This study presents an integrated waste-to-energy strategy for the sustainable conversion of the biodegradable organic fraction of municipal solid waste (BOFMSW) into biohydrogen (Bio.H2) and biomethane (Bio.CH4) through a two-stage continuous stirred dark fermentation (DF) process. The first-stage bioreactor was inoculated with Clostridium Thermocellum selectively enriched in a 2-bromoethanesulfonic acid (BESA) medium, and the influence of bimetallic ion catalysts NiCl2 + FeCl2 and NiCl2 + FeSO4 was evaluated at various concentrations (25, 50, 75, and 100 mg/L). The catalyst combination NiCl2 + FeCl2 at 75 mg/L produced the maximum Bio.H2 yield of 3162 L, representing a 69% enhancement compared with the catalyst-free substrate. At this optimal catalytic concentration, the percentage of H2 in the gas composition was 69.26%. The second-stage bioreactor utilized the effluent from the first stage for Bio.CH4 generation, achieving the highest cumulative yield of 729 L at 50 mg/L NiCl2 + FeCl2, which was 59% higher than that of the catalyst-free substrate. The two-stage process achieved an overall COD removal efficiency of 93.18%, demonstrating the system’s effective capacity for energy recovery. Fourier Transform Infrared (FTIR) and Field Emission Scanning Electron Microscopy (FESEM) analyses confirmed the biochemical and morphological degradation of complex organics into volatile fatty acids, illustrating efficient substrate conversion and microbial proliferation. The final digested slurry, rich in nitrogen, phosphorus, and potassium, was found suitable for use as a bio-fertilizer, supporting nutrient recycling and soil enrichment. This integrated process not only improved energy recovery efficiency but also achieved near-zero waste discharge, combining waste-to-energy and waste-to-resource approaches. The developed system demonstrates strong potential for pilot-scale implementation of Bio.H2, and Bio.CH4 for co-production from municipal solid waste (MSW), offering a circular bioeconomy pathway toward low-carbon, sustainable urban waste management.

Extracellular vesicles (EVs) are cell-released lipid-wrapped nano- to micro-sized particles without self-replication ability. Plant cells secrete EVs (plant EVs, PEVs) during normal development of plants and in plant response to external stimuli. Distinct from plant-derived nanoparticles, here we narrow the definition of PEVs, which are naturally secreted by cells, excluding those from disrupted cells or artificial vesicles with properties similar to those of EVs. We focus on PEV classification, isolation methods, and their biogenesis, cargos, biological functions, and applications. In addition, we discuss the challenges and opportunities in this field.

Marine bacteria alternate between planktonic and surface-attached lifestyles, facing continuous phage predation. However, how these lifestyles shape resistance evolution remains poorly understood. Using a Roseobacter model strain, we demonstrate that surface-attached populations exhibit 26-fold higher survivability than planktonic counterparts during lytic phage infection. This advantage emerges through the evolution of heterogeneous subpopulations exhibiting diverse resistance phenotypes, a pattern absent in planktonic populations. Whole-genome sequencing of 139 heritable phage-resistant mutants revealed fundamentally divergent mutational patterns, with planktonic populations predominantly harboring tandem repeat mutations, whereas surface-attached populations favor non-coding mutations. Despite this, both lifestyles independently converged on mutations in the CtrA phosphorelay system, identifying CtrA as a previously unrecognized evolutionary target of phage-driven selection and triggering planktonic-to-surface-attached switch. Further analyses revealed systematic downregulation of motility genes and enhancement of biofilm formation, mechanistically linking phage resistance to lifestyle transitions. The identified CtrA mutations occur in regions highly conserved across ecologically important marine Alphaproteobacteria (Rhodobacterales) that are known to switch between planktonic and surface-attached states, suggesting lifestyle-dependent evolutionary trajectories may broadly shape phage resistance in marine ecosystems. Marine bacteria are often under constant phage predation. Li et al. present that surface-attached populations exhibit 26-fold higher survivability than planktonic counterparts during lytic phage infection. They identify CtrA as an evolutionary target for phage-driven selection towards an attached lifestyle.

While the impact of non-antibiotic drugs on gut bacteria is well-known, their mechanisms of action remain poorly characterized, and effective mitigation strategies for drug-induced dysbiosis are still limited. Here, we screened bacteria-derived drug-target protein homologs (BDTPHs) mapped to 63 target proteins and 107 associated drugs to quantify “drug–BDTPH–bacterium” interactions. These interactions were validated by co-culture experiments using 10 drugs and 25 strains, enzyme assays, and genetic perturbations in Escherichia coli. Ex vivo and in vivo testing with six drugs showed that over 50% of affected genera exhibited high affinity, indicating microbiota alterations through the “drug–BDTPH–bacterium” axis. Leveraging this quantitative interaction framework, we identified a strain of Bifidobacterium animalis that can competitively bind methotrexate through high-affinity BDTPH, thereby effectively alleviating gut microbiota dysbiosis in vivo. Our findings elucidate a mechanism by which non-antibiotic drug effects on bacterial growth, and suggest a universal homology-based competition strategy to restore drug-disrupted microbiota. Here, the authors uncover a mechanism by which drug-target homologs mediate non-antibiotic drug effects on bacterial growth, and suggest a universal homology-based competition strategy to reverse MTX-induced microbiota dysbiosis.

The discovery of antibiotics and their subsequent therapeutic use revolutionized our ability to treat once deadly infectious diseases, and antibiotics have become one of the most commonly prescribed drug classes. Unfortunately, these compounds not only target pathogenic strains, but also non-pathogenic bacteria that fulfill important functions for the human host. As such, antibiotic treatment can cause severe collateral damage, resulting in dysbiosis, for example, in the human gut microbiome. Given the immense importance of the gut microbiome for human health, antibiotic-induced dysbiosis can cause a variety of detrimental health outcomes. In addition, antibiotic (over-)use causes selection of antibiotic-resistant strains, and the human gut microbiome has become a major reservoir for resistance determinants that can transfer to pathogenic isolates and cause hard-to-treat infections. In this review, we describe various adverse effects that antibiotic use has on the human gut microbiome, how we can approach this problem experimentally, and discuss pathways to mitigate antibiotic-induced collateral damage.

Feedforward loops (FFLs) and feedback loops (FBLs) are ubiquitous network motifs that mediate signal filtering, pulse generation, and state switching; yet, how coupling FBLs to FFLs produces robust multistability—a key mechanism for cellular decision-making—remains unclear. Here, we systematically investigate coupled FFL–FBL architectures by focusing on two prevalent FFL types, each with AND or OR logic, yielding four distinct frameworks. For each framework, we enumerate all 36 = 729 possible circuits, corresponding to three possible states (activation, inhibition, or absence) for each of six feedback edges, formulate each circuit as a system of ordinary differential equations, and quantify robustness as the proportion of 100,000 randomly sampled parameter sets exhibiting multistability. Our results reveal two key principles. First, positive self-activation is a primary driver of multistability, but the identity of the critical node(s) depends on the FFL type and logic. Second, coherent FFLs support multistability more readily than incoherent ones, whereas the choice between AND and OR logic has a comparatively weaker effect. Notably, we identify representative high-performing circuits within each framework and find that a small set of circuit designs remain robustly multistable across all four frameworks. These findings advance the theoretical understanding of motif design and provide practical guidelines for engineering synthetic multistable circuits.