Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources

peer-reviewedKefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.The Alimentary Pharmabiotic Centre is a research centre funded by Science Foundation Ireland (SFI), through the Irish Government’s National Development Plan. The authors and their work were supported by SFI CSET grant APC CSET 2 grant 07/CE/B1368

Parents’ experiences of introducing toddlers to fruits and vegetables through repeated exposure, with and without prior visual familiarization to foods: evidence from daily diaries

While repeated exposure is an established method for inducing food acceptance in young children, little is known about parents’ experiences of repeatedly offering new or disliked foods at home. In this study, parents kept structured diary records during a 15-day period in which they offered their 2-year-old child daily tastes of one fruit and one vegetable. We explored how children’s acceptance of foods (measured in terms of willingness to taste, liking and intake) and the ease and enjoyment of the process for parents changed from the early (days 1-5) to middle (days 6-10) to later (days 11-15) phases of exposure. In addition, we explored whether prior visual familiarization to foods affected children’s behavior and/or parents’ experiences during exposure. Families were randomly assigned to look at a picture book about one to-be-exposed food for the two weeks prior to the exposure phase (‘fruit book’ and ‘vegetable book’ groups) or to a control group, who did not receive a book. Measures obtained from parents’ diary records revealed increases in willingness to taste and intake of vegetables and increased liking of both fruits and vegetables with greater exposure. Prior visual familiarization to vegetables further boosted children’s willingness to taste and liking of vegetables, and the ease and enjoyment of introducing these for parents. Children’s acceptance of foods and parents’ positivity during exposure predicted children’s liking and intake of foods 3 months later. Results confirm the potential for vegetable picture books to support parents in engaging with repeated exposure regimes and in successfully introducing vegetables into toddlers’ diets

Targeted advertisement of chlamydia screening on social media: A mixed-methods analysis

Objective Chlamydia is one of the most common sexually transmitted infections in teenagers and young adults. This study used a mixed-methods analysis to investigate targeted promotion of chlamydia home-testing on social media. Methods Our first study, in which face-to-face interviews with young women were conducted, sought to explore their attitudes and preferences towards social media-based health promotion. Our second study used Facebook and Google analytics to examine visits to a chlamydia testing page (where chlamydia testing kits could be ordered online), both before and after a targeted Facebook-based health promotion campaign was conducted. Results The interviews revealed Facebook to be the preferred choice of social media, with participants perceiving it to be a powerful and far-reaching platform for social interaction. Participants also highlighted several aspects of promotional content to be important at increasing engagement with the target population, including appropriate use of colour, level of interactivity, use of humour and anonymity. The website analysis showed a 277% increase in the direct entrance on the chlamydia testing kit page and a 41% increase in chlamydia test kit orders, in comparison with the baseline period prior to the intervention. Conclusions The findings support social media as an engaging medium for the online promotion of chlamydia self-testing and implicate Facebook advertising as a useful tool in addition to community-based chlamydia screening services. Future research needs to identify whether targeted social media-based health promotion could lead to higher chlamydia diagnosis rate in comparison to traditional communication channels

The Effect of Dietary Supplementation with Spent Cider Yeast on the Swine Distal Gut Microbiome

peer-reviewedBackground: There is an increasing need for alternatives to antibiotics for promoting animal health, given the increasing problems associated with antibiotic resistance. In this regard, we evaluated spent cider yeast as a potential probiotic for modifying the gut microbiota in weanling pigs using pyrosequencing of 16S rRNA gene libraries. Methodology and Principal Findings: Piglets aged 24–26 days were assigned to one of two study groups; control (n = 12) and treatment (n = 12). The control animals were fed with a basal diet and the treatment animals were fed with basal diet in combination with cider yeast supplement (500 ml cider yeast containing ,7.6 log CFU/ml) for 21 days. Faecal samples were collected for 16s rRNA gene compositional analysis. 16S rRNA compositional sequencing analysis of the faecal samples collected from day 0 and day 21 revealed marked differences in microbial diversity at both the phylum and genus levels between the control and treatment groups. This analysis confirmed that levels of Salmonella and Escherichia were significantly decreased in the treatment group, compared with the control (P,0.001). This data suggest a positive influence of dietary supplementation with live cider yeast on the microbial diversity of the pig distal gut. Conclusions/Significance: The effect of dietary cider yeast on porcine gut microbial communities was characterized for the first time using 16S rRNA gene compositional sequencing. Dietary cider yeast can potentially alter the gut microbiota, however such changes depend on their endogenous microbiota that causes a divergence in relative response to that given diet.This work was funded by Enterprise Ireland, under the Commercialisation Fund (Contract No: CFTD/05/117), the Irish Government under the National Development Plan, 2000–2006, the European Research and Development Fund and Science Foundation Ireland (SFI).European Research and Development Fun

In silico analysis highlights the frequency and diversity of type 1 lantibiotic gene clusters in genome sequenced bacteria

<p>Abstract</p> <p>Background</p> <p>Lantibiotics are lanthionine-containing, post-translationally modified antimicrobial peptides. These peptides have significant, but largely untapped, potential as preservatives and chemotherapeutic agents. Type 1 lantibiotics are those in which lanthionine residues are introduced into the structural peptide (LanA) through the activity of separate lanthionine dehydratase (LanB) and lanthionine synthetase (LanC) enzymes. Here we take advantage of the conserved nature of LanC enzymes to devise an <it>in silico </it>approach to identify potential lantibiotic-encoding gene clusters in genome sequenced bacteria.</p> <p>Results</p> <p>In total 49 novel type 1 lantibiotic clusters were identified which unexpectedly were associated with species, genera and even phyla of bacteria which have not previously been associated with lantibiotic production.</p> <p>Conclusions</p> <p>Multiple type 1 lantibiotic gene clusters were identified at a frequency that suggests that these antimicrobials are much more widespread than previously thought. These clusters represent a rich repository which can yield a large number of valuable novel antimicrobials and biosynthetic enzymes.</p

Relatedness between the two-component lantibiotics lacticin 3147 and staphylococcin C55 based on structure, genetics and biological activity

BACKGROUND: Two component lantibiotics, such as the plasmid-encoded lacticin 3147 produced by Lactococcus lactis DPC3147 and staphylococcin C55 produced by Staphylococcus aureus C55, represent an emerging subgroup of bacteriocins. These two bacteriocins are particularly closely related, exhibiting 86% (LtnA1 and C55α) and 55% (LtnA2 and C55β) identity in their component peptides. The aim of this study was to investigate, for the first time for any two component bacteriocins, the significance of the relatedness between these two systems. RESULTS: So close is this relatedness that the hybrid peptide pairs LtnA1:C55β and C55α:LtnA2 were found to have activities in the single nanomolar range, comparing well with the native pairings. To determine whether this flexibility extended to the associated post-translational modification/processing machinery, the staphylococcin C55 structural genes were directly substituted for their lacticin 3147 counterparts in the ltn operon on the large conjugative lactococcal plasmid pMRC01. It was established that the lacticin LtnA1 post-translational and processing machinery could produce functionally active C55α, but not C55β. In order to investigate in closer detail the significance of the differences between LtnA1 and C55α, three residues in LtnA1 were replaced with the equivalent residues in C55α. Surprisingly, one such mutant LtnA1-Leu21Ala was not produced. This may be significant given the positioning of this residue in a putative lipid II binding loop. CONCLUSION: It is apparent, despite sharing striking similarities in terms of structure and activity, that these two complex bacteriocins display some highly dedicated features particular to either system

Adolescents' views of food and eating: Identifying barriers to healthy eating

This is a postprint version of the article. The official published version can be accessed from the link below - © 2006 The Association for Professionals in Services for Adolescents Published by Elsevier Ltd.Contemporary Western society has encouraged an obesogenic culture of eating amongst youth. Multiple factors may influence an adolescent's susceptibility to this eating culture, and thus act as a barrier to healthy eating. Given the increasing prevalence of obesity amongst adolescents, the need to reduce these barriers has become a necessity. Twelve focus group discussions of single-sex groups of boys or girls ranging from early to-mid adolescence (N = 73) were employed to identify key perceptions of, and influences upon, healthy eating behaviour. Thematic analysis identified four key factors as barriers to healthy eating. These factors were: physical and psychological reinforcement of eating behaviour; perceptions of food and eating behaviour; perceptions of contradictory food-related social pressures; Q perceptions of the concept of healthy eating itself. Overall, healthy eating as a goal in its own right is notably absent from the data and would appear to be elided by competing pressures to eat unhealthily and to lose weight. This insight should inform the development of future food-related communications to adolescents. (c) 2006 The Association for Professionals in Services for Adolescents.Funding from Safefood: the food safety promotion board is acknowledged

Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome.

peer-reviewedLactobacilli constitute a large genus of Gram-positive lactic acid bacteria which have widespread roles ranging from gut commensals to starters in fermented foods. A combination of in silico and laboratory-based screening allowed us to determine the overall bacteriocin producing potential of representative strains of each species of the genus. The genomes of 175 lactobacilli and 38 associated species were screened for the presence of antimicrobial producing genes and combined with screening for antimicrobial activity against a range of indicators. There also appears to be a link between the strains’ environment and bacteriocin production, with those from the animal and human microbiota encoding over twice as many bacteriocins as those from other sources. Five novel bacteriocins were identified belonging to differing bacteriocin classes, including two-peptide bacteriocins (muricidin and acidocin X) and circular bacteriocins (paracyclicin). In addition, there was a clear clustering of helveticin type bacteriolysins in the Lactobacillus acidophilus group of species. This combined in silico and in vitro approach to screening has demonstrated the true diversity and complexity of bacteriocins across the genus. It also highlights their biological importance in terms of communication and competition between closely related strains in diverse complex microbial environments

The altered gut microbiota in adults with cystic fibrosis

peer-reviewedBackground Cystic Fibrosis (CF) is an autosomal recessive disease that affects the function of a number of organs, principally the lungs, but also the gastrointestinal tract. The manifestations of cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction in the gastrointestinal tract, as well as frequent antibiotic exposure, undoubtedly disrupts the gut microbiota. To analyse the effects of CF and its management on the microbiome, we compared the gut microbiota of 43 individuals with CF during a period of stability, to that of 69 non-CF controls using 454-pyrosequencing of the 16S rRNA gene. The impact of clinical parameters, including antibiotic therapy, on the results was also assessed. Results The CF-associated microbiome had reduced microbial diversity, an increase in Firmicutes and a reduction in Bacteroidetes compared to the non-CF controls. While the greatest number of differences in taxonomic abundances of the intestinal microbiota was observed between individuals with CF and the healthy controls, gut microbiota differences were also reported between people with CF when grouped by clinical parameters including % predicted FEV1 (measure of lung dysfunction) and the number of intravenous (IV) antibiotic courses in the previous 12 months. Notably, CF individuals presenting with severe lung dysfunction (% predicted FEV1 ≤ 40%) had significantly (p < 0.05) reduced gut microbiota diversity relative to those presenting with mild or moderate dysfunction. A significant negative correlation (−0.383, Simpson’s Diversity Index) was also observed between the number of IV antibiotic courses and gut microbiota diversity. Conclusions This is one of the largest single-centre studies on gut microbiota in stable adults with CF and demonstrates the significantly altered gut microbiota, including reduced microbial diversity seen in CF patients compared to healthy controls. The data show the impact that CF and it's management have on gut microbiota, presenting the opportunity to develop CF specific probiotics to minimise microbiota alterations.The authors and their work were supported by the Science Foundation of Ireland and funded by the Centre for Science, Engineering and Technology (SFI-CSET) grant 02/CE/B124 and by FP7 funded CFMATTERS (Cystic Fibrosis Microbiome-determined Antibiotic Therapy Trial in Exacerbations: Results Stratified, Grant Agreement no. 603038)

Draft genome sequence of Bacillus thuringiensis DPC6431, producer of the bacteriocin thuricin CD

We report the draft genome sequence of Bacillus thuringiensis DPC6431, a producer of the anticlostridial bacteriocin thuricin CD and isolated from a human fecal sample. The assembly comprises 96 contigs for a total of 5,581,839 bp, with 32.5% G+C content