A5101616148- Microbial Community Ecology and Physiology
- Microbial bioremediation and biosurfactants
- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Nail Diseases and Treatments
- Phytase and its Applications
- Water Treatment and Disinfection
- Dermatology and Skin Diseases
- Microbial Fuel Cells and Bioremediation
- Microbial Metabolic Engineering and Bioproduction
- Environmental remediation with nanomaterials
- Chemical Analysis and Environmental Impact
- Salivary Gland Disorders and Functions
- Protein purification and stability
- Oral microbiology and periodontitis research
- Methane Hydrates and Related Phenomena
- Oral Health Pathology and Treatment
- Protein Hydrolysis and Bioactive Peptides
- Aquaculture Nutrition and Growth
- Viral Infectious Diseases and Gene Expression in Insects
- Biofuel production and bioconversion
- Semiconductor materials and devices
- Plant nutrient uptake and metabolism
- Veterinary Oncology Research
- Radioactive element chemistry and processing
Shanghai University of Engineering Science
2024
University of Pennsylvania
2023
City University of Hong Kong
2023
Moog (United States)
2020-2022
University of Toronto
1994-2020
University of Birmingham
2019
Google (United States)
2013
University of Ottawa
2007-2008
Clarke University
1981
Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, consequently have great potential for the study of microbial communities. However, best approaches analysis long-read metagenomic data unknown. Additionally, rigorous evaluation bioinformatics tools is hindered by a lack from validated samples with known composition.We sequenced 2 commercially available mock communities containing 10 species (ZymoBIOMICS Microbial Community Standards) Oxford Nanopore...
ABSTRACT Summary Microbiome studies continue to provide tremendous insight into the importance of microorganism populations macroscopic world. High-throughput DNA sequencing technology (i.e., Next-generation Sequencing) has enabled cost-effective, rapid assessment microbial when combined with bioinformatic tools capable identifying taxa and calculating diversity composition biological environmental samples. Ribosomal RNA gene sequencing, where 16S 18S rRNA sequences are used identify...
Dehalococcoides mccartyi strains are obligate organohalide-respiring bacteria harboring multiple distinct reductive dehalogenase (RDase) genes within their genomes. A major challenge is to identify substrates for the enzymes encoded by these RDase genes. We demonstrate an approach that involves blue native polyacrylamide gel electrophoresis (BN-PAGE) followed enzyme activity assays with slices and subsequent identification of proteins in using liquid chromatography coupled tandem mass...
Two novel reductive dehalogenases (RDases) that are highly similar to each other but catalyse distinct dechlorination reactions were identified from Dehalobacter-containing mixed cultures. These two RDases partially purified crude protein extracts of anaerobic dechlorinating enrichment cultures using blue native polyacrylamide gel electrophoresis. Gel slices assayed for activity, and associated proteins liquid chromatography tandem mass spectrometry with the metagenome parent culture as...
This study analyzed the complex bacterial and fungal microbiota of healthy clinically affected canine ear skin samples. A total 589 samples were included: 257 swab (128 vs. 129 affected) 332 (172 160 using next-generation sequencing (NGS) to determine both relative absolute abundances bacteria fungi present in highlighted cases was characterized by an overall loss microbial diversity, high biomass, with overgrowth certain members microbiota. The observed phenotype these best described...
Organohalide respiring bacteria (OHRB) express reductive dehalogenases for energy conservation and growth. Some of these enzymes catalyze the dehalogenation chlorinated brominated pollutants in anaerobic subsurface environments, providing a valuable ecosystem service. Dehalococcoides mccartyi strains have been most extensively studied owing to their ability dechlorinate all ethenes - notably carcinogenic vinyl chloride ethene. The genomes OHRB, particularly obligate often harbour multiple...
The genes encoding both the cytosolic and mitochondrial serine hydroxymethyltransferases (SHM2 SHM1, respectively) a third unidentified gene of yeast Saccharomyces cerevisiae have been isolated their nucleotide sequences determined. Analysis predicted amino acid sequence amino-terminal regions, comparison with other SHMT enzymes, subcellular fractionation studies all suggested that SHM1 encodes SHMT, while SHM2 enzyme. but not has putative GCN4 sites upstream TATA box, suggesting regulation...
Chloroform (CF) is a widespread groundwater contaminant not susceptible to aerobic degradation. Under anoxic conditions, CF can undergo abiotic and cometabolic transformation but detoxification generally achieved. The recent discovery of distinct Dehalobacter strains that respire dichloromethane (DCM) ferment DCM nonchlorinated products promises bioremediation plumes feasible. To track both strains, 16S rRNA gene-based qPCR assays specific for either strain were designed validated. A...
To compare the bacteriome of oral cavity in healthy dogs and with various stages periodontal disease.Dogs without disease (n = 12) or mild (10), moderate (19), severe (10) disease.The maxillary arcade each dog was sampled a sterile swab, swabs were submitted for next-generation DNA sequencing targeting V1-V3 region 16S rRNA gene.714 bacterial species from 177 families identified. The 3 most frequently found Actinomyces sp (48/51 samples), Porphyromonas cangingivalis (47/51 Campylobacter...
Typically, the assembly and closure of a complete bacterial genome requires substantial additional effort spent in wet lab for gap resolution polishing. Assembly is further confounded by subspecies polymorphism when starting from metagenome sequence data. In this paper, we describe an silico gap-resolution strategy that can substantially improve assembly. This resolves gaps scaffolds using pre-assembled contigs, followed verification with read mapping. It capable resolving caused repetitive...
Compound specific isotope analysis (CSIA) has been applied to monitor bioremediation of groundwater contaminants and provide insight into mechanisms transformation chlorinated ethanes. To date there is little information on its applicability for methanes. Moreover, published enrichment factors (ε) observed during the biotic abiotic degradation alkanes, such as carbon tetrachloride (CT); 1,1,1-trichloroethane (1,1,1-TCA); 1,1-dichloroethane (1,1-DCA), range from -26.5‰ -1.8‰ illustrate a...
Otitis media (OM) and externa (OE) are painful, recurrent ear conditions. As most otitis publications focus on the bacterial content of childhood ears, there remains a dearth information regarding adult microbiome including both bacteria fungi. This study compares outer healthy adults to affected by OE OM using intergenic-transcribed-spacer (ITS) 16S-rDNA sequencing. The core consists prokaryote Cutibacterium acnes eukaryotic Malassezia arunalokei , M . globosa restricta mycobiome is...
Long-read metagenomic sequencing is a powerful approach for cataloging the microbial diversity present in complex microbiomes, including human gut microbiome. We performed deep-sequencing experiment using PacBio HiFi reads to obtain metagenome-assembled genomes (MAGs) from pooled long-read metagenome assembly two methods (hifiasm-meta, metMDBG), used improved bioinformatic and proximity ligation binning strategies cluster contigs identify MAGs, developed novel framework compare consolidate...
Many reductive dehalogenases (RDases) have been identified in organohalide-respiring microorganisms, and yet their substrates, specific activities, conditions for expression are not well understood. We tested whether RDase varied depending on the substrate-exposure history of dechlorinating communities. For this purpose, we used enrichment culture KB-1 maintained trichloroethene (TCE), as subcultures intermediates cis-dichloroethene (cDCE) vinyl chloride (VC). contains a TCE-to-cDCE...
Previous studies have suggested the involvement of viral and bacterial components in initiation progression feline chronic gingivostomatitis (FCGS), but role fungi remains entirely unknown. This pilot study aimed to investigate bacteriome mycobiome oral health disease. Physical exams, including assessment, privately owned, clinically healthy (CH) cats (n = 14) affected by FCGS were performed. Using a sterile swab, tissue surfaces CH sampled submitted for 16S rRNA ITS-2 next-generation DNA...
The genomes of two closely related Dehalobacter strains (strain CF and strain DCA) were assembled from the metagenome an anaerobic enrichment culture that reductively dechlorinates chloroform (CF), 1,1,1-trichloroethane (1,1,1-TCA) 1,1-dichloroethane (1,1-DCA). 3.1 Mbp (that 1,1,1-TCA) DCA 1,1-DCA) each contain 17 putative reductive dehalogenase homologous (rdh) genes. These systematically compared to three other available organohalide-respiring (Dehalobacter restrictus PER-K23, sp. E1...
Background: Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, consequently have great potential for the study of microbial communities. However, best approaches analysis long-read metagenomic data unknown. Additionally, rigorous evaluation bioinformatics tools is hindered by a lack from validated samples with known composition. Methods: We sequenced two commercially-available mock communities containing ten species (ZymoBIOMICS Microbial Community...
Abstract Background Urine from clinically healthy dogs is not sterile. Characterizing microbial diversity and abundance within this population of important to define normal reference ranges for urine. Objectives To establish composition relative representation bacterial fungal microbiomes in urine dogs. Animals Fifty Methods Analytic study. sampling via cystocentesis. Comprehensive evaluation including standard urinalysis, culture sensitivity, next‐generation sequencing (NGS), bioinformatics...
Over the past three years we have seen twelve patients who become depressed while taking cimetidine. Clinically depression is similar to that in a Primary Affective Disorder. Two representative cases are presented. It suggested cimetidine has precipitated depressive reaction vulnerable patients. Tricyclic antidepressants effective relieving depression. postulated cimetidine, by blocking H 2 receptors CNS, produces an imbalance between 1 and . This may be etiological factor precipitating...
To investigate the mycobiome of oral cavity in healthy dogs and with various stages periodontal disease.51 without disease (n = 12) or mild (10), moderate (19), severe (10) disease.The whole maxillary arcade each dog was sampled a sterile swab, swabs were submitted for next-generation DNA sequencing targeting internal transcribed spacer 2 region commercial platform.Fungi detected all samples, total 320 fungal species from 135 families data set. No single found samples. The 3 most frequently...
Bacteroidales strain CF is the most abundant nondechlorinating organism in a Dehalobacter-containing enrichment culture that consistently reductively dechlorinates >50 mg/liter chloroform or 1,1,1-trichloroethane (methyl chloroform). We assembled and closed complete genome sequence of this from metagenomic sequencing data for cultures. This predicted to ferment l-lactate ethanol.