A5026524856- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Water Treatment and Disinfection
- Genomics and Phylogenetic Studies
- Child Nutrition and Water Access
- Vibrio bacteria research studies
- Mycobacterium research and diagnosis
- Molecular Biology Techniques and Applications
- Antibiotic Resistance in Bacteria
- Bacterial Identification and Susceptibility Testing
- Inflammatory Bowel Disease
- Genetics, Bioinformatics, and Biomedical Research
- Pharmaceutical and Antibiotic Environmental Impacts
- Actinomycetales infections and treatment
- Bacteriophages and microbial interactions
- Clostridium difficile and Clostridium perfringens research
- Salmonella and Campylobacter epidemiology
- Cancer therapeutics and mechanisms
- Advanced Electron Microscopy Techniques and Applications
- Clinical Nutrition and Gastroenterology
- Environmental DNA in Biodiversity Studies
- Tuberculosis Research and Epidemiology
- Glycosylation and Glycoproteins Research
- Food Security and Health in Diverse Populations
- Computational Drug Discovery Methods
University of Glasgow
2016-2020
University of Birmingham
2014-2017
Czech Academy of Sciences, Institute of Microbiology
2015
The study of microbial communities has been revolutionised in recent years by the widespread adoption culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder these sequence-based approaches is presence contamination DNA extraction kits other laboratory reagents. In this we demonstrate that contaminating ubiquitous commonly used reagents, varies greatly composition between different kit batches, critically impacts results obtained...
Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected large outbreak enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This was linked to community, national and European-wide cases. Hospital with are at high risk, require rapid response. initially investigated this by whole-genome sequencing using novel protocol on the Illumina MiSeq; we then integrated these data from surveillance sequencing, thereby...
OBJECTIVES: Exploring associations between the gut microbiota and colonic inflammation assessing sequential changes during exclusive enteral nutrition (EEN) may offer clues into microbial origins of Crohn’s disease (CD). METHODS: Fecal samples (n=117) were collected from 23 CD 21 healthy children. From children fecal before, EEN, when patients returned to their habitual diets. Microbiota composition functional capacity characterized using sequencing 16SrRNAgene shotgun metagenomics. RESULTS:...
Abstract Background Amplicon sequencing on Illumina platforms leverages their deep and multiplexing capacity but is limited in genetic resolution due to short read lengths. While Oxford Nanopore or Pacific Biosciences overcome this limitation, application has been higher error rates lower data output. Results In study, we introduce an amplicon workflow, i.e., NanoAmpli-Seq, that builds the intramolecular-ligated nanopore consensus (INC-Seq) approach demonstrate its for full-length 16S rRNA...
Limiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without using disinfectant. The impact of these contrasting approaches on the microbiome not systematically understood. We use genome-resolved metagenomics to compare structure, metabolic traits, and population genomes samples from bulk across multiple full-scale disinfected non-disinfected systems. Microbial communities cluster at structural-...
The effect that traditional and modern DNA extraction methods have on applications to study the role of gut microbiota in health disease is a topic current interest. Genomic was extracted from three faecal samples one probiotic capsule using popular methods; chaotropic (CHAO) method, phenol/chloroform (PHEC) extraction, proprietary kit (QIAG). performance each these yield quality, composition quantitative PCR, deep sequencing 16S rRNA gene, analysis pipeline evaluated. CHAO yielded highest...
The lack of success in target-based screening approaches to the discovery antibacterial agents has led reemergence phenotypic as a successful approach identifying bioactive, compounds. A challenge though with this route is then identify molecular target(s) and mechanism action hits. This target identification, or deorphanization step, often essential further optimization validation studies. Direct experimental identification hit complex, precisely because properties specificity are not yet...
Studying the gut microbiota in unaffected relatives of people with Crohn's disease (CD) may advance our understanding role bacteria aetiology.Faecal composition (16S rRNA gene sequencing), genetic functional capacity (shotgun metagenomics) and faecal short chain fatty acids (SCFA) were compared adult CD children (CDR, n = 17) healthy controls, unrelated to patients (HUC, 14). The characteristics 19 used as a benchmark 'dysbiosis'.The CDR was less diverse (p 0.044) than that HUC group. Local...
Abstract The study of microbial communities has been revolutionised in recent years by the widespread adoption culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder these sequence-based approaches is presence contamination DNA extraction kits other laboratory reagents. In this we demonstrate that contaminating ubiquitous commonly used kits, varies greatly composition between different kit batches, critically impacts results...
Staphylococci are a major constituent of the nasal microbiome and frequent cause hospital-acquired infection. Antibiotic surgical prophylaxis is administered prior to surgery reduce patient's risk postoperative The impact on staphylococcal largely unknown. Here, we report species present in revealed by novel culture independent technique. Daily samples from 18 hospitalised patients, six whom received no antibiotics 12 antibiotic (flucloxacillin gentamicin or teicoplanin +/- gentamicin), were...
Abstract Antimicrobial resistance (AMR) in drinking water has received less attention than counterparts the urban cycle. While culture-based techniques or gene-centric PCR have been used to probe impact of treatment approaches (e.g., disinfection) on AMR water, our knowledge there is no systematic comparison traits between disinfected and disinfectant residual-free systems. We use metagenomics assess associations residuals prevalence its host association full-scale distribution systems...
ABSTRACT Limiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without the use of disinfectant. The impact these contrasting approaches on microbiome not systematically understood. We utilized genome-resolved metagenomics to compare structure, metabolic traits, and population genomes microbiomes across multiple full-scale systems utilizing two-distinct control strategies. Microbial communities...
Abstract Background Amplicon sequencing on Illumina platforms leverages their deep and multiplexing capacity, but is limited in genetic resolution due to short read lengths. While Oxford Nanopore or Pacific Biosciences overcome this limitation, application has been higher error rates smaller data output. Results In study, we introduce an amplicon workflow, i.e., NanoAmpli-Seq, that builds Intramolecular-ligated Consensus Sequencing (INC-Seq) approach demonstrate its for full-length 16S rRNA...
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