Resistant starch is a dietary fiber that escapes digestion in the small intestine and undergoes fermentation by gut microbiota in the colon, producing beneficial short-chain fatty acids (SCFAs). Among the various types of resistant starch, resistant starch type 5 (RS5) has gained significant attention due to its unique and stable structural and functional properties. RS5 is a self-assembled V-type inclusion complex formed when amylose helices encapsulate guest molecules. This formation occurs through non-covalent interactions after the native starch structure is disrupted, and a guest compound is introduced. This structure provides enhanced resistance to enzymatic digestion, slows fermentation, and facilitates targeted release of bioactive molecules, making it effective in modulating gut health. RS5 promotes the proliferation of beneficial gut microbiota while suppressing pathogenic species, leading to increased SCFAs production, mostly butyrate, acetate, and propionate, which maintain intestinal integrity, reduces inflammation, and supports metabolic regulation. RS5 also contributes to preventing and managing chronic diseases such as obesity, type 2 diabetes, and colorectal cancer. While prior research has focused on its preparation methods and physicochemical characteristics, the influence of RS5 on gut microbiota and host health remains inadequately explored. This review summarizes the formation, classification, and structural diversity of RS5 complexes and how these factors influence digestibility and fermentation kinetics. Furthermore, it explores how RS5 modulates the composition and metabolic activity of the gut microbiota, enhancing SCFAs production. By comparing RS5 with other RS types, this review highlights its superior prebiotic potential and supports RS5-based functional food development for improving gut and metabolic health, targeting gut microecology.

Following the Fukushima Daiichi nuclear power plant accident, radioactive cesium was released into the environment, prompting intensified efforts to identify cesium-resistant microorganisms. During these studies, we isolated a cesium-resistant Escherichia coli strain, designated ZX-1, which exhibits remarkable tolerance to cesium concentrations exceeding 700 mM. As no prior reports of cesium-resistant E. coli exist, this finding suggests the presence of a previously unrecognized resistance mechanism. This study aims to elucidate the molecular basis of cesium resistance in ZX-1.

RNA-seq analysis comparing ZX-1 with its parental strain, the commercial E. coli Mach1™, revealed constitutive upregulation of the guanidinium exporter gene gdx in ZX-1. Reanalysis of the whole-genome sequence identified a 20-bp deletion upstream of the gdx open reading frame, likely disrupting formation of the guanidinium riboswitch P2 loop and resulting in constitutive gdx expression.

To evaluate gdx function, the gene was cloned into the expression vector pBAD24 and expressed in E. coli. The resulting gdx-expressing strain exhibited even greater cesium resistance than ZX-1. Functional assays demonstrated that this strain mediates not only guanidinium/H⁺ antiport activity but also Cs⁺/H⁺ antiport activity. Cesium resistance was further enhanced in the presence of guanidinium, consistent with riboswitch-mediated induction of gdx.

Collectively, these findings provide evidence for a novel cesium efflux mechanism in E. coli and uncover an unexpected role of the guanidinium exporter Gdx in cesium export. These insights may facilitate the discovery of additional cesium-resistant microorganisms and broaden the potential for future applications.

The interaction and co-evolution between human gut bacteria and their phages shape the dynamic gut microbiome, exerting a significant impact on human health. However, the underlying mechanisms are largely unexplored. In particular, a bacteria-phage interaction model of the Bacteroidota phylum and the Microviridae phages is lacking, limiting our understanding of their ecological roles in human gut. In this study, we isolated a Bacteroidota-infecting Microviridae phage ϕHBP1 from human feces. Infection of its host Bacteroides fragilis with ϕHBP1 drives multiple genomic structural variations, which are correlated with host resistance to ϕHBP1. In turn, our phage evolution assay in B. fragilis H1 obtained ϕHBP1 mutants that carry mutations within the capsid and pilot proteins and can reinfect the resistant bacterial population. Together, our findings provide novel insights into an antagonistic co-evolution mechanism between gut phage and bacteria, and hold important implications for diversifying phages through evolution to target resistant bacteria in phage therapy.

Bacillus subtilis is widely used in industrial fermentation and probiotic applications; however, phage contamination poses a substantial economic threat. To address this, we isolated three phages (PJNB030, PJNB031, and PJNB032) from a contaminated B. subtilis fermentation broth and characterized their biological properties. Phenotypic analyses indicated broad pH stability (pH 4-10), variable thermal tolerance, and differential UV sensitivity. Replication kinetics revealed latent periods of 10-20 min and burst sizes ranging from 50 to 73 PFU/cell. Genomic sequencing identified linear dsDNA genomes (64-165 kb) with GC content ranging from 33.5 to 47.4%. Phylogenomic and comparative genomic analyses revealed that these phages were located on distinct branches. Deletion of pgcA (which encodes α-phosphoglucomutase) rendered cells completely resistant to PJNB031 and PJNB032, whereas it reduced PJNB030 infectivity (plaque formation efficiency) by approximately six orders of magnitude. Adsorption assays confirmed that the binding of PJNB031 and PJNB032 to ΔpgcA mutants was abolished, whereas PJNB030 retained partial adsorption capacity. In conclusion, this study identified wall teichoic acid as the primary receptor for these phages and established pgcA deletion as an effective strategy for engineering phage-resistant B. subtilis strains. Our findings provide critical insights into the mitigation of phage contamination in industrial bioprocesses.

Hachiman systems provide innate antiphage immunity across prokaryotic domains. The system encodes a HamA nuclease and a HamB helicase both of which exhibit great diversity in sequence. Phylogenetic analyses of HamA and HamB proteins revealed similar phylogenetic trees for both proteins, falling into three major types. Close examination of one of the subclades identified a distinct subfamily in which most of these Hachiman systems stands alone, however, Hachiman in the Streptococcus genus is combined with PezAT, a distinct pneumococcal epsilon zeta toxin-antitoxin system, yielding the Pez-Ham system. Investigation of a S. thermophilus Pez-Ham system revealed that only the Hachiman system is required for mediating antiphage defence. Biochemical characterization of encoded proteins, i.e., HamA or HamB individually or in protein complex revealed that the HamA nuclease is inactive alone, but upon the formation of heterologous dimer with HamB, the resulting protein complex effectively cleaves DNAs of various forms with a broad specificity (5′-CNNNG-3′), and the nuclease activity is greatly facilitated by ATP-binding in HamB and to a less degree by ATP hydrolysis. Genetic investigations further showed, while the Pez system did not function in antiphage immunity in Escherichia coli, the system repressed the expression of Hachiman, and thereby balancing the trade-off between the fitness cost and the effectiveness of antiphage defence.

Polyethylene (PE) is one of the most widely used plastics worldwide and is valued for its versatility, durability, and cost-effectiveness. However, the chemical stability of PE combined with its widespread use makes it a persistent environmental pollutant that contributes to the accumulation of plastic waste in terrestrial and marine ecosystems. The escalating issue of plastic pollution has underscored the importance of developing sustainable solutions, of which PE biodegradation has emerged as a promising avenue for mitigating the environmental burden of recalcitrant polyolefins. This review systematically summarizes the recent advances in the biodegradation and bioconversion of PE, focusing on methods for evaluating degradation efficiency, the mechanisms by which microorganisms and enzymes contribute to PE degradation, and the microbial and enzymatic resources identified to date. In addition, we discuss physicochemical strategies that enhance degradation efficiency and their integration with biological approaches, as well as the potential applications of emerging biotechnological tools in PE degradation. The integration of cutting-edge biotechnological tools such as synthetic biology and machine learning with traditional biodegradation methods holds great potential for accelerating PE degradation rates and achieving more sustainable plastic waste management.

Mevalonolactone (MVAL) is a high-value feedstock for the cosmetic industry, with (R)-(-)-MVAL as the sole bioactive enantiomer. Chemical synthesis, which is the traditional method for MVAL production, is hindered by cumbersome procedures, low chiral purity, and sensitivity to humidity. Microbial fermentation via fermentative mevalonate (MVA) accumulation followed by in vitro acid-catalyzed lactonization has emerged as a promising alternative for producing optically pure (R)-(-)-MVAL. Strategies for MVA overproduction in microbial systems are reviewed, including the selection of chassis strains and enzymes for the MVA biosynthetic pathway, metabolic engineering approaches for strain improvement, optimization of fermentation processes, and downstream processes for MVA-to-MVAL lactonization. Finally, prospects for advancing microbial MVAL production are discussed.

Genetically encoded biosensors provide powerful tools for coupling desired phenotypes to detectable outputs and have been extensively developed to detect a wide range of natural and unnatural products. When integrated with diverse high-throughput screening (HTS) approaches, these biosensors enable efficient product-driven screening across various throughputs, thereby expediting the engineering and optimization of microbial cell factories to produce various target compounds. For effective HTS of microbial cell factories, biosensors need to possess certain crucial characteristics. The performance features of biosensors significantly influence their application potential in HTS and can be precisely engineered through synthetic biology strategies. Furthermore, to ensure biosensor-driven HTS, additional engineering and optimizations of the biosensors are often required to increase the success rate and reduce false positives in the screening process. This review discusses the essential features of genetically encoded biosensors designed for HTS and then summarizes the latest advances in biosensor engineering for HTS purposes via synthetic biology strategies. Following this, the challenges and optimization of biosensors to adapt to different HTS processes are also discussed and exemplified. Finally, the key concerns and research prospects of developing biosensors for HTS applications are highlighted. Overall, this review provides comprehensive guidance on the engineering of genetically encoded biosensors and their applications in HTS for developing microbial cell factories to produce diverse target compounds.

Bacterial growth modulation is crucial in microbial synthetic biology. In this study, we found that glutamate is an extremely poor carbon source for Escherichia coli and Bacillus subtilis. The slow growth on glutamate can be effectively overcome by the heterologous expression of glutamate transporters from Vibrio natriegens. Our results revealed that cross-species substrate transporters could be employed to shift bacterial cellular resource allocation, offering a potential genetic strategy for modulating microbial biomass growth.