1,753 results on '"Phylosymbiosis"'
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2. Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome
- Author
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Sadeghi, Javad, Chaganti, Subba Rao, Johnson, Timothy B., and Heath, Daniel D.
- Published
- 2023
- Full Text
- View/download PDF
3. Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome
- Author
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Javad Sadeghi, Subba Rao Chaganti, Timothy B. Johnson, and Daniel D. Heath
- Subjects
Host-microbe ,Microbial communities ,Microbial ecology ,Microbiome ,Phylosymbiosis ,QR100-130 - Abstract
Abstract Background While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation. Results We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes. Conclusions Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstract
- Published
- 2023
- Full Text
- View/download PDF
4. Limited Evidence for Microbial Transmission in the Phylosymbiosis between Hawaiian Spiders and Their Microbiota
- Author
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Perez-Lamarque, Benoît, Krehenwinkel, Henrik, Gillespie, Rosemary G, and Morlon, Hélène
- Subjects
Microbiology ,Biological Sciences ,Infection ,Good Health and Well Being ,Animals ,Phylogeny ,Hawaii ,Spiders ,Microbiota ,Infectious Disease Transmission ,Vertical ,microbiota ,phylosymbiosis ,vertical transmission ,Hawaiian arthropods ,endosymbionts ,host filtering - Abstract
The degree of similarity between the microbiotas of host species often mirrors the phylogenetic proximity of the hosts. This pattern, referred to as phylosymbiosis, is widespread in animals and plants. While phylosymbiosis was initially interpreted as the signal of symbiotic transmission and coevolution between microbes and their hosts, it is now recognized that similar patterns can emerge even if the microbes are environmentally acquired. Distinguishing between these two scenarios, however, remains challenging. We recently developed HOME (host-microbiota evolution), a cophylogenetic model designed to detect vertically transmitted microbes and host switches from amplicon sequencing data. Here, we applied HOME to the microbiotas of Hawaiian spiders of the genus Ariamnes, which experienced a recent radiation on the archipelago. We demonstrate that although Hawaiian Ariamnes spiders display a significant phylosymbiosis, there is little evidence of microbial vertical transmission. Next, we performed simulations to validate the absence of transmitted microbes in Ariamnes spiders. We show that this is not due to a lack of detection power because of the low number of segregating sites or an effect of phylogenetically driven or geographically driven host switches. Ariamnes spiders and their associated microbes therefore provide an example of a pattern of phylosymbiosis likely emerging from processes other than vertical transmission. IMPORTANCE How host-associated microbiotas assemble and evolve is one of the outstanding questions of microbial ecology. Studies aiming at answering this question have repeatedly found a pattern of "phylosymbiosis," that is, a phylogenetic signal in the composition of host-associated microbiotas. While phylosymbiosis was often interpreted as evidence for vertical transmission and host-microbiota coevolution, simulations have now shown that it can emerge from other processes, including host filtering of environmentally acquired microbes. However, distinguishing the processes driving phylosymbiosis in nature remains challenging. We recently developed a cophylogenetic method that can detect vertical transmission. Here, we applied this method to the microbiotas of recently diverged spiders from the Hawaiian archipelago, which display a clear phylosymbiosis pattern. We found that none of the bacterial operational taxonomic units is vertically transmitted. We show with simulations that this result is not due to methodological artifacts. Thus, we provide a striking empirical example of phylosymbiosis emerging from processes other than vertical transmission.
- Published
- 2022
5. Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia
- Author
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Ross, Ashley A., Müller, Kirsten M., Weese, J. Scott, and Neufeld, Josh D.
- Published
- 2018
6. A bird’s-eye view of phylosymbiosis : weak signatures of phylosymbiosis among all 15 species of cranes
- Author
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Trevelline, Brian K., Sosa, Jahree, Hartup, Barry K., and Kohl, Kevin D.
- Published
- 2020
7. Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan’s Great Rift Valley
- Author
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Enas Al-khlifeh, Sanaz Khadem, Bela Hausmann, and David Berry
- Subjects
bioclimatic zone ,gut microbiota ,host phylogeny ,microbiome ,phylosymbiosis ,Microbiology ,QR1-502 - Abstract
Host phylogeny and the environment play vital roles in shaping animal microbiomes. However, the effects of these variables on the diversity and richness of the gut microbiome in different bioclimatic zones remain underexplored. In this study, we investigated the effects of host phylogeny and bioclimatic zone on the diversity and composition of the gut microbiota of two heterospecific rodent species, the spiny mouse Acomys cahirinus and the house mouse Mus musculus, in three bioclimatic zones of the African Great Rift Valley (GRV). We confirmed host phylogeny using the D-loop sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. Phylogenetic analysis supported the morphological identification of the rodents and revealed a marked genetic difference between the two heterospecific species. We found that bioclimatic zone had a significant effect on the gut microbiota composition while host phylogeny did not. Microbial alpha diversity of heterospecific hosts was highest in the Mediterranean forest bioclimatic zone, followed by the Irano–Turanian shrubland, and was lowest in the Sudanian savanna tropical zone. The beta diversity of the two rodent species showed significant differences across the Mediterranean, Irano–Turanian, and Sudanian regions. The phyla Firmicutes and Bacteroidetes were highly abundant, and Deferribacterota, Cyanobacteria and Proteobacteria were also prominent. Amplicon sequence variants (ASVs) were identified that were unique to the Sudanian bioclimatic zone. The core microbiota families recovered in this study were consistent among heterospecific hosts. However, diversity decreased in conspecific host populations found at lower altitudes in Sudanian bioclimatic zone. The composition of the gut microbiota is linked to the adaptation of the host to its environment, and this study underscores the importance of incorporating climatic factors such as elevation and ambient temperature, in empirical microbiome research and is the first to describe the rodent gut microbiome from the GRV.
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- 2023
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8. Gut Microbiota in Decapod Shrimps: Evidence of Phylosymbiosis
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Tang, Yuanyuan, Ma, Ka Yan, Cheung, Man Kit, Yang, Chien-Hui, Wang, Yaqin, Hu, Xuelei, Kwan, Hoi Shan, and Chu, Ka Hou
- Published
- 2021
- Full Text
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9. Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities
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Kohl, Kevin D.
- Published
- 2020
10. An introduction to phylosymbiosis
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Lim, Shen Jean and Bordenstein, Seth R.
- Published
- 2020
11. Evidence of phylosymbiosis in Formica ants
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Raphaella Jackson, Patapios A. Patapiou, Gemma Golding, Heikki Helanterä, Chloe K. Economou, Michel Chapuisat, and Lee M. Henry
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phylosymbiosis ,endosymbiont ,ant ,microbiome ,evolution ,Microbiology ,QR1-502 - Abstract
IntroductionInsects share intimate relationships with microbes that play important roles in their biology. Yet our understanding of how host-bound microbial communities assemble and perpetuate over evolutionary time is limited. Ants host a wide range of microbes with diverse functions and are an emerging model for studying the evolution of insect microbiomes. Here, we ask whether phylogenetically related ant species have formed distinct and stable microbiomes.MethodsTo answer this question, we investigated the microbial communities associated with queens of 14 Formica species from five clades, using deep coverage 16S rRNA amplicon sequencing.ResultsWe reveal that Formica species and clades harbor highly defined microbial communities that are dominated by four bacteria genera: Wolbachia, Lactobacillus, Liliensternia, and Spiroplasma. Our analysis reveals that the composition of Formica microbiomes mirrors the phylogeny of the host, i.e., phylosymbiosis, in that related hosts harbor more similar microbial communities. In addition, we find there are significant correlations between microbe co-occurrences.DiscussionOur results demonstrate Formica ants carry microbial communities that recapitulate the phylogeny of their hosts. Our data suggests that the co-occurrence of different bacteria genera may at least in part be due to synergistic and antagonistic interactions between microbes. Additional factors potentially contributing to the phylosymbiotic signal are discussed, including host phylogenetic relatedness, host-microbe genetic compatibility, modes of transmission, and similarities in host ecologies (e.g., diets). Overall, our results support the growing body of evidence that microbial community composition closely depends on the phylogeny of their hosts, despite bacteria having diverse modes of transmission and localization within the host.
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- 2023
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12. Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification.
- Author
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Tsang CTT, Hui TKL, Chung NM, Yuen WT, and Tsang LM
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- Animals, Bacteria classification, Bacteria genetics, Wetlands, Brachyura microbiology, Symbiosis, Gastrointestinal Microbiome genetics, RNA, Ribosomal, 16S genetics, Phylogeny
- Abstract
The acquisition of microbial symbionts enables animals to rapidly adapt to and exploit novel ecological niches, thus significantly enhancing the evolutionary fitness and success of their hosts. However, the dynamics of host-microbe interactions and their evolutionary implications remain largely underexplored in marine invertebrates. Crabs of the family Sesarmidae (Crustacea: Brachyura) are dominant inhabitants of mangrove forests and are considered keystone species there. Their rapid diversification, particularly after adopting a plant-feeding lifestyle, is believed to have been facilitated by symbiotic gut microbes, enabling successful colonization of intertidal and terrestrial environments. To investigate the patterns and mechanisms shaping the microbial communities and the role of microbes in the evolution of Sesarmidae, we characterized and compared the gut microbiome compositions across 43 crab species from Sesarmidae and other mangrove-associated families using 16S metabarcoding. We found that the gut microbiome assemblages in crabs are primarily determined by host identity, with a secondary influence from environmental factors such as microhabitat and sampling location, and to a lesser extent influenced by biological factors such as sex and gut region. While patterns of phylosymbiosis (i.e. when microbial community relationships recapitulate the phylogeny of their hosts) were consistently observed in all beta-diversity metrics analysed, the strength of phylosymbiosis varied across crab families. This suggests that the bacterial assemblages in each family were differentially shaped by different degrees of host filtering and/or other evolutionary processes. Notably, Sesarmidae displayed signals of cophylogeny with its core gut bacterial genera, which likely play crucial functional roles in their hosts by providing lignocellulolytic enzymes, essential amino acids, and fatty acids supplementation. Our results support the hypothesis of microbial contribution to herbivory and terrestrialization in mangrove crabs, highlighting the tight association and codiversification of the crab holobiont., (© 2024 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)
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- 2024
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13. Phylosymbiosis: The Eco-Evolutionary Pattern of Insect–Symbiont Interactions
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Man Qin, Liyun Jiang, Gexia Qiao, and Jing Chen
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microbial community structure ,phylosymbiosis pattern ,stochastic effect ,codiversification ,ecological filtering ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Insects harbor diverse assemblages of bacterial and fungal symbionts, which play crucial roles in host life history. Insects and their various symbionts represent a good model for studying host–microbe interactions. Phylosymbiosis is used to describe an eco-evolutionary pattern, providing a new cross-system trend in the research of host-associated microbiota. The phylosymbiosis pattern is characterized by a significant positive correlation between the host phylogeny and microbial community dissimilarities. Although host–symbiont interactions have been demonstrated in many insect groups, our knowledge of the prevalence and mechanisms of phylosymbiosis in insects is still limited. Here, we provide an order-by-order summary of the phylosymbiosis patterns in insects, including Blattodea, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera. Then, we highlight the potential contributions of stochastic effects, evolutionary processes, and ecological filtering in shaping phylosymbiotic microbiota. Phylosymbiosis in insects can arise from a combination of stochastic and deterministic mechanisms, such as the dispersal limitations of microbes, codiversification between symbionts and hosts, and the filtering of phylogenetically conserved host traits (incl., host immune system, diet, and physiological characteristics).
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- 2023
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14. Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria
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Pérez-Carrascal, Olga M., Tromas, Nicolas, Terrat, Yves, Moreno, Elisa, Giani, Alessandra, Corrêa Braga Marques, Laisa, Fortin, Nathalie, and Shapiro, B. Jesse
- Published
- 2021
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15. Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria
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Olga M. Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Elisa Moreno, Alessandra Giani, Laisa Corrêa Braga Marques, Nathalie Fortin, and B. Jesse Shapiro
- Subjects
Microcystis ,Cyanobacteria ,Phylosymbiosis ,Co-phylogeny ,Microbiome ,Phycosphere ,Microbial ecology ,QR100-130 - Abstract
Abstract Background Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria—their microbiome. However, the nature of the relationship between Microcystis and its microbiome remains unclear. Is it a long-term, evolutionarily stable association? Which partners benefit? Here we report the genomic diversity of 109 individual Microcystis colonies—including cyanobacteria and associated bacterial genomes—isolated in situ and without culture from Lake Champlain, Canada and Pampulha Reservoir, Brazil. Results We identified 14 distinct Microcystis genotypes from Canada, of which only two have been previously reported, and four genotypes specific to Brazil. Microcystis genetic diversity was much greater between than within colonies, consistent with colony growth by clonal expansion rather than aggregation of Microcystis cells. We also identified 72 bacterial species in the microbiome. Each Microcystis genotype had a distinct microbiome composition, and more closely related genotypes had more similar microbiomes. This pattern of phylosymbiosis could be explained by co-phylogeny in only two out of the nine most prevalent associated bacterial genera, Roseomonas and Rhodobacter. These phylogenetically associated genera could enrich the metabolic repertoire of Microcystis, for example by encoding the biosynthesis of complementary carotenoid molecules. In contrast, other colony-associated bacteria showed weaker signals of co-phylogeny, but stronger evidence of horizontal gene transfer with Microcystis. These observations suggest that acquired genes are more likely to be retained in both partners (Microcystis and members of its microbiome) when they are loosely associated, whereas one gene copy is sufficient when the association is physically tight and evolutionarily long-lasting. Conclusions We have introduced a method for culture-free isolation of single colonies from nature followed by metagenomic sequencing, which could be applied to other types of microbes. Together, our results expand the known genetic diversity of both Microcystis and its microbiome in natural settings, and support their long-term, specific, and potentially beneficial associations. Video Abstract
- Published
- 2021
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16. Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis
- Author
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Boscaro, V., Holt, C. C., Van Steenkiste, N. W. L., Herranz, M., Irwin, N. A. T., Àlvarez-Campos, P., Grzelak, K., Holovachov, O., Kerbl, A., Mathur, V., Okamoto, N., Piercey, R. S., Worsaae, K., Leander, B. S., and Keeling, P. J.
- Published
- 2022
- Full Text
- View/download PDF
17. Evidence of phylosymbiosis in Formica ants
- Author
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Jackson, R. (Raphaella), Patapiou, P. A. (Patapios A.), Golding, G. (Gemma), Helanterä, H. (Heikki), Economou, C. K. (Chloe K.), Chapuisat, M. (Michel), Henry, L. M. (Lee M.), Jackson, R. (Raphaella), Patapiou, P. A. (Patapios A.), Golding, G. (Gemma), Helanterä, H. (Heikki), Economou, C. K. (Chloe K.), Chapuisat, M. (Michel), and Henry, L. M. (Lee M.)
- Abstract
Introduction: Insects share intimate relationships with microbes that play important roles in their biology. Yet our understanding of how host-bound microbial communities assemble and perpetuate over evolutionary time is limited. Ants host a wide range of microbes with diverse functions and are an emerging model for studying the evolution of insect microbiomes. Here, we ask whether phylogenetically related ant species have formed distinct and stable microbiomes. Methods: To answer this question, we investigated the microbial communities associated with queens of 14 Formica species from five clades, using deep coverage 16S rRNA amplicon sequencing. Results: We reveal that Formica species and clades harbor highly defined microbial communities that are dominated by four bacteria genera: Wolbachia, Lactobacillus, Liliensternia, and Spiroplasma. Our analysis reveals that the composition of Formica microbiomes mirrors the phylogeny of the host, i.e., phylosymbiosis, in that related hosts harbor more similar microbial communities. In addition, we find there are significant correlations between microbe co-occurrences. Discussion: Our results demonstrate Formica ants carry microbial communities that recapitulate the phylogeny of their hosts. Our data suggests that the co-occurrence of different bacteria genera may at least in part be due to synergistic and antagonistic interactions between microbes. Additional factors potentially contributing to the phylosymbiotic signal are discussed, including host phylogenetic relatedness, host-microbe genetic compatibility, modes of transmission, and similarities in host ecologies (e.g., diets). Overall, our results support the growing body of evidence that microbial community composition closely depends on the phylogeny of their hosts, despite bacteria having diverse modes of transmission and localization within the host.
- Published
- 2023
18. Phylosymbiosis and metabolomics resolve phenotypically plastic and cryptic sponge species in the genus Agelas across the Caribbean basin.
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Pankey MS, Gochfeld DJ, Gastaldi M, Macartney KJ, Clayshulte Abraham A, Slattery M, and Lesser MP
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- Animals, Phylogeny, Caribbean Region, West Indies, Coral Reefs, Agelas, Porifera genetics
- Abstract
Fundamental to holobiont biology is recognising how variation in microbial composition and function relates to host phenotypic variation. Sponges often exhibit considerable phenotypic plasticity and also harbour dense microbial communities that function to protect and nourish hosts. One of the most prominent sponge genera on Caribbean coral reefs is Agelas. Using a comprehensive set of morphological (growth form, spicule), chemical and molecular data on 13 recognised species of Agelas in the Caribbean basin, we were able to define only five species (=clades) and found that many morphospecies designations were incongruent with phylogenomic and population genetic analyses. Microbial communities were also strongly differentiated between phylogenetic species, showing little evidence of cryptic divergence and relatively low correlation with morphospecies assignment. Metagenomic analyses also showed strong correspondence to phylogenetic species, and to a lesser extent, geographical and morphological characters. Surprisingly, the variation in secondary metabolites produced by sponge holobionts was explained by geography and morphospecies assignment, in addition to phylogenetic species, and covaried significantly with a subset of microbial symbionts. Spicule characteristics were highly plastic, under greater impact from geographical location than phylogeny. Our results suggest that while phenotypic plasticity is rampant in Agelas, morphological differences within phylogenetic species affect functionally important ecological traits, including the composition of the symbiotic microbial communities and metabolomic profiles., (© 2024 John Wiley & Sons Ltd.)
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- 2024
- Full Text
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19. Limited Evidence for Microbial Transmission in the Phylosymbiosis between Hawaiian Spiders and Their Microbiota
- Author
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Benoît Perez-Lamarque, Henrik Krehenwinkel, Rosemary G. Gillespie, and Hélène Morlon
- Subjects
microbiota ,phylosymbiosis ,vertical transmission ,host filtering ,Hawaiian arthropods ,endosymbionts ,Microbiology ,QR1-502 - Abstract
ABSTRACT The degree of similarity between the microbiotas of host species often mirrors the phylogenetic proximity of the hosts. This pattern, referred to as phylosymbiosis, is widespread in animals and plants. While phylosymbiosis was initially interpreted as the signal of symbiotic transmission and coevolution between microbes and their hosts, it is now recognized that similar patterns can emerge even if the microbes are environmentally acquired. Distinguishing between these two scenarios, however, remains challenging. We recently developed HOME (host-microbiota evolution), a cophylogenetic model designed to detect vertically transmitted microbes and host switches from amplicon sequencing data. Here, we applied HOME to the microbiotas of Hawaiian spiders of the genus Ariamnes, which experienced a recent radiation on the archipelago. We demonstrate that although Hawaiian Ariamnes spiders display a significant phylosymbiosis, there is little evidence of microbial vertical transmission. Next, we performed simulations to validate the absence of transmitted microbes in Ariamnes spiders. We show that this is not due to a lack of detection power because of the low number of segregating sites or an effect of phylogenetically driven or geographically driven host switches. Ariamnes spiders and their associated microbes therefore provide an example of a pattern of phylosymbiosis likely emerging from processes other than vertical transmission. IMPORTANCE How host-associated microbiotas assemble and evolve is one of the outstanding questions of microbial ecology. Studies aiming at answering this question have repeatedly found a pattern of “phylosymbiosis,” that is, a phylogenetic signal in the composition of host-associated microbiotas. While phylosymbiosis was often interpreted as evidence for vertical transmission and host-microbiota coevolution, simulations have now shown that it can emerge from other processes, including host filtering of environmentally acquired microbes. However, distinguishing the processes driving phylosymbiosis in nature remains challenging. We recently developed a cophylogenetic method that can detect vertical transmission. Here, we applied this method to the microbiotas of recently diverged spiders from the Hawaiian archipelago, which display a clear phylosymbiosis pattern. We found that none of the bacterial operational taxonomic units is vertically transmitted. We show with simulations that this result is not due to methodological artifacts. Thus, we provide a striking empirical example of phylosymbiosis emerging from processes other than vertical transmission.
- Published
- 2022
- Full Text
- View/download PDF
20. Phylosymbiosis shapes skin bacterial communities and pathogen-protective function in Appalachian salamanders
- Author
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Osborne, Owen G, primary, Jiménez, Randall R, additional, Byrne, Allison Q, additional, Gratwicke, Brian, additional, Ellison, Amy, additional, and Muletz-Wolz, Carly R, additional
- Published
- 2024
- Full Text
- View/download PDF
21. Insights Into the Species-Specific Microbiota of Greenideinae (Hemiptera: Aphididae) With Evidence of Phylosymbiosis
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Man Qin, Jing Chen, Liyun Jiang, and Gexia Qiao
- Subjects
phylosymbiosis signal ,microbiota variation ,aphid species-specific ,host plant ,symbiont diversity ,Microbiology ,QR1-502 - Abstract
Aphids and their symbionts represent an outstanding model for studies of insect–symbiont interactions. The aphid microbiota can be shaped by aphid species, geography and host plants. However, the relative importance of phylogenetic and ecological factors in shaping microbial community structures is not well understood. Using Illumina sequencing of the V3–V4 hypervariable region of the 16S rRNA gene, we characterized the microbial compositions of 215 aphid colonies representing 53 species of the aphid subfamily Greenideinae from different regions and plants in China, Nepal, and Vietnam. The primary endosymbiont Buchnera aphidicola and secondary symbiont Serratia symbiotica dominated the microbiota of Greenideinae. We simultaneously explored the relative contribution of host identity (i.e., aphid genus and aphid species), geography and host plant to the structures of bacterial, symbiont and secondary symbiont communities. Ordination analyses and statistical tests highlighted the strongest impact of aphid species on the microbial flora in Greenideinae. Furthermore, we found a phylosymbiosis pattern in natural Greenideinae populations, in which the aphid phylogeny was positively correlated with microbial community dissimilarities. These findings will advance our knowledge of host-associated microbiota assembly across both host phylogenetic and ecological contexts.
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- 2022
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22. Spider phylosymbiosis: divergence of widow spider species and their tissues’ microbiomes
- Author
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Sara J. Dunaj, Brian R. Bettencourt, Jessica E. Garb, and Robert M. Brucker
- Subjects
Phylosymbiosis ,Host-microbe interactions ,Black widow spiders ,Common house spider ,Hologenome ,Metatranscriptomics ,Evolution ,QH359-425 - Abstract
Abstract Background Microbiomes can have profound impacts on host biology and evolution, but to date, remain vastly understudied in spiders despite their unique and diverse predatory adaptations. This study evaluates closely related species of spiders and their host-microbe relationships in the context of phylosymbiosis, an eco-evolutionary pattern where the microbial community profile parallels the phylogeny of closely related host species. Using 16S rRNA gene amplicon sequencing, we characterized the microbiomes of five species with known phylogenetic relationships from the family Theridiidae, including multiple closely related widow spiders (L. hesperus, L. mactans, L. geometricus, S. grossa, and P. tepidariorum). Results We compared whole animal and tissue-specific microbiomes (cephalothorax, fat bodies, venom glands, silk glands, and ovary) in the five species to better understand the relationship between spiders and their microbial symbionts. This showed a strong congruence of the microbiome beta-diversity of the whole spiders, cephalothorax, venom glands, and silk glands when compared to their host phylogeny. Our results support phylosymbiosis in these species and across their specialized tissues. The ovary tissue microbial dendrograms also parallel the widow phylogeny, suggesting vertical transfer of species-specific bacterial symbionts. By cross-validating with RNA sequencing data obtained from the venom glands, silk glands and ovaries of L. hesperus, L. geometricus, S. grossa, and P. tepidariorum we confirmed that several microbial symbionts of interest are viably active in the host. Conclusion Together these results provide evidence that supports the importance of host-microbe interactions and the significant role microbial communities may play in the evolution and adaptation of their hosts.
- Published
- 2020
- Full Text
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23. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge
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Michael P. Doane, Megan M. Morris, Bhavya Papudeshi, Lauren Allen, Dnyanada Pande, John M. Haggerty, Shaili Johri, Abigail C. Turnlund, Meredith Peterson, Dovi Kacev, Andy Nosal, Deni Ramirez, Kevin Hovel, Julia Ledbetter, Amanda Alker, Jackeline Avalos, Kristi Baker, Shruti Bhide, Emma Billings, Steven Byrum, Molly Clemens, Amelia Juliette Demery, Lais Farias Oliveira Lima, Oscar Gomez, Omar Gutierrez, Selena Hinton, Donald Kieu, Angie Kim, Rebeca Loaiza, Alexander Martinez, Jordan McGhee, Kristine Nguyen, Sabrina Parlan, Amanda Pham, Rosalyn Price-Waldman, Robert A. Edwards, and Elizabeth A. Dinsdale
- Subjects
Microbiome ,Phylosymbiosis ,Metagenomics ,Elasmobranch skin ,Teleost ,Vertebrate fishes ,Microbial ecology ,QR100-130 - Abstract
Abstract Background The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes. Results We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch’s average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes. Conclusion Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales. Video abstract
- Published
- 2020
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24. Gut microbial communities of American pikas (Ochotona princeps): Evidence for phylosymbiosis and adaptations to novel diets
- Author
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Kohl, Kevin D., Varner, Johanna, Wilkening, Jennifer L., and Dearing, M. Denise
- Published
- 2018
25. Spider phylosymbiosis: divergence of widow spider species and their tissues’ microbiomes
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Dunaj, Sara J., Bettencourt, Brian R., Garb, Jessica E., and Brucker, Robert M.
- Published
- 2020
- Full Text
- View/download PDF
26. Disentangling the mechanisms underlying phylosymbiosis in mammals.
- Author
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Mallott EK
- Subjects
- Animals, Phylogeny, Mammals genetics, Oxygen, RNA, Ribosomal, 16S, Symbiosis genetics, Microbiota
- Abstract
Mammalian gut microbial communities are frequently found to be host-specific-microbial community compositions are more similar within than between host species-and some individual microbial taxa consistently associate with a single or small set of host species. The ecoevolutionary dynamics that result in this pattern of phylosymbiosis or host specificity have been proposed, but robust tests of the mechanisms driving these relationships are lacking. In this issue of Molecular Ecology, Mazel et al. (2023) combine large amplicon sequencing data sets with bacterial phenotypic traits to test whether microbial dispersal patterns contribute to the host specificity of the gut microbiome. They find that both transmission mode and oxygen tolerance are predictive of how specialized a microbe is. Horizontally transmitted, oxygen-tolerant microbes are more likely to be generalists, and vertically transmitted anaerobes are more likely to be limited to a few host species. This creative use of publicly available data provides a roadmap for testing hypotheses about the mechanisms underlying phylosymbiosis., (© 2023 John Wiley & Sons Ltd.)
- Published
- 2024
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27. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge
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Doane, Michael P., Morris, Megan M., Papudeshi, Bhavya, Allen, Lauren, Pande, Dnyanada, Haggerty, John M., Johri, Shaili, Turnlund, Abigail C., Peterson, Meredith, Kacev, Dovi, Nosal, Andy, Ramirez, Deni, Hovel, Kevin, Ledbetter, Julia, Alker, Amanda, Avalos, Jackeline, Baker, Kristi, Bhide, Shruti, Billings, Emma, Byrum, Steven, Clemens, Molly, Demery, Amelia Juliette, Lima, Lais Farias Oliveira, Gomez, Oscar, Gutierrez, Omar, Hinton, Selena, Kieu, Donald, Kim, Angie, Loaiza, Rebeca, Martinez, Alexander, McGhee, Jordan, Nguyen, Kristine, Parlan, Sabrina, Pham, Amanda, Price-Waldman, Rosalyn, Edwards, Robert A., and Dinsdale, Elizabeth A.
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- 2020
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28. Phylosymbiosis: The Eco-Evolutionary Pattern of Insect–Symbiont Interactions.
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Qin, Man, Jiang, Liyun, Qiao, Gexia, and Chen, Jing
- Subjects
- *
LIFE history theory , *MICROBIAL communities , *HYMENOPTERA , *LEPIDOPTERA , *DIPTERA - Abstract
Insects harbor diverse assemblages of bacterial and fungal symbionts, which play crucial roles in host life history. Insects and their various symbionts represent a good model for studying host–microbe interactions. Phylosymbiosis is used to describe an eco-evolutionary pattern, providing a new cross-system trend in the research of host-associated microbiota. The phylosymbiosis pattern is characterized by a significant positive correlation between the host phylogeny and microbial community dissimilarities. Although host–symbiont interactions have been demonstrated in many insect groups, our knowledge of the prevalence and mechanisms of phylosymbiosis in insects is still limited. Here, we provide an order-by-order summary of the phylosymbiosis patterns in insects, including Blattodea, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera. Then, we highlight the potential contributions of stochastic effects, evolutionary processes, and ecological filtering in shaping phylosymbiotic microbiota. Phylosymbiosis in insects can arise from a combination of stochastic and deterministic mechanisms, such as the dispersal limitations of microbes, codiversification between symbionts and hosts, and the filtering of phylogenetically conserved host traits (incl., host immune system, diet, and physiological characteristics). [ABSTRACT FROM AUTHOR]
- Published
- 2023
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29. The Bacterial Microbiome of the Coral Skeleton Algal Symbiont Ostreobium Shows Preferential Associations and Signatures of Phylosymbiosis
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Pushpakumara, BLDU, Tandon, K, Willis, A, Verbruggen, H, Pushpakumara, BLDU, Tandon, K, Willis, A, and Verbruggen, H
- Abstract
Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.
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- 2023
30. Schistosomiasis Vector Snails and Their Microbiota Display a Phylosymbiosis Pattern
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Camille Huot, Camille Clerissi, Benjamin Gourbal, Richard Galinier, David Duval, and Eve Toulza
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microbiota ,phylosymbiosis ,metabarcoding ,Planorbid snails ,tripartite interactions ,schistosomiasis ,Microbiology ,QR1-502 - Abstract
Planorbidae snails are the intermediate host for the trematode parasite of the Schistosoma genus, which is responsible for schistosomiasis, a disease that affects both humans and cattle. The microbiota for Schistosoma has already been described as having an effect on host/parasite interactions, specifically through immunological interactions. Here, we sought to characterize the microbiota composition of seven Planorbidae species and strains. Individual snail microbiota was determined using 16S ribosomal DNA amplicon sequencing. The bacterial composition was highly specific to the host strain with limited interindividual variation. In addition, it displayed complete congruence with host phylogeny, revealing a phylosymbiosis pattern. These results were confirmed in a common garden, suggesting that the host highly constrains microbial composition. This study presents the first comparison of bacterial communities between several intermediate snail hosts of Schistosoma parasites, paving the way for further studies on the understanding of this tripartite interaction.
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- 2020
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31. Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.
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Al-Khlifeh E, Khadem S, Hausmann B, and Berry D
- Abstract
Host phylogeny and the environment play vital roles in shaping animal microbiomes. However, the effects of these variables on the diversity and richness of the gut microbiome in different bioclimatic zones remain underexplored. In this study, we investigated the effects of host phylogeny and bioclimatic zone on the diversity and composition of the gut microbiota of two heterospecific rodent species, the spiny mouse Acomys cahirinus and the house mouse Mus musculus , in three bioclimatic zones of the African Great Rift Valley (GRV). We confirmed host phylogeny using the D-loop sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. Phylogenetic analysis supported the morphological identification of the rodents and revealed a marked genetic difference between the two heterospecific species. We found that bioclimatic zone had a significant effect on the gut microbiota composition while host phylogeny did not. Microbial alpha diversity of heterospecific hosts was highest in the Mediterranean forest bioclimatic zone, followed by the Irano-Turanian shrubland, and was lowest in the Sudanian savanna tropical zone. The beta diversity of the two rodent species showed significant differences across the Mediterranean, Irano-Turanian, and Sudanian regions. The phyla Firmicutes and Bacteroidetes were highly abundant, and Deferribacterota, Cyanobacteria and Proteobacteria were also prominent. Amplicon sequence variants (ASVs) were identified that were unique to the Sudanian bioclimatic zone. The core microbiota families recovered in this study were consistent among heterospecific hosts. However, diversity decreased in conspecific host populations found at lower altitudes in Sudanian bioclimatic zone. The composition of the gut microbiota is linked to the adaptation of the host to its environment, and this study underscores the importance of incorporating climatic factors such as elevation and ambient temperature, in empirical microbiome research and is the first to describe the rodent gut microbiome from the GRV., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2023 Al-khlifeh, Khadem, Hausmann and Berry.)
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- 2023
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32. Diverse coral reef invertebrates exhibit patterns of phylosymbiosis
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O’Brien, Paul A., Tan, Shangjin, Yang, Chentao, Frade, Pedro R., Andreakis, Nikos, Smith, Hillary A., Miller, David J., Webster, Nicole S., Zhang, Guojie, and Bourne, David G.
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- 2020
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33. Evidence of phylosymbiosis in Formica ants
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Jackson, Raphaella, Patapiou, Patapios A., Golding, Gemma, Helanterä, Heikki, Economou, Chloe K., Chapuisat, Michel, Henry, Lee M., Organismal and Evolutionary Biology Research Programme, Evolution, Sociality & Behaviour, and Tvärminne Zoological Station
- Subjects
Microbiology (medical) ,Endosymbiont ,Phylosymbiosis ,Evolution ,1181 Ecology, evolutionary biology ,ant ,endosymbiont ,evolution ,microbiome ,phylosymbiosis ,Ant ,Microbiome ,Microbiology - Abstract
IntroductionInsects share intimate relationships with microbes that play important roles in their biology. Yet our understanding of how host-bound microbial communities assemble and perpetuate over evolutionary time is limited. Ants host a wide range of microbes with diverse functions and are an emerging model for studying the evolution of insect microbiomes. Here, we ask whether phylogenetically related ant species have formed distinct and stable microbiomes.MethodsTo answer this question, we investigated the microbial communities associated with queens of 14 Formica species from five clades, using deep coverage 16S rRNA amplicon sequencing.ResultsWe reveal that Formica species and clades harbor highly defined microbial communities that are dominated by four bacteria genera: Wolbachia, Lactobacillus, Liliensternia, and Spiroplasma. Our analysis reveals that the composition of Formica microbiomes mirrors the phylogeny of the host, i.e., phylosymbiosis, in that related hosts harbor more similar microbial communities. In addition, we find there are significant correlations between microbe co-occurrences.DiscussionOur results demonstrate Formica ants carry microbial communities that recapitulate the phylogeny of their hosts. Our data suggests that the co-occurrence of different bacteria genera may at least in part be due to synergistic and antagonistic interactions between microbes. Additional factors potentially contributing to the phylosymbiotic signal are discussed, including host phylogenetic relatedness, host-microbe genetic compatibility, modes of transmission, and similarities in host ecologies (e.g., diets). Overall, our results support the growing body of evidence that microbial community composition closely depends on the phylogeny of their hosts, despite bacteria having diverse modes of transmission and localization within the host.
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- 2023
34. Phylosymbiosis and the microbiome of the native Australian stingless bee Tetragonula carbonaria
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Tarlinton, Boyd and Tarlinton, Boyd
- Abstract
Tetragonula carbonaria (Smith 1854) is a native Australian stingless bee, hosting a diverse range of bacterial symbionts. T. carbonaria is used as a model to explore how relationships between host insects and the microbiome occur and can be detected within a single species, shedding light on how host-microbiome associations arise and are maintained across the corbiculate bees. Host-microbiome relationships are considered through the lens of phylosymbiosis. Methods for detecting phylosymbiosis are explored; different bioinformatics and statistical techniques are compared, with implications for future studies. Bayesian modelling is used to predict possible routes of acquisition of bee symbionts.
- Published
- 2021
35. Phylosymbiosis in the Rhizosphere Microbiome Extends to Nitrogen Cycle Functional Potential
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Mikayla Van Bel, Amanda E. Fisher, Laymon Ball, J. Travis Columbus, and Renaud Berlemont
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phylosymbiosis ,rhizosphere ,microbiome ,nitrogen cycling ,Poaceae ,Chloridoideae ,Biology (General) ,QH301-705.5 - Abstract
Most plants rely on specialized root-associated microbes to obtain essential nitrogen (N), yet not much is known about the evolutionary history of the rhizosphere–plant interaction. We conducted a common garden experiment to investigate the plant root–rhizosphere microbiome association using chloridoid grasses sampled from around the world and grown from seed in a greenhouse. We sought to test whether plants that are more closely related phylogenetically have more similar root bacterial microbiomes than plants that are more distantly related. Using metagenome sequencing, we found that there is a conserved core and a variable rhizosphere bacterial microbiome across the chloridoid grasses. Additionally, phylogenetic distance among the host plant species was correlated with bacterial community composition, suggesting the plant hosts prefer specific bacterial lineages. The functional potential for N utilization across microbiomes fluctuated extensively and mirrored variation in the microbial community composition across host plants. Variation in the bacterial potential for N fixation was strongly affected by the host plants’ phylogeny, whereas variation in N recycling, nitrification, and denitrification was unaffected. This study highlights the evolutionary linkage between the N fixation traits of the microbial community and the plant host and suggests that not all functional traits are equally important for plant–microbe associations.
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- 2021
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36. Phylosymbiosis drives the distribution of pathogen-protective bacteria in Appalachian salamanders
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Osborne, Owen, primary, Jiménez, Randall, additional, Byrne, Allison, additional, Gratwicke, Brian, additional, Ellison, Amy, additional, and Muletz-Wolz, Carly, additional
- Published
- 2024
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37. Subspecies divergence, hybridisation and the spatial environment shape phylosymbiosis in the microbiome of house mice
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Ferreira, Susana C. M., primary, Jarquín-Díaz, Víctor Hugo, additional, Planillo, Aimara, additional, Ďureje, Ľudovít, additional, Martincová, Iva, additional, Kramer-Schadt, Stephanie, additional, Forslund, Sofia K, additional, and Heitlinger, Emanuel, additional
- Published
- 2023
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38. Disentangling the mechanisms underlying phylosymbiosis in mammals
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Mallott, Elizabeth K., primary
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- 2023
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39. Gut microbiomes of captive primates show phylosymbiosis, respond to dietary sugar reduction, and select for host-specific dietary microbes.
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Bornbusch, Sally L, Muletz-Wolz, Carly R, Lopez-Bondarchuk, Ekaterina, Maslanka, Michael T, and Kendrick, Erin L
- Subjects
- *
PRIMATES , *MICROORGANISMS , *BACTERIAL population , *GUT microbiome , *BACTERIAL communities , *ANIMAL housing , *FLAVOBACTERIALES - Abstract
Host-associated microbiomes are influenced by evolutionary history and proximate factors such as diet and environment. Zoos house animals in relatively standardized and manipulatable environments, making zoo populations valuable for studying microbiomes. Using a small population of five, closely related primate species housed under nearly identical environments, we investigated gut microbiome variation regarding (a) congruence between host evolutionary history and gut bacterial composition (i.e. phylosymbiosis), (b) a longitudinal reduction in dietary sugar intake, and (c) ingestion of bacteria from dietary sources. We found that the primate gut microbiomes varied across individuals and showed phylosymbiosis. When animals were fed diets with reduced sugar and increased fibre, we found host-specific changes in taxonomically distinct microbes (Phascolarctobacterium, Megasphaera , and Sharpea). Yet, these bacterial genera share similar functional potential (fibre degradation), indicating that the distinct bacterial communities may fulfill similar functions. Although all individuals received the same diet, the diet-associated bacteria in primate gut microbiomes were distinct across individuals of different species, suggesting a mechanism that selects for unique dietary microbes to persist in animal guts. Our findings show that the microbiomes of a small, captive primate population housed under uniform environmental conditions still show patterns congruent with combined influences of evolutionary history and diet. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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40. The Phylosymbiosis Pattern Between the Fig Wasps of the Same Genus and Their Associated Microbiota
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Jiaxing Li, Xianqin Wei, Dawei Huang, and Jinhua Xiao
- Subjects
insect ,host-associated microbiota ,holobiont ,16S rDNA ,coevolution ,Wolbachia ,Microbiology ,QR1-502 - Abstract
Microbial communities can be critical for many metazoans, which can lead to the observation of phylosymbiosis with phylogenetically related species sharing similar microbial communities. Most of the previous studies on phylosymbiosis were conducted across the host families or genera. However, it is unclear whether the phylosymbiosis signal is still prevalent at lower taxonomic levels. In this study, 54 individuals from six species of the fig wasp genus Ceratosolen (Hymenoptera: Agaonidae) collected from nine natural populations and their associated microbiota were investigated. The fig wasp species were morphologically identified and further determined by mitochondrial CO1 gene fragments and nuclear ITS2 sequences, and the V4 region of 16S rRNA gene was sequenced to analyze the bacterial communities. The results suggest a significant positive correlation between host genetic characteristics and microbial diversity characteristics, indicating the phylosymbiosis signal between the phylogeny of insect hosts and the associated microbiota in the lower classification level within a genus. Moreover, we found that the endosymbiotic Wolbachia carried by fig wasps led to a decrease in bacterial diversity of host-associated microbial communities. This study contributes to our understanding of the role of host phylogeny, as well as the role of endosymbionts in shaping the host-associated microbial community.
- Published
- 2022
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41. Phylosymbiosis Impacts Adaptive Traits in Nasonia Wasps
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Edward J. van Opstal and Seth R. Bordenstein
- Subjects
Nasonia ,evolution ,microbiome ,phylosymbiosis ,Microbiology ,QR1-502 - Abstract
ABSTRACT Phylosymbiosis is defined as microbial community relationships that recapitulate the phylogeny of hosts. As evidence for phylosymbiosis rapidly accumulates in different vertebrate and invertebrate holobionts, a central question is what evolutionary forces cause this pattern. We use intra- and interspecific gut microbiota transplants to test for evidence of selective pressures that contribute to phylosymbiosis. We leverage three closely related species of the parasitoid wasp model Nasonia that recently diverged between 0.4 and 1 million years ago: N. vitripennis, N. giraulti, and N. longicornis. Upon exposure of germfree larvae to heat-inactivated microbiota from intra- or interspecific larvae, we measure larval growth, pupation rate, and adult reproductive capacity. We report three key findings: (i) larval growth significantly slows when hosts receive an interspecific versus intraspecific gut microbiota, (ii) marked decreases in pupation and resulting adult survival occur from interspecific gut microbiota exposure, and (iii) adult reproductive capacities including male fertility and longevity are unaffected by early life exposure to an interspecific microbiota. Overall, these findings reveal developmental and survival costs to Nasonia upon larval exposures to interspecific microbiota and provide evidence that selective pressures on phenotypes produced by host-microbiota interactions may underpin phylosymbiosis. IMPORTANCE Phylosymbiosis is an ecoevolutionary hypothesis and emerging pattern in animal-microbiota studies whereby the host phylogenetic relationships parallel the community relationships of the host-associated microbiota. A central prediction of phylosymbiosis is that closely related hosts exhibit a lower microbiota beta diversity than distantly related hosts. While phylosymbiosis has emerged as a widespread trend in a field often challenged to find trends across systems, two critical and understudied questions are whether or not phylosymbiosis is consequential to host biology and if adaptive evolutionary forces underpin the pattern. Here, using germfree rearing in the phylosymbiosis model Nasonia, we demonstrate that early life exposure to heat-inactivated microbiota from more distantly related species poses more severe developmental and survival costs than microbiota from closely related or the same species. This study advances a functional understanding of the consequences and potential selective pressures underpinning phylosymbiosis.
- Published
- 2019
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42. Mechanisms governing avian phylosymbiosis: Genetic dissimilarity based on neutral and MHC regions exhibits little relationship with gut microbiome distributions of Galápagos mockingbirds
- Author
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Fleischer, Ramona; https://orcid.org/0000-0003-1657-9347, Risely, Alice; https://orcid.org/0000-0002-0731-2934, Hoeck, Paquita E A, Keller, Lukas F; https://orcid.org/0000-0002-0149-0174, Sommer, Simone, Fleischer, Ramona; https://orcid.org/0000-0003-1657-9347, Risely, Alice; https://orcid.org/0000-0002-0731-2934, Hoeck, Paquita E A, Keller, Lukas F; https://orcid.org/0000-0002-0149-0174, and Sommer, Simone
- Abstract
The gut microbiome of animals, which serves important functions but can also contain potential pathogens, is to varying degrees under host genetic control. This can generate signals of phylosymbiosis, whereby gut microbiome composition matches host phylogenetic structure. However, the genetic mechanisms that generate phylosymbiosis and the scale at which they act remain unclear. Two non‐mutually exclusive hypotheses are that phylosymbiosis is driven by immunogenetic regions such as the major histocompatibility complex (MHC) controlling microbial composition, or by spatial structuring of neutral host genetic diversity via founder effects, genetic drift, or isolation by distance. Alternatively, associations between microbes and host phylogeny may be generated by their spatial autocorrelation across landscapes, rather than the direct effects of host genetics. In this study, we collected MHC, microsatellite, and gut microbiome data from separate individuals belonging to the Galápagos mockingbird species complex, which consists of four allopatrically distributed species. We applied multiple regression with distance matrices and Bayesian inference to test for correlations between average genetic and microbiome similarity across nine islands for which all three levels of data were available. Clustering of individuals by species was strongest when measured with microsatellite markers and weakest for gut microbiome distributions, with intermediate clustering of MHC allele frequencies. We found that while correlations between island‐averaged gut microbiome composition and both microsatellite and MHC dissimilarity existed across species, these relationships were greatly weakened when accounting for geographic distance. Overall, our study finds little support for large‐scale control of gut microbiome composition by neutral or adaptive genetic regions across closely related bird phylogenies, although this does not preclude the possibility that host genetics shapes gut microbiome
- Published
- 2020
43. Exploration of whole-genome data of vertebrate gut microbiome reveals dynamics of strain phylosymbiosis
- Author
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Chiu, Jeffrey Huey-Chuan, Knight, Rob1, Allen, Eric, Chiu, Jeffrey Huey-Chuan, Chiu, Jeffrey Huey-Chuan, Knight, Rob1, Allen, Eric, and Chiu, Jeffrey Huey-Chuan
- Abstract
The gut microbiota is a complex community of microbial species inhabiting the digestive tract. Each microbial species is further composed of microbes with slightly different genetic variants also known as strains. While most evolutionary studies of the gut microbiome occur at the community-level or focused on narrow clades of vertebrates, few studies have examined the evolution of wildlife and their gut microbiome at the strain-level across the animal kingdom. In this exploratory study, we examine a wildlife gut metagenomic dataset to investigate the evolutionary dynamics of bacterial species and their respective host. In particular, this is the first examination of whether there is significant congruence between the phylogeny of bacterial strains and that of their respective hosts, which we refer to as strain phylosymbiosis, across the animal kingdom. Our analysis of the most abundant bacteria in our dataset revealed Akkermansia muciniphila and Bacteroides vulgatus exhibited strong signals of strain phylosymbiosis.
- Published
- 2021
44. Schistosomiasis Vector Snails and Their Microbiota Display a Phylosymbiosis Pattern
- Author
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Huot, Camille, Clerissi, Camille, Gourbal, Benjamin, Galinier, Richard, Duval, David, Toulza, Eve, Huot, Camille, Clerissi, Camille, Gourbal, Benjamin, Galinier, Richard, Duval, David, and Toulza, Eve
- Abstract
Planorbidae snails are the intermediate host for the trematode parasite of the Schistosoma genus, which is responsible for schistosomiasis, a disease that affects both humans and cattle. The microbiota for Schistosoma has already been described as having an effect on host/parasite interactions, specifically through immunological interactions. Here, we sought to characterize the microbiota composition of seven Planorbidae species and strains. Individual snail microbiota was determined using 16S ribosomal DNA amplicon sequencing. The bacterial composition was highly specific to the host strain with limited interindividual variation. In addition, it displayed complete congruence with host phylogeny, revealing a phylosymbiosis pattern. These results were confirmed in a common garden, suggesting that the host highly constrains microbial composition. This study presents the first comparison of bacterial communities between several intermediate snail hosts of Schistosoma parasites, paving the way for further studies on the understanding of this tripartite interaction
- Published
- 2020
- Full Text
- View/download PDF
45. Microbiota associated with meiofaunal nemerteans reveals evidence of phylosymbiosis
- Author
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Leasi, Francesca, primary, Eckert, Ester, additional, Norenburg, Jon, additional, Thomas, W Kelley, additional, Sevigny, Joseph, additional, Hall, Jeff, additional, Wirshing, Herman, additional, and Fontaneto, Diego, additional
- Published
- 2023
- Full Text
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46. Microclimate Shapes the Phylosymbiosis of Rodent Gut Microbiota in Jordan’s Great Rift Valley
- Author
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Al-khlifeh, Enas, primary, Khadem, Sanaz, additional, Hausmann, Bela, additional, and Berry, David, additional
- Published
- 2023
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47. Evaluating cpn60 for high-resolution profiling of the mammalian skin microbiome and detection of phylosymbiosis.
- Author
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Umbach AK, Fernando C, Hill JE, and Neufeld JD
- Abstract
Despite being the most widely used phylogenetic marker for amplicon-based profiling of microbial communities, limited phylogenetic resolution of the 16S rRNA gene limits its use for studies of host-microbe co-evolution. In contrast, the cpn60 gene is a universal phylogenetic marker with greater sequence variation capable of species-level resolution. This research compared mammalian skin microbial profiles generated from cpn60 and 16S rRNA gene sequencing approaches, testing for patterns of phylosymbiosis that suggest co-evolutionary host-microbe associations. An ~560 bp fragment of the cpn60 gene was amplified with universal primers and subjected to high-throughput sequencing. Taxonomic classification of cpn60 sequences was completed using a naïve-Bayesian QIIME2 classifier created for this project, trained with an NCBI-supplemented curated cpn60 database (cpnDB_nr). The cpn60 dataset was then compared to published 16S rRNA gene amplicon data. Beta diversity comparisons of microbial community profiles generated with cpn60 and 16S rRNA gene amplicons were not significantly different, based on Procrustes analysis of Bray-Curtis and UniFrac distances. Despite similar relationships among skin microbial profiles, improved phylogenetic resolution provided by the cpn60 gene sequencing permitted observations of phylosymbiosis between microbial community profiles and their mammalian hosts that were not previously observed with 16S rRNA gene profiles. Subsequent investigation of Staphylococcaceae taxa using the cpn60 gene showed increased phylogenetic resolution compared the 16S rRNA gene profiles, revealing potential co-evolutionary host-microbe associations. Overall, our results demonstrate that 16S rRNA and cpn60 marker genes generate comparable microbial community composition patterns while cpn60 better facilitates analyses, such as phylosymbiosis, that require increased phylogenetic resolution., (© 2023. The Author(s).)
- Published
- 2023
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48. Genomes of Gut Bacteria from Nasonia Wasps Shed Light on Phylosymbiosis and Microbe-Assisted Hybrid Breakdown
- Author
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Karissa L. Cross, Brittany A. Leigh, E. Anne Hatmaker, Aram Mikaelyan, Asia K. Miller, and Seth R. Bordenstein
- Subjects
Proteus ,Providencia ,Nasonia ,gut bacteria ,microbiome ,phage ,Microbiology ,QR1-502 - Abstract
ABSTRACT Phylosymbiosis is a cross-system trend whereby microbial community relationships recapitulate the host phylogeny. In Nasonia parasitoid wasps, phylosymbiosis occurs throughout development, is distinguishable between sexes, and benefits host development and survival. Moreover, the microbiome shifts in hybrids as a rare Proteus bacterium in the microbiome becomes dominant. The larval hybrids then catastrophically succumb to bacterium-assisted lethality and reproductive isolation between the species. Two important questions for understanding phylosymbiosis and bacterium-assisted lethality in hybrids are (i) do the Nasonia bacterial genomes differ from other animal isolates and (ii) are the hybrid bacterial genomes the same as those in the parental species? Here, we report the cultivation, whole-genome sequencing, and comparative analyses of the most abundant gut bacteria in Nasonia larvae, Providencia rettgeri and Proteus mirabilis. Characterization of new isolates shows Proteus mirabilis forms a more robust biofilm than Providencia rettgeri and that, when grown in coculture, Proteus mirabilis significantly outcompetes Providencia rettgeri. Providencia rettgeri genomes from Nasonia are similar to each other and more divergent from pathogenic, human associates. Proteus mirabilis from Nasonia vitripennis, Nasonia giraulti, and their hybrid offspring are nearly identical and relatively distinct from human isolates. These results indicate that members of the larval gut microbiome within Nasonia are most similar to each other, and the strain of the dominant Proteus mirabilis in hybrids is resident in parental species. Holobiont interactions between shared, resident members of the wasp microbiome and the host underpin phylosymbiosis and hybrid breakdown. IMPORTANCE Animal and plant hosts often establish intimate relationships with their microbiomes. In varied environments, closely related host species share more similar microbiomes, a pattern termed phylosymbiosis. When phylosymbiosis is functionally significant and beneficial, microbial transplants between host species and host hybridization can have detrimental consequences on host biology. In the Nasonia parasitoid wasp genus, which contains a phylosymbiotic gut community, both effects occur and provide evidence for selective pressures on the holobiont. Here, we show that bacterial genomes in Nasonia differ from other environments and harbor genes with unique functions that may regulate phylosymbiotic relationships. Furthermore, the bacteria in hybrids are identical to those in parental species, thus supporting a hologenomic tenet that the same members of the microbiome and the host genome impact phylosymbiosis, hybrid breakdown, and speciation.
- Published
- 2021
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49. Insights into the gut bacterial communities of spider from wild with no evidence of phylosymbiosis
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Vikas Kumar, Inderjeet Tyagi, and Kaomud Tyagi
- Subjects
Phylum ,Firmicutes ,Cytochrome c oxidase subunit I ,Zoology ,Bacillus ,Spiders ,Biology ,biology.organism_classification ,Actinobacteria ,Gut Microbiome ,Phylosymbiosis ,Araneidae ,Prevotella ,bacteria ,Original Article ,Proteobacteria ,General Agricultural and Biological Sciences ,Bacterial phyla ,Arthropods - Abstract
In the present study, an effort has been made to elucidate the gut bacterial diversity of twelve species of the family Araneidae under three subfamilies collected from 5 states of India along with their predicted metabolic role in functional metabolism. Further, we also compared the host species phylogeny based on partial cytochrome c oxidase subunit I (COI) sequences with the gut bacteria composition dendrogram to decipher the phylosymbiotic relationships. Analysis revealed the presence of 22 bacterial phyla, 145 families, and 364 genera in the gut, with Proteobacteria, Firmicutes, Actinobacteria, and Deinococcus-Thermus as the highest abundant phyla. Moreover, phylum Bacteriodetes was dominated only in Cyclosa mulmeinensis and Chlamydiae in Neoscona bengalensis. At the genus level, Bacillus, Acinetobacter, Cutibacterium, Pseudomonas, and Staphylococcus were the most dominant genera. Furthermore, the genus Prevotella was observed only in Cyclosa mulmeinensis, and endosymbiont Wolbachia only in Eriovixia laglaizei. The differential abundance analysis (DeSeq2) revealed the 19 significant ASVs represented by the genera like Acinetobacter, Vagoccoccus, Prevotella, Staphylococcus, Curvibacter, Corynebacterium, Paracoccus, Streptococcus, Microbacterium, and Pseudocitrobacter. The inter- and intra-subfamilies comparison based on diversity indices (alpha and beta diversity) revealed that the subfamily Araneinae have high richness and diversity than Argiopinae and Gasteracanthinae. The phylosymbiotic analysis revealed that there is no congruence between the gut bacteria composition dendrogram with their host phylogeny.
- Published
- 2021
50. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny
- Author
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F. Joseph Pollock, Ryan McMinds, Styles Smith, David G. Bourne, Bette L. Willis, Mónica Medina, Rebecca Vega Thurber, and Jesse R. Zaneveld
- Subjects
Science - Abstract
Associations between corals and symbiotic microorganisms could be driven by the environment or shared evolutionary history. Here, the authors examine relationships between coral phylogenies and associated microbiomes, finding evidence of phylosymbiosis in microbes from coral skeleton and tissue, but not mucus.
- Published
- 2018
- Full Text
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