A5056818748- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Inflammatory Bowel Disease
- Clostridium difficile and Clostridium perfringens research
- Immunodeficiency and Autoimmune Disorders
- Microscopic Colitis
- Diet and metabolism studies
- Acute Myeloid Leukemia Research
- Helicobacter pylori-related gastroenterology studies
- Methane Hydrates and Related Phenomena
- Peatlands and Wetlands Ecology
- Genetic factors in colorectal cancer
- Probiotics and Fermented Foods
- Coastal wetland ecosystem dynamics
- Soil Carbon and Nitrogen Dynamics
- Drug Transport and Resistance Mechanisms
- Genomics and Phylogenetic Studies
- Gastrointestinal motility and disorders
- Single-cell and spatial transcriptomics
- Infrared Target Detection Methodologies
- Hematopoietic Stem Cell Transplantation
- Frailty in Older Adults
- Heavy metals in environment
- Mine drainage and remediation techniques
- Alzheimer's disease research and treatments
University of Chicago
2020-2025
Argonne National Laboratory
2014-2024
UNSW Sydney
2013-2023
Univerzitná Nemocnica Louisa Pasteura
2016
University of Pavol Jozef Šafárik
2016
United States Department of Energy
2014
Illinois Wesleyan University
2010
Large quantities of immunoglobulin A (IgA) are constitutively secreted by intestinal plasma cells to coat and contain the commensal microbiota, yet specificity these antibodies remains elusive. Here we profiled reactivities single murine IgA cloning characterizing large numbers monoclonal antibodies. IgAs were not specific individual bacterial taxa but rather polyreactive, with broad reactivity a diverse, defined, subset microbiota. These arose at low frequencies among naïve B selected into...
Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there large gaps in our knowledge their diversity ecology. The 'Biomes Australian Soil Environments' (BASE) project has generated a database microbial with associated metadata across extensive environmental gradients at continental scale. As the characterisation microbes rapidly expands, BASE provides an evolving platform for interrogating integrating function. currently amplicon sequences contextual data...
Mucosal biopsy is the most common sampling technique used to assess microbial communities associated with intestinal mucosa. Biopsies disrupt epithelium and can be complications such as bleeding. sample a limited area of mucosa, which lead potential bias. In contrast mucosal biopsy, brush less invasive provides greater coverage, if it provide equivalent community data, would preferable biopsies. We compared samples collected from mucosa using either cytology or forceps. paired patients...
Abstract In preceding efforts, we demonstrated that antibiotic (ABX) cocktail-mediated perturbations of the gut microbiome in two independent transgenic lines, termed APP SWE / PS1 ΔE9 and APPPS1-21, leads to a reduction Aβ deposition male mice. To determine whether these observed reductions cerebral amyloidosis are specific any individual or require synergistic effects several antibiotics, treated APPPS1-21 mice with either ABX an cocktail assessed amyloid deposition. Specifically, were...
Abstract Even in the setting of optimal resuscitation high-income countries severe sepsis and septic shock have a mortality 20–40%, with antibiotic resistance dramatically increasing this risk. To develop reference dataset enabling identification common bacterial targets for therapeutic intervention, we applied standardized genomic, transcriptomic, proteomic metabolomic technological framework to multiple clinical isolates four sepsis-causing pathogens: Escherichia coli , Klebsiella...
Hyperoxaluria is a major risk factor for kidney stones and has no specific therapy, although Oxalobacter formigenes colonization associated with reduced stone risk. O. interacts colonic epithelium induces oxalate secretion, thereby reducing urinary excretion, via an unknown secretagogue. The difficulties in sustaining underscore the need to identify derived factors inducing secretion. We therefore evaluated effects of culture conditioned medium (CM) on apical 14 C-oxalate uptake by human...
Bile acids (BAs) are cholesterol-derived molecules that aid in digestion and nutrient absorption, regulate host metabolic processes, influence physiology of the gut microbiota. Both its microbiome contribute to enzymatic modifications shape chemical diversity BAs gut. Several bacterial species have been reported conjugate standard amino BAs, but it was not known if bacteria other amine classes. Here, we show
Abstract Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria , Archaea and Eukarya assemblages. Sequence is linked to extensive physical, biological chemical oceanographic contextual information. Samples collected monthly seasonally from multiple depths at...
Total proctocolectomy with ileal pouch anal anastomosis is the standard of care for patients severe ulcerative colitis. We generated a cell-type-resolved transcriptional and epigenetic atlas pouches using scRNA-seq scATAC-seq data from paired biopsy samples segment above (pre-pouch) (male=4, female=2), biopsies terminal ileum ascending colon healthy individuals (male=3, female=3) serving as reference. Our study finds an additional population absorptive secretory epithelial cells within but...
Defining the health of gut microbiome or microbial organ has been elusive and controversial. This in turn makes defining dysbiosis (imbalances microbiota) an enigma particularly determining what, how, when to intervene restore eubiosis. Taxonomical profiles microbiota have typically used but are unreliable because highly variable interindividual taxa arbitrary functional assignments generalized groups. We therefore developed a metabolomic marker panel, selected through supervised,...
Crohn's disease, a major class of Inflammatory bowel is chronic condition affecting millions, with >50% the patients experiencing relapses marked by inflammation. Our cellular atlas (380,000 cells) terminal ileum and ascending colon mucosa from 46 Crohns' disease non-disease donors across various clinical condition, decipher heterogeneity for recurrent refractory We identified an inflammatory cascade mediated follicle-associated enterocytes in inflamed ileum, involving pro-inflammatory...
Microbial communities that inhabit environments such as soil can contain thousands of distinct taxa, yet little is known about how this diversity maintained in response to environmental perturbations changes the availability carbon. By utilizing aerobic substrate arrays examine effect carbon amendment on microbial taken from six (soil a temperate prairie and forest, tropical forest soil, subalpine surface water palustrine emergent wetland), we examined inoculum source shape composition...
The aim of this study is to prove the involvement immune response in etiopathogenesis some cochleovestibular disorders by a demonstration antibodies against inner ear antigens and identify benefits immunosuppressive therapy.McCabe 1979 postulated hypothesis autoimmune disease.Sodium dodecyl sulfate polyacrylamid gel electrophoresis immunoblotting were used examine serum 74 subjects for presence antigens. divided into three groups: A--subjects with idiopathic progressive sensorineural hearing...
Myelodysplastic neoplasms (MDSs) and chronic myelomonocytic leukemia (CMML) are clonal disorders driven by progressively acquired somatic mutations in hematopoietic stem cells (HSCs). Hypomethylating agents (HMAs) can modify the clinical course of MDS CMML. Clinical improvement does not require eradication mutated may be related to improved differentiation capacity HSCs. However, patients with established disease it is unclear whether (1) HSCs multiple progress through comparable frequency...
This study has found numerous novel genetic variants of GA-insensitive dwarfing genes with potential agricultural value for crop improvement. The cultivar, Spica is a tall genotype and possesses the wild-type Rht-A1a, Rht-B1a Rht-D1a. cultivar Quarrion null mutant in DELLA motif each 3 genomes. first report Rht-A1. In addition, mutants which differ from reported alleles Rht-B1b, Rht-B1e Rht-D1b have been Quarrion, Carnamah Whistler. accession, Aus1408 an allele Rht-B1 mutation conserved...
Inflammatory bowel diseases (IBD) are chronic inflammatory disorders where predictive biomarkers for the disease development and clinical course sorely needed of prevention early intervention strategies that can be implemented to improve outcomes. Since gut microbiome alterations reflect and/or contribute impending host health changes, we examined whether microbiota metagenomic profiles would provide more robust measures predicting outcomes in colitis-prone hosts. Using interleukin (IL) 10...
Increasing use and mining of antimony (Sb) has resulted in greater concern involving its fate transport the environment. Antimony(V) (III) are two most environmentally relevant oxidation states, but little is known about redox transitions between natural systems. To better understand behavior anoxic environments, transformations Sb(V) were studied biotic abiotic reactors. The reactors contained (2 mM as KSb(OH)6), ferrihydrite (50 Fe(III)), sulfate (10 mM), lactate that inoculated with...
Total proctocolectomy with ileal pouch anal anastomosis (IPAA) is the standard of care for patients severe treatment resistant ulcerative colitis (UC). Despite improvements in patient outcomes, about 50% will develop inflammation within 1-2 years following surgery. Establishment UC pouches associated profound histological changes mucosa. A detailed characterization these on a cellular and molecular level crucial an improved understanding physiology diseases management.We generated...
Bile acids (BAs) are cholesterol-derived molecules that aid in digestion and nutrient absorption, regulate host metabolic processes, influence physiology of the gut microbiota. Both its microbiome contribute to enzymatic modifications shape chemical diversity BAs gut. Several bacterial species have been reported conjugate standard amino BAs, but it was not known if bacteria other amine classes. Here, we show