Assembly of gut-derived bacterial communities follows “early-bird” resource utilization dynamics

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Янв. 14, 2023

Diet can impact host health through changes to the gut microbiota, yet we lack mechanistic understanding linking nutrient availability and microbiota composition. Here, use thousands of microbial communities cultured in vitro from human feces uncover simple assembly rules develop a predictive model community composition upon addition single nutrients central carbon metabolism complex medium. Community membership was largely determined by donor feces, whereas relative abundances were supplemental source. The absolute abundance most taxa independent supplementing nutrient, due ability fast-growing organisms quickly exhaust their niche medium then exploit monopolize Relative dominant could be predicted nutritional preferences growth dynamics species isolation, exceptions consistent with strain-level variation capabilities. Our study reveals that follows utilization provides framework for manipulating commensal perturbations.

Язык: Английский

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Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth

eLife, Год журнала: 2024, Номер 12

Опубликована: Янв. 22, 2024

The structure and diversity of microbial communities are intrinsically hierarchical due to the shared evolutionary history their constituents. This is typically captured through taxonomic assignment phylogenetic reconstruction, sources information that frequently used group microbes into higher levels organization in experimental natural communities. Connecting community joint ecological dynamics abundances these groups a central problem ecology. However, how depends on scale observation at which defined has never been systematically examined. Here, we macroecological approach quantitatively characterize among disparate environments across scales. We found measures biodiversity given can be consistently predicted using minimal model ecology, Stochastic Logistic Model growth (SLM). result suggests SLM more appropriate null-model for than alternatives such as Unified Neutral Theory Biodiversity. Extending within-scale results, examined relationship between calculated different scales (e.g. genus vs. family), an empirical pattern previously evaluated context Diversity Begets (DBD) hypothesis (Madi et al., 2020). richness estimates assuming independence members, demonstrating DBD sufficiently explained null Contrastingly, only by including correlations members consequence interactions) predict results this study novel patterns establish sharp demarcation recently proposed not affected interactions.

Язык: Английский

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The optimization of microbial functions through rational environmental manipulations

Molecular Microbiology, Год журнала: 2024, Номер 122(3), С. 294 - 303

Опубликована: Фев. 19, 2024

Abstract Microorganisms play a central role in biotechnology and it is key that we develop strategies to engineer optimize their functionality. To this end, most efforts have focused on introducing genetic manipulations microorganisms which are then grown either monoculture or mixed‐species consortia. An alternative strategy microbial processes rationally the environment microbes grow. The multidimensional, including factors such as temperature, pH, salinity, nutrient composition, etc. These environmental all influence growth phenotypes of they generally “interact” with one another, combining effects complex, non‐additive ways. In piece, overview origins consequences these “interactions” between discuss how been built into statistical, bottom‐up predictive models function identify optimal conditions for monocultures We also “top‐down” approaches, algorithms, finding combinations factors. By providing brief summary state field, hope stimulate further work rational manipulation optimization environment.

Язык: Английский

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Characterizing a stable five-species microbial community for use in experimental evolution and ecology

Microbiology, Год журнала: 2024, Номер 170(9)

Опубликована: Сен. 19, 2024

Model microbial communities are regularly used to test ecological and evolutionary theory as they easy manipulate have fast generation times, allowing for large-scale, high-throughput experiments. A key assumption most model is that stably coexist, but this rarely tested experimentally. Here we report the (dis)assembly of a five-species community from metacommunity soil microbes can be future Using reciprocal invasion-from-rare experiments show all species coexist demonstrate stable long time (~600 generations). Crucially work, each identified by their plate morphologies, even after >1 year in co-culture. We characterise pairwise interactions produce high-quality reference genomes species. This questions ecology evolution.

Язык: Английский

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Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology

Frontiers in Microbiology, Год журнала: 2021, Номер 12

Опубликована: Апрель 9, 2021

Recent advances in robotics and affordable genomic sequencing technologies have made it possible to establish quantitatively track the assembly of enrichment communities high-throughput. By conducting community experiments up thousands synthetic habitats, where extrinsic sources variation among replicates can be controlled, we now study reproducibility predictability microbial at different levels organization, its relationship with nutrient composition other ecological drivers. Through a dialog mathematical models, high-throughput are bringing us closer goal developing quantitative predictive theory assembly. In this short review, present an overview recent research on growing field, highlighting connection between suggesting directions for future work.

Язык: Английский

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Interactions between Culturable Bacteria Are Predicted by Individual Species’ Growth

mSystems, Год журнала: 2023, Номер 8(2)

Опубликована: Фев. 23, 2023

In order to understand the function and structure of microbial communities, one must know all pairwise interactions that occur between different species within community, as these shape community’s functioning. However, measuring can be an extremely difficult task especially when dealing with big complex communities.

Язык: Английский

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When can higher‐order interactions produce stable coexistence?

Ecology Letters, Год журнала: 2024, Номер 27(6)

Опубликована: Июнь 1, 2024

Abstract Most ecological models are based on the assumption that species interact in pairs. Diverse communities, however, can have higher‐order interactions, which two or more jointly impact growth of a third species. A pitfall common pairwise approach is it misses interactions potentially responsible for maintaining natural diversity. Here, we explore stability properties systems where guarantee specified set abundances feasible equilibrium dynamics. Even these lead to equilibria do not necessarily produce stable coexistence. Instead, likely be when weak facilitative. Correlations between and permit robust coexistence even diverse systems. Our work only reveals challenges generating through but also uncovers interaction patterns enable

Язык: Английский

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Diversity begets diversity under microbial niche construction

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Фев. 15, 2022

Abstract Microbial interactions are expected to modulate microbial diversity, but whether they inhibit or stimulate further diversity in complex communities, and how, remains poorly understood. By assembling communities multiple identical habitats with a single limiting nutrient, here we provide direct evidence for the role of niche construction cross-feeding driving positive relationship between community focal lineage communities. Combining these experiments simulations, show that this is not inevitable depends on underlying metabolic structure by-product secretions uptake different taxonomic levels.

Язык: Английский

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Metabolic Plasticity Shapes Microbial Communities across a Temperature Gradient

The American Naturalist, Год журнала: 2024, Номер 204(4), С. 381 - 399

Опубликована: Июнь 28, 2024

AbstractA central challenge in community ecology is understanding and predicting the effects of abiotic factors on assembly. In particular, microbial communities play a role ecosystem, but we do not understand how changing like temperature are going to affect composition or function. this article, studied self-assembly multiple synthetic environments changes based metabolic responses different functional groups along gradient. many communities, coexist through partitioning carbon sources an emergent trophic structure (cross-feeding). system, respirofermentative bacteria display preference for sugars supplied as only source secrete secondary (organic acids) that more efficiently consumed by obligate respirators. As consequence structure, plasticity respirofermenters has downstream consequences relative abundance respirators across temperatures. We found temperatures can largely be described increase fermentation by-products with increasing from bacteria. This research highlights importance trade-offs species interactions dynamics gradients.

Язык: Английский

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Preferential use of organic acids over sugars by soil microbes in simulated root exudation

Soil Biology and Biochemistry, Год журнала: 2025, Номер unknown, С. 109738 - 109738

Опубликована: Фев. 1, 2025

Язык: Английский

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