Phages are typically classified as temperate, integrating into host genomes, or lytic, replicating and killing bacteria; for this reason, lytic phages are not expected in bacterial genome sequences. Here we analyse 3.6 million bacterial genome assemblies from 1,226 species and find 119,510 lytic phage genomes, which we term bacterial assembly-associated phage sequences. This represents a ~5-fold increase in the number of phages with associated hosts and raises questions about fundamental aspects of phage biology. Our analyses of bacterial assembly-associated phage sequences revealed previously undescribed phage clusters, including clusters distantly related to Salmonella Goslarviruses in Escherichia coli and Shigella, while also substantially expanding known genera such as Seoulvirus (from 16 to >300 members). Close relatives of lytic phages used therapeutically were also detected, suggesting clinical isolate sequencing unknowingly archives potential phage candidates. The discovery of complete, lytic phage genomes within bacterial assemblies challenges assumptions about the nature of the lytic lifestyle and reveals an untapped reservoir of phages. Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle.

Understanding microbial phenotypes from genomic data is crucial for studying co-evolution, ecology, and pathology. This study presents a scalable approach that integrates literature-extracted information with genomic data, combining natural language processing and functional genome analysis. We applied this method to publicly available data, providing novel insights into predicting microbial phenotypes. We fine-tuned transformer-based language models to analyze 3.83 million open-access scientific articles, extracting a phenotypic network of bacterial strains. This network maps relationships between strains and traits such as pathogenicity, metabolism, and biome preference. By annotating their reference genomes, we predicted key genes influencing these traits. Our findings align with known phenotypes, reveal novel correlations, and uncover genes involved in disease and host associations. The network’s interconnectivity provides deeper understanding of microbial communities and allowed identification of hub species through inferred trophic connections that are difficult to infer experimentally. This work demonstrates the potential of machine learning for uncovering cross-species gene–phenotype patterns. As microbial genomic data and literature expand, such methods will be essential for extracting meaningful insights and advancing microbiology research. In summary, this integrative approach can accelerate discovery and understanding in microbial genomics. Ultimately, such techniques will facilitate the study of microbial ecology, co-evolutionary processes, and disease pathogenesis to an unprecedented depth.

Acid resistance is crucial for enterobacteria to withstand host acidic environments during infection, including the gastrointestinal tract and macrophage phagosomes. A key acid resistance mechanism of the facultative intracellular pathogen Salmonella is the expression of the arginine decarboxylase AdiA. While AdiA confers acid resistance via an H+-consuming reaction, we discover that the 3′-untranslated region (UTR) of adiA mRNA is processed by RNase E into a regulatory small RNA, AdiZ. Through RNA–RNA interactome profiling and transcriptomic analysis, followed by in vitro structural probing and in vivo validations, we demonstrate that AdiZ directly base-pairs with and negatively regulates ptsG, pykF, and dmsA mRNAs involved in glucose uptake, glycolysis, and anaerobic respiration, respectively. Intriguingly, AdiZ is induced and facilitates Salmonella survival within macrophages, where acidic and hypoxic stresses prevail. Thus, simultaneous expression of AdiA and AdiZ from a single mRNA ties arginine-dependent acid resistance to metabolic reprogramming of Salmonella in the host intracellular niches.

Biodegradable bioplastics have emerged as promising alternatives to conventional plastics in the current scenario of growing demand for sustainable materials. However, the high costs associated with their production still interfere with the proper dissemination of these materials. The present review will deal with the different aspects of the production of biodegradable bioplastics in biorefineries as an approach for cost reduction and low waste generation, aligning with circular bioeconomy principles. By employing different types of biomass and conversion processes, bioplastics and their composites can be considered a valuable product in biorefineries, demonstrated by actual case studies and functional industries.

Heterotrophic nanoflagellates are the chief agents of bacterivory in the aquatic microbial loop but remain underrepresented in culture collections and in genomic databases. We isolated and characterized a representative of the previously uncultured freshwater Cryptomonad Group 1 (CRY1a) lineage using a genome-streamlined, ultra-small and abundant microbe Planktophila versatilis as a prey and Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) probe–based screening. This isolate, Tyrannomonas regina, is one of the most dominant ubiquitous heterotrophic cryptomonads in freshwaters. It is a small heterotrophic nanoflagellate (ca. 3–5 μm) and has the smallest genome of any cryptomonad sequenced thus far. The compact genome (ca. 69 Mb) revealed no traces of a photosynthetic lifestyle, consistent with its phylogenomic placement as a sister clade to cryptophytes that are characterized by the acquisition of a red-algal symbiont. Moreover, in comparison to its photosynthetic counterparts, its genome presents substantially lower repeat content and endogenous viral elements. Genomes of two giant viruses, Tyrannovirus reginensis GV1 and GV2, were also recovered from the same culture and represent a viral genus that has been described so far solely by metagenome-recovered genomes. Collectively, these findings provide insights into genomic ancestry and evolution, widespread ecological impact, and interactions of an elusive protist lineage and illustrate the advantages of culture-centric approaches towards unfolding complex tapestries of life in the microbial world.

Bacteria have a variety of mechanisms for limiting predation by phages. SpbK is a Toll/interleukin-1 receptor (TIR) domain-containing antiphage defence protein from Bacillus subtilis that provides protection against the temperate phage SPβ via abortive infection. Here we structurally characterise SpbK and its interaction with the SPβ protein YonE. We demonstrate that SpbK is an NADase that produces both ADP-ribose (ADPR) and canonical cyclic ADPR with a N1-glycosidic bond (cADPR, also referred to as N1-cADPR). Combining cryo-EM, in silico predictions, site-directed mutagenesis, and phage infection assays, we show that formation of two-stranded head-to-tail assemblies of SpbK TIR domains is required for both NADase activity and antiphage defence. We also demonstrate that YonE is a dodecameric portal protein that activates the NADase function of SpbK by facilitating TIR domain clustering. Collectively, our results provide insight into how bacterial TIR NADases recognise phage infection. SpbK protects Bacillus subtilis from phage infection by depleting NAD⁺. In this study, the authors uncover the molecular mechanisms underlying SpbK’s self association-dependent NADase activity and its activation by the SPβ phage portal protein YonE.

Methane emissions from rice paddies represent a critical environmental concern in agriculture. Although genetic strategies for mitigating emissions have gained attention, the specific microbial and molecular mechanisms remain underexplored. Here, we investigated how the gs3 loss-of-function allele in the near-isogenic rice line Milyang360 modulates rhizosphere and endosphere microbial communities under distinct nitrogen regimes. Field experiments revealed that Milyang360 consistently reduced methane emissions compared with its parental line, Saeilmi, particularly under low-nitrogen conditions. Integrated plant transcriptomic and rhizosphere metagenomic analyses, including the reconstruction of Metagenome-Assembled Genomes, demonstrated that the gs3 allele upregulated genes related to root hair elongation or promoting microbial symbiosis. This physiological change limited substrate availability for methanogens and facilitated the colonization by beneficial microorganisms. Consequently, we observed a functional shift in the microbiome, characterized by the enrichment of methanotrophs and nitrogen-fixing bacteria. This microbial restructuring was most prominent under low-nitrogen conditions, indicating a strong genotype by environment interaction. Our findings highlight the gs3 allele’s dual role in reducing methane emissions and improving nitrogen use efficiency by recruiting a beneficial microbiome. This study provides a clear mechanistic link between a plant gene and rhizosphere ecology, offering a promising genetic target for developing sustainable, low emission rice cultivars. 

High expression of heterologous proteins is often achieved by integrating multiple copies of a gene into a host. However, such multicopy systems are prone to genetic instability due to homologous recombination between identical sequences. We present the multisequence ChimeraMap (MScMap), an algorithm for designing multiple synonymous coding sequences that minimizes recombination risk while maintaining high expression. MScMap extends the ChimeraMap framework by selecting diverse nucleotide blocks from a host genome to encode the target protein, balancing host adaptation and sequence dissimilarity. We introduce heuristics for block selection and concatenation to reduce long common substrings, a known driver of recombination. Our method outperforms a multi-objective evolutionary algorithm in both genetic stability and predicted expression across a wide range of human proteins while being significantly faster. We also show that MScMap can also be used to reduce sequence repeats within a single coding sequence. A web tool for single and multicopy coding sequence optimization is available online.

This work aims to improve RNA synthesis and manufacturing, exemplified by T7 RNA polymerase-driven in vitro transcription. We developed a novel, plasmid-compatible co-tethering strategy that functionally couples RNA polymerase to its promoter DNA immobilized on a solid matrix. As demonstrated recently, co-tethering enhances promoter binding, increases RNA yield, and suppresses RNA re-binding, especially under high-salt conditions, thereby reducing double-stranded RNA by-products. The system leverages asymmetric end-labeling of linearized plasmid DNA using a simple “Klenow fill-in” reaction with modified nucleotides, enabling stable attachment of DNA to both RNA polymerase and solid support (magnetic beads). The immobilized co-tethered polymerase–DNA complex supports efficient transcription initiation in high-salt environments (which further reduces RNA re-binding), yielding RNA of high purity. Co-tethered complex remains functionally stable over extended storage and multiple transcription cycles (10-20 rounds), re-using the enzyme–DNA catalyst. Transcripts of lengths (0.8, 5.6, and 8.6 kb) are efficiently produced. Highly sensitive in vitro assays with immune cells confirm low immunogenicity and strong translational output, while in vivo validation using a novel Matrigel-plugged mouse model demonstrates robust expression and safety. With a simple modification to the DNA template, the reusable, co-tethered enzyme–DNA catalytic complex streamlines mRNA manufacturing by producing RNA of higher purity from the outset.

Retrons are tripartite bacterial systems composed of non-coding RNA (ncRNA), reverse transcriptase (RT), and effector proteins with diverse enzymatic domains. Here, we characterized Retron-Eco11, a type III-A3 retron associated with a phosphoribosyltransferase-like effector, and demonstrated that it mediates antiphage defense and can be harnessed for genome editing. All three components—ncRNA, RT, and effector—are essential for defense. Retron-Eco11 protects Escherichia coli against multiple phages and is specifically activated by structurally related, phage-encoded helicases, including UvsW and D10 from phages T4 and T5. We show that these helicases trigger effector-mediated toxicity, leading to abortive infection, which is associated with phosphoribosyl pyrophosphate depletion due to PRTase activation, thereby altering nucleotide metabolism. UvsW interacts directly with multicopy single-stranded DNA, and effector protein activation requires the catalytic activity of phage-encoded helicases. Our data indicate that activation occurs without detectable effector release or measurable changes in the composition of the Retron complex. Beyond its defensive role, Retron-Eco11 enables targeted genome editing in bacterial and eukaryotic cells, underscoring the biological relevance and biotechnological potential of type III-A3 retrons.