A5009977791- Gut microbiota and health
- Diet and metabolism studies
- Clostridium difficile and Clostridium perfringens research
- Gastrointestinal motility and disorders
- Nutritional Studies and Diet
- Probiotics and Fermented Foods
- Microscopic Colitis
- Genomics and Phylogenetic Studies
- Inflammatory Bowel Disease
- Pediatric health and respiratory diseases
- Colorectal Cancer Screening and Detection
- Mycobacterium research and diagnosis
- Gene expression and cancer classification
- Infant Nutrition and Health
- Nutrition and Health in Aging
- Frailty in Older Adults
- Helicobacter pylori-related gastroenterology studies
- Tryptophan and brain disorders
- Metabolomics and Mass Spectrometry Studies
- Obesity, Physical Activity, Diet
- Dietary Effects on Health
- Food Security and Health in Diverse Populations
- Molecular Biology Techniques and Applications
- Bioinformatics and Genomic Networks
- Cancer Research and Treatments
Bon Secours Hospital Cork
2018-2023
University College Cork
2013-2022
APC Microbiome Institute
2015-2022
4D Pharma (United Kingdom)
2022
National University of Ireland
2017-2021
University College Dublin
2006-2010
<h3>Objectives</h3> Habitual diet plays a major role in shaping the composition of gut microbiota, and also determines repertoire microbial metabolites that can influence host. The typical Western corresponds to an omnivore; however, Mediterranean (MD), common culture, is date nutritionally recommended dietary pattern includes high-level consumption cereals, fruit, vegetables legumes. To investigate potential benefits MD this cross-sectional survey, we assessed microbiota metabolome cohort...
The commensal microbiota, host immunity and metabolism participate in a signalling network, with diet influencing each component of this triad. In addition to diet, many elements modern lifestyle influence the gut microbiota but degree which exercise affects population is unclear. Therefore, we explored for their impact on microbiota.Since extremes often accompany addressed issue by studying professional athletes from an international rugby union squad. Two groups were included control...
<h3>Background and aims</h3> Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder that may be triggered by enteric pathogens has also been linked to alterations in the microbiota host immune response. The authors performed detailed analysis of faecal IBS control subjects correlated findings with key clinical physiological parameters. <h3>Design</h3> used pyrosequencing determine composition 37 patients (mean age years; 26 female subjects; 15 diarrhoea-predominant...
<h3>Objective</h3> A signature that unifies the colorectal cancer (CRC) microbiota across multiple studies has not been identified. In addition to methodological variance, heterogeneity may be caused by both microbial and host response differences, which was addressed in this study. <h3>Design</h3> We prospectively studied colonic expression of specific genes using faecal mucosal samples ('ON' 'OFF' tumour, proximal distal) from 59 patients undergoing surgery for CRC, 21 individuals with...
Objective Ageing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We others have shown that frailty co-varies with alterations in the gut microbiota a manner accelerated consumption restricted diversity diet. The Mediterranean diet (MedDiet) associated health. In NU-AGE project, we investigated if 1-year MedDiet intervention could alter reduce Design profiled 612 non-frail or pre-frail subjects across five European...
Background and aims Microbiota alterations are linked with colorectal cancer (CRC) notably higher abundance of putative oral bacteria on colonic tumours. However, it is not known if mucosa-associated taxa indeed orally derived, such cases a distinct subset patients or the microbiome generally suitable for screening CRC. Methods We profiled microbiota in swabs, mucosae stool from individuals CRC (99 subjects), polyps (32) controls (103). Results Several were differentially abundant compared...
The gut is the most extensively studied niche of human microbiome. aim this study was to characterise initial microbiota development a cohort breastfed infants (n = 192) from 1 24 weeks age. V4-V5 region 16S rRNA amplicon Illumina sequencing and, in parallel, bacteriological culture. metabolomic profile infant urine at 4 age also examined by LC-MS. Full-term (FT), spontaneous vaginally delivered (SVD) infants' remained stable both phylum and genus levels during 24-week period examined. FT...
Abstract Lactobacilli are a diverse group of species that occupy nutrient-rich niches associated with humans, animals, plants and food. They used widely in biotechnology food preservation, being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear identity uncertain relationships between them other commercially important lactic acid bacteria. The capacity for biotransformations catalysed is an untapped resource. Here we report the genome...
Frailty is arguably the biggest problem associated with population ageing, and associates gut microbiome composition in elderly care-dependent individuals. Here we characterize frailty associations microbiota a younger community dwelling population, to identify targets for intervention encourage healthy ageing. We analysed 16S rRNA gene sequence data derived from faecal samples obtained 728 female twins. was quantified using index (FI). Mixed effects models were used diversity, operational...
Numerous feature selection methods have been applied to the identification of differentially expressed genes in microarray data. These include simple fold change, classical t-statistic and moderated t-statistics. Even though these return gene lists that are often dissimilar, few direct comparisons exist. We present an empirical study which we compare some most commonly used methods. apply 9 publicly available datasets, compare, both produced how perform class prediction test datasets. In...
The composition and function of the human gut microbiota has been linked to health disease. We previously identified correlations between habitual diet, gradients in an unstratified cohort 178 elderly subjects. To refine our understanding diet-microbiota associations differential taxon abundance, we adapted iterative bi-clustering algorithm (iterative binary bclustering gene sets (iBBiG)) applied it data from 732 faecal samples 371 ELDERMET subjects, including longitudinal samples. thus...
Interaction between disease-microbiome associations and ageing has not been explored in detail. Here, using age/region-matched sub-sets, we analysed the gut microbiome differences across five major diseases a multi-cohort dataset constituting more than 2500 individuals from 20 to 89 years old. We show that display specific age-centric trends. Ageing-associated alterations towards disease-like configuration occur colorectal cancer patients, thereby masking disease signatures. identified...
Irritable bowel syndrome (IBS) is a heterogeneous disorder, but diagnoses and determination of subtypes are made based on symptoms. We profiled the fecal microbiomes patients with without IBS to identify biomarkers this disorder.We collected urine samples from 80 (Rome IV criteria; 16-70 years old) 65 matched individuals (control individuals), along anthropometric, medical, dietary information. Shotgun 16S ribosomal RNA amplicon sequencing were performed feces, whereas metabolites analyzed...
To investigate compositional differences in the gut microbiota associated with bone homeostasis and fractures a cohort of older adults.Faecal profiles were determined from 181 individuals osteopenia (n = 61) or osteoporosis 60), an age- gender-matched group normal BMD 60). Analysis 16S (V3-V4 region) amplicon dataset classified to genus level was used identify significantly differentially abundant taxa. Adjustments made for potential confounding variables identified literature using several...
Lactobacilli are gram-positive bacteria that a subdominant element in the human gastrointestinal microbiota, and which commonly used food industry. Some lactobacilli considered probiotic, have been associated with health benefits. However, there is very little culture-independent information on how consumed probiotic microorganisms might affect entire intestinal microbiota. We therefore studied impact of administration Lactobacillus salivarius UCC118, microorganism well characterized for its...
Taxonomic classification is a corner stone for the characterisation and comparison of microbial communities. Currently, most existing methods are either slow, restricted to specific communities, highly sensitive taxonomic inconsistencies, or limited genus level classification. As crucial microbiota information hinging on high-level resolution it imperative increase species wherever possible.In response this need we developed SPINGO, flexible stand-alone software dedicated high-resolution...
In this study, we characterized the gut microbiota in six healthy Irish thoroughbred racehorses and showed it to be dominated by phyla Firmicutes, Bacteroidetes, Proteobacteria, Verrucomicrobia, Actinobacteria, Euryarchaeota, Fibrobacteres Spirochaetes. Moreover, all horses harboured Clostridium, Fibrobacter, Faecalibacterium, Ruminococcus, Eubacterium, Oscillospira, Blautia Anaerotruncus, Coprococcus, Treponema Lactobacillus spp. Notwithstanding sample size, was noteworthy that core species...
There are complex interactions between aging, frailty, diet, and the gut microbiota; modulation of microbiota by diet could lead to healthier aging. The purpose this study was test effect diets differing in sugar, fat, fiber content upon mice humanized with from healthy or frail older people. We also performed a 6-month dietary supplementation three human cohorts representing distinct life-stages.Mice were colonized then underwent an 8-week intervention either high-fiber/low-fat typical...