• 16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

      Fouhy, Fiona; Clooney, Adam G; STANTON, CATHERINE; Claesson, Marcus J.; Cotter, Paul D.; European Union; Science Foundation Ireland; 603038; SFI/12/RC/2273; SFI/11/PI/1137 (Biomed Central, 24/06/2016)
      Background Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the community. Numerous factors, including DNA extraction method, primer sequences and sequencing platform employed, can affect the accuracy of the results achieved. The aim of this study was to determine the impact of these three factors on 16S rRNA gene sequencing results, using mock communities and mock community DNA. Results The use of different primer sequences (V4-V5, V1-V2 and V1-V2 degenerate primers) resulted in differences in the genera and species detected. The V4-V5 primers gave the most comparable results across platforms. The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. Data generated from DNA extracted using the 2 extraction methods were very similar. Conclusions Microbiota compositional data differed depending on the primers and sequencing platform that were used. The results demonstrate the risks in comparing data generated using different sequencing approaches and highlight the merits of choosing a standardised approach for sequencing in situations where a comparison across multiple sequencing runs is required.
    • The altered gut microbiota in adults with cystic fibrosis

      Burke, D.G.; Fouhy, Fiona; Harrison, M. J; Rea, Mary; Cotter, Paul D.; O'Sullivan, Orla; STANTON, CATHERINE; Hill, Cian J; Shanahan, Fergus; Plant, Barry J.; et al. (Biomed Central, 09/03/2017)
      Background 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.
    • Analysis of Health Benefits Conferred by Lactobacillus Species from Kefir

      Cotter, Paul D.; Slattery, Conor; O'Toole, Paul W.; Department of Agriculture, Food and Marine; Science Foundation Ireland; APC Microbiome Ireland; Vistamilk; Enterprise Ireland; European Union; 818368 (MDPI, 2019-06-01)
      Lactobacilli are among the most common microorganisms found in kefir; a traditional fermented milk beverage produced locally in many locations around the world. Kefir has been associated with a wide range of purported health benefits; such as antimicrobial activity; cholesterol metabolism; immunomodulation; anti-oxidative effects; anti-diabetic effects; anti-allergenic effects; and tumor suppression. This review critically examines and assesses these claimed benefits and mechanisms with regard to particular Lactobacillus species and/or strains that have been derived from kefir; as well as detailing further potential avenues for experimentation.
    • Antifungal Peptides as Therapeutic Agents

      Fernández de Ullivarri, Miguel; Arbulu, Sara; Garcia-Gutierrez, Enriqueta; Cotter, Paul D.; Science Foundation Ireland; European Union; Teagasc Walsh Fellowship Programme; SFI/12/RC/2273; 754535; 2015066 (Frontiers Media SA, 2020-03-17)
      Fungi have been used since ancient times in food and beverage-making processes and, more recently, have been harnessed for the production of antibiotics and in processes of relevance to the bioeconomy. Moreover, they are starting to gain attention as a key component of the human microbiome. However, fungi are also responsible for human infections. The incidence of community-acquired and nosocomial fungal infections has increased considerably in recent decades. Antibiotic resistance development, the increasing number of immunodeficiency- and/or immunosuppression-related diseases and limited therapeutic options available are triggering the search for novel alternatives. These new antifungals should be less toxic for the host, with targeted or broader antimicrobial spectra (for diseases of known and unknown etiology, respectively) and modes of actions that limit the potential for the emergence of resistance among pathogenic fungi. Given these criteria, antimicrobial peptides with antifungal properties, i.e., antifungal peptides (AFPs), have emerged as powerful candidates due to their efficacy and high selectivity. In this review, we provide an overview of the bioactivity and classification of AFPs (natural and synthetic) as well as their mode of action and advantages over current antifungal drugs. Additionally, natural, heterologous and synthetic production of AFPs with a view to greater levels of exploitation is discussed. Finally, we evaluate the current and potential applications of these peptides, along with the future challenges relating to antifungal treatments.
    • Aquaculture Production of the Brown Seaweeds Laminaria digitata and Macrocystis pyrifera: Applications in Food and Pharmaceuticals

      Purcell-Meyerink, Diane; Packer, Michael A.; Wheeler, Thomas T.; Hayes, Maria; Teagasc; European Union; 754380 (Multidisciplinary Digital Publishing Institute, 2021-02-28)
      Seaweeds have a long history of use as food, as flavouring agents, and find use in traditional folk medicine. Seaweed products range from food, feed, and dietary supplements to pharmaceuticals, and from bioenergy intermediates to materials. At present, 98% of the seaweed required by the seaweed industry is provided by five genera and only ten species. The two brown kelp seaweeds Laminaria digitata, a native Irish species, and Macrocystis pyrifera, a native New Zealand species, are not included in these eleven species, although they have been used as dietary supplements and as animal and fish feed. The properties associated with the polysaccharides and proteins from these two species have resulted in increased interest in them, enabling their use as functional foods. Improvements and optimisations in aquaculture methods and bioproduct extractions are essential to realise the commercial potential of these seaweeds. Recent advances in optimising these processes are outlined in this review, as well as potential future applications of L. digitata and, to a greater extent, M. pyrifera which, to date, has been predominately only wild-harvested. These include bio-refinery processing to produce ingredients for nutricosmetics, functional foods, cosmeceuticals, and bioplastics. Areas that currently limit the commercial potential of these two species are highlighted
    • Characterisation of Seasonal Mytilus edulis By-Products and Generation of Bioactive Hydrolysates

      Naik, Azza Silotry; Mora, Leticia; Hayes, Maria; Bord Iascaigh Mhara; European Union; 17/SRDP/002 2018-2020 (MDPI AG, 2020-10-01)
      Mussel cultivation results in tons of by-product, with 27% of the harvest considered as reject material. In this study, mussel by-products considered to be undersized (mussels with a cooked meat yield <30%), mussels with broken shells and barnacle-fouled mussels were collected from three different locations in the west, north-west and south-west of Ireland. Samples were hydrolysed using controlled temperatures and agitation, and the proteolytic enzyme Protamex® was added at an enzyme:substrate ratio of 1:50 (w:v). The hydrolysates were freeze-dried and analysed for protein content and amino acid composition, lipid content and fatty acid methyl ester (FAME) composition, ash and techno-functional and bioactive activities. The degree of hydrolysis was determined using the Adler-Nissen pH stat method and was found to be between 2.41% ± 0% and 7.55% ± 0.6%. Mussel by-products harvested between February and May 2019 had protein contents ranging from 36.76% ± 0.41% to 52.19% ± 1.78%. The protein content of mussels collected from July to October (the spawning season) ranged from 59.07% ± 1.375% to 68.31% ± 3.42%. The ratio of essential to nonessential amino acids varied from 0.68–0.96 and it was highest for a sample collected in November from the west of Ireland. All the hydrolysate samples contained omega-3 polyunsaturated fatty acids (PUFA), especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), which are known anti-inflammatory agents. Selected hydrolysates which had angiotensin-converting enzyme I (ACE-I; EC 3.4.15.1) and dipeptidyl peptidase IV (DPP-IV; EC 3.4.14.5) inhibitory activities were filtered using 3-kDa membrane filtration and the permeate fraction was sequenced using mass spectrometry (MS). Identified peptides were >7 amino acids in length. Following BIOPEP database mining, 91% of the by-product mussel peptides identified were found to be previously identified DPP-IV and ACE-I inhibitory peptides, and this was confirmed using in vitro bioassays. The ACE-I inhibitory activity of the by-product mussel hydrolysates ranged from 22.23% ± 1.79% to 86.08% ± 1.59% and the most active hydrolysate had an ACE-I inhibitory concentration (IC50) value of 0.2944 mg/mL compared to the positive control, captopril. This work demonstrates that by-product mussel hydrolysates have potential for use as health-promoting ingredients.
    • Collective unconscious: How gut microbes shape human behavior

      Dinan, Timothy G.; Stilling, Roman M.; STANTON, CATHERINE; Cryan, John F.; Science Foundation Ireland; Health Research Board; European Union; SFI/12/RC/2273; HRA_POR/2011/23; HRA_POR/2012/32; et al. (Elsevier, 2015-03-03)
      The human gut harbors a dynamic and complex microbial ecosystem, consisting of approximately 1 kg of bacteria in the average adult, approximately the weight of the human brain. The evolutionary formation of a complex gut microbiota in mammals has played an important role in enabling brain development and perhaps sophisticated social interaction. Genes within the human gut microbiota, termed the microbiome, significantly outnumber human genes in the body, and are capable of producing a myriad of neuroactive compounds. Gut microbes are part of the unconscious system regulating behavior. Recent investigations indicate that these microbes majorly impact on cognitive function and fundamental behavior patterns, such as social interaction and stress management. In the absence of microbes, underlying neurochemistry is profoundly altered. Studies of gut microbes may play an important role in advancing understanding of disorders of cognitive functioning and social interaction, such as autism.
    • Collective unconscious: How gut microbes shape human behavior

      Dinan, Timothy G.; Stilling, Roman M.; STANTON, CATHERINE; Cryan, John F.; Science Foundation Ireland; Health Research Board of Ireland; European Union; SFI/12/RC/2273; HRA_POR/2011/23; HRA_POR/2012/32 (Elsevier BV, 2015-04)
      The human gut harbors a dynamic and complex microbial ecosystem, consisting of approximately 1 kg of bacteria in the average adult, approximately the weight of the human brain. The evolutionary formation of a complex gut microbiota in mammals has played an important role in enabling brain development and perhaps sophisticated social interaction. Genes within the human gut microbiota, termed the microbiome, significantly outnumber human genes in the body, and are capable of producing a myriad of neuroactive compounds. Gut microbes are part of the unconscious system regulating behavior. Recent investigations indicate that these microbes majorly impact on cognitive function and fundamental behavior patterns, such as social interaction and stress management. In the absence of microbes, underlying neurochemistry is profoundly altered. Studies of gut microbes may play an important role in advancing understanding of disorders of cognitive functioning and social interaction, such as autism.
    • Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

      Clooney, Adam G; Fouhy, Fiona; Sleator, Roy D.; O'Driscoll, Aisling; STANTON, CATHERINE; Cotter, Paul D.; Claesson, Marcus J.; Science Foundation Ireland; European Union; SFI/12/RC/2273; et al. (PLOS, 05/02/2016)
      Rapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number ofmethodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemistry version, read length, insert size, and analysis pipelines, amongst others. This increase in variability threatens to compromise both the reproducibility and the comparability of studies conducted. Here we perform the first reported study comparing both amplicon and shotgun sequencing for the three leading next-generation sequencing technologies. These were applied to six human stool samples using Illumina HiSeq, MiSeq and Ion PGM shotgun sequencing, as well as amplicon sequencing across two variable 16S rRNA gene regions. Notably, we found that the factor responsible for the greatest variance inmicrobiota composition was the chosen methodology rather than the natural inter-individual variance, which is commonly one of the most significant drivers in microbiome studies. Amplicon sequencing suffered from this to a large extent, and this issue was particularly apparent when the 16S rRNA V1-V2 region amplicons were sequenced withMiSeq. Somewhat surprisingly, the choice of taxonomic binning software for shotgun sequences proved to be of crucial importance with even greater discriminatory power than sequencing technology and choice of amplicon. Optimal N50 assembly values for the HiSeq was obtained for 10million reads per sample, whereas the applied MiSeq and PGM sequencing depths proved less sufficient for shotgun sequencing of stool samples. The latter technologies, on the other hand, provide a better basis for functional gene categorisation, possibly due to their longer read lengths. Hence, in addition to highlighting methodological biases, this study demonstrates the risks associated with comparing data generated using different strategies. We also recommend that laboratories with particular interests in certain microbes should optimise their protocols to accurately detect these taxa using different techniques.
    • Complete Genome Sequences of vB_LmoS_188 and vB_LmoS_293, Two Bacteriophages with Specificity for Listeria monocytogenes Strains of Serotypes 4b and 4e

      Casey, A.; Kieran, Jordan; Coffey, Aidan; McAuliffe, Olivia; European Union; Safefood; PROMISE 265877; FOODSEG 266061 (American Society for Microbiology, 09/04/2015)
      Listeria monocytogenes is responsible for the rare disease listeriosis, which is associated with the consumption of contaminated food products. We report here the complete genome sequences of vB_LmoS_188 and vB_LmoS_293, phages isolated from environmental sources and that have host specificity for L. monocytogenes strains of the 4b and 4e serotypes.
    • Delivery of β-carotene to the in vitro intestinal barrier using nanoemulsions with lecithin or sodium caseinate as emulsifiers

      Gasa-Falcon, Ariadna; Arranz, Elena; Odriozola-Serrano, Isabel; Martín-Belloso, Olga; Giblin, Linda; Ministerio de Economía y Competitividad; Enterprise Ireland; European Union; Science Foundation Ireland; Agencia de Gestio d’Ajuts Universitaris I de Recerca; et al. (Elsevier BV, 2021-01)
      To increase the intestinal delivery of dietary β-carotene, there is a need to develop nanostructured food systems to encapsulate this fat soluble bioactive. The aim of this study was to evaluate the bioacessibility and bioavailability across the intestinal barrier of β-carotene-enriched nanoemulsions stabilised with two emulsifiers (lecithin or sodium caseinate) by coupling an in vitro gastrointestinal digestion with two in vitro cell culture models (Caco-2 or co-culture of Caco-2/HT29-MTX). Nanoemulsions stabilised with lecithin had significantly higher β-carotene in the gastrointestinal digested micellar fraction, lower β-carotene in the Caco-2 (and Caco-2/HT29-MTX) apical compartment and significantly higher β-carotene in Caco-2 cellular content compared to β-carotene-enriched nanoemulsions stabilised with sodium caseinate. Finally, to assess anti-inflammatory activity of digested nanoemulsions, lipopolysaccharide stimulated macrophages were exposed to Caco- 2 basolateral samples with levels of TNF-α and IL-β, subsequently quantified. A TNF-α response from stimulated THP-1 macrophages was elicited by basolateral samples, regardless the emulsifier used to formulate nanoemulsions. This study demonstrated that β-carotene permeability is influenced by the food derived emulsifier used for stabilising nanoemulsions, indicating that composition may be a critical factor for β-carotene delivery.
    • Delivery of β-carotene to the in vitro intestinal barrier using nanoemulsions with lecithin or sodium caseinate as emulsifiers

      Gasa-Falcon, Ariadna; Arranz, Elena; Odriozola-Serrano, Isabel; Martín-Belloso, Olga; Giblin, Linda; Fondo Europeo de Desarrollo Regional; Ministerio de Economía y Competitividad; European Union; Enterprise Ireland; Science Foundation Ireland; et al. (Elsevier, 2021-01-13)
      To increase the intestinal delivery of dietary β-carotene, there is a need to develop nanostructured food systems to encapsulate this fat soluble bioactive. The aim of this study was to evaluate the bioacessibility and bioavailability across the intestinal barrier of β-carotene-enriched nanoemulsions stabilised with two emulsifiers (lecithin or sodium caseinate) by coupling an in vitro gastrointestinal digestion with two in vitro cell culture models (Caco-2 or co-culture of Caco-2/HT29-MTX). Nanoemulsions stabilised with lecithin had significantly higher β-carotene in the gastrointestinal digested micellar fraction, lower β-carotene in the Caco-2 (and Caco-2/HT29-MTX) apical compartment and significantly higher β-carotene in Caco-2 cellular content compared to β-carotene-enriched nanoemulsions stabilised with sodium caseinate. Finally, to assess anti-inflammatory activity of digested nanoemulsions, lipopolysaccharide stimulated macrophages were exposed to Caco- 2 basolateral samples with levels of TNF-α and IL-β, subsequently quantified. A TNF-α response from stimulated THP-1 macrophages was elicited by basolateral samples, regardless the emulsifier used to formulate nanoemulsions. This study demonstrated that β-carotene permeability is influenced by the food derived emulsifier used for stabilising nanoemulsions, indicating that composition may be a critical factor for β-carotene delivery.
    • Development of enterococci and production of tyramine during the manufacture and ripening of Cheddar cheese

      Rea, Mary; Franz, C.M.A.P.; Holzapfel, W.H.; Cogan, Tim; European Union; CT97-3078 (Teagasc (Agriculture and Food Development Authority), Ireland, 2004)
      The effect of six strains of enterococci (three strains of Enterococcus faecalis, and one strain each of Ec. faecium, Ec. durans and Ec. casseliflavus) on flavour development and tyramine production in Cheddar cheese during manufacture and ripening was studied in two trials. No strain produced gelatinase or haemolysin and all of them grew well during manufacture reaching 107 colony forming units (cfu)/g in 6 h, after which they remained more or less constant during at least 48 weeks of ripening. There was no relationship between tyramine production in a broth containing tyrosine and tyramine production in the cheese. All strains, except Ec. casseliflavus, produced tyramine in the cheese, with the greatest concentration (162 mg/kg) being produced by Ec. durans after 9 months ripening at 8 ºC. There was no statistically significant difference (P > 0.05) between the flavour of the control cheese and any cheese containing an enterococcus. Nevertheless, cheese made with Ec. faecium E-24 received the best score in each trial at both time points. No off-flavours were found. Regarding proteolysis, only Ec. faecalis E-140 showed significant (P < 0.05) increases in both phosphotungstic acid and pH 4.6 soluble N. It is concluded that enterococci have little effect on the flavour of Cheddar cheese.
    • Dietary Supplementation with a Magnesium-Rich Marine Mineral Blend Enhances the Diversity of Gastrointestinal Microbiota

      Crowley, Erin; Long-Smith, Caitriona; Murphy, Amy; Patterson, Elaine; Murphy, Kiera; O’Gorman, Denise; Stanton, Catherine; Nolan, Yvonne; Science Foundation Ireland; European Union; et al. (MDPI AG, 2018-06-20)
      Accumulating evidence demonstrates that dietary supplementation with functional food ingredients play a role in systemic and brain health as well as in healthy ageing. Conversely, deficiencies in calcium and magnesium as a result of the increasing prevalence of a high fat/high sugar “Western diet” have been associated with health problems such as obesity, inflammatory bowel diseases, and cardiovascular diseases, as well as metabolic, immune, and psychiatric disorders. It is now recognized that modulating the diversity of gut microbiota, the population of intestinal bacteria, through dietary intervention can significantly impact upon gut health as well as systemic and brain health. In the current study, we show that supplementation with a seaweed and seawater-derived functional food ingredient rich in bioactive calcium and magnesium (0.1% supplementation) as well as 70 other trace elements, significantly enhanced the gut microbial diversity in adult male rats. Given the significant impact of gut microbiota on health, these results position this marine multi-mineral blend (MMB) as a promising digestive-health promoting functional food ingredient.
    • Early Gut Microbiota Perturbations Following Intrapartum Antibiotic Prophylaxis to Prevent Group B Streptococcal Disease

      Mazzola, Giuseppe; Murphy, Kiera; Ross, R Paul; Di Gioia, Diana; Biavati, Bruno; Corvaglia, Luigi T.; Faldella, Giacomo; STANTON, CATHERINE; Department of Agriculture, Food and the Marine; European Union; et al. (PLOS, 22/06/2016)
      The faecal microbiota composition of infants born to mothers receiving intrapartum antibiotic prophylaxis with ampicillin against group B Streptococcus was compared with that of control infants, at day 7 and 30 of life. Recruited newborns were both exclusive breastfed and mixed fed, in order to also study the effect of dietary factors on the microbiota composition. Massive parallel sequencing of the V3-V4 region of the 16S rRNA gene and qPCR analysis were performed. Antibiotic prophylaxis caused the most marked changes on the microbiota in breastfed infants, mainly resulting in a higher relative abundance of Enterobacteriaceae, compared with control infants (52% vs. 14%, p = 0.044) and mixed-fed infants (52% vs. 16%, p = 0.13 NS) at day 7 and in a lower bacterial diversity compared to mixed-fed infants and controls. Bifidobacteria were also particularly vulnerable and abundances were reduced in breastfed (p = 0.001) and mixed-fed antibiotic treated groups compared to non-treated groups. Reductions in bifidobacteria in antibiotic treated infants were also confirmed by qPCR. By day 30, the bifidobacterial population recovered and abundances significantly increased in both breastfed (p = 0.025) and mixed-fed (p = 0.013) antibiotic treated groups, whereas Enterobacteriaceae abundances remained highest in the breastfed antibiotic treated group (44%), compared with control infants (16%) and mixed-fed antibiotic treated group (28%). This study has therefore demonstrated the short term consequences of maternal intrapartum antibiotic prophylaxis on the infant faecal microbial population, particularly in that of breastfed infants.
    • The Effect of Dietary Supplementation with Spent Cider Yeast on the Swine Distal Gut Microbiome

      Upadrasta, Aditya; O'Sulivan, Lisa; O'Sullivan, Orla; Sexton, Noel; Lawlor, Peadar G; Hill, Colin; Fitzgerald, Gerald F; STANTON, CATHERINE; Ross, R Paul; Enterprise Ireland; et al. (PLOS, 09/10/2013)
      Background: 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.
    • The Effect of Feeding Bt MON810 Maize to Pigs for 110 Days on Intestinal Microbiota

      Buzoianu, Stefan G.; Walsh, Maria C.; Rea, Mary; O'Sullivan, Orla; Crispie, Fiona; Cotter, Paul D.; Ross, R Paul; Gardiner, Gillian E.; Lawlor, Peadar G; European Union; et al. (PLOS, 04/05/2012)
      Objective To assess the effects of feeding Bt MON810 maize to pigs for 110 days on the intestinal microbiota. Methodology/Principal Findings Forty male pigs (~40 days old) were blocked by weight and litter ancestry and assigned to one of four treatments; 1) Isogenic maize-based diet for 110 days (Isogenic); 2) Bt maize-based diet (MON810) for 110 days (Bt); 3) Isogenic maize-based diet for 30 days followed by a Bt maize-based diet for 80 days (Isogenic/Bt); 4) Bt maize-based diet for 30 days followed by an isogenic maize-based diet for 80 days (Bt/Isogenic). Enterobacteriaceae, Lactobacillus and total anaerobes were enumerated in the feces using culture-based methods on days 0, 30, 60 and 100 of the study and in ileal and cecal digesta on day 110. No differences were found between treatments for any of these counts at any time point. The relative abundance of cecal bacteria was also determined using high-throughput 16 S rRNA gene sequencing. No differences were observed in any bacterial taxa between treatments, with the exception of the genus Holdemania which was more abundant in the cecum of pigs fed the isogenic/Bt treatment compared to pigs fed the Bt treatment (0.012 vs 0.003%; P≤0.05). Conclusions/Significance Feeding pigs a Bt maize-based diet for 110 days did not affect counts of any of the culturable bacteria enumerated in the feces, ileum or cecum. Neither did it influence the composition of the cecal microbiota, with the exception of a minor increase in the genus Holdemania. As the role of Holdemania in the intestine is still under investigation and no health abnormalities were observed, this change is not likely to be of clinical significance. These results indicate that feeding Bt maize to pigs in the context of its influence on the porcine intestinal microbiota is safe.
    • The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations

      Fouhy, Fiona; Deane, Jennifer; Rea, Mary; O'Sullivan, Orla; Ross, R Paul; O'Callaghan, Grace; Plant, Barry J.; STANTON, CATHERINE; Science Foundation Ireland; European Union; et al. (PLoS, 06/03/2015)
      Background High-throughput sequencing has enabled detailed insights into complex microbial environments, including the human gut microbiota. The accuracy of the sequencing data however, is reliant upon appropriate storage of the samples prior to DNA extraction. The aim of this study was to conduct the first MiSeq sequencing investigation into the effects of faecal storage on the microbiota, compared to fresh samples. Culture-based analysis was also completed. Methods Seven faecal samples were collected from healthy adults. Samples were separated into fresh (DNA extracted immediately), snap frozen on dry ice and frozen for 7 days at -80°C prior to DNA extraction or samples frozen at -80°C for 7 days before DNA extraction. Sequencing was completed on the Illumina MiSeq platform. Culturing of total aerobes, anaerobes and bifidobacteria was also completed. Results No significant differences at phylum or family levels between the treatment groups occurred. At genus level only Faecalibacterium and Leuconostoc were significantly different in the fresh samples compared to the snap frozen group (p = 0.0298; p = 0.0330 respectively). Diversity analysis indicated that samples clustered based on the individual donor, rather than by storage group. No significant differences occurred in the culture-based analysis between the fresh, snap or -80°C frozen samples. Conclusions Using the MiSeq platform coupled with culture-based analysis, this study highlighted that limited significant changes in microbiota occur following rapid freezing of faecal samples prior to DNA extraction. Thus, rapid freezing of samples prior to DNA extraction and culturing, preserves the integrity of the microbiota.
    • Enduring Behavioral Effects Induced by Birth by Caesarean Section in the Mouse

      Morais, Livia H.; Golubeva, Anna V.; Moloney, Gerard M; Stanton, Catherine; Dinan, Timothy G.; Cryan, John F.; Science Foundation Ireland; European Union; Department of Agriculture, Food and the Marine; Science without Borders; et al. (2020-08-20)
      Birth by Caesarean (C)-section impacts early gut microbiota colonization and is associated with an increased risk of developing immune and metabolic disorders. Moreover, alterations of the microbiome have been shown to affect neurodevelopmental trajectories. However, the long-term effects of C-section on neurobehavioral processes remain unknown. Here, we demonstrated that birth by C-section results in marked but transient changes in microbiome composition in the mouse, in particular, the abundance of Bifidobacterium spp. was depleted in early life. Mice born by C-section had enduring social, cognitive, and anxiety deficits in early life and adulthood. Interestingly, we found that these specific behavioral alterations induced by the mode of birth were also partially corrected by co-housing with vaginally born mice. Finally, we showed that supplementation from birth with a Bifidobacterium breve strain, or with a dietary prebiotic mixture that stimulates the growth of bifidobacteria, reverses selective behavioral alterations in C-section mice. Taken together, our data link the gut microbiota to behavioral alterations in C-section-born mice and suggest the possibility of developing adjunctive microbiota-targeted therapies that may help to avert long-term negative consequences on behavior associated with C-section birth mode.
    • Evaluation of Phage Therapy in the Context of Enterococcus faecalis and Its Associated Diseases

      Bolocan, Andrei S.; Upadrasta, Aditya; de Almeida Bettio, Pedro H.; Clooney, Adam G.; Draper, Lorraine A.; Ross, R. Paul; Hill, Colin; Science Foundation Ireland; European Union; Janssen Biotech, Inc.; et al. (MDPI, 2019-04-20)
      Bacteriophages (phages) or bacterial viruses have been proposed as natural antimicrobial agents to fight against antibiotic-resistant bacteria associated with human infections. Enterococcus faecalis is a gut commensal, which is occasionally found in the mouth and vaginal tract, and does not usually cause clinical problems. However, it can spread to other areas of the body and cause life-threatening infections, such as septicemia, endocarditis, or meningitis, in immunocompromised hosts. Although E. faecalis phage cocktails are not commercially available within the EU or USA, there is an accumulated evidence from in vitro and in vivo studies that have shown phage efficacy, which supports the idea of applying phage therapy to overcome infections associated with E. faecalis. In this review, we discuss the potency of bacteriophages in controlling E. faecalis, in both in vitro and in vivo scenarios. E. faecalis associated bacteriophages were compared at the genome level and an attempt was made to categorize phages with respect to their suitability for therapeutic application, using orthocluster analysis. In addition, E. faecalis phages have been examined for the presence of antibiotic-resistant genes, to ensure their safe use in clinical conditions. Finally, the domain architecture of E. faecalis phage-encoded endolysins are discussed.