Search

Biodegradable templates are sought for targeted antibiotic administration/delivery in bone infections to avoid detrimental reactions during bone regeneration. We investigated two key-aspects in this direction: 1) the optimal antibiotic delineation, with thermal stability equivalent to the temperature involved for templates preparation and 2) the antibacterial templates development by a two-step homogenization process. The selected antibiotic – ampicillin (AMP) was mechanically and then thermally mixed with the prime materials: poly(lactic acid) (PLA) – the polymeric matrix, biogenic bovine bone-derived hydroxyapatite (HA, particles <40 μm), and graphene nanoplatelets (GnP, micrometric range). For the first time, all materials were used in simultaneous modulated ratios for the synthesis of PLA/AMP (1–5 wt.%)/HA (0–30 wt.%)/GnP (0–3 wt.%) composites. The influence of the concomitant materials modulation was surveyed through several assays. The FTIR-ATR spectroscopy depicted a three-level model of overlapping structures asserting the solid molecular cross-linking between all materials, without structural alterations induced to any material (XRD analysis). The addition of AMP to the PLA matrix caused a slight particle conglomeration, alleviated through GnP addition. The microporous HA particles supported the adhesion to the PLA matrix and promoted the AMP particles' entrapment/attachment. Linked to the enhanced wettability of the composite materials, the phosphate buffered saline solution (PBS) degradation profiles revealed a pronounced burst during the first 14–28 days of incubation and a long-term, low-level process hereafter. Thus, the formation of pores and cavities were signalled along with the HA particles' fragmentation. The released AMP (percentage) pictured an ascending trendline during the 24 h of analysis, at all targeted ratios. The preservation of AMP features at 200 °C was endorsed by the strong antibacterial activity of composite materials against Staphylococcus aureus (S. Aureus) growth and the medium response against Escherichia coli (E. Coli) – the higher the drug release, the higher the inhibitory effect on bacteria evolution. • Novel development of PLA/AMP/HA/GnP composite materials. • Influence of AMP/HA/GnP ratio on the physico-chemical features, and degradation profiles. • Extensive investigations on composite thin plates correlated to the antibacterial activity. • Synergistic inhibitory sequel against S. Aureus , dependent on the AMP ratio. [ABSTRACT FROM AUTHOR]

The bacterial type 6 secretion system (T6SS) is a toxin-injecting nanoweapon that mediates competition in plant-and animal-associated microbial communities. Bacteria can evolve de novo resistance against T6SS attacks, but resistance is far from universal in natural communities, suggesting key features of T6SS weaponry may act to limit its evolution. Here, we combine ecoevolutionary modeling and experimental evolution to examine how toxin type and multiplicity in Acinetobacter baylyi attackers shape resistance evolution in susceptible Escherichia coli competitors. In both our models and experiments, we find that combinations of multiple distinct toxins limit resistance evolution by creating genetic bottlenecks, driving resistant lineages extinct before they can reach high frequency. We also show that, paradoxically, single-toxin attackers can drive the evolution of cross-resistance, protecting bacteria against unfamiliar toxin combinations, even though such evolutionary pathways were inaccessible against multitoxin attackers. Our findings indicate that, comparable to antimicrobial and anticancer combination therapies, multitoxin T6SS arsenals function to limit resistance evolution in competing microbes. This helps us to understand why T6SSs remain widespread and effective weapons in microbial communities, and why many T6SS-armed bacteria encode functionally diverse anticompetitor toxins. [ABSTRACT FROM AUTHOR]

The bacteria-phage arm race drives the evolution of diverse bacterial defenses. This study identifies and characterizes the defense hotspots in Acinetobacter baumannii using a reference-free approach. Among 4383 high-quality genomes, we found a total of 17,430 phage defense systems and with 54.54% concentrated in 21 hotspots. These hotspots exhibit distinct preferences for different defense systems, and co-occurrence patterns suggest synergistic interactions. Additionally, the mobile genetic elements are abundant around these hotspots, likely facilitating horizontal transfer and evolution of defense systems. The number of hotspots increases in species phylogenetically closer to Acinetobacter baumannii, but the number of defense systems per hotspot varies due to particular selective pressures. These findings provide critical insights into the genetic organization of phage defense systems, contributing to a broader understanding of bacterial immunity and the evolutionary dynamics that shape Acinetobacter genomes. This knowledge lays the foundation for developing targeted interventions to combat antibiotic resistance Acinetobacter baumannii. This study identifies phage resistance hotspots in Acinetobacter baumannii. Analysis of 4383 genomes found 17,430 systems, 54.54% in 21 hotspots, showing diverse defense systems, co-occurrence patterns, and selective adaptation to environmental pressures. [ABSTRACT FROM AUTHOR]

In this article, we develop a computational approach for estimating the most likely trajectories describing rare events that correspond to the emergence of non-dominant genotypes. This work is based on the large deviations approach for discrete Markov chains describing the genetic evolution of large bacterial populations. We demonstrate that a gradient descent algorithm developed in this article results in the fast and accurate computation of most likely trajectories for a large number of bacterial genotypes. We supplement our analysis with extensive numerical simulations demonstrating the computational advantage of the designed gradient descent algorithm over other, more simplified, approaches. [ABSTRACT FROM AUTHOR]

The increase in antibiotic resistance in recent years, mainly due to the non-rational use of antibiotics, is one of the most important global public health threats. In this paper, we propose a mathematical dynamic random model describing the antibiotic resistance evolution of a bacteria and where antibiotic consumption is included is the main driving force in the resistance increase. The random model is solved using the Random Variable Transformation technique and is applied to study the case of Acinetobacter baumannii bacterium resistant to the antibiotic colistin in Valencia, Spain. Using the Multi-Objective Particle Swarm Optimization algorithm, the model has been calibrated with the A. baumannii colistin-resistance and colistin consumption data series. With the optimal model, four possible 7-year future scenarios with different antibiotic consumption trends have been simulated. The model results show how reducing antibiotic consumption does not easily stop the increase in resistance. [ABSTRACT FROM AUTHOR]

Multidrug resistance in Pseudomonas aeruginosa, a high-priority pathogen per the World Health Organization, poses a global threat due to carbapenem resistance and limited antibiotic treatments. Using the bioinformatic tools CRISPRCasFinder, CRISPRCasTyper, CRISPRloci, and CRISPRImmunity, we analyzed the genome of P. aeruginosa PAO1 and revealed an orphan CRISPR system, suggesting it may be a remnant of a type IV system due to the presence of the DinG protein. This system comprises two CRISPR arrays and noteworthy DinG and Cas3 proteins, supporting recent evidence about the association between type IV and I CRISPR systems. Additionally, we demonstrated a co-evolutionary relationship between the orphan CRISPR system in P. aeruginosa PAO1 and the mobile genetic element and prophages identified. One self-targeting spacer was identified, often associated with bacterial evolution and autoimmunity, and no Acr proteins. This research opens avenues for studying how these CRISPR arrays regulate pathogenicity and for developing alternative strategies using its endogenous orphan CRISPR system against carbapenem-resistant P. aeruginosa strains. [ABSTRACT FROM AUTHOR]

Incompatible plasmids play a crucial role in the horizontal transfer of antibiotic resistance in bacteria, particularly in Gram-negative bacteria, and have thus attracted considerable attention in the field of microbiological research. In the 1970s, these plasmids, housing an array of resistance genes and genetic elements, were predominantly discovered. They exhibit a broad presence in diverse host bacteria, showcasing diversity in geographic distribution and the spectrum of antibiotic resistance genes. The complex genetic structure of plasmids further accelerates the accumulation of resistance genes in Gram-negative bacteria. This article offers a comprehensive review encompassing the discovery process, host distribution, geographic prevalence, carried resistance genes, and the genetic structure of different types incompatible plasmids, including IncA, IncC, IncF, IncL, IncM, IncH, and IncP. It serves as a valuable reference for enhancing our understanding of the role of these different types of plasmids in bacterial evolution and the dissemination of antibiotic resistance. [ABSTRACT FROM AUTHOR]

Why microbes harm their hosts is a fundamental question in evolutionary biology with broad relevance to our understanding of infectious diseases. Several hypotheses have been proposed to explain this "evolution of virulence." In this perspective, we reexamine one of these hypotheses in the specific context of the human gut microbiome, namely short-sighted evolution. According to the short-sighted evolution hypothesis, virulence is a product of niche expansion within a colonized host, whereby variants of commensal microbes establish populations in tissues and sites where the infection causes morbidity or mortality. This evolution is short-sighted in that the evolved variants that infect those tissues and sites are not transmitted to other hosts. The specific hypothesis that we propose is that some bacteria responsible for invasive infections and disease are the products of the short-sighted evolution of commensal bacteria residing in the gut microbiota. We present observations in support of this hypothesis and discuss the challenges inherent in assessing its general application to infections and diseases associated with specific members of the gut microbiota. We then describe how this hypothesis can be tested using genomic data and animal model experiments and outline how such studies will serve to provide fundamental information about both the evolution and genetic basis of virulence, and the bacteria of intensively studied yet poorly understood habitats including the gut microbiomes of humans and other mammals. [ABSTRACT FROM AUTHOR]

Aminoacyl‐tRNA synthetases (aaRSs) are universally essential enzymes that synthesize aminoacyl‐tRNA substrates for protein synthesis. Although most organisms require a single aaRS gene for each proteinogenic amino acid to translate their genetic information, numerous species encode multiple gene copies of an aaRS. Growing evidence indicates that organisms acquire extra aaRS genes to sustain or adapt to their unique lifestyle. However, predicting and defining the function of repeated aaRS genes remains challenging due to their potentially unique physiological role in the host organism and the inconsistent annotation of repeated aaRS genes in the literature. Here, we carried out comparative, phylogenetic, and functional studies to determine the activity of coexisting paralogs of tryptophanyl‐, tyrosyl‐, seryl‐, and prolyl‐tRNA synthetases encoded in several human pathogenic bacteria. Our analyses revealed that, with a few exceptions, repeated aaRSs involve paralogous genes with distinct phylogenetic backgrounds. Using a collection of Escherichia coli strains that enabled the facile characterization of aaRS activity in vivo, we found that, in almost all cases, one aaRS displayed transfer RNA (tRNA) aminoacylation activity, whereas the other was not compatible with E. coli. Together, this work illustrates the challenges of identifying, classifying, and predicting the function of aaRS paralogs and highlights the complexity of aaRS evolution. Moreover, these results provide new insights into the potential role of aaRS paralogs in the biology of several human pathogens and foundational knowledge for the investigation of the physiological role of repeated aaRS paralogs across bacteria. [ABSTRACT FROM AUTHOR]

Abstract—Issues related to the spread of antibiotic resistance genes in environmental microbial communities are considered. "Hotspots" of adaptive evolution, accumulation, and spread of antibiotic-resistant bacteria and genetic material of antibiotic resistance are highlighted. Such "hotspots" include anthropogenic ecosystems, such as municipal wastewater treatment plants, municipal solid waste landfills, livestock enterprises, and agrocenoses. The influence of various types of pollutants and biotic factors on enhancement of mutagenesis and horizontal transfer of antibiotic resistance genes is considered. The role of mobile genetic elements in mobilization and accelerated spread of resistance determinants is shown. Special attention is paid to the role of oxidative stress and stress regulons, which are activated for realization and control of molecular genetic mechanisms of adaptive evolution of bacteria and the horizontal distribution of genetic material in bacterial populations. Oxidative stress is identified as one of the main activators of genome destabilization and adaptive evolution of bacteria. [ABSTRACT FROM AUTHOR]

Horizontal gene transfer is one of the most important drivers of bacterial evolution. Transformation by uptake of extracellular DNA is traditionally not considered to be an effective mode of gene acquisition, simply because extracellular DNA is degraded in a matter of days when it is suspended in e.g. seawater. Recently the age span of stored DNA was increased to at least 2 Ma. Here, we show that Acinetobacter baylyi can incorporate 60 bp DNA fragments adsorbed to common sedimentary minerals and that the transformation frequencies scale with mineral surface properties. Our work highlights that ancient environmental DNA can fuel the evolution of contemporary bacteria. In contrast to heritable stochastic mutations, the processes by which bacteria acquire new genomic material during times of increased stress and needs, indicate a non-random mechanism that may propel evolution in a non-stochastic manner. [ABSTRACT FROM AUTHOR]

Aerobic composting is a key strategy to the sustainable use of livestock manure, which is however constrained by the slow kinetics. Microbe-aided thermophilic composting provides an attractive solution to this problem. In this study, we identified key thermophilic bacteria capable of accelerating manure composting based on the deciphering of manure bacterial community evolution in a thermophilic system. High-throughput sequencing showed a significant evolution of manure bacterial community structure with the increasing heating temperature. Firmicutes were substantially enriched by the heating, particularly some known thermotolerant bacterial species, such as Novibacillus thermophiles , Bacillus thermolactis , and Ammoniibacillus agariperforans. Correspondingly, through function prediction, we found bacterial taxa with cellulolytic and xylanolytic activities were significantly higher in the thermophilic process relative to the initial stage. Subsequently, a total of 47 bacteria were isolated in situ and their phylogenetic affiliation and degradation capacity were determined. Three isolates were back inoculated to the manure, resulting in shortened composting process from 5 to 3 days with Germination Index increased up to 134%, and improved compost quality particularly in wheat growth promoting. Comparing to the mesophilic and thermophilic Bacillus , the genomes of the three isolates manifested some features similar to the thermophiles, including smaller genome size and mutation of specific genes that enhance heat tolerance. This study provide robust evidence that microbe-aided thermophilic composting is capable to accelerate manure composting and improve the quality of compost, which represents a new hope to the sustainable use of manure from the meat industry. [ABSTRACT FROM AUTHOR]

Rainfall, evaporation, tides and waves make the soil at coastlines show dynamic unsaturated characteristics. In order to cope with landslides, collapses, and coastline receding, microbially induced calcium carbonate precipitation (MICP) was recently implemented to reinforce the soil in slopes and coastal zones using a spraying method. However, most of the researches on MICP focus on soil with a static saturation degree, and there are few numerical researches about the MICP reactions under dynamic saturation degree. Therefore, a coupled numerical model capable of describing the evolutions of bacteria, substance, calcium carbonate (CaCO3), porosity, and permeability in unsaturated soil over time reasonably was developed based on the convective–diffusion–reaction theory and the Richards' equation. The effect of MICP reactions on the parameters α, n, θs, θr in van Genuchten-Mualem (VG) model was considered. A large cylinder test (30 × 75 cm) about reinforcing sand based on the spraying method was carried out to validate the model. The CaCO3 distribution of the MICP infiltration and mineralization was fully reproduced and the concept of critical depth (Zcr) was proposed. The initial porosity, initial bacterial concentration, and spraying rate were the main parameters affecting the CaCO3 distribution and critical depth Zcr. When the bacterial concentration increased, the maximum CaCO3 content, critical depth Zcr, and normalized permeability coefficient (k/k0) indicated exponential increase, exponential increase, and exponential decrease. The saturated permeability coefficient of the sand was determined by the maximum calcium carbonate. The normalized permeability coefficient (k/k0) and critical depth Zcr showed an exponential decrease and a power function increase with the increase of the maximum CaCO3 content. [ABSTRACT FROM AUTHOR]

The advent of novel high-resolution physicochemical techniques and the integration of omics technologies into biomedical research have opened avenues for investigating the mechanisms underlying bacterial survival in vitro and in vivo, subjected to the influence of biotic and abiotic stressors. This encompasses axenic cultures, microbial communities, and holobionts. The development of innovative methodological platforms has facilitated the acquisition of unique data relevant to both fundamental and applied scientific fields. The experimental results indicated a remarkably high level of genomic plasticity in microorganisms and the potential for the evolution of bacterial virulence under selective pressure. These findings have significantly impacted our understanding of the arsenal of self-defense tools in bacteria and the prioritization of research in this field. The increasing quantity of factual material now necessitates a shift in focus from pathogens to the broader category of commensal bacteria, which are used as probiotics in various fields, including medicine, agriculture, and the food industry. The possibility of large-scale genomic reorganization and progressive evolution of virulence in these bacteria under stressful conditions, as well as their modulation of host cell signaling systems and suppression of innate immunity, negative regulation of key cell cycle controllers, disruption of the structure of the intestinal microbiota and intestinal homeostasis, highlight the obvious insufficiency of our knowledge about the "logic of life" of symbionts and the mechanisms of their interaction with eukaryotic cells. This may compromise the ideas of several practical applications. This underscores the importance of comprehensive studies of commensals, their potential for plasticity in different environmental conditions, and the ways in which they communicate and interact with regulatory networks of higher organisms. It also highlights the need to develop a standardization for assessing the safety of probiotics. The review addresses these issues. [ABSTRACT FROM AUTHOR]

This review aimed to identify newly discovered bacteria from individuals with periodontal/peri-implant diseases and organize them into new clusters (GF-MoR complexes) to update Socransky's complexes (1998). For methodological development, the PCC (Population, Concept, Context) strategy was used for the focus question construction: "In patients with periodontal and/or peri-implant disease, what bacteria (microorganisms) were detected through laboratory assays?" The search strategy was applied to PubMed/MEDLINE, PubMed Central, and Embase. The search key terms, combined with Boolean markers, were (1) bacteria, (2) microbiome, (3) microorganisms, (4) biofilm, (5) niche, (6) native bacteria, (7) gingivitis), (8) periodontitis, (9) peri-implant mucositis, and (10) peri-implantitis. The search was restricted to the period 1998–2024 and the English language. The bacteria groups in the oral cavity obtained/found were retrieved and included in the GF-MoR complexes, which were based on the disease/condition, presenting six groups: (1) health, (2) gingivitis, (3) peri-implant mucositis, (4) periodontitis, (5) peri-implantitis, and (6) necrotizing and molar–incisor (M-O) pattern periodontitis. The percentual found per group refers to the number of times a specific bacterium was found to be associated with a particular disease. A total of 381 articles were found: 162 articles were eligible for full-text reading (k = 0.92). Of these articles, nine were excluded with justification, and 153 were included in this review (k = 0.98). Most of the studies reported results for the health condition, periodontitis, and peri-implantitis (3 out of 6 GF-MoR clusters), limiting the number of bacteria found in the other groups. Therefore, it became essential to understand that bacterial colonization is a dynamic process, and the bacteria present in one group could also be present in others, such as those observed with the bacteria found in all groups (Porphyromonas gingivalis, Tannarela forsythia, Treponema denticola, and Aggregatibacter actinomycetemcomitans) (GF-MoR's red triangle). The second most observed bacteria were grouped in GF-MoR's blue triangle: Porphyromonas spp., Prevotela spp., and Treponema spp., which were present in five of the six groups. The third most detected bacteria were clustered in the grey polygon (GF-MoR's grey polygon): Fusobacterium nucleatum, Prevotella intermedia, Campylobacter rectus, and Eikenella corrodens. These three geometric shapes had the most relevant bacteria to periodontal and peri-implant diseases. Specifically, per group, GF-MoR's health group had 58 species; GF-MoR's gingivitis group presented 16 bacteria; GF-MoR's peri-implant mucositis included 17 bacteria; GF-MoR's periodontitis group had 101 different bacteria; GF-MoR's peri-implantitis presented 61 bacteria; and the last group was a combination of necrotizing diseases and molar–incisor (M-I) pattern periodontitis, with seven bacteria. After observing the top seven bacteria of all groups, all of them were found to be gram-negative. Groups 4 and 5 (periodontitis and peri-implantitis) presented the same top seven bacteria. For the first time in the literature, GF-MoR's complexes were presented, gathering bacteria data according to the condition found and including more bacteria than in Socransky's complexes. Based on this understanding, this study could drive future research into treatment options for periodontal and peri-implant diseases, guiding future studies and collaborations to prevent and worsen systemic conditions. Moreover, it permits the debate about the evolution of bacterial clusters. [ABSTRACT FROM AUTHOR]

Bacterial infections are a growing problem, and antibiotic drugs can be widely used to fight bacterial infections. However, the overuse of antibiotics and the evolution of bacteria have led to the emergence of drug-resistant bacteria, severely reducing the effectiveness of treatment. Therefore, it is very important to develop new effective antibacterial strategies to fight multi-drug resistant bacteria. Nanozyme is a kind of enzyme-like catalytic nanomaterials with unique physical and chemical properties, high stability, structural diversity, adjustable catalytic activity, low cost, easy storage and so on. In addition, nanozymes also have excellent broad-spectrum antibacterial properties and good biocompatibility, showing broad application prospects in the field of antibacterial. In this paper, we reviewed the research progress of antibacterial application of nanozymes. At first, the antibacterial mechanism of nanozymes was summarized, and then the application of nanozymes in antibacterial was introduced. Finally, the challenges of the application of antibacterial nanozymes were discussed, and the development prospect of antibacterial nanozymes was clarified. [ABSTRACT FROM AUTHOR]

Addressing the global antimicrobial resistance (AMR) crisis requires a multifaceted innovative approach to mitigate impacts on public health, healthcare and economic systems. In the complex evolution of AMR, biofilms and the acquisition of antimicrobial resistance genes (ARGs) play a pivotal role. Aeromonas is a major AMR player that often forms biofilm, harbors ARGs and is frequently detected in wastewater. Existing wastewater treatment plants (WWTPs) do not have the capacity to totally eliminate antimicrobial-resistant bacteria favoring the evolution of ARGs in wastewater. Besides facilitating the emergence of AMR, biofilms contribute significantly to biofouling process within the activated sludge of WWTP bioreactors. This paper presents the inhibition of biofilm formation, the expression of biofilm-linked genes and ARGs by phytochemicals andrographolide, docosanol, lanosterol, quercetin, rutin and thymohydroquinone. Aeromonas species were isolated and purified from activated sludge samples. The ARGs were detected in the isolated Aeromonas species through PCR. Aeromonas biofilms were quantified following the application of biocompounds through the microtiter plate assay. qPCR analyses of related genes were done for confirmation. Findings showed that the natural compounds inhibited the formation of biofilms and reduced the expression of genes linked to biofilm production as well as ARGs in wastewater Aeromonas. This indicates the efficacy of these compounds in targeting and controlling both ARGs and biofilm formation, highlighting their potential as innovative solutions for combating antimicrobial resistance and biofouling. [ABSTRACT FROM AUTHOR]

The phenomenon of exclusion allows conjugative plasmids to selectively impede the entry of identical or related elements into their host cell to prevent the resulting instability. Entry exclusion blocks DNA translocation into the recipient cell, whereas surface exclusion destabilizes the mating pair. IncC conjugative plasmids largely contribute to the dissemination of antibiotic-resistance genes in Gammaproteobacteria. IncC plasmids are known to exert exclusion against their relatives, including IncC and IncA plasmids, yet the entry exclusion factor eexC alone does not account for the totality of the exclusion phenotype. In this study, a transposon-directed insertion sequencing approach identified sfx as necessary and sufficient for the remaining exclusion phenotype. Sfx is an exclusion factor unrelated to the ones described to date. A cell fractionation assay localized Sfx in the outer membrane. Reverse transcription PCR and beta-galactosidase experiments showed that sfx is expressed constitutively at a higher level than eexC. A search in Gammaproteobacteria genomes identified Sfx homologs encoded by IncC, IncA and related, untyped conjugative plasmids and an uncharacterized family of integrative and mobilizable elements that likely rely on IncC plasmids for their mobility. Mating assays demonstrated that sfx is not required in the donor for exclusion, ruling out Sfx as the exclusion target. Instead, complementation assays revealed that the putative adhesin TraN in the donor mediates the specificity of surface exclusion. Mating assays with TraN homologs from related untyped plasmids from Aeromonas spp. and Photobacterium damselae identified two surface exclusion groups, with each Sfx being specific of TraN homologs from the same group. Together, these results allow us to better understand the apparent incompatibility between IncA and IncC plasmids and to propose a mechanistic model for surface exclusion mediated by Sfx in IncC plasmids and related elements, with implications for the rampant dissemination of antibiotic resistance. Author summary: Bacterial conjugation plays a pivotal role in the evolution of bacterial populations. The circulation of drug resistance genes bolsters the emergence of multidrug-resistant pathogens, with which contemporary medicine struggles to cope. Exclusion is a natural process preventing the redundant acquisition of a plasmid via conjugation by a host harbouring an identical or similar plasmid. Although exclusion has been known for the past half-century, the mechanisms involved remain poorly understood. This study describes an exclusion factor, Sfx, encoded by IncC, IncA and related conjugative plasmids and by unrelated integrative and mobilizable elements. We report that Sfx is a lipoprotein of the recipient that selectively inhibits conjugation based on the adhesin TraN expressed at the surface of the donor. We propose a mechanistic model for Sfx-mediated exclusion. Ultimately, a better understanding of exclusion could facilitate the design of conjugation inhibitors targeting mating pair formation to curb the circulation of drug-resistance genes in healthcare settings, agriculture, animal husbandry and food and drug production. [ABSTRACT FROM AUTHOR]

Flagella are highly complex rotary molecular machines that enable bacteria to not only migrate to optimal environments but also to promote range expansion, competitiveness, virulence, and antibiotic survival. Flagellar motility is an energy-demanding process, where the sum of its production (biosynthesis) and operation (rotation) costs has been estimated to total ~10% of the entire energy budget of an Escherichia coli cell. The acquisition of such a costly adaptation process is expected to secure short-term benefits by increasing competitiveness and survival, as well as long-term evolutionary fitness gains. While the role of flagellar motility in bacterial survival has been widely reported, its direct influence on the rate of evolution remains unclear. We show here that both production and operation costs contribute to elevated mutation rates. Our findings suggest that flagellar movement may be an important player in tuning the rate of bacterial evolution. [ABSTRACT FROM AUTHOR]

Many insects are obligatorily associated with and dependent on specific microbial species as essential mutualistic partners. In the host insects, such microbial mutualists are usually maintained in specialized cells or organs, called bacteriocytes or symbiotic organs. Hence, potentially exponential microbial growth cannot be realized but must be strongly constrained by spatial and resource limitations within the host cells or tissues. How such endosymbiotic bacteria grow, divide, and proliferate is important for understanding the interactions and dynamics underpinning intimate host-microbe symbiotic associations. Here we report that Blattabacterium, the ancient and essential endosymbiont of cockroaches, exhibits unexpectedly high rates of cell division (20%-58%) and, in addition, the cell division is asymmetric (average asymmetry index >1.5) when isolated from the German cockroach Blattella germanica. The asymmetric division of endosymbiont cells at high frequencies was observed irrespective of host tissues (fat bodies vs ovaries) or developmental stages (adults vs nymphs vs embryos) of B. germanica, and also observed in several different cockroach species. By contrast, such asymmetric and frequent cell division was observed neither in Buchnera, the obligatory bacterial endosymbiont of aphids, nor in Pantoea, the obligatory bacterial gut symbiont of stinkbugs. Comparative genomics of cell division-related genes uncovered that the Blattabacterium genome lacks the Min system genes that determine the cell division plane, which may be relevant to asymmetric cell division. These observations combined with comparative symbiont genomics provide insight into what processes and regulations may underpin the growth, division, and proliferation of such bacterial mutualists continuously constrained under within-host conditions. IMPORTANCE Diverse insects are dependent on specific bacterial mutualists for their survival and reproduction. Due to the long-lasting coevolutionary history, such symbiotic bacteria tend to exhibit degenerative genomes and suffer uncultivability. Because of their microbiological fastidiousness, the cell division patterns of such uncultivable symbiotic bacteria have been poorly described. Here, using fine microscopic and quantitative morphometric approaches, we report that, although bacterial cell division usually proceeds through symmetric binary fission, Blattabacterium, the ancient and essential endosymbiont of cockroaches, exhibits frequent and asymmetric cell division. Such peculiar cell division patterns were not observed with other uncultivable essential symbiotic bacteria of aphids and stinkbugs. Gene repertoire analysis revealed that the molecular machinery for regulating the bacterial cell division plane are lost in the Blattabacterium genome, suggesting the possibility that the general trend toward the reductive genome evolution of symbiotic bacteria may underpin their bizarre cytological/morphological traits. [ABSTRACT FROM AUTHOR]

Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping community interactions, but offer little toward controlling them—an important step in the translation of synthetic strains into natural contexts. Toxin–antitoxin (TA) systems serve as ubiquitous and diverse agents of selection; however, their utility is limited by their erratic distribution in hosts. Here we examine the heterogeneous distribution of TAs as a consequence of their mobility. By systematically mapping TA systems across a 10,000 plasmid network, we find HGT communities have unique and predictable TA signatures. We propose these TA signatures arise from plasmid competition and have further potential to signal the degree to which plasmids, hosts, and phage interact. To emphasize these relationships, we construct an HGT network based solely on TA similarity, framing specific selection markers in the broader context of bacterial communities. This work both clarifies the evolution of TA systems and unlocks a common framework for manipulating community interactions through TA compatibility. [ABSTRACT FROM AUTHOR]

Continuous directed evolution of base editors (BEs) has been successful in bacteria cells, but not yet in mammalian cells. Here, we report the development of a Continuous Directed Evolution system in Mammalian cells (CDEM). CDEM enables the BE evolution in a full-length manner with Cas9 nickase. We harness CDEM to evolve the deaminases of cytosine base editor BE3 and adenine base editors, ABEmax and ABE8e. The evolved cytidine deaminase variants on BE4 architecture show not only narrowed editing windows, but also higher editing purity and low off-target activity without a trade-off in on-targeting activity. The evolved ABEmax and ABE8e variants exhibit narrowed or shifted editing windows to different extents, and lower off-target effects. The results illustrate that CDEM is a simple but powerful approach to continuously evolve BEs without size restriction in the mammalian environment, which is advantageous over continuous directed evolution system in bacteria cells. Continuous directed evolution of base editors (BEs) has been successful in bacteria cells, but not yet in mammalian cells. Here, the authors report a Continuous Directed Evolution system in Mammalian cells (CDEM) enabling the BE evolution in a full-length manner with Cas9 nickase. [ABSTRACT FROM AUTHOR]

Bacterial evolution, particularly in hospital settings, is leading to an increase in multidrug resistance. Understanding the basis for this resistance is critical as it can drive discovery of new antibiotics while allowing the clinical use of known antibiotics to be optimized. Here, we report a photoactive chemical probe for superresolution microscopy that allows for the in situ probing of antibiotic-induced structural disruption of bacteria. Conjugation between a spiropyran (SP) and galactose via click chemistry produces an amphiphilic photochromic glycoprobe, which self-assembles into glycomicelles in water. The hydrophobic inner core of the glycomicelles allows encapsulation of antibiotics. Photoirradiation then serves to convert the SP to the corresponding merocyanine (MR) form. This results in micellar disassembly allowing for release of the antibiotic in an on-demand fashion. The glycomicelles of this study adhere selectively to the surface of a Gram-negative bacterium through multivalent sugar-lectin interaction. Antibiotic release from the glycomicelles then induces membrane collapse. This dynamic process can be imaged in situ by superresolution spectroscopy owing to the "fluorescence blinking" of the SP/MR photochromic pair. This research provides a high-precision imaging tool that may be used to visualize how antibiotics disrupt the structural integrity of bacteria in real time. [ABSTRACT FROM AUTHOR]

When examining bacterial genomes for evidence of past selection, the results depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed by dN/dS, the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with opposite implications for dynamical intuition and applications of dN/dS. Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain the dN/ dS decay given only dozens of locally fluctuating selective pressures, which is realistic in the context of Bacteroides genomes. The success of the adaptive reversion model argues for interpreting low values of dN/dS obtained from long timescales with caution as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short timescales. [ABSTRACT FROM AUTHOR]

Epigenetic mechanisms can generate bacterial lineages capable of spontaneously switching between distinct phenotypes. Currently, mathematical models and simulations propose epigenetic switches as a mechanism of adaptation to deal with fluctuating environments. However, bacterial evolution experiments for testing these predictions are lacking. Here, we exploit an epigenetic switch in Salmonella enterica, the opvAB operon, to show clear evidence that OpvAB bistability persists in changing environments but not in stable conditions. Epigenetic control of transcription in the opvAB operon produces OpvABOFF (phage-sensitive) and OpvABON (phage-resistant) cells in a reversible manner and may be interpreted as an example of bet-hedging to preadapt Salmonella populations to the encounter with phages. Our experimental observations and computational simulations illustrate the adaptive value of epigenetic variation as an evolutionary strategy for mutation avoidance in fluctuating environments. In addition, our study provides experimental support to game theory models predicting that phenotypic heterogeneity is advantageous in changing and unpredictable environments. [ABSTRACT FROM AUTHOR]

Accumulation processes, where many potentially coupled features are acquired over time, occur throughout the sciences, from evolutionary biology to disease progression, and particularly in the study of cancer progression. Existing methods for learning the dynamics of such systems typically assume limited (often pairwise) relationships between feature subsets, cross-sectional or untimed observations, small feature sets, or discrete orderings of events. Here we introduce HyperTraPS-CT (Hypercubic Transition Path Sampling in Continuous Time) to compute posterior distributions on continuous-time dynamics of many, arbitrarily coupled, traits in unrestricted state spaces, accounting for uncertainty in observations and their timings. We demonstrate the capacity of HyperTraPS-CT to deal with cross-sectional, longitudinal, and phylogenetic data, which may have no, uncertain, or precisely specified sampling times. HyperTraPS-CT allows positive and negative interactions between arbitrary subsets of features (not limited to pairwise interactions), supporting Bayesian and maximum-likelihood inference approaches to identify these interactions, consequent pathways, and predictions of future and unobserved features. We also introduce a range of visualisations for the inferred outputs of these processes and demonstrate model selection and regularisation for feature interactions. We apply this approach to case studies on the accumulation of mutations in cancer progression and the acquisition of anti-microbial resistance genes in tuberculosis, demonstrating its flexibility and capacity to produce predictions aligned with applied priorities. Author summary: Many important processes in biology and medicine involve a progressive buildup of features over time. These might be, for example, the accumulation of different mutations as cancer progresses, or the evolution of bacteria to be resistant to more and more drugs. Here we introduce an algorithm called HyperTraPS-CT that allows us to use data to learn the details of how these features build up over time. The algorithm provides information on which features affect each other, which come early and which come late, and what might happen in the future. It is more flexible than several existing approaches, and can be used across many different scentific situations; we demonstrate its use in learning about leukemia progression and tuberculosis drug resistance. This approach has the potential to help make useful predictions about how new instances of these processes will evolve, about data which can't be observed due to technological limitations, and about possible mechanisms that determine how features interact. [ABSTRACT FROM AUTHOR]

Healthy state is priority in today's world which can be achieved using effective medicines. But due to overuse and misuse of antibiotics, a menace of resistance has increased in pathogenic microbes. World Health Organization (WHO) has announced ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) as the top priority pathogens as these have developed resistance against certain antibiotics. To combat such a global issue, it is utmost important to identify novel therapeutic strategies/agents as an alternate to such antibiotics. To name certain antibiotic adjuvants including: inhibitors of beta–lactamase, efflux pumps and permeabilizers for outer membrane can potentially solve the antibiotic resistance problems. In this regard, inhibitors of lytic domain of lytic transglycosylases provide a novel way to not only act as an alternate to antibiotics but also capable of restoring the efficiency of previously resistant antibiotics. Further, use of bacteriophages is another promising strategy to deal with antibiotic resistant pathogens. Taking in consideration the alternatives of antibiotics, a green synthesis nanoparticle-based therapy exemplifies a good option to combat microbial resistance. As horizontal gene transfer (HGT) in bacteria facilitates the evolution of new resistance strains, therefore identifying the mechanism of resistance and development of inhibitors against it can be a novel approach to combat such problems. In our perspective, host-directed therapy (HDT) represents another promising strategy in combating antimicrobial resistance (AMR). This approach involves targeting specific factors within host cells that pathogens rely on for their survival, either through replication or persistence. As many new drugs are under clinical trials it is advisable that more clinical data and antimicrobial stewardship programs should be conducted to fully assess the clinical efficacy and safety of new therapeutic agents. [ABSTRACT FROM AUTHOR]

The tannery industry produces one of the worst contaminants, and unsafe disposal in nearby waterbodies and landfills has become an imminent threat to public health, especially when the resulting multidrug-resistant bacteria and heavy metals enter community settings and animal food chains. In this study, we have collected 10 tannery wastewater (TWW) samples and 10 additional non-tannery wastewater (NTW) samples to compare the chemical oxygen demand (COD), pH, biological oxygen demand (BOD), dissolved oxygen (DO), total dissolved solids (TDS), chromium concentration, bacterial load, and antibiotic resistance profiles. While COD, pH, and chromium concentration data were previously published from our lab, this part of the study uncovers that TWW samples had a significantly higher bacterial load, compared to the non-tannery wastewater samples (5.89 × 104 and 9.38 × 103 cfu/mL, respectively), higher BOD and TDS values, and significantly lower DO values. The results showed that 53.4, 46.7, 40.0, and 40.0% of the TWW isolates were resistant to ceftriaxone, erythromycin, nalidixic acid, and azithromycin, respectively. On the other hand, 20.0, 30.0, 50.0, and 40.0% of the NTW isolates were resistant to the same antibiotics, respectively. These findings suggest that the TWW isolates were more resistant to antibiotics than the NTW isolates. Moreover, the TWW isolates exhibited higher multidrug resistance than the NTW isolates, 33.33, and 20.00%, respectively. Furthermore, spearman correlation analysis depicts that there is a negative correlation between BOD and bacterial load up to a certain level (r = − 0.7749, p = 0.0085). In addition, there is also a consistent negative correlation between COD and bacterial load (r = − 0.7112, p = 0.0252) and TDS and bacterial load (r = − 0.7621, p = 0.0104). These findings suggest that TWW could pose a significant risk to public health and the environment and highlight the importance of proper wastewater treatment in tannery industries. [ABSTRACT FROM AUTHOR]

The successful evolution of KPC-2 in bacteria has limited the clinical practice of carbapenems. This dilemma deteriorated the prognosis of associated infections and hence attracted increasing attention from researchers to explore alternative therapeutic options. Here, the enzyme inhibition assay was first performed to screen for a potent KPC-2 inhibitor. The synergistic effect of the candidate with carbapenems was further confirmed by checkboard minimum inhibitory concentration (MIC) assay, time-killing assay, disk diffusion method, and live/dead bacteria staining analysis. The mechanisms by which the candidate acts were subsequently explored through molecular dynamics (MD) simulations, etc. Our study found that Ginkgolic Acid (C13:0) (GA) exhibited effective KPC-2 inhibitory activity in both laboratory strain and clinical strain containing KPC-2. It could potentiate the killing effect of carbapenems on KPC-2-positive Klebsiella pnenmoniae (K. pnenmoniae). Further explorations revealed that GA could competitively bind to the active pocket of KPC-2 with meropenem (MEM) via residues Trp104, Gly235, and Leu166. The secondary structure and functional groups of KPC-2 were subsequently altered, which may be the main mechanism by which GA exerted its KPC-2 inhibitory effect. In addition, GA was also found to synergize with MEM to disrupt membrane integrity and increase membrane permeability, which may be another mechanism by which GA reinforced the bactericidal ability of carbapenems. Our study indicated that GA was a significant KPC-2 inhibitor that could prolong the lifespan of carbapenems and improve the prognosis of patients. [ABSTRACT FROM AUTHOR]

The editorial in Frontiers in Microbiology explores microbial stress tolerance mechanisms, focusing on responses to metal, acidic, and oxidative stress in bacteria and fungi. Studies include investigations on the effects of chromium on gut microbiota, metal(loid) toxicity in Escherichia coli, and the response of Vibrio cholerae to heavy metals. The research also delves into the stress responses of Streptococcus pneumoniae, Rhodobacter species, and other pathogens, shedding light on adaptation mechanisms and potential therapeutic targets for infectious diseases and bioremediation. The authors emphasize the importance of further research into microbial stress responses for advancements in environmental and health sciences. [Extracted from the article]

Mobile genetic elements shape microbial gene repertoires and populations. Recent results reveal that many, possibly most, microbial mobile genetic elements require helpers to transfer between genomes, which we refer to as Hitcher Genetic Elements (hitchers or HGEs). They may be a large fraction of pathogenicity and resistance genomic islands, whose mechanisms of transfer have remained enigmatic for decades. Together with their helper elements and their bacterial hosts, hitchers form tripartite networks of interactions that evolve rapidly within a parasitism–mutualism continuum. In this emerging view of microbial genomes as communities of mobile genetic elements many questions arise. Which elements are being moved, by whom, and how? How often are hitchers costly hyper-parasites or beneficial mutualists? What is the evolutionary origin of hitchers? Are there key advantages associated with hitchers' lifestyle that justify their unexpected abundance? And why are hitchers systematically smaller than their helpers? In this essay, we start answering these questions and point ways ahead for understanding the principles, origin, mechanisms, and impact of hitchers in bacterial ecology and evolution. Microbial evolution is shaped by mobile genetic elements, but recent work shows that many of these depend in turn on other mobile genetic elements. These chains of functional dependencies raise numerous questions in terms of genetics, molecular biology, ecology and co-evolutionary processes. [ABSTRACT FROM AUTHOR]

Cronobacter condimenti are environmental commensals that have not been associated with any clinical infections. To date, they are the least understood and described Cronobacter species within the genus. The objective of this study was to use a draft genome sequence (DGS) of the Cronobacter condimenti strain s37 to screen for genes encoding for antibiotic resistance, virulence, response to environmental stress, and biofilm formation. The strain was isolated in Poland from commercial small radish sprouts. This is the second genome of this species available in the GenBank database. The comparative genome analysis (cgMLST) of C. condimenti s37 with other Cronobacter spp. including the pathogenic species C. sakazakii and the plant-associated closely related genera Franconibacter and Siccibacter was also performed. The assembled and annotated genome of the C. condimenti s37 genome was 4,590,991 bp in length, with a total gene number of 4384, and a GC content of 55.7%. The s 37 genome encoded for genes associated with resistance to stressful environmental conditions (metal resistance genes: zinc, copper, osmotic regulation, and desiccation stress), 17 antimicrobial resistance genes encoding resistance to various classes of antibiotics and 50 genes encoding for the virulence factors. The latter were mainly genes associated with adhesion, chemotaxis, hemolysis, and biofilm formation. Cg-MLST analysis (3991 genes) revealed a greater similarity of C. condimenti s37 to S. turicensis, F. pulveris, and C. dublinensis than to other species of the genus Cronobacter. Studies on the diversity, pathogenicity, and virulence of Cronobacter species isolated from different sources are still insufficient and should certainly be continued. Especially the analysis of rare strains such as s37 is very important because it provides new information on the evolution of these bacteria. Comparative cgMLST analysis of s37 with other Cronobacter species, as well as closely related genera Franconibacter and Siccibacter, complements the knowledge on their adaptability to specific environments such as desiccation. [ABSTRACT FROM AUTHOR]

Group B Streptococcus (GBS) is a major human and animal pathogen that threatens public health and food security. Spill-over and spill-back between host species is possible due to adaptation and amplification of GBS in new niches but the evolutionary and functional mechanisms underpinning those phenomena are poorly known. Based on analysis of 1,254 curated genomes from all major GBS host species and six continents, we found that the global GBS population comprises host-generalist, host-adapted and host-restricted sublineages, which are found across host groups, preferentially within one host group, or exclusively within one host group, respectively, and show distinct levels of recombination. Strikingly, the association of GBS genomes with the three major host groups (humans, cattle, fish) is driven by a single accessory gene cluster per host, regardless of sublineage or the breadth of host spectrum. Moreover, those gene clusters are shared with other streptococcal species occupying the same niche and are functionally relevant for host tropism. Our findings demonstrate (1) the heterogeneity of genome plasticity within a bacterial species of public health importance, enabling the identification of high-risk clones; (2) the contribution of inter-species gene transmission to the evolution of GBS; and (3) the importance of considering the role of animal hosts, and the accessory gene pool associated with their microbiota, in the evolution of multi-host bacterial pathogens. Collectively, these phenomena may explain the adaptation and clonal expansion of GBS in animal reservoirs and the risk of spill-over and spill-back between animals and humans. Author summary: Group B Streptococcus (GBS) is a bacterium that represents a health and food security threat in three major host groups: humans (in particular neonates), bovines, and fishes. However, the genomic mechanisms driving adaptation to these hosts remain unclear. Here, we use powerful statistical approaches to compare genomes of GBS from around the world. We found that GBS' ability to exchange genes is a good indicator of how well it can adapt to different hosts. Additionally, three groups of genes appear crucial for GBS to infect either humans, cows, or fishes, regardless of the bacterial strain. These gene groups are also found in other similar bacteria that live in the same hosts or environments. Where a functional role is already known for two gene groups in humans and bovines, respectively, it is shown here for the first time for the third gene group in fishes. Our findings demonstrate the importance of considering the role of animals in the evolution of multi-host bacterial pathogens like GBS. Gene exchange between bacteria infecting multiple hosts represents a high threat to human health, as high-risk types of GBS could adapt and expand in animals, which could then act as reservoirs for highly pathogenic human infections. [ABSTRACT FROM AUTHOR]

Tunnel waste constitutes a prevalent by‐product of highway construction in high‐altitude mountainous and hilly regions. Sulphide minerals exhibit a unique distribution pattern within the alpine hills. Consequently, tunnel excavation can disrupt the stability of these sulphide minerals, rendering the tunnel waste susceptible to generating secondary environmental hazards during stockpiling. This research delves into the migration and transformation dynamics of potential environmental pollutants in tunnel waste through geoenvironmental simulation techniques. Controlled variables were employed to simulate various conditions, including surface illumination, internal anaerobiosis, water content and aerobic environments. The study's findings indicate that the presence of pyrite in the waste stream primarily drives the secondary contamination of the tunnel waste. Pyrite within the slag tends to react and form sulphuric acid in the stockpile environment, thus creating an acidic milieu that exacerbates the release of existing contaminants. The emergence of an anaerobic environment and a photocatalytic system composed of Fe/Ti substances in the waste stream serves to further accelerate pollutant release. This study thoroughly investigates the primary causes of environmental pollution during the stockpiling of tunnel slag and assesses the potential environmental impact scenarios. The outcomes of this research offer substantial theoretical and empirical support for the management of slag generated during the tunnel construction process. [ABSTRACT FROM AUTHOR]

Microbes are key drivers of global biogeochemical cycles, and their functional roles arey dependent on temperature. Large population sizes and rapid turnover rates mean that the predominant response of microbes to environmental warming is likely to be evolutionary, yet our understanding of evolutionary responses to temperature change in microbial systems is rudimentary. Natural microbial communities are diverse assemblages of interacting taxa. However, most studies investigating the evolutionary response of bacteria to temperature change are focused on monocultures. Here, we utilize high-throughput experimental evolution of bacteria in both monoculture and community contexts along a thermal gradient to determine how interspecific interactions influence the thermal adaptation of community members. We found that community-evolved isolates tended toward higher maximum growth rates across the temperature gradient compared to their monoculture-evolved counterparts. We also saw little evidence of systematic evolutionary change in the shapes of bacterial thermal tolerance curves along the thermal gradient. However, the effect of community background and selection temperature on the evolution of thermal tolerance curves was variable and highly taxon-specific,with some taxa exhibiting pronounced changes in thermal tolerance while others were less impacted. We also found that temperature acted as a strong environmental filter, resulting in the local extinction of taxa along the thermal gradient, implying that temperature-driven ecological change was a key factor shaping the community background upon which evolutionary selection can operate. These findings offer novel insight into how community background impacts thermal adaptation. [ABSTRACT FROM AUTHOR]

Opportunistic pathogens are environmental microbes that are generally harmless and only occasionally cause disease. Unlike obligate pathogens, the growth and survival of opportunistic pathogens do not rely on host infection or transmission. Their versatile lifestyles make it challenging to decipher how and why virulence has evolved in opportunistic pathogens. The coincidental evolution hypothesis postulates that virulence results from exaptation or pleiotropy, i.e. traits evolved for adaptation to living in one environment that have a different function in another. In particular, adaptation to avoid or survive protist predation has been suggested to contribute to the evolution of bacterial virulence (the training ground hypothesis). Here, we used experimental evolution to determine how the selective pressure imposed by a protist predator impacts the virulence and fitness of a ubiquitous environmental opportunistic bacterial pathogen that has acquired multidrug resistance: Serratia marcescens. To this aim, we evolved S. marcescens in the presence or absence of generalist protist predator, Tetrahymena thermophila. After 60 d of evolution, we evaluated genotypic and phenotypic changes by comparing evolved S. marcescens with the ancestral strain. Whole-genome shotgun sequencing of the entire evolved populations and individual isolates revealed numerous cases of parallel evolution, many more than statistically expected by chance, in genes associated with virulence. Our phenotypic assays suggested that evolution in the presence of a predator maintained virulence, whereas evolution in the absence of a predator resulted in attenuated virulence. We also found a significant correlation between virulence, biofilm formation, growth, and grazing resistance. Overall, our results provide evidence that bacterial virulence and virulence-related traits are maintained by selective pressures imposed by protist predation. [ABSTRACT FROM AUTHOR]

Pollinators are thought to be the main drivers of floral evolution. Flowers are also colonized by abundant communities of microbes that can affect the interaction between plants and their pollinators. Very little is known, however, about how flower-colonizing microbes influence floral evolution. Here we performed a 6-generation experimental evolution study using fast-cycling Brassica rapa, in which we factorially manipulated the presence of pollinators and flower microbes to determine how pollinators and microbes interact in driving floral evolution. We measured the evolution of 6 morphological traits, as well as the plant mating system and flower attractiveness. Only one of the 6 traits (flower number) evolved in response to pollinators, while microbes did not drive the evolution of any trait, nor did they interact with pollinators in driving the evolution of morphological traits. Moreover, we did not find evidence that pollinators or microbes affected the evolution of flower attractiveness to pollinators. However, we found an interactive effect of pollinators and microbes on the evolution of autonomous selfing, a trait that is expected to evolve in response to pollinator limitations. Overall, we found only weak evidence that microbes mediate floral evolution. However, our ability to detect an interactive effect of pollinators and microbes might have been limited by weak pollinator-mediated selection in our experimental setting. Our results contrast with previous (similar) experimental evolution studies, highlighting the susceptibility of such experiments to drift and to experimental artefacts. [ABSTRACT FROM AUTHOR]

The Clostridium perfringens epidemic threatens biosecurity and causes significant economic losses. C. perfringens infections are linked to more than one hundred million cases of food poisoning annually, and 8–60% of susceptible animals are vulnerable to infection, resulting in an economic loss of more than 6 hundred million USD. The enzymes and toxins (>20 species) produced by C. perfringens play a role in intestinal colonization, immunological evasion, intestinal micro-ecosystem imbalance, and intestinal mucosal disruption, all influencing host health. In recent decades, there has been an increase in drug resistance in C. perfringens due to antibiotic misuse and bacterial evolution. At the same time, traditional control interventions have proven ineffective, highlighting the urgent need to develop and implement new strategies and approaches to improve intervention targeting. Therefore, an in-depth understanding of the spatial and temporal evolutionary characteristics, transmission routes, colonization dynamics, and pathogenic mechanisms of C. perfringens will aid in the development of optimal therapeutic strategies and vaccines for C. perfringens management. Here, we review the global epidemiology of C. perfringens, as well as the molecular features and roles of various virulence factors in C. perfringens pathogenicity. In addition, we emphasize measures to prevent and control this zoonotic disease to reduce the transmission and infection of C. perfringens. [ABSTRACT FROM AUTHOR]

The overuse of antibiotics has the effect of accelerating the evolution of bacteria and the development of superresistant bacteria. Consequently, there is an urgent need to develop new and efficient non-antibiotic-based antimicrobial agents. The Ga-TCPP framework (Frameworks) materials (GaTF) were prepared by a self-assembly method using gallium chloride (GaCl3) and tetrakis(4-carboxyphenyl)porphyrin (TCPP) as raw materials. GaTF exhibited dual antimicrobial activities, comprising gallium ions and photodynamic forces. The GaTF @ PC was modified on its surface using phosphatidylcholines (PC) to achieve good biocompatibility. GaTF@PC can effectively produce single-linear oxygen when irradiated with a 655 nm light source and gradually dissociates in phosphate buffer to release Ga3+. The effects of material concentration and light intensity on antimicrobial properties were investigated using Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) as experimental strains. The antimicrobial experiments demonstrated a positive correlation between the antimicrobial effect of GaTF@PC and both the material concentration and light intensity. At a concentration of 30 µg · mL-1, irradiation with a 655 nm light source at a light intensity of 100 mW · cm-2 for 10 minutes resulted in antibacterial rates of over 99% for both E. coli and S. aureus. [ABSTRACT FROM AUTHOR]

Nature is home to a variety of microorganisms that create materials under environmentally friendly conditions. While this offers an attractive approach for sustainable manufacturing, the production of materials by native microorganisms is usually slow and synthetic biology tools to engineer faster microorganisms are only available when prior knowledge of genotype-phenotype links is available. Here, we utilize a high-throughput directed evolution platform to enhance the fitness of whole microorganisms under selection pressure and identify genetic pathways to enhance the material production capabilities of native species. Using Komagataeibacter sucrofermentans as a model cellulose-producing microorganism, we show that our droplet-based microfluidic platform enables the directed evolution of these bacteria toward a small number of cellulose overproducers from an initial pool of 40,000 random mutants. Sequencing of the evolved strains reveals an unexpected link between the cellulose-forming ability of the bacteria and a gene encoding a protease complex responsible for protein turnover in the cell. The ability to enhance the fitness of microorganisms toward a specific phenotype and to unravel genotype-phenotype links makes this high-throughput directed evolution platform a promising tool for the development of new strains for the sustainable manufacturing of materials. [ABSTRACT FROM AUTHOR]

Chlamydiae are a large group of obligate endosymbionts of eukaryotes that includes the Chlamydiaceae family, comprising several animal pathogens. Among Chlamydiaceae, Chlamydia trachomatis causes widespread ocular and urogenital infections in humans. Like many bacterial pathogens, all Chlamydiae manipulate host cells by injecting them with type III secretion effector proteins. We previously characterized the C. trachomatis effector CteG, which localizes at the host cell Golgi and plasma membrane during distinct phases of the chlamydial infectious cycle. Here, we show that CteG is a Chlamydiaceae-specific effector with over 60 homologs phylogenetically categorized into two distinct clades (CteG I and CteG II) and exhibiting several inparalogs and outparalogs. Notably, cteG I homologs are syntenic to C. trachomatis cteG, whereas cteG II homologs are syntenic among themselves but not with C. trachomatis cteG. This indicates a complex evolution of cteG homologs, which is unique among C. trachomatis effectors, marked by numerous events of gene duplication and loss. Despite relatively modest sequence conservation, nearly all tested CteG I and CteG II proteins were identified as type III secretion substrates using Yersinia as a heterologous bacterial host. Moreover, most of the type III secreted CteG I and CteG II homologs were delivered by C. trachomatis into host cells, where they localized at the Golgi region and cell periphery. Overall, this provided insights into the evolution of bacterial effectors and revealed a Chlamydiaceae family of type III secreted proteins that underwent substantial divergence during evolution while conserving the capacity to localize at specific host cell compartments. [ABSTRACT FROM AUTHOR]

Transcriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, we use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level. We find that single-cell transcript abundances are influenced by bacterial growth state and plasmid carriage. Moreover, plasmid carriage constrains the formation of bacterial subpopulations. Plasmid genes, including those with core functions such as replication and maintenance, exhibit transcriptional heterogeneity associated with cell activity. Notably, we identify a cell subpopulation that does not transcribe conjugal plasmid transfer genes, which may help reduce plasmid burden on a subset of cells. Our study advances the understanding of plasmid-mediated subpopulation dynamics and provides insights into the plasmid-bacteria interplay. Transcriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, Cyriaque et al. use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level, providing insights into plasmid-bacteria dynamics. [ABSTRACT FROM AUTHOR]

Living organisms ranging from bacteria to animals have developed their own ways to accumulate and store phosphate during evolution, in particular as the polyphosphate (polyP) granules in bacteria. Degradation of polyP into phosphate is involved in phosphorus cycling, and exopolyphosphatase (PPX) is the key enzyme for polyP degradation in bacteria. Thus, understanding the structure basis of PPX is crucial to reveal the polyP degradation mechanism. Here, it is found that PPX structure varies in the length of ɑ‐helical interdomain linker (ɑ‐linker) across various bacteria, which is negatively correlated with their enzymatic activity and thermostability – those with shorter ɑ‐linkers demonstrate higher polyP degradation ability. Moreover, the artificial DrPPX mutants with shorter ɑ‐linker tend to have more compact pockets for polyP binding and stronger subunit interactions, as well as higher enzymatic efficiency (kcat/Km) than that of DrPPX wild type. In Deinococcus‐Thermus, the PPXs from thermophilic species possess a shorter ɑ‐linker and retain their catalytic ability at high temperatures (70 °C), which may facilitate the thermophilic species to utilize polyP in high‐temperature environments. These findings provide insights into the interdomain linker length‐dependent evolution of PPXs, which shed light on enzymatic adaption for phosphorus cycling during natural evolution and rational design of enzyme. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance is a pressing concern that poses a significant threat to global public health, necessitating the exploration of alternative strategies to combat drug-resistant microbial infections. Recently, antimicrobial peptides (AMPs) have gained substantial attention as possible replacements for conventional antibiotics. Because of their pharmacodynamics and killing mechanisms, AMPs display a lower risk of bacterial resistance evolution compared with most conventional antibiotics. However, bacteria display different mechanisms to resist AMPs, and the role of metabolic pathways in the resistance mechanism is not fully understood. This review examines the intricate relationship between metabolic genes and AMP resistance, focusing on the impact of metabolic pathways on various aspects of resistance. Metabolic pathways related to guanosine pentaphosphate (pppGpp) and guanosine tetraphosphate (ppGpp) [collectively (p)ppGpp], the tricarboxylic acid (TCA) cycle, haem biosynthesis, purine and pyrimidine biosynthesis, and amino acid and lipid metabolism influence in different ways metabolic adjustments, biofilm formation and energy production that could be involved in AMP resistance. By targeting metabolic pathways and their associated genes, it could be possible to enhance the efficacy of existing antimicrobial therapies and overcome the challenges exhibited by phenotypic (recalcitrance) and genetic resistance toward AMPs. Further research in this area is needed to provide valuable insights into specific mechanisms, uncover novel therapeutic targets, and aid in the fight against antimicrobial resistance. [ABSTRACT FROM AUTHOR]

The emergence of new infectious diseases poses a major threat to humans, animals, and broader ecosystems. Defining factors that govern the ability of pathogens to adapt to new host species is therefore a crucial research imperative. Pathogenic bacteria are of particular concern, given dwindling treatment options amid the continued expansion of antimicrobial resistance. In this review, we summarize recent advancements in the understanding of bacterial host species adaptation, with an emphasis on pathogens of humans and related mammals. We focus particularly on molecular mechanisms underlying key steps of bacterial host adaptation including colonization, nutrient acquisition, and immune evasion, as well as suggest key areas for future investigation. By developing a greater understanding of the mechanisms of host adaptation in pathogenic bacteria, we may uncover new strategies to target these microbes for the treatment and prevention of infectious diseases in humans, animals, and the broader environment. [ABSTRACT FROM AUTHOR]

Anthrax is an acute infectious zoonotic disease caused by Bacillus anthracis, a bacterium that is considered a potential biological warfare agent. Bacillus bacteriophages shape the composition and evolution of bacterial communities in nature and therefore have important roles in the ecosystem community. B. anthracis phages are not only used in etiological diagnostics but also have promising prospects in clinical therapeutics or for disinfection in anthrax outbreaks. In this study, two temperate B. anthracis phages, vB_BanS_A16R1 (A16R1) and vB_BanS_A16R4 (A16R4), were isolated and showed siphovirus-like morphological characteristics. Genome sequencing showed that the genomes of phages A16R1 and A16R4 are 36,569 bp and 40,059 bp in length, respectively. A16R1 belongs to the genus Wbetavirus, while A16R4 belongs to the genus Hubeivirus and is the first phage of that genus found to lyse B. anthracis. Because these two phages can comparatively specifically lyse B. anthracis, they could be used as alternative diagnostic tools for identification of B. anthracis infections. [ABSTRACT FROM AUTHOR]

As a common foodborne pathogen, infection with L. monocytogenes poses a significant threat to human life and health. The objective of this study was to employ comparative genomics to unveil the biodiversity and evolutionary characteristics of L. monocytogenes strains from different regions, screening for potential target genes and mining novel target genes, thus providing significant reference value for the specific molecular detection and therapeutic targets of L. monocytogenes strains. Pan-genomic analysis revealed that L. monocytogenes from different regions have open genomes, providing a solid genetic basis for adaptation to different environments. These strains contain numerous virulence genes that contribute to their high pathogenicity. They also exhibit relatively high resistance to phosphonic acid, glycopeptide, lincosamide, and peptide antibiotics. The results of mobile genetic elements indicate that, despite being located in different geographical locations, there is a certain degree of similarity in bacterial genome evolution and adaptation to specific environmental pressures. The potential target genes identified through pan-genomics are primarily associated with the fundamental life activities and infection invasion of L. monocytogenes, including known targets such as inlB, which can be utilized for molecular detection and therapeutic purposes. After screening a large number of potential target genes, we further screened them using hub gene selection methods to mining novel target genes. The present study employed eight different hub gene screening methods, ultimately identifying ten highly connected hub genes (bglF_1, davD, menE_1, tilS, dapX, iolC, gshAB, cysG, trpA, and hisC), which play crucial roles in the pathogenesis of L. monocytogenes. The results of pan-genomic analysis showed that L. monocytogenes from different regions exhibit high similarity in bacterial genome evolution. The PCR results demonstrated the excellent specificity of the bglF_1 and davD genes for L. monocytogenes. Therefore, the bglF_1 and davD genes hold promise as specific molecular detection and therapeutic targets for L. monocytogenes strains from different regions. [ABSTRACT FROM AUTHOR]

Freshwater availability is essential, and its maintenance has become an enormous challenge. Due to population growth and climate changes, freshwater sources are becoming scarce, imposing the need for strategies for its reuse. Currently, the constant discharge of waste into water bodies from human activities leads to the dissemination of pathogenic bacteria, negatively impacting water quality from the source to the infrastructure required for treatment, such as the accumulation of biofilms. Current water treatment methods cannot keep pace with bacterial evolution, which increasingly exhibits a profile of multidrug resistance to antibiotics. Furthermore, using more powerful disinfectants may affect the balance of aquatic ecosystems. Therefore, there is a need to explore sustainable ways to control the spreading of pathogenic bacteria. Bacteriophages can infect bacteria and archaea, hijacking their host machinery to favor their replication. They are widely abundant globally and provide a biological alternative to bacterial treatment with antibiotics. In contrast to common disinfectants and antibiotics, bacteriophages are highly specific, minimizing adverse effects on aquatic microbial communities and offering a lower cost-benefit ratio in production compared to antibiotics. However, due to the difficulty involving cultivating and identifying environmental bacteriophages, alternative approaches using NGS metagenomics in combination with some bioinformatic tools can help identify new bacteriophages that can be useful as an alternative treatment against resistant bacteria. In this review, we discuss advances in exploring the virome of freshwater, as well as current applications of bacteriophages in freshwater treatment, along with current challenges and future perspectives. [ABSTRACT FROM AUTHOR]