Alterations in gut microbiota have been linked to chronic kidney disease (CKD), but large-scale studies and mechanistic insights are limited. Here we analyzed gut metagenome data from 1,550 older individuals (aged 65–93 years) with comprehensive kidney function measurements. Segatella copri was positively associated with kidney function through microbial ammonia metabolism-related pathways and the asnA gene, which encodes an ammonia-assimilating enzyme. These associations were replicated in two external studies. In mice, ammonia supplementation increased serum levels of creatinine and blood urea nitrogen, accelerating CKD progression. In vitro cultures of S. copri or asnA-overexpressing Escherichia coli reduced ammonia concentrations, which was markedly attenuated in asnA-knockout S. copri. Gavage of either S. copri or asnA-overexpressing E. coli, but not asnA-knockout S. copri, mitigated ammonia-induced CKD progression in mice. These findings highlight the role of gut microbial ammonia metabolism in CKD pathogenesis and underscore the therapeutic potential of microbial-based interventions. Using human data and mice models, it was revealed that assimilation of ammonia by a gut microbe prevents its harmful accumulation that can impair kidney function.

The gut microbiota serves as a critical interface between lifestyle factors and host physiology. Despite extensive research on individual domains including diet, sleep, and exercise, an integrated understanding of their synergistic effects on microbial communities remains incomplete. This knowledge gap limits our ability to develop targeted microbiome-based interventions for metabolic and immune-related disorders.  To address this gap, we conducted a comprehensive evaluation of peer-reviewed literature from 2000 to present, identified through systematic searches of PubMed, Web of Science, and Scopus using key terms related to gut microbiota and lifestyle interventions. Our analysis focused on studies incorporating microbiome profiling techniques, controlled lifestyle interventions, and multi-omics data integration. The review prioritized mechanistic insights from both clinical and preclinical investigations while critically assessing methodological approaches across the field.  High-fiber dietary patterns consistently promoted the abundance of beneficial, short-chain fatty acid-producing bacteria, though with notable inter-individual variation. Circadian rhythm disruption was associated with reduced microbial diversity and expansion of pro-inflammatory bacterial taxa, paralleling increases in systemic inflammation markers. Athletic populations demonstrated unique microbial signatures characterized by enhanced metabolic potential, with distinct taxonomic profiles emerging across different sport disciplines.  This work synthesizes current evidence into a novel framework for understanding lifestyle-microbiota interactions, while identifying key challenges in study design and data interpretation. We propose standardized methodological approaches for future investigations and outline translational strategies for personalized microbiota modulation. These insights advance the potential for targeted microbial interventions to optimize metabolic and immune health outcomes.

Nature has evolved an exquisite yet limited set of chemical reactions that underpin the function of all living organisms. By contrast, the field of synthetic organic chemistry can access reactivity not observed in nature, and integration of these abiotic reactions within living systems offers an elegant solution to the sustainable synthesis of many industrial chemicals from renewable feedstocks. Here we report a biocompatible Lossen rearrangement that is catalysed by phosphate in the bacterium Escherichia coli for the transformation of activated acyl hydroxamates to primary amine-containing metabolites in living cells. Through auxotroph rescue, we demonstrate how this new-to-nature reaction can be used to control microbial growth and chemistry by generating the essential metabolite para-aminobenzoic acid. The Lossen rearrangement substrate can also be synthesized from polyethylene terephthalate and applied to whole-cell biocatalytic reactions and fermentations generating industrial small molecules (including the drug paracetamol), paving the way for a general strategy to bioremediate and upcycle plastic waste in native and engineered biological systems. Biocompatible chemistry merges chemo-catalytic reactions with cellular metabolism for sustainable small-molecule synthesis. Now a biocompatible Lossen rearrangement has been demonstrated to control bacterial cell growth and chemistry and applied to the remediation and upcycling of polyethylene terephthalate plastic waste in whole-cell reactions and fermentations to produce valuable industrial chemicals, including the drug paracetamol.

Bacterial small RNAs (sRNA) are key regulators of gene expression, interacting with target messenger RNAs (mRNAs) through imperfect base pairing. Unlike other non-coding RNAs such as microRNAs and PIWI-interacting RNAs, bacterial sRNAs exhibit significant sequence and structural diversity, complicating functional predictions. Recent high-throughput profiling of the sRNA interactome has accentuated this problem by revealing a highly complex network of sRNA interactions. It is clear that there is an incredible diversity of sRNA interactions with different RNA classes in vivo, including different interaction modes with mRNAs. In this review, we attempt to summarize the known sequence and structural features that contribute to sRNA function in bacteria. As many of these features drive recruitment of protein partners, we necessarily focus on interactions with chaperones and ribonucleases, the best studied being Hfq and RNase E. Where possible, we have included examples outside this well-studied system as diversity and rule breaking appear to be central themes of sRNA biology. Understanding the sequences and structures that drive sRNA function will enhance our ability to predict regulatory outcomes, and this may inform the development of effective RNA therapeutics that are inspired by bacterial sRNA mechanisms.

Type IIS restriction enzyme-mediated DNA assembly is efficient but has sequence constraints and can result in unwanted sequence scars. To overcome these drawbacks, we developed UniClo, a type IIS restriction enzyme-mediated method for universal and flexible DNA assembly. This is achieved through a combination of vector engineering, DNA methylation using recombinant methylases, and steric blockade using CRISPR–dCas9 technology to regulate this methylation. Type IIS restriction enzyme sites within fragments to be assembled are methylated using recombinant methylases, while the fragment-flanking outer sites are protected from methylation by a recombinant dCas9–sgRNA complex. During the subsequent assembly reaction, only the protected flanking sites are cut as only they are unmethylated. Fragments are correctly assembled, despite containing internal sites for the single type IIS restriction enzyme used for the one-pot assembly. The assembled plasmid can be used as a donor plasmid in a subsequent assembly round with the same type IIS restriction enzyme and the assembly vector engineering ensures removal of potential scars by a trimming process. This simplifies assembly design and only three vectors are required for any multi-round assembly. These vectors all use the same pair of overhangs. UniClo provides a simple scarless approach for hierarchical assembly of any sequence and has wide potential application.

Transgenic plants are essential for both basic and applied plant biology. Recently, fluorescent and colorimetric markers were developed to enable nondestructive identification of transformed seeds and accelerate the generation of transgenic plant lines. Yet, transformation often results in the integration of multiple copies of transgenes in the plant genome. Multiple transgene copies can lead to transgene silencing and complicate the analysis of transgenic plants by requiring researcher to track multiple T-DNA loci in future generations. Thus, to simplify analysis of transgenic lines, plant researchers typically screen transformed plants for lines where the T-DNA inserted in a single locus — an analysis that involves laborious manual counting of fluorescent and non-fluorescent seeds for screenable markers.  To expedite T-DNA segregation analysis, we developed SeedSeg, an image analysis tool that uses a segmentation algorithm to count the number of transformed and wild-type seeds in an image. SeedSeg runs a chi-squared test to determine the number of T-DNA loci. Parameters can be adjusted to optimize for different brightness intensities and seed sizes. By automating the seed counting process, SeedSeg reduces the manual labor associated with identifying transgenic lines containing a single T-DNA locus. SeedSeg is adaptable to different seed sizes and visual transgene markers, making it a versatile tool for accelerating plant research.

Understanding the relationships between bacteria, their ecological and genomic traits, and their environment, is important to elucidate microbial community dynamics and their roles in ecosystem functioning. Here, we examined the relationships between soil properties and bacterial traits within highly managed agricultural soil systems subjected to arable crop rotations or management as permanent grass. We assessed the bacterial communities using metabarcoding and assigned each amplicon trait scores for rRNA copy number, genome size, and GC content, which are classically associated with potential growth rates and specialisation. We also calculated the niche breadth trait of each amplicon as a measure of social ubiquity within the examined samples. Within this soil system, we demonstrated that pH was the primary driver of bacterial traits. The weighted mean trait scores of the samples revealed that bacterial communities associated with soils at lower pH (<7) tended to have larger genomes (potential plasticity), have more rRNA (higher growth rate potential), and are more ubiquitous (have less niche specialisation) than the bacterial communities from higher pH soils. Our findings highlight not only the association between pH and bacterial community composition but also the importance of pH in driving community functionality by directly influencing genomic and niche traits.

Numerous important environments harbor low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems. In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize contaminants.

Eukaryotic Argonautes (eAgos) have traditionally been characterized by their ability to utilize RNA guides to identify RNA targets, thereby engaging in post-transcriptional gene silencing pathways. While some eAgos have been demonstrated to use DNA guides for RNA cleavage, the ability of eAgos to cleave DNA targets remains unclear. In this study, we characterized CsAgo, an eAgo protein derived from thermophilic eukaryote Chaetomiumsp. MPI-CAGE-AT-0009, demonstrating a novel ability to cleave both DNA and RNA targets in vitro. Guided by short single-stranded DNA (ssDNA) or RNA, CsAgo exhibits robust RNA cleavage activity at 20–90°C in vitro. CsAgo can effectively cleave ssDNA guided by RNA guides at 20–50°C in vitro. Notably, CsAgo can utilize DNA guides to effectively cleave ssDNA, plasmid double-stranded DNA (dsDNA), and linear dsDNA at ≥80°C in vitro. Based on its ability to cleave dsDNA at high temperatures, CsAgo demonstrates versatility and efficacy in simplifying routine cloning workflows. Additionally, we have developed a CsAgo-based nucleic acid detection method based on a Pyrococcus furiosus Ago-mediated nucleic acid detection method, which exhibits a high sensitivity of six copies/reaction. These results suggest that eAgos include that, in theory, can be utilized for potential DNA-targeting applications. This not only enhances our understanding of eAgos but also expands the toolkit for DNA manipulation.

DNA replication is a fundamental process in all living organisms. As the most diverse and abundant biological entities on Earth, bacteriophages may utilize unconventional methods for genome replication. In this study, we identified a novel DNA replicase, GP55, from lactococcal phage 1706. GP55 comprises a helicase domain, a distinctive archaeo-eukaryotic primase domain, and a family B DNA polymerase domain, collectively exhibiting helicase, primase, and DNA polymerase activities, along with intrinsic 3′–5′ exonuclease activity. Notably, the helicase activity of GP55 is UTP/dTTP-dependent rather than ATP-dependent and facilitates strand displacement during DNA synthesis. GP55 exhibits a unique primase activity, recognizing specific but less stringent DNA sequences and preferring GTP for the initiation of RNA primer synthesis. Additionally, a newly identified α-helix domain, composed of two pairs of parallel α-helices, was found to be essential for its primase activity. The multiple activities enable GP55 to efficiently synthesize DNA de novo in the presence of dNTPs and NTPs. This study reveals a concise strategy employed by bacteriophages for genome replication using multifunctional replicases.