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1,509 results for “Host associated”
Geography, seasonality, and host-associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal
<p>The Canadian Arctic is an extreme environment with low floral and faunal diversity characterized by major seasonal shifts in temperature, moisture and daylight. Muskoxen (<i>Ovibos moschatus</i>) are one of few large herbivores able to survive this harsh environment. Microbiome research of the gastrointestinal tract may hold clues as to how muskoxen exist in the Arctic, but also how this species may respond to rapid environmental changes. In this study, we investigated the effects of season (spring/summer/winter), year (2007-2016), and host genetic structure on population-level microbiome variation in muskoxen from the Canadian Arctic. We utilized 16S rRNA gene sequencing to characterize the fecal microbial communities of 78 male muskoxen encompassing two population genetic clusters.<a name="_Hlk534564036"> These clusters are defined by Arctic Mainland and Island populations, including; 1) two mainland sampling locations of the Northwest Territories and Nunavut; and 2) four locations of Victoria Island. </a>Between these geographic populations, we found that differences in the microbiome reflected host-associated genetic cluster with evidence of migration. Within populations, seasonality influenced bacterial diversity with no significant differences between years of sampling. We found evidence of pathogenic bacteria, with significantly higher presence in mainland samples. Our findings demonstrate the effects of seasonality and the role of host population-level structure in driving fecal microbiome differences in a large Arctic mammal.</p>
Experimental parasite community perturbation reveals associations between Sin Nombre virus and gastrointestinal nematodes in a rodent reservoir host
<p>Individuals are often co-infected with several parasite species, yet measuring within-host interactions remains difficult in the wild. Consequently, the impact of such interactions on host fitness and epidemiology are often unknown. We used anthelmintic drugs to experimentally reduce nematode infection and measured the effects on both nematodes and the important zoonosis Sin Nombre virus (SNV) in its primary reservoir (<i>Peromyscus spp.</i>). Treatment significantly reduced nematode infection, but increased SNV seroprevalence. Furthermore, mice that were co-infected with both nematodes and SNV were in better condition and survived up to four times longer than uninfected or singly-infected mice. These results highlight the importance of investigating multiple parasites for understanding interindividual variation and epidemiological dynamics in reservoir populations with zoonotic transmission potential.</p>
Tick microbiomes in neotropical forest fragments are best explained by tick-associated and environmental factors rather than host blood source
<p>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. <i>Francisella </i>and <i>Rickettsia </i>were highly prevalent, but their proportional abundance differed greatly among tick species and we found both positive and negative co-occurrence between members of these two genera. Other tick endosymbionts (e.g. <i>Coxiella</i>, <i>Rickettsiella</i>) were associated with specific tick species. In addition, we detected <i>Anaplasma</i> and <i>Bartonella </i>in several tick species. Our results indicate that the microbial composition and richness of Neotropical ticks are principally related to intrinsic factors (tick species, 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.</p>
Data from: Does sex-biased dispersal account for the lack of geographic and host-associated differentiation in introduced populations of an aphid parasitoid?
Host recognition and use in female parasitoids strongly relies on host fidelity, a plastic behavior which can significantly restrict the host preferences of parasitoids, thus reducing the gene flow between parasitoid populations attacking different insect hosts. However, the effect of migrant males on the genetic differentiation of populations has been frequently ignored in parasitoids, despite its known impact on gene flow between populations. Hence, we studied the extent of gene flow mediated by female and male parasitoids by assessing sibship relationships among parasitoids within and between populations, and its impact on geographic and host-associated differentiation in the aphid parasitoid Aphidius ervi. We report evidences of a high gene flow among parasitoid populations on different aphid hosts and geographic locations. The high gene flow among parasitoid populations was found to be largely male mediated, suggested by significant differences in the distribution of full-sib and paternal half-sib dyads of parasitoid populations.
Data from: A heritable symbiont and host-associated factors shape fungal endophyte communities across spatial scales
1. Although microbial ecologists are intensely interested in the processes governing microbial community assembly, progress has been limited by a lack of studies that span multiple geographical scales and levels of biological organization. 2. We used high throughput sequencing to characterize foliar fungal endophyte communities and host plant genetic structure both within, and among, 24 populations of spotted locoweed (Astragalus lentiginosus) across the Great Basin Desert. 3. Across the Great Basin, both within, and among populations of the host plant, fungal endophyte richness was predicted by plant size and variation in the seed-borne, heritable fungus, Alternaria fulva, which produces the bioactive alkaloid swainsonine. 4. The degree of between-plant turnover in the endophyte community was inversely related to host plant inbreeding and average plant size, and positively related to the relative abundance of A. fulva. Plant size was inversely related to endophyte community richness, both among, and within populations. The genetic and physical distance between host populations was not predictive of differences in fungal community structure. 5. Synthesis: Through pairing intensive local- and regional sampling, we uncovered a primacy of deterministic forces imposed by a heritable symbiont on the community structure of locoweed endophytes.
Data from: Risk alleles for tuberculosis infection associate with reduced immune reactivity in a wild mammalian host
Integrating biological processes across scales remains a central challenge in disease ecology. Genetic variation drives differences in host immune responses, which, along with environmental factors, generates temporal and spatial infection patterns in natural populations that epidemiologists seek to predict and control. However, genetics and immunology are typically studied in model systems, whereas population-level patterns of infection status and susceptibility are uniquely observable in nature. Despite obvious causal connections, organizational scales from genes to host outcomes to population patterns are rarely linked explicitly. Here we identify two loci near genes involved in macrophage (phagocyte) activation and pathogen degradation that additively increase risk of bovine tuberculosis infection by up to 9-fold in wild African buffalo. Furthermore, we observe genotype-specific variation in IL-12 production indicative of variation in macrophage activation. Here we provide measurable differences in infection resistance at multiple scales by characterizing the genetic and inflammatory variation driving patterns of infection in a wild mammal.
Genotypic variation in an ecologically important parasite is associated with host species, lake, and spore size
<p>Genetic variation in parasites has important consequences for host-parasite interactions. Prior studies of the ecologically important parasite <i>Metschnikowia bicuspidata</i> have suggested low genetic variation in the species. Here, we collected <i>M. bicuspidata</i> from two host species (<i>Daphnia dentifera</i> and <i>Ceriodaphnia dubia</i>) and two regions (Michigan and Indiana, USA). Within a lake, outbreaks tended to occur in one host species but not the other. Using microsatellite markers, we identified six parasite genotypes grouped within three distinct clades, one of which was rare. Of the two main clades, one was generally associated with <i>D. dentifera,</i> with lakes in both regions containing a single genotype. The other <i>M. bicuspidata</i> clade was mainly associated with <i>C. dubia</i>, with a different genotype dominating in each region. Despite these associations, both <i>D. dentifera-</i> and <i>C. dubia</i>-associated genotypes were found infecting both hosts in lakes. However, in lab experiments, the <i>D. dentifera</i>-associated genotype infected both <i>D. dentifera</i> and <i>C. dubia</i>, but the <i>C. dubia</i>-associated genotype, which had spores that were approximately 30% smaller, did not infect <i>D. dentifera. </i>We hypothesize that variation in spore size might help explain patterns of cross-species transmission. Future studies exploring the causes and consequences of variation in spore size may help explain patterns of infection and the maintenance of genotypic diversity in this ecologically important system.</p>
Cultivation of host-associated bacteria under sulfide-enriched microoxic and anoxic conditions
<p>Three images of cell colonies on culture plates inoculated with gill tissue homogenate from <em>Bathymodiolus brooksi</em>. The colonies grew under the following conditions: </p> <ul> <li>IMG_2467: microoxic, low H2S, low ammonium</li> <li>IMG_2468: microoxic, low H2S, low ammonium, organics</li> <li>IMG_2474: microoxic, low H2S, high ammonium, organics, 1 mM thiosulfate</li> </ul> <p>Image of a control plate without cultures inoculated with heat sterilized aliquot of <em>Bathymodiolus brooksi</em> gill homogenate:</p> <ul> <li>IMG_2475</li> </ul> <p>Two images of pH controls plated with homogenization medium that did not contain gill homogenate:</p> <ul> <li>IMG_2477: phenol red</li> <li>IMG_2479: bromothymol blue</li> </ul> <p>Two close up photos of colonies on agar plates</p> <ul> <li>IMG_2485</li> <li>IMG_2488</li> </ul>
Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation
<p>Summary statistics for "Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation" </p><p>Files are organized in the following directory structure:</p><p><strong>G2G/</strong> - Summary statistics of G2G associations (SNPs, HLA, and gene-level analysis). </p><p><strong>HLA/ </strong>- Peptide binding prediction results</p><p><strong>preS1_haplotypes/ - </strong>Resolved intra-host haplotypes of the preS1 binding region. </p><p><strong>DnDs/</strong> - Calculation of intra-host positive selection, within the preS1 binding region. </p><p> </p>
A cohort-based study of host gene expression: tumor suppressor and innate immune/inflammatory pathways associated with the HIV reservoir size
<p>The major barrier to an HIV cure is the HIV reservoir: latently-infected cells that persist despite effective antiretroviral therapy (ART). Most prior studies of host genetic predictors of HIV control have focused on "elite controllers," rare individuals able to control virus in the absence of ART. However, there have been few genetic studies among ART-suppressed non-controllers, who make up the majority of people living with HIV (PLWH). We performed host RNA sequencing and HIV reservoir quantification (total DNA [tDNA], unspliced RNA [usRNA], intact DNA) from peripheral CD4+ T cells from 191 HIV+ ART-suppressed non-controllers. After adjusting for nadir CD4+ count, timing of ART initiation, and genetic ancestry, we identified two host genes for which higher expression was significantly associated with smaller total DNA viral reservoir size, <em>P3H3</em> and <em>NBL1</em>, both known tumor suppressor genes. We then identified 17 host genes for which lower expression was associated with higher residual transcription (HIV usRNA). These included novel associations with membrane channel (<em>KCNJ2</em>, <em>GJB2</em>), inflammasome (<em>IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9, CXCL3, CXCL10</em>), and innate immunity (TLR7) genes (FDR-adjusted q<0.05). Gene set enrichment analyses further identified significant associations of HIV usRNA with TLR4/microbial translocation (q=0.006), IL-1/NRLP3 inflammasome (q=0.008), and IL-10 (q=0.037) signaling. Protein validation assays using ELISA and multiplex cytokine assays supported these observed inverse host gene correlations, with P3H3, IL-10, and TNF-a protein associations achieving statistical significance (p<0.05). Of note, plasma IL-10 was also significantly inversely associated with HIV DNA (p=0.016). HIV intact DNA was not associated with differential host gene expression, although this may have been due to a large number of undetectable values in our study. Further data are needed to validate these findings, including functional genomic studies, larger cohorts including underrepresented PLWH in research, and those including dedicated assays to measure the replication-competent HIV reservoir.</p>
Figure 1 in DNA barcoding, visual-guide resource, new localities and host associations of genus Periglischrus Oudemans, 1902 (Acari: Mesostigmata, Spinturnicidae) from Minas Gerais, Brazil
Figure 1 Geographical distribution of sampling localities ofPeriglischrus spp.
Post-association barrier to host switching maintained despite strong selection in a novel mutualism
<p class="MsoNormal"><span>Following a host shift, repeated co-passaging of a mutualistic pair is expected to increase fitness over time in one or both species.<span> </span>Without adaptation, a novel association may be evolutionarily short-lived as it is likely to be outcompeted by native pairings.<span> </span>Here we test whether experimental evolution can rescue a low-fitness novel pairing between two sympatric species of <em>Steinernema</em> nematodes and their symbiotic <em>Xenorhabdus</em> bacteria.<span> </span>Despite low mean fitness in the novel association, considerable variation in nematode reproduction was observed across replicate populations.<span> </span>We selected the most productive infections, co-passaging this novel mutualism nine times to determine whether selection could improve fitness of either or both partners.<span> </span>We found that neither partner showed increased fitness over time.<span> </span>Our results suggest that the variation in association success was not heritable and that mutational input was insufficient to allow evolution to facilitate this host shift.<span> </span>Thus, post-association costs of host switching may represent a formidable barrier to novel partnerships among sympatric mutualists. </span></p>
Host-parasite interactions between a copepod (Pharodes tortugensis) and small reef-associated gobies (Coryphopterus) in the British Virgin Islands
<p>The effects of parasitic copepods on free-living hosts are infrequently documented, and the copepod Pharodes tortugensis has remained virtually unstudied since described. For the first time, we document its host range in the British Virgin Islands (BVI), the prevalence and intensity of infections on wild hosts, and its impacts on host morphology and performance. Infections were observed on four benthic gobies in the BVI (<em>Coryphopterus glaucofraenum</em>, <em>C. venezuelae</em>, <em>C. dicrus</em> and <em>C. eidolon</em>) but not on other host species previously reported from other parts of the western Atlantic. Infected gobies were widespread in the BVI (detected at 33 of 52 sites, prevalence from 1–25%) but extremely rare elsewhere in the Caribbean (detected at 2 of 16 sites, prevalence <0.006%). As is typical of macroparasite infections, <em>P. tortugensis</em> was over-dispersed in BVI host populations (mean intensity = 4.7, range = 1–17). Infections were most common in juvenile and female hosts, and rarely found in larger male hosts. The copepods attach in the branchial chamber of the goby; female copepods show high attachment fidelity to the ventral surface of the chamber, while male copepods attached most often to the first two gill arches and in the branchial chamber adjacent to the female. Infections caused substantial damage to the host's branchial chamber and gill filaments. Parasitized gobies also had larger livers and smaller gonads than unparasitized individuals of similar length. The changes in organ mass of infected gobies were not sizeable enough to affect total body mass, and host condition (the body-length vs. body-mass relationship) was similar for gobies with and without infections. Parasitized gobies were, however, significantly smaller in body mass at a given age, reflecting slower overall growth. Effects of <em>P. tortugensis</em> on individual hosts were broadly similar to those of other parasitic copepods that infect fish gills and, for unknown reasons, the BVI appears to be a persistent hotspot of infections on these goby hosts.</p>
Cross-continental comparison of parasite communities in a wide-ranging carnivore suggests associations with prey diversity and host density
<p><span>Parasites are integral to ecosystem functioning yet often overlooked. Improved understanding of host-parasite associations is important, particularly for wide-ranging species for which host range shifts and climate change could alter host-parasite interactions and their effects on ecosystem function. </span></p> <p><span>Among the most widely distributed mammals with diverse diets, grey wolves (<i>Canis lupus</i>) host parasites that are transmitted among canids and via prey species. Grey wolf-parasite associations may therefore influence the population dynamics and ecological functions of both wolves and their prey. Our goal was to identify large-scale processes that shape host-parasite interactions across populations, with the grey wolf as a model organism. </span></p> <p><span>By compiling data from various studies, we examined the faecal prevalence of gastrointestinal parasites in six wolf populations from two continents in relation to wolf density, diet diversity, and other ecological conditions.</span></p> <p><span>As expected, we found that the faecal prevalence of parasites transmitted directly to wolves via contact with other canids or their excreta was positively associated with wolf density. Contrary to our expectations, the faecal prevalence of parasites transmitted via prey was negatively associated with prey diversity. We also found that parasite communities reflected landscape characteristics and specific prey items available to wolves. </span></p> <p><span>Several parasite taxa identified in this study, including hookworms and coccidian protozoans, can cause morbidity and mortality in canids, especially in pups, or in combination with other stressors. The density-prevalence relationship for parasites with simple lifecycles may reflect a regulatory role of gastrointestinal parasites on wolf populations. Our result that faecal prevalence of parasites was lower in wolves with more diverse diets could provide insight into the mechanisms by which biodiversity may regulate disease. A diverse suite of predator-prey interactions could regulate the effects of parasitism on prey populations and mitigate the transmission of infectious agents, including zoonoses, spread via trophic interactions. </span></p>
High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal
<p>Host-specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among-host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly-transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host-specialist seal louse (<em>Echinophthirius horridus</em>) infesting the Saimaa ringed seal (<em>Phoca hispida saimensis</em>), which is endemic to Lake Saimaa in Finland and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among-host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population-genetic analyses of the seals themselves.</p>
A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae
<p>European flat oyster (<em>Ostrea edulis</em>) is an ecologically and economically important marine bivalve, that has been severely affected by the intracellular parasite <em>Bonamia ostreae</em>. In this study, a flat oyster SNP array (~14,000 SNPs) was used to validate previously reported outlier loci for divergent selection associated with <em>B. ostreae</em> exposure in the Northeast Atlantic Area. A total of 134 wild and hatchery individuals from the North Sea, collected in naïve (NV) and long-term affected (LTA) areas, were analysed. Genetic diversity and differentiation were related to the sampling origin (wild vs hatchery) when using neutral markers, and to bonamiosis status (NV vs LTA) when using outlier loci for divergent selection. Two genetic clusters appeared intermingled in all sampling locations when using outlier loci and their frequency was associated with their bonamiosis status. When both clusters were compared, outlier datasets showed high genetic divergence (FST > 0.25) unlike neutral loci (FST not ≠ 0). Moreover, the cluster associated with LTA samples showed much higher genetic diversity and significant heterozygote excess with outlier loci, but not with neutral data. Most outliers mapped on chromosome 8 (OE-C8) of the flat oyster genome, supporting a main genomic region underlying resilience to bonamiosis. Furthermore, differentially expressed genes previously reported between NV and LTA strains showed higher mapping density on OE-C8. A range of relevant immune functions were specifically enriched among genes annotated on OE-C8, providing hypotheses for resilience mechanisms to an intracellular parasite. The results suggest that marker-assisted selection could be applied to breed resilient strains of <em>O. edulis</em> to bonamiosis, if lower parasite load and/or higher viability of the LTA genetic cluster following <em>B. ostreae</em> infection is demonstrated.</p>
Data from: Comparative host-pathogen associations of Snake Fungal Disease in sympatric species of water snakes (Nerodia)
<p>The ascomycete fungus <em>Ophidiomyces ophiodiicola</em> (<em>Oo</em>) is the causative agent of ophidiomycosis (Snake Fungal Disease), which has been detected globally. However, surveillance efforts in the central U.S., specifically Texas, have been minimal. The threatened and rare Brazos water snake (<em>Nerodia harteri harteri</em>) is one of the most range restricted snakes in the U.S. and is sympatric with two wide-ranging congeners, <em>N. erythrogaster transversa</em> and <em>N. rhombifer</em>, in north central Texas; thus, providing an opportunity to test comparative host-pathogen associations in this system. To accomplish this, we surveyed a portion of the Brazos river drainage (~400 river km) over 29 months and tested 150 Nerodia individuals for the presence of <em>Oo </em>via quantitative PCR and recorded any potential signs of <em>Oo </em>infection. We found <em>Oo </em>was distributed across the entire range of <em>N. h. harteri,</em> <em>Oo</em> prevalence was 46% overall, and there was a significant association between <em>Oo </em>occurrence and signs of infection in our sample. Models indicated adults had a higher probability of <em>Oo </em>infection than juveniles and subadults, and adult <em>N. h. harteri</em> had a higher probability of infection than adult <em>N. rhombifer</em> but not higher than adult <em>N. e. transversa</em>. High <em>Oo </em>prevalence estimates (94.4%) in adult <em>N. h. harteri </em>has implications for their conservation and management owing to their patchy distribution, comparatively low genetic diversity, and threats from anthropogenic habitat modification.</p>
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought
<p><strong><span>Plants are colonized by distinct pathogenic and commensal microbiomes across different regions of the globe, but the factors driving their geographic variation are largely unknown. Using 16S rDNA and shotgun sequencing, we characterized the associations of the <em>Arabidopsis thaliana</em> leaf microbiome with host genetics and climate variables from 267 populations in the species’ native range across Europe. Comparing the distribution of the 575 major bacterial amplicon variants (phylotypes), we discovered that microbiome composition in <em>A. thaliana</em> segregates along a latitudinal gradient. The latitudinal clines in microbiome composition are predicted by metrics of drought, but also by the spatial genetics of the host. To validate the relative effects of drought and host genotype we conducted a common garden field study, finding 10% of the core bacteria to be affected directly by drought, and 20% to be affected by host genetic associations with drought. These data provide a valuable resource for the plant microbiome field, with the identified associations suggesting that drought can directly and indirectly shape genetic variation in A. thaliana via the leaf microbiome.</span></strong></p>
Fig. 1 in Host specificity studies on Gynaikothrips (Thysanoptera: Phlaeothripidae) associated with leaf galls of cultivated Ficus (Rosales: Moraceae) trees
Fig. 1. Pronotal posteroangular setae showing variation in length.
Fig. 2. Four Ficus benjamina plants inside a in Host specificity studies on Gynaikothrips (Thysanoptera: Phlaeothripidae) associated with leaf galls of cultivated Ficus (Rosales: Moraceae) trees
Fig. 2. Four Ficus benjamina plants inside a collapsible cage.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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