Biology subjects

Foster, K. R.

Publications and source records attributed to Foster, K. R..

14 recordsLinked to original sources

bioRxiv2026

Division of labor during bacterial warfare

Division of labor is commonly associated with cooperative behavior, yet one of its most extreme forms occurs during bacterial warfare, where a subset of cells undergoes suicidal lysis to release toxins. Why bacteria divide labor among a few cells rather than producing toxin uniformly remains unknown. Here, we combine timelapse microscopy and simulations, to understand the division of labor during bacterial warfare using bacteriocin (colicin) production by the gut bacterium Escherichia coli as a model system. At the single-cell level, we find that lytic toxin production is a tightly regulated event: only cells that commit to lysis produce significant toxin and then lysis only occurs once a large amount of toxin has been made. This high threshold ensures each sacrifice delivers a large dose, which is released in a rapid burst from a lysing cell. While such burst-like release appears to provide no advantage over uniform labor in well-mixed conditions, we show it becomes extremely effective in spatially structured populations where the rapid release of toxin by one cell can generate lethal concentrations locally and eliminate competitors. Finally, we explain why the lysing fraction remains so small. While an increase in the producing cells increases toxin levels, it also increases the probability of local patch extinctions. The division of labor during bacterial warfare, therefore, enables powerful localized killing while safeguarding the population from self-destruction.

microbiology↗

bioRxiv2025

Reprogrammed SimCells for Antimicrobial Therapy

Antimicrobial resistance (AMR) is a critical global health challenge. In this study, we developed a novel platform based on chromosome-free and non-replicating simple cells (SimCells, size 1-2 {micro}m) and mini-SimCells (size 100-400 nm) for targeted pathogen elimination. Engineered with surface-displayed nanobodies, SimCells and mini-SimCells selectively bind bacteria expressing specific antigens (e.g., OmpA in E. coli). The selective interactions facilitate close SimCell-pathogen proximity, enabling two antimicrobial mechanisms: direct injection of toxic effectors into bacterial cytoplasm via a heterologous expression of type VI secretion system (T6SS), and enzymatic conversion of aspirin into catechol by engineered salicylate hydroxylase, leading to sustained local production of hydrogen peroxide (H2O2). Our results demonstrate that both reprogrammed SimCells and mini-SimCells can eliminate target E. coli with high specificity and efficiency. Multi-dose reprogrammed mini-SimCell treatment led to a 103-fold selective reduction of targeted bacteria in mixed microbial communities, with minimal disruption to non-target bacteria. We demonstrate that reprogrammed mini-SimCells, engineered with nanobody targeting outer membrane protein OmpA of the clinically relevant multidrug resistant pathogen E. coli ST131, achieved elimination efficiencies over 97% at 24 and 48 hrs. This modularised plug-and-play antimicrobial platform provides a highly specific, efficient and adaptable solution for combating diverse AMR pathogens. Significance StatementAntimicrobial-resistant (AMR) bacteria cause millions of deaths worldwide annually, representing a critical global health challenge. In this study, we developed a novel therapeutic platform using two types of chromosome-free, non-replicating engineered bacterial cells: SimCells (1-2 {micro}m) and mini-SimCells (100-400 nm). These SimCells were engineered to selectively bind to targeted E. coli, facilitating precise delivery of toxic proteins via a Type VI secretion system (T6SS) and localised generation of hydrogen peroxide from aspirin. We demonstrate that mini-SimCells eliminated over 97% of a targeted AMR strain within 48 hours. Moreover, multiple-dose administration achieved a selective 103-fold reduction of targeted E. coli in mixed microbial communities. This modular plug-and-play platform offers an adaptable solution against diverse multi-drug-resistant pathogens.

synthetic biology↗

bioRxiv2024

Bacterial warfare is associated with virulence and antimicrobial resistance

Bacteria have evolved a diverse array of mechanisms to inhibit and kill competitors, commonly known as bacterial weapons. However, why some bacteria carry weapons while others do not remains poorly understood. Here we explore this question using the bacteriocins of E. coli as a model system, which are both well studied and have large well-annotated genomic resources. While bacteriocins are found widely across E. coli strains, we find that carriage is particularly associated with pathogenic extra-intestinal (ExPEC) strains, including many clinically-important pandemic strains. These pathogenic strains commonly carry large plasmids that encode the bacteriocins but also virulence factors, including siderophores, and antimicrobial resistance mechanisms. Across all E. coli strains, we find many orphan immunity proteins, which protect against bacteriocins and suggest that bacterial warfare is important in nature. We also present evidence that bacteriocin toxins readily move between strains via plasmid transfer and even between plasmids via transposons. Finally, we show that several E. coli bacteriocins are widely shared with the pathogen Salmonella enterica, further cementing the link to virulence. Our work suggests that the bacteriocins of E. coli are important antibacterial weapons for dangerous antimicrobial-resistant strains.

microbiology↗

bioRxiv2024

Horizontal gene transfer can reshape bacterial warfare

Bacteria commonly use molecular weaponry to kill or inhibit competitors. Genes encoding many of these weapons can be transmitted horizontally, but the impact on bacterial warfare is not understood. Here, we develop an ecological model of bacterial warfare where there is potential for horizontal gene transfer. Our model predicts that weapon gene transfer from an attacker to a target strain is possible, but at a low rate such that transfer has a negligible impact on competition outcomes. We tested the model empirically using a transmissible plasmid encoding colicin E2, a potent antibacterial toxin produced by Escherichia coli. As predicted by the model, we find that toxin plasmid transfer is feasible during warfare, but the resulting transconjugants remain rare. However, exploring the model further reveals realistic conditions where transfer has major impacts. Specifically, the model predicts that whenever competing strains have access to some unique nutrients, transconjugants can proliferate and reach high abundances. In support of these predictions, short- and long-term experiments show that transconjugants can thrive when nutrient competition is relaxed. Our work shows how horizontal gene transfer can reshape bacterial warfare in a way that can benefit a weapon gene but not the bacteria that carries it.

microbiology↗

bioRxiv2024

A simple regulatory network coordinates a bacterial stress response in space and time

Bacteria employ diverse gene regulatory networks to protect themselves from stressful environments. While transcriptomics and proteomics show that the expression of different genes can shift strongly in response to stress, the underlying logic of large regulatory networks is difficult to understand from bulk measurements performed at discrete time points. As a result, it remains challenging to predict how these regulatory networks function at a system level. Here we use time-resolved single-cell imaging to explore the functioning of a key bacterial stress response: The Escherichia coli response to oxidative stress. Our work reveals a striking diversity in the expression dynamics of genes in the regulatory network, with differences in the timing, magnitude, and direction of expression changes. Nevertheless, we find that these patterns have a simple underlying logic. Firstly, all genes exhibit a transient increase in their protein levels simply due to the slowing down of cell growth under stress. Controlling for this effect reveals three classes of gene regulation driven by the transcription factor OxyR. Downregulated genes drop in expression level, while upregulated genes either show pulsatile expression that decays rapidly or gradual induction, dependent upon transcription factor binding dynamics. These classes appear to serve distinct functional roles in cell populations. Pulsatile genes are stress-sensitive and activate rapidly and transiently in a few cells, which provides an initial protection for cell groups. Gradually upregulated genes are less sensitive and induce more evenly generating a lasting protection that involves a larger number of cells. Our study shows how bacterial populations use simple regulatory principles to coordinate a stress response in space and time.

systems biology↗

bioRxiv2024

Bacteria use spatial sensing to direct chemotaxis on surfaces

Planktonic bacteria navigate chemical gradients using temporal sensing to detect changes in concentration over time as they swim. Here we show that surface-attached bacteria use a fundamentally different mode of sensing during chemotaxis. We combined microfluidic experiments, massively parallel cell tracking, and fluorescent reporters to study how Pseudomonas aeruginosa senses chemical gradients during pili-based "twitching" chemotaxis on surfaces. First, we asked whether surface-attached cells use temporal sensing by exposing them to temporal chemical gradients generated via Taylor-Aris dispersion. However, we find that temporal changes in concentration do not induce changes in motility, indicating that twitching cells do not sense chemical gradients like swimming bacteria do. We, therefore, designed experiments to test whether cells can detect chemical gradients across the length of their bodies. In these experiments, we follow the localisation of a fluorescent protein fusion to quantify the chemotactic behaviour of stationary cells in an alternating chemical gradient. We find that P. aeruginosa cells can directly sense differences in concentration across the lengths of their bodies, even in the presence of strong temporal fluctuations. Our work reveals that P. aeruginosa cells are capable of spatial sensing, thus overturning the widely held notion that bacterial cells are too small to directly sense chemical gradients in space.

microbiology↗

bioRxiv2023

Cell motility greatly empowers bacterial contact weapons

Many bacteria kill competitors using short-range weapons, such as the Type VI Secretion System (T6SS) and Contact Dependent Inhibition (CDI). While these can deliver powerful toxins, they rely on direct contact between attacker and target cells. We hypothesised that movement enables attackers to contact more targets and thus greatly empower their weapons. To explore this, we developed individual-based and continuum models to show that motility greatly improves contact-dependent toxin delivery through two underlying processes. First, genotypic mixing increases the inter-strain contact probability of attacker and sensitive cells. Second, target switching ensures attackers constantly attack new cells, instead of repeatedly hitting the same cell. We test our predictions with the pathogen Pseudomonas aeruginosa, using genetically engineered strains to study the interaction between CDI and twitching motility. As predicted, we find that motility massively improves the effectiveness of CDI, in some cases up to 10,000-fold. Moreover, we demonstrate that both mixing processes occur using timelapse single-cell microscopy and quantify their relative importance by combining experimental data with our models. Our work shows how bacteria combine cell movement with contact-based weapons to launch powerful attacks on their competitors.

microbiology↗

bioRxiv2023

Community ecology of phages on a clonal bacterial host

Bacteriophages are the most abundant and diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. Here, we have discovered a general mechanism that allows phage diversity to outstrip the diversity of their bacterial hosts. We assembled and passaged dozens of diverse phage communities on a single, non-coevolving strain of Escherichia coli until the phage communities reached equilibrium. In all cases, we found multiple phage species coexisted stably, despite competition for a single, clonal host population. Coexistence within these communities was supported through host phenotypic heterogeneity, whereby phages specialized on cells adopting different growth phenotypes. Our experiments reveal a rich community ecology of bacteriophages where multiple phage species coexist and interact at the scale of a single bacterial host. One-Sentence SummaryDiverse communities of phages emerge stably and consistently on a clonal bacterial host, enabled by phenotypic heterogeneity.

microbiology↗

bioRxiv2022

Bows and swords: why bacteria carry short and long-range weapons

Bacteria possess a diverse range of mechanisms for inhibiting competitors, including bacteriocins, tailocins, the type VI secretion system, and contact-dependent inhibition. Why bacteria have evolved such a wide array of weapon systems remains a mystery. Here we develop an agent-based model to compare short-range weapons that require cell-cell contact, with long-range weapons that rely on diffusion. Our models predict that contact weapons are useful when an attacking strain is outnumbered, facilitating invasion and establishment. By contrast, ranged weapons tend to only be effective when attackers are abundant. We test our predictions with the opportunistic pathogen Pseudomonas aeruginosa, which naturally carries multiple weapons, including contact-dependent inhibition (CDI) and diffusing tailocins. As predicted, short-range CDI functions better at low frequency, while long-range tailocins require high frequency and cell density to function effectively. Head-to-head competitions between the two weapon types further support our predictions: a tailocin attacker only defeats CDI when it is numerically dominant, but then we find it can be devastating. Finally, we show that the two weapons work well together when one strain employs both. We conclude that short and long-range weapons serve different functions and allow bacteria to fight both as individuals and as a group.

microbiology↗

bioRxiv2022

Collective protection against the type VI secretion system in bacteria

Bacteria commonly face attacks from other strains using the type VI secretion system (T6SS), a molecular speargun that stabs and intoxicates competitors. Here we show how bacteria can work together to collectively defend themselves against these attacks. This project began with an outreach activity: while developing an online computer game of bacterial warfare, we noticed that one strategist ( Slimy) that made extracellular polymeric substances (EPS) was able to resist attacks from another strategist that employed the T6SS ( Stabby). This observation motivated us to model this scenario more formally, using dedicated agent-based simulations. The model predicts that EPS production can serve as a collective defence mechanism, which protects both producing cells and neighbouring cells that do not make EPS. We then tested our model with a synthetic community that contains a T6SS-wielding attacker (Acinetobacter baylyi), and two T6SS-sensitive target strains (Escherichia coli) that either secrete EPS, or not. As predicted by our modelling, we find that the production of EPS leads to collective protection against T6SS attacks, where EPS producers protect each other and nearby non-producers. We identify two processes that explain this protection: EPS sharing between cells and a second general mechanism whereby groups of resistant cells shield susceptible cells ( flank protection). Our work shows how EPS-producing bacteria can work together to defend themselves from the type VI secretion system.

microbiology↗

bioRxiv2021

Reconfigurable microfluidic circuits for isolating and retrieving cells of interest

Microfluidic devices are widely used in many fields of biology, but a key limitation is that cells are typically surrounded by solid walls, making it hard to access those that exhibit a specific phenotype for further study. Here, we provide a general and flexible solution to this problem that exploits the remarkable properties of microfluidic circuits with fluid walls - transparent interfaces between culture media and an immiscible fluorocarbon that are easily pierced with pipets. We provide two proofs-of-concept in which specific cell sub-populations are isolated and recovered: i) murine macrophages chemotaxing towards complement component 5a, and ii) bacteria (Pseudomonas aeruginosa) in developing biofilms that migrate towards antibiotics. We build circuits in minutes on standard Petri dishes, add cells, pump in laminar streams so molecular diffusion creates attractant gradients, acquire time-lapse images, and isolate desired sub-populations in real-time by building fluid walls around migrating cells with an accuracy of tens of micrometres using 3D-printed adaptors that convert conventional microscopes into wall-building machines. Our method allows live cells of interest to be easily extracted from microfluidic devices for downstream analyses.

bioengineering↗

bioRxiv2021

Suicidal chemotaxis in bacteria

Bacteria commonly live in communities on surfaces where steep gradients of antibiotics and other chemical compounds routinely occur. While many species of bacteria can move on surfaces, we know surprisingly little about how such antibiotic gradients affect cell motility. Here we study the behaviour of the opportunistic pathogen Pseudomonas aeruginosa in stable spatial gradients of a range of antibiotics by tracking thousands of cells in microfluidic devices as they form biofilms. Unexpectedly, these experiments reveal that individual bacteria use pili-based ( twitching) motility to actively navigate towards regions with higher antibiotic concentrations. Our analyses suggest that this biased migration is driven, at least in part, by a direct response to the antibiotics. Migrating cells can reach antibiotic concentrations hundreds of times higher than their minimum inhibitory concentration in a few hours and remain highly motile. However, isolating these cells - using fluid-walled microfluidic devices that can be reconfigured in situ - suggests that these bacteria are terminal and not able to reproduce. In spite of moving towards their death, we show that migrating cells are capable of entering a suicidal program to release bacteriocins that are used to kill other bacteria. Our work suggests that bacteria respond to antibiotics as if they come from a competing colony growing in the neighbourhood, inducing them to invade and attack. As a result, clinical antibiotics have the potential to serve as a bait that lures bacteria to their death.

microbiology↗

bioRxiv2020

Droplet printing reveals the importance of micron-scale structure for bacterial ecology

Bacteria often live in diverse communities where the spatial arrangement of strains and species is considered critical for their ecology, including whether strains can coexist, which are ecologically dominant, and how productive they are as a community1,2. However, a test of the importance of spatial structure requires manipulation at the fine scales at which this structure naturally occurs3-8. Here we develop a droplet-based printing method to arrange different bacterial genotypes across a sub-millimetre array. We use this to test the importance of fine-scale spatial structure by printing strains of the gut bacterium Escherichia coli that naturally compete with one another using protein toxins9,10. This reveals that the spatial arrangement of bacterial genotypes is important for ecological outcomes. Toxin-producing strains largely eliminate susceptible non-producers when genotypes are well-mixed. However, printing strains side-by-side creates an ecological refuge such that susceptible strains can coexist with toxin producers, even to the extent that a susceptible strain outnumbers the toxin producer. Head-to-head competitions between toxin producers also reveals strong effects, where spatial structure can make the difference between one strain winning and mutual destruction. Finally, we print different potential barriers between two competing strains to understand why space is so important. This reveals the importance of processes that limit the free diffusion of molecules. Specifically, we show that cells closest to a toxin producer bind to and capture toxin molecules, which creates a refuge for their clonemates. Our work provides a new method to generate customised bacterial communities with defined spatial distributions, and reveals that micron-scale changes in these distributions can drive major shifts in their ecology.

microbiology↗

bioRxiv2020

The Evolution of Mass Cell Suicide in Bacterial Warfare

Behaviours that reliably cause the death of an actor are typically strongly disfavoured by natural selection, and yet many bacteria undergo cell lysis to release anti-competitor toxins [1-4]. This behaviour is most easily explained if only a few cells die to release toxins and help their clonemates, but the number of cells that actually lyse during bacterial warfare is unknown. The challenge is that one cannot distinguish cells that have undergone programmed suicide from those that were simply killed by a competitors toxin. We developed a two-colour fluorescence reporter assay in Escherichia coli to overcome this problem. Surprisingly, this revealed conditions where nearly all cells undergo programmed lysis. Adding a DNA-damaging toxin (DNase colicin) to a focal strain causes it to engage in mass cell suicide where around 85% of cells lyse to release their own toxin. Time-lapse 3D confocal microscopy revealed that self-lysis occurs at even higher frequencies (~94%) at the interface between competing colonies. We sought to understand how such high levels of cell suicide could be favoured by natural selection. Exposing E. coli that do not perform lysis to the DNase colicin revealed that mass lysis only occurs when cells are going to die anyway from toxin exposure. From an evolutionary perspective, this renders the behaviour cost-free as these cells have zero reproductive potential. This explains how mass cell suicide can evolve, as any small benefit to surviving clonemates can lead to the strategy being favoured by natural selection. Our findings have strong parallels to the suicidal attacks of social insects [5-8], which are also performed by individuals with low reproductive potential, suggesting convergent evolution in these very different organisms. HIGHLIGHTSO_LIA novel assay can detect Escherichia coli undergoing cell suicide to release toxins C_LIO_LIWe quantified the frequency of suicidal self-lysis during competitions C_LIO_LIUnder some conditions, nearly all cells will self-lyse to release toxins C_LIO_LISelf-lysis makes evolutionary sense as cells will die anyway from competitors toxins C_LI

microbiology↗