Soil microbiomes and one health

Nature Reviews Microbiology, Journal Year: 2022, Volume and Issue: 21(1), P. 6 - 20

Published: Aug. 23, 2022

Language: Английский

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Diet and depression: exploring the biological mechanisms of action

Molecular Psychiatry, Journal Year: 2020, Volume and Issue: 26(1), P. 134 - 150

Published: Nov. 3, 2020

Language: Английский

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Alpha-, beta-, and gamma-diversity of bacteria varies across habitats

PLoS ONE, Journal Year: 2020, Volume and Issue: 15(9), P. e0233872 - e0233872

Published: Sept. 23, 2020

Bacteria are essential parts of ecosystems and the most diverse organisms on planet. Yet, we still do not know which habitats support highest diversity bacteria across multiple scales. We analyzed alpha-, beta-, gamma-diversity bacterial assemblages using 11,680 samples compiled by Earth Microbiome Project. found that soils contained richness within a single sample (alpha-diversity), but sediment displayed gamma-diversity. Sediment, biofilms/mats, inland water exhibited variation in community composition among geographic locations (beta-diversity). Within soils, agricultural lands, hot deserts, grasslands, shrublands richness, while forests, cold tundra biomes consistently harbored fewer species. Surprisingly, encompassed similar levels beta-diversity as other soil biomes. These patterns were robust to alpha- beta- metrics used taxonomic binning approach. Overall, results idea spatial environmental heterogeneity is an important driver diversity.

Language: Английский

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Phage-mediated horizontal gene transfer and its implications for the human gut microbiome

Gastroenterology report, Journal Year: 2022, Volume and Issue: 10

Published: Jan. 1, 2022

Horizontal gene transfer (HGT) in the microbiome has profound consequences for human health and disease. The spread of antibiotic resistance genes, virulence, pathogenicity determinants predominantly occurs by way HGT. Evidence exists extensive horizontal gut microbiome. Phage transduction is a type HGT event which bacteriophage transfers non-viral DNA from one bacterial host cell to another. abundance tailed bacteriophages suggests that could act as significant mode Here we review detail known mechanisms phage-mediated HGT, namely specialized generalized transduction, lateral gene-transfer agents, molecular piracy, well methods used detect discuss its potential implications

Language: Английский

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Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 22, 2023

Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates abundance of their impact on plant health. Here combined field surveys experiments investigate relationships properties structure function contrasting health outcomes. We find that acidification largely impacts bacterial communities reduces capacity soils combat fungal pathogens. In vitro assays microbiomes from acidified further highlight declined ability suppress Fusarium, globally important pathogen. Similarly, when inoculate healthy plants an microbiome, show greatly reduced prevent pathogen invasion. Finally, metagenome sequencing untargeted metabolomics reveals down regulation genes associated synthesis sulfur compounds reduction key traits related metabolism in acidic soils. Our findings suggest changes disruption specific microbial processes induced by can play critical role for

Language: Английский

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Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: April 29, 2024

Abstract Agriculture contributes to a decline in local species diversity and above- below-ground biotic homogenization. Here, we conduct continental survey using 1185 soil samples compare microbial communities from natural ecosystems (forest, grassland, wetland) with converted agricultural land. We combine our results global meta-analysis of available sequencing data that cover more than 2400 across six continents. Our combined demonstrate land conversion taxonomic functional homogenization bacteria, mainly driven by the increase geographic ranges taxa croplands. find 20% phylotypes are decreased 23% increased conversion, croplands enriched Chloroflexi, Gemmatimonadota, Planctomycetota, Myxcoccota Latescibacterota . Although there is no significant difference composition between land, genes involved nitrogen fixation, phosphorus mineralization transportation depleted cropland. provide insight into consequences land-use change on diversity.

Language: Английский

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Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: April 25, 2024

Abstract The root-associated microbiota plays an important role in the response to environmental stress. However, underlying mechanisms controlling interaction between salt-stressed plants and are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean ( Glycine soja ), we demonstrate that highly conserved microbes dominated Pseudomonas enriched root rhizosphere of plant. Two corresponding isolates confirmed enhance salt tolerance soybean. Shotgun metagenomic metatranscriptomic sequencing reveal motility-associated genes, mainly chemotaxis flagellar assembly, significantly expressed salt-treated samples. We further find roots stressed secreted purines, especially xanthine, which induce motility isolates. Moreover, exogenous application for xanthine non-stressed results enrichment, reproducing shift root. Finally, mutant analysis shows related gene cheW is required toward enhancing tolerance. Our study proposes recruits beneficial species exudating key metabolites (i.e., purine) against

Language: Английский

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Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics

Microbiome, Journal Year: 2020, Volume and Issue: 8(1)

Published: April 2, 2020

Abstract Background The Arctic and Antarctic are the two most geographically distant bioregions on earth. Recent sampling efforts following metagenomics have shed light global ocean microbial diversity function, yet microbiota of polar regions has not been included in such analyses. Results Here a metagenomic study seawater samples ( n = 60) collected from different depths at 28 locations zones was performed, together with metagenomes Tara Oceans. More than 7500 (19%) seawater-derived operational taxonomic units could be identified Oceans datasets, more 3,900,000 protein-coding gene orthologs had no hits Ocean Microbial Reference Gene Catalog. Analysis 214 metagenome assembled genomes (MAGs) recovered microbiomes, revealed strains that prevalent while nearly undetectable temperate seawater. Metabolic pathway reconstruction for these microbes suggested versatility saccharide lipids biosynthesis, nitrate sulfate reduction, CO 2 fixation. Comparison between microbiomes antibiotic resistance genes were enriched functions like DNA recombination Antarctic. Conclusions Our data highlight occurrence dominant locally unique functional traits environmental adaption, provide foundation analyzing microbiome complete perspective.

Language: Английский

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Structural diversity, functional aspects and future therapeutic applications of human gut microbiome

Archives of Microbiology, Journal Year: 2021, Volume and Issue: 203(9), P. 5281 - 5308

Published: Aug. 17, 2021

Language: Английский

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Decay of SARS-CoV-2 RNA along the wastewater treatment outfitted with Upflow Anaerobic Sludge Blanket (UASB) system evaluated through two sample concentration techniques

The Science of The Total Environment, Journal Year: 2020, Volume and Issue: 754, P. 142329 - 142329

Published: Sept. 15, 2020

Language: Английский

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