A5001947512- Gut microbiota and health
- Biofuel production and bioconversion
- Enzyme Production and Characterization
- Microbial Metabolic Engineering and Bioproduction
- Probiotics and Fermented Foods
- Clostridium difficile and Clostridium perfringens research
- Metabolomics and Mass Spectrometry Studies
- Diet and metabolism studies
- Microbial Metabolites in Food Biotechnology
- Gout, Hyperuricemia, Uric Acid
- Glycosylation and Glycoproteins Research
- Catalysis for Biomass Conversion
- Porphyrin Metabolism and Disorders
- Bioinformatics and Genomic Networks
- Pituitary Gland Disorders and Treatments
- Amino Acid Enzymes and Metabolism
- Acupuncture Treatment Research Studies
- Advanced Cellulose Research Studies
- Adrenal Hormones and Disorders
- Alcohol Consumption and Health Effects
- Enzyme Structure and Function
- Food composition and properties
- Immune Cell Function and Interaction
- Molecular Biology Techniques and Applications
- GABA and Rice Research
Stanford University
2016-2025
University of Illinois Urbana-Champaign
2007-2022
Energy Biosciences Institute
2009-2022
Stanford Medicine
2022
ORCID
2020
Chan Zuckerberg Initiative (United States)
2018
Center for Genomic Science
2010-2014
University of Illinois System
2013
Urbana University
2010
Beijing Chaoyang Emergency Medical Center
2010
Abstract The combustion of fossil‐derived fuels has a significant impact on atmospheric carbon dioxide (CO 2 ) levels and correspondingly is an important contributor to anthropogenic global climate change. Plants have evolved photosynthetic mechanisms in which solar energy used fix CO into carbohydrates. Thus, biofuels, derived from plant biomass, can be considered potentially neutral process. One the major limitations for efficient conversion biomass biofuels recalcitrant nature cell wall,...
Significance Many millions of people take probiotics over the counter, but very little is known about what they do and whether really work. Here we show that in mice, introducing Bifidobacterium , one most commonly used probiotics, not only colonizes gut, also alters entire microbiotic landscape. We previously found this treatment rescues mice from an otherwise fatal inflammatory syndrome brought on by anti–CTLA-4 antibody, a checkpoint inhibitor often causes autoimmunity humans undergoing...
Significance Fermentation of dietary fiber in the lower gut humans is a critical process for function and integrity both bacterial community host cells. Here we demonstrate that two human commensal Bacteroides are equipped with unique enzymes allow degradation xylan, common hemicellulose diets. Furthermore, identify novel carbohydrate-binding module (CBM) family disrupts catalytic domain glycoside hydrolase 10 (GH10) endoxylanase facilitates hydrolytic activity enzyme. The conservation...
Clostridial metabolite production The clostridia are Firmicute bacterial commensals commonly found in the mammalian gut. Clostridia produce a range of metabolites that diffuse into host's circulation and have been difficult to manipulate genetically, but Guo et al. successfully developed CRISPR-Cas9 deletion system Clostridium sporogenes (see Perspective by Henke Clardy). authors used mutants mass spectrometry elucidate clostridial synthesis several different branched short-chain fatty acids...
Enzymatic depolymerization of lignocellulose by microbes in the bovine rumen and human colon is critical to gut health function within host. Prevotella bryantii B(1)4 a bacterium that efficiently degrades soluble xylan. To identify genes harnessed this degrade xylan, transcriptomes P. cultured on either wheat arabinoxylan or mixture its monosaccharide components were compared DNA microarray RNA sequencing approaches. The most highly induced formed cluster contained putative outer membrane...
Abstract The bacterial species living in the gut mediate many aspects of biological processes such as nutrition and activation adaptive immunity. In addition, commensal fungi residing intestine also influence host health. Although interaction bacterium fungus has been shown, its precise mechanism during colonization human remains largely unknown. Here, we show between fungal for utilization dietary components driving their efficient growth intestine. Next generation sequencing fecal samples...
Abstract The enteric pathogen Clostridioides difficile ( Cd ) is responsible for a toxin-mediated infection that causes more than 200,000 recorded hospitalizations and 13,000 deaths in the United States every year 1 . However, can colonize gut absence of disease symptoms. Prevalence asymptomatic colonization by toxigenic healthy populations high; carriers are at increased risk compared to noncolonized individuals may be reservoir transmission 2,3 Elucidating molecular mechanisms which...
The human gut microbiota produces dozens of small molecules that circulate in blood, accumulate to comparable levels as pharmaceutical drugs, and influence host physiology. Despite the importance these metabolites health disease, origin most microbially-produced their fate remains largely unknown. Here, we uncover a host-microbe co-metabolic pathway for generation hippuric acid, one abundant organic acids mammalian urine. Combining stable isotope tracing with bacterial genetics, demonstrate...
γδ T cells are essential for immune defense and modulating physiological processes. While they have the potential to recognize large numbers of antigens through somatic gene rearrangement, which trigger most cell response remain unidentified, role antigen recognition in function is contentious. Here, we show that some receptors (TCRs) exhibit polyspecificity, recognizing multiple ligands diverse molecular nature. These include haptens, metabolites, neurotransmitters, posttranslational...
Abstract Anaerobic bacteria from the human microbiome produce a wide array of molecules at high concentrations that can directly or indirectly affect host. The production these molecules, mostly derived their primary metabolism, is frequently encoded in metabolic gene clusters (MGCs). However, despite importance microbiome-derived metabolites, no tool existed to predict responsible for production. For this reason, we recently introduced gutSMASH. gutSMASH 41 different known pathways,...
Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars its core growth strategy remains unclear. To obtain a comprehensive view of the network E . , we generated complementary resources: defined culture media, metabolomics profiles strain isolates, curated genome-scale reconstruction. Stable isotope-resolved...
We measured expression and used biochemical characterization of multiple carbohydrate esterases by the xylanolytic rumen bacterium Prevotella ruminicola 23 grown on an ester-enriched substrate to gain insight into esterase activities this hemicellulolytic bacterium. The P. genome contains 16 genes predicted encode activity, based microarray data, four these were upregulated >2-fold at transcriptional level during growth oligosaccharide (XOS(FA,Ac)) from corn relative a nonesterified fraction...
ABSTRACT Xylan is an abundant plant cell wall polysaccharide and a dominant component of dietary fiber. Bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate degradation this complex heteropolymer. These xylanases typically derive from glycoside hydrolase (GH) families 10 11; however, analysis genome sequence xylan-degrading gut bacterium Bacteroides intestinalis DSM 17393 revealed presence two putative GH8 xylanases. In current study, we demonstrate that...