Making the Best of Aggression: The Many Dimensions of Bacterial Toxin Regulation

Interactions between diet and gut microbiota in cancer

Dietary patterns and specific dietary components, in concert with the gut microbiota, can jointly shape susceptibility, resistance and therapeutic response to cancer. Which diet-microbial interactions contribute to or mitigate carcinogenesis and how they work are important questions in this growing field. Here we interpret studies of diet-microbial interactions to assess dietary determinants of intestinal colonization by opportunistic and oncogenic bacteria. We explore how diet-induced expansion of specific gut bacteria might drive colonic epithelial tumorigenesis or create immuno-permissive tumour milieus and introduce recent findings that provide insight into these processes. Additionally, we describe available preclinical models that are widely used to study diet, microbiome and cancer interactions. Given the rising clinical interest in dietary modulations in cancer treatment, we highlight promising clinical trials that describe the effects of different dietary alterations on the microbiome and cancer outcomes.

Interactions between commensal Enterococcus faecium and Enterococcus lactis and clinical isolates of Enterococcus faecium

Enterococcus faecium (Efm) is a versatile pathogen, responsible for multidrug-resistant infections, especially in hospitalized immunocompromised patients. Its population structure has been characterized by diverse clades (A1, A2, and B (reclassified as E. lactis (Ela)), adapted to different environments, and distinguished by their resistomes and virulomes. These features only partially explain the predominance of clade A1 strains in nosocomial infections. We investigated in vitro interaction of 50 clinical isolates (clade A1 Efm) against 75 commensal faecal isolates from healthy humans (25 clade A2 Efm and 50 Ela). Only 36% of the commensal isolates inhibited clinical isolates, while 76% of the clinical isolates inhibited commensal isolates. The most apparent overall differences in inhibition patterns were presented between clades. The inhibitory activity was mainly mediated by secreted, proteinaceous, heat-stable compounds, likely indicating an involvement of bacteriocins. A custom-made database targeting 76 Bacillota bacteriocins was used to reveal bacteriocins in the genomes. Our systematic screening of the interactions between nosocomial and commensal Efm and Ela on a large scale suggests that, in a clinical setting, nosocomial strains not only have an advantage over commensal strains due to their possession of AMR genes, virulence factors, and resilience but also inhibit the growth of commensal strains.

In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes

Due to their potential application as an alternative to antibiotics, bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by bacteria, have received much attention in recent years. To identify bacteriocins within marine bacteria, most of the studies employed a culture-based method, which is more time-consuming than the in silico approach. For that, the aim of this study was to identify potential bacteriocin gene clusters and their potential producers in 51 marine Bacillota (formerly Firmicutes) genomes, using BAGEL4, a bacteriocin genome mining tool. As a result, we found out that a majority of selected Bacillota (60.78%) are potential bacteriocin producers, and we identified 77 bacteriocin gene clusters, most of which belong to class I bacteriocins known as RiPPs (ribosomally synthesized and post-translationally modified peptides). The identified putative bacteriocin gene clusters are an attractive target for further in vitro research, such as the production of bacteriocins using a heterologous expression system.

Gut Distribution, Impact Factor, and Action Mechanism of Bacteriocin-Producing Beneficial Microbes as Promising Antimicrobial Agents in Gastrointestinal Infection

Gastrointestinal (GI) infection by intestinal pathogens poses great threats to human health, and the therapeutic use of antibiotics has reached a bottleneck due to drug resistance. The developments of antimicrobial peptides produced by beneficial bacteria have drawn attention by virtue of effective, safe, and not prone to developing resistance. Though bacteriocin as antimicrobial agent in gut infection has been intensively investigated and reviewed, reviews on that of bacteriocin-producing beneficial microbes are very rare. It is important to explicitly state the prospect of bacteriocin-producing microbes in prevention of gastrointestinal infection towards their application in host. This review discusses the potential of gut as an appropriate resource for mining targeted bacteriocin-producing microbes. Then, host-related factors affecting the bacteriocin production and activity of bacteriocin-producing microbes in the gut are summarized. Accordingly, the multiple mechanisms (direct inhibition and indirect inhibition) behind the preventive effects of bacteriocin-producing microbes on gut infection are discussed. Finally, we propose several targeted strategies for the manipulation of bacteriocin-producing beneficial microbes to improve their performance in antimicrobial outcomes. We anticipate an upcoming emergence of developments and applications of bacteriocin-producing beneficial microbes as antimicrobial agent in gut infection induced by pathogenic bacteria.

Interbacterial competition mediated by the type VIIb secretion system

Successful occupancy of a given niche requires the colonising bacteria to interact extensively with the biotic and abiotic environment, including other resident microbes. Bacteria have evolved a range of protein secretion machines for this purpose with eleven such systems identified to date. The type VIIb secretion system (T7SSb) is utilised by Bacillota to secrete a range of protein substrates, including antibacterial toxins targeting closely related strains, and the system as a whole has been implicated in a range of activities such as iron acquisition, intercellular signalling, host colonisation and virulence. This review covers the components and secretion mechanism of the T7SSb, the substrates of these systems and their roles in Gram-positive bacteria, with a focus on interbacterial competition.

The toxicological spectrum of the Bacillus cereus toxin cereulide points towards niche-specific specialisation

Most microbes share their environmental niches with very different forms of life thereby engaging in specialised relationships to enable their persistence. The bacterium Bacillus cereus occurs ubiquitously in the environment with certain strain backgrounds causing foodborne and opportunistic infections in humans. The emetic lineage of B. cereus is capable of producing the toxin cereulide, which evokes emetic illnesses. Although food products favouring the accumulation of cereulide are known, the ecological role of cereulide and the environmental niche of emetic B. cereus remain elusive. To better understand the ecology of cereulide-producing B. cereus, we systematically assayed the toxicological spectrum of cereulide on a variety of organisms belonging to different kingdoms. As cereulide is a potassium ionophore, we further tested the effect of environmental potassium levels on the action of cereulide. We found that adverse effects of cereulide exposure are species-specific, which can be exacerbated with increased environmental potassium. Additionally, we demonstrate that cereulide is produced within an insect cadaver indicating its potential ecological function for a saprophytic lifestyle. Collectively, distinct cereulide susceptibilities of other organisms may reflect its role in enabling competitive niche specialization of emetic B. cereus.

Structural and biosynthetic diversity of plantaricins from Lactiplantibacillus

Lactiplantibacillus plantarum (L. plantarum) produces an antimicrobial peptide known as plantaricin. Plantaricin-producing L. plantarum is of interest for its gut-friendly nature, wide range of sugar utilization, palatability, and probiotic attributes, making it a better candidate for the food industry. Numerous strains of plantaricin-producing L. plantarum have been isolated from different ecological niches and found to follow different mechanisms for plantaricin production. The mechanism of plantaricin production is sensitive to environmental factors; therefore, any alteration in the optimum conditions can inhibit/halt bacteriocin production. To regain the lost or hidden plantaricin-producing character of the L. plantarum strains under ideal laboratory conditions, it is essential to understand the mechanism of plantaricin production. Previously, discrete information on various mechanisms of plantaricin production has been elaborated. However, based on the literature analysis, we observed that a systematic classification of plantaricins produced by L. plantarum is not explored. Hence, we aim to collect information about rapidly emerging plantaricins and distribute them among the different classes of bacteriocin, followed by classifying them based on different mechanisms of plantaricin production. This may help scaleup the bacteriocin production at industrial levels, which is otherwise challenging to achieve. This will also help the reader understand plantaricins and their mechanism of plantaricin production to a deeper extent and to characterize/reproduce the peptide where plantaricin production is a hidden character. KEY POINTS: • L. plantarum produces the antimicrobial compound plantaricin. • L. plantarum has different regulatory operons which control plantaricin production. • Based on the regulatory operon, the mechanism of plantaricin production is different.

The cAMP receptor protein (CRP) enhances the competitive nature of Salmonella Typhimurium

The cAMP receptor protein (CRP) is a global regulatory protein. We evaluated the role of CRP in starvation physiology in Salmonella Typhimurium. The Δcrp mutant survived 10 days of starvation. However, in a co-culture with the wild type in nutrient-rich medium, Δcrp died within 48 h. Similar co-culture results were observed with Escherichia coli and Staphylococcus aureus. Our study showed that the Δcrp mutant was not killed by toxins and the Type IV secretion system of the WT. The possibility of viable but non-culturable cells (VBNC) was also ruled out. However, when the overall metabolism of the co-culture was slowed down (anaerobic condition, inhibition by antibiotics and low temperature) that improved the survival of Δcrp in co-culture. But one more significant observation was that the Δcrp mutant survived in nutrient-free co-culture conditions. These two observations suggest that CRP protein is essential for efficient nutrient assimilation in a competitive environment. The cells without CRP protein are unable to evaluate the energy balance within the cell, and the cell spends energy to absorb nutrients. But the wild type cell absorbs nutrients at a faster rate than Δcrp mutant. This leads to a situation wherein the Δcrp is spending energy to absorb the nutrients but is unable to compete with the wild type. This futile metabolism leads to death. Hence, this study shows that CRP is a metabolism modulator in a complex nutrient environment. This study also highlights the need for innovative growth conditions to understand the unique function of a gene.

Horizontal Transfer of Bacteriocin Biosynthesis Genes Requires Metabolic Adaptation To Improve Compound Production and Cellular Fitness

Biosynthetic gene clusters (BGCs) encoding the production of bacteriocins are widespread among bacterial isolates and are important genetic determinants of competitive fitness within a given habitat. Staphylococci produce a tremendous diversity of compounds, and the corresponding BGCs are frequently associated with mobile genetic elements, suggesting gain and loss of biosynthetic capacity. Pharmaceutical biology has shown that compound production in heterologous hosts is often challenging, and many BGC recipients initially produce small amounts of compound or show reduced growth rates. To assess whether transfer of BGCs between closely related Staphylococcus aureus strains can be instantly effective or requires elaborate metabolic adaptation, we investigated the intraspecies transfer of a BGC encoding the ribosomally synthesized and posttranslationally modified peptide (RiPP) micrococcin P1 (MP1). We found that acquisition of the BGC by S. aureus RN4220 enabled immediate MP1 production but also imposed a metabolic burden, which was relieved after prolonged cultivation by adaptive mutation. We used a multiomics approach to study this phenomenon and found adaptive evolution to select for strains with increased activity of the tricarboxylic acid cycle (TCA), which enhanced metabolic fitness and levels of compound production. Metabolome analysis revealed increases of central metabolites, including citrate and α-ketoglutarate in the adapted strain, suggesting metabolic adaptation to overcome the BGC-associated growth defects. Our results indicate that BGC acquisition requires genetic and metabolic predispositions, allowing the integration of bacteriocin production into the cellular metabolism. Inappropriate metabolic characteristics of recipients can entail physiological burdens, negatively impacting the competitive fitness of recipients within natural bacterial communities. IMPORTANCE Human microbiomes are critically associated with human health and disease. Importantly, pathogenic bacteria can hide in human-associated communities and can cause disease when the composition of the community becomes unbalanced. Bacteriocin-producing commensals are able to displace pathogens from microbial communities, suggesting that their targeted introduction into human microbiomes might prevent pathogen colonization and infection. However, to develop probiotic approaches, strains are needed that produce high levels of bioactive compounds and retain cellular fitness within mixed bacterial communities. Our work offers insights into the metabolic burdens associated with the production of the bacteriocin micrococcin P1 and highlights evolutionary strategies that increase cellular fitness in the context of production. Metabolic adaptations are most likely broadly relevant for bacteriocin producers and need to be considered for the future development of effective microbiome editing strategies.

The type-VI secretion system of the beneficial symbiont Vibrio fischeri

The mutualistic symbiosis between the Hawaiian bobtail squid Euprymna scolopes and the marine bacterium Vibrio fischeri is a powerful experimental system for determining how intercellular interactions impact animal-bacterial associations. In nature, this symbiosis features multiple strains of V. fischeri within each adult animal, which indicates that different strains initially colonize each squid. Various studies have demonstrated that certain strains of V. fischeri possess a type-VI secretion system (T6SS), which can inhibit other strains from establishing symbiosis within the same host habitat. The T6SS is a bacterial melee weapon that enables a cell to kill adjacent cells by translocating toxic effectors via a lancet-like apparatus. This review describes the progress that has been made in understanding the factors that govern the structure and expression of the T6SS in V. fischeri and its effect on the symbiosis.

Transcriptional organization and regulation of the Pseudomonas putida K1 type VI secretion system gene cluster

The type VI secretion system (T6SS) is an antimicrobial molecular weapon that is widespread in Proteobacteria and offers competitive advantages to T6SS-positive micro-organisms. Three T6SSs have recently been described in Pseudomonas putida KT2440 and it has been shown that one, K1-T6SS, is used to outcompete a wide range of phytopathogens, protecting plants from pathogen infections. Given the relevance of this system as a powerful and innovative mechanism of biological control, it is critical to understand the processes that govern its expression. Here, we experimentally defined two transcriptional units in the K1-T6SS cluster. One encodes the structural components of the system and is transcribed from two adjacent promoters. The other encodes two hypothetical proteins, the tip of the system and the associated adapters, and effectors and cognate immunity proteins, and it is also transcribed from two adjacent promoters. The four identified promoters contain the typical features of σ70-dependent promoters. We have studied the expression of the system under different conditions and in a number of mutants lacking global regulators. P. putida K1-T6SS expression is induced in the stationary phase, but its transcription does not depend on the stationary σ factor RpoS. In fact, the expression of the system is indirectly repressed by RpoS. Furthermore, it is also repressed by RpoN and the transcriptional regulator FleQ, an enhancer-binding protein typically acting in conjunction with RpoN. Importantly, expression of the K1-T6SS gene cluster is positively regulated by the GacS-GacA two-component regulatory system (TCS) and repressed by the RetS sensor kinase, which inhibits this TCS. Our findings identified a complex regulatory network that governs T6SS expression in general and P. putida K1-T6SS in particular, with implications for controlling and manipulating a bacterial agent that is highly relevant in biological control.

Presence and absence of type VI secretion systems in bacteria

The type VI secretion system (T6SS) is a molecular puncturing device that enables Gram-negative bacteria to kill competitors, manipulate host cells and take up nutrients. Who would want to miss such superpowers? Indeed, many studies show how widespread the secretion apparatus is among microbes. However, it is becoming evident that, on multiple taxonomic levels, from phyla to species and strains, some bacteria lack a T6SS. Here, we review who does and does not have a type VI secretion apparatus and speculate on the dynamic process of gaining and losing the secretion system to better understand its spread and distribution across the microbial world.

Investigating cell autonomy in microorganisms

Cell-cell signaling in microorganisms is still poorly characterized. In this Methods paper, we describe a genetic procedure for detecting cell-nonautonomous genetic effects, and in particular cell-cell signaling, termed the chimeric colony assay (CCA). The CCA measures the effect of a gene on a biological response in a neighboring cell. This assay can measure cell autonomy for range of biological activities including transcript or protein accumulation, subcellular localization, and cell differentiation. To date, the CCA has been used exclusively to investigate colony patterning in the budding yeast Saccharomyces cerevisiae. To demonstrate the wider potential of the assay, we applied this assay to two other systems: the effect of Grr1 on glucose repression of GAL1 transcription in yeast and the effect of rpsL on stop-codon translational readthrough in Escherichia coli. We also describe variations of the standard CCA that address specific aspects of cell-cell signaling, and we delineate essential controls for this assay. Finally, we discuss complementary approaches to the CCA. Taken together, this Methods paper demonstrates how genetic assays can reveal and explore the roles of cell-cell signaling in microbial processes.

Antimicrobial Potential of the Genera Geobacillus and Parageobacillus, as Well as Endolysins Biosynthesized by Their Bacteriophages

In the recent decades, antibiotic resistance has emerged and spread rapidly among clinically relevant pathogens. The natural ability of bacteria to transmit resistance determinants through horizontal gene transfer poses constant challenges to drug development. Natural molecules produced by soil microorganisms continue to be a key source of new antimicrobial agents. In this context, bacteria from the Geobacillus and Parageobacillus genera deserve special attention. Although there is commercial and industrial interest in these microorganisms, the full range of antibacterial compounds biosynthesized by the Geobacillus and Parageobacillus species remains largely unexplored. The aim of this review is to present the strong antimicrobial potential of these bacteria and endolysins produced by their bacteriophages.

Pseudomonas aeruginosa rhamnolipid micelles deliver toxic metabolites and antibiotics into Staphylococcus aureus

Efficient delivery of toxic compounds to bacterial competitors is essential during interspecies microbial warfare. Rhamnolipids (RLPs) are glycolipids produced by Pseudomonas and Burkholderia species involved in solubilization and uptake of environmental aliphatic hydrocarbons and perform as biosurfactants for swarming motility. Here, we show that RLPs produced by Pseudomonas aeruginosa associate to form micelles. Using high-resolution microscopy, we found that RLP micelles serve as carriers for self-produced toxic compounds, which they deliver to Staphylococcus aureus cells, thereby enhancing and accelerating S. aureus killing. RLPs also potentiated the activity of lincosamide antibiotics, suggesting that RLP micelles may transport not only self-produced but also heterologous compounds to target competing bacterial species

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Pseudomonas aeruginosa rhamnolipids form micelles

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Rhamnolipid micelles delivery pyochelin into S. aureus cells

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Rhamnolipid micelles potentiate activity of lincosamide antibiotics against S. aureus

Higher-order effects, continuous species interactions, and trait evolution shape microbial spatial dynamics

Persistently diverse microbial communities are one of biology’s great puzzles. Using a modeling framework that accommodates high mutation rates and a continuum of species traits, we studied microbial communities in which antagonistic interactions occur via the production of, inhibition of, and vulnerability to toxins (e.g., antibiotics). Mutation size and mobility enhanced microbial diversity and temporal persistence to extraordinarily high levels. These findings—including the discovery that the duration of the transient phase in community assembly provides a guide to equilibrial diversity—highlight the potentially critical role that antagonistic interactions play in promoting the diversity of bacterial systems. Such interactions, together with resource-driven interactions and spatial structure, may drive the enigmatic levels of biodiversity seen in microbial systems.

The assembly and maintenance of microbial diversity in natural communities, despite the abundance of toxin-based antagonistic interactions, presents major challenges for biological understanding. A common framework for investigating such antagonistic interactions involves cyclic dominance games with pairwise interactions. The incorporation of higher-order interactions in such models permits increased levels of microbial diversity, especially in communities in which antibiotic-producing, sensitive, and resistant strains coexist. However, most such models involve a small number of discrete species, assume a notion of pure cyclic dominance, and focus on low mutation rate regimes, none of which well represent the highly interlinked, quickly evolving, and continuous nature of microbial phenotypic space. Here, we present an alternative vision of spatial dynamics for microbial communities based on antagonistic interactions—one in which a large number of species interact in continuous phenotypic space, are capable of rapid mutation, and engage in both direct and higher-order interactions mediated by production of and resistance to antibiotics. Focusing on toxin production, vulnerability, and inhibition among species, we observe highly divergent patterns of diversity and spatial community dynamics. We find that species interaction constraints (rather than mobility) best predict spatiotemporal disturbance regimes, whereas community formation time, mobility, and mutation size best explain patterns of diversity. We also report an intriguing relationship among community formation time, spatial disturbance regimes, and diversity dynamics. This relationship, which suggests that both higher-order interactions and rapid evolution are critical for the origin and maintenance of microbial diversity, has broad-ranging links to the maintenance of diversity in other systems.

Ribosomally synthesized peptides, foreground players in microbial interactions: recent developments and unanswered questions

It is currently well established that multicellular organisms live in tight association with complex communities of microorganisms including a large number of bacteria. These are immersed in complex interaction networks reflecting the relationships established between them and with host organisms; yet, little is known about the molecules and mechanisms involved in these mutual interactions. Ribosomally synthesized peptides, among which bacterial antimicrobial peptides called bacteriocins and microcins have been identified as contributing to host-microbe interplays, are either unmodified or post-translationally modified peptides. This review will unveil current knowledge on these ribosomal peptide-based natural products, their interplay with the host immune system, and their roles in microbial interactions and symbioses. It will include their major structural characteristics and post-translational modifications, the main rules of their maturation pathways, and the principal ecological functions they ensure (communication, signalization, competition), especially in symbiosis, taking select examples in various organisms. Finally, we address unanswered questions and provide a framework for deciphering big issues inspiring future directions in the field.

The microbiome-shaping roles of bacteriocins

The microbiomes on human body surfaces affect health in multiple ways. They include not only commensal or mutualistic bacteria but also potentially pathogenic bacteria, which can enter sterile tissues to cause invasive infection. Many commensal bacteria produce small antibacterial molecules termed bacteriocins that have the capacity to eliminate specific colonizing pathogens; as such, bacteriocins have attracted increased attention as potential microbiome-editing tools. Metagenome-based and activity-based screening approaches have strongly expanded our knowledge of the abundance and diversity of bacteriocin biosynthetic gene clusters and the properties of a continuously growing list of bacteriocin classes. The dynamic acquisition, diversification or loss of bacteriocin genes can shape the fitness of a bacterial strain that is in competition with bacteriocin-susceptible bacteria. However, a bacteriocin can only provide a competitive advantage if its fitness benefit exceeds the metabolic cost of production, if it spares crucial mutualistic partner strains and if major competitors cannot develop resistance. In contrast to most currently available antibiotics, many bacteriocins have only narrow activity ranges and could be attractive agents for precision therapy and prevention of infections. A common scientific strategy involving multiple disciplines is needed to uncover the immense potential of microbiome-shaping bacteriocins.

Revisiting the steps of Salmonella gut infection with a focus on antagonistic interbacterial interactions

A commensal microbial community is established in the mammalian gut during its development, and these organisms protect the host against pathogenic invaders. The hallmark of noninvasive Salmonella gut infection is the induction of inflammation via effector proteins secreted by the type III secretion system, which modulate host responses to create a new niche in which the pathogen can overcome the colonization resistance imposed by the microbiota. Several studies have shown that endogenous microbes are important to control Salmonella infection by competing for resources. However, there is limited information about antimicrobial mechanisms used by commensals and pathogens during these in vivo disputes for niche control. This review aims to revisit the steps that Salmonella needs to overcome during gut colonization-before and after the induction of inflammation-to achieve an effective infection. We focus on a series of reported and hypothetical antagonistic interbacterial interactions in which both contact-independent and contact-dependent mechanisms might define the outcome of the infection.

A quantitative decision theory of animal conflict

Interactions between individuals are thought to shape evolution and speciation through natural selection, but little is known about how an individual (or player) strategically interacts with others to maximize its payoff. We develop a simple decision-theoretic model that generates four hypotheses about the choice of an optimal behavioral strategy by a player in response to the strategies of other players. The golden threshold hypothesis suggests that 62% is the critical threshold determining the transition of a larger player's strategy in reaction to its smaller dove-like partner. Below this critical point, the larger one exploits the smaller one, whereas above it, the larger one chooses to cooperate with the smaller one. The competition-to-cooperation shift hypothesis states that a larger player never cooperates with a smaller hawk-like player unless the former is reversely surpassed in size by the latter by 75%. The Fibonacci retracement mark hypothesis proposes that, faced with a larger dove-like player, a smaller player chooses to either cooperate or cheat, depending on whether its size relative to the larger player is less or more than 38%. The surrender-resistance hypothesis suggests that, in reaction to a larger hawk-like player, a smaller player can either gain some benefit from resistance or is sacrificed by choosing to surrender. We test these hypotheses by re-analyzing body mass data of full-sib fishes that were co-cultured in a common water pool. Pairwise analysis of these co-existing fishes broadly suggests the prediction of our hypotheses. Taken together, our model unveils detectable yet previously unknown quantitative mechanisms that mediate the strategic choice of animal behavior in populations or communities. Given the ubiquitous nature of biological interactions occurring at different levels of organizations and the paucity of quantitative approaches to understand them, results by our decision-theoretic model represent an initial step towards the deeper understanding of how biological entities interact with each other to drive their evolution.

Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion

Interference competition among bacteria requires a highly specialized, narrow-spectrum weaponry when targeting closely-related competitors while sparing individuals from the same clonal population. Here we investigated mechanisms by which environmentally important Pseudomonas bacteria with plant-beneficial activity perform kin interference competition. We show that killing between phylogenetically closely-related strains involves contractile phage tail-like devices called R-tailocins that puncture target cell membranes. Using live-cell imaging, we evidence that R-tailocins are produced at the cell center, transported to the cell poles and ejected by explosive cell lysis. This enables their dispersal over several tens of micrometers to reach targeted cells. We visualize R-tailocin-mediated competition dynamics between closely-related Pseudomonas strains at the single-cell level, both in non-induced condition and upon artificial induction. We document the fatal impact of cellular self-sacrifice coupled to deployment of phage tail-like weaponry in the microenvironment of kin bacterial competitors, emphasizing the necessity for microscale assessment of microbial competitions.

Bacillus cereus: Epidemiology, Virulence Factors, and Host-Pathogen Interactions

The toxin-producing bacterium Bacillus cereus is an important and neglected human pathogen and a common cause of food poisoning. Several toxins have been implicated in disease, including the pore-forming toxins hemolysin BL (HBL) and nonhemolytic enterotoxin (NHE). Recent work revealed that HBL binds to the mammalian surface receptors LITAF and CDIP1 and that both HBL and NHE induce potassium efflux and activate the NLRP3 inflammasome, leading to pyroptosis. These mammalian receptors, in part, contribute to inflammation and pathology. Other putative virulence factors of B. cereus include cytotoxin K, cereulide, metalloproteases, sphingomyelinase, and phospholipases. In this review, we highlight the latest progress in our understanding of B. cereus biology, epidemiology, and pathogenesis, and discuss potential new directions for research in this field.

Microbial regulation of natural antibiotic resistance: Understanding the protist-bacteria interactions for evolution of soil resistome

The emergence, evolution and spread of antibiotic resistance genes (ARGs) in the environment represent a global threat to human health. Our knowledge of antibiotic resistance in human-impacted ecosystems is rapidly growing with antibiotic use, organic fertilization and wastewater irrigation identified as key selection pressures. However, the importance of biological interactions, especially predation and competition, as a potential driver of antibiotic resistance in the natural environment with limited anthropogenic disturbance remains largely overlooked. Stress-affected bacteria develop resistance to maximize competition and survival, and similarly bacteria may develop resistance to fight stress under the predation pressure of protists, an essential component of the soil microbiome. In this article, we summarized the major findings for the prevalence of natural ARGs on our planet and discussed the potential selection pressures driving the evolution and development of antibiotic resistance in natural settings. This is the first article that reviewed the potential links between protists and the antibiotic resistance of bacteria, and highlighted the importance of predation by protists as a crucial selection pressure of antibiotic resistance in the absence of anthropogenic disturbance. We conclude that an improved ecological understanding of the protists-bacteria interactions and other biological relationships would greatly expand our ability to predict and mitigate the environmental antibiotic resistance under the context of global change.

Proteus mirabilis outcompetes Klebsiella pneumoniae in artificial urine medium through secretion of ammonia and other volatile compounds

Klebsiella pneumoniae and Proteus mirabilis form mixed biofilms in catheter-associated urinary tract infections. However, co-inoculation of P. mirabilis with K. pneumoniae in artificial urine medium (AUM) resulted in a drastic reduction of K. pneumoniae cells in both biofilm and planktonic growth. Here, the mechanism behind this competitive interaction was studied. Both pH and aqueous ammonia (NH_3aq) increased in mixed cultures (to 9.3 and 150 mM, respectively), while K. pneumoniae viable cells dramatically diminished over time (>6-log reduction, p < 0.05). Mixed cultures developed in either 2-(N-morpholino) ethanesulfonic acid (MES)-buffered AUM (pH 6.5) or AUM without urea did not show bacterial competition, evidencing that the increase in pH and/or NH_3aq concentration play a role in the competitive interaction. Viability of K. pneumoniae single-species cultures decreased 1.5-log in alkaline AUM containing 150 mM NH_3aq after 24 h inoculation, suggesting that ammonia is involved in this inter-species competition. Besides NH_3aq, additional antimicrobials should be present to get the whole competitive effect. Supernatants from P. mirabilis-containing cultures significantly diminished K. pneumoniae viability in planktonic cultures and affected biofilm biomass (p < 0.05). When subjected to evaporation, these supernatants lost their antimicrobial activity suggesting the volatile nature of the antimicrobial compounds. Exposure of K. pneumoniae to volatile compounds released by P. mirabilis significantly decreased cell viability in both planktonic and biofilm cultures (p < 0.05). The current investigation also evidenced a similar bactericidal effect of P. mirabilis volatiles over Escherichia coli and Morganella morganii. Altogether, these results evidence the secretion of ammonia and other volatile compounds by P. mirabilis, with antimicrobial activity against gram-negative uropathogens including K. pneumoniae. This investigation provides novel insight into competitive inter-species interactions that are mediated by production of volatile molecules.

The cost and benefit of quorum sensing-controlled bacteriocin production in Lactobacillus plantarum

Bacteria eliminate competitors via 'chemical warfare' with bacteriocins. Some species appear to adjust bacteriocin production conditionally in response to the social environment. We tested whether variation in the cost and benefit of producing bacteriocins could explain such conditional behaviour, in the bacteria Lactobacillus plantarum. We found that: (a) bacterial bacteriocin production could be upregulated by either the addition of a synthetic autoinducer peptide (PLNC8IF; signalling molecule), or by a plasmid which constitutively encodes for the production of this peptide; (b) bacteriocin production is costly, leading to reduced growth when grown in poor and, to a lesser extent, in rich media; (c) bacteriocin production provides a fitness advantage, when grown in competition with sensitive strains; and (d) the fitness benefits provided by bacteriocin production are greater at higher cell densities. These results show how the costs and benefits of upregulating bacteriocin production can depend upon abiotic and biotic conditions.

Toxin production spontaneously becomes regulated by local cell density in evolving bacterial populations

The production of anticompetitor toxins is widespread among bacteria. Because production of such toxins is costly, it is typically regulated. In particular, many toxins are produced only when the local cell density is high. It is unclear which selection pressures shaped the evolution of density-dependent regulation of toxin production. Here, we study the evolution of toxin production, resistance and the response to a cell-density cue in a model of an evolving bacterial population with spatial structure. We present results for two growth regimes: (i) an undisturbed, fixed habitat in which only small fluctuations of cell density occur, and (ii) a serial-transfer regime with large fluctuations in cell density. We find that density-dependent toxin production can evolve under both regimes. However, the selection pressures driving the evolution of regulation differ. In the fixed habitat, regulation evolves because it allows cells to produce toxin only when opportunities for reproduction are highly limited (because of a high local cell density), and the effective fitness costs of toxin production are hence low. Under serial transfers, regulation evolves because it allows cells to switch from a fast-growing non-toxic phenotype when colonising a new habitat, to a slower-growing competitive toxic phenotype when the cell density increases. Colonies of such regulating cells rapidly expand into unoccupied space because their edges consist of fast-growing, non-toxin-producing cells, but are also combative because cells at the interfaces with competing colonies do produce toxin. Because under the two growth regimes different types of regulation evolve, our results underscore the importance of growth conditions in the evolution of social behaviour in bacteria.

Bacteria live in microbial communities, in which they compete with many other microbes for nutrients and space. In this competitive environment, almost all known bacterial strains produce toxins that impair or kill other bacteria. This chemical warfare is thought to be one of the major factors shaping microbial diversity. Many toxins are produced only if the local density of bacteria is high. To achieve this, bacteria respond to cell-density cues: signalling molecules or other indicators of the presence of other cells. Here, we use a computational model to study the evolution of density-based regulation of toxin production in bacterial populations. We show that such regulation can arise under various growth conditions, and analyse the selection pressures driving its evolution. In particular, we find that if bacteria regularly need to colonise a new habitat, density-based regulation allows them to express a fast-growing, non-toxic phenotype when expanding into uncolonised territory, and a slower-growing, toxin-producing phenotype when competing with other strains. Colonies of regulating cells show a typical structure, with cells of the fast-growing, sensitive phenotype at their expanding edges, and toxin-producing cells in the colony interior and at interfaces between colonies.