Spatial structure increases the benefits of antibiotic production in<i>Streptomyces</i>*

Westhoff, Sanne; Otto, Simon B.; Swinkels, Aram; Bode, Bo; Wezel, Gilles P. van; Rozen, Daniel E.

doi:10.1111/evo.13817

Cited by 23 publications

(16 citation statements)

References 41 publications

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“…It is important, however, that each round of culture be long enough to allow the benefits of compound production to accrue, lest the disruption of spatial structure in passages have a negative effect on selection for public goods production. (See Westhoff et al [27]. ) As the optimal values for the diffusion resistance (for cells, nutrients, and compounds) and nutrient concentrations of the medium, the densities of producer and target, and the degree of resistance of the target cannot be precisely determined a priori , and evolution has a stochastic component, it is advisable to run the evolution experiment in a high-throughput manner with different levels of the above-mentioned parameters, as well as a large number of replicates.…”

Section: Discussionmentioning

confidence: 99%

Evolving Antibiotics against Resistance: a Potential Platform for Natural Product Development?

Waldetoft

Gurney

Lachance

et al. 2019

mBio

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To avoid an antibiotic resistance crisis, we need to develop antibiotics at a pace that matches the rate of evolution of resistance. However, the complex functions performed by antibiotics—combining, e.g., penetration of membranes, counteraction of resistance mechanisms, and interaction with molecular targets—have proven hard to achieve with current methods for drug development, including target-based screening and rational design.

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Section: Discussionmentioning

confidence: 99%

Evolving Antibiotics against Resistance: a Potential Platform for Natural Product Development?

Waldetoft

Gurney

Lachance

et al. 2019

mBio

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“…It will also be crucial to examine these responses in experiments that more closely approximate the natural environment, including environments with increased spatial heterogeneity and decreased diffusion, and where local interactions are maintained over longer periods of time. Similarly, an important next step is determine how these social interactions influence competitive outcomes, as has been done for constitutive antibiotic production between competing species (1,2,36). Together, these approaches will lead to a fuller understanding of the role of antibiotic production in natural soils and the factors that maintain microbial diversity.…”

Section: Effect Of Resource Stress On Inhibitionmentioning

confidence: 99%

“…It can also be driven by secreted toxins, like antibiotics or bacteriocins, that kill or inhibit competitors. Antibiotics and bacteriocins can allow producing strains to invade established habitats or repel invasion by other strains (1,2).…”

Section: Introductionmentioning

confidence: 99%

Competition sensing alters antibiotic production inStreptomyces

Westhoff

Kloosterman

Hoesel

et al. 2020

Preprint

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Corresponding authors: Sanne Westhoff and Daniel E. Rozen s.westhoff@biology.leidenuniv.nl and d.e.rozen@biology.leidenuniv.nl ABSTRACTOne of the most important ways that bacteria compete for resources and space is by producing antibiotics that inhibit competitors. Because antibiotic production is costly, the biosynthetic gene clusters coordinating their synthesis are under strict regulatory control and often require "elicitors" to induce expression, including cues from competing strains.Although these cues are common, they are not produced by all competitors and so the phenotypes causing induction remain unknown. By studying interactions between 24 antibiotic-producing Streptomyces we show that inhibition between competitors is common and occurs more frequently if strains are closely related. Next, we show that antibiotic production is more likely to be induced by cues from strains that are closely related or that share biosynthetic gene clusters. Unexpectedly, antibiotic production is less likely to be induced by antagonistic competitors, indicating that cell damage is not a general cue for induction. In addition to induction, antibiotic production often decreased in the presence of a competitor, although this response was not associated with genetic relatedness or overlap in biosynthetic gene clusters. Finally, we show that resource limitation increases the probability that antibiotic production declines. Our results clarify that social cues and resource availability are crucial determinants of interference competition in Streptomyces.

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“…Here, a 10 μm well diameter was chosen to confine a small number of interacting cells together at length scales similar to those found in multi-species biofilms (Tolker-Nielsen and Molin, 2000), confinement at these length scales often facilitates inter-cellular interactions (Westhoff et al, 2020). Cells are then trapped within the wells using a previously developed photodegradable polyethylene glycol (PEG)-based membrane (van der Vlies et al, 2019), co-cultured, and then focal strain growth in each well is tracked with time lapse fluorescent microscopy (TLFM).…”

Section: Introductionmentioning

confidence: 99%

Simultaneous Discovery of Positive and Negative Interactions Among Rhizosphere Bacteria Using Microwell Recovery Arrays

et al. 2021

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Understanding microbe-microbe interactions is critical to predict microbiome function and to construct communities for desired outcomes. Investigation of these interactions poses a significant challenge due to the lack of suitable experimental tools available. Here we present the microwell recovery array (MRA), a new technology platform that screens interactions across a microbiome to uncover higher-order strain combinations that inhibit or promote the function of a focal species. One experimental trial generates 104 microbial communities that contain the focal species and a distinct random sample of uncharacterized cells from plant rhizosphere. Cells are sequentially recovered from individual wells that display highest or lowest levels of focal species growth using a high-resolution photopolymer extraction system. Interacting species are then identified and putative interactions are validated. Using this approach, we screen the poplar rhizosphere for strains affecting the growth of Pantoea sp. YR343, a plant growth promoting bacteria isolated from Populus deltoides rhizosphere. In one screen, we montiored 3,600 microwells within the array to uncover multiple antagonistic Stenotrophomonas strains and a set of Enterobacter strains that promoted YR343 growth. The later demonstrates the unique ability of the platform to discover multi-membered consortia that generate emergent outcomes, thereby expanding the range of phenotypes that can be characterized from microbiomes. This knowledge will aid in the development of consortia for Populus production, while the platform offers a new approach for screening and discovery of microbial interactions, applicable to any microbiome.

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Spatial structure increases the benefits of antibiotic production inStreptomyces*

Cited by 23 publications

References 41 publications

Evolving Antibiotics against Resistance: a Potential Platform for Natural Product Development?

Evolving Antibiotics against Resistance: a Potential Platform for Natural Product Development?

Competition sensing alters antibiotic production inStreptomyces

Simultaneous Discovery of Positive and Negative Interactions Among Rhizosphere Bacteria Using Microwell Recovery Arrays

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