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Gopal N.,Teagasc | Gopal N.,University College Cork | Hill C.,University College Cork | Hill C.,APC Microbiome Institute | And 5 more authors.
Frontiers in Microbiology | Year: 2015

Milk produced in udder cells is sterile but due to its high nutrient content, it can be a good growth substrate for contaminating bacteria. The quality of milk is monitored via somatic cell counts and total bacterial counts, with prescribed regulatory limits to ensure quality and safety. Bacterial contaminants can cause disease, or spoilage of milk and its secondary products. Aerobic spore-forming bacteria, such as those from the genera Sporosarcina, Paenisporosarcina, Brevibacillus, Paenibacillus, Geobacillus and Bacillus, are a particular concern in this regard as they are able to survive industrial pasteurization and form biofilms within pipes and stainless steel equipment. These single or multiple-species biofilms become a reservoir of spoilage microorganisms and a cycle of contamination can be initiated. Indeed, previous studies have highlighted that these microorganisms are highly prevalent in dead ends, corners, cracks, crevices, gaskets, valves and the joints of stainless steel equipment used in the dairy manufacturing plants. Hence, adequate monitoring and control measures are essential to prevent spoilage and ensure consumer safety. Common controlling approaches include specific cleaning-in-place processes, chemical and biological biocides and other novel methods. In this review, we highlight the problems caused by these microorganisms, and discuss issues relating to their prevalence, monitoring thereof and control with respect to the dairy industry. © 2015 Gopal, Hill, Ross, Beresford, Fenelon and Cotter.


Ryan P.M.,Teagasc | Ross R.P.,APC Microbiome Institute | Fitzgerald G.F.,APC Microbiome Institute | Caplice N.M.,University College Cork | And 2 more authors.
Current Opinion in Clinical Nutrition and Metabolic Care | Year: 2015

Purpose of review Health promoting functional food ingredients for cardiovascular health are generally aimed at modulating lipid metabolism in consumers. However, significant advances have furthered our understanding of the mechanisms involved in development, progression, and treatment of cardiovascular disease. In parallel, a central role of the gut microbiota, both in accelerating and attenuating cardiovascular disease, has emerged. Recent findings Modulation of the gut microbiota, by use of prebiotics and probiotics, has recently shown promise in cardiovascular disease prevention. Certain prebiotics can promote a short chain fatty acid profile that alters hormone secretion and attenuates cholesterol synthesis, whereas bile salt hydrolase and exopolysaccharideproducing probiotics have been shown to actively correct hypercholesterolemia. Furthermore, specific microbial genera have been identified as potential cardiovascular disease risk factors. This effect is attributed to the ability of certain members of the gut microbiota to convert dietary quaternary amines to trimethylamine, the primary substrate of the putatively atherosclerosis-promoting compound trimethylamine-N-oxide. In this respect, current research is indicating trimethylamine-depleting Achaea - termed Archeabiotics as a potential novel dietary strategy for promoting heart health. Summary The microbiota offers a modifiable target, which has the potential to progress or prevent cardiovascular disease development. Whereas host-Targeted interventions remain the standard, current research implicates microbiota-mediated therapies as an effective means of modulating cardiovascular health. Copyright © 2015 Wolters Kluwer Health, Inc. All rights reserved.


O' Mahony S.M.,University College Cork | O' Mahony S.M.,APC Microbiome Institute | Stilling R.M.,APC Microbiome Institute | Dinan T.G.,APC Microbiome Institute | And 3 more authors.
Birth Defects Research Part C - Embryo Today: Reviews | Year: 2015

Many childhood diseases such as autism spectrum disorders, allergic disease, and obesity are on the increase. Although environmental factors are thought to play a role in this increase. The mechanisms at play are unclear but increasing evidence points to an interaction with the gastrointestinal microbiota as being potentially important. Recently this community of bacteria and perturbation of its colonization in early life has been linked to a number of diseases. Many factors are capable of influencing this colonization and ultimately leading to an altered gut microbiota which is known to affect key systems within the body. The impact of the microbial composition of our gastrointestinal tract on systems outside the gut is also becoming apparent. Here we highlight the factors that are capable of impacting on microbiota colonization in early-life and the developing systems that are affected and finally how this may be involved in the manifestation of childhood diseases. © 2015 Wiley Periodicals, Inc.


Sherwin E.,APC Microbiome Institute | Rea K.,APC Microbiome Institute | Dinan T.G.,APC Microbiome Institute | Cryan J.F.,APC Microbiome Institute | Cryan J.F.,University College Cork
Current Opinion in Gastroenterology | Year: 2016

Purpose of review There is an increasing realization that the microorganisms which reside within our gut form part of a complex multidirectional communication network with the brain known as the microbiome-gut-brain axis. In this review, we focus on recent findings which support a role for this axis in modulating neurodevelopment and behavior. Recent findings A growing body of research is uncovering that under homeostatic conditions and in response to internal and external stressors, the bacterial commensals of our gut can signal to the brain through a variety of mechanisms to influence processes such neurotransmission, neurogenesis, microglia activation, and modulate behavior. Moreover, the mechanisms underlying the ability of stress to modulate the microbiota and also for microbiota to change the set point for stress sensitivity are being unraveled. Dysregulation of the gut microbiota composition has been identified in a number of psychiatric disorders, including depression. This has led to the concept of bacteria that have a beneficial effect upon behavior and mood (psychobiotics) being proposed for potential therapeutic interventions. Summary Understanding the mechanisms by which the bacterial commensals of our gut are involved in brain function may lead to the development of novel microbiome-based therapies for these mood and behavioral disorders. Copyright © 2016 Wolters Kluwer Health, Inc. All rights reserved.


PubMed | University College Cork, Teagasc, Cork University Maternity Hospital, APC Microbiome Institute and Mercy University Hospital
Type: Case Reports | Journal: Pediatrics | Year: 2015

Sulfhemoglobinemia is a rare disorder characterized by the presence of sulfhemoglobin in the blood. It is typically drug-induced and may cause hypoxia, end-organ damage, and death through oxygen deprivation. We present here a case of non-drug-induced sulfhemoglobinemia in a 7-day-old preterm infant complicated by hemolytic anemia. Microbiota compositional analysis of fecal samples to investigate the origin of hydrogen sulphide revealed the presence of Morganella morganii at a relative abundance of 38% of the total fecal microbiota at the time of diagnosis. Mmorganii was not detected in the fecal samples of 40 age-matched control preterm infants. Mmorganii is an opportunistic pathogen that can cause serious infection, particularly in immunocompromised hosts such as neonates. Strains of Mmorganii are capable of producing hydrogen sulphide, and virulence factors include the production of a diffusible -hemolysin. The infant in this case survived intact through empirical oral and intravenous antibiotic therapy, probiotic administration, and red blood cell transfusions. This coincided with a reduction in the relative abundance of Mmorganii to 3%. Neonatologists should have a high index of suspicion for intestinal pathogens in cases of non-drug-induced sulfhemoglobinemia and consider empirical treatment of the intestinal microbiota in this potentially lethal condition.


PubMed | University College Cork, APC Microbiome Institute and Karolinska Institutet
Type: Journal Article | Journal: Schizophrenia bulletin | Year: 2016

Despite the biological plausibility of an association between obstetric mode of delivery and psychosis in later life, studies to date have been inconclusive. We assessed the association between mode of delivery and later onset of psychosis in the offspring. A population-based cohort including data from the Swedish National Registers was used. All singleton live births between 1982 and 1995 were identified (n= 1,345,210) and followed-up to diagnosis at age 16 or later. Mode of delivery was categorized as: unassisted vaginal delivery (VD), assisted VD, elective Caesarean section (CS) (before onset of labor), and emergency CS (after onset of labor). Outcomes included any psychosis; nonaffective psychoses (including schizophrenia only) and affective psychoses (including bipolar disorder only and depression with psychosis only). Cox regression analysis was used reporting partially and fully adjusted hazard ratios (HR) with 95% confidence intervals (CI). Sibling-matched Cox regression was performed to adjust for familial confounding factors. In the fully adjusted analyses, elective CS was significantly associated with any psychosis (HR 1.13, 95% CI 1.03, 1.24). Similar findings were found for nonaffective psychoses (HR 1.13, 95% CI 0.99, 1.29) and affective psychoses (HR 1.17, 95% CI 1.05, 1.31) ((2)for heterogeneityP= .69). In the sibling-matched Cox regression, this association disappeared (HR 1.03, 95% CI 0.78, 1.37). No association was found between assisted VD or emergency CS and psychosis. This study found that elective CS is associated with an increase in offspring psychosis. However, the association did not persist in the sibling-matched analysis, implying the association is likely due to familial confounding by unmeasured factors such as genetics or environment.


PubMed | University College Cork and APC Microbiome Institute
Type: Journal Article | Journal: Birth defects research. Part C, Embryo today : reviews | Year: 2016

Many childhood diseases such as autism spectrum disorders, allergic disease, and obesity are on the increase. Although environmental factors are thought to play a role in this increase. The mechanisms at play are unclear but increasing evidence points to an interaction with the gastrointestinal microbiota as being potentially important. Recently this community of bacteria and perturbation of its colonization in early life has been linked to a number of diseases. Many factors are capable of influencing this colonization and ultimately leading to an altered gut microbiota which is known to affect key systems within the body. The impact of the microbial composition of our gastrointestinal tract on systems outside the gut is also becoming apparent. Here we highlight the factors that are capable of impacting on microbiota colonization in early-life and the developing systems that are affected and finally how this may be involved in the manifestation of childhood diseases.


News Article | November 11, 2015
Site: www.nature.com

Researchers studying communities of microbes need to up their game. That was the argument made by two articles published on 28 October in Science1 and Nature2, which called for national and international initiatives that would unite microbiome researchers and move the field forward. The initiatives would help researchers to develop better, standardized ways to study microbial communities so that scientists can make meaningful comparisons of data sets across different studies. Some researchers were sceptical. Nick Loman, a bacterial geneticist at the University of Birmingham, UK, tweeted: But the proponents say that the two articles are just starting points for broader discussion in the field. Microbiome studies focus on the bacteria and other microbes living in sites ranging from soil to the human mouth. In the Science piece, US researchers argued that for microbiology to move beyond descriptive studies towards hypothesis- and application-driven science, the field needs to bring in scientists from other disciplines and create tools that manipulate microbial communities and their genes. The authors proposed that a national Unified Microbiome Initiative (UMI) would develop and implement these tools, and called for new funding mechanisms for interdisciplinary research. The Nature article, by authors in the United States, Germany and China, responds to the US researchers’ proposal by calling for an International Microbiome Initiative (IMI). This would coordinate the efforts of a global, interdisciplinary group of scientists, including the UMI, allowing researchers to share data. “By pooling data from scientists from around the world, an IMI would generate much more knowledge than could one country alone,” the authors write. Several scientists greeted the proposals with enthusiasm, including Roman Stilling, a postdoctoral fellow at the APC Microbiome Institute at University College Cork, Ireland. He said in an e-mail to Nature: “Standardization may help ensure reproducibility and may help other researchers with guidelines to follow when they want to start working on the microbiome too.” But Patrick Schloss, a microbiologist at the University of Michigan in Ann Arbor, questioned the need for a global initiative, tweeting: Schloss later tempered his tweets in a blog post, writing that he and others are already developing tools to study microbial data and pursuing hypothesis-driven work. He wrote that funding for interdisciplinary microbiome research would be “awesome”, but added in an interview that a lot of details are missing from the proposals. “In fairness, we don’t really know much about what is being planned,” Schloss says, adding that the proposals seem primarily to be a call for government support, rather than a concrete plan. “There’s no funding mandate, there’s nothing really. Just a bunch of ideas,” he says. These are works in progress, says microbial ecologist Jack Gilbert at the University of Chicago in Illinois, a co-author of the Science article. “To put down immediately at this point that we have a clear funding method, this is what we want to fund, these are the research areas we think are valid, would have been crass,” Gilbert says. Gilbert hopes that the proposals — and the online back-and-forth — will stimulate further discussion and the creation of new research programmes. “No one is saying that we’re going to fundamentally transform the way you do science. We’re saying we’re going to fundamentally transform the way science is funded and the way multidisciplinary science can be implemented,” he says. “This is starting a conversation.” Other scientists expressed concern that standardizing methods and data sharing might stifle creativity in a rapidly evolving field. Loman wrote in an e-mail to Nature that there are often good reasons for methodological differences between microbiologists studying different ecosystems such as the gut or soil. “Should we standardise on one protocol?” he adds. “We don’t even know what the right technique is for many niches.” And as Noah Fierer, a microbial ecologist at the University of Colorado, Boulder, added in a blog post: “Methods are constantly changing (hopefully improving) and many of these improvements come from smaller labs that may not be directly involved in the consortium that decides the consensus methods.” These criticisms of the call for standardization surprised Nicole Dubilier, a co-author of the Nature piece who is a microbiologist at the Max Planck Institute for Marine Microbiology in Bremen, Germany. “If there’s one thing that will help the field, it’s standardization,” she says. “Standardization is the key to comparing results.” Some scientists poked fun at the grand aims of the initiatives. Josh Neufeld, a microbial ecologist at the University of Waterloo in Canada, tweeted:


Parente E.,University of Basilicata | Cocolin L.,University of Turin | De Filippis F.,University of Naples Federico II | Zotta T.,CNR Institute of Food Sciences | And 8 more authors.
International Journal of Food Microbiology | Year: 2016

Amplicon targeted high-throughput sequencing has become a popular tool for the culture-independent analysis of microbial communities. Although the data obtained with this approach are portable and the number of sequences available in public databases is increasing, no tool has been developed yet for the analysis and presentation of data obtained in different studies. This work describes an approach for the development of a database for the rapid exploration and analysis of data on food microbial communities. Data from seventeen studies investigating the structure of bacterial communities in dairy, meat, sourdough and fermented vegetable products, obtained by 16S rRNA gene targeted high-throughput sequencing, were collated and analysed using Gephi, a network analysis software. The resulting database, which we named FoodMicrobionet, was used to analyse nodes and network properties and to build an interactive web-based visualisation. The latter allows the visual exploration of the relationships between Operational Taxonomic Units (OTUs) and samples and the identification of core- and sample-specific bacterial communities. It also provides additional search tools and hyperlinks for the rapid selection of food groups and OTUs and for rapid access to external resources (NCBI taxonomy, digital versions of the original articles). Microbial interaction network analysis was carried out using CoNet on datasets extracted from FoodMicrobionet: the complexity of interaction networks was much lower than that found for other bacterial communities (human microbiome, soil and other environments). This may reflect both a bias in the dataset (which was dominated by fermented foods and starter cultures) and the lower complexity of food bacterial communities. Although some technical challenges exist, and are discussed here, the net result is a valuable tool for the exploration of food bacterial communities by the scientific community and food industry. © 2015 Published by Elsevier B.V.


Bourrie B.C.T.,University of Alberta | Bourrie B.C.T.,Teagasc | Willing B.P.,University of Alberta | Cotter P.D.,Teagasc | Cotter P.D.,APC Microbiome Institute
Frontiers in Microbiology | Year: 2016

Kefir is a complex fermented dairy product created through the symbiotic fermentation of milk by lactic acid bacteria and yeasts contained within an exopolysaccharide and protein complex called a kefir grain. As with other fermented dairy products, kefir has been associated with a range of health benefits such as cholesterol metabolism and angiotensin-converting enzyme (ACE) inhibition, antimicrobial activity, tumor suppression, increased speed of wound healing, and modulation of the immune system including the alleviation of allergy and asthma. These reports have led to increased interest in kefir as a focus of research and as a potential probiotic-containing product. Here, we review those studies with a particular emphasis on the microbial composition and the health benefits of the product, as well as discussing the further development of kefir as an important probiotic product. © 2016 Bourrie, Willing and Cotter.

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