mSphere最新文献

Heat shock factor (HSF)-type regulators are stress-responsive transcription factors widely distributed among eukaryotes, including fungi. They carry a four-stranded winged helix-turn-helix DNA-binding domain considered as the signature domain for HSFs. The genome of the opportunistic yeast Candida albicans encodes four HSF members, namely, Sfl1, Sfl2, Skn7, and the essential regulator, Hsf1. C. albicans HSFs do not only respond to heat shock and/or temperature variation but also to CO₂ levels, oxidative stress, and quorum sensing, acting this way as central decision makers. In this minireview, I follow on the heels of my mSphere of Influence commentary (2020) to provide an overview of the repertoire of HSF regulators in Saccharomyces cerevisiae and C. albicans and describe how their genetic perturbation in C. albicans, coupled with genome-wide expression and location analyses, allow to map their transcriptional circuitry. I highlight how they can regulate, in common, a crucial developmental program: filamentous growth.

Myeloid phagocytes are essential for antifungal immunity against pulmonary Aspergillus fumigatus and systemic Candida albicans infections. However, the molecular mechanisms underlying fungal clearance by phagocytes remain incompletely understood. In this study, we investigated the role of Perforin-2 (Mpeg1) in antifungal immunity. We found that Mpeg1^-/- mice generated on a mixed C57BL/6J-DBA/2 background exhibited enhanced survival, reduced lung fungal burden, and greater neutrophil fungal killing activity compared to wild-type C57BL/6J (B6) mice, suggesting that Perforin-2 may impair antifungal immune responses. However, when we compared Mpeg1^-/- mice with co-housed Mpeg^+/+ littermate controls, these differences were no longer observed, indicating that initial findings were likely influenced by differences in the murine genetic background or the microbiota composition. Furthermore, Perforin-2 was dispensable for antifungal immunity during C. albicans bloodstream infection. These results suggest that Perforin-2 is not essential for host defense against fungal infections in otherwise immune-competent mice.

Importance: Humans encounter fungal pathogens daily and rely on innate immune cells to clear Aspergillus fumigatus, the leading cause of mold pneumonia worldwide, and Candida albicans, the most common cause of fungal bloodstream infections. The World Health Organization has classified A. fumigatus and C. albicans as critical priority fungal pathogens due to the emergence of drug resistance and the increasing number of susceptible individuals across the globe. The mechanisms by which innate immune cells clear these fungal pathogens remain incompletely defined. In this study, we examined the role of a pore-forming protein called Perforin-2 in host defense against these fungal pathogens, in part because Perforin-2 has been implicated in antibacterial host defense. Our findings reveal that Perforin-2 is dispensable for antifungal immunity against respiratory A. fumigatus and systemic C. albicans infections in mice, suggesting that the antimicrobial activity of Perforin-2 does not extend to these two fungal pathogens.

Thousands of complete genome sequences for strains of a species that are now available enable the advancement of pangenome analytics to a new level of sophistication. We collected 2,377 publicly available complete genomes of Escherichia coli for detailed pangenome analysis. The core genome and accessory genomes consisted of 2,398 and 5,182 genes, respectively. We developed a machine learning approach to define the accessory genes characterizing the major phylogroups of E. coli plus Shigella: A, B1, B2, C, D, E, F, G, and Shigella. The analysis resulted in a detailed structure of the genetic basis of the phylogroups' differential traits. This pangenome structure was largely consistent with a housekeeping-gene-based MLST distribution, sequence-based Mash distance, and the Clermont quadruplex classification. The rare genome (consisting of genes found in <6.8% of all strains) consisted of 163,619 genes, about 79% of which represented variations of 315 underlying transposon elements. This analysis generated a mathematical definition of the genetic basis for a species.

Importance: The comprehensive analysis of the pangenome of Escherichia coli presented in this study marks a significant advancement in understanding bacterial genetic diversity. By employing machine learning techniques to analyze 2,377 complete E. coli genomes, the study provides a detailed mapping of core, accessory, and rare genes. This approach reveals the genetic basis for differential traits across phylogroups, offering insights into pathogenicity, antibiotic resistance, and evolutionary adaptations. The findings enhance the potential for genome-based diagnostics and pave the way for future studies aimed at achieving a global genetic definition of bacterial phylogeny.

Ningning Liu works in the field of fungal infection and cancer progression, with a particular focus on the mechanism of host-pathogen interaction. In this mSphere of influence article, he reflects on how papers entitled "The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL," by B. Aykut, S. Pushalkar, R. Chen, Q. Li, et al. (Nature 574:264-267, 2019, https://doi.org/10.1038/s41586-019-1608-2), and "A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors," by A. B. Dohlman, J. Klug, M. Mesko, I. H. Gao, et al. (Cell 185:3807-3822.E12, 2022, https://doi.org/10.1016/j.cell.2022.09.015), emphasized the non-negligible role of fungi in the host and demonstrated a connection between fungi and cancer. These researches arouse his interest in seeking the novel fungal pathogen lurking inside tumors and understanding the unexplored mechanisms behind the severe fungal infections in cancer patients.

The underlying interactions that occur to maintain skin microbiome composition, function, and overall skin health are largely unknown. Often, these types of interactions are mediated by microbial metabolites. Cobamides, the vitamin B₁₂ family of cofactors, are essential for metabolism in many bacteria but are only synthesized by a fraction of prokaryotes, including certain skin-associated species. Therefore, we hypothesize that cobamide sharing mediates skin community dynamics. Preliminary work predicts that several skin-associated Corynebacterium species encode de novo cobamide biosynthesis and that their abundance is associated with skin microbiome diversity. Here, we show that commensal Corynebacterium amycolatum produces cobamides and that this synthesis can be tuned by cobalt limitation. To demonstrate cobamide sharing by C. amycolatum, we employed a co-culture assay using an E. coli cobamide auxotroph and showed that C. amycolatum produces sufficient cobamides to support Escherichia coli growth, both in liquid co-culture and when separated spatially on solid medium. We also generated a C. amycolatum non-cobamide-producing strain (cob^-) using UV mutagenesis that contains mutated cobamide biosynthesis genes cobK (precorrin-6X reductase) and cobO (corrinoid adenosyltransferase) and confirm that disruption of cobamide biosynthesis abolishes the support of E. coli growth through cobamide sharing. Our study provides a unique model to study metabolite sharing by microorganisms, which will be critical for understanding the fundamental interactions that occur within complex microbiomes and for developing approaches to target the human microbiota for health advances.

Importance: The human skin serves as a crucial barrier for the body and hosts a diverse community of microbes known as the skin microbiome. The interactions that occur to maintain a healthy skin microbiome are largely unknown but are thought to be driven in part, by nutrient sharing between species in close association. Here we show that the skin-associated bacteria Corynebacterium amycolatum produces and shares cobalamin, a cofactor essential for survival in organisms across all domains of life. This study provides a unique model to study metabolite sharing by skin microorganisms, which will be critical for understanding the fundamental interactions that occur within the skin microbiome and for developing therapeutic approaches aiming to engineer and manipulate the skin microbiota.

Dietary fibers influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructo-oligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic. Despite being well studied, we do not yet have a complete picture of all FOS-consuming gut bacterial taxa. To identify new bacterial consumers, we used a short exposure of microbial communities in a stool sample to FOS or galactomannan as the sole carbon source to induce glycan metabolism genes. We then performed metatranscriptomics, paired with whole metagenomic sequencing, and 16S amplicon sequencing. The short incubation was sufficient to cause induction of genes involved in carbohydrate metabolism, like carbohydrate-active enzymes (CAZymes), including glycoside hydrolase family 32 genes, which hydrolyze fructan polysaccharides like FOS and inulin. Interestingly, FOS metabolism transcripts were notably overexpressed in Blautia species not previously reported to be fructan consumers. We therefore validated the ability of different Blautia species to ferment fructans by monitoring their growth and fermentation in defined media. This pulse metatranscriptomics approach is a useful method to find novel consumers of prebiotics and increase our understanding of prebiotic metabolism by CAZymes in the gut microbiota.

Importance: Complex carbohydrates are key contributors to the composition of the human gut microbiota and play an essential role in the microbiota's effects on host health. Understanding which bacteria consume complex carbohydrates, or glycans, provides a mechanistic link between dietary prebiotics and their beneficial health effects, an essential step for their therapeutic application. Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. We identified novel consumers of fructo-oligosaccharide among Blautia species, expanding our understanding of this well-known glycan. Our approach can be applied to identify consumers of understudied glycans and expand our prebiotic repertoire. It can also be used to study prebiotic glycans directly in stool samples in distinct patient populations to help delineate the prebiotic mechanism.

The bacteria living in the human gut are essential for host health. Though the composition and metabolism of these bacteria are well described in both healthy hosts and those with intestinal disease, less is known about the metabolic activity of the gut bacteria prior to, and during, disease development-especially regarding gut bacterial replication. Here, we use a recently developed single-cell technique alongside existing metagenomics-based tools to identify, track, and quantify replicating gut bacteria both ex vivo and in situ in the dextran sodium sulfate (DSS) mouse model of colitis. We show that the proportion of replicating gut bacteria decreases when mice have the highest levels of inflammation and returns to baseline levels as mice begin recovering. In addition, we report significant alterations in the composition of the replicating gut bacterial community ex vivo during colitis development. On the taxa level, we observe significant changes in the abundance of taxa such as the mucus-degrading Akkermansia and the poorly described Erysipelatoclostridium genus. We further demonstrate that many taxa exhibit variable replication rates in situ during colitis, including Akkermansia muciniphila. Lastly, we show that colitis development is positively correlated with increases in the presence and abundance of bacteria in situ which are predicted to be fast replicators. This could suggest that taxa with the potential to replicate quickly may have an advantage during intestinal inflammation. These data support the need for additional research using activity-based approaches to further characterize the gut bacterial response to intestinal inflammation and its consequences for both the host and the gut microbial community.IMPORTANCEIt is well known that the bacteria living inside the gut are important for human health. Indeed, the type of bacteria that are present and their metabolism are different in healthy people versus those with intestinal disease. However, less is known about how these gut bacteria are replicating, especially as someone begins to develop intestinal disease. This is particularly important as it is thought that metabolically active gut bacteria may be more relevant to health. Here, we begin to address this gap using several complementary approaches to characterize the replicating gut bacteria in a mouse model of intestinal inflammation. We reveal which gut bacteria are replicating, and how quickly, as mice develop and recover from inflammation. This work can serve as a model for future research to identify how actively growing gut bacteria may be impacting health, or why these particular bacteria tend to thrive during intestinal inflammation.

Mathematical models can provide insights into complex interactions and dynamics within microbial communities to complement and extend experimental laboratory approaches. For dental biofilms, they can give a basis for evaluating biofilm growth or the transition from health to disease. We have developed mathematical models to simulate the transition toward a cariogenic microbial biofilm, modeled as the overgrowth of Streptococcus mutans within a five-species dental community. This work builds on experimental data from a continuous flow reactor with hydroxyapatite coupons for biofilm growth, in a chemically defined medium with varying concentrations of glucose and lactic acid. The biofilms formed on the coupons were simulated using individual-based models (IbMs), with bacterial growth modeled using experimentally measured kinetic parameters. The IbM assumes that the maximum theoretical growth yield for biomass is dependent on the local concentration of reactants and products, while the growth rates were described using traditional Monod equations. We have simulated all the conditions studied experimentally, considering different initial relative abundance of the five species, and also different initial clustering in the biofilm. The simulation results only reproduced the experimental dominance of S. mutans at high glucose concentration after we considered the species-specific effect of pH on growth rates. This highlights the significance of the aciduric property of S. mutans in the development of caries. Our study demonstrates the potential of combining in vitro and in silico studies to gain a new understanding of the factors that influence dental biofilm dynamics.IMPORTANCEWe have developed in silico models able to reproduce the relative abundance measured in vitro in the synthetic dental biofilm communities growing in a chemically defined medium. The advantage of this combination of in vitro and in silico models is that we can study the influence of one parameter at a time and aim for direct validation. Our work demonstrates the utility of individual-based models for simulating diverse conditions affecting dental biofilm scenarios, such as the frequency of glucose intake, sucrose pulsing, or integration of pathogenic or probiotic species. Although in silico models are reductionist approaches, they have the advantage of not being limited in the scenarios they can test by the ethical consideration of an in vivo system, thus significantly contributing to dental biofilm research.

This study investigates a previously unreported stress signal transduced as crosstalk between the cell wall integrity (CWI) pathway and the septation initiation network (SIN). Echinocandins, which target cell wall synthesis, are widely used to treat mycoses. Their efficacy, however, is species specific. Our findings suggest that this is due largely to CWI-SIN crosstalk and the ability of filamentous species to fortify with septa in response to echinocandin stress. To better understand this crosstalk, we used a microscopy-based assay to measure septum density, aiming to understand the septation response to cell wall stress. The echinocandin micafungin, an inhibitor of β-(1,3)-glucan synthase, was employed to induce this stress. We observed a strong positive correlation between micafungin treatment and septum density in wild-type strains. This finding suggests that CWI activates SIN under cell wall stress, increasing septum density to protect against cell wall failure. More detailed investigations, with targeted knockouts of CWI and SIN signaling proteins, enabled us to identify crosstalk occurring between the CWI kinase, MpkA, and the SIN kinase, SepH. This discovery of the previously unknown crosstalk between the CWI and SIN pathways not only reshapes our understanding of fungal stress responses, but also unveils a promising new target pathway for the development of novel antifungal strategies.

Importance: Echinocandin-resistant species pose a major challenge in clinical mycology by rendering one of only four lines of treatment, notably one of the two that are well-tolerated, ineffective in treating systemic mycoses of these species. Previous studies have demonstrated that echinocandins fail against highly polarized fungi because they target only apical septal compartments. It is known that many filamentous species respond to cell wall stress with hyperseptation. In this work, we show that echinocandin resistance hinges on this dynamic response, rather than on innate septation alone. We also describe, for the first time, the signaling pathway used to deploy the hyperseptation response. By disabling this pathway, we were able to render mycelia susceptible to echinocandin stress. This work enhances our microbiological understanding of filamentous fungi and introduces a potential target to overcome echinocandin-resistant species.