| 1. |
- Andersson, Martin N, et al.
(author)
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Sex- and tissue-specific profiles of chemosensory gene expression in a herbivorous gall-inducing fly (Diptera: Cecidomyiidae)
- 2014
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15, s. 1-19
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Journal article (peer-reviewed)abstract
- Background: The chemical senses of insects mediate behaviors that are closely linked to survival and reproduction. The order Diptera contains two model organisms, the vinegar fly Drosophila melanogaster and the mosquito Anopheles gambiae, whose chemosensory genes have been extensively studied. Representing a third dipteran lineage with an interesting phylogenetic position, and being ecologically distinct by feeding on plants, the Hessian fly (Mayetiola destructor Say, Diptera: Cecidomyiidae) genome sequence has recently become available. Among plant-feeding insects, the Hessian fly is unusual in ‘reprogramming’ the plant to create a superior food and in being the target of plant resistance genes, a feature shared by plant pathogens. Chemoreception is essential for reproductive success, including detection of sex pheromone and plant-produced chemicals by males and females, respectively. Results: We identified genes encoding 122 odorant receptors (OR), 28 gustatory receptors (GR), 39 ionotropic receptors (IR), 32 odorant binding proteins, and 7 sensory neuron membrane proteins in the Hessian fly genome. We then mapped Illumina-sequenced transcriptome reads to the genome to explore gene expression in male and female antennae and terminal abdominal segments. Our results reveal that a large number of chemosensory genes have up-regulated expression in the antennae, and the expression is in many cases sex-specific. Sex-specific expression is particularly evident among the Or genes, consistent with the sex-divergent olfactory-mediated behaviors of the adults. In addition, the large number of Ors in the genome but the reduced set of Grs and divergent Irs suggest that the short-lived adults rely more on long-range olfaction than on short-range gustation. We also report up-regulated expression of some genes from all chemosensory gene families in the terminal segments of the abdomen, which play important roles in reproduction. Conclusions: We show that a large number of the chemosensory genes in the Hessian fly genome have sex- and tissue-specific expression profiles. Our findings provide the first insights into the molecular basis of chemoreception in plant-feeding flies, representing an important advance toward a more complete understanding of olfaction in Diptera and its links to ecological specialization.
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| 2. |
- Bensch, Staffan, et al.
(author)
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The genome of Haemoproteus tartakovskyi and its relationship to human malaria parasites
- 2016
-
In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 8:5, s. 73-1361
-
Journal article (peer-reviewed)abstract
- The phylogenetic relationships among hemosporidian parasites, including the origin of Plasmodium falciparum, the most virulent malaria parasite of humans, have been heavily debated for decades. Studies based on multiple-gene sequences have helped settle many of these controversial phylogenetic issues. However, denser taxon sampling and genome-wide analyses are needed to confidently resolve the evolutionay relationships among hemosporidian parasites. Genome sequences of several Plasmodium parasites are available but only for species infecting primates and rodents. To root the phylogenetic tree of Plasmodium, genomic data from related parasites of birds or reptiles are required. Here, we use a novel approach to isolate parasite DNA from microgametes and describe the first genome of a bird parasite in the sister genus to Plasmodium, Haemoproteus tartakovskyi Similar to Plasmodium parasites, H. tartakovskyi has a small genome (23.2 Mb, 5,990 genes) and a GC content (25.4%) closer to P. falciparum (19.3%) than to Plasmodium vivax (42.3%). Combined with novel transcriptome sequences of the bird parasite Plasmodium ashfordi, our phylogenomic analyses of 1,302 orthologous genes demonstrate that mammalian-infecting malaria parasites are monophyletic, thus rejecting the repeatedly proposed hypothesis that the ancestor of Laverania parasites originated from a secondary host shift from birds to humans. Genes and genomic features previously found to be shared between P. falciparum and bird malaria parasites, but absent in other mammal malaria parasites, are therefore signatures of maintained ancestral states. We foresee that the genome of H. tartakovskyi will open new directions for comparative evolutionary analyses of malarial adaptive traits.
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| 3. |
- Ferreira, Francisco C., et al.
(author)
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Transcriptional response of individual Hawaiian Culex quinquefasciatus mosquitoes to the avian malaria parasite Plasmodium relictum
- 2022
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In: Malaria Journal. - : Springer Nature. - 1475-2875. ; 21
-
Journal article (peer-reviewed)abstract
- Background: Plasmodium parasites that cause bird malaria occur in all continents except Antarctica and are primarily transmitted by mosquitoes in the genus Culex. Culex quinquefasciatus, the mosquito vector of avian malaria in HawaiModified Letter Turned Commai, became established in the islands in the 1820s. While the deadly effects of malaria on endemic bird species have been documented for many decades, vector-parasite interactions in avian malaria systems are relatively understudied.Methods: To evaluate the gene expression response of mosquitoes exposed to a Plasmodium infection intensity known to occur naturally in HawaiModified Letter Turned Commai, offspring of wild-collected Hawaiian Cx. quinquefasciatus were fed on a domestic canary infected with a fresh isolate of Plasmodium relictum GRW4 from a wild-caught Hawaiian honeycreeper. Control mosquitoes were fed on an uninfected canary. Transcriptomes of five infected and three uninfected individual mosquitoes were sequenced at each of three stages of the parasite life cycle: 24 h post feeding (hpf) during ookinete invasion; 5 days post feeding (dpf) when oocysts are developing; 10 dpf when sporozoites are released and invade the salivary glands.Results: Differential gene expression analyses showed that during ookinete invasion (24 hpf), genes related to oxidoreductase activity and galactose catabolism had lower expression levels in infected mosquitoes compared to controls. Oocyst development (5 dpf) was associated with reduced expression of a gene with a predicted innate immune function. At 10 dpf, infected mosquitoes had reduced expression levels of a serine protease inhibitor, and further studies should assess its role as a Plasmodium agonist in C. quinquefasciatus. Overall, the differential gene expression response of Hawaiian Culex exposed to a Plasmodium infection intensity known to occur naturally in HawaiModified Letter Turned Commai was low, but more pronounced during ookinete invasion.Conclusions: This is the first analysis of the transcriptional responses of vectors to malaria parasites in non-mammalian systems. Interestingly, few similarities were found between the response of Culex infected with a bird Plasmodium and those reported in Anopheles infected with human Plasmodium. The relatively small transcriptional changes observed in mosquito genes related to immune response and nutrient metabolism support conclusions of low fitness costs often documented in experimental challenges of Culex with avian Plasmodium.
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| 4. |
- Fountain‐Jones, Nicholas M., et al.
(author)
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Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions
- 2024
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In: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 33:2
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Journal article (peer-reviewed)abstract
- The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.
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| 5. |
- Hellgren, Olof, et al.
(author)
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De novo synthesis of thiamine (vitamin B1) is the ancestral state in Plasmodium parasites – evidence from avian haemosporidians
- 2018
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In: Parasitology. - 0031-1820. ; 145:8, s. 1084-1089
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Journal article (peer-reviewed)abstract
- Parasites often have reduced genomes as their own genes become redundant when utilizing their host as a source of metabolites, thus losing their own de novo production of metabolites. Primate malaria parasites can synthesize vitamin B1 (thiamine) de novo but rodent malaria and other genome-sequenced apicomplexans cannot, as the three essential genes responsible for this pathway are absent in their genomes. The unique presence of functional thiamine synthesis genes in primate malaria parasites and their sequence similarities to bacterial orthologues, have led to speculations that this pathway was horizontally acquired from bacteria. Here we show that the genes essential for the de novo synthesis of thiamine are found also in avian Plasmodium species. Importantly, they are also present in species phylogenetically basal to all mammalian and avian Plasmodium parasites, i.e. Haemoproteus. Furthermore, we found that these genes are expressed during the blood stage of the avian malaria infection, indicating that this metabolic pathway is actively transcribed. We conclude that the ability to synthesize thiamine is widespread among haemosporidians, with a recent loss in the rodent malaria species.
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| 6. |
- Hellgren, Olof, et al.
(author)
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De novo synthesis of thiamine (vitamin B1) is the ancestral state in Plasmodium parasites – evidence from avian haemosporidians
- 2017
-
In: Parasitology. - : Cambridge University Press (CUP). - 0031-1820 .- 1469-8161. ; 145:8, s. 1084-1089
-
Journal article (peer-reviewed)abstract
- Parasites often have reduced genomes as their own genes become redundant when utilizing their host as a source of metabolites, thus losing their own de novo production of metabolites. Primate malaria parasites can synthesize vitamin B1 (thiamine) de novo but rodent malaria and other genome-sequenced apicomplexans cannot, as the three essential genes responsible for this pathway are absent in their genomes. The unique presence of functional thiamine synthesis genes in primate malaria parasites and their sequence similarities to bacterial orthologues, have led to speculations that this pathway was horizontally acquired from bacteria. Here we show that the genes essential for the de novo synthesis of thiamine are found also in avian Plasmodium species. Importantly, they are also present in species phylogenetically basal to all mammalian and avian Plasmodium parasites, i.e. Haemoproteus. Furthermore, we found that these genes are expressed during the blood stage of the avian malaria infection, indicating that this metabolic pathway is actively transcribed. We conclude that the ability to synthesize thiamine is widespread among haemosporidians, with a recent loss in the rodent malaria species.
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| 7. |
- Leray, Matthieu, et al.
(author)
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Natural experiments and long-term monitoring are critical to understand and predict marine host–microbe ecology and evolution
- 2021
-
In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 19:8, s. e3001322-e3001322
-
Journal article (peer-reviewed)abstract
- Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.
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| 8. |
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| 9. |
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| 10. |
- Naepflin, Kathrin, et al.
(author)
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Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales
- 2019
-
In: PeerJ. - 2167-8359. ; 7
-
Journal article (peer-reviewed)abstract
- Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.
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| 11. |
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| 12. |
- Sigeman, Hanna, et al.
(author)
-
Insights into avian incomplete dosage compensation : Sex-biased gene expression coevolves with sex chromosome degeneration in the common whitethroat
- 2018
-
In: Genes. - : MDPI AG. - 2073-4425. ; 9:8
-
Journal article (peer-reviewed)abstract
- Non-recombining sex chromosomes (Y and W) accumulate deleterious mutations and degenerate. This poses a problem for the heterogametic sex (XY males; ZW females) because a single functional gene copy often implies less gene expression and a potential imbalance of crucial expression networks. Mammals counteract this by dosage compensation, resulting in equal sex chromosome expression in males and females, whereas birds show incomplete dosage compensation with significantly lower expression in females (ZW). Here, we study the evolution of Z and W sequence divergence and sex-specific gene expression in the common whitethroat (Sylvia communis), a species within the Sylvioidea clade where a neo-sex chromosome has been formed by a fusion between an autosome and the ancestral sex chromosome. In line with data from other birds, females had lower expression than males at the majority of sex-linked genes. Results from the neo-sex chromosome region showed thatWgametologs have diverged functionally to a higher extent than their Z counterparts, and that the female-to-male expression ratio correlated negatively with the degree of functional divergence of these gametologs. We find it most likely that sex-linked genes are being suppressed in females as a response to W chromosome degradation, rather than that these genes experience relaxed selection, and thus diverge more, by having low female expression. Overall, our data of this unique avian neo-sex chromosome system suggest that incomplete dosage compensation evolves, at least partly, through gradual accumulation of deleterious mutations at the W chromosome and declining female gene expression.
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| 13. |
- Sigvald, Roland, et al.
(author)
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Molecular identification of bloodmeals and species composition in Culicoides biting midges
- 2013
-
In: Medical and Veterinary Entomology. - : Wiley. - 0269-283X .- 1365-2915. ; 27, s. 104-112
-
Journal article (peer-reviewed)abstract
- Investigations of host preferences in haematophagous insects, including Culicoides biting midges (Diptera: Ceratopogonidae), are critical in order to assess transmission routes of vector-borne diseases. In this study, we collected and morphologically identified 164 blood-engorged Culicoides females caught in both light traps and permanent 12-m high suction traps during 20082010 in Sweden. Molecular analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene in the biting midges was performed to verify species classification, discern phylogenetic relationships and uncover possible cryptic species. Bloodmeal analysis using universal vertebrate cytochrome b primers revealed a clear distinction in host selection between mammalophilic and ornithophilic Culicoides species. Host sequences found matches in horse (n = 59), sheep (n = 39), cattle (n = 26), Eurasian elk (n = 1) and 10 different bird species (n = 18). We identified 15 Culicoides species previously recorded in Scandinavia and four additional species haplotypes that were distinctly different from the described species. All ornithophilic individuals (n = 23) were caught exclusively in the suction traps, as were, interestingly, almost all mammalophilic species (n = 41), indicating that many biting midge species may be able to cover long distances after completing a bloodmeal. These results add new information on the composition of Culicoides species and their host preferences and their potential long-distance dispersal while blood-engorged.
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| 14. |
- Videvall, Elin, et al.
(author)
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Butterfly monitoring using systematically placed transects in contrasting climatic regions - Exploring an established spatial design for sampling
- 2016
-
In: Nature Conservation. - : Pensoft Publishers. - 1314-6947 .- 1314-3301. ; 14, s. 41-62
-
Journal article (peer-reviewed)abstract
- Butterfly monitoring schemes are recording programs initiated to monitor nationwide butterfly abundance and distribution patterns, often with help from volunteers. The method generates high-resolution data, but may be associated with a degree of habitat sampling bias if volunteers prefer to survey areas perceived to be high-quality butterfly habitats. This can result in habitats becoming underrepresented in the data set, leading to less information about the butterfly populations there. In the present study, we investigate the possibility of applying a spatial design used by the Swedish Bird Survey for nationwide, gridbased sampling, with a goal to get butterfly monitoring data covering a representative sample of different habitats. We surveyed four 2×2 km sampling squares, split into 100 m segments, in the southernmost region of Sweden (Scania) and four in the northernmost region (Norrbotten). The grid-based transects were compared with volunteer-selected transects in a G IS analysis using a refined Swedish version of CORINE land cover data to see how well these two transect designs represent true habitat coverage. A total of 53 km transect was monitored, resulting in 490 individuals and 29 different species recorded. We found that transect cover correlated significantly with overall land cover using both monitoring methods, though standardised transects outperformed volunteer-selected transects in habitat representation in Scania, but not in Norrbotten. Butterflies were found to aggregate significantly in specific habitats, but with contrasting results for the two geographically different regions. Grasslands in both regions generated a high number of recorded butterflies, although so did clear-cut and residential areas in Norrbotten as well. The highest number of individuals recorded per transect was found in bogs in Scania. This study emphasises the value of complementing free site selection monitoring schemes with spatially representative schemes such as the Swedish Bird Survey, and sheds some light on general habitat preferences for Swedish butterflies in two contrasting climatic regions. Copyright Elin Videvall et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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| 15. |
- Videvall, Elin, et al.
(author)
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Coprophagy rapidly matures juvenile gut microbiota in a precocial bird
- 2023
-
In: Evolution Letters. - : Oxford University Press. - 2056-3744. ; 7:4, s. 240-251
-
Journal article (peer-reviewed)abstract
- Coprophagy is a behavior where animals consume feces, and has been observed across a wide range of species, including birds and mammals. The phenomenon is particularly prevalent in juveniles, but the reasons for this remain unclear. One hypothesis is that coprophagy enables offspring to acquire beneficial gut microbes that aid development. However, despite the potential importance of this behavior, studies investigating the effects in juveniles are rare. Here we experimentally test this idea by examining how ingestion of adult feces by ostrich chicks affects their gut microbiota development, growth, feeding behavior, pathogen abundance, and mortality. We conducted extensive longitudinal experiments for 8 weeks, repeated over 2 years. It involved 240 chicks, of which 128 were provided daily access to fresh fecal material from adults and 112 were simultaneously given a control treatment. Repeated measures, behavioral observations, and DNA metabarcoding of the microbial gut community, both prior to and over the course of the experiment, allowed us to evaluate multiple aspects of the behavior. The results show that coprophagy causes (a) marked shifts to the juvenile gut microbiota, including a major increase in diversity and rapid maturation of the microbial composition, (b) higher growth rates (fecal-supplemented chicks became 9.4% heavier at 8 weeks old), (c) changes to overall feeding behavior but no differences in feed intake, (d) lower abundance of a common gut pathogen (Clostridium colinum), and (e) lower mortality associated with gut disease. Together, our results suggest that the behavior of coprophagy in juveniles is highly beneficial and may have evolved to accelerate the development of gut microbiota.
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| 16. |
- Videvall, Elin, et al.
(author)
-
Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
- 2017
-
In: mSystems. - 2379-5077. ; 2:6
-
Journal article (peer-reviewed)abstract
- The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of direct PCR for measuring host microbiomes have not yet been investigated other than in humans with 454 sequencing. Here, we conduct a comprehensive evaluation of the microbial communities obtained with direct PCR and the widely used Mo Bio PowerSoil DNA extraction kit in five distinct gut sample types (ileum, cecum, colon, feces, and cloaca) from 20 juvenile ostriches, using 16S rRNA Illumina MiSeq sequencing. We found that direct PCR was highly comparable over a range of measures to the DNA extraction method in cecal, colon, and fecal samples. However, the two methods significantly differed in samples with comparably low bacterial biomass: cloacal and especially ileal samples. We also sequenced 100 replicate sample pairs to evaluate repeatability during both extraction and PCR stages and found that both methods were highly consistent for cecal, colon, and fecal samples (rs > 0.7) but had low repeatability for cloacal (rs = 0.39) and ileal (rs = -0.24) samples. This study indicates that direct PCR provides a fast, cheap, and reliable alternative to conventional DNA extraction methods for retrieving 16S rRNA data, which can aid future gut microbiome studies. IMPORTANCE The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly.
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| 17. |
- Videvall, Elin, et al.
(author)
-
Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
- 2017
-
In: mSystems. - : American Society for Microbiology. - 2379-5077. ; 2:6
-
Journal article (peer-reviewed)abstract
- The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly.
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| 18. |
- Videvall, Elin, et al.
(author)
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Early-life gut dysbiosis linked to juvenile mortality in ostriches
- 2020
-
In: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 8:1
-
Journal article (peer-reviewed)abstract
- Background: Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbiosis, and if particular gut regions or specific time periods during ontogeny are more susceptible. We also know very little of this process in non-model organisms, despite an increasing realization of the general importance of gut microbiota for health. Methods: Here, we examine the changes that occur in the microbiome during dysbiosis in different parts of the gastrointestinal tract in a long-lived bird with high juvenile mortality, the ostrich (Struthio camelus). We evaluated the 16S rRNA gene composition of the ileum, cecum, and colon of 68 individuals that died of suspected enterocolitis during the first 3 months of life (diseased individuals), and of 50 healthy individuals that were euthanized as age-matched controls. We combined these data with longitudinal environmental and fecal sampling to identify potential sources of pathogenic bacteria and to unravel at which stage of development dysbiosis-associated bacteria emerge. Results: Diseased individuals had drastically lower microbial alpha diversity and differed substantially in their microbial beta diversity from control individuals in all three regions of the gastrointestinal tract. The clear relationship between low diversity and disease was consistent across all ages in the ileum, but decreased with age in the cecum and colon. Several taxa were associated with mortality (Enterobacteriaceae, Peptostreptococcaceae, Porphyromonadaceae, Clostridium), while others were associated with health (Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, Turicibacter, Roseburia). Environmental samples showed no evidence of dysbiosis-associated bacteria being present in either the food, water, or soil substrate. Instead, the repeated fecal sampling showed that pathobionts were already present shortly after hatching and proliferated in individuals with low microbial diversity, resulting in high mortality several weeks later. Conclusions: Identifying the origins of pathobionts in neonates and the factors that subsequently influence the establishment of diverse gut microbiota may be key to understanding dysbiosis and host development. [MediaObject not available: See fulltext.]
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| 19. |
- Videvall, Elin
(author)
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Evolutionary genomics of host-microbe interactions
- 2018
-
Doctoral thesis (other academic/artistic)abstract
- The microbes living inside hosts have highly important consequences for host health and fitness. From the host’s perspective, some microbes exhibit mutualistic tendencies, others parasitic, and some commensal, but this is context-dependent and opportunistic lifestyles are widespread in nature. Our knowledge of how hosts interact molecularly with different microbes is, however, poor, and little research has been done on non-model organisms from a genomic and community-wide perspective. In this PhD thesis, I investigate host-microbe interactions from multiple angles, and utilize high-throughput sequencing techniques to paint a broad, overarching picture of the relationship between hosts and microbes. My PhD comprised two related projects, 1) host-microbiome interactions and 2) host-parasite interactions. In the former, I have evaluated how to best sample and measure the gut microbiomes of avian hosts (Paper I and II). Different sections of the ostrich gastrointestinal tract were characterized and shown to harbour divergent microbial communities (Paper I, II, and IV). I have further demonstrated that the gut microbiome of juvenile ostriches is colonized in a successional manner and gradually develops over time (Paper III), and is strongly linked to growth and mortality (Paper III and IV). In the second project I described the avian transcriptome response to malaria infection over time and to parasites with different virulence (Paper V and VI). Birds with malaria infection experience a range of transcriptional changes that involves for example the immune system, stress response, cell death regulation, and regulatory genes. To evaluate the molecular response of the malaria parasite, I assembled the blood transcriptome of Plasmodium ashfordi and showed that parasite gene expression is host-specific (Paper VII). This transcriptome was subsequently used, together with a genome assembly of Haemoproteus tartakovskyi, to construct a phylogeny of haemosporidian parasites which showed strong support for a monophyletic clade of mammalian malaria parasites (Paper VIII). Finally, the assembled transcriptome and genome were utilized to identify thiamine biosynthesis enzymes in avian Plasmodium (Paper IX), and to demonstrate that the avian Plasmodium parasites exhibit the most AT-rich genes of eukaryotes (Paper X). In summary, this work offers new insights into host-microbiome and host-parasite interactions, and enables a greater understanding of the multifaceted relationship between hosts and their microbes.
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| 20. |
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| 21. |
- Videvall, Elin, et al.
(author)
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Host transcriptional responses to high-and low-virulent avian malaria parasites
- 2020
-
In: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 195:6, s. 1070-1084
-
Journal article (peer-reviewed)abstract
- The transcriptional response of hosts to genetically similar pathogens can vary substantially, with important implications for disease severity and host fitness. A low pathogen load can theoretically elicit both high and low host responses, as the outcome depends on both the effectiveness of the host at suppressing the pathogen and the ability of the pathogen to evade the immune system. Here, we investigate the transcriptional response of Eurasian siskins (Spinus spinus) to two closely related lineages of the malaria parasite Plasmodium relictum. Birds were infected with either the high-virulent lineage P. relictum SGS1, the low-virulent sister lineage P. relictum GRW4, or sham-injected (controls). Blood samples for RNA sequencing were collected at four time points during the course of infection, totaling 76 transcriptomes from 19 birds. Hosts infected with SGS1 experienced up to 87% parasitemia and major transcriptome shifts throughout the infection, and multiple genes showed strong correlation with parasitemia. In contrast, GRW4-infected hosts displayed low parasitemia (maximum 0.7%) with a minor transcriptional response. We furthermore demonstrate that the baseline gene expression levels of hosts prior to infection were irrelevant as immunocompetence markers, as they could not predict future pathogen load. This study shows that the magnitude of the host transcriptional response can differ markedly from related parasites with different virulence, and it enables a better understanding of the molecular interactions taking place between hosts and parasites.
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| 22. |
- Videvall, Elin, et al.
(author)
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Impact of ionizing radiation on the environmental microbiomes of Chornobyl wetlands
- 2023
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In: Environmental Pollution. - : Elsevier. - 0269-7491 .- 1873-6424. ; 330
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Journal article (peer-reviewed)abstract
- Radioactive contamination has the potential to cause damage to DNA and other biomolecules. Anthropogenic sources of radioactive contamination include accidents in nuclear power plants, such as the one in Chornobyl in 1986 which caused long-term radioactive pollution. Studies on animals within radioactive zones have provided us with a greater understanding of how wildlife can persevere despite chronic radiation exposure. However, we still know very little about the effects of radiation on the microbial communities in the environment. We examined the impact of ionizing radiation and other environmental factors on the diversity and composition of environmental microbiomes in the wetlands of Chornobyl. We combined detailed field sampling along a gradient of radiation together with 16S rRNA high-throughput metabarcoding. While radiation did not affect the alpha diversity of the microbiomes in sediment, soil, or water, it had a significant effect on the beta diversity in all environment types, indicating that the microbial composition was affected by ionizing radiation. Specifically, we detected several microbial taxa that were more abundant in areas with high radiation levels within the Chor-nobyl Exclusion Zone, including bacteria and archaea known to be radioresistant. Our results reveal the existence of rich and diverse microbiomes in Chornobyl wetlands, with multiple taxonomic groups that are able to thrive despite the radioactive contamination. These results, together with additional field and laboratory-based ap-proaches examining how microbes cope with ionizing radiation will help to forecast the functionality and re-naturalization dynamics of radiocontaminated environments.
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| 23. |
- Videvall, Elin, et al.
(author)
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Major shifts in gut microbiota during development and its relationship to growth in ostriches
- 2019
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 28:10, s. 2653-2667
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Journal article (peer-reviewed)abstract
- The development of gut microbiota during ontogeny is emerging as an important process influencing physiology, immunity and fitness in vertebrates. However, knowledge of how bacteria colonize the juvenile gut, how this is influenced by changes in the diversity of gut bacteria and to what extent this influences host fitness, particularly in nonmodel organisms, is lacking. Here we used 16S rRNA gene sequencing to describe the successional development of the faecal microbiome in ostriches (Struthio camelus, n = 66, repeatedly sampled) over the first 3 months of life and its relationship to growth. We found a gradual increase in microbial diversity with age that involved multiple colonization and extinction events and a major taxonomic shift in bacteria that coincided with the cessation of yolk absorption. Comparisons with the microbiota of adults (n = 5) revealed that the chicks became more similar in their microbial diversity and composition to adults as they aged. There was a five-fold difference in juvenile growth during development, and growth during the first week of age was strongly positively correlated with the abundance of the genus Bacteroides and negatively correlated with Akkermansia. After the first week, the abundances of six phylogenetically diverse families (Peptococcaceae, S24-7, Verrucomicrobiae, Anaeroplasmataceae, Streptococcaceae, Methanobacteriaceae) were associated with subsequent reductions in chick growth in an age-specific and transient manner. These results have broad implications for our understanding of the development of gut microbiota and its associations with animal growth.
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| 24. |
- Videvall, Elin, et al.
(author)
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Measuring the gut microbiome in birds : Comparison of faecal and cloacal sampling
- 2018
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In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 18:3, s. 424-434
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Journal article (peer-reviewed)abstract
- The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling; however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high-throughput 16S rRNA sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of Gammaproteobacteria and fewer Clostridia relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of each sampling method in measuring the abundance of different bacterial taxa was highly variable: Bacteroidetes was the most highly correlated phylum between all three gut sections and both methods, whereas Actinobacteria, for example, was only strongly correlated between faecal and colon samples. Based on our results, we recommend sampling faeces, whenever possible, as this sample type provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique accurately portrayed the bacterial community of the ileum nor the caecum illustrates the difficulty in noninvasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies.
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| 25. |
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