Toxicity drives facilitation between 4 bacterial species

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(32), P. 15979 - 15984

Published: July 3, 2019

Competition between microbes is extremely common, with many investing in mechanisms to harm other strains and species. Yet positive interactions species have also been documented. What makes help or each currently unclear. Here, we studied the 4 bacterial capable of degrading metal working fluids (MWF), an industrial coolant lubricant, which contains growth substrates as well toxic biocides. We were surprised find only neutral Using mathematical modeling further experiments, show that this community likely due toxicity MWF, whereby species' detoxification benefited others by facilitating their survival, such they could grow degrade MWF better when together. The addition nutrients, reduction toxicity, more instead resulted competitive behavior. Our work provides support stress gradient hypothesis showing how harsh, environments can strongly favor facilitation microbial mask underlying interactions.

Language: Английский

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Trophic Interactions and the Drivers of Microbial Community Assembly

Current Biology, Journal Year: 2020, Volume and Issue: 30(19), P. R1176 - R1188

Published: Oct. 1, 2020

Despite numerous surveys of gene and species content in heterotrophic microbial communities, such as those found animal guts, oceans, or soils, it is still unclear whether there are generalizable biological ecological processes that control their dynamics function. Here, we review experimental theoretical advances to argue networks trophic interactions, which the metabolic excretions one primary resource for another, constitute central drivers community assembly. Trophic interactions emerge from deconstruction complex forms organic matter into a wealth smaller intermediates, some released environment serve nutritional buffet community. The structure emergent network rate at resources supplied many features assembly, including relative contributions competition cooperation emergence alternative states. Viewing assembly through lens also has important implications spatial communities well functional redundancy taxonomic groups. Given ubiquity across environments, they impart common logic can enable development more quantitative predictive ecology.

Language: Английский

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Massively parallel screening of synthetic microbial communities

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(26), P. 12804 - 12809

Published: June 11, 2019

Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic are combinatorially constructed assayed high throughput. However, assembling many combinations of microbes logistically complex difficult achieve on timescale commensurate microbial growth. Here, introduce kChip, droplets-based platform that performs rapid, massively parallel, bottom-up construction communities. We first show kChip enables phenotypic characterization across conditions. Next, screen ∼100,000 multispecies comprising up 19 soil isolates, identified sets promote growth model plant symbiont

Language: Английский

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Emerging strategies for precision microbiome management in diverse agroecosystems

Nature Plants, Journal Year: 2021, Volume and Issue: 7(3), P. 256 - 267

Published: March 8, 2021

Language: Английский

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Ecological modelling approaches for predicting emergent properties in microbial communities

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(7), P. 855 - 865

Published: May 16, 2022

Language: Английский

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Design of synthetic human gut microbiome assembly and butyrate production

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: May 31, 2021

The capability to design microbiomes with predictable functions would enable new technologies for applications in health, agriculture, and bioprocessing. Towards this goal, we develop a model-guided approach synthetic human gut production of the health-relevant metabolite butyrate. Our data-driven model quantifies microbial interactions impacting growth butyrate separately, providing key insights into ecological mechanisms driving production. We use our explore vast community space using design-test-learn cycle identify high butyrate-producing communities. can accurately predict assembly across wide range species richness. Guided by model, constraints on richness molecular factors production, including hydrogen sulfide, environmental pH, resource competition. In sum, provides flexible generalizable framework understanding predicting metabolic functions.

Language: Английский

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Interspecies bacterial competition regulates community assembly in the C. elegans intestine

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(7), P. 2131 - 2145

Published: Feb. 15, 2021

From insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role health and disease. To further our understanding how intestinal assemble function, we study the C. elegans microbiota with bottom-up approach by feeding this nematode monocultures as well mixtures two eight species. We find bacteria colonizing monoculture do not always co-cultures due interspecies interactions. Moreover, community diversity increases, ability colonize worm gut becomes less than interactions for determining assembly. explore host-microbe adaptation, compare isolated from non-native isolates, success colonization is determined more species' taxonomy isolation source. Lastly, comparing assembled microbiotas mutants, innate immunity via p38 MAPK pathway decreases abundances yet has little influence on composition. These results highlight interactions, so adaptation or environmental filtering, dominant assembly microbiota.

Language: Английский

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Genomic structure predicts metabolite dynamics in microbial communities

Cell, Journal Year: 2022, Volume and Issue: 185(3), P. 530 - 546.e25

Published: Jan. 31, 2022

Language: Английский

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A Survey on Hypergraph Representation Learning

ACM Computing Surveys, Journal Year: 2023, Volume and Issue: 56(1), P. 1 - 38

Published: June 22, 2023

Hypergraphs have attracted increasing attention in recent years thanks to their flexibility naturally modeling a broad range of systems where high-order relationships exist among interacting parts. This survey reviews the newly born hypergraph representation learning problem, whose goal is learn function project objects—most commonly nodes—of an input hyper-network into latent space such that both structural and relational properties network can be encoded preserved. We provide thorough overview existing literature offer new taxonomy embedding methods by identifying three main families techniques, i.e., spectral, proximity-preserving, (deep) neural networks. For each family, we describe its characteristics our insights single yet flexible framework then discuss peculiarities individual methods, as well pros cons. review tasks, datasets, settings which embeddings are typically used. finally identify open challenges would inspire further research this field.

Language: Английский

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Higher-order organization of multivariate time series

Nature Physics, Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 2, 2023

Language: Английский

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