Microbial Cell最新文献

Mucormycosis is a life-threatening infection caused by certain members of the fungal order Mucorales, with increased incidence in recent years. Individuals with untreated diabetes mellitus, and patients treated with deferoxamine are particularly susceptible to this infection. Elevated free iron concentrations in serum contribute to the development of mucormycosis. Pathogenic fungi have evolved multiple mechanisms to acquire and utilize free iron or extract it from the various iron-binding molecules within the host. The utilization of hydroxamate siderophores as xenosiderophores may contribute to the development of mucormycosis. The genome of Mucor lusitanicus encodes one Sit1 siderophore transporter. In this study, the role of the sit1 gene was characterized by generating knockout mutants using CRISPR-Cas9. Relative transcript level of the sit1 gene significantly increased in the presence of deferoxamine- and deferasirox-iron complexes. Lack of sit1 resulted in altered germination of spores and growth ability, and decreased virulence. Furthermore, absence of the gene caused elevated transcript levels of a ferric reductase (FRE), a low-affinity iron permease (FET4) and a copper dependent iron oxidase (FET3). Our result suggests that expressions of the genes involved in iron uptake affect each other. The lack of Sit1 resulted in an increased transcript level of the FRE3 gene, which may be able to reduce iron from the siderophore-iron complex. The reduced and liberated iron may be then taken up by activated FET4a. This study highlights the significance of understanding the iron acquisition mechanisms of pathogenic fungi to develop effective treatments for fungal infections.

The interaction between intratumoral microbiome and the tumor microenvironment (TME) has furthered our understanding of tumor ecology. Yet, the implications of their interaction for lung cancer management remain unclear. In the current work, we collected host transcriptome samples and matched intratumoral microbiome samples, as well as detailed clinical metadata from The Cancer Genome Atlas (TCGA) of 478 patients with lung adenocarcinoma (LUAD). Utilizing the multiomics integration approach, we comprehensively investigated the crosstalk between the TME and intratumoral microbiome in patients with LUAD. First, we developed a prognostic model based on the TME signatures (TMEindex) that clearly distinguished clinical, survival, and response to immunotherapy of patients with LUAD. Additionally, we found profound differences in intratumoral microbiota signatures, including alpha- and beta-diversity, among patients with different survival risks based on the TME signatures. In depth, we detected that genera Luteibacter and Chryseobacterium were strongly negatively and positively associated with patients' survival risk, respectively, suggesting their opposing roles in cancer progression. Moreover, we developed a model that fused intratumoral microbial abundance information with TME signatures, called intratumoral microbiome-modified TMEindex (IMTMEindex), leading in predicting patient overall survival at 1-, 3-, and 5-years. Future clinical profiling of the specific intratumoral microbes in the TME could improve prognosis, inform immunotherapy, and facilitate the development of novel therapeutics for LUAD.

Persister cells are a subpopulation of bacteria capable of surviving antibiotic treatments and are thought to contribute to disease chronicity and symptom relapse of chronic conditions. Crohn's disease (CD) is a multifactorial chronic inflammatory condition of the gastrointestinal tract, and adherent-invasive Escherichia coli (AIEC) have emerged as a key contributor to its pathogenesis. AIEC can survive, replicate, and produce persister cells within macrophages; however, beyond the LF82 reference strain, little is known about the persistence phenotype and its variability among AIEC strains. In this study, the survival of two AIEC reference strains was analyzed following ciprofloxacin treatment, a fluoroquinolone antibiotic commonly used in CD therapy. In addition, four AIEC clinical isolates and two non-AIEC E. coli pathotypes were included for comparison. We investigated the roles of the resident antibiotic resistance plasmid, the stress response protein HtrA, and macrophage-induced persister formation. Our results revealed broad variability in persister cell formation among AIEC strains. Remarkably, the reference NRG857c strain exhibits a threateningly high-persistence phenotype, with persistence levels 200-fold higher than LF82 and certain clinical isolates. Neither the antibiotic resistance plasmid nor HtrA were required for this phenotype. Moreover, unlike LF82, NRG857c did not exhibit increased persistence following macrophage internalization. Overall, our findings demonstrate the presence of distinct persistence phenotypes among AIEC strains and identify NRG857c as a high-persistence variant. These observations underscore the need to consider bacterial persistence in the management of CD, particularly given the potential presence of AIEC strains with elevated persistence capabilities.

Trypanosoma cruzi, the causing agent of Chagas disease, is the only known trypanosomatid pathogenic to humans having a complete histidine to glutamate pathway, which involves a series of four enzymatic reactions that convert histidine into downstream metabolites, including urocanate, 4-imidazolone-5-propionate, N-formimino-L-glutamate and L-glutamate. Recent studies have highlighted the importance of this pathway in ATP production, redox balance, and the maintenance of cellular homeostasis in T. cruzi. In this work, we focus on the first step of the histidine degradation pathway, which is performed by the enzyme histidine ammonia lyase. Here we determined the kinetic and biochemical parameters of the T. cruzi histidine ammonia-lyase. By generating null mutants of this enzyme using CRISPR-Cas9 we observed that disruption of the first step of the histidine degradation pathway completely abolishes the capability of this parasite to metabolise histidine, compromising the use of this amino acid as an energy and carbon source. Additionally, we showed that the knockout of the histidine ammonia lyase affects metacyclogenesis when histidine is the only metabolizable source and diminishes trypomastigote infection in vitro.

Caffeine can modulate cell cycle progression, override DNA damage checkpoint signalling and increase chronological lifespan (CLS) in various model systems. Early studies suggested that caffeine inhibits the phosphatidylinositol 3-kinase-related kinase (PIKK) Rad3 to override DNA damage-induced cell cycle arrest in fission yeast. We have previously suggested that caffeine modulates cell cycle progression and lifespan by inhibiting the Target of Rapamycin Complex 1 (TORC1). Nevertheless, whether this inhibition is direct or not, has remained elusive. TORC1 controls metabolism and mitosis timing by integrating nutrients and environmental stress response (ESR) signalling. Nutritional or other stresses activate the Sty1-Ssp1-Ssp2 (AMP-activated protein kinase complex, AMPK) pathway, which inhibits TORC1 and accelerates mitosis through Sck2 inhibition. Additionally, activation of the ESR pathway can extend lifespan in fission yeast. Here, we demonstrate that caffeine indirectly activates Ssp1, Ssp2 and the AMPKβ regulatory subunit Amk2 to advance mitosis. Ssp2 is phosphorylated in an Ssp1-dependent manner following exposure to caffeine. Furthermore, Ssp1 and Amk2, are required for resistance to caffeine under conditions of prolonged genotoxic stress. The effects of caffeine on DNA damage sensitivity are uncoupled from mitosis in AMPK pathway mutants. We propose that caffeine interacts synergistically with other genotoxic agents to increase DNA damage sensitivity. Our findings show that caffeine accelerates mitotic division and is beneficial for CLS through AMPK. Direct pharmacological targeting of AMPK may serve towards healthspan and lifespan benefits beyond yeasts, given the highly conserved nature of this key regulatory cellular energy sensor.

Nitrogen metabolism in Saccharomyces cerevisiae is tightly regulated to optimize the utilization of available nitrogen sources. Uga3 is a known transcription factor involved in the gamma-aminobutyric acid (GABA) pathway; however, its broader role in nitrogen metabolism remains unclear. Here, we demonstrate that Uga3 influences arginine biosynthesis, linking its function beyond GABA utilization when cells grow with proline as the sole and poor nitrogen source. Using a combination of intracellular amino acid quantification, proteomics, and gene expression analysis, we show that the absence of Uga3 leads to a significant increase in intracellular arginine levels and the up-regulation of ARG5,6, a key gene in the arginine biosynthesis pathway. Proteomic analysis of uga3∆ cells reveals differential expression of multiple nitrogen metabolism-related proteins, suggesting a broader regulatory role for Uga3. Surprisingly, chromatin immunoprecipitation (ChIP) assays indicate that Uga3 does not directly bind the ARG5,6 promoter, implying an indirect regulatory mechanism. These findings expand the known functions of Uga3, positioning it as a key player in the coordinated regulation of nitrogen metabolism. Given the impact of nitrogen availability on industrial fermentation processes, our results provide new insights into optimizing yeast performance under nitrogen-limited conditions.

TDP-43 is linked to human diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). Expression of TDP-43 in yeast is known to be toxic, cause cells to elongate, form liquid-like aggregates, and inhibit autophagy and TOROID formation. Here, we used the apt1∆ aah1∆ yeast model of inborn errors of metabolism, previously shown to lead to intracellular adenine accumulation and adenine amyloid-like fiber formation, to explore interactions with TDP-43. Results show that the double deletion shifts the TDP-43 aggregates from liquid-like droplets toward a more amyloid-like state. At the same time the deletions reduce TDP-43's effects on toxicity, cell morphology, autophagy, and TOROID formation without affecting the level of TDP-43. This suggests that the liquid-like droplets rather than amyloid-like TDP-43 aggregates are responsible for the deleterious effects in yeast. How the apt1∆ aah1∆ deletions alter TDP-43 aggregate formation is not clear. Possibly, it results from adenine and TDP-43 fiber interactions as seen for other heterologous fibers. This work offers new insights into the potential interactions between metabolite-based amyloids and pathological protein aggregates, with broad implications for understanding protein misfolding diseases.

Vaginal microbiota involves seven communities-state types (CST), four dominated by Lactobacillus. L. crispatus, particularly, offers enhanced protection against infections. Recurrent vulvovaginal candidiasis and trichomoniasis affect millions of people annually, often asymptomatically, facilitating infection spread and leading complications. Co-culture, the technique of cultivating different microbial populations together to mimic real-life conditions, enables the study of microorganism interactions, including inhibitory or promotive effects on pathogens. This review compiles data on co-culture techniques to analyze interactions among Lactobacillus spp., Candida spp., and Trichomonas vaginalis. PubMed was searched using medical subject headings (MESH) terms, 'co-culture', 'coculture,' 'cocultivation,' 'co-incubation,' and 'Trichomonas vaginalis', 'Candida spp.', 'Lactobacillus spp.'. Articles were selected based on relevance to vaginal health, English language, availability, and use of co-culture or co-incubation techniques in the past 24 years. Co-culture and co-incubation studies over the past 24 years have advanced our understanding of microbiota-host, pathogen-host, and pathogen-host-microbiota interactions. These studies reveal that microbiota composition impacts infections, with the microbiota producing substances against pathogens and pathogens developing stress tolerance mechanisms. They elucidate pathogen virulence factors, interactions with immune cells, and how ecological relationships between microorganisms can enhance pathogenicity.

The cervicovaginal microbiome (CVM) is increasingly being considered as an important aspect of women's health, particularly in relation to the risk and progression of sexually transmitted infections (STIs). CVM composition varies significantly between individuals and is shaped by factors including diet, age, environmental exposures, and lifestyle. Understanding these influences may shed light on how microbial imbalances contribute to infection susceptibility and the development of reproductive health disorders. Five distinct community state types (CSTs) classify common CVM compositions. Most CSTs (I, II, III, V) are characterized by a dominant Lactobacillus species and are associated with better or neutral reproductive health, including reduced coincident detection of STIs such as Chlamydia trachomatis. In contrast, CST IV is composed of diverse, predominantly anaerobic, microbial species and is associated with CVM dysbiosis, bacterial vaginosis, and a heightened risk of STI acquisition. This review examines the complex interplay between the CVM, C. trachomatis infection, and host immune responses, highlighting the role of metabolites such as short-chain and long-chain fatty acids, indole, and iron in modulating pathogen survival and host defenses. Additionally, the impacts of CVM composition on C. trachomatis persistence, ascension, and clearance are discussed, alongside co-infection dynamics with pathogens like Neisseria gonorrhoeae and Mycoplasma genitalium.

Shiga toxin-producing Escherichia coli (STEC) is a major food-borne pathogen causing human diseases ranging from diarrhea to life-threatening complications, mainly in young children. Colonization, virulence, and interactions of STEC strains with human gut microbiota are pivotal during infection but remain poorly described, particularly in children, the most affected population. In this work, we evaluated changes in the microbiota and metabolome composition in the in vitro gut model: Toddler ARtificial COLon (T-ARCOL) infected with EHEC O157:H7 strain EDL 933. Stool samples collected from children with STEC-positive diarrhea and stool from the same children after recovery from the diarrheal episode (n=5) were used to inoculate the T-ARCOL model. STEC colonization was progressively reduced throughout fermentation in T-ARCOL with diarrhea or recovery fecal samples. Beta diversity showed that the diarrhea-associated microbiota was significantly distinct from the recovery microbiota and exhibited a lower α-diversity. In contrast to recovery conditions, diarrheal conditions were characterized by an increased abundance of potential pathobionts such as members of the Clostridiaceae family and higher acetate, succinate, and N-acetylneuraminic acid levels. Our results provide new evidence of the impact of EHEC in the microbiota and metabolome dynamics in an in vitro gut model that could be useful in understanding their physiopathology in this at-risk population, considering inter-individual variabilities in gut microbiota.