A5064966691- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Probiotics and Fermented Foods
- Bacterial Genetics and Biotechnology
- Microscopic Colitis
- Bacteriophages and microbial interactions
- Gastrointestinal motility and disorders
- Microbial Community Ecology and Physiology
- Wastewater Treatment and Nitrogen Removal
- Genomics and Phylogenetic Studies
- Anaerobic Digestion and Biogas Production
- Viral gastroenteritis research and epidemiology
- RNA and protein synthesis mechanisms
- Protist diversity and phylogeny
- Helicobacter pylori-related gastroenterology studies
- Bacterial biofilms and quorum sensing
- Microbial Fuel Cells and Bioremediation
- Infant Nutrition and Health
- Microbial Metabolites in Food Biotechnology
- Hydrogen's biological and therapeutic effects
- Animal Ecology and Behavior Studies
- Escherichia coli research studies
- Pediatric health and respiratory diseases
- Fatty Acid Research and Health
- Cancer Research and Treatments
University of Nebraska–Lincoln
2019-2025
Baylor College of Medicine
2015-2024
Massachusetts Institute of Technology
2004-2014
Michigan State University
2003-2014
Ecologie Microbienne Lyon
2008
Health First
2008
H-Net: Humanities & Social Sciences Online
2008
We sought to identify the fungi that colonize healthy GI tracts and have a sustained influence on diverse functions of gut microbiome. Instead, we found all in stool volunteers could be explained by their presence oral dietary sources our results, together with those from other analyses, support model there is little or no gastrointestinal colonization fungi. This may due Westernization, primate evolution, fungal ecology, and/or strong defenses immune system. Importantly, tract often...
ABSTRACT Treatment with antibiotics is a major risk factor for Clostridioides difficile infection, likely due to depletion of the gastrointestinal microbiota. Two microbiota-mediated mechanisms thought limit C. colonization include conversion conjugated primary bile salts into secondary toxic growth and competition between microbiota limiting nutrients. Using continuous flow model that simulates nutrient conditions distal colon, we investigated how treatment 6 clinically used influenced...
Horizontal gene transfer contributes to the evolution of bacterial species. Mobile genetic elements play an important role in horizontal transfer, and characterization regulation these should provide insight into conditions that influence evolution. We characterized a mobile element, ICEBs1, Gram-positive bacterium Bacillus subtilis found it is functional integrative conjugative element (ICE) capable transferring Listeria identified two promote ICEBs1 transfer: induce global DNA damage...
Continuous-flow culture models are one tool for studying complex interactions between members of human fecal microbiotas because they allow studies to be completed during an extended period time under conditions where pH, nutrient availability, and washout waste products dead cells can controlled. Because many the existing well-validated continuous-flow large complex, we were interested in developing a simpler system that would microbial community dynamics examined higher throughput while...
Summary The mobile genetic element ICE Bs1 is an integrative and conjugative (a transposon) found in the Bacillus subtilis chromosome. SOS response RapI‐PhrI sensory system activate gene expression, excision transfer by inactivating repressor protein ImmR. Although ImmR similar to many characterized phage repressors, we that, unlike these inactivation of requires ‐encoded anti‐repressor ImmA (YdcM). was needed for degradation B. . Coexpression Escherichia coli or co‐incubation purified...
Summary ICE Bs1 is a mobile genetic element found in the chromosome of Bacillus subtilis . Excision and transfer regulated by global DNA damage response intercellular peptide signalling. We identified characterized repressor, ImmR (formerly YdcN), encoded represses transcription genes required for excision transfer, both activates its own transcription. regulates within binding to several sites region that contains promoters immR xis (encoding excisionase). In addition, we confers immunity...
To what extent genotypic differences translate to phenotypic variation remains a poorly understood issue of paramount importance for several cornerstone concepts microbiology including the species definition. Here, we take advantage completed genomic sequences, expressed proteomic profiles, and physiological studies 10 closely related Shewanella strains provide quantitative insights into this issue. Our analyses revealed that, despite extensive horizontal gene transfer within these genomes,...
ABSTRACT Clostridium difficile infection is the most common cause of severe cases antibiotic-associated diarrhea (AAD) and a significant health burden. Recent increases in rate C. have paralleled emergence specific phylogenetic clade strains (ribotype 027; North American pulsed-field electrophoresis 1 [NAP1]; restriction endonuclease analysis [REA] group BI). Initial reports indicated that ribotype 027 were associated with increased morbidity mortality might be hypervirulent. Although...
Clostridium difficile disease is the leading antibiotic-associated cause of diarrhea and nosocomial acquired infection in western world. The per annum burden USA alone amounts to 250,000 cases with 14,000 ascribed deaths medical costs excess a billion dollars. Novel models for study C. are therefore pertinent. Germ free C57BL/6 mice gavaged healthy human fecal microbiota maintained stable "humanized" over multiple generations when housed under specific pathogen-free (SPF) conditions. As...
Integration of antibiotic and probiotic therapy has the potential to lessen public health burden antimicrobial-associated diseases. Clostridium difficile infection (CDI) represents an important example where rational design next-generation probiotics is being actively pursued prevent disease recurrence. Because intrinsic resistance clinically relevant antibiotics used treat CDI (vancomycin, metronidazole, fidaxomicin) a desired trait in such species, we screened several bacteria identified...
It is widely accepted that the pathogen Clostridioides difficile exploits an intestinal environment with altered microbiota, but details of these microbe–microbe interactions are unclear. Adherence and colonization mucus has been demonstrated for several enteric pathogens it possible mucin-associated microbes may be working in concert C. difficile. We showed ribotype-027 adheres to MUC2 glycans using fecal bioreactors, we identified associates mucin-degrading microbes. was found chemotax...
Kombucha is a popular fermented tea that has attracted considerable attention due, in part, to its suggested health benefits. Previous results from animal models led us hypothesize kombucha may reduce blood sugar levels humans with diabetes. The objective of this pilot clinical study was evaluate for anti-hyperglycemic activities adults diabetes mellitus type II.The organized as prospective randomized double-blinded crossover at single-center urban hospital system. Participants (n = 12) were...
ABSTRACT In Bacillus subtilis , extracellular peptide signaling regulates several biological processes. Secreted Phr peptides are imported into the cell and act intracellularly to antagonize activity of regulators known as Rap proteins. B. encodes proteins peptides, processes regulated by many these unknown. We used DNA microarrays characterize roles that rap - phr modules play in regulating gene expression. found rapK-phrK expression a number genes activated response regulator ComA. ComA...
Summary ICE Bs1 is an integrative and conjugative element (conjugative transposon) integrated into trnS‐leu2 in Bacillus subtilis . In response to DNA damage or high concentrations of potential mating partners, can excise transfer various recipients, including other species. We found that excision occurs by site‐specific recombination within 60 bp direct repeats mark the junctions between chromosomal DNA. Excision required two genes, int (integrase, ydcL ), predicted encode a tyrosine...
Abstract Fungal infections are a major health problem that often begin in the gastrointestinal tract. Gut microbe interactions early childhood critical for proper immune responses, yet there is little known about development of fungal population from infancy into childhood. Here, as part TEDDY (The Environmental Determinants Diabetes Young) study, we examine stool samples 888 children 3 to 48 months and find considerable differences between fungi bacteria. The metagenomic relative abundance...
Summary The Bacillus subtilis proteins DnaD and DnaB are essential for replication initiation conserved in low G+C content Gram‐positive bacteria. Previous work indicated that involved helicase loading during the process of restarting stalled forks. We have investigated roles at oriC vivo . Using chromatin immunoprecipitation (ChIP), we found functions needed to load replicative To investigate further initiation, isolated characterized suppressors temperature sensitivity dnaD dnaB mutant...
Abstract Mechanistic investigations of host-microbe interactions in the human gut are limited by current co-culture model systems. The intestinal epithelium requires oxygen for viability, while bacteria facultative or obligate anaerobes. ability to host-commensal under dynamic conditions is critical understanding host-pathogen gut. Here, we demonstrate a simple, cost-effective method co-culturing anaerobic with enteroid monolayers variable conditions. Enteroid-Anaerobe Co-Culture (EACC)...
Clostridioides difficile is a common cause of acute gastrointestinal (GI) inflammation in mammals, which can have detrimental effects on host health. The molecular mechanisms GI colonization by C. , including interactions with cells and secreted mucin glycoproteins. associates the mucus layer vivo will associate epithelial mucosal surfaces vitro . Previously, we found substantial defect binding to for mutants major flagellar subunit, fliC while mutation subunit type IV pili, pilA1, showed...
While antibiotics play important roles in treating infections, disruption of the gastrointestinal microbiota during antibiotic treatment can lead to negative health consequences. However, for many antibiotics, spectrum activity has been determined select isolates rather than range microbes that populate tract. Here, we examined response communities using two different model systems, human fecal minibioreactors and associated mice. Communities established 12 donors were exposed classes...
Dietary fibers play a significant role in shaping the composition and function of microbial communities human colon. Our understanding specific chemical traits dietary that influence diversity, interactions, remains limited. Toward filling this knowledge gap, we developed novel measure, termed Chemical Subunits Linkages (CheSL) Shannon to characterize effects carbohydrate complexity on fecal bacteria cultured vitro under controlled, continuous flow conditions using media systematically...