Diversity, connectivity and negative interactions define robust microbiome networks across land, stream, and sea

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

In this era of rapid global change, factors influencing the stability ecosystems and their functions have come into spotlight. For decades relationship between complexity has been investigated in modeled empirical systems, yet results remain largely context dependent. To overcome we leverage a multiscale inventory fungi bacteria ranging from single sites along an environmental gradient, to habitats inclusive land, sea stream, entire watershed. We use networks assess microbiome robustness identify fundamental principles stability. demonstrate that while some facets are positively associated with robustness, others not. Beyond positive biodiversity x relationships find number "gatekeeper" species or those highly connected central within networks, proportion predicted negative interactions universal indicators robust microbiomes. With potential promise engineering address challenges human ecosystem health properties microbiomes for future experimental studies may enhance emphasize features beyond additional characteristics such as adaptability should be considered these efforts.

Language: Английский

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Is precision microbiome medicine just around the corner?

Nature Reviews Gastroenterology & Hepatology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 4, 2025

Language: Английский

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Metagenomic insights into the assembly, function, and key taxa of bacterial community in full-scale pesticide wastewater treatment processes

Environmental Research, Journal Year: 2025, Volume and Issue: unknown, P. 121037 - 121037

Published: Feb. 1, 2025

Language: Английский

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Cattle Slurry Application Increases Soil Ecosystem Resistance to Flooding

Published: Jan. 1, 2025

Language: Английский

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Microbial community structure and nitrogen cycling in an area affected by the tailings dam collapse under a rehabilitation process

Applied Soil Ecology, Journal Year: 2025, Volume and Issue: 209, P. 106045 - 106045

Published: March 24, 2025

Language: Английский

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Salt stress alters the selectivity of mature pecan for the rhizosphere community and its associated functional traits

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: March 26, 2025

Introduction Salt stress is a major global environmental factor limiting plant growth. Rhizosphere bacteria, recruited from bulk soil, play pivotal role in enhancing salt resistance herbaceous and crop species. However, whether the rhizosphere bacterial community of mature tree can respond to stress, particularly saline-alkalitolerant trees, remains unexplored. Pecan ( Carya illinoinensis ), an important commercially cultivated nut tree, considered saline-alkali tolerant. Methods trees (12 years) were subjected different NaCl concentrations for 12 weeks. Collected samples included roots, leaves, fruit. Amplicon sequencing data shotgun metagenomic obtained investigated: 1) microbial communities various ecological niches pecan trees; 2) characteristic bacteria associated functional traits when suffered stress. Results discussion We characterized pecan-associated microbiome (i.e., fruit, leaf, root, soil) first time. These findings suggest that niche-based processes, such as habitat selection, drive fungal assembly tissues. reduced diversity, altered composition, shifted pecan’s selective pressure on Proteobacteria Actinobacteria . Shotgun further revealed response This study enhances our understanding tree-associated microbiomes supports theory shaping may be strategy saline-alkali-tolerant resist provide insights into tolerance potential applications, development bio-inoculants, managing saline environments agricultural contexts.

Language: Английский

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Enhanced propionate and butyrate metabolism in cecal microbiota contributes to cold-stress adaptation in sheep

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: April 24, 2025

During cold stress, gut microbes play crucial roles in orchestrating energy metabolism to enhance environmental adaptation. In sheep, hindgut ferment carbohydrates generate short-chain fatty acids (SCFAs) as an source. However, the mechanisms by which and their metabolites interact with host facilitate adaptation environments remain ambiguous. Herein, we simulated a winter environment (- 20 °C) provided rationed diet compare between Hulunbuir Hu sheep. Our findings show that exposure enhances SCFA sheep cecum. acetate, butyrate, total concentrations increased, whereas propionate butyrate notable increase SCFAs. Notably, concentration was higher than under stress. Following exposure, proinflammatory cytokine IL-1β levels increased both breeds. addition, showed IL-10, exhibited elevated secretory IgA levels. The cecal microbiota responded differently, no changes alpha beta diversity, considerable alterations. abundance of fungi, specifically Blastocystis sp. subtype 4, decreased, several Lachnospiraceae species (Roseburia hominis, Faecalicatena contorta, Ruminococcus gnavus) involved increased. Pathways related carbohydrate metabolism, such starch sucrose galactose pentose glucuronate interconversions, were upregulated. Treponema bryantii, Roseburia 499, Prevotella copri upregulation pathways amino acid metabolism. Cold node connectivity within symbiotic networks breeds, network vulnerability microbial community decrease influence stochastic processes on assembly, corresponding role selection. Conversely, shift evident Further transcriptomic analysis revealed distinct regulatory protein synthesis, thermogenesis substantially By contrast, immune conservation through reduced ribosome synthesis. Correlation indicated holds central position networks, exhibiting more complex tightly regulated involving SCFAs, microbiota, functions, transcriptomes. Partial least squares path modeling altered transcriptomes affecting SCFAs cytokines. this study suggest acetate fermentation rely tissue for exhibit diversity function, leading This may promote physiological innate defense, balancing heat loss enhancing

Language: Английский

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Absolute abundance unveilsBasidiobolusas a cross-domain bridge indirectly bolstering gut microbiome homeostasis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 28, 2024

Abstract The host microbiome is integral to metabolism, immune function, and resilience against pathogens. However, reliance on relative abundance (RA) estimate host-associated microbiomes introduces compositional biases, while limited tools for absolute (AA) quantification hinder broader applications. To address these challenges, we developed DspikeIn ( https://github.com/mghotbi/DspikeIn ), an R package paired with a versatile wet-lab methodology AA quantification. Using RA compare core distributions across herpetofauna orders their natural histories revealed starkly distinct results, driven by aggregate effects, including inherited biases in additional multifactorial influences. Focusing two closely related Desmognathus species demonstrated that enhanced resolution differential analyses minimized false discovery rates (FDR) when identifying enriched taxa gut microbiomes. Keystone identified through network associations also differed between data. For example, Lactococcus Cetobacterium were members Anura Caudata, Basidiobolus Mortierella Chelonia Squamata, facilitating adaptation diverse environments, insights undetectable AA-based analysis further removing the subnetwork increased negative interactions, highlighting its role promoting homeostasis cross-domain connectivity. Despite low redundancy, node exhibited high betweenness, efficiency, degree, serving as critical bridge linking disconnected nodes or modules indirectly supporting stability, consistent Burt’s structural hole theory. represents transformative tool research, enabling transition from delivering more accurate, consistent, comparable results studies. Graphical abstract cheatsheet

Language: Английский

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The microbiome of a perennial cereal differs from annual winter wheat only in the root endosphere

ISME Communications, Journal Year: 2024, Volume and Issue: 5(1)

Published: Dec. 19, 2024

Abstract The intensification of agriculture has led to environmental degradation, including the loss biodiversity. This prompted interest in perennial grain cropping systems address and mitigate some these negative impacts. In order determine if cultivation promotes a higher microbial diversity, we assessed endophytic microbiota crop (intermediate wheatgrass, Thinopyrum intermedium L.) comparison its annual counterpart, wheat (Triticum aestivum L.). study covered three sampling sites pan-European gradient (Sweden, Belgium, France), two plant genotypes, compartments (roots, stems, leaves), time points. We observed that host genotype effect was mainly evident belowground compartment, only lesser extent aboveground tissues, with similar pattern at all sites. Moreover, intermediate wheatgrass roots harbored different bacterial community composition diversity richness compared their counterparts. root influenced by not several soil chemical parameters, such as carbon:nitrogen ratio, but also respiration dehydrogenase activity. Consistent findings across space suggest stable mechanisms assembly associated cropping, underscoring potential role supporting biodiversity within sustainable agricultural systems.

Language: Английский

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