Microbial Biotechnology最新文献

Enterococcus species, natural inhabitants of the human gut, have become major causes of life-threatening bloodstream infections (BSIs) and the third most frequent cause of hospital-acquired bacteremia. The rise of high-level gentamicin resistance (HLGR) in enterococcal isolates complicates treatment and revives bacteriophage therapy. This study isolated and identified forty E. faecalis clinical isolates, with 30% exhibiting HLGR. The HLGR5 isolate, resistant to fosfomycin, vancomycin, and linezolid, was used to isolate the vB_EfaS_SZ1 phage from effluent water. This phage specifically lysed 42% of HLGR isolates. vB_EfaS_SZ1 demonstrated beneficial traits, including thermal stability, acid-base tolerance, a short latent period, and a large burst size. The phage genome comprises a 40,942 bp linear double-stranded DNA with 65 open reading frames (ORFs). The genome closely resembled Enterococcus phages, classifying it within the Efquatrovirus genus. Phage-antibiotic synergy was assessed using checkerboard assays and time-killing analyses, revealing enhanced bacteriolytic activity of ampicillin and fosfomycin, with significant reductions in minimum inhibitory concentration values. In a mouse bacteremia model, phage-antibiotic combinations significantly reduced E. faecalis liver burden compared to monotherapies. Histopathological analysis confirmed therapeutic synergy, showing reduced inflammation and improved hepatocyte regeneration. These findings underscore the potential of phage vB_EfaS_SZ1 as an adjunct to antibiotic therapy for resistant enterococcal bacteremia.

Acetaminophen induced acute liver injury (ALI) has a high incidence and is a serious medical problem, but there is a lack of effective treatment. The enterohepatic axis is one of the targets of recent attention due to its important role in liver diseases. Disulfiram (DSF) is a multitarget drug that has been proven to play a role in a variety of liver diseases and can affect intestinal flora, but whether it can alleviate ALI is not clear. We utilised bacterial 16S rRNA gene profiling, antimicrobial treatments, and faecal microbiota transplantation tests to explore whether DSF therapy for ALI is dependent on gut microbiota. Our findings indicate that DSF primarily restores intestinal microbiome balance by modulating the abundance of Akkermansia muciniphila (A. muciniphila), leading to significant alleviation of ALI symptoms in a gut microbiota dependent manner. We also found that A. muciniphila can promote the activation of PI3K/Akt pathway, correct the Bcl-2/Bax ratio, and further inhibit hepatocyte apoptosis. In conclusion, DSF ameliorates ALI by modulating the intestinal microbiome and activating the PI3K/AKT pathway through A. muciniphila.

While rising greenhouse gases cause climate change, global economies ask for resilient solutions for the business of the future. Biomanufacturing may well serve as a pillar of a circular economy with minimised environmental impact. Therefore, innovations of the lab need to successfully bridge the imminent 'death-valley of innovation' for making commercial production happen. This editorial aims to prepare the ground for prospective developments so as to the seed of novel ideas will prosper.

Antimicrobial peptides (AMPs) are promising candidates to combat multidrug-resistant pathogens. However, the high cost of extensive wet-lab screening has made AI methods for identifying and designing AMPs increasingly important, with machine learning (ML) techniques playing a crucial role. AI approaches have recently revolutionised this field by accelerating the discovery of new peptides with anti-infective activity, particularly in preclinical mouse models. Initially, classical ML approaches dominated the field, but recently there has been a shift towards deep learning (DL) models. Despite significant contributions, existing reviews have not thoroughly explored the potential of large language models (LLMs), graph neural networks (GNNs) and structure-guided AMP discovery and design. This review aims to fill that gap by providing a comprehensive overview of the latest advancements, challenges and opportunities in using AI methods, with a particular emphasis on LLMs, GNNs and structure-guided design. We discuss the limitations of current approaches and highlight the most relevant topics to address in the coming years for AMP discovery and design.

The increasing threat of antibiotic resistance underscores the urgent need for innovative strategies to combat infectious diseases, including the development of antivirulants. Microbial pathogens rely on their virulence factors to initiate and sustain infections. Antivirulants are small molecules designed to target virulence factors, thereby attenuating the virulence of infectious microbes. The bacterial type IV pilus (T4P), an extracellular protein filament that depends on the T4P machinery (T4PM) for its biogenesis, dynamics and function, is a key virulence factor in many significant bacterial pathogens. While the T4PM presents a promising antivirulence target, the systematic identification of inhibitors for its multiple protein constituents remains a considerable challenge. Here we report a novel high-throughput screening (HTS) approach for discovering T4P inhibitors. It uses Pseudomonas aeruginosa, a high-priority pathogen, in combination with its T4P-targeting phage, φKMV. Screening of a library of 2168 compounds using an optimised protocol led to the identification of tuspetinib, based on its deterrence of the lysis of P. aeruginosa by φKMV. Our findings show that tuspetinib also inhibits two additional T4P-targeting phages, while having no effect on a phage that recognises lipopolysaccharides as its receptor. Additionally, tuspetinib impedes T4P-mediated motility in P. aeruginosa and Acinetobacter species without impacting growth or flagellar motility. This bacterium-phage pairing approach is applicable to a broad range of virulence factors that are required for phage infection, paving ways for the development of advanced chemotherapeutics against antibiotic-resistant infections.

Advancing microbiome-gut-brain axis science requires systematic, rational and translational approaches to bridge the critical knowledge gaps currently preventing full exploitation of the gut microbiome as a tractable therapeutic target for gastrointestinal, mental and brain health. Current research is still marked by many open questions that undermine widespread application to humans. For example, the lack of mechanistic understanding of probiotic effects means it remains unclear why even apparently closely related strains exhibit different effects in vivo. For the therapeutic application of live microbial psychobiotics, consensus on their application as adjunct treatments to conventional neuromodulators, use in unmedicated populations or in at-risk cohorts with sub-clinical symptomatology is warranted. This missing information on both sides of the therapeutic equation when treating central nervous system (CNS) conditions makes psychobiotic research challenging, especially when compared to other pharmaceutical or functional food approaches. Expediting the transition from positive preclinical data to proven benefits in humans includes interpreting the promises and pitfalls of animal behavioural assays, as well as navigating mechanism-informed decision making to select the right microbe(s) for the job. In this review, we consider how these decisions can be supported in light of information accrued from a range of clinical studies across healthy, at-risk and pathological study populations, where specific strains have been evaluated in the context of gastrointestinal physiology, brain function and behaviour. Examples of successful, partial and unsuccessful translation from bench to bedside are considered. We also discuss the developments in in silico analyses that have enhanced our understanding of the gut microbiome and that have moved research towards pinpointing the host-microbe interactions most important for optimal gut-brain axis function. Combining this information with knowledge from functional assays across in vitro and ex vivo domains and incorporating model organisms can prime the discovery pipelines with the most promising and rationally selected psychobiotic candidates.

Prof. Manuel Espinosa Padrón (1942-2024): A superb plasmid biologist and a gentle colossus.

Using synthetic biology techniques, bacteria have been engineered to serve as microrobots for diagnosing diseases and delivering treatments. These engineered bacteria can be used individually or in combination as microbial consortia. The components within these consortia complement each other, enhancing diagnostic accuracy and providing synergistic effects that improve treatment efficacy. The application of microbial therapies in cancer, intestinal diseases, and metabolic disorders underscores their significant potential. The impact of these therapies on the host's native microbiota is crucial, as engineered microbes can modulate and interact with the host's microbial environment, influencing treatment outcomes and overall health. Despite numerous advancements, challenges remain. These include ensuring the long-term survival and safety of bacteria, developing new chassis microbes and gene editing techniques for non-model strains, minimising potential toxicity, and understanding bacterial interactions with the host microbiota. This mini-review examines the current state of engineered bacteria and microbial consortia in disease diagnosis and treatment, highlighting advancements, challenges, and future directions in this promising field.

Sterol composition plays a crucial role in determining the ability of yeast cells to withstand high temperatures, an essential trait in biotechnology. Using a targeted evolution strategy involving fluconazole (FCNZ), an inhibitor of the sterol biosynthesis pathway, and the immunosuppressant FK506, we aimed to enhance thermotolerance in an industrial baker's yeast population by modifying their sterol composition. This approach yielded six isolates capable of proliferating in liquid YPD with μ_max values ranging from 0.072 to 0.236 h^-1 at 41.5°C, a temperature that completely inhibits the growth of the parental strain. The clones were categorised into two groups based on their respiratory competence or deficiency, the latter associated with mtDNA loss, an event seemingly linked to FCNZ and heat tolerance. Genome sequencing and ploidy-level analysis of all strains revealed aneuploidies, copy number variations (CNVs), and single nucleotide polymorphisms (SNPs). Notably, all evolved clones exhibited specific point mutations in MPM1 (P50S) and PDR1 (F749S). CRISPR-Cas9 experiments confirmed the role of the pdr1^F749S mutation in the FCNZ-tolerance phenotype and demonstrated that Mpm1 is required for growth at high temperatures. However, no apparent heat tolerance benefit was observed from single or combined mutations in these genes, supporting the hypothesis that thermotolerance is mediated by multiple interacting mechanisms. In this context, all evolved clones exhibited altered sterol profiles, with differences observed between respiratory-competent and -deficient strains. In conclusion, our experimental evolution generated thermotolerant and fully competent strains and identified factors that could influence fluconazole and heat growth.

The discovery at the end of the 20th century of genes that induce cell death revolutionised the biocontaintment of genetically manipulated bacteria for environmental or agricultural applications. These bacterial 'killer' genes were then assayed for their potential to target and control malignant cells in human cancers. The identification of the bacteriomes in different human organs and tissues, coupled with the observation that bacteria tend to accumulate near tumours, has opened new avenues for anti-cancer strategies. This progress, along with recent insights into how cancer cells evade immune response, has prompted innovative therapeutic approaches. Tumour microenvironments are typically nutrient-rich, characterised by low oxygen tensions and very resistant to immune responses. Two recent studies in MBT highlight the promise of using Salmonella typhimurium and Escherichia coli as vectors in novel cancer treatments. Engineered S. typhimurium strains can generate adjuvant flagellin-antigen complexes that function as in situ vaccines, hence increasing the immunogenic responses within tumour environment. Similarly, gut E. coli can be used as vectors to targert tumour cells in colon cancer, enabling both diagnostic applications and localised treatments. Both approaches hold significant potential to improve patient survival outcomes.