Multistability and regime shifts in microbial communities explained by competition for essential nutrients

Dubinkina, Veronika; Fridman, Yulia; Pandey, Parth Pratim; Maslov, Sergei

doi:10.1101/687574

Cited by 17 publications

(34 citation statements)

References 48 publications

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“…There are many plausible biological mechanisms one could add to a purely trophic community model that could explain the existence of alternative states, also known as 'multistability'. These mechanisms could involve, for instance, phenotypic plasticity [95], simultaneous competition for multiple resources [96], metabolic trade-offs [89], or higher-order interactions [97]. Here, we choose to highlight two simple mechanisms that we think are likely to be ubiquitous across microbiomes: mutual antagonism and positive feedback loops (Figure 4).…”

Section: Assembly Dynamics Of Trophic Systemsmentioning

confidence: 99%

Trophic Interactions and the Drivers of Microbial Community Assembly

et al. 2020

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

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Section: Assembly Dynamics Of Trophic Systemsmentioning

confidence: 99%

Trophic Interactions and the Drivers of Microbial Community Assembly

et al. 2020

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“…The essential resources can be either light and other nutrients, or the nutrients themselves such as nitrogen and phosphorus. Model extensions can include resource pulsing, diffusion gradients within the medium or water column, and large numbers of consumer species and nutrient conditions (Dubinkina et al, 2019;Stojsavljevic et al, 2019).…”

Section: Broader Context Within Consumer-resource Modelsmentioning

confidence: 99%

Estrogen as an Essential Resource and the Coexistence of ER+ and ER– Cancer Cells

Kareva

Brown

2021

Front. Ecol. Evol.

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Diagnosis of estrogen sensitivity in breast cancer is largely predicated on the ratio of ER+ and ER– cancer cells obtained from biopsies. Estrogen is a growth factor necessary for cell survival and division. It can also be thought of as an essential resource that can act in association with other nutrients, glucose, glutamine, fatty acids, amino acids, etc. All of these nutrients, collectively or individually, may limit the growth of the cancer cells (Liebig’s Law of the Minimum). Here we model estrogen susceptibility in breast cancer as a consumer-resource interaction: ER+ cells require both estrogen and glucose as essential resources, whereas ER– only require the general resource. The model predicts that when estrogen is the limiting factor, other nutrients may go unconsumed and available at higher levels, thus permitting the invasion of ER– cells. Conversely, when ER– cells are less efficient on glucose than ER+ cells, then ER– cells limited by glucose may be susceptible to invasion by ER+ cells, provided that sufficient levels of estrogen are available. ER+ cells will outcompete ER– cells when estrogen is abundant, resulting in low concentrations of interstitial glucose within the tumor. In the absence of estrogen, ER– cells will outcompete ER+ cells, leaving a higher concentration of interstitial glucose. At intermediate delivery rates of estrogen and glucose, ER+ and ER– cells are predicted to coexist. In modeling the dynamics of cells in the same tumor with different resource requirements, we can apply concepts and terms familiar to many ecologists. These include: resource supply points, R∗, ZNGI (zero net growth isoclines), resource depletion, and resource uptake rates. Based on the circumstances favoring ER+ vs. ER– breast cancer, we use the model to explore the consequences of therapeutic regimens that may include hormonal therapies, possible roles of diet in changing cancer cell composition, and potential for evolutionarily informed therapies. More generally, the model invites the viewpoint that cancer’s eco-evolutionary dynamics are a consumer-resource interaction, and that other growth factors such as EGFR or androgens may be best viewed as essential resources within these dynamics.

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“…One potential mechanism to explain microbiome shifts and their persistence is multistability (7)(8)(9)(10)(11)(12)(13), the concept that several steady states can exist for an identical set of system parameters ( Fig. 1).…”

Section: Introductionmentioning

confidence: 99%

Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community

et al. 2020

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Major changes in the microbiome are associated with health and disease. Some microbiome states persist despite seemingly unfavorable conditions, such as the proliferation of aerobe-anaerobe communities in oxygen-exposed environments in wound infections or small intestinal bacterial overgrowth. Mechanisms underlying transitions into and persistence of these states remain unclear. Using two microbial taxa relevant to the human microbiome, we combine genome-scale mathematical modeling, bioreactor experiments, transcriptomics, and dynamical systems theory to show that multistability and hysteresis (MSH) is a mechanism describing the shift from an aerobe-dominated state to a resilient, paradoxically persistent aerobe-anaerobe state. We examine the impact of changing oxygen and nutrient regimes and identify changes in metabolism and gene expression that lead to MSH and associated multi-stable states. In such systems, conceptual causation-correlation connections break and MSH must be used for analysis. Using MSH to analyze microbiome dynamics will improve our conceptual understanding of stability of microbiome states and transitions between states.

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Multistability and regime shifts in microbial communities explained by competition for essential nutrients

Cited by 17 publications

References 48 publications

Trophic Interactions and the Drivers of Microbial Community Assembly

Trophic Interactions and the Drivers of Microbial Community Assembly

Estrogen as an Essential Resource and the Coexistence of ER+ and ER– Cancer Cells

Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community

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