Lactobacilli have long been regarded as promising probiotic bacteria due to their safety profile, host compatibility, and beneficial roles in modulating human health. However, the therapeutic efficacy of wild-type probiotics remains constrained by limited target specificity, lack of control over their activity, and variability in clinical responses. Recent advances in synthetic biology have enabled the possibility of overcoming these constraints through precise engineering of bacterial functions, such as therapeutics production. Despite these advances, significant challenges remain in engineering lactobacilli, including limited genetic toolkits, species- and strain-dependent variability, and uncertainty regarding the stability and safety of engineered strains. This review discusses the current landscape of engineering lactobacilli for therapeutic applications, with particular emphasis on candidates undergoing clinical evaluation. Furthermore, it outlines key technical hurdles to overcome and suggests potential solutions to accelerate their translation into clinically effective and reliable microbial therapeutics.
Microbial communities often maintain ecosystem functions despite environmental fluctuations and compositional turnover. This robustness is frequently attributed to functions being encoded and provided by multiple members of the community, a phenomenon referred to as functional redundancy. Yet functional redundancy does not by itself explain whether a function will be maintained after a perturbation. A central challenge is therefore to understand when such functional overlap among taxa can translate into compensation and functional robustness.Here, we argue that addressing this challenge requires moving beyond asking whether redundancy is present to asking under which ecological conditions redundant providers are maintained and can buffer function. This requires focusing on clearly defined functions, identifying the taxa that provide them, and understanding the processes that determine whether these providers persist, are lost, or are replaced under changing conditions. From this perspective, the potential for redundancy to support functional robustness depends on whether providers differ in their responses to environmental perturbations, avoid coupled loss through interaction-network effects, and are maintained over relevant timescales through coexistence, turnover, or immigration.These conditions can be examined through the lens of trait-based ecology, interaction-network theory, and coexistence theory. They are jointly shaped by how a focal function is connected to trait distributions and species interactions, including resource competition. As a result, the relationship between functional redundancy and microbial community dynamics is inherently function-specific. This perspective shifts the focus from quantifying redundancy alone to testing when redundant providers can actually persist, compensate, and realize functions under change.
Lactic acid bacteria (LAB) are globally recognized for their essential roles in food fermentation and impact on human health. Recent evidence identifies bacterial extracellular vesicles (EVs) as unique functional entities, serving as key mediators in microbe-host interactions.LAB-EV biogenesis is primarily driven by mechanisms that compromise cell-wall integrity, including prophage-encoded holin-endolysin systems and autolysin activity. EVs as nano-sized particles exert diverse beneficial effects by inhibiting pathogens, shaping microbiota composition, reinforcing the intestinal epithelial barrier, and modulating host immunity. Their ability to cross biological barriers and reach distal organs also implies systemic impacts. Consequently, LAB-EVs are emerging as a versatile platform for next-generation postbiotics and delivery systems, capable of protecting and transporting bioactive compounds.The interpretation of the effects conveyed by LAB-EVs requires critical considerations regarding mechanistic depth and cargo heterogeneity. A so-far overlooked factor is the influence of bacteriophage elements, which can influence both biogenesis pathways and host immune signatures. To successfully transition toward industrial and clinical applications, research must shift from observational studies to rigorous mechanistic evaluations and standardized production strategies, such as the use of prophage-cured strains or the development of artificial EV-mimics. This review synthesizes recent advances in LAB-EV biology and outlines the considerations necessary to harness these nano-couriers as valuable tools in modern biomedicine and food science.
Bacteria continuously acquire foreign DNA through horizontal gene transfer, yet its successful integration depends on regulatory mechanisms that balance genome protection with evolutionary innovation. Xenogeneic silencers are central to this process: they preferentially bind AT-rich DNA, a common feature of many horizontally acquired genetic elements, and repress its transcription. Recent studies, however, reveal a much broader regulatory repertoire. Beyond transcriptional repression, these proteins contribute to chromosome organization by forming higher-order nucleoprotein complexes and phase-separated condensates that shape bacterial nucleoid architecture. Furthermore, they play roles in regulating bacteriophage infection cycles, including mechanisms by which phages hijack host silencing activities for their own benefit. Their extensive regulatory reach, spanning virulence genes, biofilm formation, specialized metabolite production, and mobile genetic elements (MGEs), underscores their central role in connecting environmental signals, including fluctuations in the second messenger c-di-GMP, with gene expression, and genome organization. The diversification of xenogeneic silencers across bacterial chromosomes, plasmids, phages, and other MGEs highlights their evolutionary significance. Together, these recent findings position xenogeneic silencers as dynamic regulatory modules that shape the fate of foreign DNA across the horizontal gene transfer network.
Microbial communities are fundamentally shaped by the diverse metabolic processes through which microbes extract energy from the chemical and light-driven potential gradients in their environment. Thus, predicting microbial community dynamics requires a quantitative framework grounded in bioenergetics and accounting for the key factors influencing metabolite concentrations in microbes’ local environment. Here, we present a perspective based on three tightly coupled factors governing microbial community metabolism: (i) the thermodynamics of redox reactions, that is, the redox tower, as a universal constraint on energy yield and reaction feasibility; (ii) external environmental and host-driven factors that set the availability of key metabolites that can act as electron donors and acceptors; and (iii) intracommunity cellular responses that alter metabolic outputs and feedback with local conditions. We emphasise that all three factors have to be integrated and considering any one without the others will only provide limited insights into community metabolisms. This integrative view needs to be incorporated into tightly coupled experiments and modelling to enable a mechanistic understanding of microbial community metabolism across environments.
Biodegradation research historically followed a reductionist approach focused on axenic (pure) cultures capable of catabolizing the specific contaminant(s) of interest. While this approach has substantially advanced our understanding of the microbiology, physiology, biochemistry, and genetics of contaminant degradation under laboratory conditions, it does not capture the complexity of natural and engineered environments. During in situ bioremediation, microbiomes are exposed to mixtures of contaminants, and microbial interactions profoundly influence contaminant transformation and fate. In anoxic environments, degradation of chlorinated compounds is often sustained by metabolic cooperation among taxonomically and physiologically distinct microorganisms. Through the exchange of metabolites such as hydrogen, formate, acetate, and other nutrients, microbial populations establish interdependent networks that overcome thermodynamic and physiological constraints, enabling self-sustaining systems of contaminant transformations that would be inefficient or impossible with individual organisms. We highlight examples of microbial interactions that underpin anaerobic catabolism of chlorinated contaminants, including systems resulting in self-sustained anaerobic bioremediation.
The need for materials that have a limited impact on the environment has led to the development of engineered living materials (ELMs), which integrate living organisms and material applications to generate functional matter. Filamentous fungi offer a promising scaffold to design ELMs, which can be produced from the bottom up, but the possibilities for introducing dynamic functionalities are limited. To solve this, multispecies ELMs can be designed, using bacteria and algae to introduce biological functions in the material. The amenability of bacteria for synthetic biology offers a suitable platform to develop novel functions, while algae can endow the material with photosynthetic properties. Due to the preexisting natural interactions between these organisms and fungi, such as lichens and fungal highways, the establishment of a consortium-based bottom-up ELM becomes feasible. In this review, we summarize the natural mutualistic interactions between fungi, algae, and bacteria and how they can be harnessed for the design and implementation of engineered living materials, using filamentous fungi as their structural backbone. Furthermore, we review the role of such interactions in industrial processes, where they have been engineered for wastewater treatment and biotechnological production. Lastly, we discuss the current challenges of engineered living materials, the advantages of consortia-based solutions, and their future perspectives.
Organ-specific immune responses are shaped by tissue microenvironments, which instruct and regulate the behaviour of tissue-resident macrophages and lymphocytes. During infection, microbes are also influenced by tissue-specific environmental signals, which may influence host-microbe interactions and infection outcome. The pathogenic fungus Candida albicans undergoes significant adaptation within the host, associated with major genetic and phenotypic changes as a result of stress responses. These underlie the ability of this yeast to evade host immune responses and establish infection. Recent evidence has pointed to C. albicans phenotypic diversity directly influencing the host microenvironment and therefore localised immune responses. In this review, we discuss organ-specific mechanisms of antifungal defence and fungal tissue-specific phenotypes and stress responses during invasive infection. We focus on C. albicans, the best studied fungal infection in multiple organs, while highlighting lessons learned from other fungal pathogens to signal important future directions for the field.
Fructophilic lactic acid bacteria (FLAB) are a group of lactic acid bacteria with unique growth characteristics, that is, poor growth on glucose. Their growth is enhanced in the presence of fructose or external electron acceptors. These organisms inhabit fructose-rich environments such as flowers, fruits, and pollinating insects, particularly honey bees. Apilactobacillus spp. and Fructobacillus spp. are representatives of FLAB, although they belong to phylogenetically distant clades. These organisms commonly possess markedly small genomes with a low number of coding DNA sequences. Furthermore, their genomes are characterized by a markedly reduced number of genes involved in carbohydrate transport and metabolism. Genome reduction in FLAB reflects convergent adaptation to fructose-rich environments rather than general genome streamlining. The two distinct FLAB genera, Fructobacillus and Apilactobacillus, independently lost more than 100 genes in statistically similar orders. In contrast, genes involved in carbohydrate and amino acid metabolism exhibited reversed orders of loss between the two genera. Furthermore, FLAB genomes lack an intact bifunctional alcohol/aldehyde dehydrogenase gene (adhE), which causes their poor growth on glucose. A comparative genomic study suggested the evolutionary process underlying adhE gene decay during adaptation to the fructose-rich environments, including pollinating insects. In conclusion, FLAB represent a unique example of habitat-driven convergent reductive evolution that can be investigated across multiple biological scales — from individual genes to whole genomes — in the diverse LAB group with a wide range of habitats, and partially share the fructophilic evolution with eukaryotic yeasts found in fructose-rich habitats.
Bacterial-fungal interactions represent fundamental ecological associations that shape microbial community structure across diverse environments. While traditionally framed through the lens of antagonism, bacteria and fungi engage in sophisticated metabolic dialogs extending far beyond simple warfare. Both primary and specialized metabolites function as context-dependent signals, nutrient resources, and modulators of cellular processes that fundamentally influence the physiology, development, and evolutionary trajectory of both fungi and bacteria. Primary metabolites mediate mutualistic relationships through cross-feeding and syntrophy, while specialized metabolites, including volatile organic compounds, lipopeptides, and phenazines, modulate fungal physiology at sub-inhibitory concentrations, reprogramming metabolic networks and triggering adaptive responses without causing cell death. At the molecular level, bacterial metabolites regulate fungal gene expression through transcriptional reprogramming, with consequences that extend to long-term evolutionary adaptation. The complexity of Bacillus-Trichoderma interactions exemplifies how these principles translate into ecological outcomes, exhibiting context-dependent transitions from competition to synergism that enhance biocontrol efficacy, plant growth promotion, and organic matter turnover. Recognizing the multifunctional nature of microbial metabolites beyond direct toxicity opens new avenues for rationally engineering cross-kingdom consortia with targeted agricultural and biotechnological applications.
Successful infection by a bacteriophage requires the injection of the phage genome into the cytoplasm of the host bacterium. To achieve this, an infecting phage must traverse the layers of the host cell envelope, including the membrane(s) and the cell wall. This process is further complicated in bacterial species that produce a proteinaceous S-layer on the outermost surface of the cell. Surprisingly little is known about the mechanistic basis of these early stages in the phage lifecycle, and even less is known about infection of S-layer producing bacteria. Recent advances in structural biology, particularly in cryoEM, have dramatically improved our understanding of the structures of both bacterial S-layers and phage virions separately, but we still lack a molecular view combining both phage and S-layer in the process of infection. Here, we review our current understanding of phage-S-layer interactions, using the human pathogen Clostridioides difficile as an example host.
Understanding the governing principles of microbial growth control is central to fundamental microbiology, biotechnology, and systems biology. Recent quantitative studies have highlighted the pivotal role of proteome allocation in microbial growth control. Rather than simply maximizing growth, microbial cells dynamically adjust their resource allocation strategies to balance multiple physiological traits due to the fundamental constraint of trade-offs. Moreover, beyond resource allocation, which largely involves ‘abundance control’, recent studies have revealed another critical regulatory layer of microbial growth — ‘activity control’, such as modulations of ribosomal elongation rates, metabolic enzyme efficiency, and the fraction of actively translating ribosomes. Integrating these quantitative principles is expected to advance a comprehensive understanding of how distinct microbial physio-types emerge across diverse ecological niches and to further guide the rational design of synthetic biology.
Cryptococcus neoformans is a prime example of accidental virulence, repurposing environmental survival strategies to persist within the hostile milieu of the human host. This review synthesizes recent advances in systems biology and infection modeling to chart the pathogen's dissemination from the lungs to distal organs along the anatomic route of infection. Upon inhalation, mammalian temperature and elevated CO2 act as host-entry signals that engage the thermotolerance and stress-response circuitry required for survival at 37°C. In the lung, capsule expansion, melanization, and trehalose-supported proteostasis underpin survival within alveolar macrophages and the establishment of latency. Morphotype diversification - including lung-predominant titan cells and the smaller 'seed' cells optimized for hematogenous spread - shapes this host encounter. During hematogenous transit, fungal cells must contend with alkaline pH and phosphate limitation, integrated through Pho4, alongside iron-mediated nutritional immunity that intersects with mitochondrial redox state, before facing Kupffer-cell-mediated hepatic filtration. At the blood-brain barrier, inositol metabolism together with hyaluronic acid, Plb1, Mpr1, and urease drives invasion, after which adaptation to copper limitation and microglial pressure governs central nervous system persistence. Beyond neuroinvasion, we highlight persistence in less frequent infection reservoirs such as the kidney and prostate, where the fungus encounters distinctchallenges, including osmotic stress and fluctuating metal availability. Finally, we outline open questions ranging from cryptococcal cytolytic effectors and vaccine development to next-generation induction therapy, and propose that large-scale gene deletion resources will be central to identifying organ-specific virulence determinants. This overview identifies the pathogen's vulnerabilities to inform the development of new treatments.
Microbial communities drive fundamental processes across the globe, from biogeochemical cycling to human health. Yet, their complexity often obscures mechanistic understanding. Synthetic communities (SynComs) have emerged as powerful tools to distill this complexity into tractable, rationally designed systems to study community function. Metabolic interactions — competition and sharing of resources between organisms — are a frequent focus of these controlled studies. The role of B vitamin cross-feeding remains a critical frontier because B vitamins are required in trace quantities for metabolism, but not all organisms can make their own, necessitating cross-feeding interactions. Here, we review recent advances in microbial ecology that use SynComs to investigate B vitamin-mediated interactions through mechanistic approaches across scales, domains of life, environments, and disciplines. We highlight key findings that demonstrate how auxotrophy, obligate cross-feeding networks, precursor sharing, exploitation and interference competition, and cell lysis together encompass B vitamin interactions. Collectively, these processes demonstrate how microbial B vitamin exchanges drive macroscale community functions like host-microbiome interdependencies. The mechanistic insights into microbial community interactions synthesized from these integrative approaches provide foundational insight into the structure and function of natural microbial communities, advancing the potential to engineer microbiomes for therapeutic and environmental applications.
Enterococcus faecalis is a human gut commensal and major opportunistic pathogen that is frequently found within polymicrobial communities at biofilm-associated infection sites, including the catheterized urinary tract, surgical and chronic wounds, the gut, and oral and mucosal niches. Its interactions with co-isolated bacteria and fungi can alter biofilm formation, antimicrobial susceptibility, immune signaling, and disease severity, yet the molecular basis of these interactions, and whether the same mechanisms recur across anatomically distinct sites, remains incompletely understood. In this review, we explore mechanistic studies of E. faecalis polymicrobial biology, organized around recurring interaction types. We first describe microbial mechanisms such as metabolic cross-feeding and iron-restricted physiology, notably ornithine/arginine exchange, lactate, and heme, as well as quorum sensing and interspecies signaling through the Fsr system, and cross-kingdom interactions with Candida albicans, emphasizing motifs that recur across different infections. We then examine host-coupled dynamics, in which the host participates mechanistically through nutritional immunity, tissue injury, immune modulation, and feedback loops that reshape the community. Throughout this review, we highlight how defined, host-relevant synthetic communities can facilitate mechanistic determinants for clinical co-occurrence, and we outline some of the limitations of current models while proposing priorities for further research.
Advances in molecular biology have expanded antimicrobial strategies that traditionally targeted proteins or metabolic pathways to now include RNA, enabling a previously unattainable precision through control of gene expression. The clinical potential of RNA-therapeutics was demonstrated during the COVID-19 pandemic, when mRNA vaccines marked a transformative milestone for RNA-based interventions for viral infections. Increasingly, similar principles are emerging for the treatment of bacterial infections. Antisense oligonucleotides (ASOs) bind complementary mRNA sequences to induce RNase H-mediated degradation or block their translation. Initially developed for genetic and neurodegenerative disorders, ASOs are now emerging as next-generation antibacterials, termed ASOBiotics, designed to silence essential bacterial genes. In this review, we explore the advances of ASO technologies with applications in bacterial pathogens, outlining design considerations while discussing the challenges and opportunities for making precision antibacterial therapeutics.
Extracellular vesicles (EVs) released by host cells are emerging as central effectors of antibacterial immunity. Through distinct biogenetic pathways, they carry selectively sorted proteins, lipids, nucleic acids, and metabolites whose composition is dynamically reshaped by the physiological state of the producing cell. Infection-derived EVs propagate inflammatory and antimicrobial signals to bystander cells, intercept secreted bacterial toxins as molecular decoys, and prime adaptive responses through antigen presentation. Conversely, bacterial pathogens have evolved counterstrategies that suppress EV release, divert cargo loading, or co-opt EVs as carriers of virulence factors, thereby converting a host defence program into a pathogenic asset. The net outcome of EV-mediated communication is highly context-dependent, varying with pathogen species, host cell type, tissue environment, and infection stage. Here, we first review evidence that EVs serve as bona fide instruments of host defence, then describe how different bacterial pathogens subvert these same pathways, and discuss methodological limitations and translational opportunities for targeting infection-derived EVs.
Bacteria employ a sophisticated arsenal of immune systems to counter bacteriophage infection. Among these systems, retron antiphage systems have emerged as a widespread class of reverse transcriptase (RT)-associated regulatory modules. Retrons are genetic elements encoding an RT and a structured noncoding RNA (ncRNA), which together generate multicopy single-stranded DNA (msDNA). In antiphage defense, an RT-msDNA module associates with its cognate effector protein to form a tripartite complex, which typically functions as a toxin-antitoxin system. Recent studies reveal a consistent defense mechanism: RT-msDNA complex functions as a molecular sentinel that senses phage-encoded triggers and regulates effector activation. Perturbation of RT-msDNA unleashes diverse cytotoxic effectors, thus inducing abortive infection (Abi) to restrict viral propagation. This review summarizes recent advances in retron activation mechanisms, effector diversity, and structural assembly, providing a comprehensive perspective on retron-mediated immunity.
