An introduction to phylosymbiosis

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2020, Volume and Issue: 287(1922), P. 20192900 - 20192900

Published: March 4, 2020

Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as ‘microbial community relationships that recapitulate phylogeny their host’, we review relevant literature and data last decade, emphasizing frequently used methods regular patterns observed analyses. Quantitative is provided by statistical evaluating higher microbiome variation between host species than within species, topological similarities dendrogram, positive association genetic beta diversity. Significant degrees are prevalent, but not universal, microbiomes plants animals from terrestrial aquatic habitats. Consistent with natural selection shaping phylosymbiosis, transplant experiments demonstrate reduced performance and/or fitness upon host–microbiome mismatches. Hybridization can also disrupt phylosymbiotic cause hybrid pathologies. The pervasiveness carries several important implications advancing knowledge eco-evolutionary processes impact interactions future applications precision microbiology. Important steps will be examine beyond bacterial communities, apply evolutionary modelling an increasingly sophisticated understanding unravel microbial mechanisms contribute pattern. This serves gateway experimental, conceptual quantitative themes outlines opportunities ripe investigation diversity disciplines.

Language: Английский

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The Effects of Temperature on Animal Gut Microbiomes

Frontiers in Microbiology, Journal Year: 2020, Volume and Issue: 11

Published: March 10, 2020

Temperature is a prominent abiotic environmental variable that drives the adaptive trajectories of animal lineages and structures composition communities. Global temperature regimes are expected to undergo rapid shifts in next century, yet for many taxa we lack an understanding consequences these predicted populations. In this review, synthesize recent evidence variation shapes function gut microbiomes, key regulators host physiology, with potential population responses climate change. Several studies spanning range taxa, including Chordata, Arthropoda, Mollusca, have reported repeatable associations between community microbiome. several cases, same microbiome been observed across distantly related suggesting existence conserved mechanisms underlying temperature-induced plasticity. Extreme temperatures can disrupt stability alpha-diversity within microbiomes individual hosts generate beta-diversity among Microbiome states resulting from extreme associated, some cases causally linked, both beneficial deleterious effects on phenotypes. We propose routes by which changes may impact fitness, colonization resistance gut, energy nutrient assimilation, life history traits. Cumulatively, available data indicate disruption be mechanism changing will fitness wild-living

Language: Английский

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Host specificity of the gut microbiome

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 19(10), P. 639 - 653

Published: May 27, 2021

Language: Английский

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Direct observation of adaptive tracking on ecological time scales in Drosophila

Science, Journal Year: 2022, Volume and Issue: 375(6586)

Published: March 17, 2022

Direct observation of evolution in response to natural environmental change can resolve fundamental questions about adaptation, including its pace, temporal dynamics, and underlying phenotypic genomic architecture. We tracked the fitness-associated phenotypes allele frequencies genome-wide 10 replicate field populations Drosophila melanogaster over generations from summer late fall. Adaptation was evident each sampling interval (one four generations), with exceptionally rapid adaptation large frequency shifts at many independent loci. The direction basis adaptive shifted repeatedly time, consistent action strong rapidly fluctuating selection. Overall, we found clear evidence tracking occurring contemporaneously change, thus demonstrating temporally dynamic nature adaptation.

Language: Английский

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Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila

eLife, Journal Year: 2021, Volume and Issue: 10

Published: June 22, 2021

To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures seasonal occurring in parallel among Drosophila melanogaster populations. Specifically, estimated allele frequencies genome-wide from flies sampled early and late the growing season 20 widely dispersed We frequency shifts across North America Europe, demonstrating that is a general phenomenon temperate fly Seasonally fluctuating polymorphisms are enriched large chromosomal inversions, find broad concordance between spatial change. The direction change at seasonally variable can be predicted by weather conditions weeks prior sampling, linking environment genomic response selection. Our results suggest an important evolutionary force affecting patterns genetic variation .

Language: Английский

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‘Multi-omics’ data integration: applications in probiotics studies

npj Science of Food, Journal Year: 2023, Volume and Issue: 7(1)

Published: June 5, 2023

Abstract The concept of probiotics is witnessing increasing attention due to its benefits in influencing the host microbiome and modulation immunity through strengthening gut barrier stimulation antibodies. These benefits, combined with need for improved nutraceuticals, have resulted extensive characterization leading an outburst data generated using several ‘omics’ technologies. recent development system biology approaches microbial science paving way integrating from different omics techniques understanding flow molecular information one level other clear on regulatory features phenotypes. limitations tendencies a ‘single omics’ application ignore influence processes justify ‘multi-omics’ selections action host. Different techniques, including genomics, transcriptomics, proteomics, metabolomics lipidomics, used studying their are discussed this review. Furthermore, rationale multi-omics integration platforms supporting analyses was also elucidated. This review showed that useful selecting functions microbiome. Hence, recommend approach holistically

Language: Английский

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The role of animal hosts in shaping gut microbiome variation

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1901)

Published: March 18, 2024

Millions of years co-evolution between animals and their associated microbial communities have shaped diversified the nature relationship. Studies continue to reveal new layers complexity in host–microbe interactions, fate which depends on a variety different factors, ranging from neutral processes environmental factors local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics mathematical modelling disentangle individual contribution ecological microbiome evolution. Within this framework, host are known be among dominant drivers composition animal species. However, extent they shape assembly evolution remains unclear. In review, we summarize our understanding how drive these dynamics conserved vary across taxa. We conclude by outlining key avenues for research highlight need implementation modifications existing theory fully capture host-associated microbiomes. This article part theme issue ‘Sculpting microbiome: determine respond colonization’.

Language: Английский

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Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research

iScience, Journal Year: 2020, Volume and Issue: 23(8), P. 101414 - 101414

Published: July 25, 2020

From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by bidirectional interactions between host and their associated microbiota. Current technology can reveal many such combining multi-omic data from both hosts microbes. However, exploring full extent these requires careful consideration study design for efficient generation optimal integration derived (meta)genomics, (meta)transcriptomics, (meta)proteomics, (meta)metabolomics. In this perspective, we introduce holo-omic approach that incorporates microbiota domains untangle interplay two. We revisit recent literature on biomolecular host-microbe discuss implementation current limitations approach. anticipate application contribute opening new research avenues discoveries in biomedicine, biotechnology, agricultural aquacultural sciences, nature conservation, as well basic ecological evolutionary research.

Language: Английский

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The study of host–microbiome (co)evolution across levels of selection

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2020, Volume and Issue: 375(1808), P. 20190604 - 20190604

Published: Aug. 9, 2020

Microorganismal diversity can be explained in large part by selection imposed from both the abiotic and biotic environments, including-in case of host-associated microbiomes-interactions with eukaryotes. As such, microbiomes usefully studied across a variety scales: within single host over time, among genotypes population, between populations species. A plethora recent studies these scales diverse systems are: (i) exemplifying importance genetics shaping microbiome composition; (ii) uncovering role key phenotypes; (iii) highlighting dynamic nature microbiome. They have also raised critical question: do complex associations fit our existing understanding evolution coevolution, or often intimate seemingly cross-generational interactions follow novel evolutionary rules those previously identified? Herein, we describe known (co)evolution host-microbiome systems, placing data extant frameworks that been developed decades study, ask whether there are unique properties require paradigm shift. By examining when how act on its as unit (termed, holobiont), find conceptual framework, which focuses individuals, well individuals groups, is generally suited for (co)evolutionary change assemblages. This article theme issue 'The evolution'.

Language: Английский

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The role of the microbiota in human genetic adaptation

Science, Journal Year: 2020, Volume and Issue: 370(6521)

Published: Dec. 4, 2020

Getting to the guts of local evolution The microbiota mammals is a product coevolution. However, humans exhibit range adaptive peculiarities that can be quite geographically specific. human also displays variety community compositions and overlapping redundant metabolic characteristics alter host physiology. For example, lactase persistence genetic characteristic European populations, but in populations lacking gene, milk sugar digestion endowed by instead. Suzuki Ley review evidence for role plays adaptation new changing circumstances. Science , this issue p. eaaz6827

Language: Английский

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