The gut microbiome governs aspects of human growth and development. While human milk's primary purpose is metabolism, it also provides nonnutritious biologics and macromolecules. This mixture includes the human milk oligosaccharides (HMOs), which are indigestible and survive the low pH of the stomach and small intestine, reaching the large intestine intact. Here, HMOs serve as prebiotics for beneficial bacteria, providing a competitive growth advantage over potential pathogens. Upon metabolizing HMOs, commensals generate short-chain fatty acids and metabolites that enhance the gut community. Therefore, HMOs work to develop and sustain the gut microbial community as a living therapeutic that prevents illness from potential microbial pathogens and modulates development of the infant gut. The goal of this targeted review is to characterize the roles HMOs play in governing bacterial and viral members of the infant gut microbiome, describing how HMOs both define a healthy microbiota and prevent microbial dysbiosis.

Solar-driven biosynthesis from carbon dioxide can facilitate sustainable chemical manufacturing. However, cell-density limits and contamination susceptibility have seriously hampered its practical implementation. Here we develop a solar–chemical hybrid-driven biosynthesis (SCHB) strategy integrating wastewater-based phosphorus recovery into biological photosynthetic metabolism for chemical production. Specifically, we incorporate the phosphite oxidation pathway into cyanobacteria to supplement additional electrons to stimulate bacterial growth. This strategy conferred contamination resistance and enabled the utilization of phosphite-rich wastewater. A series of chemicals including raspberry ketone, indigo and its derivatives were effectively synthesized via SCHB, and the synthesis efficiency was promoted by a factor of up to 305%. Furthermore, the scalability of SCHB was demonstrated at the 500-litre level with real wastewater, which synchronized chemical production with nutrient recovery. Life-cycle assessment and techno-economic analysis indicated notable environmental benefits and economic feasibility. This study potentially opens a viable approach for the sustainable biosynthesis of chemicals. Bio-photosynthesis has the potential to achieve sustainable chemical production, but technical challenges remain. This work proposes a solar–chemical hybrid-driven biosynthesis strategy to achieve efficient chemical production from wastewater and carbon dioxide.

Microbial cell factories offer a sustainable route to plant-derived natural products, but yield drift and strain degeneration persist. Growth-coupled biosynthesis can continuously enrich high producers, yet specific product-responsive biosensors remain scarce and their population-level effects are unclear. Here, we describe a rapid transcriptome-mining workflow that, as proof-of-concept, delivers yeast biosensors for glycyrrhetinic acid and medicarpin. By fine-tuning PDR5 promoter, we expand the dynamic range of the glycyrrhetinic acid sensor and wire it to an essential gene, establishing a growth-addiction circuit that increases titer by 46.8 % after subculture. Single-cell transcriptome reveals that the evolved strain population exhibits a completely different division of labor compared to the initial strain. Coupling does not eliminate phenotypic heterogeneity; instead, it amplifies a dedicated sub-population marked by discrete transcriptional signatures. Deletion of genes highly expressed in non-producing cells or enrichment of high-producing cell clusters can further boost population-level production. This study provides both a generalizable biosensor-discovery platform and single-cell-guided strategies for stabilizing and optimizing natural-product cell factories. Growth-coupled biosynthesis in microbes can stabilise production yields, yet their population-level effects are unclear. Here the authors use ScRNA-seq to reveal that an evolved glycyrrhetinic acid-producing growth-coupled yeast strain population achieves division of labor.

Sustainable materials are needed to address the serious economic and safety risks of microbial metal corrosion. Colonizing metal surfaces with biofilms of noncorrosive microbes was previously shown to reduce aerobic, abiotic corrosion. However, the ability of biofilms to thwart highly corrosive anaerobic microbes is untested. Here we report on a strain of Escherichia coli genetically modified for enhanced metal adherence and adaptively evolved to tolerate sulfide. The E. coli biofilms effectively inhibited all known major routes for anaerobic microbial iron corrosion, including proton and sulfide attack, as well as the highly aggressive corrosion of electroactive microbes that directly extract electrons from Fe0. The E. coli biofilms prevented corrosion much better than biofilms of other microorganisms previously reported to reduce aerobic, abiotic corrosion. The results highlight the possibility of tailoring biofilm properties to function as effective sustainable, self-healing coatings to safeguard critical metal infrastructure.

Prime editing has emerged as a precise and powerful genome editing tool, offering a favorable gene editing profile compared to other Cas9-based approaches. Here we report several nCas9-DNA polymerase fusion proteins and their engineered versions to create a simple and efficient two-component chimeric oligonucleotide-directed editing (CODE) system. CODE contains a derivative of Bst DNA polymerase engineered for increased thermostability and processivity as well as a chimeric pegRNA (cpegRNA) for programmable search and replace genome editing. Additionally, CODEMax(exo+) features a 5’ to 3’ exonuclease activity that promotes effective strand invasion and repair outcomes favoring the incorporation of the desired edit. We demonstrate that CODEs can perform small insertions, deletions, and substitutions with improved efficiency compared to PEMax at many loci in HEK293T cells with plasmid- and RNP-based delivery. We also show that CODEMax can successfully modify mouse and bovine embryos with up to 9.3% precise editing. Further optimization of CODEMax systems may enhance editing outcomes in embryos and other challenging contexts. Overall, CODEs complement existing prime editors to expand the toolbox for genome manipulations without double-stranded breaks. Gene editing technologies enable precise DNA modifications but remain limited by efficiency, precision of intended edits, and flexibility. Here, authors develop chimeric oligonucleotide-directed and Cas polymerase-based systems that enhance programmable gene correction across cells and embryos.

High-salinity conditions frequently impair the fermentation performance of Saccharomyces cerevisiae in industrial processes involving high-osmolarity substrates. Identifying genetic determinants that enhance salt tolerance is therefore essential for the development of robust yeast cell factories. In this study, a comparative transcriptomic analysis was performed to investigate the transcriptional responses of a salt-tolerant strain, E-158, and its parental strain, KF-7, under 1.25 M NaCl stress, with the aim of identifying potential targets for strain engineering. Comparative transcriptomic analysis revealed extensive transcriptional differences between E-158 and KF-7 under high-salt conditions, involving central carbon and nitrogen metabolism, peroxisome-associated oxidative stress responses, ion transport, cell wall-related processes, and sporulation-related pathways. Based on these profiles, two transcription factors (CUP9 and ZNF1) and three functional genes (DAL1, IDP2, and CTA1) were selected for functional validation. Overexpression or deletion of the transcription factors, as well as overexpression of the functional genes, was carried out in KF-7. Fermentation experiments under 1.25 M NaCl demonstrated that all engineered strains outperformed the parental strain. Among them, overexpression of CTA1 resulted in the greatest improvement, with glucose consumption and ethanol production increased by 35.04% and 45.66%, respectively, after 96 h of fermentation. This study demonstrates that comparative transcriptomics can serve as an effective strategy for identifying engineering targets associated with salt tolerance in S. cerevisiae. The evaluated genes provide potential targets for strain improvement and offer insights for the rational design of yeast cell factories suited for high-salinity biofuel and bioproduct fermentation processes.

Our double-stranded DNA (dsDNA) genomes are famously compacted by proteins in the nuclei of our cells, resulting in meters of dsDNA being confined in micron-sized volumes. The most prevalent form of viral genomes, however, is single-stranded RNA (ssRNA), which is compacted at significantly higher density in protective protein shells with nanometer dimensions. In this review, we discuss the special nature of ssRNA that allows it to be spontaneously packaged in this way by co-self-assembly with viral capsid protein (CP). We focus on the few viruses whose nucleocapsids can be reconstituted from their purified CP and ssRNA genomes and whose CPs can spontaneously package heterologous RNA into virus-like particles (VLPs). These VLPs are then compared with their cell-synthesized versions, with lentivirus and adeno-associated virus vector particles, and with nucleocapsids formed by nonviral proteins whose messenger RNAs are put under directed evolutionary pressure to be packaged by them in cellulo.

Genome-scale and multigene transcriptional regulation are crucial technologies in metabolic engineering. However, in E. coli, a stable and universal tool for whole-genome transcriptional activation, and an in situ tool for multigene regulation remain lacking. Here, we present CAGER, a versatile clustered regularly interspaced short palindromic repeats-associated transposases (CAST)-mediated gene regulation toolkit. Through rational mutagenesis, we mitigate the intrinsic transcriptional interference in the left end of CAST system derived from Vibrio cholerae. Using promoters or terminators as cargoes, CAGER constructs the genome-wide activation (3272 genes) or termination (3339 genes) libraries, from which new activation or inhibition targets relevant to cellular acetic acid assimilation are identified. Furthermore, with the aid of M13 phage and the promoter library, CAGER facilitates rapid in situ multigene expression diversification. Applied to lycopene synthesis, a library targeting seven genomic sites is constructed within 24 h, achieving a 73.6-fold yield increase. This work highlights the modifiability of CAST elements and broadens CAST’s application in transcriptional regulation.

The production of methane, a potent greenhouse gas, by ruminants during feed digestion is designated enteric methane emissions (EME) and is mainly produced by the rumen microbiome. Reliably recording EME in large populations is currently cost-prohibitive, hampering farming decisions aimed at reducing EME. Here, we perform comprehensive analyses on host genetics, KEGG orthology groups (KOs) from the rumen metagenome, and EME of more than 800 cows from Australia and Spain. We report that the rumen microbiome explains up to 34% of the EME variance, and when combined with the host genome, the variance explained is up to 59% with prediction accuracies of up to 0.40. The results support a recursive model, where both the host genome and rumen metagenome explain EME. The isometric log-ratio transformation of KOs may potentially better capture relationships between host genetics and the rumen microbiome than the centered log-ratio transformation, and BayesR yielded slightly higher microbe‑explained EME variance than best linear unbiased prediction. A forward simulation estimated to reach 90% of EME prediction accuracy with 6,000 animals with rumen microbiomes and host genomes, which could open opportunities for developing strategies to reduce EME. Our study contributes to the foundation for reducing EME, supporting global warming mitigation. Ruminal microbial genes and cattle (Bos taurus) genetics predict about 60% of enteric methane emission variation between animals, supporting strategies aimed at reducing these emissions.

From aircraft to neural networks, engineers are often inspired by biological systems; however, literature often conflates inspiration with scientific evidence. Here, I propose a transparent and consistent reporting framework for bio-inspired design that can accelerate technological progress and stimulate collaborative scientific pursuits. From aircraft to neural networks, engineers are often inspired by biological systems; however, literature often conflates inspiration with scientific evidence. Christina Harvey proposes a transparent and consistent reporting framework for bio-inspired design that can accelerate technological progress and stimulate collaborative scientific pursuits.

Triggering immune response through generation of signal molecules is a common immune strategy across all domains of life. In the bacterial type IV Thoeris antiphage system, a Toll/interleukin-1 receptor (TIR)-domain protein produces adenosine 5’-diphosphate-cyclo[N7:1”]-ribose (N7-cADPR) as the immune signal to activate a Caspase-like effector. Here, we identified an inhibitor of type IV Thoeris through a phage mating assay that allows a sensitive phage to acquire anti-defense genes from related resistant phages. The inhibitor (hereafter TadIV-1) functions as a sponge that sequesters the N7-cADPR signal to inhibit Caspase activation. Structural analyses of TadIV-1 indicate a distinctive signal binding mechanism, wherein the binding pocket comprises its N-terminal flexible loop. In addition, phages lacking TadIV-1 can escape type IV Thoeris sensing through mutation in the capsid vertex protein. Collectively, this work expands the phage anti-defense arsenal with a unique immune signal sequestration mechanism and provides insights into phage invasion recognition mechanism of type IV Thoeris. The bacterial type-IV Thoeris system produces, in response to phage infection, a signal molecule that triggers protein degradation and stops viral replication. Here, the authors identify a phage protein that sequesters the signal, thus blocking the antiviral response.