Microbial Biotechnology最新文献

Fusobacterium, a gram-negative anaerobic bacillus in mouth, gastrointestinal tract and elsewhere, has long been considered as opportunistic pathogen. Increasing evidence indicate the association of Fusobacterium with human diseases, especially cancer. However, previous studies demonstrated contradictory prevalent features of Fusobacterium species in normal and patient population. To address this dissonance, we developed a high-precision multiplex PCR assay that allows concurrent identification of five species of Fusobacterium (F. nucleatum, F. mortiferum, F. ulcerans, F. varium and F. necrophorum) and four subspecies of F. nucleatum (nucleatum, animalis, vincentii and polymorphum). By employing the PCR method, we investigated the prevalent features of Fusobacterium communities in Southern Chinese population and cancer patients. Surprisingly, we found F. nucleatum was dominant in both Southern Chinese population and cancer patients, and discovered the correlations of Fusobacterium species to host conditions. Moreover, F. mortiferum exhibited better diagnostic performance for cancers compared to other species, and the combination of F. mortiferum, F. nucleatum, body mass index and haemoglobin by a logistic regression model showed excellent diagnostic performances for cancers. Additionally, we determined the compositional features and loads of Fusobacterium communities in paired tumour, adjacent tissues and normal tissues of colorectal cancer and lung cancer. Hence, we developed a high-precision multiplex PCR assay to profile Fusobacterium in human faeces and tumour, and demonstrate its prevalence in Southern Chinese population with correlations to host conditions and cancers.

Isobutanol, a promising biofuel with higher energy content than ethanol, presents a sustainable alternative through biosynthesis. However, enhancing yield remains challenging due to the inefficiencies in microbial synthesis. This study introduces a transcription factor-based biosensor using the AlkS-PalkB system in Escherichia coli, which correlates green fluorescence with isobutanol concentration. Employing directed evolution, we modified AlkS to detect isobutanol, significantly improving biosensor specificity. Initial modifications increased the dynamic response from non-detectable to a 2.60-fold change. Subsequent optimisations through site-directed mutagenesis and promoter engineering further enhanced this response to a 5.56-fold change, equivalent to a 114% increase. Although engineered for isobutanol detection with high sensitivity, the engineered biosensor retains responsiveness to several short-chain alcohols. This biosensor provides a foundation for high-throughput screening of isobutanol and other short-chain alcohol-producing strains, though additional improvements in selectivity and operating range may be required for efficient implementation.

Black soldier fly larvae (BSFL) can efficiently convert organic waste into biomass and reduce pathogenic bacteria in organic waste. The microbial composition of the substrate and the gut of BSFL is a pivotal factor in determining the efficacy of BSFL in pathogen elimination. However, there are insufficient data on the gut microbiology of BSFL in relation to pathogen inhibition. To address this gap, we investigated the dynamics of Salmonella during the conversion of chicken manure by BSFL and examined the role of intestinal bacterial communities and core bacteria in reducing Salmonella levels. The results indicate that BSFL treatment can reduce the amount of Salmonella in chicken manure, with the gut microbiome of the BSFL playing a crucial role in this reduction. Combining metagenomic analysis with culturomics methods, we isolated 158 strains from the larval gut, in which seven gut bacteria belonging to the genus Bacillus can promote BSFL to reduce Salmonella. In reinoculation and validation experiments, the combination of BSFL and Bacillus velezensis A2 enhanced the elimination of Salmonella from chicken manure and larvae. This study provides insight into how BSFL can reduce pathogenic bacteria in chicken manure and suggests that pairing BSFL with functional microorganisms can improve the biosafety of organic waste conversion by BSFL.

Microorganisms drive the biotransformation of dissolved organic matter (DOM) during organic wastes composting, yet the role of phages with different lifestyles (i.e., temperate and virulent) in this process remains poorly understood. Here, bulk metagenomic sequencing combined with electrospray ionisation (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to investigate the dynamics of temperate and virulent phage communities, microbial functional traits represented by the growth yield (Y)–resource acquisition (A)–stress tolerance (S) life-history strategies (Y-A-S) framework, and molecular changes in DOM composition, as well as their potential linkages during the composting of a rice chaff and chicken manure mixture. Our results revealed that the ratio of temperate/virulent phage, microbial Y/A strategy, and microbial-/plant-derived DOM components exhibited highly consistent dynamic patterns, all peaking during mid-composting stage when temperatures are elevated and remaining low at the initial and final stages. Random forest analysis further identified the ratio of temperate/virulent phages and the microbial Y/A strategy as key predictors of the variance in microbial Y/A trade-offs and microbial−/plant-derived DOM components, accounting for 10% and 13% of the explained variance, respectively. Together, our results demonstrate that an increased prevalence of temperate phages promoted the microbial Y-strategy and the accumulation of microbial-derived DOM components, while a greater dominance of virulent phages favoured the A-strategy and plant-derived DOM enrichment. These findings offer new insights into the ecological role of phages in mediating material transformation during organic waste composting.

Halomonas species have recently emerged as attractive candidates for next-generation industrial biotechnology, due to their ability to thrive under high-salt conditions, which allows for fermentation under open, unsterile conditions. However, their genetic manipulation has long been hindered by difficulties in genetic transformation. In this study, we report the development of a highly efficient electroporation protocol for Halomonas elongata DSM 2581. By optimising competent cell preparation and electroporation parameters, and using plasmid DNA purified from dam/dcm methylation-deficient Escherichia coli, we achieved a maximum transformation efficiency of 2.8 × 10⁸ ± 0.2 × 10⁸ CFU/μg DNA—the highest efficiency reported for any Halomonas species to date. Notably, we observed that growing cells in low-salt medium and harvesting them at late-stationary phase considerably improved electroporation efficiency. Moreover, we further demonstrated that the use of non-methylated plasmids helped evade the defence systems of H. elongata DSM 2581 that target foreign DNA. Importantly, the protocol proved transferable to other industrially relevant strains, achieving efficiencies of 5.3 × 10⁷ ± 0.1 × 10⁷ and 5.4 × 10⁶ ± 1.2 × 10⁶ CFU/μg DNA in Halomonas boliviensis LC1 and Halomonas campaniensis LS21, respectively. Altogether, this work establishes a robust, high-efficiency electroporation method for Halomonas spp., facilitating future genetic manipulation and strain engineering work, as well as encouraging further research into underexplored Halomonas species.

The continued increase in atmospheric CO₂ concentrations has intensified global efforts to develop sustainable biotechnologies that capture and reutilise carbon rather than releasing it. While photosynthetic microorganisms provide a renewable route for CO₂ fixation into organic products, heterotrophic fermentation remains the industrial standard due to its high productivity, controllability and scalability. Consequently, integrating the carbon efficiency of autotrophic processes with the productivity of heterotrophic systems may represent a promising strategy toward circular biomanufacturing. Here, we developed a gas-linked co-culture system designed to spatially separate heterotrophic and autotrophic metabolisms while enabling gas-phase CO₂ exchange between them. This configuration allowed CO₂ released during heterotrophic metabolism to be reutilised in autotrophic metabolism, supporting cooperative carbon cycling. Compared to non-linked controls, the gas-linked system enhanced biomass accumulation and nearly doubled the production of value-added metabolites—namely polyhydroxybutyrate (PHB) and carotenoids—while reducing net CO₂ emissions by 20.62%. Although further optimisation is necessary to approach a fully net-zero process, this study demonstrates that gas-phase integration of trophically distinct cultures offers a promising platform for circular carbon biorefineries.

Monitoring acetic acid (AC) in fermentation processes is essential as excessive AC accumulation, particularly during alcoholic fermentation, can disrupt fermentation and lead to spoilage. However, conventional detection methods such as steam distillation, GC–MS, and HPLC are costly, time-consuming, and require liquid-phase samples, limiting their use for real-time monitoring and early identification of AC buildup. Here, we present an alternative tool for AC detection using a whole-cell bacterial biosensor, which utilises the YwbIR transcriptional regulator from Bacillus subtilis . The designed biosensor exhibits high sensitivity, manifesting a linear response with (R² = 0.97) from 0 to 1.0 g/L and a 5–8 fold induction at wine spoilage-relevant concentrations. It retains functionality in ethanol-rich matrices (up to 14.5% v/v) and enables headspace detection. Specificity assays and molecular docking analyses confirm high affinity for AC over other volatile fatty acids. This biosensor offers a low-cost solution for real-time AC monitoring, allowing timely intervention before spoilage occurs and supporting improved quality assurance in fermentation-driven food and beverage production.

Selenium (Se) is an essential trace element whose toxicity depends on its oxidation state. Microorganisms detoxify Se(VI) and Se(IV) by reducing them to elemental selenium [Se(0)], forming selenium nanoparticles (SeNPs) with antimicrobial activity. Stenotrophomonas bentonitica BII-R7 exhibits remarkable tolerance and reduction capacity toward toxic Se oxyanions, making it a promising candidate for bioremediation and green nanotechnology. In this study, cells exposed to Se(IV) were fractionated into cytoplasmic and membrane components and analysed at 24, 168 and 720 h. Spherical SeNPs were observed in the cytoplasm, while irregular aggregates formed in the membrane fraction, suggesting compartment-specific reduction pathways. The delayed formation of SeNPs in membranes supports a time-dependent, multimodal mechanism. Homogeneous biogenic SeNPs (160–180 nm) produced by intact S. bentonitica cells exhibited antimicrobial activity against Escherichia coli CET101 and Staphylococcus aureus ATCC 25923. Flow cytometry revealed strong, time-dependent cytotoxicity. In E. coli, SeNPs induced 21.1% membrane depolarization, 62.8% ROS accumulation and DNA damage at 48 h, indicating a ROS-mediated mechanism. In contrast, S. aureus showed early membrane depolarization at 12 h, with only 4.37% active cells and minimal ROS levels, and a significant drop in viability at 24 h (31.3%), suggesting a ROS-independent mechanism driven by membrane disruption. These findings highlight the strain-specific toxicity of SeNPs and their potential as eco-friendly, broad-spectrum antimicrobials.

The first forms of life on Earth were microbial, preceding the evolution of multicellular life by more than two billion years. Based on our current understanding of the origin of life, it is likely that the first life forms on any extraterrestrial world would also be microbial. Due to the extreme temperatures, radiation or aridity on most planetary surfaces, such extraterrestrial microbes would most likely dwell in subsurface environments. Earth's subsurface features a wide range of environments, including deep marine sediments, crustal aquifers, rock fracture fluids, hydrocarbon reservoirs, caves and permafrost soils. These environments are known to host an immense diversity of life forms, predominantly microbes that survive or even thrive under extreme conditions and energy scarcity. Life's ability to endure and possibly evolve in Earth's subsurface lends credence to the possible existence of life beyond our planet and provides a blueprint for the extraterrestrial life forms and biosignatures we might expect. The exploration of space via extraterrestrial samples analysed on Earth, in situ extraterrestrial analyses, and remote sensing continue to advance our search for and understanding of potential biosignatures on other planetary bodies. But by investigating Earth's deep, dark and isolated ecosystems, we not only broaden our understanding of life's adaptability but also refine our strategies and technologies for detecting life on other planets and moons. Subsurface exploration is not just a frontier of Earth science—it is a cornerstone of astrobiology and in the pursuit of understanding the multitude of processes that could create and sustain life anywhere. In this opinion article, we discuss the latest highlights in subsurface research and technology, how Earth's subsurface environments serve as models for potential environments on other planetary bodies, why insights into subsurface microbiomes inform the search for life elsewhere, and which technologies and developments will advance the field in the future.

Plasmid vectors are to this day the fundamental tools in molecular biology, but their selection is often guided by convenience rather than informed choice. This article revisits the architectural and functional features that determine plasmid performance i.e., origins of replication, copy number, cargo capacity, selection markers, and stability systems. We outline how these elements shape host range, expression dynamics, and metabolic burden, particularly as synthetic biology increasingly targets non-model bacteria. The growing need for reliable, portable vectors has driven the development of broad-host-range backbones, streamlined modular architectures such as SEVA, and alternatives to antibiotic-based selection. We also examine strategies to enhance long-term stability, including toxin–antitoxin systems and chromosomal integration via mini-transposons, recombinase-assisted platforms, and CRISPR-associated transposases. The convergence of standardization and customization, enabled by advances in DNA synthesis and emerging AI-assisted plasmid design tools is discussed also. These innovations promise flexible vector engineering tailored to diverse microbial chassis. Yet, a deeper, systems-level understanding of plasmid–host interactions will be necessary to ensure robust deployment of engineered functions in laboratory, industrial, and environmental settings.