The gut virome in Irritable Bowel Syndrome differs from that of controls.

Irritable Bowel Syndrome (IBS), the most common gastrointestinal disorder, is diagnosed solely on symptoms. Potentially diagnostic alterations in the bacterial component of the gut microbiome (the bacteriome) are associated with IBS, but despite the known role of the virome (particularly bacteriophages), in shaping the gut bacteriome, few studies have investigated the virome in IBS. We performed metagenomic sequencing of fecal Virus-Like Particles (VLPs) from 55 patients with IBS and 51 control individuals. We detected significantly lower alpha diversity of viral clusters comprising both known and novel viruses (viral 'dark matter') in IBS and a significant difference in beta diversity compared to controls, but not between IBS symptom subtypes. The three most abundant bacteriophage clusters belonged to the Siphoviridae, Myoviridae, and Podoviridae families (Order Caudovirales). A core virome (defined as a cluster present in at least 50% of samples) of 5 and 12 viral clusters was identified in IBS and control subjects, respectively. We also identified a subset of viral clusters that showed differential abundance between IBS and controls. The virome did not co-vary significantly with the bacteriome, with IBS clinical subtype, or with Bile Acid Malabsorption status. However, differences in the virome could be related back to the bacteriome as analysis of CRISPR spacers indicated that the virome alterations were at least partially related to the alterations in the bacteriome. We found no evidence for a shift from lytic to lysogenic replication of core viral clusters, a phenomenon reported for the gut virome of patients with Inflammatory Bowel Disease. Collectively, our data show alterations in the virome of patients with IBS, regardless of clinical subtype, which may facilitate development of new microbiome-based therapeutics.

The fecal mycobiome in patients with Irritable Bowel Syndrome.

Alterations of the gut microbiota have been reported in various gastrointestinal disorders, but knowledge of the mycobiome is limited. We investigated the gut mycobiome of 80 patients with Irritable Bowel Syndrome (IBS) in comparison with 64 control subjects. The fungal-specific internal transcribed spacer 1 (ITS-1) amplicon was sequenced, and mycobiome zero-radius operational taxonomic units (zOTUs) were defined representing known and unknown species and strains. The fungal community was sparse and individual-specific in all (both IBS and control) subjects. Although beta-diversity differed significantly between IBS and controls, no difference was found among clinical subtypes of IBS or in comparison with the mycobiome of subjects with bile acid malabsorption (BAM), a condition which may overlap with IBS with diarrhoea. The mycobiome alterations co-varied significantly with the bacteriome and metabolome but were not linked with dietary habits. As a putative biomarker of IBS, the predictive power of the fecal mycobiome in machine learning models was significantly better than random but insufficient for clinical diagnosis. The mycobiome presents limited therapeutic and diagnostic potential for IBS, despite co-variation with bacterial components which do offer such potential.

Diet-microbiota-health interactions in older subjects: implications for healthy aging.

With modern medicine and an awareness of healthy lifestyle practices, people are living longer and generally healthier lives than their ancestors. These successes of modern medicine have resulted in an increasing proportion of elderly in society. Research groups around the world have investigated the contribution of gut microbial communities to human health and well-being. It was established that the microbiota composition of the human gut is modulated by lifestyle factors, especially diet. The microbiota composition and function, acting in concert with direct and indirect effects of habitual diet, is of great importance in remaining healthy and active. This is not a new concept, but until now the scale of the potential microbiota contribution was not appreciated. There are an estimated ten times more bacteria in an individual than human cells. The bacterial population is relatively stable in adults, but the age-related changes that occur later in life can have a negative impact on host health. This loss of the adult-associated microbiota correlates with measures of markers of inflammation, frailty, co-morbidity and nutritional status. This effect may be greater than that of diet or in some cases genetics alone. Collectively, the recent studies show the importance of the microbiota and associated metabolites in healthy aging and the importance of diet in its modulation.

Food and nutrient intake of Irish community-dwelling elderly subjects: who is at nutritional risk?

OBJECTIVES: To assess the dietary intakes of Irish community-dwelling elderly individuals, participating in the ELDERMET project. DESIGN: Cross-sectional study. SETTING: Cork city and county region of southern Ireland. PARTICIPANTS: Two hundred and eight (94 males, 114 females) community-dwelling subjects aged 64-93 yrs. MEASUREMENTS: Dietary intake was assessed using a validated semi-quantitative food frequency questionnaire (FFQ). Anthropometric data were recorded. Nutritional status was assessed using the Mini Nutritional Assessment (MNA). RESULTS: A high rate of overweight/obesity was observed in this population group. Consumption of energy-dense, low-nutrient foods was excessive among this population group. Older elderly subjects (≥75 yrs) consumed significantly (P<0.01) more desserts/sweets than younger elderly (64-74 yrs). Intakes of dietary fat and saturated fat were high while dairy food consumption was inadequate in both males and females. Elderly females typically had a more nutrient-dense diet than males. A considerable proportion of subjects, particularly males, had inadequate intakes of calcium, magnesium, vitamin D, folate, zinc and vitamin C. CONCLUSION: The data indicate that the diet of Irish community-dwelling elderly individuals is sub-optimal with respect to nutrient intake, and excessive in terms of fat intake, with implications for the health status of this population group. Reductions in dietary fat and increased low fat dairy food intakes are recommended for the prevention of diet-related disease in older persons. In addition, strategies to improve a number of sub-optimal micronutrient intakes need to be developed and implemented, particularly among elderly males.

The core faecal bacterial microbiome of Irish Thoroughbred racehorses.

UNLABELLED: In this study, we characterized the gut microbiota in six healthy Irish thoroughbred racehorses and showed it to be dominated by the phyla Firmicutes, Bacteroidetes, Proteobacteria, Verrucomicrobia, Actinobacteria, Euryarchaeota, Fibrobacteres and Spirochaetes. Moreover, all the horses harboured Clostridium, Fibrobacter, Faecalibacterium, Ruminococcus, Eubacterium, Oscillospira, Blautia Anaerotruncus, Coprococcus, Treponema and Lactobacillus spp. Notwithstanding the sample size, it was noteworthy that the core microbiota species assignments identified Fibrobacter succinogenes, Eubacterium coprostanoligenes, Eubacterium hallii, Eubacterium ruminantium, Oscillospira guillermondii, Sporobacter termiditis, Lactobacillus equicursoris, Treponema parvum and Treponema porcinum in all the horses. This is the first study of the faecal microbiota in the Irish thoroughbred racehorse, a significant competitor in the global bloodstock industry. The information gathered in this pilot study provides a foundation for veterinarians and other equine health-associated professionals to begin to analyse the microbiome of performance of racehorses. This study and subsequent work may lead to alternate dietary approaches aimed at minimizing the risk of microbiota-related dysbiosis in these performance animals. SIGNIFICANCE AND IMPACT OF THE STUDY: Although Irish thoroughbreds are used nationally and internationally as performance animals, very little is known about the core faecal microbiota of these animals. This is the first study to characterize the bacterial microbiota present in the Irish thoroughbred racehorse faeces and elucidate a core microbiome irrespective of diet, animal management and geographical location.