Paul W. O’Toole
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View article: Evaluating the rumen microbial community of genetically divergent spring-calving dairy cows grazing grass-only or grass-clover swards at different stages of the grazing season
Evaluating the rumen microbial community of genetically divergent spring-calving dairy cows grazing grass-only or grass-clover swards at different stages of the grazing season Open
The current study used a culture-independent methodology to investigate the rumen microbiome composition in two genetically divergent groups of spring-calving dairy cows, high (€218) and low (€157) Economic Breeding Index (EBI), grazing tw…
View article: Iron-saturated bovine lactoferrin preserves microbiota diversity and healthy ageing-associated taxa in an in vitro colon model of elderly gut microbiota (Iron-saturated bovine lactoferrin impact on elderly gut microbiota)
Iron-saturated bovine lactoferrin preserves microbiota diversity and healthy ageing-associated taxa in an in vitro colon model of elderly gut microbiota (Iron-saturated bovine lactoferrin impact on elderly gut microbiota) Open
Lactoferrin is a multifunctional milk protein receiving increased interest in recent years because of its potential as a functional food ingredient to reduce the prevalence of iron deficiency, while providing additional health benefits inc…
View article: Identifying the non-Bifidobacterial hallmarks of a Bifidobacterium-receptive gut microbiome
Identifying the non-Bifidobacterial hallmarks of a Bifidobacterium-receptive gut microbiome Open
Bifidobacteria are key health-associated members of the human gut and widely used as probiotics, but their colonization success varies across individuals, partly due to baseline microbiome composition. In this analysis encompassing 51,058 …
View article: Do all trainers think the same? Exploring use of the Think Aloud method to understand colonoscopy trainer thought processes
Do all trainers think the same? Exploring use of the Think Aloud method to understand colonoscopy trainer thought processes Open
Colonoscopy is a complex skill to teach. Understanding trainer cognition is an important factor in determining the level of trainer competence. This study aimed to explore colonoscopy trainer thoughts as they observed trainee performance u…
View article: Investigating interaction between genotype and microbiome profile in Irish honeybees
Investigating interaction between genotype and microbiome profile in Irish honeybees Open
View article: A Review of Diet and Foraged Pollen Interactions with the Honeybee Gut Microbiome
A Review of Diet and Foraged Pollen Interactions with the Honeybee Gut Microbiome Open
The honeybee Apis mellifera is a globally vital pollinator for flowering plants and crops, but it is currently facing mounting threats to survival due to habitat anthropization, emerging pathogens, and climate change. Over the past decade,…
View article: Effects of Prebiotics and a Synthetic Microbiome Consortium on the Composition and Metabolites of the Elderly Gut Microbiota In Vitro
Effects of Prebiotics and a Synthetic Microbiome Consortium on the Composition and Metabolites of the Elderly Gut Microbiota In Vitro Open
A 24 h artificial colon fermentation was performed to assess the effects of a prebiotic MIX and synthetic consortium (S7) on gut microbiota composition and microbial metabolite production in clinically stratified older adults (healthy and …
View article: aurora: a machine learning gwas tool for analyzing microbial habitat adaptation
aurora: a machine learning gwas tool for analyzing microbial habitat adaptation Open
View article: Toward a health-associated core keystone index for the human gut microbiome
Toward a health-associated core keystone index for the human gut microbiome Open
A robust index of gut microbiome taxa encompassing their association with host health and microbiome resilience would be valuable for development and optimization of microbiome-based therapeutics. Here we present a single ranked order for …
View article: Associations Between the Gut Microbiome, Inflammation, and Cardiovascular Profiles in People With Human Immunodeficiency Virus
Associations Between the Gut Microbiome, Inflammation, and Cardiovascular Profiles in People With Human Immunodeficiency Virus Open
Background Inflammation and innate immune activation are associated with chronic human immunodeficiency virus (HIV) infection, despite effective treatment. Although gut microbiota alterations are linked to systemic inflammation, their rela…
View article: In vitro digestibility of bioprocessed brewer’s spent yeast: Demonstrating protein quality and gut microbiome modulation potential
In vitro digestibility of bioprocessed brewer’s spent yeast: Demonstrating protein quality and gut microbiome modulation potential Open
With an ever-increasing global population and dwindling natural resources, a shift towards more sustainable food systems is required. Important aspects to aid in this transition are the reduction of food waste, and a movement towards non-a…
View article: HIV, the gut microbiome and clinical outcomes, a systematic review
HIV, the gut microbiome and clinical outcomes, a systematic review Open
Background Effective antiretroviral therapy (ART) has improved the life expectancy of people with HIV (PWH). However, this population is now experiencing accelerated age‐related comorbidities, contributed to by chronic immune activation an…
View article: International consensus statement on microbiome testing in clinical practice
International consensus statement on microbiome testing in clinical practice Open
View article: Dysrupted microbial tryptophan metabolism associates with SARS-CoV-2 acute inflammatory responses and long COVID
Dysrupted microbial tryptophan metabolism associates with SARS-CoV-2 acute inflammatory responses and long COVID Open
Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and risk of long COVID has been associated with the depletion or over-abundance of specific taxa within the gut microbiome. However, the microbial me…
View article: Healthy and Unhealthy Aging and the Human Microbiome
Healthy and Unhealthy Aging and the Human Microbiome Open
An altered gut microbiome is a feature of many multifactorial diseases, and microbiome effects on host metabolism, immune function, and possibly neurological function are implicated. Increased biological age is accompanied by a change in t…
View article: Yeast <i>β</i>-glucan supplementation lowers insulin resistance without altering microbiota composition compared with placebo in subjects with type II diabetes: a phase I exploratory study
Yeast <i>β</i>-glucan supplementation lowers insulin resistance without altering microbiota composition compared with placebo in subjects with type II diabetes: a phase I exploratory study Open
The increased global prevalence of type II diabetes mellitus (T2DM) is associated with consumption of low fibre ‘Western diets’. Characteristic metabolic parameters of these individuals include insulin resistance, high fasting and postpran…
View article: Genome sequence of the New Zealand cheese isolate and candidate probiotic strain <i>Lactiplantibacillus plantarum</i> FNZ042
Genome sequence of the New Zealand cheese isolate and candidate probiotic strain <i>Lactiplantibacillus plantarum</i> FNZ042 Open
The complete genome sequence of the candidate probiotic strain Lactiplantibacillus plantarum FNZ042 was determined using a hybrid genome assembly comprising data from Illumina and PacBio sequencing platforms. The genome assembly comprised …
View article: Genome sequence of the New Zealand raw milk isolate and candidate probiotic strain <i>Lactococcus lactis</i> FNZ339
Genome sequence of the New Zealand raw milk isolate and candidate probiotic strain <i>Lactococcus lactis</i> FNZ339 Open
The complete genome sequence of the candidate probiotic strain Lactococcus lactis FNZ339 was determined using a hybrid genome assembly comprising data from Illumina and Oxford Nanopore Technologies sequencing platforms. The genome assembly…
View article: Cross‐Cohort Gut Microbiome Signatures of Irritable Bowel Syndrome Presentation and Treatment
Cross‐Cohort Gut Microbiome Signatures of Irritable Bowel Syndrome Presentation and Treatment Open
Irritable bowel syndrome (IBS) is a prevalent disorder of gut‐brain interaction without a reliable cure. Evidence suggests that an alteration of the gut microbiome may contribute to IBS pathogenesis, motivating the development of microbiom…
View article: State of the art and the future of microbiome-based biomarkers: a multidisciplinary Delphi consensus
State of the art and the future of microbiome-based biomarkers: a multidisciplinary Delphi consensus Open
Although microbiome signatures have been identified in various contexts (ie, pathogenesis of non-communicable diseases and treatment response), qualified microbiome-based biomarkers are currently not in use in clinical practice. The Human …
View article: Disease-associated microbiome signature species in the gut
Disease-associated microbiome signature species in the gut Open
There is an accumulation of evidence that the human gut microbiota plays a role in maintaining health, and that an altered gut microbiota (sometimes called dysbiosis) associates with risk for many noncommunicable diseases. However, the dyn…
View article: Towards a Health-Associated Core Keystone (HACK) index for the human gut microbiome
Towards a Health-Associated Core Keystone (HACK) index for the human gut microbiome Open
Variations in the normal gut microbiome and the existence of context-dependent disease associations have confounded the identification of microbiome markers of health. A reliable indexing of taxa based on their association with host health…
View article: Probiotic Lactobacilli activate Formyl-Peptide Receptor 2
Probiotic Lactobacilli activate Formyl-Peptide Receptor 2 Open
Changes in the composition of the human microbiota can negatively impact human health. Probiotic bacteria like many lactobacilli help prevent or repair dysbiosis but it is largely unclear which molecules of these bacteria mediate the probi…
View article: Ageing, microbes and health
Ageing, microbes and health Open
The human gut microbiome is a modifier of the risk for many non‐communicable diseases throughout the lifespan. In ageing, the effect of the microbiome appears to be more pronounced because of the lower physiological reserve. Microbial meta…
View article: Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables
Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables Open
Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the r…
View article: Kefir4All, a citizen science initiative to raise awareness of the roles that microbes play in food fermentation
Kefir4All, a citizen science initiative to raise awareness of the roles that microbes play in food fermentation Open
Microorganisms are ubiquitous in nature and are central to human, animal, environmental, and planetary health. They play a particularly important role in the food chain and the production of high-quality, safe, and health-promoting foods, …
View article: High-quality MAGs assembled from raw milk metagenomes
High-quality MAGs assembled from raw milk metagenomes Open
High-quality MAGs assembled from raw milk metagenomes. Assembly of Metagenome Assembled Genomes (MAGs) was done using metaSPAdes (3.13), followed by binning with MetaBAT2 (2.12.1) and quality assessment with checkM (1.0.18). High-quality M…
View article: Microbe Profile: The Lactobacillaceae
Microbe Profile: The Lactobacillaceae Open
Graphical abstract Phylogeny, host association and genome size in the Lactobacillaceae . The phylogenetic tree of 287 unique species and 15 strains with unassigned species was built using concatenated alignment of amino acid sequences of c…
View article: Engraftment of aging-related human gut microbiota and the effect of a seven-species consortium in a pre-clinical model
Engraftment of aging-related human gut microbiota and the effect of a seven-species consortium in a pre-clinical model Open
Human aging is characterized by gut microbiome alteration and differential loss of gut commensal species associated with the onset of frailty. The administration of cultured commensal strains to replenish lost taxa could potentially promot…
View article: Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov.
Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov. Open
The methanogenic strain Mx-05T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It sha…