Embracing the unknown: disentangling the complexities of the soil microbiome

Nature Reviews Microbiology, Год журнала: 2017, Номер 15(10), С. 579 - 590

Опубликована: Авг. 21, 2017

Язык: Английский

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Keystone taxa as drivers of microbiome structure and functioning

Nature Reviews Microbiology, Год журнала: 2018, Номер 16(9), С. 567 - 576

Опубликована: Май 22, 2018

Язык: Английский

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The gut microbiota in anxiety and depression – A systematic review

Clinical Psychology Review, Год журнала: 2020, Номер 83, С. 101943 - 101943

Опубликована: Окт. 29, 2020

Язык: Английский

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Understanding and exploiting plant beneficial microbes

Current Opinion in Plant Biology, Год журнала: 2017, Номер 38, С. 155 - 163

Опубликована: Июнь 14, 2017

After a century of incremental research, technological advances, coupled with need for sustainable crop yield increases, have reinvigorated the study beneficial plant-microbe interactions attention focused on how microbiomes alter plant phenotypes. We review recent advances in microbiome and describe potential applications increasing productivity. The phylogenetic diversity is increasingly well characterized, their functional becoming more accessible. Large culture collections are available controlled experimentation, to come. Genetic resources being brought bear questions function. expect that microbial amendments varying complexities will expose rules governing contributing growth promotion disease resistance, enabling agriculture.

Язык: Английский

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Rarefaction, Alpha Diversity, and Statistics

Frontiers in Microbiology, Год журнала: 2019, Номер 10

Опубликована: Окт. 23, 2019

Understanding the drivers of diversity is a fundamental question in ecology. Extensive literature discusses different methods for describing and documenting its effects on ecosystem health function. However, it widely believed that depends intensity sampling. I discuss statistical perspective diversity, framing an environment as unknown parameter, discussing bias variance plug-in rarefied estimates. describe state addressing these problems, focusing analysis microbial diversity. argue latent variable models can address issues with variance, but corrections need to be utilized well. encourage ecologists use estimates account unobserved species, measurement error compare across ecosystems.

Язык: Английский

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Perturbations in Gut Microbiota Composition in Psychiatric Disorders

JAMA Psychiatry, Год журнала: 2021, Номер 78(12), С. 1343 - 1343

Опубликована: Сен. 15, 2021

Evidence of gut microbiota perturbations has accumulated for multiple psychiatric disorders, with signatures proposed as potential biomarkers. However, no attempts have been made to evaluate the specificity these across range conditions.

Язык: Английский

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Biophysical processes supporting the diversity of microbial life in soil

FEMS Microbiology Reviews, Год журнала: 2017, Номер 41(5), С. 599 - 623

Опубликована: Июль 10, 2017

Soil, the living terrestrial skin of Earth, plays a central role in supporting life and is home to an unimaginable diversity microorganisms. This review explores key drivers for microbial soils under different climates land-use practices at scales ranging from soil pores landscapes. We delineate special features as habitat (focusing on bacteria) consequences communities. covers recent modeling advances that link physical processes with (termed biophysical processes). Readers are introduced concepts governing water organization associated transport properties dispersion ranges often determined by spatial highly dynamic aqueous phase. The narrow hydrological windows wetting phase connectedness crucial resource distribution longer range Feedbacks between activity their immediate environment responsible emergence stabilization structure-the scaffolding ecological functioning. synthesize insights historical contemporary studies provide outlook challenges opportunities developing quantitative framework predict component

Язык: Английский

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The soil microbiome — from metagenomics to metaphenomics

Current Opinion in Microbiology, Год журнала: 2018, Номер 43, С. 162 - 168

Опубликована: Фев. 15, 2018

Soil microorganisms carry out important processes, including support of plant growth and cycling carbon other nutrients. However, the majority soil microbes have not yet been isolated their functions are largely unknown. Although metagenomic sequencing reveals microbial identities functional gene information, it includes DNA from with vastly varying physiological states. Therefore, metagenomics is only predictive community potential. We posit that next frontier lies in understanding metaphenome, product combined genetic potential microbiome available resources. Here we describe examples opportunities towards gaining metaphenome.

Язык: Английский

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Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance

mBio, Год журнала: 2018, Номер 9(4)

Опубликована: Июль 30, 2018

The alpha diversity of ecologic communities is affected by many biotic and abiotic drivers and, in turn, affects ecosystem functioning. Yet, patterns host-associated microbial (microbiomes) are poorly studied the appropriateness general theory untested. Expanding to include microbiomes essential as a frequently cited metric their status. Here, we review newly analyze reports for animal gut microbiomes. We demonstrate that both diet body size affect but physiology (fermenter versus simple) most important driver. also assess advantages various metrics. importance often assumed has not been tested outright. Therefore, close discussing how integrate into field biodiversity-ecosystem functioning more clearly understand when why host supports diverse communities.

Язык: Английский

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Dysbiosis and Its Discontents

mBio, Год журнала: 2017, Номер 8(5)

Опубликована: Окт. 10, 2017

ABSTRACT Dysbiosis is a key term in human microbiome research, especially when patterns are associated with disease states. Although some questions have been raised about how this applied, its use continues undiminished the literature. We investigate ways which researchers discuss dysbiosis and then assess impact of different concepts on research. After an overview term’s historical roots, we conduct quantitative qualitative analyses large selection contemporary statements. categorize both short definitions longer conceptual statements dysbiosis. Further analysis allows us to identify problematic implications used, particularly regard causal hypotheses normal-abnormal distinctions. suggest that should reflect carefully they dysbiosis, order for field continue develop greater predictive scope explanatory depth.

Язык: Английский

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