Bacteriocins: evolution, ecology, and application

Peptide-Based Formulation from Lactic Acid Bacteria Impairs the Pathogen Growth in Ananas Comosus (Pineapple)

Worldwide, street vending commerce has grown exponentially, representing in some countries, including Ecuador, a significant proportion of food consumed by the urban population. Pineapple is one of the common fruits sold as ready-to-eat slices by ambulant vendors in the street or on public transport at risk of contamination by various microorganisms. Previously, we selected Lactobacillus plantarum UTNCys5-4 and Lactococcus lactis subsp. lactis Gt28 strains producing peptides with high capacity to inhibit pathogen growth in vitro. In this study, the effect of different edited formulations containing a mixture of Cys5-4/Gt28 peptides was evaluated in vitro and ex vitro against a pathogenic cocktail containing E. coli (2), Salmonella (2) and Shigella (1). The growth of bacterial cocktail co-inoculated with cell-free supernatant containing peptides (formulation T1) and precipitated peptides (formulation T6), in a ratio of Cys5-4/Gt28:1:1 (v/v), results in a decrease of total cell viability with 1.85 and 1.2 log CFU/mL orders of magnitude at 6 h of incubation. About the same decrease (1.9 log CFU/g) was observed when pineapple slices artificially inoculated with the pathogenic cocktail were coated with T1 formulation, indicating the capacity to diminish simultaneous pathogens in situ, thus demonstrating its great biological control and protection. However, the E. coli cell counts reduced by 2.08 log CFU/g while Salmonella and Shigella cell counts reduced by 1.43 and 1.91 log CFU/g, respectively, at 5 days of refrigeration. In the untreated pineapple slices, the total cell density was maintained during storage, suggesting the adaptation of the pathogens to the fruit matrix. The peptide-based formulation exerted a bacteriolytic mode of action inducing pathogenic cell death. The results indicate that coating pineapple slices with peptide-based formulation is a promising approach to protect them from further contamination by microbial spoilage as well as an alternative to increase the food safety.

Deciphering the Role of Colicins during Colonization of the Mammalian Gut by Commensal E. coli

Colicins are specific and potent toxins produced by Enterobacteriaceae that result in the rapid elimination of sensitive cells. Colicin production is commonly found throughout microbial populations, suggesting its potential importance for bacterial survival in complex microbial environments. Nonetheless, as colicin biology has been predominately studied using synthetic models, it remains unclear how colicin production contributes to survival and fitness of a colicin-producing commensal strain in a natural environment. To address this gap, we took advantage of MP1, an E. coli strain that harbors a colicinogenic plasmid and is a natural colonizer of the murine gut. Using this model, we validated that MP1 is competent for colicin production and then directly interrogated the importance of colicin production and immunity for MP1 survival in the murine gut. We showed that colicin production is dispensable for sustained colonization in the unperturbed gut. A strain lacking colicin production or immunity shows minimal fitness defects and can resist displacement by colicin producers. This report extends our understanding of the role that colicin production may play for E. coli during gut colonization and suggests that colicin production is not essential for a commensal to persist in its physiologic niche in the absence of exogenous challenges.

Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae

The plant pathogen, Pseudomonas syringae (Ps), together with related Ps species, infects and attacks a wide range of agronomically important crops, including tomato, kiwifruit, pepper, olive and soybean, causing economic losses. Currently, chemicals and introduced resistance genes are used to protect plants against these pathogens but have limited success and may have adverse environmental impacts. Consequently, there is a pressing need to develop alternative strategies to combat bacterial disease in crops. One such strategy involves using narrow-spectrum protein antibiotics (so-called bacteriocins), which diverse bacteria use to compete against closely related species. Here, we demonstrate that one bacteriocin, putidacin L1 (PL1), can be expressed in an active form at high levels in Arabidopsis and in Nicotiana benthamiana in planta to provide effective resistance against diverse pathovars of Ps. Furthermore, we find that Ps strains that mutate to acquire tolerance to PL1 lose their O-antigen, exhibit reduced motility and still cannot induce disease symptoms in PL1-transgenic Arabidopsis. Our results provide proof-of-principle that the transgene-mediated expression of a bacteriocin in planta can provide effective disease resistance to bacterial pathogens. Thus, the expression of bacteriocins in crops might offer an effective strategy for managing bacterial disease, in the same way that the genetic modification of crops to express insecticidal proteins has proven to be an extremely successful strategy for pest management. Crucially, nearly all genera of bacteria, including many plant pathogenic species, produce bacteriocins, providing an extensive source of these antimicrobial agents.

Quantitative proteomic analysis reveals the influence of plantaricin BM-1 on metabolic pathways and peptidoglycan synthesis in Escherichia coli K12

Plantaricin BM-1 is a class IIa bacteriocin with a strong bactericidal effect on gram-positive bacteria. Although plantaricin BM-1 also inhibits the growth of some gram-negative bacteria, including Escherichia coli, the mechanism is not clear. In this study, we used tandem mass tag-based quantitative proteomics analysis to examine the inhibitory mechanism of plantaricin BM-1 against E. coli K12, and evaluated the morphological effects by electron microscopy. The results demonstrated that plantaricin BM-1 inhibits the growth of E. coli K12 by bacteriostatic action, mainly acting on the surface of the cell wall, leading to its collapse. Proteomic analysis identified 976 differentially expressed proteins (>1.2-fold change, p < 0.05) under treatment with plantaricin BM-1, including 490 up-regulated proteins and 486 down-regulated proteins. These proteins were mainly involved in peptidoglycan synthesis and energy metabolism pathways, including amino acid, glyoxylate and dicarboxylate, ABC transporter, and quorum-sensing pathways. Specifically, plantaricin BM-1 treatment significantly improved peptidoglycan synthesis and enhanced the tricarboxylic acid cycle in E. coli K12, and altered the expression of cell membrane proteins. These results provide new insight into the inhibition mechanism of class IIa bacteriocins on gram-negative bacteria, which can lay the foundation for its broader use as an alternative to conventional antibiotics.

Changes in Bacterial Populations and Their Metabolism over 90 Sequential Cultures on Wheat-Based Thin Stillage

Wheat-based thin stillage (W-TS) is a liquid co-product of wheat fermentation for ethanol production, which typically contains substantial amounts of glycerol. Two-stage fermentation, via endemic microorganisms, can be used in processes to convert this compound to more valuable products and simplify the enrichment process through the clarification of the medium and concentration of particles as a protein-rich concentrate. We recultured bacteria 90 times (72 h at 37 °C) on fresh W-TS to determine the stability of the culture and metabolic processes. Next-generation sequencing of W-TS revealed the presence of a predominant Lactobacillus community that rapidly displaced competing microorganisms (e.g., Pediococcus) in subsequent fermentations. These organisms produced bacteriocins (e.g., helveticin J, interpreted through the presence of bacteriocin genes) and acidified the fermentation broth (through the production of succinic acid: 1.7 g/L, lactic acid: 1.8 g/L, and acetic acid: 4.1 g/L). Furthermore, the microbial community produced cobalamin (inferred through sequencing) and converted glycerol (10 g/L reduced to 3.5 g/L after 72 h) to 1,3-propanediol (6.1 g/L after 72 h). Altogether, Lactobacilli were identified as the predominant endemic microorganisms in W-TS after the first 10 cultures. The community was stable and provided a novel approach to increase the value of organic solutes in W-TS.

Intrapopulation Antagonism Can Reduce the Growth and Aggressiveness of the Wheat Head Blight Pathogen Fusarium graminearum

Fusarium graminearum is a causal agent of Fusarium head blight (FHB), a disease that reduces yield and quality of cereal crops and contaminates grain with mycotoxins that pose health risks to humans and livestock. Interpopulation antagonistic interactions between isolates that produce different trichothecene mycotoxins can reduce FHB in wheat, but it is not known if interactions between isolates with a shared population identity that produce the same trichothecenes have a similar effect. Using isolates from the predominant F. graminearum populations in North America (NA1 and NA2), we examined intrapopulation interactions by comparing growth, disease progression, and toxin production of individual isolates with multi-isolate mixes. In vitro, mycelial growth was significantly greater when most NA1 and NA2 isolates were cultured individually versus when cultured as a mixture of isolates from the same population. In susceptible wheat Norm, FHB generally progressed faster in heads inoculated with an individual isolate versus a multi-isolate mixture, but the antagonistic effect of intrapopulation interactions was more pronounced for NA1 than NA2 isolates. By contrast, in moderately resistant wheat Alsen, mixtures of isolates from either population caused obvious reductions in FHB development. Mycotoxin contamination was not consistently affected by intrapopulation interactions and varied depending on the interacting isolates from either population. Our results indicate that antagonistic intrapopulation interactions can influence FHB in controlled environmental conditions. Understanding if the regional composition of pathogen populations similarly influences FHB in the field could improve disease forecasting and management practices.

Dynamics of ColicinE2 production and release determine the competitive success of a toxin-producing bacterial population

The release of toxins is one mechanism used by bacterial species to establish dominance over competitors, but how the dynamics of toxin expression determine the competitive success of a toxin-producing population is largely unknown. Here, we investigate how the expression dynamics of ColicinE2 - a toxic bacteriocin - affect competition between toxin-producing and toxin-sensitive strains of Escherichia coli. We demonstrate that, in addition to genetic modifications in the toxin expression system, alterations of the growth medium can be used to modulate the timing of toxin production and the amount of toxin released. Thus cells that release the toxin at later times can accumulate more colicin. In experiments, we found that delaying toxin release does not significantly alter competition outcome. However, our theoretical analysis allowed us to assess the relative contributions of release time and toxin level to the competitive success of the producer strain, that might counteract each other in experiments. The results reveal that the importance of delaying toxin release lies in increasing the toxin amount. This is a more effective strategy for the toxin-producing strain than prompt discharge of the colicin. In summary, our study shows how the toxin release dynamics influence the competitive success of the toxin-producing bacterial population.

In vitro assessment of the bioactivities of sericin protein extracted from a bacterial silk-like biopolymer

Sericin is one of the main components of silk proteins, which has numerous biomedical applications because of its antioxidant, anticancer and antimicrobial properties. We recently isolated and characterized a novel silk-like protein named BNES. It is of non-animal origin and is like a bacterial polymeric silk. Sericin is a very popular protein compound that is effective in treating cancerous tumors. The process of extracting it from natural silk produced by silkworms or spiders is both complex and expensive. From the published scientific literature, it has been shown that sericin has not been previously extracted from a bacterial source. In the present study, sericin was extracted from bacteria capable of producing a biopolymer named BNES whose chemical composition is like that of natural silk and its bio-therapeutic effects were evaluated for the first time. The antioxidant activity of BNES measured by DPPH and ABTS assays showed IC50 values of 0.38 and 0.41 mg mL-1, respectively. BNES displayed satisfactory cytotoxic effect against four cancer cell lines, including Huh-7, Caco-2, MCF-7 and A549 cells, with IC50 values in the ranges of ca. 0.62 ± 0.17, 0.72 ± 0.27, 0.76 ± 0.36 and 0.83 ± 0.31 mg mL-1, respectively, after 24 h of treatment and 0.51 ± 0.22, 0.49 ± 0.19, 0.41 ± 0.25 and 0.55 ± 0.38, respectively, after 48 h of treatment, without affecting normal cells (WI38 cells). The antitumor activity of BNES was established to be an apoptosis-dependent mechanism determined via cellular morphology alterations, cell cycle arrest in the sub-G1 phase and nuclear staining with highly fluorescent fragments. The antimicrobial effects of BNES were examined with yeast and Gram-negative and Gram-positive bacteria. The results confirmed its antimicrobial activity against all tested organisms at concentrations of up to 1.33 mg mL-1. The competitive advantage of the bacterial sericin BNES over sericin extracted from spider or silkworm sources is that it can be produced in very large quantities through large-scale bio-fermenters, which reduces the expected cost of production, in addition to having sustainable bacterial production source.

Gene expression noise in a complex artificial toxin expression system

Gene expression is an intrinsically stochastic process. Fluctuations in transcription and translation lead to cell-to-cell variations in mRNA and protein levels affecting cellular function and cell fate. Here, using fluorescence time-lapse microscopy, we quantify noise dynamics in an artificial operon in Escherichia coli, which is based on the native operon of ColicinE2, a toxin. In the natural system, toxin expression is controlled by a complex regulatory network; upon induction of the bacterial SOS response, ColicinE2 is produced (cea gene) and released (cel gene) by cell lysis. Using this ColicinE2-based operon, we demonstrate that upon induction of the SOS response noise of cells expressing the operon is significantly lower for the (mainly) transcriptionally regulated gene cea compared to the additionally post-transcriptionally regulated gene cel. Likewise, we find that mutations affecting the transcriptional regulation by the repressor LexA do not significantly alter the population noise, whereas specific mutations to post-transcriptionally regulating units, strongly influence noise levels of both genes. Furthermore, our data indicate that global factors, such as the plasmid copy number of the operon encoding plasmid, affect gene expression noise of the entire operon. Taken together, our results provide insights on how noise in a native toxin-producing operon is controlled and underline the importance of post-transcriptional regulation for noise control in this system.

Preparation of phosphatidylcholine nanovesicles containing bacteriocin CAMT2 and their anti-listerial activity

A novel bacteriocin CAMT2, produced by Bacillus amyloliquefaciens ZJHD3-06, has potential as a natural biopreservative for the control of food-borne spoilage and pathogenic bacteria. To avoid interaction of CAMT2 with components of food that may adversely impact its antibacterial activity, CAMT2 was encapsulated into nanovesicles prepared from soybean phosphatidylcholine. The encapsulation of CAMT2 exhibited a limited impact on functional structure and crystallinity of bacteriocin CAMT2, but a high anti-listerial activity in agar, and increase its stability in food at refrigeration temperature (4 °C). The results also showed that both encapsulated and free CAMT2 had good anti-listerial effect in skim milk at refrigeration temperature. However, encapsulated CAMT2 performed better than free CAMT2 against Listeria in whole milk. These results showed that nano-encapsulation is an effective method of protecting bacteriocin from fat in milk and retaining its antimicrobial efficacy.

A PGPR-Produced Bacteriocin for Sustainable Agriculture: A Review of Thuricin 17 Characteristics and Applications

A wide range of prokaryotes produce and excrete bacteriocins (proteins with antimicrobial activity) to reduce competition from closely related strains. Application of bacteriocins is of great importance in food industries, while little research has been focused on the agricultural potential of bacteriocins. A number of bacteriocin producing bacteria are members of the phytomicrobiome, and some strains are plant growth promoting rhizobacteria (PGPR). Thuricin 17 is a single small peptide with a molecular weight of 3.162 kDa, a subclass IId bacteriocin produced by Bacillus thuringiensis NEB17, isolated from soybean nodules. It is either cidal or static to a wide range of prokaryotes. In this way, it removes key competition from the niche space of the producer organism. B. thuringiensis NEB17 was isolated from soybean root nodules, and thus is a member of the phytomicrobiome. Interestingly, thuricin 17 is not active against a wide range of rhizobial strains involved in symbiotic nitrogen fixation with legumes or against other PGPR. In addition, it stimulates plant growth, particularly in the presence of abiotic stresses. The stresses it assists with include key ones associated with climate change (drought, high temperature, and soil salinity). Hence, in the presence of stress, it increases the size of the overall niche space, within plant roots, for B. thuringiensis NEB17. Through its anti-microbial activity, it could also enhance plant growth via control of specific plant pathogens. None of the isolated bacteriocins have been examined as broadly as thuricin 17 on plant growth promotion. Thus, this review focuses on the effect of thuricin 17 as a microbe to plant signal that assists crop plants in managing stress and making agricultural systems more climate change resilient.

Steering eco-evolutionary game dynamics with manifold control

Feedback loops between population dynamics of individuals and their ecological environment are ubiquitously found in nature and have shown profound effects on the resulting eco-evolutionary dynamics. By incorporating linear environmental feedback law into the replicator dynamics of two-player games, recent theoretical studies have shed light on understanding the oscillating dynamics of the social dilemma. However, the detailed effects of more general nonlinear feedback loops in multi-player games, which are more common especially in microbial systems, remain unclear. Here, we focus on ecological public goods games with environmental feedbacks driven by a nonlinear selection gradient. Unlike previous models, multiple segments of stable and unstable equilibrium manifolds can emerge from the population dynamical systems. We find that a larger relative asymmetrical feedback speed for group interactions centred on cooperators not only accelerates the convergence of stable manifolds but also increases the attraction basin of these stable manifolds. Furthermore, our work offers an innovative manifold control approach: by designing appropriate switching control laws, we are able to steer the eco-evolutionary dynamics to any desired population state. Our mathematical framework is an important generalization and complement to coevolutionary game dynamics, and also fills the theoretical gap in guiding the widespread problem of population state control in microbial experiments.

The importance of antimicrobial compounds produced by beneficial bacteria on the biocontrol of phytopathogens

Bacteria produce antimicrobial compounds to compete for nutrients and space in a particular habitat. Antagonistic interactions can be evaluated by several methodologies including the double-layer agar and simultaneous inhibition assays. Among the well-known inhibitory substances produced by bacteria are the broad-spectrum antibiotics, organic acids, siderophores, antifungal, and bacteriocins. The most studied bacterial genera able to produce these inhibitory substances are Enterococcus, Lactococcus, Streptomyces, Bacillus, Pseudomonas, Klebsiella, Escherichia, and Burkholderia. Some beneficial bacteria can promote plant growth and degrade toxic compounds in the environment representing an attractive solution to diverse issues in agriculture and soil pollution, particularly in fields with damaged soils where pesticides and fertilizers have been indiscriminately used. Beneficial bacteria may increase plant health by inhibiting pathogenic microorganisms; some examples include Gluconacetobacter diazotrophicus, Azospirullum brasilense, Pseudomonas fluorescens, Pseudomonas protegens, and Burkholderia tropica. However, most studies showing the antagonistic potential of these bacteria have been performed in vitro, and just a few of them have been evaluated in association with plants. Several inhibitory substances involved in pathogen antagonism have not been elucidated yet; in fact, we know only 1 % of the bacterial diversity in a natural environment leading us to assume that many other inhibitory substances remain unexplored. In this review, we will describe the characteristics of some antimicrobial compounds produced by beneficial bacteria, the principal methodologies performed to evaluate their production, modes of action, and their importance for biotechnological purposes.

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.

100 Years Since Tolaas: Bacterial Blotch of Mushrooms in the 21st Century

Among the biotic constraints of common mushroom (Agaricus bisporus) production, bacterial blotch is considered the most important mushroom disease in terms of global prevalence and economic impact. Etiology and management of bacterial blotch has been a major concern since its original description in 1915. Although Pseudomonas tolaasii is thought to be the main causal agent, various Pseudomonas species, as well as organisms from other genera have been reported to cause blotch symptoms on mushroom caps. In this review, we provide an updated overview on the etiology, epidemiology, and management strategies of bacterial blotch disease. First, diversity of the causal agent(s) and utility of high throughput sequencing-based approaches in the precise characterization and identification of blotch pathogen(s) is explained. Further, due to the limited options for use of conventional pesticides in mushroom farms against blotch pathogen(s), we highlight the role of balanced threshold of relative humidity and temperature in mushroom farms to combat the disease in organic and conventional production. Additionally, we discuss the possibility of the use of biological control agents (either antagonistic mushroom-associated bacterial strains or bacteriophages) for blotch management as one of the sustainable approaches for 21^st century agriculture. Finally, we aim to elucidate the association of mushroom microbiome in cap development and productivity on one hand, and blotch incidence/outbreaks on the other hand.

Identification and characterisation of capidermicin, a novel bacteriocin produced by Staphylococcus capitis

One hundred human-derived coagulase negative staphylococci (CoNS) were screened for antimicrobial activity using agar-based deferred antagonism assays with a range of indicator bacteria. Based on the findings of the screen and subsequent well assays with cell free supernatants and whole cell extracts, one strain, designated CIT060, was selected for further investigation. It was identified as Staphylococcus capitis and herein we describe the purification and characterisation of the novel bacteriocin that the strain produces. This bacteriocin which we have named capidermicin was extracted from the cell-free supernatant of S. capitis CIT060 and purified to homogeneity using reversed-phase high performance liquid chromatography (RP-HPLC). Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometric (MS) analysis revealed that the capidermicin peptide has a mass of 5,464 Da. Minimal inhibitory concentration (MIC) experiments showed that capidermicin was active in the micro-molar range against all the Gram-positive bacteria that were tested. Antimicrobial activity was retained over a range of pHs (2–11) and temperatures (10–121°C x 15 mins). The draft genome sequence of S. capitis CIT060 was determined and the genes predicted to be involved in the biosynthesis of capidermicin were identified. These genes included the predicted capidermicin precursor gene, and genes that are predicted to encode a membrane transporter, an immunity protein and a transcriptional regulator. Homology searches suggest that capidermicin is a novel member of the family of class II leaderless bacteriocins.

Amphibian skin-associated Pigmentiphaga: Genome sequence and occurrence across geography and hosts

The bacterial communities colonizing amphibian skin have been intensively studied due to their interactions with pathogenic chytrid fungi that are causing drastic amphibian population declines. Bacteria of the family Alcaligenaceae, and more specifically of the genus Pigmentiphaga, have been found to be associated specifically to arboreal frogs. Here we analyze their occurrence in a previously assembled global skin microbiome dataset from 205 amphibian species. Pigmentiphaga made up about 5% of the total number of reads in this global dataset. They were mostly found in unrelated arboreal frogs from Madagascar (Mantellidae and Hyperoliidae), but also occurred at low abundances on Neotropical frogs. Based on their 16S sequences, most of the sequences belong to a clade within Pigmentiphaga not assignable to any type strains of the five described species of the genus. One isolate from Madagascar clustered with Pigmentiphaga aceris (>99% sequence similarity on 16S rRNA gene level). Here, we report the full genome sequence of this bacterium which, based on 16S sequences of >97% similarity, has previously been found on human skin, floral nectar, tree sap, stream sediment and soil. Its genome consists of a single circular chromosome with 6,165,255 bp, 5,300 predicted coding sequences, 57 tRNA genes, and three rRNA operons. In comparison with other known Pigmentiphaga genomes it encodes a higher number of genes associated with environmental information processing and cellular processes. Furthermore, it has a biosynthetic gene cluster for a nonribosomal peptide syntethase, and bacteriocin biosynthetic genes can be found, but clusters for β-lactones present in other comparative Pigmentiphaga genomes are lacking.

Crude extracts of metabolites from co-cultures of lactic acid bacteria are highly antagonists of Listeria monocytogenes

Listeria monocytogenes is a pathogen difficult to control, due to its resistance to extreme conditions. The antimicrobial activity of a mixture of metabolites produced by lactic acid bacteria was evaluated against L. monocytogenes. Bacterial combined cultures in 1:1 ratio of Lactobacillus plantarum and Weissella cibaria (treatment LP + WC) and mixtures in ratio 1:1:1 of Lactobacillus brevis, L. plantarum, and W. cibaria, (treatment (LB + LP + WC) were grown by discontinuous fermentation, at 32 °C for 48 h. At 1, 2, 6, 12, 24 and 48 h of fermentation, samples were taken, the biomass was separated from the metabolites, and the antimicrobial activity of the metabolites was measured in vitro against L. monocytogenes. For comparison, experimental data published in the literature corresponding to monocultures of L. brevis (L.B), L. plantarum (LP) and W. cibaria (WC) were used. The antimicrobial activity was measured by a surface diffusion technique using absorbent paper discs impregnated with 60 μl from each metabolite and placed on the TSA agar surface (36 °C, 24 h). The metabolites from the microbial mixtures showed statistical differences with respect to their respective monocultures. With the treatment (LP + WC) an inhibition diameter of 2.54 cm was obtained at 12 h of fermentation, this value was higher than those obtained in the monoculture LP (2.19 cm), and WC (2.44 cm), during the same period. In the mixture (LB + LP + WC) during the first 12 h of fermentation, the antimicrobial activity was higher (2.12–2.28 cm) than the antimicrobial activity of the monoculture LB (1.66–2.23 cm). The use of metabolites from the co-culture of L brevis, L. plantarum and W. cibaria under the evaluated conditions, potentiate the antimicrobial activity of L. brevis against L. monocytogenes, therefore, they are promising in bio-preservation.

PARAGEN 1.0: A Standardized Synthetic Gene Library for Fast Cell-Free Bacteriocin Synthesis

The continuous emergence of microbial resistance to our antibiotic arsenal is widely becoming recognized as an imminent threat to global human health. Bacteriocins are antimicrobial peptides currently under consideration as real alternatives or complements to common antibiotics. These peptides have been much studied, novel bacteriocins are regularly reported and several genomic databases on these peptides are currently updated. Despite this, to our knowledge, a physical collection of bacteriocins that would allow testing and comparing them for different applications does not exist. Rapid advances in synthetic biology in combination with cell-free protein synthesis technologies offer great potential for fast protein production. Based on the amino acid sequences of the mature peptide available in different databases, we have built a bacteriocin gene library, called PARAGEN 1.0, containing all the genetic elements required for in vitro cell-free peptide synthesis. Using PARAGEN 1.0 and a commercial kit for cell-free protein synthesis we have produced 164 different bacteriocins. Of the bacteriocins synthesized, 54% have shown antimicrobial activity against at least one of the indicator strains tested, including Gram-positive and Gram-negative bacteria representing commonly used lab strains, industrially relevant microorganisms, and known pathogens. This bacteriocin collection represents a streamlined pipeline for selection, production, and screening of bacteriocins as well as a reservoir of ready-to-use antimicrobials against virtually any class of relevant bacteria.

Unveiled feather microcosm: feather microbiota of passerine birds is closely associated with host species identity and bacteriocin-producing bacteria

The functional relevance of microbiota is a key aspect for understanding host-microbiota interactions. Mammalian skin harbours a complex consortium of beneficial microorganisms known to provide health and immune-boosting advantages. As yet, however, little is known about functional microbial communities on avian feathers, including their co-evolution with the host and factors determining feather microbiota (FM) diversity. Using 16S rRNA profiling, we investigated how host species identity, phylogeny and geographic origin determine FM in free-living passerine birds. Moreover, we estimated the relative abundance of bacteriocin-producing bacteria (BPB) and keratinolytic feather damaging bacteria (FDB) and evaluated the ability of BPB to affect FM diversity and relative abundance of FDB. Host species identity was associated with feather bacterial communities more strongly than host geographic origin. FM functional properties differed in terms of estimated BPB and FDB relative abundance, with both showing interspecific variation. FM diversity was negatively associated with BPB relative abundance across species, whereas BPB and FDB relative abundance was positively correlated. This study provides the first thorough evaluation of antimicrobial peptides-producing bacterial communities inhabiting the feather integument, including their likely potential to mediate niche-competition and to be associated with functional species-specific feather microbiota in avian hosts.

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.

Evolution of increased virulence is associated with decreased spite in the insect-pathogenic bacterium Xenorhabdus nematophila

Disease virulence may be strongly influenced by social interactions among pathogens, both during the time course of an infection and evolutionarily. Here, we examine how spiteful bacteriocin production in the insect-pathogenic bacterium Xenorhabdus nematophila is evolutionarily linked to its virulence. We expected a negative correlation between virulence and spite owing to their inverse correlations with growth. We examined bacteriocin production and growth across 14 experimentally evolved lineages that show faster host-killing relative to their ancestral population. Consistent with expectations, these more virulent lineages showed reduced bacteriocin production and faster growth relative to the ancestor. Further, bacteriocin production was negatively correlated with growth across the examined lineages. These results strongly support an evolutionary trade-off between virulence and bacteriocin production and lend credence to the view that disease management can be improved by exploiting pathogen social interactions.

Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges

Describing the role of plasmids and their contribution to the exchange of genetic material among bacteria is essential for understanding the fields of plasmid epidemiology, microbial ecology, and commercial and synthetic microbiology. Broad-host-range (BHR) plasmids are those that are found not only in a single bacterial species, but in members of different taxonomic groups and are of significant interest to researchers in many fields. We applied a novel approach to computationally identify new BHR plasmids, in which we searched for highly similar cognate plasmids within a comprehensive plasmid database. After identifying 125 plasmid groups with highly similar cognates found in multiple taxa, we closely examined BHR plasmids found in multiple families. The majority of our identified BHR plasmids are found in members of the Enterobacteriaceae and closely related taxa, while three BHR plasmids of potential commercial significance were found in two species of Cyanobacteria. One plasmid with an exceptionally broad host range was found in both Gram-positive and Gram-negative bacterial species. This analysis demonstrates the utility of this method in identifying new BHR plasmids while highlighting unknown ranges of previously documented plasmids.

The case for class II bacteriocins: A biophysical approach using "suicide probes" in receptor-free hosts to study their mechanism of action

Class II bacteriocins are unmodified membrane-active peptides that act over a narrow spectrum of target bacteria. They bind a specific receptor protein on the membrane to form a pore, leading to membrane permeabilization and cell death. However, little is known about the molecular events triggering the pore formation after the bacteriocin recognizes the receptor. It is not clear yet if the pore is the same receptor forced into an open conformation or if the pore results from the bacteriocin insertion and oligomeric assembly in the lipid bilayer. In order to reveal which model is more suitable to explain the toxicity mechanism, in this work we use chimeric peptides, resulting from the fusion of the bitopic membrane protein EtpM with different class II bacteriocins: enterocin CRL35, pediocin PA-1 and microcin V. E. coli strains lacking the specific receptors for these bacteriocins were chosen as expression hosts. As these constructs display a lethal effect when they are heterologously expressed, they are called "suicide probes". The results suggest that, indeed, the specific receptor would act as a docking molecule more than as a structural piece of the pore, as long as the bacteriocin is somehow anchored to the membrane. These set of chimeric peptides also represent an in vivo system that allows to study the interaction of the bacteriocins with real bacterial membranes, instead of model membranes. Hence, the effects of these suicide probes in membrane fluidity and transmembrane potential were also assessed, using fluorescence spectroscopy. The data show that the different suicide probes are able to increase phospholipid order and depolarize the membranes of receptor-free bacterial cells.

Colicin Z, a structurally and functionally novel colicin type that selectively kills enteroinvasive Escherichia coli and Shigella strains

Colicin production in Escherichia coli (E. coli) strains represents an important trait with regard to microbial survival and competition in the complex intestinal environment. A novel colicin type, colicin Z (26.3 kDa), was described as a product of an original producer, extraintestinal E. coli B1356 strain, isolated from the anorectal abscess of a 17 years-old man. The 4,007 bp plasmid (pColZ) was completely sequenced and colicin Z activity (cza) and colicin Z immunity (czi) genes were identified. The cza and czi genes are transcribed in opposite directions and encode for 237 and 151 amino acid-long proteins, respectively. Colicin Z shows a narrow inhibitory spectrum, being active only against enteroinvasive E. coli (EIEC) and Shigella strains via CjrC receptor recognition and CjrB- and ExbB-, ExbD-mediated colicin translocation. All tested EIEC and Shigella strains isolated between the years 1958–2010 were sensitive to colicin Z. The lethal effect of colicin Z was found to be directed against cell wall peptidoglycan (PG) resulting in PG degradation, as revealed by experiments with Remazol Brilliant Blue-stained purified peptidoglycans and with MALDI-TOF MS analyses of treated PG. Colicin Z represents a new class of colicins that is structurally and functionally distinct from previously studied colicin types.

Privatization of public goods can cause population decline

Microbes commonly deploy a risky strategy to acquire nutrients from their environment, involving the production of costly public goods that can be exploited by neighbouring individuals. Why engage in such a strategy when an exploitation-free alternative is readily available whereby public goods are kept private? We address this by examining metabolism of Saccharomyces cerevisiae in its native form and by creating a new three-strain synthetic community deploying different strategies of sucrose metabolism. Public-metabolizers digest resources externally, private-metabolizers internalize resources before digestion, and cheats avoid the metabolic costs of digestion but exploit external products generated by competitors. A combination of mathematical modelling and ecological experiments reveal that private-metabolizers invade and take over an otherwise stable community of public-metabolizers and cheats. However, owing to the reduced growth rate of private-metabolizers and population bottlenecks that are frequently associated with microbial communities, privatizing public goods can become unsustainable, leading to population decline.

Identifying antimicrobial peptides using word embedding with deep recurrent neural networks

MOTIVATION

Antibiotic resistance constitutes a major public health crisis, and finding new sources of antimicrobial drugs is crucial to solving it. Bacteriocins, which are bacterially produced antimicrobial peptide products, are candidates for broadening the available choices of antimicrobials. However, the discovery of new bacteriocins by genomic mining is hampered by their sequences' low complexity and high variance, which frustrates sequence similarity-based searches.

RESULTS

Here we use word embeddings of protein sequences to represent bacteriocins, and apply a word embedding method that accounts for amino acid order in protein sequences, to predict novel bacteriocins from protein sequences without using sequence similarity. Our method predicts, with a high probability, six yet unknown putative bacteriocins in Lactobacillus. Generalized, the representation of sequences with word embeddings preserving sequence order information can be applied to peptide and protein classification problems for which sequence similarity cannot be used.

AVAILABILITY AND IMPLEMENTATION

Data and source code for this project are freely available at: https://github.com/nafizh/NeuBI.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A microcin processing peptidase-like protein of the cyanobacterium Synechococcus elongatus is essential for secretion of biofilm-promoting proteins

Small secreted compounds, e.g. microcins, are characterized by a double-glycine (GG) secretion motif that is cleaved off upon maturation. Genomic analysis suggests that small proteins that possess a GG motif are widespread in cyanobacteria; however, the roles of these proteins are largely unknown. Using a biofilm-proficient mutant of the cyanobacterium Synechococcus elongatus PCC 7942 in which the constitutive biofilm self-suppression mechanism is inactivated, we previously demonstrated that four small proteins, Enable biofilm formation with a GG motif (EbfG1-4), each with a GG motif, enable biofilm formation. Furthermore, a peptidase belonging to the C39 family, Peptidase transporter enabling Biofilm (PteB), is required for secretion of these proteins. Here, we show that the microcin processing peptidase-like protein encoded by gene Synpcc7942_1127 is also required for biofilm development - inactivation of this gene in the biofilm-proficient mutant abrogates biofilm development. Additionally, this peptidase-like protein (denoted EbfE - enables biofilm formation peptidase) is required for secretion of the EbfG biofilm-promoting small proteins. Given their protein-domain characteristics, we suggest that PteB and EbfE take part in a maturation-secretion system, with PteB being located to the cell membrane while EbfE is directed to the periplasmic space via its secretion signal.

Partial Characterization of Novel Bacteriocin SF1 Produced by Shigella flexneri and Their Lethal Activity on Members of Gut Microbiota

A strain of Shigella flexneri producing bacteriocin was isolated from a patient with diarrhea. The main objective of this study was to isolate and partially characterize the bacteriocin. The producing microorganism was identified using biochemical, serological, and molecular methods. The lethal activity of the S. flexneri strain was studied using the drop method. This bacterial strain showed activity against different strains of E. coli and B. fragilis. Using immunological techniques, it was determined that S. flexneri belongs to serotype 2a, and by PCR, the presence of the ipaH plasmid was determined. By chromatographic techniques, it was determined that the bacteriocin is a peptide of high purity with a molecular weight of 66294.094 Da. The amino acid composition and sequence were determined by the Edman reaction, and a sequence of 619 amino acid residues was obtained. Only in five positions of this sequence, the amino acid glutamine changed to glutamic acid with respect to colicin U produced by S. boydii. From an ecological point of view, it could be assumed that SF1 bacteriocin contributes to eliminate some members of the normal microbiota of the human intestine, facilitating colonization and then producing the invasion process that characterizes the pathogenicity of Shigella.

Biological properties and production of bacteriocins-like-inhibitory substances by Lactobacillus sp. strains from human vagina

AIMS

The aim of this study was to characterize Lactobacillus strains for their biological properties and amensalistic activities against genital and nongenital pathogens.

METHODS AND RESULTS

For the purpose, some special characteristics (H2 O2 , biofilm and antimicrobial substances production) as well as safety properties of 112 lactobacilli were evaluated. All the strains had good amensalistic characteristics, in particular cell-free supernatants of 10 strains showed antibacterial activity against bacteria, as well as Candida sp. Moreover, these 10 strains were excellent biofilm producers.

CONCLUSIONS

These results provide evidence for the possible use as probiotics for vaginal co-therapy in case of dysbiosis.

SIGNIFICANCE AND IMPACT OF THE STUDY

Recently, the problem of antibiotic resistance is constantly increasing, even though resources and energy are invested in order to increase knowledge on the mechanisms of action. Bacteriocins have a rapid mechanism of action, act at extremely low concentrations, are generally sensitive to proteases and they usually have a narrow killing spectrum; these characteristics reduce the possibility of the bacterium to develop resistance. This study is focused on the feasibility of a high production of antimicrobial substances and their characterization in order to be exploited as a therapeutic alterative or in co-therapy with antibiotics in case of vaginal dysbiosis.

Virulence Plasmids of the Pathogenic Clostridia

The clostridia cause a spectrum of diseases in humans and animals ranging from life-threatening tetanus and botulism, uterine infections, histotoxic infections and enteric diseases, including antibiotic-associated diarrhea, and food poisoning. The symptoms of all these diseases are the result of potent protein toxins produced by these organisms. These toxins are diverse, ranging from a multitude of pore-forming toxins to phospholipases, metalloproteases, ADP-ribosyltransferases and large glycosyltransferases. The location of the toxin genes is the unifying theme of this review because with one or two exceptions they are all located on plasmids or on bacteriophage that replicate using a plasmid-like intermediate. Some of these plasmids are distantly related whilst others share little or no similarity. Many of these toxin plasmids have been shown to be conjugative. The mobile nature of these toxin genes gives a ready explanation of how clostridial toxin genes have been so widely disseminated both within the clostridial genera as well as in the wider bacterial community.

Antimicrobial activity of nest-lining feathers is enhanced by breeding activity in avian nests

The use of feathers as nest material has been proposed as a kind of self-medication strategy because antimicrobial-producing microorganisms living on feathers may defend offspring against pathogenic infections. In this case, it is expected that density of antimicrobial-producing bacteria, and their antimicrobial effects, are higher in feathers that line the nests than in eggshells. Moreover, we know that feather pigmentation and breeding activity may influence density and antimicrobial production of bacteria. To test these predictions, we analyzed bacterial densities and antimicrobial activity of bacterial colonies isolated from bird eggshells and nest-lining feathers against bacterial strains comprising potential pathogens. Samples were collected from spotless starling (Sturnus unicolor) nests, and from artificial nests to isolate the effects of breeding activity on bacterial communities. The composition of feathers lining the nests was experimentally manipulated to create groups of nests with pigmented feathers, with unpigmented feathers, with both types of feathers or without feathers. Although we did not detect an effect of experimental feather treatments, we found that bacterial colonies isolated from feathers were more active against the tested bacterial strains than those isolated from eggshells. Moreover, bacterial density on feathers, keratinolytic bacteria on eggshells and antimicrobial activity of colonies isolated were higher in starling nests than in artificial nests. These results suggest that antimicrobial activity of bacteria growing on nest-lining feathers would be one of the mechanisms explaining the previously detected antimicrobial effects of this material in avian nests, and that breeding activity results in nest bacterial communities with higher antimicrobial activity.

Nosocomial bloodstream infection and the emerging carbapenem-resistant pathogen Ralstonia insidiosa

Background

Ralstonia picketti, Ralstonia mannitolilytica, and Ralstonia insidiosa have recently been regarded as emerging pathogens of infectious diseases, in particular as the pathogens responsible for nosocomial infection in immunocompromised patients. R. insidiosa differs from R. picketti and R. mannitolilytica, and its related infections are rarely reported.

Methods

Clinical data from two nosocomial bloodstream infection cases were extracted and analyzed. The causable isolates were identified by the VITEK 2 Compact system, matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and molecular identification methods using PCR with universal and species-specific primers. Antimicrobial susceptibility testing was performed using the broth microdilution method. Both of the isolates were subjected to whole genome sequencing using a HiSeq X10 Sequencer. Antimicrobial resistance genes, virulence factors, and plasmid replicons were identified from assembled genomes. A real-time RT-PCR experiment and a cloning experiment were conducted to explore the related class D β-lactamase-encoding genes.

Results

Both patients recovered under therapy with antibiotics. Isolates were initially misidentified as R. mannitolilytica by the VITEK 2 Compact system rather than R. insidiosa, as identified by both MALDI-TOF MS and 16S rRNA gene sequencing. Both isolates were resistant to aminoglycosides, β-lactams, and polymyxin B. One isolate harboring bla_OXA-570 was resistant to carbapenems. The whole genome sequencing data confirmed species identification based on average nucleotide identity (ANI) and revealed two variants of class D β-lactamase-encoding gene bla_OXA (bla_OXA-573 and bla_OXA-574). The real-time RT-PCR experiment showed no difference in gene expression between bla_OXA-570 and bla_OXA-573 in our strains. The cloning experiment showed that variant OXA-573 had no carbapenem hydrolase activity.

Conclusions

We described two cases of nosocomial bloodstream infection caused by R. insidiosa strains. MALDI-TOF MS was cost-effective for rapid species identification. Clinicians should be aware that R. insidiosa can be resistant to commonly used antibiotics, even carbapenems.

Muscle characteristics in chicks challenged with Salmonella Enteritidis and the effect of preventive application of the probiotic Enterococcus faecium

The present study was conducted to assess the effects of the probiotic Enterococcus faecium AL41 (EF) and of the enteric pathogen Salmonella Enteritidis PT4 (SE) on the development of posthatch pectoralis major muscle (PM) of broiler chicks. The four experimental groups were control (CON), EF, SE, and EF+SE (EFSE). EF and SE were given per os from days 1 to 7 and at day 4 posthatch, respectively. Muscle samples from 6 chicks per group were taken at day 8 (D8) and day 11 (D11) to evaluate PM myofiber growth, capillarization, DNA, RNA, and protein content, as well as enzyme activities (isocitrate dehydrogenase, lactate dehydrogenase, creatine kinase). PM growth rate was 7.45 ± 2.7 g/d in non-SE groups (CON, EF) and 5.10 ± 1.82 g/d in SE-infected groups (P < 0.02). Compared with group CON, application of bacteria (groups EF and SE) reduced the fiber cross-sectional area (246 and 262 vs. 347 ± 19 μm2) and the number of myonuclei per fiber (0.66 and 0.64 vs. 0.79 ± 0.03). At D11, hypertrophic myofiber growth normalized in the EF group, but negative effects persisted in SE and EFSE birds contributing to lower daily PM gain. In addition, SE infection strongly disturbed PM capillarization. Negative effects on capillary cross-sectional area and on the area (%) covered by capillaries persisted until D11 in the SE group, whereas pre-feeding of EF restored capillarization in the EFSE group to control levels. We conclude that supplementation of the probiotic bacteria EF AL41 had positive effects on PM capillarization and, thus, on delivery of O2, supply of nutrients, and removal of metabolites. Supplementation of probiotic bacteria might therefore reduce energetic stress and improve muscle health and meat quality during SE infection.

Coexistence and Pattern Formation in Bacterial Mixtures with Contact-Dependent Killing

Multistrain microbial communities often exhibit complex spatial organization that emerges because of the interplay of various cooperative and competitive interaction mechanisms. One strong competitive mechanism is contact-dependent neighbor killing enabled by the type VI secretion system. It has been previously shown that contact-dependent killing can result in bistability of bacterial mixtures so that only one strain survives and displaces the other. However, it remains unclear whether stable coexistence is possible in such mixtures. Using a population dynamics model for two interacting bacterial strains, we found that coexistence can be made possible by the interplay of contact-dependent killing and long-range growth inhibition, leading to the formation of various cellular patterns. These patterns emerge in a much broader parameter range than that required for the linear Turing-like instability, suggesting this may be a robust mechanism for pattern formation.

Characterization of Subtilin L-Q11, a Novel Class I Bacteriocin Synthesized by Bacillus subtilis L-Q11 Isolated From Orchard Soil

Bacteriocins are peptides or proteins synthesized by bacterial ribosomes that show killing or inhibitory activities against different groups of bacteria. Bacteriocins are considered potential alternatives to traditional antibiotics, preservatives in pharmaceutical and food industries. A strain L-Q11 isolated from orchard soil was phylogenetically characterized as Bacillus subtilis based on 16S rRNA gene sequencing analysis. A novel class I bacteriocin (Subtilin L-Q11), was identified and purified from L-Q11 cell-free supernatant in a four-step procedure, including salt precipitation, cation exchange, gel filtration, and reverse-phase high-performance liquid chromatography (RP-HPLC). The molecular mass (3,552.9 Da) of this novel bacteriocin was determined by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The purified Subtilin L-Q11 exhibited optimal features in pH tolerance, thermostability, and sensitivity to proteases. Further, Subtilin L-Q11 showed inhibitory activities against a number of bacteria including some human pathogens and food spoilage bacteria, in particular Staphylococcus aureus. All these important features make this novel bacteriocin a potential candidate for the development of a new antibacterial drug or food preservative in the future.

Overview of the Antimicrobial Compounds Produced by Members of the Bacillus subtilis Group

Over the last seven decades, applications using members of the Bacillus subtilis group have emerged in both food processes and crop protection industries. Their ability to form survival endospores and the plethora of antimicrobial compounds they produce has generated an increased industrial interest as food preservatives, therapeutic agents and biopesticides. In the growing context of food biopreservation and biological crop protection, this review suggests a comprehensive way to visualize the antimicrobial spectrum described within the B. subtilis group, including volatile compounds. This classification distinguishes the bioactive metabolites based on their biosynthetic pathways and chemical nature: i.e., ribosomal peptides (RPs), volatile compounds, polyketides (PKs), non-ribosomal peptides (NRPs), and hybrids between PKs and NRPs. For each clade, the chemical structure, biosynthesis and antimicrobial activity are described and exemplified. This review aims at constituting a convenient and updated classification of antimicrobial metabolites from the B. subtilis group, whose complex phylogeny is prone to further development.

Social evolution under demographic stochasticity

How social traits such as altruism and spite evolve remains an open question in evolutionary biology. One factor thought to be potentially important is demographic stochasticity. Here we provide a general theoretical analysis of the role of demographic stochasticity in social evolution. We show that the evolutionary impact of stochasticity depends on how the social action alters the recipient’s life cycle. If the action alters the recipient’s death rate, then demographic stochasticity always favours altruism and disfavours spite. On the other hand, if the action alters the recipient’s birth rate, then stochasticity can either favour or disfavour both altruism and spite depending on the ratio of the rate of population turnover to the population size. Finally, we also show that this ratio is critical to determining if demographic stochasticity can reverse the direction of selection upon social traits. Our analysis thus provides a general understanding of the role of demographic stochasticity in social evolution.

Explaining the evolution of social traits such as altruism and spite remains a key outstanding problem in evolutionary biology. Here we develop a simple theory for the effect of demographic stochasticity (random variation in an individual’s birth and death rates) on the evolution of social traits. Our results provide a clear set of predictions: whether a social trait is favoured or disfavoured is determined by how the social action alters the recipient’s life cycle. If the social action alters the recipient’s death rate, then altruism is favoured and spite disfavoured. If instead the social action alters the recipient’s birth rate, then both altruism and spite can be either favoured or disfavoured—the precise outcome depends upon the ratio of the population turnover rate to the population size.

Effects and immune responses of probiotic treatment in ruminants

Gut microbial colonization and establishment are vital to ruminant health and production. This review article focuses on current knowledge and methods used to understand and manipulate the gut microbial community in ruminant animals, with a special focus on probiotics treatment. This review highlights the most promising of studies in this area, including gut microbial colonization and establishment, effect of gastrointestinal tract microbial community on host mucosal innate immune function, impact of feeding strategies on gut microbial community, current probiotic treatments in ruminants, methods to manipulate the gut microbiota and associated antimicrobial compounds, and models and cell lines used in understanding the host immune response to probiotic treatments. As a lot of work in this area was done in humans and mice, this review article also includes up-to-date knowledge from relevant studies in human and mouse models. This review is a useful resource for scientists working in the areas of ruminant nutrition and health, and to researchers investigating the microbial ecology and its relation to animal health.

Localized recombination drives diversification of killing spectra for phage-derived syringacins

To better understand the potential for antagonistic interactions between members of the same bacterial species, we have surveyed bacteriocin killing activity across a diverse suite of strains of the phytopathogen Pseudomonas syringae. Our data demonstrate that killing activity from phage-derived bacteriocins of P. syringae (R-type syringacins) is widespread. Despite a high overall diversity of bacteriocin activity, strains can broadly be classified into five main killing types and two main sensitivity types. Furthermore, we show that killing activity switches frequently between strains and that switches correlate with localized recombination of two genes that together encode the proteins that specify bacteriocin targeting. Lastly, we demonstrate that phage-derived bacteriocin killing activity can be swapped between strains simply through expression of these two genes in trans. Overall, our study characterizes extensive diversity of killing activity for phage-derived bacteriocins of P. syringae across strains and highlights the power of localized recombination to alter phenotypes that mediate strain interactions during evolution of natural populations and communities.

Pseudomonas bacteriocin syringacin M released upon desiccation suppresses the growth of sensitive bacteria in plant necrotic lesions

Bacteriocins are regarded as important factors mediating microbial interactions, but their exact role in community ecology largely remains to be elucidated. Here, we report the characterization of a mutant strain, derived from Pseudomonas syringae pv. tomato DC3000 (Pst), that was incapable of growing in plant extracts and causing disease. Results showed that deficiency in a previously unannotated gene saxE led to the sensitivity of the mutant to Ca²⁺ in leaf extracts. Transposon insertions in the bacteriocin gene syrM, adjacent to saxE, fully rescued the bacterial virulence and growth of the ΔsaxE mutant in plant extracts, indicating that syrM‐saxE encode a pair of bacteriocin immunity proteins in Pst. To investigate whether the syrM‐saxE system conferred any advantage to Pst in competition with other SyrM‐sensitive pathovars, we compared the growth of a SyrM‐sensitive strain co‐inoculated with Pst strains with or without the syrM gene and observed a significant syrM‐dependent growth reduction of the sensitive bacteria on plate and in lesion tissues upon desiccation–rehydration treatment. These findings reveal an important biological role of SyrM‐like bacteriocins and help to understand the complex strategies used by P. syringae in adaptation to the phyllosphere niche in the context of plant disease.

Commensal Enterobacteriaceae Protect against Salmonella Colonization through Oxygen Competition

Neonates are highly susceptible to infection with enteric pathogens, but the underlying mechanisms are not resolved. We show that neonatal chick colonization with Salmonella enterica serovar Enteritidis requires a virulence-factor-dependent increase in epithelial oxygenation, which drives pathogen expansion by aerobic respiration. Co-infection experiments with an Escherichia coli strain carrying an oxygen-sensitive reporter suggest that S. Enteritidis competes with commensal Enterobacteriaceae for oxygen. A combination of Enterobacteriaceae and spore-forming bacteria, but not colonization with either community alone, confers colonization resistance against S. Enteritidis in neonatal chicks, phenocopying germ-free mice associated with adult chicken microbiota. Combining spore-forming bacteria with a probiotic E. coli isolate protects germ-free mice from pathogen colonization, but the protection is lost when the ability to respire oxygen under micro-aerophilic conditions is genetically ablated in E. coli. These results suggest that commensal Enterobacteriaceae contribute to colonization resistance by competing with S. Enteritidis for oxygen, a resource critical for pathogen expansion.