Diet–microbiota interactions and personalized nutrition

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 17(12), P. 742 - 753

Published: Sept. 20, 2019

Language: Английский

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PICRUSt2: An improved and customizable approach for metagenome inference

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2019, Volume and Issue: unknown

Published: June 15, 2019

One major limitation of microbial community marker gene sequencing is that it does not provide direct information on the functional composition sampled communities. Here, we present PICRUSt2 ( https://github.com/picrust/picrust2 ), which expands capabilities original PICRUSt method 1 to predict potential a based profiles. This updated and implementation includes several improvements over previous algorithm: an expanded database families reference genomes, new approach now compatible with any OTU-picking or denoising algorithm, novel phenotype predictions. Upon evaluation, was more accurate than PICRUSt1 other current approaches overall. also flexible allows addition custom databases. We highlight these important caveats regarding use predicted metagenomes, are related inherent challenges analyzing metagenome data in general.

Language: Английский

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Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats

mBio, Journal Year: 2020, Volume and Issue: 11(1)

Published: Jan. 6, 2020

In this comprehensive survey of microbiomes >900 species, including 315 mammals and 491 birds, we find a striking convergence the birds animals that fly. nonflying mammals, diet short-term evolutionary relatedness drive microbiome, many microbial species are specific to particular kind mammal, but flying break pattern with microbes shared across different little correlation either or hosts. This finding suggests adaptation flight breaks long-held relationships between hosts their microbes.

Language: Английский

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Applying the core microbiome to understand host–microbe systems

Journal of Animal Ecology, Journal Year: 2020, Volume and Issue: 89(7), P. 1549 - 1558

Published: April 5, 2020

Abstract The host‐associated core microbiome was originally coined to refer common groups of microbes or genes that were likely be particularly important for host biological function. However, the term has evolved encompass variable definitions across studies, often identifying key with respect their spatial distribution, temporal stability ecological influence, as well contribution function and fitness. A major barrier reaching a consensus over how define its relevance biological, evolutionary theory is lack precise terminology associated definitions, persistent association Common, microbiomes can together generate insights into processes act independently function, while functional host‐adapted cores distinguish between facultative near‐obligate symbionts differ in effects on This commentary summarizes five broad have been applied literature, highlighting strengths limitations advancing our understanding host–microbe systems, noting where they are overlap, discussing potential No one definition capture range population. Applied together, reveal different layers microbial organization from which we begin understand govern interactions.

Language: Английский

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The Gut Microbiota and Unhealthy Aging: Disentangling Cause from Consequence

Cell Host & Microbe, Journal Year: 2020, Volume and Issue: 28(2), P. 180 - 189

Published: Aug. 1, 2020

Language: Английский

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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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Evolutionary and Ecological Consequences of Gut Microbial Communities

Annual Review of Ecology Evolution and Systematics, Journal Year: 2019, Volume and Issue: 50(1), P. 451 - 475

Published: Aug. 29, 2019

Animals are distinguished by having guts—organs that must extract nutrients from food yet also bar invasion pathogens. Most guts colonized nonpathogenic microorganisms, but the functions of these microbes, or even reasons why they occur in gut, vary widely among animals. Sometimes microorganisms have codiversified with hosts; sometimes live mostly elsewhere environment. Either way, gut often benefit hosts. Benefits may reflect evolutionary addiction, whereby hosts incorporate into normal developmental processes. But benefits include novel ecological capabilities; for example, many metazoan clades exist virtue communities enabling new dietary niches. immensely their dependence on lacking them entirely to using as obligate development, nutrition, protection. Many consequences can be ascribed microbial community processes and host's ability shape

Language: Английский

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Covariation of diet and gut microbiome in African megafauna

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(47), P. 23588 - 23593

Published: Nov. 4, 2019

A major challenge in biology is to understand how phylogeny, diet, and environment shape the mammalian gut microbiome. Yet most studies of nonhuman microbiomes have relied on relatively coarse dietary categorizations focused either individual wild populations or captive animals that are sheltered from environmental pressures, which may obscure effects variation microbiome composition diverse natural communities. We analyzed plant bacterial DNA fecal samples an assemblage 33 sympatric large-herbivore species (27 native, 6 domesticated) a semiarid East African savanna, enabled high-resolution assessment seasonal both diet composition. Phylogenetic relatedness strongly predicted (r = 0.91) was weakly but significantly correlated with 0.20). Dietary diversity did not predict across within any except kudu; however, species. found spectrum sensitivity at diet-microbiome nexus: Seasonal changes explained 25% Species' positions (and deviations from) this were obviously driven by body size, digestive strategy, composition; domesticated tended exhibit greater turnover than wildlife. Our results reveal marked differences influence degree covariation free-ranging megafauna, well canonical predictors nutritional ecology.

Language: Английский

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Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: Jan. 23, 2021

Abstract Background Adaptive shifts in gut microbiome composition are one route by which animals adapt to seasonal changes food availability and diet. However, outside of dietary shifts, other potential environmental drivers microbial have rarely been investigated, particularly organisms living their natural environments. Results Here, we generated the largest wild nonhuman primate dataset date identify diversity function 758 samples collected from Ethiopian geladas ( Theropithecus gelada ). Because live a cold, high-altitude environment low-quality grass-based diet, they face extreme thermoregulatory energetic constraints. We tested how proxies (rainfall) stress (temperature) predicted geladas. The covaried with rainfall temperature pattern that suggests distinct responses challenges. Microbial were driven differences main components diet across seasons: rainier periods, was dominated cellulolytic/fermentative bacteria specialized digesting grass, while during dry periods break down starches found underground plant parts. Temperature had comparatively smaller, but detectable, effect on microbiome. During cold bacterial genes involved energy, amino acid, lipid metabolism increased, suggesting stimulation fermentation activity when nutritional co-occurred, potentially helping maintain energy balance challenging periods. Conclusion Together, these results shed light extent microbiota plasticity provides metabolic flexibility host, might be key factor thriving changing On longer evolutionary timescale, such provided may also allowed members adopt colonize new grassland habitats East Africa.

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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