Assembly Graph as the Rosetta Stone of Ecological Assembly

Опубликована: Авг. 2, 2024

Ecological assembly---the process of ecological community formation through species introductions---has recently seen exciting theoretical advancements across dynamical, informational, and probabilistic approaches. However, these theories often remain inaccessible to non-theoreticians, they lack a unifying lens. Here, I introduce the assembly graph as an integrative tool connect emerging theories. The visually represents dynamics, where nodes symbolize combinations edges represent transitions driven by introductions. Through lens graphs, review how processes reduce uncertainty in random arrivals (informational approach), identify graphical properties that guarantee coexistence examine class dynamical models constrain topology graphs (dynamical quantify transition probabilities with incomplete information (probabilistic approach). To facilitate empirical testing, also methods decompose complex into smaller, measurable components, well computational tools for deriving graphs. In sum, this math-light progress aims catalyze research towards predictive understanding assembly.

Язык: Английский

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Multistability driven by cooperative growth in microbial communities

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

Опубликована: Дек. 13, 2023

Abstract Microbial communities often exhibit more than one possible stable composition for the same set of external conditions 1-7 . In human microbiome, persistent changes in species and abundance are associated with health disease states 8 The main drivers these alternative remain relatively unknown 9 Here we experimentally demonstrate that a cross-kingdom community, composed six relevant to respiratory tract, displays four each dominated by different species. pairwise coculture, observe widespread bistability among pairs, providing natural origin multistability full community. contrast common association between antagonism, experiments reveal many positive interactions within community members. We find multiple display self-facilitation, or cooperative growth, modeling predicts this could drive observed as well non-canonical outcomes. A tailored biochemical screening assay reveals glutamate supplementation either reduces eliminates cooperativity growth several species, confirm such extent across pairs Our findings provide mechanistic explanation how rather competitive can underlie microbial communities.

Язык: Английский

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What makes a temperate phage an effective bacterial weapon?

mSystems, Год журнала: 2024, Номер 9(6)

Опубликована: Май 10, 2024

Temperate bacteriophages (phages) are common features of bacterial genomes and can act as self-amplifying biological weapons, killing susceptible competitors thus increasing the fitness their hosts (lysogens). Despite prevalence, however, key characteristics an effective temperate phage weapon remain unclear. Here, we use systematic mathematical analyses coupled with experimental tests to understand what makes weapon. We find that effectiveness is controlled by life history traits-in particular, probability lysis induction rate-but optimal combination traits varies initial frequency a lysogen within population. As consequence, certain weapons be detrimental when rare yet beneficial common, while subtle changes in individual completely reverse impact on fitness. confirm predictions our model experimentally, using phages isolated from clinically relevant Liverpool epidemic strain

Язык: Английский

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Full factorial construction of synthetic microbial communities

Опубликована: Сен. 30, 2024

Constructing combinatorially complete species assemblages is often necessary to dissect the complexity of microbial interactions and find optimal consortia. At moment, this accomplished through either painstaking, labor intensive liquid handling procedures, or use state-of-the-art microfluidic devices. Here we present a simple, rapid, low-cost, highly accessible methodology for assembling all possible combinations library strains, which can be implemented with basic laboratory equipment. To demonstrate usefulness methodology, construct set consortia from eight Pseudomonas aeruginosa empirically measure community-function landscape biomass productivity, identify highest yield community, that lead its function. This easy implement, inexpensive will make assembly easily laboratories.

Язык: Английский

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Environment‐Organism Feedbacks Drive Changes in Ecological Interactions

Ecology Letters, Год журнала: 2024, Номер 28(1)

Опубликована: Дек. 31, 2024

Ecological interactions are foundational to our understanding of community composition and function. While known change depending on the environmental context, it has generally been assumed that external factors responsible for driving these dependencies. Here, we derive a theoretical framework which instead focuses how intrinsic changes caused by organisms themselves alter interaction values. Our central concept is 'instantaneous interaction', captures feedback between current state organismal growth, generating spatiotemporal context-dependencies as modify their environment over time and/or space. We use small microbial communities illustrate this can predict time-dependencies in toxin degradation system, relate time- spatial-dependencies crossfeeding communities. By re-centring relationship environment, predicts variations wherever intrinsic, organism-driven dominates drivers.

Язык: Английский

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Modelling interactions that determine core gut microbiome stability to predict microbiome perturbation by opportunistic pathogens

Опубликована: Июль 15, 2024

The gut microbiome plays a crucial role in host homeostasis, with implications for nutrition, immune development, metabolism, and protection against pathogens. Changes composition are associated health after microbial shifts, opportunistic pathogens have unique chance to invade overgrow the However, complexity of inhibits understanding cause consequence. This study describes species interaction model predict stability. method aids perturbation by Escherichia coli Bacteroides ovatus validate predictions co-culture growth experiments. Despite their inherent differences rates commensals, both E. B. can successfully an established consortium. mechanisms invasion differ; replaces original consortium bacterium, whereas integrates into microbiome. research enhances our processes stability health.

Язык: Английский

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Editorial overview: Systems and synthetic biology of microbial cells and communities

Current Opinion in Microbiology, Год журнала: 2024, Номер 80, С. 102517 - 102517

Опубликована: Июль 18, 2024

Язык: Английский

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Full factorial construction of synthetic microbial communities

Опубликована: Сен. 30, 2024

Constructing combinatorially complete species assemblages is often necessary to dissect the complexity of microbial interactions and find optimal consortia. At moment, this accomplished through either painstaking, labor intensive liquid handling procedures, or use state-of-the-art microfluidic devices. Here we present a simple, rapid, low-cost, highly accessible methodology for assembling all possible combinations library strains, which can be implemented with basic laboratory equipment. To demonstrate usefulness methodology, construct set consortia from eight Pseudomonas aeruginosa empirically measure community-function landscape biomass productivity, identify highest yield community, that lead its function. This easy implement, inexpensive will make assembly easily laboratories.

Язык: Английский

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Ecological Scaling of Temporal Fluctuations with Bacterial Abundance in Gut Microbiota Depends on Functional Properties of Individual Microbial Species and Bacterial Communities

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 29, 2024

Abstract Macroecological relationships that describe various statistical associations between species’ abundances, their spatial, and temporal variability are among the most general laws in ecology biology. One of commonly observed is a power-law scaling means variances species known as Taylor’s law. law has been across many ecosystems, from diverse plant animal ecosystems to complex microbial communities. While mathematical models have proposed explain potential origins law, what determines its exponents not understood. Here, we use trajectories human baboon gut microbiota analyze relationship functional properties individual bacterial communities with species-specific community-level The Taylor characterizes – for each abundance host organisms. On other hand, organism multiple variances. For community find power strongly associated certain nutrient-degrading enzymes gut. Notably, our results demonstrate availability metabolizing starch glycogen significantly increases scaling. We also depends on properties. Specifically, observe lower larger metabolic networks, able grow number carbon sources, particular functions, such glutamine folate metabolism. Overall, study reveals capabilities biosynthetic properties, which likely related ecological roles microbiota.

Язык: Английский

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Environment-organism feedbacks drive changes in ecological interactions

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

Опубликована: Ноя. 2, 2023

Abstract Ecological interactions, the impact of one organism on growth and death another, underpin our understanding long-term composition functional properties communities. In recent years, context-dependency interactions – their tendency to change values in different environments, locations at times has become an increasingly important theme ecological research. However, overarching theoretical assumption been that external environmental factors are responsible for driving these changes. Here, we derive a interaction framework which teases apart separate roles played by extrinsic inputs intrinsic changes driven organisms within environment itself. At heart theory is ‘instantaneous interaction’, quantity captures feedback between it. limit intrinsic, organismdriven dominates over drivers, find this can give rise temporal spatial context-dependencies as modify time and/or space. We use small synthetic microbial communities model ecosystems demonstrate power framework, using it predict time-dependent intra-specific toxin degradation system relate dependencies crossfeeding Our helps explain ubiquity systems where population such placing equal footing inhabit

Язык: Английский

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