Browsing by Subject "Gastrointestinal Microbiome"
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Item Changes in the Gut Metabolic Landscape Drive Inflammation-Associated Dysbiosis and Host Responses(2020-12-01T06:00:00.000Z) Hughes, Elizabeth Rose; Sperandio, Vanessa; Pfeiffer, Julie K.; Alto, Neal; Winter, Sebastian E.Intestinal inflammation is frequently associated with alterations in composition of gut microbial communities, termed dysbiosis. Inflammation-associated dysbiosis is characterized by an expansion of facultative anaerobic bacteria in the Proteobacteria phylum, such as Escherichia coli. A dysbiotic microbiota has been linked to increased disease severity in the context of inflammatory bowel disease. However, the mechanisms responsible for inflammation-associated dysbiosis and its impact on disease are incompletely understood. Utilizing bioinformatic analyses of gut microbiota composition and mechanistic studies with Escherichia coli as a model organism in murine models, we uncovered two metabolic pathways that are unique to intestinal inflammation and responsible for changes in microbiota composition. Aerobic respiration coupled with formate oxidation, and utilization of molecular hydrogen fuel expansion of Escherichia coli populations during intestinal inflammation. The impact of oxygen leakage into the gut lumen on obligate anaerobic bacterial metabolism was additionally investigated. In vitro metabolite measurements and use of bacterial genetics indicated formate production increased in Bacteroides exposed to low oxygen levels. Formate measurements and exogenous delivery of formate in mice suggested that intestinal formate levels increase during inflammation and may exacerbate disease. However, further study is required. In conclusion, we identified key changes that occur during non-infectious inflammation in the gut metabolic landscape, illustrating the importance of understanding bacterial metabolism in order to understand host-microbiota interactions.Item Dysbiosis-Associated Changes in Host Metabolism Produce Lactate to Support Enterobacterial Expansion During Inflammation(2019-04-04) Gillis, Caroline Catherine; Hendrixson, David R.; Winter, Sebastian E.; Sperandio, Vanessa; Burstein, EzraThe lumen of the gastrointestinal tract is heavily colonized by microbes, termed the gut microbiota. Under normal conditions, fermentative anaerobes constitute the majority of the gut microbiota. However, during inflammation there is a change in the nutritional environment of the gut that enables the outgrowth of facultative aerobic Enterobacteriaceae through respiratory metabolism. Salmonella enterica serovar Typhimurium (S. Tm) is a pathogenic member of the Enterobacteriaceae family that benefits from inflammation. We found that S. Tm uses lactate as a nutrient during infection, which maximizes colonization of the gut. During S. Tm infection, a profound change in the microbial community of the gut occurs. In particular, butyrate-producing Clostridia species are depleted. Butyrate is the preferred substrate for β-oxidation by intestinal epithelial cells (IEC). In the absence of butyrate, IEC perform a fermentative metabolism that produces lactate as a waste product. Lactate is then used in conjunction with oxygen as a terminal electron acceptor to support growth of S. Tm in the murine gut lumen. We next investigated the regulation of lactate utilization in S. Tm. We found that the lactate utilization genes (lldPRD), were inducible by electron acceptors and L-lactate. The transcriptional response to L-lactate was coordinated by the regulatory protein LldR, which maximized colonization of the murine gut. Under anaerobic conditions, lldPRD expression was repressed by the two-component system ArcAB. Commensal members of the Enterobacteriaceae family also expand during non-infectious colitis. We investigated whether lactate was also produced during non-infectious colitis and if commensal Enterobacteriaceae could use this nutrient. Butyrate was depleted and lactate was abundant in a murine model of colitis. Metagenomic sequencing demonstrated that lactate dehydrogenase genes were more abundant in the microbiome of inflamed mice than control mice. We next began to characterize putative lactate dehydrogenases in E. coli. We identified several putative lactate dehydrogenases, however, their role in E. coli fitness requires further study. In conclusion, we identified an important host-derived nutrient that promotes S. Tm fitness during infection and may serve as a nutrient for commensal Enterobacteriaceae during non-infectious colitis. This illustrates the importance of nutrient acquisition for Enterobacteriaceae during inflammatory colonization of the gut.Item Factors Governing Gastrointestinal Colonization of Candida albicans(December 2021) Mishra, Animesh Anand; Hendrixson, David R.; Hooper, Lora V.; Winter, Sebastian E.; Koh, Andrew Y.Candida albicans can colonize the human gastrointestinal tract (GI) and cause disseminated infections in immunocompromised hosts. Depletion of specific gut commensal microbiota is associated with or results in increased C. albicans burden in the gut and increased likelihood of dissemination in human patients and mice, respectively. The exact mechanisms by which gut microbiota mediate C. albicans colonization resistance in the gut, however, are unknown. Here, we show that gut microbiota-derived short chain fatty acids (SCFA) directly inhibit C. albicans growth in vitro. SCFA inhibit C. albicans hexose uptake and induce intracellular acidification. In contrast, SCFA promote C. albicans GI colonization resistance in vivo but only when an intact gut microbiome is present. SCFA induce gut microbiota composition changes that promote C. albicans colonization resistance. Commensal gut microbiota unable to produce SCFA have a diminished capacity to reduce C. albicans GI colonization. Prebiotic therapy results in increased GI SCFA levels which enhance C. albicans GI clearance. This work also describes two C. albicans isolates 529L and CHN1 that can stably colonize the murine GI tract without the use of antibiotics. These clinical isolates have a higher resistance to antimicrobial peptide CRAMP compared to the most commonly studied C. albicans laboratory strain SC5314. Thus, the work sheds light on mechanisms that might be critical in governing C. albicans gastrointestinal colonization levels. It provides mechanistic insights into the importance of gut microbiota-derived metabolites in maintaining C. albicans colonization resistance and may have therapeutic implications for modulating C. albicans gastrointestinal colonization levels in order to prevent invasive candidiasis in immunocompromised patients. Further, C. albicans strain-specific difference in colonization ability appears to depend on the sensitivity to these host immune effectors. The described isolates can further serve as valuable tools to probe the mechanisms of C. albicans gastrointestinal colonization without the intervention of any antibiotics.Item Immune Checkpoint Blockade Induces Gut Microbiota Translocation That Augments Extraintestinal Anti-Tumor Immunity(2023-05-01T05:00:00.000Z) Choi, Yongbin; Yan, Nan; Koh, Andrew Y.; Hooper, Lora V.; Winter, Sebastian E.Gut microbiota are critical for effective immune checkpoint blockade therapy (ICT) for cancer. The mechanisms by which gut microbiota augment extraintestinal anti-cancer immune responses, however, are largely unknown. Here, we find that ICT induces the translocation of specific endogenous gut microbiota into secondary lymphoid organs and subcutaneous melanoma tumors. Mechanistically, ICT induces lymph node remodeling and dendritic cell (DC) activation which facilitates the translocation of a selective subset of gut bacteria to extraintestinal tissues which promote optimal anti-tumor T-cell responses in both the tumor-draining lymph nodes (TDLN) and the primary tumor. Antibiotic treatment results in decreased gut microbiota translocation into MLN and TDLN, diminished DC and effector CD8+ T cell responses, and attenuated response to ICT. Our findings illuminate a key mechanism by which gut microbiota promote extraintestinal anti-cancer immunity.Item Interplay Between Tryptophan Metabolites and the Virulence Factors of Enteric Pathogens(2020-08-01T05:00:00.000Z) Kumar, Aman; Winter, Sebastian E.; Sperandio, Vanessa; Conrad, Nicholas; Tu, BenjaminThe human gut consists of a complex milieu of several small molecules that helps in shaping its overall chemistry and biogeography. Trillions of bacteria, collectively known as the gut microbiota, colonize this landscape and occupy a specific niche. Small molecules derived from diet, gut microbial metabolism, and host metabolic activity have an impact on dictating the underlying gut microbiome composition. Gut bacterial populations effectively sense these molecular signatures and modulate gene expression to colonize this niche. An invading intestinal pathogen, to effectively colonize the gut, must sense and respond to the molecular signatures in the gut, which leads to effective colonization and infection. Diet is the principal source of energy by the intake of three main nutrients: carbohydrates, proteins, and fats. Tryptophan is an essential amino acid taken from the diet and plays an important role in protein biosynthesis. Tryptophan is also metabolized to different small molecules and its metabolic products are known to be present in high concentrations in the body. Upon ingestion, tryptophan is readily available in the luminal environment of the gut. Abundant levels of tryptophan are also absorbed by intestinal epithelial cells and is made available in different cellular compartments for normal physiological processes. Tryptophan present in the gut lumen can be further metabolized to numerous small molecules by the action of the gut microbial metabolic activity. Indole is one of the most abundant tryptophan-derived metabolites present in the gut and is absorbed by the host epithelial cells. The host can also metabolize tryptophan to various small molecules including serotonin that is made available in the gut lumen upon release from the host cells. Bacteria in the gut sense these bacterial and host-derived small molecules to colonize and maintain their niche. Similarly, an invading food-borne pathogen such as Enterohemorrhagic Escherichia coli (EHEC), which causes gastroenteritis by primarily colonizing the human colon, sense these small molecules and respond in a way that is conducive for its colonization and virulence gene expression. The role of these highly abundant tryptophan-derived small molecules in dictating the infectivity of an enteric pathogen remains unknown. Because the concentrations of these small molecules naturally present in the body are in the range of the drug concentrations that are used to treat certain diseases, it is possible to repurpose the information gained from these studies to treat intestinal infections. In the present study, we focused on two highly abundant tryptophan-derived small molecules present in the gut. Indole is derived from bacterial metabolism while serotonin is present via the action of host metabolism of tryptophan. Indole and serotonin are structurally similar and therefore may have similar effects against a pathogen in vivo. Indeed, we identified that both indole and serotonin decrease the virulence of the human pathogen Enterohemorrhagic E. coli (EHEC) and the mouse pathogen Citrobacter rodentium. We used multiple strategies including genetic manipulation, pharmacological inhibitors, and knock-out murine models to show that both indole and serotonin are inhibitory signals for virulence gene expression in EHEC and C. rodentium. We further investigated the mechanism used by these pathogens to sense these signals. We identified the first bacterial receptor for both indole and serotonin, and showed that these signals are sensed by a bacterial membrane bound histidine kinase CpxA. Upon sensing indole or serotonin, CpxA dephosphorylates itself and the transcription factor CpxR. In its phosphorylated state, CpxR directly activates expression of the virulence genes, its dephosphorylation prevents its action, decreasing expression of these genes. Together, our studies highlight the importance of sensing small molecules and understanding the gut biogeography by invading pathogens to successfully colonize the gut.Item The microbiome and spondyloarthritis(2015-10-30) Reimold, AndreasItem Regulation of Body Composition by the Microbiota and the Circadian Clock(2017-11-21) Wang, Yuhao; Green, Carla B.; Liu, Yi; Wan, Yihong; Hooper, Lora V.The intestinal microbiota has been identified as an environmental factor that markedly impacts energy storage and body fat accumulation, yet the underlying mechanisms remain unclear. In this dissertation, I show that the microbiota regulates body composition through the circadian transcription factor NFIL3 in intestinal epithelial cells. First, epithelial NFIL3 promotes lipid absorption and export in the intestine by regulating a circadian expression program of epithelial lipid metabolic genes. Second, Nfil3 transcription oscillates diurnally in intestinal epithelial cells and the amplitude of the circadian oscillation is controlled by the microbiota through group 3 innate lymphoid cells (ILC3), STAT3, and the epithelial cell circadian clock. These findings provide mechanistic insight into how the intestinal microbiota regulates body composition and establish NFIL3 as an essential molecular link among the microbiota, the circadian clock, and host metabolism.Item Unique Aspects of Intestinal Biology That Influence Enteric Virus Infection(2021-05-01T05:00:00.000Z) Woods Acevedo, Mikal Aaron; Orchard, Robert C.; Pfeiffer, Julie K.; Schoggins, John W.; Winter, Sebastian E.Enteric viruses are human pathogens that pose a significant global health problem. In this work, I explore how unique facets of host biology influence enteric virus infection, ranging from intestinal microbiota to circadian rhythms. To examine these factors, I used coxsackievirus B3 (CVB3) and poliovirus, which serve as a powerful model viruses to understand virus-host interactions. CVB3 and poliovirus are nonenveloped single-stranded positive-sense RNA viruses, which spread through the fecal-oral route. While many enteric virus infections are mild, some can be severe or even fatal. Thus it is important to study which factors impact enteric virus infection. Throughout my dissertation I used a variety of mouse models to answer a multitude of questions related to what factors influence enteric virus infection. To study the microbiota-mediated enhancement of CVB3 infection, I used different methods of antibiotic depletion in mice. We determined that two related enteric viruses, CVB3 and poliovirus, differ in their requirements of the microbiota. Furthermore, I studied the antiviral effects of antibiotics in vitro and in vivo and found that while antibiotics are not antiviral for CVB3 in cell culture, they are antiviral for CVB3 in a mouse model. Finally, by infecting mice at different times of day, we determined that host circadian rhythms influence enteric virus susceptibility. In conclusion, using model enteric viruses, such as CVB3 and poliovirus, I elucidated multiple unique aspects of host biology, ranging from microbiota to circadian rhythms, that influence viral replication and pathogenesis.Item [UT Southwestern Medical Center News](2009-08-19) Shear, Kristen Holland