Aug 2026· Nature Biotechnology· 0 citations· 77 references
Medicine
TL;DR
This work identifies a panel of strong constitutive promoters that drive robust gene expression across diverse clostridial strains and develops an inducible promoter system that enables precise, tunable gene regulation and facilitates the implementation of CRISPR-Cas gene-deletion systems.
An inducible genome-editing framework exploiting the endogenous Cas9 system of Apilactobacillus kunkeei, a key member of the honeybee microbiota, is established and the toolkit available for harnessing endogenous CRISPR-Cas systems in genetically recalcitrant, non-model gram-positive bacteria is expanded.
Mahesh S. Iyer, Erik Hagström, Kristina Näslund et al.· Applied and Environmental Mi...· 0 citations
Although horizontal gene transfer drives bacterial diversification, its contribution to chromosome-scale variation in human gut commensals remains unclear. This study demonstrated that human-associated bifidobacteria undergo extensive chromosomal transfer through natural transformation. Comparative genomics of coexisting Bifidobacterium pseudocatenulatum isolates from a single individual revealed extensive recombination signatures between the lineages. We experimentally reproduced this recombination by co-culturing strains, resulting in the transfer of multiple chromosomal regions and generation of mosaic genomes. Individual recombination tracts reached up to 247 kb per site, with cumulative replacements accounting for up to 28.9% of the recipient chromosome. These transfers occurred with heat-killed donors or purified DNA and were abolished by DNase, thereby identifying natural transformation as the underlying mechanism. Furthermore, we observed that environmental factors strongly influenced transformation frequency, suggesting that gut environmental conditions play a role regulating this process. Using natural transformation, we established a simple markerless genome-editing method that enables efficient gene deletions. Deletions of the Tad pili, ComEA-ComEC, or DprA-ComM-YraN gene clusters abolished transformation, defining the core machinery. The conservation of these genes across the genus Bifidobacterium and experimental demonstration of natural transformation in Bifidobacterium longum and Bifidobacterium breve indicate that natural transformation capacity is widespread within the genus. Our findings establish natural transformation as a key mechanism that promotes genome plasticity and contributes to adaptive evolution in bifidobacteria, thereby expanding our current understanding of horizontal gene transfer in the human gut microbiota.
Yohei Watanabe, Kento Orihara, N. Tsukuda et al.· The ISME Journal· 0 citations
A novel marker recycling cassette is reported for Aspergillus species that enables highly efficient gene disruption and marker recycling by combining a doxycycline-inducible Cre/ loxP system with a uracil biosynthesis pathway and counterselection using uracil analogs.
The engineering of microorganisms is undergoing a fundamental paradigm shift, transitioning from the construction of static cell factories to the programming of dynamically responsive living materials. However, translating molecular interventions into robust macroscopic functions requires overcoming distinct microbial-specific barriers, including delivery bottlenecks and genetic stability. In this review, we establish a unified Edit-Reprogram-Functionalize conceptual framework that systematically delineates transient genetic regulation from permanent genomic engineering. We critically examine the evolutionary trajectories of five foundational technologies: plasmid engineering, CRISPR-Cas systems, base editors, prime editors, and enzyme engineering. Rather than analyzing these toolsets in isolation, we map their convergence into an integrated engineering continuum that drives the precise synthesis of two distinct output classes: engineered living microbial materials and robust microbial metabolite-derived materials. By evaluating representative breakthroughs-from ultrasound-actuated bacterial therapeutics to ultra-tough, biosynthesized protein composites-through the strict lens of host-dependent constraints, we reveal the mechanistic principles governing successful preclinical translation. Finally, we propose an actionable roadmap centered on systemic miniaturization, closed-loop control, and multi-scale integration, providing a definitive blueprint for the next generation of precision medicine, advanced biomanufacturing, and ecological remediation.
Yangyang Du, Yunjia Shi, Dazhi Chen et al.· Small· 0 citations
Transposons are fundamental genetic elements that have profoundly shaped the architecture of eukaryotic genomes. Yeasts and filamentous fungi have emerged as important chassis organisms for bioingredient production in synthetic biology and metabolic engineering. In this review, we summarise the current understanding and future opportunities in the development of transposon-based tools for genome engineering in these fungal systems. Fungal inverted terminal repeat (ITR) DNA transposons, as well as long terminal repeat (LTR) and non-LTR retrotransposons, can accelerate genomic mutagenesis, facilitating the screening of superior genotypes and phenotypes. CRISPR-associated transposons (CASTs) hold considerable potential for site-specific integration of large transgenes, bypassing the limitations imposed by low homologous recombination (HR) efficiency in non-Saccharomyces hosts. Overall, transposon-based tools represent a valuable and underexplored avenue to accelerate genome engineering and strain development in yeasts and filamentous fungi.
Bingyin Peng, Masahiro Tominaga, Chengqiang Wang et al.· Yeast· 1 citation
How HGT has significantly shaped the genome evolution of Saccharomyces cerevisiae is highlighted, providing key traits relevant to fermentation processes and how detecting HGT events helps to understand yeast genome plasticity and to identify useful “foreign” DNA, which can be manipulated to create novel yeast strains with enhanced fermentation performance, flavour profiles, or stress tolerance.
A. Grassi, U. Rogo, M. Fambrini et al.· World Journal of Microbiolog...· 0 citations
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