactions in wild plant populations.

Amplicon-Based Next Generation Sequencing for Rapid Identification of Rickettsia and Ectoparasite Species from Entomological Surveillance in Thailand

BACKGROUND

Next generation sequencing (NGS) technology has been used for a wide range of epidemiological and surveillance studies. Here, we used amplicon-based NGS to species identify Rickettsia and their arthropod hosts from entomological surveillance.

METHODS

During 2015-2016, we screened 1825 samples of rodents and ectoparasites collected from rodents and domestic mammals (dog, cat, and cattle) across Thailand for Rickettsia. The citrate synthase gene was amplified to identify Rickettsia to species, while the Cytochrome Oxidase subunit I (COI) and subunit II (COII) genes were used as target genes for ectoparasite identification. All target gene amplicons were pooled for library preparation and sequenced with Illumina MiSeq platform.

RESULT

The highest percentage of Rickettsia DNA was observed in fleas collected from domestic animals (56%) predominantly dogs. Only a few samples of ticks from domestic animals, rodent fleas, and rodent tissue were positive for Rickettisia DNA. NGS based characterization of Rickettsia by host identified Rickettsia asembonensis as the most common bacteria in positive fleas collected from dogs (83.2%) while "Candidatus Rickettsia senegalensis" was detected in only 16.8% of Rickettsia positive dog fleas. Sequence analysis of COI and COII revealed that almost all fleas collected from dogs were Ctenocephalides felis orientis. Other Rickettsia species were detected by NGS including Rickettsia heilongjiangensis from two Haemaphysalis hystricis ticks, and Rickettsia typhi in two rodent tissue samples.

CONCLUSION

This study demonstrates the utility of NGS for high-throughput sequencing in the species characterization/identification of bacteria and ectoparasite for entomological surveillance of rickettsiae. A high percentage of C. f. orientis are positive for R. asembonensis. In addition, our findings indicate there is a risk of tick-borne Spotted Fever Group rickettsiosis, and flea-borne murine typhus transmission in Tak and Phangnga provinces of Thailand.

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 networks inferred from environmental DNA data for biomonitoring ecosystem change: Strengths and pitfalls

Environmental DNA contains information on the species interaction networks that support ecosystem functions and services. Next-generation biomonitoring proposes the use of this data to reconstruct ecological networks in real time and then compute network-level properties to assess ecosystem change. We investigated the relevance of this proposal by assessing: (i) the replicability of DNA-based networks in the absence of ecosystem change, and (ii) the benefits and shortcomings of community- and network-level properties for monitoring change. We selected crop-associated microbial networks as a case study because they support disease regulation services in agroecosystems and analysed their response to change in agricultural practice between organic and conventional systems. Using two statistical methods of network inference, we showed that network-level properties, especially β-properties, could detect change. Moreover, consensus networks revealed robust signals of interactions between the most abundant species, which differed between agricultural systems. These findings complemented those obtained with community-level data that showed, in particular, a greater microbial diversity in the organic system. The limitations of network-level data included (i) the very high variability of network replicates within each system; (ii) the low number of network replicates per system, due to the large number of samples needed to build each network; and (iii) the difficulty in interpreting links of inferred networks. Tools and frameworks developed over the last decade to infer and compare microbial networks are therefore relevant to biomonitoring, provided that the DNA metabarcoding data sets are large enough to build many network replicates and progress is made to increase network replicability and interpretation.

Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

The ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.

In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses

During the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo-mock community (33 arthropod taxa from 16 orders), and guano-based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano-based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one-third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints.

A novel Borrelia species, intermediate between Lyme disease and relapsing fever groups, in neotropical passerine-associated ticks

Lyme disease (LD) and relapsing fevers (RF) are vector-borne diseases caused by bacteria of the Borrelia genus. Here, we report on the widespread infection by a non-described Borrelia species in passerine-associated ticks in tropical rainforests of French Guiana, South America. This novel Borrelia species is common in two tick species, Amblyomma longirostre and A. geayi, which feed on a broad variety of neotropical mammal and bird species, including migratory species moving to North America. The novel Borrelia species is divergent from the LD and RF species, and is more closely related to the reptile- and echidna-associated Borrelia group that was recently described. Genome sequencing showed that this novel Borrelia sp. has a relatively small genome consisting of a 0.9-Mb-large chromosome and an additional 0.3 Mb dispersed on plasmids. It harbors an RF-like genomic organization but with a unique mixture of LD- and RF-specific genes, including genes used by RF Borrelia for the multiphasic antigen-switching system and a number of immune-reactive protein genes used for the diagnosis of LD. Overall, our data indicate that this novel Borrelia is an intermediate taxon between the LD and RF species that may impact a large host spectrum, including American mammals. The designation "Candidatus Borrelia mahuryensis" is proposed for this species.

Spatio-temporal trends in richness and persistence of bacterial communities in decline-phase water vole populations

Understanding the driving forces that control vole population dynamics requires identifying bacterial parasites hosted by the voles and describing their dynamics at the community level. To this end, we used high-throughput DNA sequencing to identify bacterial parasites in cyclic populations of montane water voles that exhibited a population outbreak and decline in 2014-2018. An unexpectedly large number of 155 Operational Taxonomic Units (OTUs) representing at least 13 genera in 11 families was detected. Individual bacterial richness was higher during declines, and vole body condition was lower. Richness as estimated by Chao2 at the local population scale did not exhibit clear seasonal or cycle phase-related patterns, but at the vole meta-population scale, exhibited seasonal and phase-related patterns. Moreover, bacterial OTUs that were detected in the low density phase were geographically widespread and detected earlier in the outbreak; some were associated with each other. Our results demonstrate the complexity of bacterial community patterns with regard to host density variations, and indicate that investigations about how parasites interact with host populations must be conducted at several temporal and spatial scales: multiple times per year over multiple years, and at both local and long-distance dispersal scales for the host(s) under consideration.

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.

DNA Metabarcoding as a Tool for Disentangling Food Webs in Agroecosystems

Better knowledge of food webs and related ecological processes is fundamental to understanding the functional role of biodiversity in ecosystems. This is particularly true for pest regulation by natural enemies in agroecosystems. However, it is generally difficult to decipher the impact of predators, as they often leave no direct evidence of their activity. Metabarcoding via high-throughput sequencing (HTS) offers new opportunities for unraveling trophic linkages between generalist predators and their prey, and ultimately identifying key ecological drivers of natural pest regulation. Here, this approach proved effective in deciphering the diet composition of key predatory arthropods (nine species.; 27 prey taxa), insectivorous birds (one species, 13 prey taxa) and bats (one species; 103 prey taxa) sampled in a millet-based agroecosystem in Senegal. Such information makes it possible to identify the diet breadth and preferences of predators (e.g., mainly moths for bats), to design a qualitative trophic network, and to identify patterns of intraguild predation across arthropod predators, insectivorous vertebrates and parasitoids. Appropriateness and limitations of the proposed molecular-based approach for assessing the diet of crop pest predators and trophic linkages are discussed.

Innovative application of nested PCR for detection of Porphyromonas gingivalis in human highly calcified atherothrombotic plaques

Atherothrombosis, leading to stroke and myocardial infarction, is responsible for most of the deaths in the world. An increased risk of atherothrombotic vascular events has been reported in patients with periodontitis. Periodontitis is a chronic multifactorial inflammatory disease, which involves a dysbiotic microbiota, and leads to a progressive destruction of the tooth-supporting apparatus. Transcient periodontal pathogen blood translocation, mainly bacteremia, has been associated with the severity of gingival inflammation. The identification of periodontal bacteria within atherothrombotic plaques is challenging and unpredictable. This review aims to summarize existing molecular technics for identifying periodontal microbiota in human atherothrombotic samples. A secondary objective is to describe a protocol for the identification of Porphyromonas gingivalis from highly calcified, atherothrombotic human samples that is based on our experience in translational cardiovascular research. Compared to direct real-time PCR, our protocol based on nested PCR has increased the detection of Porphyromonas gingivalis by 22.2% with good specificity.

Microbial community structure reveals instability of nutritional symbiosis during the evolutionary radiation of Amblyomma ticks

Mutualistic interactions with microbes have facilitated the adaptation of major eukaryotic lineages to restricted diet niches. Hence, ticks with their strictly blood-feeding lifestyle are associated with intracellular bacterial symbionts through an essential B vitamin supplementation. In this study, examination of bacterial diversity in 25 tick species of the genus Amblyomma showed that three intracellular bacteria, Coxiella-like endosymbionts (LE), Francisella-LE and Rickettsia, are remarkably common. No other bacterium is as uniformly present in Amblyomma ticks. Almost all Amblyomma species were found to harbour a nutritive obligate symbiont, Coxiella-LE or Francisella-LE, that is able to synthesize B vitamins. However, despite the co-evolved and obligate nature of these mutualistic interactions, the structure of microbiomes does not mirror the Amblyomma phylogeny, with a clear exclusion pattern between Coxiella-LE and Francisella-LE across tick species. Coxiella-LE, but not Francisella-LE, form evolutionarily stable associations with ticks, commonly leading to co-cladogenesis. We further found evidence for symbiont replacements during the radiation of Amblyomma, with recent, and probably ongoing, invasions by Francisella-LE and subsequent replacements of ancestral Coxiella-LE through transient co-infections. Nutritional symbiosis in Amblyomma ticks is thus not a stable evolutionary state, but instead arises from conflicting origins between unrelated but competing symbionts with similar metabolic capabilities.

Monitoring of enterovirus diversity in wastewater by ultra-deep sequencing: An effective complementary tool for clinical enterovirus surveillance

In a one-year (October 2014-October 2015) pilot study, we assessed wastewater monitoring with sustained sampling for analysis of global enterovirus (EV) infections in an urban community. Wastewater was analysed by ultra-deep sequencing (UDS) after PCR amplification of the partial VP1 capsid protein gene. The nucleotide sequence analysis showed an unprecedented diversity of 48 EV types within the community, which were assigned to the taxonomic species A (n = 13), B (n = 23), and C (n = 12). During the same period, 26 EV types, of which 22 were detected in wastewater, were identified in patients referred to the teaching hospital serving the same urban population. Wastewater surveillance detected a silent circulation of 26 EV types including viruses reported in clinically rare respiratory diseases. Wastewater monitoring as a supplementary procedure can complement clinical surveillance of severe diseases related to non-polio EVs and contribute to the final stages of poliomyelitis eradication.

Technical pitfalls that bias comparative microbial community analyses of aquatic disease Ian Hewson

The accessibility of high-throughput DNA sequencing technologies has attracted the application of comparative microbial analyses to study diseases. These studies present a window into host microbiome diversity and composition that can be used to address ecological theory in the context of host biology and behavior. Recently, comparative microbiome studies have been used to study non-vertebrate aquatic diseases to elucidate microorganisms potentially involved in disease processes or in disease prevention. These investigations suffer from many well-described biases, especially prior to sequence analyses, that could lead to misleading conclusions. Microbiome-focused studies of aquatic metazoan diseases provide valuable documentation of microbial ecology, although, they are only a starting point for establishing disease etiology, which demands quantitative validation through targeted approaches. The microbiome approach to understanding disease is most useful after laboratory diagnostics guided by pathology have failed to identify a causative agent. This opinion piece presents several technical pitfalls which may affect wider interpretation of microbe-host interactions through comparative microbial community analyses and provides recommendations, based on studies in non-aquatic systems, for incorporation into future aquatic disease research.

Cryptosporidium parvum-Infected Neonatal Mice Show Gut Microbiota Remodelling Using High-Throughput Sequencing Analysis: Preliminary Results

BACKGROUND

During the last decade, the scientific community has begun to investigate the composition and role of gut microbiota in normal health and disease. These studies have provided crucial information on the relationship between gut microflora composition and intestinal parasitic infection, and have demonstrated that many enteric pathogen infections are associated with altered gut microflora composition. In this study, we investigated the effects of Cryptosporidium parvum infection (zoonotic protozoan affecting a large range of vertebrates) on both qualitative and quantitative composition of gut microbiota in a CD-1 neonatal mouse model.

METHODS

5-day-old neonate mice were experimentally infected with 10⁵Cryptosporidium parvum Iowa oocysts by oesophageal gavage. The intestinal microbiota of both infected (Cp+) and uninfected (Cp-) mice groups was examined by high-throughput sequencing of the bacterial 16S rDNA gene V3-V4 hypervariable region.

RESULTS

The most consistent change in the microbiota composition of Cp+ mice was the increased proportion of bacterial communities belonging to the Phylum Bacteroidetes. In contrast, the microbiota of Cp- mice was associated with increased proportions of several Firmicutes and Actinobacteria phyla members.

CONCLUSION

For the first time, our study provides evidence of an association between cryptosporidial infection and gut dysbiosis, thus contributing valuable knowledge to the as-yet little-explored field of Cryptosporidium-microbiota interactions in a neonatal mouse model.

Surface sterilization methods impact measures of internal microbial diversity in ticks

BACKGROUND

Ticks are obligate blood feeders transmitting major pathogens worldwide. Over the past few years, considerable research efforts have focused on the diversity, distribution and impact of gut and intracellular bacterial symbionts on tick development and tick-borne pathogen transmission. The study of this internal microbiome requires the use of a sterilization method to remove external (i.e. cuticular) microbes present on the tick's surface and to avoid any further contamination. Several sterilization methods exist, including ethanol- or bleach-based treatments that are both effective in killing microbes but with different potential effects on DNA denaturation.

METHODS

We examined how these different sterilization methods impact the measure of internal microbial diversity hosted by the Cayenne tick Amblyomma cajennense (sensu stricto). Bacterial barcoding investigations based on 16S rRNA gene sequences were conducted on two batches of 50 individuals each: Ticks of the first batch were sterilized with bleach diluted at 1% and the second batch with 70% ethanol. Tick external microbiome was also determined from cuticle smearing and water samples used for tick washing.

RESULTS

Bacterial barcoding investigations showed major differences between ethanol- and bleach-treated specimens. Both methods led to the detection of major intracellular bacteria associated with A. cajennense (s.s.) but ethanol-treated ticks always harbored a higher bacterial diversity than bleach-treated ticks. Further examinations of tick gut and tick external microbiome revealed that ethanol-based surface sterilization method is inefficient to eliminate the DNA of external bacteria.

CONCLUSIONS

We herein provide evidence that studies investigating the internal microbiome of ticks should consider bleach as the gold standard to efficiently remove cuticular bacterial DNA. Indeed, this method does not impact the internal bacterial diversity hosted by ticks and is thus a better method than the ethanol-based one for studying the internal microbiome.

Issues and current standards of controls in microbiome research

Good scientific practice is important in all areas of science. In recent years this has gained more and more attention, especially considering the 'scientific reproducibility crisis'. While most researchers are aware of the issues with good scientific practice, not all of these issues are necessarily clear, and the details can be very complicated. For many years it has been accepted to perform and publish sequencing based microbiome studies without including proper controls. Although in recent years more scientists realize the necessity of implementing controls, this poses a problem due to the complexity of the field. Another concern is the inability to properly interpret the information gained from controls in microbiome studies. Here, we will discuss these issues and provide a comprehensive overview of problematic points regarding controls in microbiome research, and of the current standards in this area.

Stochastic processes govern bacterial communities from the blood of pikas and from their arthropod vectors

Vector-borne microbes influence pathogen transmission and blood microbiomes, thereby affecting the emergence of infectious diseases. Thus, understanding the relationship between host and vector microbiomes is of importance. In this study, we investigated the bacterial community composition, diversity and assembly of the flea (Rhadinopsylla dahurica vicina), torsalo (Hypoderma curzonial), and the blood and gut of their shared pika host, Ochotona curzoniae. Bartonella, Sphingomonas and Bradyrhizobium were enriched in blood, while Wolbachia and Fusobacterium were more abundant in fleas and torsaloes. Most of potential pathogenic microbes (belonging to Fusobacterium, Rickettsia, Kingella, Porphyromonas, Bartonella and Mycoplasma) were present in the blood of pikas and their vectors. Blood communities were more similar to those from fleas than other sample types and were independent of host factors or geographical sites. Notably, blood microbes originate mainly from fleas rather than gut or torsaloes. Interestingly, the community assembly of blood, fleas or torsaloes was primarily governed by stochastic processes, while the gut microbiome was determined by deterministic processes. Ecological drift plays a dominant role in the assembly of blood and flea microbiomes. These results reflect the difficulty for predicting and regulating the microbial ecology of fleas for the prevention of potential microbiome-associated diseases.

Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding

An accurate estimation of parasitism rates and diversity of parasitoids of crop insect pests is a prerequisite for exploring processes leading to efficient natural biocontrol. Traditional methods such as rearing have been often limited by taxonomic identification, insect mortality and intensive work, but the advent of high-throughput sequencing (HTS) techniques, such as DNA metabarcoding, is increasingly seen as a reliable and powerful alternative approach. Little has been done to explore the benefits of such an approach for estimating parasitism rates and parasitoid diversity in an agricultural context. In this study, we compared the composition of parasitoid species and parasitism rates between rearing and DNA metabarcoding of host eggs and larvae of the millet head miner, Heliocheilus albipunctella De Joannis (Lepidoptera, Noctuidae), collected from millet fields in Senegal. We first assessed the detection threshold for the main ten endoparasitoids, by sequencing PCR products obtained from artificial dilution gradients of the parasitoid DNAs in the host moth. We then assessed the potential of DNA metabarcoding for diagnosing parasitism rates in samples collected from the field. Under controlled conditions, our results showed that relatively small quantities of parasitoid DNA (0.07 ng) were successfully detected within an eight-fold larger quantity of host DNA. Parasitoid diversity and parasitism rate estimates were always higher for DNA metabarcoding than for host rearing. Furthermore, metabarcoding detected multi-parasitism, cryptic parasitoid species and differences in parasitism rates between two different sampling sites. Metabarcoding shows promise for gaining a clearer understanding of the importance and complexity of host-parasitoid interactions in agro-ecosystems, with a view to improving pest biocontrol strategies.

Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing

DNA metabarcoding of faecal samples is being successfully used to study the foraging niche of species. We assessed the ability of two benchtop high-throughput sequencing (HTS) platforms, to identify a large taxonomic array of food items from domestic cats Felis silvestris catus, including prey and human-related food taxa (pet food and leftovers leaving undetectable solid remains in faeces). Scats from a captive feeding trial (n = 41) and from free-ranging individuals (n = 326) were collected and analysed using a cytb mini-barcode in independent PCR replicates on the Ion PGM and the MiSeq platforms. Outputs from MiSeq were more sensitive and reproducible than those from Ion PGM due to a higher sequencing depth and sequence quality on MiSeq. DNA from intact prey taxa was detected more often (82% of the expected occurrences) than DNA from pet food (54%) and raw fish and meat (31%). We assumed that this variability was linked to different degree of DNA degradation: The Ion PGM detected significantly less human-linked food, birds, field voles, murids and shrews in the field-collected samples than the MiSeq platform. Pooling the replicates from both platforms and filtering the data allowed identification of at least one food item in 87.4% of the field-collected samples. Our DNA metabarcoding approach identified 29 prey taxa, of which 25 to species level (90% of items) including 9 rodents, 3 insectivores, 12 birds and 1 reptile and 33 human-related food taxa of which 23 were identified to genus level (75% of items). Our results demonstrate that using HTS platforms such as MiSeq, which provide reads of sufficiently high quantity and quality, with sufficient numbers of technical replicates, is a robust and non-invasive approach for further dietary studies on animals foraging on a wide range of food items in anthropogenic landscapes.

Identification of Leptospira and Bartonella among rodents collected across a habitat disturbance gradient along the Inter-Oceanic Highway in the southern Amazon Basin of Peru

Background

The southern Amazon Basin in the Madre de Dios region of Peru has undergone rapid deforestation and habitat disruption, leading to an unknown zoonotic risk to the growing communities in the area.

Methodology/Principal findings

We surveyed the prevalence of rodent-borne Leptospira and Bartonella, as well as potential environmental sources of human exposure to Leptospira, in 4 communities along the Inter-Oceanic Highway in Madre de Dios. During the rainy and dry seasons of 2014–2015, we captured a total of 97 rodents representing 8 genera in areas that had experienced different degrees of habitat disturbance. Primarily by using 16S metagenomic sequencing, we found that most of the rodents (78%) tested positive for Bartonella, whereas 24% were positive for Leptospira; however, the patterns differed across seasons and the extent of habitat disruption. A high prevalence of Bartonella was identified in animals captured across both trapping seasons (72%–83%) and the relative abundance was correlated with increasing level of land disturbance. Leptospira-positive animals were more than twice as prevalent during the rainy season (37%) as during the dry season (14%). A seasonal fluctuation across the rainy, dry, and mid seasons was also apparent in environmental samples tested for Leptospira (range, 55%–89% of samples testing positive), and there was a high prevalence of this bacteria across all sites that were sampled in the communities.

Conclusions/Significance

These data indicate the need for increased awareness of rodent-borne disease and the potential for environmental spread along the communities in areas undergoing significant land-use change.

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

We aimed to develop a framework, based on graph theory, to capture the ecological meaning behind pure pair comparisons of microbiome-derived data. As a proof of concept, we applied the framework to analyze the co-occurrence of bacteria in either Ixodes ricinus ticks or the spleen of one of their main hosts, the vole Myodes glareolus. As a secondary lymphoid organ, the spleen acts as a filter of blood and represents well the exposure to microorganisms circulating in the blood; including those acquired and transmitted by ticks during feeding. The microbiome of 301 and 269 individual tick and vole samples, respectively, were analyzed using next generation sequencing (NGS) of 16S rRNA. To assess the effect of habitat on ecological communities of bacteria associated to ticks and voles, two different biotopes were included in the study, forest, and ecotone. An innovative approach of NGS data analysis combining network analysis and phylogenies of co-occuring of bacteria was used to study associations between bacteria in individual samples. Of the 126 bacterial genera found in ticks and voles, 62% were shared by both species. Communities of co-occurring bacteria were always more phylogenetically diverse in ticks than in voles. Interestingly, ~80% of bacterial phylogenetic diversity was found in ~20% of ticks. This pattern was not observed in vole-associated bacteria. Results revealed that the microbiome of I. ricinus is only slightly related to that of M. glareolus and that the biotope plays the most important role in shaping the bacterial communities of either ticks or voles. The analysis of the phylogenetic signal of the network indexes across the 16S rRNA-derived tree of bacteria suggests that the microbiome of both ticks and voles has high phylogenetic diversity and that closest bacterial genera do not co-occur. This study shows that network analysis is a promising tool to unravel complex microbial communities associated to arthropod vectors and vertebrate hosts.

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

We aimed to develop a framework, based on graph theory, to capture the ecological meaning behind pure pair comparisons of microbiome-derived data. As a proof of concept, we applied the framework to analyze the co-occurrence of bacteria in either Ixodes ricinus ticks or the spleen of one of their main hosts, the vole Myodes glareolus. As a secondary lymphoid organ, the spleen acts as a filter of blood and represents well the exposure to microorganisms circulating in the blood; including those acquired and transmitted by ticks during feeding. The microbiome of 301 and 269 individual tick and vole samples, respectively, were analyzed using next generation sequencing (NGS) of 16S rRNA. To assess the effect of habitat on ecological communities of bacteria associated to ticks and voles, two different biotopes were included in the study, forest, and ecotone. An innovative approach of NGS data analysis combining network analysis and phylogenies of co-occuring of bacteria was used to study associations between bacteria in individual samples. Of the 126 bacterial genera found in ticks and voles, 62% were shared by both species. Communities of co-occurring bacteria were always more phylogenetically diverse in ticks than in voles. Interestingly, ~80% of bacterial phylogenetic diversity was found in ~20% of ticks. This pattern was not observed in vole-associated bacteria. Results revealed that the microbiome of I. ricinus is only slightly related to that of M. glareolus and that the biotope plays the most important role in shaping the bacterial communities of either ticks or voles. The analysis of the phylogenetic signal of the network indexes across the 16S rRNA-derived tree of bacteria suggests that the microbiome of both ticks and voles has high phylogenetic diversity and that closest bacterial genera do not co-occur. This study shows that network analysis is a promising tool to unravel complex microbial communities associated to arthropod vectors and vertebrate hosts.

Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls

Workflows for microbiome community profiling by high-throughput sequencing are prone to sample mix-ups and cross-contamination due to the complexity of the procedures and large number of samples typically analyzed in parallel. We employed synthetic 16S rRNA gene spike-in controls to establish a method for tracking of sample identity and detection of cross-contamination in microbiome community profiling assays based on 16S rRNA gene amplicon sequencing (16S-seq). Results demonstrated that combinatorial sample tracking mixes (STMs) can be reliably resolved by Illumina sequencing and faithfully represent their sample of origin. In a single-blinded experiment, addition of STMs at low levels was shown to be sufficient to unambiguously identify and resolve swapped samples. Using artificial admixtures of individually SMT-tagged samples, we further established the ability to detect and quantify cross-contamination down to a level of approximately 1%. The utility of our technique was underscored through detection of an unplanned case of cross-contamination that occurred during this study. By enabling detection of sample mix-ups and cross-contamination throughout 16S-seq workflows, the present technique thus assures provenance of sequence data on a per-sample basis. The method can be readily implemented in standard 16S-seq workflows and its routine application is expected to enhance the reliability of 16S-seq data.

Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia

Skin forms a critical protective barrier between a mammal and its external environment. Baseline data on the mammalian skin microbiome elucidates which microorganisms are found on healthy skin and provides insight into mammalian evolutionary history. To our knowledge, this study represents the largest existing mammalian skin microbiome survey. Our findings demonstrate that human skin is distinct, not only from other Primates, but from all 10 mammalian orders sampled. Identifying significant similarities between branching of mammalian phylogenetic trees and relatedness trees for their corresponding microbial communities raises the possibility that mammals have experienced coevolution between skin microbiota and their corresponding host species.

Skin is the largest organ of the body and represents the primary physical barrier between mammals and their external environment, yet the factors that govern skin microbial community composition among mammals are poorly understood. The objective of this research was to generate a skin microbiota baseline for members of the class Mammalia, testing the effects of host species, geographic location, body region, and biological sex. Skin from the back, torso, and inner thighs of 177 nonhuman mammals was sampled, representing individuals from 38 species and 10 mammalian orders. Animals were sampled from farms, zoos, households, and the wild. The DNA extracts from all skin swabs were amplified by PCR and sequenced, targeting the V3-V4 regions of bacterial and archaeal 16S rRNA genes. Previously published skin microbiome data from 20 human participants, sampled and sequenced using an identical protocol to the nonhuman mammals, were included to make this a comprehensive analysis. Human skin microbial communities were distinct and significantly less diverse than all other sampled mammalian orders. The factor most strongly associated with microbial community data for all samples was whether the host was a human. Within nonhuman samples, host taxonomic order was the most significant factor influencing skin microbiota, followed by the geographic location of the habitat. By comparing the congruence between host phylogeny and microbial community dendrograms, we observed that Artiodactyla (even-toed ungulates) and Perissodactyla (odd-toed ungulates) had significant congruence, providing evidence of phylosymbiosis between skin microbial communities and their hosts.

Complexity and biosemiotics in evolutionary ecology of zoonotic infectious agents

More is not automatically better. Generation and accumulation of information reflecting the complexity of zoonotic diseases as ecological systems do not necessarily lead to improved interpretation of the obtained information and understanding of these complex systems. The traditional conceptual framework for analysis of diseases ecology is neither designed for, nor adaptable enough, to absorb the mass of diverse sources of relevant information. The multidirectional and multidimensional approaches to analyses form an inevitable part in defining a role of zoonotic pathogens and animal hosts considering the complexity of their inter-relations. And the more data we have, the more involved the interpretation needs to be. The keyword for defining the roles of microbes as pathogens, animals as hosts, and environmental parameters as infection drivers is "functional importance." Microbes can act as pathogens toward their host only if/when they recognize the animal organism as the target. The same is true when the host recognizes the microbe as a pathogen rather than harmless symbiont based on the context of its occurrence in that host. Here, we propose conceptual tools developed in the realm of the interdisciplinary sciences of complexity and biosemiotics for extending beyond the currently dominant mindset in ecology and evolution of infectious diseases. We also consider four distinct hierarchical levels of perception guiding how investigators can approach zoonotic agents, as a subject of their research, representing differences in emphasizing particular elements and their relations versus more unified systemic approaches.

Microbiota Diversity Within and Between the Tissues of Two Wild Interbreeding Species

Understanding the role of microbiota as reproductive barriers or sources of adaptive novelty in the fundamental biological phenomenon of speciation is an exciting new challenge necessitating exploration of microbiota variation in wild interbreeding species. We focused on two interbreeding cyprinid species, Chondrostoma nasus and Parachondrostoma toxostoma, which have geographic distributions characterized by a mosaic of hybrid zones. We described microbiota diversity and composition in the three main teleost mucosal tissues, the skin, gills and gut, in the parental parapatric populations. We found that tissue type was the principal determinant of bacterial community composition. In particular, there was strong microbiota differentiation between external and internal tissues, with secondary discrimination between the two species. These findings suggest that specific environmental and genetic filters associated with each species have shaped the bacterial communities, potentially reflecting deterministic assemblages of bacteria. We defined the core microbiota common to both Chondrostoma species for each tissue, highlighting the occurrence of microbe-host genome interactions at this critical level for studies of the functional consequences of hybridization. Further investigations will explore to what extend these specific tissue-associated microbiota signatures could be profoundly altered in hybrids, with functional consequences for post-mating reproductive isolation in relation to environmental constraints.

Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis

Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the "all at once" taxonomic identification of bats and their arthropod prey for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods, and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity and amplification biases. Our parallel identification strategy of predators and prey reduces the risk of mis-assigning prey to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing "chirosurveillance" and conservation strategies.

Tick-, Flea-, and Louse-Borne Diseases of Public Health and Veterinary Significance in Nigeria

Mosquito-borne diseases are common high-impact diseases in tropical and subtropical areas. However, other non-mosquito vector-borne pathogens (VBPs) may share their geographic distribution, seasonality, and clinical manifestations, thereby contributing their share to the morbidity and mortality caused by febrile illnesses in these regions. The purpose of this work was to collect and review existing information and identify knowledge gaps about tick, flea-, and louse-borne diseases of veterinary and public health significance in Nigeria. Full-length articles about VBPs were reviewed and relevant information about the vectors, their hosts, geographic distribution, seasonality, and association(s) with human or veterinary diseases was extracted. Specific laboratory tools used for detection and identification of VBPs in Nigeria were also identified. A total of 62 original publications were examined. Substantial information about the prevalence and impacts of ticks and fleas on pet and service dogs (18 articles), and livestock animals (23 articles) were available; however, information about their association with and potential for causing human illnesses was largely absent despite the zoonotic nature of many of these peri-domestic veterinary diseases. Recent publications that employed molecular methods of detection demonstrated the occurrence of several classic (Ehrlichia canis, Rickettsia africae, Bartonella sp.) and emerging human pathogens (R. aeschlimannii, Neoehrlichia mikurensis) in ticks and fleas. However, information about other pathogens often found in association with ticks (R. conorii) and fleas (R. typhi, R. felis) across the African continent was lacking. Records of louse-borne epidemic typhus in Nigeria date to 1947; however, its current status is not known. This review provides an essential baseline summary of the current knowledge in Nigeria of non-mosquito VBPs, and should stimulate improvements in the surveillance of the veterinary and human diseases they cause in Nigeria. Due to increasing recognition of these diseases in other African countries, veterinary and public health professionals in Nigeria should expand the list of possible diseases considered in patients presenting with fever of unknown etiology.

Ecological and sanitary impacts of bacterial communities associated to biological invasions in African commensal rodent communities

Changes in host-parasite ecological interactions during biological invasion events may affect both the outcome of invasions and the dynamics of exotic and/or endemic infections. We tested these hypotheses, by investigating ongoing house mouse (Mus musculus domesticus) and black rat (Rattus rattus) invasions in Senegal (West Africa). We used a 16S gene rRNA amplicon sequencing approach to study potentially zoonotic bacterial communities in invasive and native rodents sampled along two well-defined independent invasion routes. We found that individual host factors (body mass and sex) were important drivers of these bacterial infections in rodents. We observed that the bacterial communities varied along invasion routes and differed between invasive and native rodents, with native rodents displaying higher overall bacterial diversity than invasive rodents. Differences in prevalence levels for some bacterial Operational Taxonomic Units (OTUs) provided support for ecological processes connecting parasitism and invasion success. Finally, our results indicated that rodent invasions may lead to the introduction of exotic bacterial genera and/or to changes in the prevalence of endemic ones. This study illustrates the difficulty of predicting the relationship between biodiversity and disease risks, and advocate for public health prevention strategies based on global pathogen surveillance followed by accurate characterization of potential zoonotic agents.

Infection of Rodents by Orientia tsutsugamushi, the Agent of Scrub Typhus in Relation to Land Use in Thailand

The relationship between land use structures and occurrence of the scrub typhus agent, Orientia tsutsugamushi, in small wild mammals was investigated in three provinces of Thailand: Buriram, Loei, and Nan. O. tsutsugamushi detection was performed using 16S ribosomal DNA (rDNA) amplicon sequencing approach using Miseq Illumina platform. In total, 387 animals (rodents and shrews) were examined for the infection. The 16S rDNA sequences of the bacterium were found in nine animals, namely Bandicota savilei, Berylmys bowersi, Leopoldamys edwardsi, Rattus exulans, R. tanezumi, and Rattus sp. phylogenetic clade 3, yielding 2.3% infection rate, with two new rodent species found infected by the bacterium in Thailand: B. bowersi and L. edwardsi. Using a generalized linear mixed model (GLMM) and Random Forest analyses for investigating the association between human-land use and occurrence of the bacterium, forest habitat appeared as a strong explicative variable of rodent infection, meaning that O. tsutsugamushi-infected animals were more likely found in forest-covered habitats. In terms of public health implementation, our results suggest that heterogenous forested areas including forest-converted agricultural land, reforestation areas, or fallows, are potential habitats for O. tsutsugamushi transmission. Further understanding of population dynamics of the vectors and their hosts in these habitats could be beneficial for the prevention of this neglected zoonotic disease.