A5063976422- Gut microbiota and health
- Biofuel production and bioconversion
- Ruminant Nutrition and Digestive Physiology
- Microbial Metabolites in Food Biotechnology
- Diet and metabolism studies
- Enzyme Production and Characterization
- Reproductive tract infections research
- Genomics and Phylogenetic Studies
- Bioenergy crop production and management
- Advanced Cellulose Research Studies
- Bacteriophages and microbial interactions
- Clostridium difficile and Clostridium perfringens research
- Polysaccharides and Plant Cell Walls
- Microbial Metabolic Engineering and Bioproduction
- Wheat and Barley Genetics and Pathology
- Studies on Chitinases and Chitosanases
- Legume Nitrogen Fixing Symbiosis
- Microbial infections and disease research
- Mycobacterium research and diagnosis
- Nutritional Studies and Diet
- Evolution and Genetic Dynamics
- Evolutionary Game Theory and Cooperation
- Animal Disease Management and Epidemiology
- Dietary Effects on Health
- Plant-Microbe Interactions and Immunity
University of Illinois Urbana-Champaign
2008-2017
Genomic Health (United States)
2015
The complex microbiome of the rumen functions as an effective system for conversion plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource degrading enzymes that could be used in production biofuels. gastrointestinal tract harbor dense microbiome. To gain greater understanding ecology metabolic potential this microbiome, we comparative metagenomics (phylotype analysis SEED subsystems-based annotations) examine randomly...
Ruminants have the remarkable ability to convert human-indigestible plant biomass into human-digestible food products, due a complex microbiome residing in rumen compartment of their upper digestive tract. Here we report discovery that components are tightly linked cows' extract energy from feed, termed feed efficiency. Feed efficiency was measured 146 milking cows and analyses taxonomic composition, gene content, microbial activity metabolomic composition performed on microbiomes 78 most...
The ingestion of a high-fat diet (HFD) and the resulting obese state can exert multitude stressors on individual including anxiety cognitive dysfunction. Though many studies have shown that exercise alleviate negative consequences HFD using metabolic readouts such as insulin glucose, paucity well-controlled rodent been published interactions with regard to behavioral outcomes. This is critical issue since some individuals assume HFD-induced problems dysfunction simply be exercised away. To...
We have previously shown that voluntary wheel running (VWR) attenuates, whereas forced treadmill (FTR) exacerbates, intestinal inflammation and clinical outcomes in a mouse model of colitis. As the gut microbiome is implicated colitis, we hypothesized VWR FTR would differentially affect microbiome. Mice (9-10/treatment) were randomly assigned to VWR, FTR, or sedentary home cage control (SED) for 6 wk. given access, ran on 40 min/day at 8-12 m/min, 5% grade. Forty-eight hours after last...
Background HLA-DRB1*0401 is associated with susceptibility, while HLA-DRB1*0402 resistance to developing rheumatoid arthritis (RA) and collagen-induced in humans transgenic mice respectively. The influence of gut-joint axis has been suggested RA, though not yet proven. Methodology/Principal Findings We have used HLA carrying susceptible -resistant HLA-DR genes explore if genetic factors their interaction gut flora can be predict susceptibility develop arthritis. Pyrosequencing the 16S rRNA...
Objective To assess the vaginal microbiome throughout full-term uncomplicated pregnancy. Methods Vaginal swabs were obtained from twelve pregnant women at 8-week intervals their pregnancies. Patients with symptoms of infection or recent antibiotic use excluded. Swabs posterior fornix and cervix 8–12, 17–21, 27–31, 36–38 weeks gestation. The microbial community was profiled using hypervariable tag sequencing V3–V5 region 16S rRNA gene, producing approximately 8 million reads on Illumina...
ABSTRACT Ruminants sustain a long-lasting obligatory relationship with their rumen microbiome dating back 50 million years. In this unique host-microbiome relationship, the host’s ability to digest its feed is completely dependent on coevolved microbiome. This extraordinary alliance raises questions regarding between ruminants’ genetics and physiology structure, composition, metabolism. To elucidate we examined association of host phylogenetic functional composition We accomplished by...
Background Bacterial vaginosis (BV) is the most common vaginal disorder of reproductive-age women. Yet cause BV has not been established. To uncover key determinants BV, we employed a multi-omic, systems-biology approach, including both deep 16S rRNA gene-based sequencing and metabolomics lavage samples from 36 These women varied demographically, behaviorally, in terms health status symptoms. Principal Findings community composition profiles reflected Nugent scores, but Amsel criteria. In...
The human gut microbiota interacts closely with diet and physiology. To better understand the mechanisms behind this relationship, microbiome research relies on complementing studies manipulations of animal models, including non-human primates. However, due to unique aspects physiology, it is likely that host-gut microbe interactions operate differently in humans Here, we show reacts a high-protein, high-fat Western than model primate, African green monkey, or vervet (Chlorocebus aethiops...
Summary Viruses are the most abundant biological entities on planet and play an important role in balancing microbes within ecosystem facilitating horizontal gene transfer. Although bacteriophages rumen environments, little is known about types of viruses present or their interaction with microbiome. We undertook random pyrosequencing virus‐enriched metagenomes (viromes) isolated from bovine fluid analysed resulting data using comparative metagenomics. A high level diversity was observed up...
Background Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which forms multi-enzyme cellulosome complex that could play an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides. Identifying major enzyme types involved degradation essential for gaining better understanding capabilities organism as well highlighting potential enzymes application improvement livestock nutrition and conversion cellulosic biomass liquid fuels....
Plant cell wall (PCW) polysaccharides and especially xylans constitute an important part of human diet. Xylans are not degraded by digestive enzymes in the upper tract therefore reach colon where they subjected to extensive degradation some members symbiotic microbiota. Xylanolytic bacteria first degraders these complex release breakdown products that can have beneficial effects on health. In order understand better how metabolize colon, this study was undertaken investigate xylan prominent...
Background The cellulosome is a multi-enzyme machine, which plays key role in the breakdown of plant cell walls many anaerobic cellulose-degrading microorganisms. Ruminococcus flavefaciens FD-1, major fiber-degrading bacterium present gut herbivores, has most intricate cellulosomal organization thus far described. Cellulosome complexes are assembled through high-affinity cohesin-dockerin interactions. More than two-hundred dockerin-containing proteins have been identified R. genome, yet...
Diet and particularly dietary fibres have an impact on the gut microbiome play important role in human health disease. Pectin is a highly consumed fibre found fruits vegetables also widely used additive food industry. Yet there no information effect of pectin microbiome. Likewise, little known pectinolytic bacteria their enzyme systems. This study was undertaken to investigate mechanisms degradation by prominent symbiont Bacteroides xylanisolvens.Transcriptomic analyses B. xylanisolvens XB1A...
Second-generation sequencing technologies have granted us greater access to the diversity and genetics of microbial communities that naturally reside endo- ecto-symbiotically with animal hosts. Substantial research has emerged describing broader trends exist within between host species their associated ecosystems, yet application these data our evolutionary understanding microbiomes appears fragmented. For most part biological perspectives are based on limited observations oversimplified...
Ruminococcus flavefaciens is a vital cellulosome-producing fibrolytic rumen bacterium. The arrangement of the cellulosomal scaffoldin gene cluster (scaC-scaA-scaB-cttA-scaE) conserved in two R. strains (17 and FD-1). Sequence analysis revealed high mosaic conservation intergenic regions that contrasted sharply with divergence structural sca sequences. Based on regions, we designed PCR primers order to examine additional (C94, B34b, C1a JM1). Using these and/or degenerate primers, scaC, scaA...
Background Ruminococcus flavefaciens is an important fibre-degrading bacterium found in the mammalian gut. Cellulolytic strains from bovine rumen have been shown to produce complex cellulosome structures that are associated with cell surface. R. 007 a highly cellulolytic strain whose ability degrade dewaxed cotton, but not Avicel cellulose, was lost following initial isolation variant 007S. The recovered after serial subculture give cotton-degrading 007C. This has allowed us investigate...
A 17-kb scaffoldin gene cluster in Ruminococcus flavefaciens strain FD-1 was compared with the homologous segment published for 17. Although general design of is identical two strains, significant differences modular architecture proteins were discovered, implying strain-specific divergence cellulosome organization.
Background The bovine rumen maintains a diverse microbial community that serves to break down indigestible plant substrates. However, those bacteria specifically adapted degrade cellulose, the major structural component of biomass, represent fraction microbiome. Previously, we proposed scaC as candidate for phylotyping Ruminococcus flavefaciens, one three cellulolytic bacterial species isolated from rumen. In present report examine dynamics and diversity scaC-types both within between cattle...
Ruminococcus albus, a cellulolytic bacterium, is critical member of the rumen community. albus lacks classical cellulosome complex, but it possesses unique family 37 carbohydrate-binding module (CBM37), which integrated into variety carbohydrate-active enzymes. We developed potential molecular tool for functional phylotyping R. population in rumen, based on variable region cel48A gene. encodes single copy CBM37-associated 48 glycoside hydrolase all known strains this bacterium. A segment...
Background: Ruminococcus flavefaciens is an important fibre-degrading bacterium found in the mammalian gut.Cellulolytic strains from bovine rumen have been shown to produce complex cellulosome structures that are associated with cell surface.R. 007 a highly cellulolytic strain whose ability degrade dewaxed cotton, but not Avicel cellulose, was lost following initial isolation variant 007S.The recovered after serial subculture give cotton-degrading 007C.This has allowed us investigate factors...