Gastrointestinal Microbiome

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  Subject Areas on Research

  • A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology. 
  • A comparative study of gut microbiomes in captive nocturnal strepsirrhines. 
  • A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome. 
  • A hands-free stool sampling system for monitoring intestinal health and disease. 
  • A longitudinal big data approach for precision health. 
  • A mole rat's gut microbiota suggests selective influence of diet on microbial niche space and evolution. 
  • A role for gut microbiota in host niche differentiation. 
  • A specific microbiota signature is associated to various degrees of ulcerative colitis as assessed by a machine learning approach. 
  • Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism. 
  • Alteration of the rat cecal microbiome during colonization with the helminth Hymenolepis diminuta. 
  • Altered bile acid profile associates with cognitive impairment in Alzheimer's disease-An emerging role for gut microbiome. 
  • Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut. 
  • Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome. 
  • Association of birth mode of delivery with infant faecal microbiota, potential pathobionts, and short chain fatty acids: a longitudinal study over the first year of life. 
  • Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome. 
  • Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model. 
  • Baby, It's Cold Outside: Host-Microbiota Relationships Drive Temperature Adaptations. 
  • Bacteria Boost Mammalian Host NAD Metabolism by Engaging the Deamidated Biosynthesis Pathway. 
  • Bacterial Aggregation Leads to Collective Elimination. 
  • Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes. 
  • Captivity humanizes the primate microbiome. 
  • Common mental disorders in irritable bowel syndrome: pathophysiology, management, and considerations for future randomised controlled trials. 
  • Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data. 
  • Composition of gut microbiota in infants in China and global comparison. 
  • Conserved anti-inflammatory effects and sensing of butyrate in zebrafish. 
  • Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. 
  • Cospeciation of gut microbiota with hominids. 
  • Cross-linkage between bacterial taxonomy and gene functions: a study of metagenome-assembled genomes of gut microbiota in adult non-alcoholic fatty liver disease. 
  • Cross-reactivity of HIV vaccine responses and the microbiome. 
  • Culture-enriched community profiling improves resolution of the vertebrate gut microbiota. 
  • Cutaneous Burn Injury Promotes Shifts in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes. 
  • Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants. 
  • Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees. 
  • Development, diet and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons. 
  • Diet-derived metabolites and mucus link the gut microbiome to fever after cytotoxic cancer treatment. 
  • Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion. 
  • Disrupted Maturation of the Microbiota and Metabolome among Extremely Preterm Infants with Postnatal Growth Failure. 
  • Distinct cellular roles for PDCD10 define a gut-brain axis in cerebral cavernous malformation. 
  • Does lipopolysaccharide-mediated inflammation have a role in OA? 
  • Dynamic linear models guide design and analysis of microbiota studies within artificial human guts. 
  • Dysregulated Microbial Fermentation of Soluble Fiber Induces Cholestatic Liver Cancer. 
  • Ecological memory of prior nutrient exposure in the human gut microbiome. 
  • Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition. 
  • Effects of microbiota-directed foods in gnotobiotic animals and undernourished children. 
  • Emerging Technologies for Gut Microbiome Research. 
  • Enteral High Fat-Polyunsaturated Fatty Acid Blend Alters the Pathogen Composition of the Intestinal Microbiome in Premature Infants with an Enterostomy. 
  • Enteroviruses: A Gut-Wrenching Game of Entry, Detection, and Evasion. 
  • Environmental Enteric Dysfunction and Growth Failure/Stunting in Global Child Health. 
  • Environmental Factors Modify the Severity of Acute DSS Colitis in Caspase-11-Deficient Mice. 
  • Environmental factors regulate Paneth cell phenotype and host susceptibility to intestinal inflammation in Irgm1-deficient mice. 
  • Epithelial delamination is protective during pharmaceutical-induced enteropathy. 
  • Expert insights: The potential role of the gut microbiome-bile acid-brain axis in the development and progression of Alzheimer's disease and hepatic encephalopathy. 
  • Faecal microbiota transplantation from metabolically compromised human donors accelerates osteoarthritis in mice. 
  • Fecal IgA, Antigen Absorption, and Gut Microbiome Composition Are Associated With Food Antigen Sensitization in Genetically Susceptible Mice. 
  • Fecal and blood microbiota profiles and presence of nonalcoholic fatty liver disease in obese versus lean subjects. 
  • Fecal microbiota diversity disruption and clinical outcomes after auto-HCT: a multicenter observational study. 
  • Feeding diversified protein sources exacerbates hepatic insulin resistance via increased gut microbial branched-chain fatty acids and mTORC1 signaling in obese mice. 
  • Fetal exposure to the maternal microbiota in humans and mice. 
  • Frontline Science: Microbiota reconstitution restores intestinal integrity after cisplatin therapy. 
  • Fructose and sugar: A major mediator of non-alcoholic fatty liver disease. 
  • Functional dyspepsia. 
  • Gastrointestinal Microbiome Disruption and Antibiotic-Associated Diarrhea in Children Receiving Antibiotic Therapy for Community-Acquired Pneumonia. 
  • Gastrointestinal hormones and the gut connectome. 
  • Gastrointestinal microbiota alteration induced by Mucor circinelloides in a murine model. 
  • General Anesthesia Alters the Diversity and Composition of the Intestinal Microbiota in Mice. 
  • Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species. 
  • Genetic Evidence That a Gut Commensal Bacterium Can Cause Colorectal Cancer. 
  • Genotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila. 
  • Global burden of irritable bowel syndrome: trends, predictions and risk factors. 
  • Got worms? Perinatal exposure to helminths prevents persistent immune sensitization and cognitive dysfunction induced by early-life infection. 
  • Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons. 
  • Gut Colonization Preceding Mucosal Barrier Injury Bloodstream Infection in Pediatric Hematopoietic Stem Cell Transplantation Recipients. 
  • Gut Microbiome over a Lifetime and the Association with Hypertension. 
  • Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. 
  • Gut microbial molecules in behavioural and neurodegenerative conditions. 
  • Gut microbial succession follows acute secretory diarrhea in humans. 
  • Gut microbiome contributions to altered metabolism in a pig model of undernutrition. 
  • Gut microbiome heritability is nearly universal but environmentally contingent. 
  • Gut microbiota dysbiosis is associated with worse emotional states in HIV infection. 
  • Gut-Innervating Nociceptor Neurons Regulate Peyer's Patch Microfold Cells and SFB Levels to Mediate Salmonella Host Defense. 
  • Gut-microbiota-microglia-brain interactions in Alzheimer's disease: knowledge-based, multi-dimensional characterization. 
  • Harnessing the microbiota to treat neurological diseases
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  • Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy. 
  • High fat diet induces microbiota-dependent silencing of enteroendocrine cells. 
  • High-fat diet-induced colonocyte dysfunction escalates microbiota-derived trimethylamine N-oxide. 
  • Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection. 
  • Human gut microbiota is associated with HIV-reactive immunoglobulin at baseline and following HIV vaccination. 
  • Impact of infection on transplantation tolerance. 
  • Indoxyl sulfate, a gut microbiome-derived uremic toxin, is associated with psychic anxiety and its functional magnetic resonance imaging-based neurologic signature. 
  • Inflammasome, Inflammation, and Tissue Homeostasis. 
  • Inflammatory Th1 and Th17 in the Intestine Are Each Driven by Functionally Specialized Dendritic Cells with Distinct Requirements for MyD88. 
  • Integrative Physiology: At the Crossroads of Nutrition, Microbiota, Animal Physiology, and Human Health. 
  • Interactions between gut microbiota and metabolites modulate cytokine network imbalances in women with unexplained miscarriage. 
  • Intersection of salt- and immune-mediated mechanisms of hypertension in the gut microbiome. 
  • Intestinal Microbiota and Relapse After Hematopoietic-Cell Transplantation. 
  • Intestinal Microbiota of Mice Influences Resistance to Staphylococcus aureus Pneumonia. 
  • Irritable Bowel Syndrome. 
  • Irritable bowel syndrome. 
  • Lactobacillus rhamnosus GG treatment improves intestinal permeability and modulates inflammatory response and homeostasis of spleen and colon in experimental model of Pseudomonas aeruginosa pneumonia. 
  • Lactose drives Enterococcus expansion to promote graft-versus-host disease. 
  • Letter: faecal microbiota transplantation for irritable bowel syndrome-room for improvement. 
  • Lipids and bariatric procedures part 1 of 2: Scientific statement from the National Lipid Association, American Society for Metabolic and Bariatric Surgery, and Obesity Medicine Association: EXECUTIVE SUMMARY. 
  • Lipids and bariatric procedures part 1 of 2: Scientific statement from the National Lipid Association, American Society for Metabolic and Bariatric Surgery, and Obesity Medicine Association: FULL REPORT. 
  • Living fabrication of functional semi-interpenetrating polymeric materials. 
  • Local habitat, not phylogenetic relatedness, predicts gut microbiota better within folivorous than frugivorous lemur lineages. 
  • Long-term stability of microbiome diversity and composition in fecal samples stored in eNAT medium. 
  • Longitudinal multi-omics of host-microbe dynamics in prediabetes. 
  • Lysosome-Rich Enterocytes Mediate Protein Absorption in the Vertebrate Gut. 
  • MAIT and Vδ2 unconventional T cells are supported by a diverse intestinal microbiome and correlate with favorable patient outcome after allogeneic HCT. 
  • Manipulating the gut microbiome to decrease uremic toxins. 
  • Maternal and Breast Milk Influences on the Infant Gut Microbiome, Enteric Health and Growth Outcomes of Rhesus Monkeys. 
  • Measuring and mitigating PCR bias in microbiota datasets. 
  • Megaphages infect Prevotella and variants are widespread in gut microbiomes. 
  • Metabolic support in the critically ill: a consensus of 19. 
  • Metabolomic signature of exposure and response to citalopram/escitalopram in depressed outpatients. 
  • Microbial colonization is required for normal neurobehavioral development in zebrafish. 
  • Microbial influences on gut development and gut-brain communication. 
  • Microbial nitrogen limitation in the mammalian large intestine. 
  • Microbial rewilding in the gut microbiomes of captive ring-tailed lemurs (Lemur catta) in Madagascar. 
  • Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020. 
  • Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas. 
  • Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation. 
  • Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha. 
  • Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake. 
  • Moving beyond microbiome-wide associations to causal microbe identification. 
  • Multi-omics analyses of radiation survivors identify radioprotective microbes and metabolites. 
  • Neuroimmunology in 2017: The central nervous system: privileged by immune connections. 
  • New insights into oxidative stress and inflammation during diabetes mellitus-accelerated atherosclerosis. 
  • No Significant Association Between the Fecal Microbiome and the Presence of Irritable Bowel Syndrome-type Symptoms in Patients with Quiescent Inflammatory Bowel Disease. 
  • Nonalcoholic Fatty Liver Disease and the Gut Microbiome. 
  • Novel antigen-presenting cell imparts Treg-dependent tolerance to gut microbiota. 
  • Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut. 
  • Pathophysiology of irritable bowel syndrome. 
  • Patterns of gut bacterial colonization in three primate species. 
  • Physiological and psychological effects of testosterone during severe energy deficit and recovery: A study protocol for a randomized, placebo-controlled trial for Optimizing Performance for Soldiers (OPS). 
  • Physiological mechanisms of sustained fumagillin-induced weight loss. 
  • Potential NICU Environmental Influences on the Neonate's Microbiome: A Systematic Review. 
  • Prebiotic galactooligosaccharides interact with mouse gut microbiota to attenuate acute graft-versus-host disease. 
  • Prebiotics for Lactose Intolerance: Variability in Galacto-Oligosaccharide Utilization by Intestinal Lactobacillus rhamnosus. 
  • Prediagnostic Antibody Responses to Fusobacterium nucleatum Proteins Are Not Associated with Risk of Colorectal Cancer in a Large U.S. Consortium. 
  • Predicting Vibrio cholerae Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study. 
  • Prevention of antibiotic-associated metabolic syndrome in mice by intestinal alkaline phosphatase. 
  • Primate phageomes are structured by superhost phylogeny and environment. 
  • Prior Dietary Practices and Connections to a Human Gut Microbial Metacommunity Alter Responses to Diet Interventions. 
  • Proteobacteria abundance during nursing predicts physical growth and brain volume at one year of age in young rhesus monkeys. 
  • Recent Metabolic Advances for Preventing and Treating Acute and Chronic Graft Versus Host Disease. 
  • Relative abundance of Akkermansia spp. and other bacterial phylotypes correlates with anxiety- and depressive-like behavior following social defeat in mice. 
  • Restoring the Microbiome in Critically Ill Patients: Are Probiotics Our True Friends When We Are Seriously Ill? 
  • Short chain fatty acids induce UCP2-mediated autophagy in hepatic cells. 
  • Short-Chain Fatty Acid Production by Gut Microbiota from Children with Obesity Differs According to Prebiotic Choice and Bacterial Community Composition. 
  • Social networks predict gut microbiome composition in wild baboons. 
  • Synchrony and idiosyncrasy in the gut microbiome of wild baboons. 
  • Systematic review with meta-analysis: efficacy of faecal microbiota transplantation for the treatment of irritable bowel syndrome. 
  • Systematic review with meta-analysis: the efficacy of prebiotics, probiotics, synbiotics and antibiotics in irritable bowel syndrome. 
  • The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos. 
  • The Gut/Lung Microbiome Axis in Obesity, Asthma, and Bariatric Surgery: A Literature Review. 
  • The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights. 
  • The Skin and Intestinal Microbiota and Their Specific Innate Immune Systems. 
  • The composition of the zebrafish intestinal microbial community varies across development. 
  • The critical role of dietary foliage in maintaining the gut microbiome and metabolome of folivorous sifakas. 
  • The function and affinity maturation of HIV-1 gp120-specific monoclonal antibodies derived from colostral B cells. 
  • The gut microbiome of extremely preterm infants randomized to the early progression of enteral feeding. 
  • The gut microbiome of nonhuman primates: Lessons in ecology and evolution. 
  • The gut microbiota is associated with immune cell dynamics in humans. 
  • The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs. 
  • The inflammatory event of birth: How oxytocin signaling may guide the development of the brain and gastrointestinal system. 
  • The influence of the brain-gut axis in inflammatory bowel disease and possible implications for treatment. 
  • The intestine is a major contributor to circulating succinate in mice. 
  • The microbe-derived short-chain fatty acids butyrate and propionate are associated with protection from chronic GVHD. 
  • The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut. 
  • The possible risks of proton pump inhibitors. 
  • The role of gut microbial community and metabolomic shifts in adaptive resistance of Atlantic killifish (Fundulus heteroclitus) to polycyclic aromatic hydrocarbons. 
  • The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota. 
  • The stepwise assembly of the neonatal virome is modulated by breastfeeding. 
  • Timing of complementary feeding is associated with gut microbiota diversity and composition and short chain fatty acid concentrations over the first year of life. 
  • Transcriptional Integration of Distinct Microbial and Nutritional Signals by the Small Intestinal Epithelium. 
  • Transcriptional programmes underlying cellular identity and microbial responsiveness in the intestinal epithelium. 
  • Transmethylamine-N-Oxide Is Associated With Diffuse Cardiac Fibrosis in People Living With HIV. 
  • Variation in gut microbiome structure across the annual hibernation cycle in a wild primate. 
  • Viable bacterial colonization is highly limited in the human intestine in utero. 
  • Viscera affectum anno: the gut beyond eating behaviours. 
  • Where the gut meets the brain. 
  • mTOR is critical for intestinal T-cell homeostasis and resistance to Citrobacter rodentium. 
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  Keywords of People

  • Grego, Sonia, Associate Research Professor in the Department of Electrical and Computer Engineering, Electrical and Computer Engineering
  • McCann, Jessica, Research Associate, Senior, Molecular Genetics and Microbiology
  • Rassadkina, Yelizaveta, Student, Molecular Genetics and Microbiology