Clostridium difficile is a major nosocomial pathogen responsible for close to half a million infections and 27,000 deaths annually in the U.S. Preceding antibiotic treatment is a major risk factor for C. difficile infection (CDI) leading to recognition that commensal microbes play a key role in resistance to CDI. Current antibiotic treatment of CDI is only partially successful due to a high rate of relapse. As a result, there is interest in understanding the effects of microbes on CDI susceptibility to support treatment of patients with probiotic microbes or entire microbial communities (e.g., fecal microbiota transplantation). The results reported here demonstrate that colonization with the human commensal fungus Candida albicans protects against lethal CDI in a murine model. Colonization with C. albicans did not increase the colonization resistance of the host. Rather, our findings showed that one effect of C. albicans colonization was to enhance a protective immune response. Mice pre-colonized with C. albicans expressed higher levels of IL-17A in infected tissue following C. difficile challenge compared to mice that were not colonized with C. albicans. Administration of cytokine IL-17A was demonstrated to be protective against lethal murine CDI in mice not colonized with C. albicans. C. albicans colonization was associated with changes in the abundance of some bacterial components of the gut microbiota. Therefore, C. albicans colonization altered the gut ecosystem, enhancing survival after C. difficile challenge. These findings demonstrate a new, beneficial role for C. albicans gut colonization.

Inside the human host, the pathogenic yeast Candida albicans colonizes predominantly oxygen-poor niches such as the gastrointestinal and vaginal tracts, but also oxygen-rich environments such as cutaneous epithelial cells and oral mucosa. This suppleness requires an effective mechanism to reversibly reprogram the primary metabolism in response to oxygen variation. Here, we have uncovered that Snf5, a subunit of SWI/SNF chromatin remodeling complex, is a major transcriptional regulator that links oxygen status to the metabolic capacity of C. albicans. Snf5 and other subunits of SWI/SNF complex were required to activate genes of carbon utilization and other carbohydrates related process specifically under hypoxia. snf5 mutant exhibited an altered metabolome reflecting that SWI/SNF plays an essential role in maintaining metabolic homeostasis and carbon flux in C. albicans under hypoxia. Snf5 was necessary to activate the transcriptional program linked to both commensal and invasive growth. Accordingly, snf5 was unable to maintain its growth in the stomach, the cecum and the colon of mice. snf5 was also avirulent as it was unable to invade Galleria larvae or to cause damage to human enterocytes and murine macrophages. Among candidates of signaling pathways in which Snf5 might operate, phenotypic analysis revealed that mutants of Ras1-cAMP-PKA pathway, as well as mutants of Yak1 and Yck2 kinases exhibited a similar carbon flexibility phenotype as did snf5 under hypoxia. Genetic interaction analysis indicated that the adenylate cyclase Cyr1, a key component of the Ras1-cAMP pathway interacted genetically with Snf5. Our study yielded new insight into the oxygen-sensitive regulatory circuit that control metabolic flexibility, stress, commensalism and virulence in C. albicans.

Colonization with the commensal fungus Candida albicans perturbs the gut-brain axis through dysregulation of endocannabinoid signaling

Prior antibiotic treatment is a risk factor for Clostridioides difficile infection (CDI); the commensal gut microbiota plays a key role in determining host susceptibility to the disease. Previous studies demonstrate that the pre-colonization of mice with a commensal fungus, Candida albicans, protects against a lethal challenge with C. difficile spores. The results reported here demonstrate that the cecum contents of antibiotic-treated mice with C. albicans colonization contained different levels of several lipid species, including non-esterified, unsaturated long-chain fatty acids compared to non-C. albicans-colonized mice. Mice fed olive oil for one week and challenged with C. difficile spores showed enhanced survival compared to PBS-fed mice. The amount of olive oil administered was not sufficient to cause weight gain or to result in significant changes to the bacterial microbiota, in contrast to the effects of a high-fat diet. Furthermore, the direct exposure of C. difficile bacteria in laboratory culture to the unsaturated fatty acid oleic acid, the major fatty acid found in olive oil, reduced the transcription of genes encoding the toxins and reduced the survival of bacteria in the post-exponential phase. Therefore, the effects of C. albicans on the metabolite milieu contributed to the attenuation of C. difficile virulence.

Bacterial strain variation exists in natural populations of bacteria and can be generated experimentally through directed or random mutation. The advent of rapid and cost-efficient whole-genome sequencing has facilitated strain-level genotyping. Even with modern tools, however, it often remains a challenge to map specific traits to individual genetic loci, especially for traits that cannot be selected under culture conditions (e.g., colonization level or pathogenicity). Using a combination of classical and modern approaches, we analyzed strain-level variation in Vibrio fischeri and identified the basis by which some strains lack the ability to utilize glycerol as a carbon source. We proceeded to reconstruct the lineage of the commonly used V. fischeri laboratory strains. Compared to the wild-type ES114 strain, we identify in ES114-L a 9.9-kb deletion with endpoints in tadB2 and glpF; restoration of the missing portion of glpF restores the wild-type phenotype. The widely used strains ESR1, JRM100, and JRM200 contain the same deletion, and ES114-L is likely a previously unrecognized intermediate strain in the construction of many ES114 derivatives. ES114-L does not exhibit a defect in competitive squid colonization but ESR1 does, demonstrating that glycerol utilization is not required for early squid colonization. Our genetic mapping approach capitalizes on the recently discovered chitin-based transformation pathway, which is conserved in the Vibrionaceae; therefore, the specific approach used is likely to be useful for mapping genetic traits in other Vibrio species.I dentifying relevant differences in bacterial strains is fundamental to determining the genetic basis of microbial phenotypes. In many cases, the number of polymorphisms between strains is so high that elucidating which locus or loci contribute to specific phenotypes cannot be achieved simply by determining the genome sequence of the isolates. This challenge is especially pronounced in identifying loci that contribute to colonization and/or pathogenicity phenotypes. The study of genomic islands has made it clear that the acquisition of large regions of DNA can profoundly influence a bacterium's ability to engage with a eukaryotic host (1, 2). Recently, it has become increasingly apparent that defined genetic changes in bacteria at individual loci, single genes, or even nucleotide changes have led to dramatic effects in the evolution of colonizing bacteria. As some examples, the acquisition of the nil locus in Xenorhabdus nematophila contributed to the species-specific association with the worm host Steinernema carpocapsae, inactivation of the RscA biofilm regulator was critical in the evolution of Yersinia pestis from Yersinia pseudotuberculosis, and acquisition of the biofilm regulation of RscS facilitated colonization of north Pacific squid by Vibrio fischeri (3-8).In most cases, identification of factors that contribute to host colonization specificity has relied first on identifying the factor as being necessary for host colonization by standard g...

Inside the human host, the pathogenic yeast Candida albicans colonizes predominantly oxygen-poor niches such as the gastrointestinal and vaginal tracts, but also oxygen-rich environments such as cutaneous epithelial cells and oral mucosa. This suppleness requires an effective mechanism to reprogram reversibly the primary metabolism in response to oxygen variation. Here, we have uncovered that Snf5, a subunit of SWI/SNF chromatin remodeling complex, is a major transcriptional regulator that links oxygen status to the metabolic capacity of C. albicans. Snf5 and other subunits of SWI/SNF complex were required to activate genes of alternative carbon utilization and other carbohydrates related process specifically under hypoxia. snf5 mutant exhibited an altered metabolome reflecting that SWI/SNF plays an essential role in maintaining metabolic homeostasis and carbon flux in C. albicans under hypoxia. Snf5 was necessary to activate the transcriptional program linked to both commensal and invasive growth. Accordingly, snf5 was unable to maintain its growth in the stomach, the cecum and the colon of mice. snf5 was also avirulent as it was unable to invade Galleria larvae or to cause damage to human enterocytes and murine macrophages. Among candidates of signaling pathways in which Snf5 might operate, phenotypic analysis revealed that mutants of Ras1-cAMP-PKA pathway, as well as mutants of Yak1 and Yck2 kinases exhibited a similar carbon flexibility phenotype as did snf5 under hypoxia. Genetic interaction analysis indicated that the adenylate cyclase Cyr1, a key component of the Ras1-cAMP pathway, but not Ras1, interacted genetically with Snf5. Our study yielded unprecedented insight into the oxygen-sensitive regulatory circuit that control metabolic flexibility, stress, commensalism and virulence in C. albicans.Author SummaryA critical aspect of eukaryotic cell fitness is the ability to sense and adapt to variations in oxygen concentrations in their local environment. Hypoxia leads to a substantial remodeling of cell metabolism and energy homeostasis, and thus, organisms must develop an effective regulatory mechanism to cope with oxygen depletion. Candida albicans is an opportunistic yeast that is the most prevalent human fungal pathogens. This yeast colonizes diverse niches inside the human host with contrasting carbon sources and oxygen concentrations. While hypoxia is the predominant conditions that C. albicans encounters inside most of the niches, the impact of this condition on metabolic flexibility, a major determinant of fungal virulence, was completely neglected. Here, we uncovered that the chromatin remodelling complex SWI/SNF is master regulatory circuit that links oxygen status to a broad spectrum of carbon utilization routes. Snf5 was essential for the maintenance of C. albicans as a commensal and also for the expression of its virulence. The oxygen-sensitive regulators identified in this work provide a framework to comprehensively understand the virulence of human fungal pathogens and represent a therapeutic value to fight fungal infections.

19Due to a limited set of antifungals available and problems in early diagnosis invasive fungal 20 infections caused by Candida species are among the most common hospital-acquired 21 infections with staggering mortality rates. Here, we describe an engineered system able to 22 sense and respond to the fungal pathogen Candida albicans, the most common cause of 23 candidemia. In doing so, we identified hydroxyphenylacetic acid (HPA) as a novel molecule 24 secreted by C. albicans. Furthermore, we engineered E. coli to be able to sense HPA 25 produced by C. albicans. Finally, we constructed a sense-and-respond system by coupling 26 the C. albicans sensor to the production of an inhibitor of hypha formation thereby reducing 27 filamentation, virulence factor expression and fungal-induced epithelial damage. This system 28 could be used as a basis for the development of novel prophylactic approaches to prevent 29 fungal infections. 30 31 32 Introduction 33 Fungal pathogens cause diverse types of infections ranging from superficial to systemic and 34 claim about 1.5 million lives per year 1 . Candida species are among the most common 35 opportunistic fungal pathogens and represent the fourth-leading cause of hospital-acquired 36bloodstream infections with mortality rates of more than 40% in immunocompromised 37 patients 1-4 . 38Candida albicans represents the main cause of candidemia, being responsible for 39 more than 40% of all cases worldwide 2 . C. albicans is a commensal colonizing the 40 gastrointestinal and genitourinary tracts of healthy individuals 5 . However, under 41 immunocompromised conditions, C. albicans can penetrate epithelia and cause severe 42 systemic infections 6 . A key virulence factor of C. albicans is its morphologic plasticity; it can 43 reversibly switch between a yeast and a filamentous or true hyphal morphology depending on 44 the environmental conditions. On epithelial surfaces, initial adhesion and subsequent 45 filamentation are required for efficient epithelial penetration 7 . In addition, several virulence 46 factors such as Candidalysin, a peptide that damages epithelial cells, are produced 47 exclusively by the hyphal form 8 . 48Difficulties associated with rapid and reliable diagnosis as well as lack of specific 49 disease manifestations contribute to the high mortality rates of systemic fungal infections 9 . 50Antifungal prophylaxis is currently applied to high risk individuals. While effective in preventing 51 Candida infections 10,11 , prolonged prophylaxis can lead to the emergence of resistant strains 52 or to an increase of species, that are intrinsically resistant to the limited set of antifungals 53 available 10,12 . Development of novel antifungals with fungistatic or fungicidal activity is limited 54 by the relative dearth of specific targets in these eukaryotic pathogens. Thus, more recently 55 approaches targeting specific virulence factors have been gaining interest. This strategy can 56 increase the number of potential targets, that are specific to the pathogen, and will...

Due to a limited set of antifungals available and problems in early diagnosis invasive fungal infections caused by Candida species are among the most common hospital-acquired infections with staggering mortality rates. Here, we describe an engineered system able to sense and respond to the fungal pathogen Candida albicans, the most common cause of candidemia. In doing so, we identified hydroxyphenylacetic acid (HPA) as a novel molecule secreted by C. albicans. Furthermore, we engineered E. coli to be able to sense HPA produced by C. albicans. Finally, we constructed a sense-and-respond system by coupling the C. albicans sensor to the production of an inhibitor of hypha formation thereby reducing filamentation, virulence factor expression and fungal-induced epithelial damage. This system could be used as a basis for the development of novel prophylactic approaches to prevent fungal infections.