A5076317634- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Probiotics and Fermented Foods
- Genomics and Phylogenetic Studies
- Methane Hydrates and Related Phenomena
- Soil Carbon and Nitrogen Dynamics
- Plant and Fungal Interactions Research
- Diet and metabolism studies
- Bacteriophages and microbial interactions
- RNA and protein synthesis mechanisms
- Helicobacter pylori-related gastroenterology studies
- Peatlands and Wetlands Ecology
- Ginseng Biological Effects and Applications
- Anaerobic Digestion and Biogas Production
- RNA modifications and cancer
- Fire effects on ecosystems
- Pharmaceutical and Antibiotic Environmental Impacts
- Microbial Metabolites in Food Biotechnology
- Gastrointestinal motility and disorders
- Polysaccharides and Plant Cell Walls
- Microbial metabolism and enzyme function
- Microbial Metabolic Engineering and Bioproduction
- Microbial Inactivation Methods
- Fecal contamination and water quality
- Antimicrobial Peptides and Activities
Eastern Regional Research Center
2022-2025
United States Department of Agriculture
2022-2025
Agricultural Research Service
2022-2025
Colorado State University
2019-2024
University of Colorado Denver
2015-2020
Abstract Microbial and viral communities transform the chemistry of Earth's ecosystems, yet specific reactions catalyzed by these biological engines are hard to decode due absence a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled Refined Annotation Metabolism), framework translate deluge microbiome-based genomic information into catalog microbial traits. To demonstrate applicability across diverse genomes, evaluated performance on defined, in silico...
Abstract The current paradigm, widely incorporated in soil biogeochemical models, is that microbial methanogenesis can only occur anoxic habitats. In contrast, here we show clear geochemical and biological evidence for methane production well-oxygenated soils of a freshwater wetland. A comparison oxic to reveal up ten times greater nine more activity oxygenated soils. Metagenomic metatranscriptomic sequencing recover the first near-complete genomes novel methanogen species, acetoclastic from...
High-throughput RNA sequencing offers broad opportunities to explore the Earth virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million virus contigs. Analysis of >330,000 RNA-dependent polymerases (RdRPs) shows that this expansion corresponds a 5-fold increase known diversity. Gene content analysis revealed multiple protein domains previously not found in viruses and implicated virus-host interactions. Extended RdRP phylogeny supports monophyly five established phyla reveals...
Abstract Forest soil microbiomes have crucial roles in carbon storage, biogeochemical cycling and rhizosphere processes. Wildfire season length, the frequency size of severe fires increased owing to climate change. Fires affect ecosystem recovery modify microbially mediated To study wildfire-dependent changes microbiomes, we characterized functional shifts microbiota (bacteria, fungi viruses) across burn severity gradients (low, moderate high severity) 1 yr post fire coniferous forests...
Triclosan is a widely used antimicrobial compound and emerging environmental contaminant. Although the role of gut microbiome in health disease increasingly well established, interaction between contaminants host largely unexplored, with unknown consequences for health. This study examined effects low, environmentally relevant levels triclosan exposure on fish microbiome. Developing fathead minnows (Pimephales promelas) were exposed to two low over 7-day exposure. Fish gastrointestinal...
Following consumption of milk, lactose, a disaccharide glucose and galactose, is hydrolyzed absorbed in the upper gastrointestinal tract. However, hydrolysis absorption are not always absolute, some lactose will enter colon where gut microbiota able to hydrolyze produce metabolic byproducts.Here, impact on healthy adults was examined, using short-term, vitro strategy fecal samples harvested from 18 donors were cultured anaerobically with without lactose. The data compiled identify...
Fructooligosaccharides (FOS) are well-known carbohydrates that promote healthy gut microbiota and have been previously demonstrated to enhance levels of Bifidobacterium Lactobacillus. Its bifidogenic properties associated with positive health outcomes such as reduced obesity anti-inflammatory properties, and, therefore, is in use a prebiotic supplement support microbiota. However, the changes age, which may lead differential responses treatments prebiotics other dietary supplements.To...
Bacterial production of gaseous hydrocarbons such as ethylene and methane affects soil environments atmospheric climate. We demonstrate that biogenic from terrestrial freshwater bacteria are directly produced by a previously unknown methionine biosynthesis pathway. This pathway, present in numerous species, uses nitrogenase-like reductase is distinct known nitrogenases reductases specifically functions C-S bond breakage to reduce ubiquitous appreciable volatile organic sulfur compounds...
Summary Despite being key contributors to biogeochemical processes, archaea are frequently outnumbered by bacteria, and consequently underrepresented in combined molecular surveys. Here, we demonstrate an approach concurrently survey the alongside bacteria with high‐resolution 16S rRNA gene sequencing, linking these community data geochemical parameters. We applied this integrated analysis hydric soils sampled across a model methane‐emitting freshwater wetland. Geochemical profiles, archaeal...
Wetland soils are one of the largest natural contributors to emission methane, a potent greenhouse gas. Currently, microbial contributions methane emissions from these systems emphasize roles acetoclastic and hydrogenotrophic methanogens, while less frequently considering methyl-group substrates (e.g., methanol methylamines). Here, we integrated laboratory field experiments explore potential for methylotrophic methanogenesis in Old Woman Creek (OWC), temperate freshwater wetland located...
Diphthamide is a modified histidine residue which uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA mRNA through ribosome. In part due to role diphthamide maintaining translational fidelity, it was previously assumed that biosynthesis genes (dph) are conserved across all eukaryotes archaea. Here, comparative analysis new existing genomes reveals some archaea (i.e., members Asgard...
Accounting for only 8% of Earth's land coverage, freshwater wetlands remain the foremost contributor to global methane emissions. Yet microorganisms and processes underlying emissions from wetland soils poorly understood. Over a five-year period, we surveyed microbial membership in situ measurements over 700 samples one most prolific methane-emitting United States. We constructed catalog 2,502 metagenome-assembled genomes (MAGs), with nearly half 72 bacterial archaeal phyla sampled...
Ammonia monooxygenase and analogous oxygenase enzymes contribute to pharmaceutical biotransformation in activated sludge. In this study, we hypothesized that methane can enhance within the benthic, diffuse periphytic sediments (i.e., "biomat") of a shallow, open-water constructed wetland. To test hypothesis, combined field-scale metatranscriptomics, porewater geochemistry, gas fluxes inform microcosms targeting activity its potential role biotransformation. field, sulfamethoxazole...
In the present research, we investigated changes in gut metabolome that occurred response to administration of
Introduction Studies have shown that a diet high in fiber and prebiotics has positive impact on human health due largely to the fermentation of these compounds by gut microbiota. One underutilized source may be rice bran, waste product processing is used most frequently as an additive livestock feed but good fibers other phenolic supplement. Previous studies focused specific extracted from bran showed soluble can improve glucose response reduce weight gain mouse models. However, less known...
In shallow, open-water engineered wetlands, design parameters select for a photosynthetic microbial biomat capable of robust pharmaceutical biotransformation, yet the contributions specific processes remain unclear. Here, we combined genome-resolved metatranscriptomics and oxygen profiling field-scale to inform laboratory inhibition microcosms amended with suite pharmaceuticals. Our analyses revealed dynamic surficial layer harboring oxic–anoxic cycling simultaneous photosynthetic,...
The current effort to valorize waste byproducts increase sustainability and reduce agricultural loss has stimulated interest in potential utilization of components as health-promoting supplements. Tomato seeds are often discarded tomato pomace, a byproduct processing, yet these known contain an array compounds with biological activity prebiotic potential. Here, extract from (TSE), acquired was evaluated for their ability effect changes on the gut microbiota using ex vivo strategy. results...
Water chlorination as a method to deter the growth of disease-causing microbes has been standard practice in United States for over century. Toxicological studies that originally designated chlorinated water safe human host failed consider its impact on developing gut microbiota. Here, this oversight was addressed through comparative assessment microbiota from post-weaned mice (B6) provided either chlorine-free or containing 1–5 mg/L chlorine. Mice had statistically significant decrease...
ABSTRACT Microbial and viral communities transform the chemistry of Earth’s ecosystems, yet specific reactions catalyzed by these biological engines are hard to decode due absence a scalable, metabolically resolved, annotation software. Here, we present DRAM ( D istilled R efined A nnotation M etabolism), framework translate deluge microbiome-based genomic information into catalog microbial traits. To demonstrate applicability across diverse genomes, evaluated performance on defined, in...
Pectins are plant polysaccharides consumed as part of a diet containing fruits and vegetables. Inside the gastrointestinal tract, pectin cannot be metabolized by mammalian cells but is fermented gut microbiota in colon with subsequent release end products including short-chain fatty acids (SCFA). The prebiotic effects have been previously evaluated reports inconsistent, most likely due to differences chemical structure which can vary molecular weight (MW) degree esterification (DE). Here,...
The genus Senna contains globally distributed plant species of which the leaves, roots, and seeds have multiple traditional medicinal nutritional uses. Notable chemical compounds derived from spp. include sennosides emodin been tested for antimicrobial effects in addition to their known laxative functions. However, studies combined components on intact human gut microbiome communities are lacking. This study evaluated Juemingzi ( sp.) extract using SIFR ® (Systemic Intestinal Fermentation...
Bile acids play a critical role in the emulsification of dietary lipids, step primary function small intestine, which is digestion and absorption food. Primary bile delivered into intestine are conjugated to enhance functionality, part, by increasing aqueous solubility preventing passive diffusion out gut lumen. acid can be disrupted microbiota via deconjugation salt hydrolases (BSHs), leading their conversion secondary through expression bacterial acid-inducible genes, process often...
The consumption of probiotics is widely encouraged due to reports their positive effects on human health. In particular, Lacticaseibacillus rhamnosus strain GG (LGG) an approved probiotic that has been reported improve health outcomes, especially for gastrointestinal disorders. However, how LGG cooperates with the gut microbiome not fully explored. To understand interaction between and its ability survive grow within microbiome, this study introduced into established microbial communities...
Introduction In traditional Chinese medicine, the rhizome of Atractylodes macrocephala (Baizhu), leaves Isatis indigotica (Daqingye), and flowers Albizia julibrissin (Hehuanhua) have been used to treat gastrointestinal illnesses, epidemics, mental health issues. Modern researchers are now exploring underlying mechanisms responsible for their efficacy. Previous studies often focused on impact purified chemicals or mixed extracts from these plants cells in tissue culture rodent models. Methods...