Klebsiella pneumoniae (Kp) is a leading cause of bacterial nosocomial infections. The rapid emergence of multidrug-resistant (MDR) Kp strains poses a significant global health threat, challenging current antibiotic-based therapies. While bacteriophage therapy offers a promising alternative, its effectiveness is often limited by the narrow host ranges of natural phages and the rapid emergence of phage resistance. Synthetic phages, with their diverse and customizable genomes, have the potential to overcome these limitations. In this study, we engineered synthetic bacteriophage variants using two in-house phage isolates, ɸ115 and ɸ100, which exhibited limited efficacy against a range of clinical Kp strains. In contrast, the synthetic phage libraries derived from the recombination of tail fiber genes and genomes of ɸ115 and ɸ100 exhibited a significantly extended host range and the ability to lyse phage resistant Kp strains. Indirect measurement of bacterial respiration as a growth indicator in presence of phage, using the OmniLog system revealed that no phage resistance Kp emerged against the synthetic phage libraries within 24 h, while other Kp strains developed resistance to the parental phages. Host range analysis, burst size measurements, and genomic DNA comparisons of individual synthetic phage isolates indicated that a short central tail fiber of ɸ100 likely plays a pivotal role in extending the host range and lysing resistant Kp strains. Our findings highlight the potential of synthetic bacteriophages to overcome the dual challenges of narrow host specificity and phage resistance. This represents a significant advancement toward developing viable phage therapeutics against MDR Kp infections.

RNAs serve versatile functional roles by virtue of their structures and dynamics. RNA computational models are typically tailored to either perform structural modeling or solve a specific class of folding problems. Here, we present PlanarFold, a coarse-grained RNA model that integrates molecular dynamics simulation in two-dimensional space with dynamic programming to explore the diverse dynamic behaviors of RNAs, achieving a speedup of more than four orders of magnitude compared with all-atom molecular dynamics models. We demonstrate that, at the secondary structure level, PlanarFold quantitatively reproduces experimental results across diverse scenarios, including the native secondary structures, thermodynamics and kinetics, mechanical properties, and co-transcriptional and de novo folding pathways. The conformational dynamics revealed by PlanarFold can provide mechanistic insight into how RNAs perform or lose functions, and offer potential targets for mutagenesis and therapeutics design, as well as guide the development of RNA-based devices. Modelling the dynamics of RNA molecules can shed light on their function. Here, the authors present PlanarFold, a fast, coarse-grained model of RNA secondary structure dynamics that can reproduces experimental measurements.

Metabolism underpins cellular function by supplying energy, biosynthetic precursors, and redox balance and in yeast there are thousands of metabolic reactions that are tightly coordinated through multilayered regulation. The yeast Saccharomyces cerevisiae has become a central model for studying metabolism and its regulation and following publication of its genome in 1996, this yeast became pivotal in systems biology. Systems biology integrates experimental data with mathematical modeling to analyze complex cellular networks. A major advance for metabolic analysis was the development of flux balance analysis and genome sequencing enabled reconstruction of the first genome-scale metabolic model (GEM) for yeast. This initial GEM described how hundreds of genes, reactions, and metabolites interact across compartments. Subsequent models, including Yeast8 and Yeast9, expanded the coverage and predictive power, and these models enable metabolic comparison, physiological analysis, omics integration, and design of strains that can be used for production of chemicals and biopharmaceuticals. Overall, S. cerevisiae remains a cornerstone of systems biology and biotechnology, with continued advances expected in integrative modeling and engineering applications.

D- and L-lactate are routinely produced as intermediates in fermentative ecosystems. However, the microbial fate of these stereoisomers remains poorly understood. Given that D-lactate is an unavoidable byproduct of digestion and a neurotoxin, understanding its microbial turnover not only holds ecological pertinence but also the potential to uncover new links between gut microbiota metabolism and host health. Here, we used chemostat bioreactors (pH 7.0, 37°C, and a solids retention time of 4 d) to enrich for lactate-consuming communities. DL-lactate-consuming consortia were enriched, characterized, and used as inoculum for duplicate bioreactors fed exclusively with D- or L-lactate. After steady-state was reached, the fed lactate stereoisomers were switched to assess community resilience. Regardless of the fed stereoisomer, the fermentation product spectra were consistent and dominated by acetate, propionate, and CO2. However, microbial communities and biomass yields diverged sharply, with a high relative abundance of Anaerotignum in D-lactate enrichments and Acidipropionibacterium and Propionibacterium in L-lactate enrichments. Notably, the biomass yield for D-lactate feeding was less than half that for L-lactate feeding, suggesting that the two isomers are metabolized through distinct biochemical pathways despite similar product spectra. Metagenomic and metaproteomic analyses confirmed divergence in D- and L-lactate conversion at both the phylogenetic and pathway levels. Our findings reveal how the stereoisomer identity of microbes shapes their niche specialization, with implications for understanding the ecology and clinical impact of lactate metabolism.

How antiviral immunity first arose in animals is a central question in evolutionary biology. Here, using the sea anemone Nematostella vectensis, we identify CARDIB, a previously uncharacterized gene located next to RLRb—a cnidarian homologue of the vertebrate RIG-I-like receptor family. This conserved genomic linkage across Anthozoa reveals an ancient coupling between immune sensing and regulation. Despite sequence similarity to vertebrate MAVS, CARDIB performs an opposing function: it represses immune genes under basal conditions yet is essential for activation upon viral challenge. CARDIB binds RLRb through a single CARD domain, forming a repressive complex. Loss of either gene abolishes antiviral transcription, disrupts apoptosis and elevates viral load under laboratory conditions. Both genes, as well as the RLRb paralogue RLRa, are essential for antiviral defence under native conditions. Phylogeny places the cnidarian CARDs distinctly from the vertebrate RLR–MAVS families, revealing an ancient mechanism that regulates the antiviral response through CARD-based signalling. Experiments in Nematostella vectensis identify CARDIB as an anthozoan-specific antiviral mediator with sequence and structural homology to the mammalian immune-activating MAVS protein but with opposing, immune-repressing functions.

The gut microbiota is implicated in adverse effects associated with low-calorie sweeteners. Yet, the direct impact of sweeteners on gut bacteria remains largely uncharacterized. Here, we report interactions between 25 phylogenetically diverse gut bacterial strains and 39 commercially used sweeteners. We tested these sweeteners individually and in combination with four commonly co-consumed compounds, viz., advantame, caffeine, vanillin, and duloxetine. Three-quarters of the tested sweeteners individually impacted the growth of at least one tested bacterial strain. Further, over 100 interactions were found between sweeteners and the four co-consumed compounds. Isosteviol, a commonly used sweetener-component, and duloxetine, an antidepressant, synergistically inhibited Roseburia intestinalis, a bacterium previously linked to glucose homeostasis, and Parabacteroides merdae, a prevalent commensal linked to healthy microbiota. Proteomic, metabolomic, and genetic analyses indicate altered small molecule transport underpinning this sweetener–drug synergy. The isosteviol-duloxetine combination also modulated metabolism of a synthetic gut bacterial community, leading to increased toxicity to HeLa cells and altered secretion of inflammation-modulatory cytokines IL-6 and IL-8 by Caco-2 cells. Our data warrant further studies on interactions between low-calorie sweeteners and common xenobiotics.

CRISPR-Cas and toxin-antitoxin systems can serve as antiviral defense mechanisms in prokaryotes. In typical toxin-antitoxin systems, toxin activation can limit phage propagation by inducing growth arrest or reduced cellular fitness, while the antitoxin neutralizes toxin activity. Here, we study potential functional synergy between a CRISPR-Cas13a system and a type II toxin-antitoxin module (HicAB) from a Leptotrichia bacterium, when heterologously expressed in E. coli, as well as in biochemical and structural analyses. We show that the antitoxin HicB exhibits toxic properties, and Cas13a directly activates HicB, triggering growth inhibition and conferring protection against bacteriophages. Structural analyses reveal that Cas13a binding promotes the spatial proximity of HicB tetramers, likely enabling its activation. The toxin HicA competitively binds to HicB, thereby inhibiting Cas13a-mediated HicB activation. Importantly, both CRISPR RNA and HicB independently suppress HicA toxicity. Structural evidence indicates that CRISPR RNA forms a hetero-tetradecameric complex with HicAB, occluding HicA’s active site and neutralizing its toxic function. Thus, our findings indicate functional synergy between distinct bacterial immune strategies. CRISPR-Cas and toxin-antitoxin systems can serve as antiviral defense mechanisms in prokaryotes. Here, the authors provide evidence of functional synergy between a CRISPR-Cas13a system and a type II toxin-antitoxin module.