The core objective of the Food Biosciences Department is to engage in advanced research and technology development in support of the Irish Agri-Food industry sector. Activities fall into three research areas: Food for Health; Cheese Microbiology and Biochemistry and Milk and Product Quality.

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Food Biosciences

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  • Genome-Wide Profiling of Enterotoxigenic Staphylococcus aureus Strains Used for the Production of Naturally Contaminated Cheeses

    Macori, Guerrino; Bellio, Alberto; Bianchi, Daniela Manila; Chiesa, Francesco; Gallina, Silvia; Romano, Angelo; Zuccon, Fabio; Cabrera-Rubio, Raúl; Cauquil, Alexandra; Merda, Déborah; et al. (MDPI AG, 2019-12-27)
    Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. More than 20 staphylococcal enterotoxins with emetic activity can be produced by specific strains responsible for staphylococcal food poisoning, one of the most common food-borne diseases. Whole genome sequencing provides a comprehensive view of the genome structure and gene content that have largely been applied in outbreak investigations and genomic comparisons. In this study, six enterotoxigenic S. aureus strains were characterised using a combination of molecular, phenotypical and computational methods. The genomes were analysed for the presence of virulence factors (VFs), where we identified 110 genes and classified them into five categories: adherence (n = 31), exoenzymes (n = 28), genes involved in host immune system evasion (n = 7); iron uptake regulatory system (n = 8); secretion machinery factors and toxins’ genes (n = 36), and 39 genes coding for transcriptional regulators related to staphylococcal VFs. Each group of VFs revealed correlations among the six enterotoxigenic strains, and further analysis revealed their accessory genomic content, including mobile genetic elements. The plasmids pLUH02 and pSK67 were detected in the strain ProNaCC1 and ProNaCC7, respectively, carrying out the genes sed, ser, and selj. The genes carried out by prophages were detected in the strain ProNaCC2 (see), ProNaCC4, and ProNaCC7 (both positive for sea). The strain ProNaCC5 resulted positive for the genes seg, sei, sem, sen, seo grouped in an exotoxin gene cluster, and the strain ProNaCC6 resulted positive for seh, a transposon-associated gene. The six strains were used for the production of naturally contaminated cheeses which were tested with the European Screening Method for staphylococcal enterotoxins. The results obtained from the analysis of toxins produced in cheese, combined with the genomic features represent a portrait of the strains that can be used for the production of staphylococcal enterotoxin-positive cheese as reference material.
  • Is there evidence for bacterial transfer via the placenta and any role in the colonization of the infant gut? – a systematic review

    Gil, Angel; Rueda, Ricardo; Ozanne, Susan E.; van der Beek, Eline M.; van Loo-Bouwman, Carolien; Schoemaker, Marieke; Marinello, Vittoria; Venema, Koen; Stanton, Catherine; Schelkle, Bettina; et al. (Taylor and Francis, 2020-08-05)
    With the important role of the gut microbiome in health and disease, it is crucial to understand key factors that establish the microbial community, including gut colonization during infancy. It has been suggested that the first bacterial exposure is via a placental microbiome. However, despite many publications, the robustness of the evidence for the placental microbiome and transfer of bacteria from the placenta to the infant gut is unclear and hence the concept disputed. Therefore, we conducted a systematic review of the evidence for the role of the placental, amniotic fluid and cord blood microbiome in healthy mothers in the colonization of the infant gut. Most of the papers which were fully assessed considered placental tissue, but some studied amniotic fluid or cord blood. Great variability in methodology was observed especially regarding sample storage conditions, DNA/RNA extraction, and microbiome characterization. No study clearly considered transfer of the normal placental microbiome to the infant gut. Moreover, some studies in the review and others published subsequently reported little evidence for a placental microbiome in comparison to negative controls. In conclusion, current data are limited and provide no conclusive evidence that there is a normal placental microbiome which has any role in colonization of infant gut.
  • Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health

    Mukherjee, Arghya; Lordan, Cathy; Ross, R. Paul; Cotter, Paul D.; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship; Science Foundation Ireland; EU; 15/F/635; 2017047; et al. (Taylor & Francis, 2020-08-23)
    Over the last two decades our understanding of the gut microbiota and its contribution to health and disease has been transformed. Among a new ‘generation’ of potentially beneficial microbes to have been recognized are members of the genus Eubacterium, who form a part of the core human gut microbiome. The genus consists of phylogenetically, and quite frequently phenotypically, diverse species, making Eubacterium a taxonomically unique and challenging genus. Several members of the genus produce butyrate, which plays a critical role in energy homeostasis, colonic motility, immunomodulation and suppression of inflammation in the gut. Eubacterium spp. also carry out bile acid and cholesterol transformations in the gut, thereby contributing to their homeostasis. Gut dysbiosis and a consequently modified representation of Eubacterium spp. in the gut, have been linked with various human disease states. This review provides an overview of Eubacterium species from a phylogenetic perspective, describes how they alter with diet and age and summarizes its association with the human gut and various health conditions.
  • Association of Habitual Dietary Fiber Intake and Fecal Microbiome Gene Abundance with Gastrointestinal Symptoms in an Irritable Bowel Syndrome Cohort

    Roy, Nicole; Heenan, Phoebe; Wall, Catherine; Young, Wayne; Carco, Caterina; Keenan, Jacqueline; Cotter, Paul; Maclean, Paul; Mullaney, Jane; Fraser, Karl; et al. (Oxford University Press (OUP), 2020-05-29)
    Objectives: Dietary fibre supplementation is recognised as important for functional gastrointestinal disorders (FGID). The exact role of the microbiome in this relationship remains unclear. We explored differences in dietary fibre intake, GI symptoms and the fecal microbiome in those with FGID.
  • Marked elevations in pro-inflammatory polyunsaturated fatty acid metabolites in females with irritable bowel syndrome

    Clarke, Gerard; Fitzgerald, Peter; Hennessy, Alan A.; Cassidy, Eugene M.; Quigley M., Eamonn M.; Ross, Paul; STANTON, CATHERINE; Cryan, John F.; Dinan, Timothy G. (Elsevier, 2021-01-04)
    Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder referred to gastroenterologists. Although the pathophysiology remains unclear, accumulating evidence points to the presence of low-level immune activation both in the gut and systemically. Circulating polyunsaturated fatty acids (PUFA) have recently attracted attention as being altered in a variety of disease states. Arachidonic acid (AA), in particular, has been implicated in the development of a pro-inflammatory profile in a number of immune-related disorders. AA is the precursor of a number of important immunomodulatory eicosanoids, including prostaglandin E2 (PGE2) and leukotriene B4 (LTB4). We investigated the hypothesis that elevated plasma AA concentrations in plasma contribute to the proposed pro-inflammatory profile in IBS. Plasma AA and related PUFA were quantified by gas chromatography analysis in IBS patients and controls. Both PGE2 and LTB4 were measured in serum using commercially available ELISA assays. AA concentrations were elevated in our patient cohort compared with healthy controls. Moreover, we demonstrated that this disturbance in plasma AA concentrations leads to downstream elevations in eicosanoids. Together, our data identifies a novel proinflammatory mechanism in irritable bowel syndrome and also suggests that elevated arachidonic acid levels in plasma may serve as putative biological markers in this condition.
  • Comparative genomics and gene-trait matching analysis of Bifidobacterium breve from Chinese children

    Liu, Rui; Yang, Bo; STANTON, CATHERINE; Ross, Paul; Zhao, Jianxin; Zhang, Hao; Chen, Wei; National Natural Science Foundation of China; National First-Class Discipline Program of Food Science and Technology; the Fundamental Research Funds for the Central Universities; et al. (Elsevier BV, 2020-08)
    Bifidobacterium breve is one of the dominant Bifidobacterial species in children. In the current work, 46 strains of B. breve isolated from fecal samples of Chinese children were analyzed using whole-genome sequencing and comparative genomics to explore their genetic diversity, as well as genotype and phenotype analysis for carbohydrate utilization and antibiotic tolerance. The phylogenetic tree was independent of region, age and feeding mode, and without any regularity in the clustering of carbohydrates and antibiotics at the genetic level. Based on genotypic-phenotypic correlation analysis, the diversity of glycosyl hydrolases and the ability of strains to metabolize carbohydrates corroborated the predominance of B. breve in the children's intestines. Simultaneously, the sensitivity of strains to antibiotics increased the understanding of its genetic features and provided a potential basis for safety evaluation.
  • Symposium review: Dairy-derived oligosaccharides—Their influence on host–microbe interactions in the gastrointestinal tract of infants

    Quinn, Erin M.; Joshi, Lokesh; Hickey, Rita M.; Teagasc Walsh Fellowship Programme; 2013059 (Elsevier, 2020-02-20)
    Oligosaccharides are the third most abundant component in human milk. It is widely accepted that they play several important protective, physiological, and biological roles, including selective growth stimulation of beneficial gut microbiota, inhibition of pathogen adhesion, and immune modulation. However, until recently, very few commercial products on the market have capitalized on these functions. This is mainly because the quantities of human milk oligosaccharides required for clinical trials have been unavailable. Recently, clinical studies have tested the potential beneficial effects of feeding infants formula containing 2′-fucosyllactose, which is the most abundant oligosaccharide in human milk. These studies have opened this field for further well-designed studies, which are required to fully understand the role of human milk oligosaccharides. However, one of the most striking features of human milk is its diversity of oligosaccharides, with over 200 identified to date. It may be that a mixture of oligosaccharides is even more beneficial to infants than a single structure. For this reason, the milk of domestic animals has become a focal point in recent years as an alternative source of complex oligosaccharides with associated biological activity. This review will focus specifically on free oligosaccharides found in bovine and caprine milk and the biological roles associated with such structures. These dairy streams are ideal sources of oligosaccharides, given their wide availability and use in so many regularly consumed dairy products. The aim of this review was to provide an overview of research into the functional role of bovine and caprine milk oligosaccharides in host–microbial interactions in the gut and provide current knowledge related to the isolation of oligosaccharides as ingredients for incorporation in functional or medical foods.
  • A Systems-Wide Analysis of Proteolytic and Lipolytic Pathways Uncovers The Flavor-Forming Potential of The Gram-Positive Bacterium Macrococcus caseolyticus subsp. caseolyticus

    Mazhar, Shahneela; Kilcawley, Kieran; Hill, Colin; McAuliffe, Olivia; Teagasc Walsh Fellowship Program; 2015055 (Frontiers Media SA, 2020-07-07)
    Macrococcus caseolyticus subsp. caseolyticus is a Gram-positive, commensal organism documented to be present as a component of the secondary microflora in fermented foods such as Ragusano and Fontina cheeses and Cantonese sausage. In these products, the organism appears to play a role in ripening and the development of the final organoleptic qualities. However, the role of this organism in flavor generation is not well understood. Therefore, the objective of this study was to investigate the role of M. caseolyticus subsp. caseolyticus in flavor compound formation through an examination of enzymatic, metabolomic and genomic data. A bank of M. caseolyticus subsp. caseolyticus strains derived from a variety of niches were examined. Enzyme activities analyzed comprised those of the proteolytic and lipolytic cascades including cell-envelope proteinase (CEP), peptidases, esterases, lipases, aminotransferases and glutamate dehydrogenase (GDH). Strain to strain variation was observed, often associated with niche. All strains, except those isolated from non-dairy sources, demonstrated high CEP activity. Such high CEP activity associated with dairy strains implies the importance of this characteristic in the adaptation of these strains to a dairy-specific niche. However, limited downstream peptidolytic activity, in addition to a limited ability to generate free amino acids (FAA) was observed across all strains, indicating weak ability of this organism to generate amino-acid derived flavor compounds. Interestingly, the strains with high CEP activity also demonstrated high esterase activity and gas chromatography-mass spectrometry (GC-MS) analysis of the volatile compounds produced when these strains were grown in lactose-free milk demonstrated differences in the range and types of volatiles produced. In contrast to this metabolic versatility, comparative genome analysis revealed the distribution of components of the proteolytic and lipolytic system in these strains to be conserved. Overall, this study demonstrates the potential of M. caseolyticus subsp. caseolyticus to generate diverse volatile flavor compounds. Additionally, the identification of the highly active strain-specific cell wall bound caseolytic proteases deriving extensive casein hydrolysis, serves as a promising avenue which can be potentially harnessed in the future to produce greater and more diverse flavor compounds.
  • Lactolisterin BU, a Novel Class II Broad-Spectrum Bacteriocin from Lactococcus lactis subsp. lactis bv. diacetylactis BGBU1-4

    Lozo, Jelena; Mirkovic, Nemanja; O'Connor, Paula M.; Malesevic, Milka; Miljkovic, Marija; Polovic, Natalija; Jovcic, Branko; Cotter, Paul D.; Kojic, Milan; Ministry of Education, Science and Technological Development of the Republic of Serbia; et al. (American Society for Microbiology, 2017-10-17)
    Lactococcus lactis subsp. lactis bv. diacetylactis BGBU1-4 produces a novel bacteriocin, lactolisterin BU, with strong antimicrobial activity against many species of Gram-positive bacteria, including important food spoilage and foodborne pathogens, such as Listeria monocytogenes, Staphylococcus aureus, Bacillus spp., and streptococci. Lactolisterin BU was extracted from the cell surface of BGBU1-4 by 2-propanol and purified to homogeneity by C18 solid-phase extraction and reversed-phase high-performance liquid chromatography. The molecular mass of the purified lactolisterin BU was 5,160.94 Da, and an internal fragment, AVSWAWQH, as determined by N-terminal sequencing, showed low-level similarity to existing antimicrobial peptides. Curing and transformation experiments revealed the presence of a corresponding bacteriocin operon on the smallest plasmid, pBU6 (6.2 kb), of strain BGBU1-4. Analysis of the bacteriocin operon revealed a leaderless bacteriocin of 43 amino acids that exhibited similarity to bacteriocin BHT-B (63%) from Streptococcus ratti, a bacteriocin with analogy to aureocin A.
  • 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.
  • Measuring Protein Content in Food: An Overview of Methods

    Hayes, Maria; Hayes (MDPI AG, 2020-09-23)
    In order to determine the quantity of protein in food, it is important to have standardized analytical methods. Several methods exist that are used in different food industries to quantify protein content, including the Kjeldahl, Lowry, Bradford and total amino acid content methods. The correct determination of the protein content of foods is important as, often, as is the case with milk, it determines the economic value of the food product and it can impact the economic feasibility of new industries for alternative protein production. This editorial provides an overview of different protein determination methods and describes their advantages and disadvantages.
  • Extraction of Protein from Four Different Seaweeds Using Three Different Physical Pre-Treatment Strategies

    O’ Connor, Jack; Meaney, Steve; Williams, Gwilym A.; Hayes, Maria (MDPI AG, 2020-04-24)
    Seaweeds are a rich source of protein and can contain up to 47% on the dry weight basis. It is challenging to extract proteins from the raw biomass of seaweed due to resilient cell-wall complexes. Four species of macroalgae were used in this study-two brown, Fucus vesiculosus and Alaria esculenta, and two red, Palmaria palmata and Chondrus crispus. Three treatments were applied individually to the macroalgal species: (I) high-pressure processing (HPP); (II) laboratory autoclave processing and (III) a classical sonication and salting out method. The protein, ash and lipid contents of the resulting extracts were estimated. Yields of protein recovered ranged from 3.2% for Fucus vesiculosus pre-treated with high pressure processing to 28.9% protein recovered for Chondrus crispus treated with the classical method. The yields of protein recovered using the classical, HPP and autoclave pre-treatments applied to Fucus vesiculosus were 35.1, 23.7% and 24.3%, respectively; yields from Alaria esculenta were 18.2%, 15.0% and 17.1% respectively; yields from Palmaria palmata were 12.5%, 14.9% and 21.5% respectively, and finally, yields from Chondrus crispus were 35.2%, 16.1% and 21.9%, respectively. These results demonstrate that while macroalgal proteins may be extracted using either physical or enzymatic methods, the specific extraction procedure should be tailored to individual species.
  • Fish By-Product Use as Biostimulants: An Overview of the Current State of the Art, Including Relevant Legislation and Regulations within the EU and USA

    Madende, Moses; Hayes, Maria; Bord Iascaigh Mhara; European Maritime Fisheries Fund; 17/SRDP/008 (MDPI AG, 2020-03-03)
    Crop production systems have adopted cost-effective, sustainable and environmentally friendly agricultural practices to improve crop yields and the quality of food derived from plants. Approaches such as genetic selection and the creation of varieties displaying favorable traits such as disease and drought resistance have been used in the past and continue to be used. However, the use of biostimulants to promote plant growth has increasingly gained attention, and the market size for biostimulants is estimated to reach USD 4.14 billion by 2025. Plant biostimulants are products obtained from different inorganic or organic substances and microorganisms that can improve plant growth and productivity and abate the negative effects of abiotic stresses. They include materials such as protein hydrolysates, amino acids, humic substances, seaweed extracts and food or industrial waste-derived compounds. Fish processing waste products have potential applications as plant biostimulants. This review gives an overview of plant biostimulants with a focus on fish protein hydrolysates and legislation governing the use of plant biostimulants in agriculture.
  • Extensive bacteriocin gene shuffling in the Streptococcus bovis/Streptococcus equinus complex reveals gallocin D with activity against vancomycin resistant enterococci

    Hill, Daragh; O’Connor, Paula M.; Altermann, Eric; Day, Li; Hill, Colin; STANTON, CATHERINE; Ross, Paul; Teagasc Walsh Fellowship Programme; Science Foundation Ireland; SFI/12/RC/2273 (Springer Science and Business Media LLC, 2020-08-10)
    Streptococcus gallolyticus LL009 produces gallocin D, a narrow spectrum two component bacteriocin with potent activity against vancomycin-resistant enterococci. Gallocin D is distinct from gallocin A, a separate two component bacteriocin produced by S. gallolyticus. Although the gene clusters encoding gallocin A and gallocin D have a high degree of gene synteny, the structural genes are highly variable and appear to have undergone gene shufing with other streptococcal species. Gallocin D was analysed in laboratory-based experiments. The mature peptides are 3,343± 1 Da and 3,019 ± 1 Da and could be readily synthesized and display activity against a vancomycin resistant Enterococcus strain EC300 with a MIC value of 1.56 µM. Importantly, these bacteriocins could contribute to the ability of S. gallolyticus to colonize the colon where they have been associated with colorectal cancer.
  • Qualitative and Quantitative Analysis of Polyphenols in Lamiaceae Plants—A Review

    Tzima, Katerina; Brunton, Nigel; Rai, Dilip; Teagasc Walsh Fellowship Programme; 2016038 (MDPI AG, 2018-03-26)
    Lamiaceae species are promising potential sources of natural antioxidants, owing to their high polyphenol content. In addition, increasing scientific and epidemiological evidence have associated consumption of foods rich in polyphenols with health benefits such as decreased risk of cardiovascular diseases mediated through anti-inflammatory effects. The complex and diverse nature of polyphenols and the huge variation in their levels in commonly consumed herbs make their analysis challenging. Innovative robust analytical tools are constantly developing to meet these challenges. In this review, we present advances in the state of the art for the identification and quantification of polyphenols in Lamiaceae species. Novel chromatographic techniques that have been employed in the past decades are discussed, ranging from ultra-high-pressure liquid chromatography to hyphenated spectroscopic methods, whereas performance characteristics such as selectivity and specificity are also summarized.
  • Prebiotic administration modulates gut microbiota and faecal short-chain fatty acid concentrations but does not prevent chronic intermittent hypoxia-induced apnoea and hypertension in adult rats

    O'Connor, Karen M.; Lucking, Eric F.; Bastiaanssen, Thomaz F.S.; Peterson, Veronica L.; Crispie, Fiona; Cotter, Paul D.; Clarke, Gerard; Cryan, John F.; O'Halloran, Ken D.; Science Foundation Ireland (Science Direct, 2020-08-30)
    Background Evidence is accruing to suggest that microbiota-gut-brain signalling plays a regulatory role in cardiorespiratory physiology. Chronic intermittent hypoxia (CIH), modelling human sleep apnoea, affects gut microbiota composition and elicits cardiorespiratory morbidity. We investigated if treatment with prebiotics ameliorates cardiorespiratory dysfunction in CIH-exposed rats. Methods Adult male rats were exposed to CIH (96 cycles/day, 6.0% O2 at nadir) for 14 consecutive days with and without prebiotic supplementation (fructo- and galacto-oligosaccharides) beginning two weeks prior to gas exposures. Findings CIH increased apnoea index and caused hypertension. CIH exposure had modest effects on the gut microbiota, decreasing the relative abundance of Lactobacilli species, but had no effect on microbial functional characteristics. Faecal short-chain fatty acid (SCFA) concentrations, plasma and brainstem pro-inflammatory cytokine concentrations and brainstem neurochemistry were unaffected by exposure to CIH. Prebiotic administration modulated gut microbiota composition and diversity, altering gut-metabolic (GMMs) and gut-brain (GBMs) modules and increased faecal acetic and propionic acid concentrations, but did not prevent adverse CIH-induced cardiorespiratory phenotypes. Interpretation CIH-induced cardiorespiratory dysfunction is not dependant upon changes in microbial functional characteristics and decreased faecal SCFA concentrations. Prebiotic-related modulation of microbial function and resultant increases in faecal SCFAs were not sufficient to prevent CIH-induced apnoea and hypertension in our model. Our results do not exclude the potential for microbiota-gut-brain axis involvement in OSA-related cardiorespiratory morbidity, but they demonstrate that in a relatively mild model of CIH, sufficient to evoke classic cardiorespiratory dysfunction, such changes are not obligatory for the development of morbidity, but may become relevant in the elaboration and maintenance of cardiorespiratory morbidity with progressive disease. Funding Department of Physiology and APC Microbiome Ireland, University College Cork, Ireland. APC Microbiome Ireland is funded by Science Foundation Ireland, through the Government's National Development Plan.
  • Microbiota and Neurodevelopmental Trajectories: Role of Maternal and Early-Life Nutrition

    Codagnone, Martin G.; STANTON, CATHERINE; O'Mahony, Siobhain M.; Dinan, Timothy G.; Cryan, John F.; Science Foundation Ireland; European Union; Nestlé Nutrition Institute; 754535; 12/RC/2273 (S. Karger AG, 2019-06-24)
    Pregnancy and early life are characterized by marked changes in body microbial composition. Intriguingly, these changes take place simultaneously with neurodevelopmental plasticity, suggesting a complex dialogue between the microbes that inhabit the gastrointestinal tract and the brain. The purpose of this chapter is to describe the natural trajectory of microbiota during pregnancy and early life, as well as review the literature available on its interaction with neurodevelopment. Several lines of evidence show that the gut microbiota interacts with diet, drugs and stress both prenatally and postnatally. Clinical and preclinical studies are illuminating how these disruptions result in different developmental outcomes. Understanding the role of the microbiota in neurodevelopment may lead to novel approaches to the study of the pathophysiology and treatment of neuropsychiatric disorders.
  • Bioprocessing of brewers’ spent grain for production of Xylanopectinolytic enzymes by Mucor sp.

    Hassan, Shady S.; Tiwari, Brijesh K; Adams, Gwylim A.; Jaiswal, Amit K.; TU Dublin; Science Foundation Ireland; 16/RC/3889 (Elsevier, 2019-12-26)
    The potential of microwave and ultrasound was evaluated for the pretreatment of brewer's spent grain (BSG). Under optimal conditions of microwave and ultrasound pretreatments, reducing sugar yields per 1 g of pretreated BSG were 64.4 ± 7 mg and 39.9 ± 6 mg, respectively. Subsequently, the pretreated BSG was evaluated as a substrate for production of Xylanopectinolytic enzymes using fungi isolated from spoiled fruits. Out of twenty-nine (29) isolates recovered, Mucor sp. (AB1) isolated from Bramley apple (Malus domestica) produced xylanopectinolytic enzymes with higher specific activity, and was selected for further studies. The highest enzyme activity (137 U/g, and 67 U/g BSG, for pectinase and xylanase, respectively) was achieved in a medium that contained 15 g of BSG, at pH 6, temperature of 30 °C, supplemented with 1% xylan or pectin for inducing the production of xylanase or pectinase, respectively. The partially purified xylanopectinolytic enzymes were optimally active at 60 °C and pH 5.
  • 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.
  • Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches

    Wang, Shuo; Yang, Bo; Ross, R. Paul; STANTON, CATHERINE; Zhao, Jianxin; Zhang, Hao; Chen, Wei; National Natural Science Foundation of China; Jiangsu Province; 31771953; et al. (MDPI AG, 2020-01-08)
    Lactobacillus ruminis is a commensal motile lactic acid bacterium living in the intestinal tract of humans and animals. Although a few genomes of L. ruminis were published, most of them were animal derived. To explore the genetic diversity and potential niche-specific adaptation changes of L. ruminis, in the current work, draft genomes of 81 L. ruminis strains isolated from human, bovine, piglet, and other animals were sequenced, and comparative genomic analysis was performed. The genome size and GC content of L. ruminis on average were 2.16 Mb and 43.65%, respectively. Both the origin and the sampling distance of these strains had a great influence on the phylogenetic relationship. For carbohydrate utilization, the human-derived L. ruminis strains had a higher consistency in the utilization of carbon source compared to the animal-derived strains. L. ruminis mainly increased the competitiveness of niches by producing class II bacteriocins. The type of clustered regularly interspaced short palindromic repeats /CRISPR-associated (CRISPR/Cas) system presented in L. ruminis was mainly subtype IIA. The diversity of CRISPR/Cas locus depended on the high denaturation of spacer number and sequence, although cas1 protein was relatively conservative. The genetic differences in those newly sequenced L. ruminis strains highlighted the gene gains and losses attributed to niche adaptations.

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