Microbiome definition re-visited: old concepts and new challenges

Microbiome, Год журнала: 2020, Номер 8(1)

Опубликована: Июнь 30, 2020

The field of microbiome research has evolved rapidly over the past few decades and become a topic great scientific public interest. As result this rapid growth in interest covering different fields, we are lacking clear commonly agreed definition term "microbiome." Moreover, consensus on best practices is missing. Recently, panel international experts discussed current gaps frame European-funded MicrobiomeSupport project. meeting brought together about 40 leaders from diverse areas, while more than hundred all world took part an online survey accompanying workshop. This article excerpts outcomes workshop corresponding embedded short historical introduction future outlook. We propose based compact, clear, comprehensive description provided by Whipps et al. 1988, amended with set novel recommendations considering latest technological developments findings. clearly separate terms microbiota provide discussion composition microbiota, heterogeneity dynamics microbiomes time space, stability resilience microbial networks, core microbiomes, functionally relevant keystone species as well co-evolutionary principles microbe-host inter-species interactions within microbiome. These broad definitions suggested unifying concepts will help to improve standardization studies future, could be starting point for integrated assessment data resulting transfer knowledge basic science into practice. Furthermore, standards important solving new challenges associated anthropogenic-driven changes planetary health, which understanding might play key role. Video Abstract.

Язык: Английский

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Simple animal models for microbiome research

Nature Reviews Microbiology, Год журнала: 2019, Номер 17(12), С. 764 - 775

Опубликована: Авг. 15, 2019

Язык: Английский

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Abundance-occupancy distributions to prioritize plant core microbiome membership

Current Opinion in Microbiology, Год журнала: 2019, Номер 49, С. 50 - 58

Опубликована: Июнь 1, 2019

Core microbiome members are consistent features of a dataset that hypothesized to reflect underlying functional relationships with the host. A review recent plant-microbiome literature reveals variety study-specific approaches used define core, which presents challenge building general framework. Abundance-occupancy distributions, in macroecology describe changes community diversity over space, offer an ecological approach for prioritizing core membership both spatial and temporal studies. Additionally, neutral models fit abundance-occupancy distributions can provide insights into deterministically selected members. We examples code systematically explore plant from distributions. Though we focus on discussions relevant microbiome, method be widely generally applied prioritize any microbiome.

Язык: Английский

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Understanding the plant-microbe interactions in environments exposed to abiotic stresses: An overview

Microbiological Research, Год журнала: 2023, Номер 271, С. 127368 - 127368

Опубликована: Март 22, 2023

Abiotic stress poses a severe danger to agriculture since it negatively impacts cellular homeostasis and eventually stunts plant growth development. stressors like drought excessive heat are expected occur more frequently in the future due climate change, which would reduce yields of important crops maize, wheat, rice may jeopardize food security human populations. The microbiomes varied taxonomically organized microbial community that is connected plants. By supplying nutrients water plants, regulating their physiology metabolism, microbiota helps plants develop tolerate abiotic stresses, can boost crop yield under stresses. In this present study, with emphasis on temperature, salt, stress, we describe current findings how stresses impact microbiomes, microbe-microbe interactions, plant-microbe interactions as way microorganisms affect metabolism plant. We also explore crucial measures must be taken applying practices faced

Язык: Английский

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The future of theoretical evolutionary game theory

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2023, Номер 378(1876)

Опубликована: Март 20, 2023

Evolutionary game theory is a truly interdisciplinary subject that goes well beyond the limits of biology. Mathematical minds get hooked up in simple models for evolution and often gradually move into other parts evolutionary biology or ecology. Social scientists realize how much they can learn from thinking transfer insight was originally generated Computer use their algorithms to explore new field where machines not only environment, but also each other. The breadth focus on few very popular issues, such as cooperation, comes at price: several insights are re-discovered different fields under labels with heroes modelling traditions. For example, reciprocity spatial structure treated differently. Will we continue develop things parallel? Or converge single set ideas, tradition eventually software repository? will these cross-fertilize other, learning engaging constructive exchange between fields? Ultimately, popularity rests its explanatory power, intuitive character models. This article part theme issue ‘Half century games: synthesis theory, application future directions’.

Язык: Английский

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Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2020, Номер 375(1798), С. 20190251 - 20190251

Опубликована: Март 23, 2020

Phylosymbiosis, where similarities in host-associated microbial communities recapitulate the phylogeny of their hosts, is a newly recognized yet pervasive pattern field host–microbe interactions. While phylosymbiosis has been documented across many systems, we still have poor understanding mechanisms that underlie this emergent pattern. Host selection microbiome widely cited mechanism, other basic ecological and evolutionary processes (dispersal, drift diversification) may also be at play. This paper discusses roles each these interactions play yielding phylosymbiotic signals hosts. Finally, will identify open questions methods are required to better understand relative contributions phylosymbiosis. Given shown relate functional components host fitness, contribute patterns important for our ecology evolution article part theme issue ‘Conceptual challenges community ecology’.

Язык: Английский

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Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts

mBio, Год журнала: 2019, Номер 10(1)

Опубликована: Янв. 28, 2019

Marine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and understand how these communities are structured. This complexity has also made challenging assign functions unravel the myriad of interactions among microbiota. Here we propose address issues by applying evidence from model systems host-microbe coevolution complex marine invertebrate microbiomes. Coevolution is reciprocal adaptation one lineage in response another can occur through interaction a its beneficial symbiont. A classic indicator codivergence microbe, this found both corals sponges. Metabolic collaboration between microbe linked appears likely holobionts, where interact with cells production degradation metabolic compounds. Neutral models useful distinguish selected microbes against background population consisting predominately random associates. Enhanced understanding their urgently required as coral reefs face unprecedented local global pressures active restoration approaches, including manipulation microbiome, proposed improve health tolerance reef species. On basis detailed review literature, three research criteria for examining invertebrates: (i) identifying stochastic deterministic components (ii) assessing (iii) confirming intimate association based on shared function.

Язык: Английский

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Microbiome-mediated plasticity directs host evolution along several distinct time scales

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2020, Номер 375(1808), С. 20190589 - 20190589

Опубликована: Авг. 9, 2020

Host-associated microbiomes influence their host's fitness in myriad ways and can be viewed as a source of phenotypic plasticity. This plasticity may allow the host to accommodate novel environmental challenges thus evolutionary adaptation. As with other modalities phenomena such Baldwin effect genetic assimilation, microbiome-mediated adaptation by facilitating accelerating it, slowing it down, or even preventing it. The dynamics involved are likely more complex than those previously studied related plasticity, involve different processes on each time scale, acquired recognition newly associated microbes immune system single- multiple-generation scales, selection transmission between hosts, acting longer scales. To date, is unclear if how any these shape evolution. opinion piece article provides conceptual framework for considering which directs evolution concludes suggestions key experimental tests presented ideas. part theme issue 'The role microbiome evolution'.

Язык: Английский

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Microbiome stability and structure is governed by host phylogeny over diet and geography in woodrats ( Neotoma spp.)

Proceedings of the National Academy of Sciences, Год журнала: 2021, Номер 118(47)

Опубликована: Ноя. 19, 2021

Significance Understanding the factors that sculpt gut microbial communities in mammals is of great interest. Here, we studied a diverse clade herbivorous rodents (woodrats, Neotoma ) with variable but well-characterized diets and habitats to quantify relative contributions host genetics, geography, diet, alongside neutral processes, structuring microbiome under natural controlled conditions. While diet geography made significant structure, phylogeny explained greatest proportion observed variation. Provision common captivity altered communities, from different species varying their resistance this perturbation. Captivity increased amount variation by phylogeny, further emphasizing extent which genetics structure mammalian microbiomes.

Язык: Английский

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Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar

Applied and Environmental Microbiology, Год журнала: 2020, Номер 86(8)

Опубликована: Фев. 4, 2020

A growing number of studies have examined variation in the microbiome to determine role modulating host health, physiology, and ecology. However, ecology microbial colonization is not fully understood rarely tested. The continued increase production farmed Atlantic salmon, coupled with increased farmed-wild salmon interactions, has accentuated need unravel potential adaptive function distinguish resident from transient gut microbes. Between compartments a system, we found majority operational taxonomic units (OTUs) that fit neutral model, Mycoplasma species among key exceptions. In wild fish, deterministic processes account for more OTU differences across life stages than those observed compartments. Unlike previous studies, our results make detailed comparisons between fish environments, while also providing insight into ecological underpinning community assembly this ecologically economically important species.

Язык: Английский

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