Microbiology - Journal Articles

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16S rRNA gene sequencing of mock microbial populations-impact of DNA extraction method, primer choice and sequencing platform
(BioMed Central, 2016-06-24) Fouhy, Fiona; Clooney, Adam G.; Stanton, Catherine; Claesson, Marcus J.; Cotter, Paul D.; Seventh Framework Programme; Science Foundation Ireland
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.
Ability of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota
(Nature Publishing Group, 2019-04-08) Alessandri, Giulia; Milani, Christian; Duranti, Sabrina; Mancabelli, Leonardo; Ranjanoro, Thibaut; Modica, Salvatore; Carnevali, Luca; Statello, Rosario; Bottacini, Francesca; Turroni, Francesca; Ossiprandi, Maria Cristina; Sgoifo, Andrea; van Sinderen, Douwe; Ventura, Marco; KitoZyme, Belgium; University of Parma, Italy; GenProbio srl
Chitin-glucan (CG) represents a natural carbohydrate source for certain microbial inhabitants of the human gut and may act as a prebiotic for a number of bacterial taxa. However, the bifidogenic activity of this substrate is still unknown. In the current study, we evaluated the ability of chitin-glucan to influence growth of 100 bifidobacterial strains belonging to those species commonly identified within the bifidobacterial communities residing in the infant and adult human gut. Such analyses were coupled with transcriptome experiments directed to explore the transcriptional effects of CG on Bifidobacterium breve 2L, which was shown to elicit the highest growth performance on this natural polysaccharide. In addition, an in vivo trial involving a rat model revealed how the colonization efficiency of this bifidobacterial strain was enhanced when the animals were fed with a diet containing CG. Altogether our analyses indicate that CG is a valuable novel prebiotic compound that may be added to the human diet in order to re-establish/reinforce bifidobacteria colonization in the mammalian gut.
The ability of Listeria monocytogenes to form biofilm on surfaces relevant to the mushroom production environment
(Elsevier, 2019-10-22) Dygico, Lionel Kenneth; Gahan, Cormac G.; Grogan, Helen; Burgess, Catherine M.; Department of Agriculture, Food and the Marine, Ireland; Food Institutional Research Measure
Due to its ubiquitous nature, Listeria monocytogenes is a threat to all fresh fruits and vegetables, including mushrooms, which are Ireland's largest horticultural crop. Although fresh cultivated mushrooms (Agaricus bisporus) have not been previously linked with listeriosis outbreaks, the pathogen still poses a threat to the industry, particularly due to its ability to form biofilms. This threat is highlighted by the multiple recalls of mushroom products caused by L. monocytogenes contamination and by previous studies demonstrating that L. monocytogenes is present in the mushroom production environment. In this study, the biofilm formation potential of L. monocytogenes strains isolated from the mushroom production environment was investigated on materials and at temperatures relevant to mushroom production. A preliminary assessment of biofilm formation of 73 mushroom industry isolates was undertaken using a crystal violet assay on polystyrene microtitre plates. The biofilm formation of a subset (n = 7) of these strains was then assessed on twelve different materials, including materials that are representative of the materials commonly found in the mushroom production environments, using the CDC biofilm reactor. Vertical scanning interferometry was used to determine the surface roughness of the chosen materials. All the strains tested using the CDC biofilm reactor were able to form biofilms on the different surfaces tested but material type was found to be a key determining factor on the levels of biofilm formed. Stainless steel, aluminium, rubber, polypropylene and polycarbonate were all able to support biofilm levels in the range of 4–4.9 log10 CFU/cm2, for seven different L. monocytogenes strains. Mushroom industry-specific materials, including growing nets and tarpaulins, were found to support biofilms levels between 4.7 and 6.7 log10 CFU/cm2. Concrete was found to be of concern as it supported 7.7 log10 CFU/cm2 of biofilm for the same strains; however, sealing the concrete resulted in an approximately 2-log reduction in biofilm levels. The surface roughness of the materials varied greatly between the materials (0.7–3.5 log10 Ra) and was found to have a positive correlation with biofilm formation (rs = 0.573) although marginally significant (P = 0.051). The results of this study indicate that L. monocytogenes can readily form biofilms on mushroom industry relevant surfaces, and additionally identifies surfaces of specific concern, where rigorous cleaning and disinfection is required.
Actinomyces produces defensin-like bacteriocins (Actifensins) with a highly degenerate structure and broad antimicrobial activity
(American Society for Microbiology, 2020-01-29) Sugrue, Ivan; O'Connor, Paula M.; Hill, Colin; Stanton, Catherine; Ross, R. Paul; Teagasc; Science Foundation Ireland; Joint Programming Initiative A healthy diet for a healthy life
We identified a strain of Actinomyces ruminicola which produces a potent bacteriocin with activity against a broad range of Gram-positive bacteria, many of which are pathogenic to animals and humans. The bacteriocin was purified and found to have a mass of 4,091 ± 1 Da with a sequence of GFGCNLITSNPYQCSNHCKSVGYRGGYCKLRTVCTCY containing three disulfide bridges. Surprisingly, near relatives of actifensin were found to be a series of related eukaryotic defensins displaying greater than 50% identity to the bacteriocin. A pangenomic screen further revealed that production of actifensin-related bacteriocins is a common trait within the genus, with 47 being encoded in 161 genomes. Furthermore, these bacteriocins displayed a remarkable level of diversity with a mean amino acid identity of only 52% between strains/species. This level of redundancy suggests that this new class of bacteriocins may provide a very broad structural basis on which to deliver and design new broad-spectrum antimicrobials for treatment of animal and human infections. IMPORTANCE: Bacteriocins (ribosomally produced antimicrobial peptides) are potential alternatives to current antimicrobials given the global challenge of antimicrobial resistance. We identified a novel bacteriocin from Actinomyces ruminicola with no previously characterized antimicrobial activity. Using publicly available genomic data, we found a highly conserved yet divergent family of previously unidentified homologous peptide sequences within the genus Actinomyces with striking similarity to eukaryotic defensins. These actifensins may provide a potent line of antimicrobial defense/offense, and the machinery to produce them could be used for the design of new antimicrobials given the degeneracy that exists naturally in their structure.
Administration of a live culture of Lactococcus lactis DPC 3147 into the bovine mammary gland stimulates the local host immune response, particularly IL-1beta and IL-8 gene expression
(Cambridge University Press, 2009-02) Beecher, Christine; Daly, Mairead; Berry, Donagh P.; Klostermann, Katja; Flynn, James; Meaney, William; Hill, Colin; McCarthy, Tommie V.; Ross, R. Paul; Giblin, Linda; Science Foundation Ireland; Teagasc; Dairy Research Trust, Ireland
Mastitis is one of the most costly diseases to the dairy farming industry. Conventional antibiotic therapy is often unsatisfactory for successful treatment of mastitis and alternative treatments are continually under investigation. We have previously demonstrated, in two separate field trials, that a probiotic culture, Lactococcus lactis DPC 3147, was comparable to antibiotic therapy to treat bovine mastitis. To understand the mode of action of this therapeutic, we looked at the detailed immune response of the host to delivery of this live strain directly into the mammary gland of six healthy dairy cows. All animals elicited signs of udder inflammation 7 h post infusion. At this time, clots were visible in the milk of all animals in the investigation. The most pronounced increase in immune gene expression was observed in Interleukin (IL)-1β and IL-8, with highest expression corresponding to peaks in somatic cell count. Infusion with a live culture of a Lc. lactis leads to a rapid and considerable innate immune response.
Advanced glycation end product intake during pregnancy and offspring allergy outcomes: prospective cohort study
(John Wiley & Sons, Inc., 2021-10-05) Venter, Carina; Pickett, Kaci; Starling, Anne; Maslin, Kate; Smith, Pete K.; Palumbo, Michaela P.; O'Mahony, Liam; Ben Abdallah, Miriam; Dabelea, Dana; National Institutes of Health; National Institute of Diabetes and Digestive and Kidney Diseases
Background: Associations have been shown between concurrent assessment of dietary intake of AGEs and childhood allergic outcomes. We examined the association between maternal AGEs intake and development of offspring asthma, wheeze, atopic dermatitis, allergic rhinitis, and food allergies, and sought to determine whether intake of AGEs was associated with cord sera cytokines/chemokines. Methods: Pregnant women ≥ 16 years were recruited in the Healthy Start study, a prospective pre-birth cohort from Colorado (N =1410). The analysis included 962 dyads with adequate diet (≥2 recalls) and allergy outcome details. AGEs intake was estimated for each mother by matching intakes reported using 24-hour dietary recalls during pregnancy to a reference database of commonly consumed foods’ AGEs values. Child diagnoses of asthma and allergies up to 8 years were obtained from electronic medical records. Cord sera cytokines and chemokines were analyzed in a subset (N = 462) of children. Results: The median [IQR] AGEs intake for the overall sample was 11919 kU/day [8293, 16573]. Unadjusted analysis showed a positive association between maternal AGEs intake in pregnancy and rhinitis up to 8 years of age (HR = 1.03; 95% CI: 1.01, 1.06), but the association was attenuated and no longer significant in adjusted models (HR = 1.01; 95% CI: 0.98, 1.04). Both adjusted and unadjusted models showed no associations between AGEs intake in pregnancy and any of the other outcomes (p>0.05). There were no significant associations between any cytokine or chemokine measured and AGEs intake or any of the outcomes studied (p>0.05). Conclusion: The study showed that maternal AGEs intake was not associated with offspring asthma and allergy outcomes. AGEs exposure during pregnancy may not have the same impact on child development to postnatal exposure.
Advances in the genomics and metabolomics of dairy lactobacilli: A review
(Elsevier Ltd., 2016-08-31) Stefanovic, Ewelina; Fitzgerald, Gerald F.; McAuliffe, Olivia; Teagasc
The Lactobacillus genus represents the largest and most diverse genera of all the lactic acid bacteria (LAB), encompassing species with applications in industrial, biotechnological and medical fields. The increasing number of available Lactobacillus genome sequences has allowed understanding of genetic and metabolic potential of this LAB group. Pangenome and core genome studies are available for numerous species, demonstrating the plasticity of the Lactobacillus genomes and providing the evidence of niche adaptability. Advancements in the application of lactobacilli in the dairy industry lie in exploring the genetic background of their commercially important characteristics, such as flavour development potential or resistance to the phage attack. The integration of available genomic and metabolomic data through the generation of genome scale metabolic models has enabled the development of computational models that predict the behaviour of organisms under specific conditions and present a route to metabolic engineering. Lactobacilli are recognised as potential cell factories, confirmed by the successful production of many compounds. In this review, we discuss the current knowledge of genomics, metabolomics and metabolic engineering of the prevalent Lactobacillus species associated with the production of fermented dairy foods. In-depth understanding of their characteristics opens the possibilities for their future knowledge-based applications.
The aliphatic amidase AmiE is involved in regulation of Pseudomonas aeruginosa virulence
(Nature Publishing Group, 2017-01-24) Clamens, Thomas; Rosay, Thibaut; Crépin, Alexandre; Grandjean, Teddy; Kentache, Takfarinas; Hardouin, Julie; Bortolotti, Perrine; Neidig, Anke; Mooij, Marlies J.; Hillion, Mélanie; Vieillard, Julien; Cosette, Pascal; Overhage, Joerg; O'Gara, Fergal; Bouffartigues, Emeline; Dufour, Alain; Chevalier, Sylvie; Guery, Benoit; Cornelis, Pierre; Feuilloley, Marc G. J.; Lesouhaitier, Olivier; Ministère de l'Education Nationale, de l'Enseignement Superieur et de la Recherche; European Regional Development Fund; Association Vaincre la Mucoviscidose; Ministère des Affaires Étrangères; Karlsruher Institut für Technologie
We have previously shown that the eukaryotic C-type natriuretic peptide hormone (CNP) regulates Pseudomonas aeruginosa virulence and biofilm formation after binding on the AmiC sensor, triggering the amiE transcription. Herein, the involvement of the aliphatic amidase AmiE in P. aeruginosa virulence regulation has been investigated. The proteome analysis of an AmiE over-producing strain (AmiE+) revealed an expression change for 138 proteins, including some that are involved in motility, synthesis of quorum sensing compounds and virulence regulation. We observed that the AmiE+ strain produced less biofilm compared to the wild type, and over-produced rhamnolipids. In the same line, AmiE is involved in P. aeruginosa motilities (swarming and twitching) and production of the quorum sensing molecules N-acyl homoserine lactones and Pseudomonas Quinolone Signal (PQS). We observed that AmiE overproduction reduced levels of HCN and pyocyanin causing a decreased virulence in different hosts (i.e. Dictyostelium discoideum and Caenorhabditis elegans). This phenotype was further confirmed in a mouse model of acute lung infection, in which AmiE overproduction resulted in an almost fully virulence decrease. Taken together, our data suggest that, in addition to its role in bacterial secondary metabolism, AmiE is involved in P. aeruginosa virulence regulation by modulating pilus synthesis and cell-to-cell communication.
Allelic variation of bile salt hydrolase genes in Lactobacillus salivarius does not determine bile resistance levels
(American Society for Microbiology, 2009-09) Fang, Fang; Li, Yin; Bumann, Mario; Raftis, Emma J.; Casey, Pat G.; Cooney, Jakki C.; Walsh, Martin A.; O'Toole, Paul W.; Science Foundation Ireland
Commensal lactobacilli frequently produce bile salt hydrolase (Bsh) enzymes whose roles in intestinal survival are unclear. Twenty-six Lactobacillus salivarius strains from different sources all harbored a bsh1 allele on their respective megaplasmids. This allele was related to the plasmid-borne bsh1 gene of the probiotic strain UCC118. A second locus (bsh2) was found in the chromosomes of two strains that had higher bile resistance levels. Four Bsh1-encoding allele groups were identified, defined by truncations or deletions involving a conserved residue. In vitro analyses showed that this allelic variation was correlated with widely varying bile deconjugation phenotypes. Despite very low activity of the UCC118 Bsh1 enzyme, a mutant lacking this protein had significantly lower bile resistance, both in vitro and during intestinal transit in mice. However, the overall bile resistance phenotype of this and other strains was independent of the bsh1 allele type. Analysis of the L. salivarius transcriptome upon exposure to bile and cholate identified a multiplicity of stress response proteins and putative efflux proteins that appear to broadly compensate for, or mask, the effects of allelic variation of bsh genes. Bsh enzymes with different bile-degrading kinetics, though apparently not the primary determinants of bile resistance in L. salivarius, may have additional biological importance because of varying effects upon bile as a signaling molecule in the host.
AllergoOncology: microbiota in allergy and cancer—A European Academy for Allergy and Clinical Immunology position paper
(Wiley, 2019-06-07) Untersmayr, Eva; Bax, Heather J.; Bergmann, Christoph; Bianchini, Rodolfo; Cozen, Wendy; Gould, Hannah J.; Hartmann, Karin; Josephs, Debra H.; Levi-Schaffer, Francesca; Penichet, Manuel L.; O'Mahony, Liam; Poli, Aurelie; Redegeld, Frank A.; Roth-Walter, Franziska; Turner, Michelle C.; Vangelista, Luca; Karagiannis, Sophia N.; Jensen-Jarolim, Erika; National Institute for Health Research; European Academy of Allergy and Clinical Immunology; Foundation for the National Institutes of Health; Deutsche Forschungsgemeinschaft; Aimwell Charitable Trust and Emailie Gutterman Memorial Endowed Fund; Departament de Salut, Generalitat de Catalunya; IGEM Therapeutics Ltd; Austrian Science Fund; Instytut Biologii Medycznej Polskiej Akademii Nauk; Cancer Research UK; Medical Research Council; Israel Science Foundation; Israel Cancer Association; American Society of Hematology; Breast Cancer Now; Stop Cancer; Israel Ministry of Science, Technology and Space “Personalized Medicine”
The microbiota can play important roles in the development of human immunity and the establishment of immune homeostasis. Lifestyle factors including diet, hygiene, and exposure to viruses or bacteria, and medical interventions with antibiotics or anti-ulcer medications, regulate phylogenetic variability and the quality of cross talk between innate and adaptive immune cells via mucosal and skin epithelia. More recently, microbiota and their composition have been linked to protective effects for health. Imbalance, however, has been linked to immune-related diseases such as allergy and cancer, characterized by impaired, or exaggerated immune tolerance, respectively. In this AllergoOncology position paper, we focus on the increasing evidence defining the microbiota composition as a key determinant of immunity and immune tolerance, linked to the risk for the development of allergic and malignant diseases. We discuss novel insights into the role of microbiota in disease and patient responses to treatments in cancer and in allergy. These may highlight opportunities to improve patient outcomes with medical interventions supported through a restored microbiome.
The altered gut microbiota in adults with cystic fibrosis
(BioMed Central, 2017-03-09) Fouhy, Fiona; Burke, Daniel G.; Harrison, M. J.; Rea, Mary C.; Cotter, Paul D.; O'Sullivan, Orla; Stanton, Catherine; Hill, Colin; Shanahan, Fergus; Plant, Barry J.; Ross, R. Paul; Science Foundation Ireland; Seventh Framework Programme; European Commission
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.
Amniotic fluid C-reactive protein as a predictor of infection in caesarean section: a feasibility study
(Nature Publishing Group, ) Marchocki, Zbigniew; Vinturache, Angela; Collins, Kevin; O'Reilly, Paddy; O'Donoghue, Keelin
This study evaluated the feasibility of maternal C-reactive protein (CRP) in amniotic fluid (AF) as a predictor of post-partum infection in women who undergo emergency or elective caesarean section (CS). AF bacterial culture and levels of hs-CRP in maternal serum and AF were evaluated in Day 0 and three days thereafter (Day 3) in 79 women undergoing CS. Univariate analyses assessed the clinical and demographic characteristics, whereas the ROC curves assessed the feasibility of hs-CRP as marker of inflammation in women who undergo CS. There was no difference in AF, Day 0, and Day 3 serum hs-CRP levels between women with sterile compared to those with bacterial growth in AF. Among women with positive AF cultures, AF and Day 0 serum hs-CRP levels were higher in women who underwent emergency compared to those who had elective CS (p = 0.04, and p = 0.02 respectively). hs-CRP in Day 0 and Day 3 serum but not in AF has a fair predictor value of infection in emergency CS only (AUC 0.767; 95% CI 0.606-0.928, and AUC 0.791; 95% CI 0.645-0.036, respectively). We conclude that AF hs-CRP is not feasible in assessing the risk of post-cesarean inflammation or infection.
Analysis of health benefits conferred by Lactobacillus species from kefir
(MDPI, 2019-06-01) Slattery, Conor; Cotter, Paul D.; O'Toole, Paul W.; Department of Agriculture, Food and the Marine; Science Foundation Ireland; Horizon 2020; Enterprise Ireland
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.
Another brick in the wall: a rhamnan polysaccharide trapped inside peptidoglycan of Lactococcus lactis
(American Society for Microbiology, 2017) Sadovskaya, Irina; Vinogradov, Evgeny; Courtin, Pascal; Armalyte, Julija; Meyrand, Mickael; Giaouris, Efstathios; Palussière, Simon; Furlan, Sylviane; Péchoux, Christine; Ainsworth, Stuart; Mahony, Jennifer; van Sinderen, Douwe; Kulakauskas, Saulius; Guérardel, Yann; Chapot-Chartier, Marie-Pierre; Agence Nationale de la Recherche; Conseil Régional, Île-de-France; Institut National de la Recherche Agronomique; Science Foundation Ireland
Polysaccharides are ubiquitous components of the Gram-positive bacterial cell wall. In Lactococcus lactis, a polysaccharide pellicle (PSP) forms a layer at the cell surface. The PSP structure varies among lactococcal strains; in L. lactis MG1363, the PSP is composed of repeating hexasaccharide phosphate units. Here, we report the presence of an additional neutral polysaccharide in L. lactis MG1363 that is a rhamnan composed of α-L-Rha trisaccharide repeating units. This rhamnan is still present in mutants devoid of the PSP, indicating that its synthesis can occur independently of PSP synthesis. High-resolution magic-angle spinning nuclear magnetic resonance (HR-MAS NMR) analysis of whole bacterial cells identified a PSP at the surface of wild-type cells. In contrast, rhamnan was detected only at the surface of PSP-negative mutant cells, indicating that rhamnan is located underneath the surface-exposed PSP and is trapped inside peptidoglycan. The genetic determinants of rhamnan biosynthesis appear to be within the same genetic locus that encodes the PSP biosynthetic machinery, except the gene tagO encoding the initiating glycosyltransferase. We present a model of rhamnan biosynthesis based on an ABC transporter-dependent pathway. Conditional mutants producing reduced amounts of rhamnan exhibit strong morphological defects and impaired division, indicating that rhamnan is essential for normal growth and division. Finally, a mutation leading to reduced expression of lcpA, encoding a protein of the LytR-CpsA-Psr (LCP) family, was shown to severely affect cell wall structure. In lcpA mutant cells, in contrast to wild-type cells, rhamnan was detected by HR-MAS NMR, suggesting that LcpA participates in the attachment of rhamnan to peptidoglycan.
Antibiotic susceptibility profiles of dairy Leuconostoc, analysis of the genetic basis of atypical resistances and transfer of genes in vitro and in a food matrix
(Public Library of Science, 2016-01-04) Flórez, Ana Belén; Campedelli, Ilenia; Delgado, Susana; Alegría, Ángel; Salvetti, Elisa; Felis, Giovanna E.; Mayo, Baltasar; Torriani, Sandra
In spite of a global concern on the transfer of antibiotic resistances (AR) via the food chain, limited information exists on this issue in species of Leuconostoc and Weissella, adjunct cultures used as aroma producers in fermented foods. In this work, the minimum inhibitory concentration was determined for 16 antibiotics in 34 strains of dairy origin, belonging to Leuconostoc mesenteroides (18), Leuconostoc citreum (11), Leuconostoc lactis (2), Weissella hellenica (2), and Leuconostoc carnosum (1). Atypical resistances were found for kanamycin (17 strains), tetracycline and chloramphenicol (two strains each), and erythromycin, clindamycin, virginiamycin, ciprofloxacin, and rifampicin (one strain each). Surprisingly, L. mesenteroides subsp. mesenteroides LbE16, showed resistance to four antibiotics, kanamycin, streptomycin, tetracycline and virginiamycin. PCR analysis identified tet(S) as responsible for tetracycline resistance in LbE16, but no gene was detected in a second tetracycline-resistant strain, L. mesenteroides subsp. cremoris LbT16. In Leuconostoc mesenteroides subsp. dextranicum LbE15, erythromycin and clindamycin resistant, an erm(B) gene was amplified. Hybridization experiments proved erm(B) and tet(S) to be associated to a plasmid of ≈35 kbp and to the chromosome of LbE15 and LbE16, respectively. The complete genome sequence of LbE15 and LbE16 was used to get further insights on the makeup and genetic organization of AR genes. Genome analysis confirmed the presence and location of erm(B) and tet(S), but genes providing tetracycline resistance in LbT16 were again not identified. In the genome of the multi-resistant strain LbE16, genes that might be involved in aminoglycoside (aadE, aphA-3, sat4) and virginiamycin [vat(E)] resistance were further found. The erm(B) gene but not tet(S) was transferred from Leuconostoc to Enterococcus faecalis both under laboratory conditions and in cheese. This study contributes to the characterization of AR in the Leuconostoc-Weissella group, provides evidence of the genetic basis of atypical resistances, and demonstrates the inter-species transfer of erythromycin resistance.
Antimicrobials for food and feed; a bacteriocin perspective
(Elsevier Ltd., 2020-01-20) O'Connor, Paula M.; Kuniyoshi, Taís M.; Oliveira, Ricardo P. S.; Hill, Colin; Ross, R. Paul; Cotter, Paul D.; Science Foundation Ireland; Fundação de Amparo à Pesquisa do Estado de São Paulo
Bacteriocins are natural antimicrobials that have been consumed via fermented foods for millennia and have been the focus of renewed efforts to identify novel bacteriocins, and their producing microorganisms, for use as food biopreservatives and other applications. Bioengineering bacteriocins or combining bacteriocins with multiple modes of action (hurdle approach) can enhance their preservative effect and reduces the incidence of antimicrobial resistance. In addition to their role as food biopreservatives, bacteriocins are gaining credibility as health modulators, due to their ability to regulate the gut microbiota, which is strongly associated with human wellbeing. Indeed the strengthening link between the gut microbiota and obesity make bacteriocins ideal alternatives to Animal Growth Promoters (AGP) in animal feed also. Here we review recent advances in bacteriocin research that will contribute to the development of functional foods and feeds as a consequence of roles in food biopreservation and human/animal health.
Antitumour responses induced by a cell-based Reovirus vaccine in murine lung and melanoma models
(BioMed Central, 2016-07-13) Campion, Ciorsdan A.; Soden, Declan; Forde, Patrick F.; Breakthrough Cancer Research, Ireland; Cork Cancer Research Centre
Background: The ever increasing knowledge in the areas of cell biology, the immune system and the mechanisms of cancer are allowing a new phase of immunotherapy to develop. The aim of cancer vaccination is to activate the host immune system and some success has been observed particularly in the use of the BCG vaccine for bladder cancer as an immunostimulant. Reovirus, an orphan virus, has proven itself as an oncolytic virus in vitro and in vivo. Over 80 % of tumour cell lines have been found to be susceptible to Reovirus infection and it is currently in phase III clinical trials. It has been shown to induce immune responses to tumours with very low toxicities. Methods: In this study, Reovirus was examined in two main approaches in vivo, in mice, using the melanoma B16F10 and Lewis Lung Carcinoma (LLC) models. Initially, mice were treated intratumourally (IT) with Reovirus and the immune responses determined by cytokine analysis. Mice were also vaccinated using a cell-based Reovirus vaccine and subsequently exposed to a tumourigenic dose of cells (B16F10 or LLC). Using the same cell-based Reovirus vaccine, established tumours were treated and subsequent immune responses and virus retrieval investigated. Results: Upregulation of several cytokines was observed following treatment and replication-competent virus was also retrieved from treated tumours. Varying levels of cytokine upregulation were observed and no replication-competent virus was retrieved in vaccine-treated mice. Prolongation of survival and delayed tumour growth were observed in all models and an immune response to Reovirus, either using Reovirus alone or a cell-based vaccine was also observed in all mice. Conclusion: This study provides evidence of immune response to tumours using a cell-based Reovirus vaccine in both tumour models investigated, B16F10 and LLC, cytokine induction was observed with prolongation of survival in almost all cases which may suggest a new method for using Reovirus in the clinic.
Archaea appear to dominate the microbiome of Inflatella pellicula deep sea sponges
(Public Library of Science, 2013) Jackson, Stephen A.; Flemer, Burkhardt; McCann, Angela; Kennedy, Jonathan; Morrissey, John P.; O'Gara, Fergal; Dobson, Alan D. W.; Department of Agriculture, Fisheries and Food, Ireland; Marine Institute
Microbes associated with marine sponges play significant roles in host physiology. Remarkable levels of microbial diversity have been observed in sponges worldwide through both culture-dependent and culture-independent studies. Most studies have focused on the structure of the bacterial communities in sponges and have involved sponges sampled from shallow waters. Here, we used pyrosequencing of 16S rRNA genes to compare the bacterial and archaeal communities associated with two individuals of the marine sponge Inflatella pellicula from the deep-sea, sampled from a depth of 2,900 m, a depth which far exceeds any previous sequence-based report of sponge-associated microbial communities. Sponge-microbial communities were also compared to the microbial community in the surrounding seawater. Sponge-associated microbial communities were dominated by archaeal sequencing reads with a single archaeal OTU, comprising similar to ∼60% and similar to ∼72% of sequences, being observed from Inflatella pellicula. Archaeal sequencing reads were less abundant in seawater (similar to ∼11% of sequences). Sponge-associated microbial communities were less diverse and less even than any other sponge-microbial community investigated to date with just 210 and 273 OTUs (97% sequence identity) identified in sponges, with 4 and 6 dominant OTUs comprising similar to ∼88% and similar to ∼89% of sequences, respectively. Members of the candidate phyla, SAR406, NC10 and ZB3 are reported here from sponges for the first time, increasing the number of bacterial phyla or candidate divisions associated with sponges to 43. A minor cohort from both sponge samples (similar to ∼0.2% and similar to ∼0.3% of sequences) were not classified to phylum level. A single OTU, common to both sponge individuals, dominates these unclassified reads and shares sequence homology with a sponge associated clone which itself has no known close relative and may represent a novel taxon.
Archaebiotics: archaea as pharmabiotics for treating chronic disease in humans?
(InTech, 2017) Ben Hania, Wajdi; Ballet, Nathalie; Vandeckerkove, Pascal; Ollivier, Bernard; O'Toole, Paul W.; Brugère, Jean-François
Recent findings highlight the role of the human gut microbiota in various disorders. For example, atherosclerosis frequently seems to be the consequence of gut microbiota–derived metabolism of some dietary components. Pharmabiotics (i.e., live/dead microbes and microbe-derived substances) and probiotics (live microorganisms with a health benefit when administered in adequate amounts) are a means to counteract these deleterious effects. Among the latter, microbes now being used or, being currently developed, are bacteria and eukaryotes (yeasts), so omitting the third domain of life—the archaea, despite their unique properties that could be of great interest to human health. Here, we promote the idea that some specific archaea are potential next-generation probiotics. This is based on an innovative example of the bioremediation of a gut microbial metabolite. Indeed, besides the fact that they are archaea (i.e. originating from a domain of life from which no pathogens of humans/animals/plants are currently known), they are rationally selected based on (i) being naturally human-hosted, (ii) having a unique metabolism not performed by other human gut microbes, (iii) depleting a deleterious atherogenic compound generated by the human gut microbiota and (iv) generating a health inert gas.
Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol
(Public Library of Science, 2013) Milani, Christian; Hevia, Arancha; Foroni, Elena; Duranti, Sabrina; Turroni, Francesca; Lugli, Gabriele A.; Sanchez, Borja; Martin, Rebeca; Gueimonde, Miguel; van Sinderen, Douwe; Margolles, Abelardo; Ventura, Marco; GenProbio srl, Italy; Fondazione Cariparma, Italy; Federation of European Microbiological Societies; Irish Research Council for Science Engineering and Technology; Regione Emilia Romagna, Italy; Science Foundation Ireland; Irish Government; Ministerio de Economía y Competitividad, Spain
Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of novel high-throughput DNA sequencing technologies, like the Ion Torrent. However, the precise representation of this bacterial community may be affected by the protocols used for DNA extraction as well as by the PCR primers employed in the amplification reaction. Here, we describe an optimized protocol for 16S rRNA gene-based profiling of the fecal microbiota.

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