APC Microbiome Ireland - 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.
Acute early-life stress results in premature emergence of adult-like fear retention and extinction relapse in infant rats
(American Psychological Association, 2013-10) Cowan, Caitlin S. M.; Callaghan, Bridget L.; Richardson, Rick; Australian Research Council; Petre Foundation; University of New South Wales
Recent studies have shown that chronic early life stress results in precocious expression of the adult-like phenotype of fear retention and inhibition. However, it is unknown whether the experience of acute early trauma has the same effects as exposure to chronic early stress. In the present study, a 24-hr period of maternal deprivation on postnatal day (P) 9 was used as an acute early life stressor. In infancy (P16-17), maternally deprived and standard-reared rats were conditioned to fear a noise paired with shock. In Experiments 1 and 2, fear to the noise was then extinguished before rats were tested for context-mediated fear renewal or stress-induced fear reinstatement. In Experiments 3a and 3b, conditioned rats were tested for fear retention 1, 7, or 14 days after training. Whereas standard-reared infants exhibited relapse-resistant extinction and infantile amnesia (i.e., behaviors typical of their age), maternally deprived infants exhibited the renewal and reinstatement effects (i.e., relapse-prone extinction) and showed good retention of fear over the 7- and 14-day intervals (i.e., infantile amnesia was reduced). In other words, similar to rats exposed to chronic early life stress, rats exposed to acute early stress expressed an adult-like profile of fear retention and inhibition during infancy. These findings suggest that similar mechanisms might be involved in the effects of acute and chronic stress on emotional development, and may have implications for our understanding and treatment of emotional disorders associated with early adversity.
Acute stress increases monocyte levels and modulates receptor expression in healthy females
(Elsevier, 2021-05) van de Wouw, Marcel; Sichetti, Marzia; Long-Smith, Caitriona M.; Ritz, Nathaniel L.; Moloney, Gerard M.; Cusack, Anne-Marie; Berding, Kirsten; Dinan, Timothy G.; Cryan, John F.; Seventh Framework Programme; Science Foundation Ireland
There has been a growing recognition of the involvement of the immune system in stress-related disorders. Acute stress leads to the activation of neuroendocrine systems, which in turn orchestrate a large-scale redistribution of innate immune cells, such as monocytes. Even though acute stress/monocyte interactions have been wellcharacterized in mice, this is not the case for humans. As such, this study aimed to investigate whether acute stress modulates blood monocyte levels in a subtype-dependent manner and whether the receptor expression of stress-related receptors is affected in humans. Blood was collected from healthy female volunteers at baseline and 1 h after the socially evaluated cold pressor test, after which blood monocyte levels and receptor expression were assessed by flow cytometry. Our results reveal a stress-induced increase in blood monocyte levels, which was independent of monocyte subtypes. Furthermore, colony stimulating factor 1 receptor (CSF-1R) and CD29 receptor expression was increased, while CD62L showed a trend towards increased expression. These results provide novel insights into how acute stress affects the innate immune system.
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.
Adult microbiota-deficient mice have distinct dendritic morphological changes: Differential effects in the amygdala and hippocampus
(Wiley, 2016-10-31) Luczynski, Pauline; Whelan, Seán O.; O'Sullivan, Colette; Clarke, Gerard; Shanahan, Fergus; Dinan, Timothy G.; Cryan, John F.; Science Foundation Ireland; Health Research Board; European Commission; GlaxoSmithKline; Pfizer; Wyeth; Mead Johnson Nutrition; National Alliance for Research on Schizophrenia and Depression; Brain and Behavior Research Foundation; Irish Government's National Development Plan
Increasing evidence implicates the microbiota in the regulation of brain and behaviour. Germ‐free mice (GF; microbiota deficient from birth) exhibit altered stress hormone signalling and anxiety‐like behaviours as well as deficits in social cognition. Although the mechanisms underlying the ability of the gut microbiota to influence stress responsivity and behaviour remain unknown, many lines of evidence point to the amygdala and hippocampus as likely targets. Thus, the aim of this study was to determine if the volume and dendritic morphology of the amygdala and hippocampus differ in GF versus conventionally colonized (CC) mice. Volumetric estimates revealed significant amygdalar and hippocampal expansion in GF compared to CC mice. We also studied the effect of GF status on the level of single neurons in the basolateral amygdala (BLA) and ventral hippocampus. In the BLA, the aspiny interneurons and pyramidal neurons of GF mice exhibited dendritic hypertrophy. The BLA pyramidal neurons of GF mice had more thin, stubby and mushroom spines. In contrast, the ventral hippocampal pyramidal neurons of GF mice were shorter, less branched and had less stubby and mushroom spines. When compared to controls, dentate granule cells of GF mice were less branched but did not differ in spine density. These findings suggest that the microbiota is required for the normal gross morphology and ultrastructure of the amygdala and hippocampus and that this neural remodelling may contribute to the maladaptive stress responsivity and behavioural profile observed in GF mice.
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 design of (nano)formulations for delivery of antisense oligonucleotides and small interfering RNA: Focus on the central nervous system
(American Chemical Society, 2021-03-18) Mendonça, Monique C. P.; Kont, Ayse; Aburto, Maria Rodriguez; Cryan, John F.; O'Driscoll, Caitríona M.; Science Foundation Ireland; European Regional Development Fund
RNA-based therapeutics have emerged as one of the most powerful therapeutic options used for the modulation of gene/protein expression and gene editing with the potential to treat neurodegenerative diseases. However, the delivery of nucleic acids to the central nervous system (CNS), in particular by the systemic route, remains a major hurdle. This review will focus on the strategies for systemic delivery of therapeutic nucleic acids designed to overcome these barriers. Pathways and mechanisms of transport across the blood-brain barrier which could be exploited for delivery are described, focusing in particular on smaller nucleic acids including antisense oligonucleotides (ASOs) and small interfering RNA (siRNA). Approaches used to enhance delivery including chemical modifications, nanocarrier systems, and target selection (cell-specific delivery) are critically analyzed. Learnings achieved from a comparison of the successes and failures reported for CNS delivery of ASOs versus siRNA will help identify opportunities for a wider range of nucleic acids and accelerate the clinical translation of these innovative therapies.
Age-associated deficits in social behaviour are microbiota-dependent
(Elsevier, 2023) Cruz-Pereira, Joana S.; Moloney, Gerard M.; Bastiaanssen, Thomaz F. S.; Boscaini, Serena; Fitzgerald, Patrick; Clarke, Gerard; Cryan, John F.; Science Foundation Ireland; Saks-Kavanaugh Foundation; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
Aging is associated with remodelling of immune and central nervous system responses resulting in behavioural impairments including social deficits. Growing evidence suggests that the gut microbiome is also impacted by aging, and we propose that strategies to reshape the aged gut microbiome may ameliorate some age-related effects on host physiology. Thus, we assessed the impact of gut microbiota depletion, using an antibiotic cocktail, on aging and its impact on social behavior and the immune system. Indeed, microbiota depletion in aged mice eliminated the age-dependent deficits in social recognition. We further demonstrate that although age and gut microbiota depletion differently shape the peripheral immune response, aging induces an accumulation of T cells in the choroid plexus, that is partially blunted following microbiota depletion. Moreover, an untargeted metabolomic analysis revealed age-dependent alterations of cecal metabolites that are reshaped by gut microbiota depletion. Together, our results suggest that the aged gut microbiota can be specifically targeted to affect social deficits. These studies propel the need for future investigations of other non-antibiotic microbiota targeted interventions on age-related social deficits both in animal models and humans.
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.
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.
Annual Research Review: Critical windows – the microbiota–gut–brain axis in neurocognitive development
(Wiley, 2019-11-26) Cowan, Caitlin S. M.; Dinan, Timothy G.; Cryan, John F.; Science Foundation Ireland; Horizon 2020
The gut microbiota is a vast, complex, and fascinating ecosystem of microorganisms that resides in the human gastrointestinal tract. As an integral part of the microbiota–gut–brain axis, it is now being recognized that the microbiota is a modulator of brain and behavior, across species. Intriguingly, periods of change in the microbiota coincide with the development of other body systems and particularly the brain. We hypothesize that these times of parallel development are biologically relevant, corresponding to ‘sensitive periods’ or ‘critical windows’ in the development of the microbiota–gut–brain axis. Specifically, signals from the microbiota during these periods are hypothesized to be crucial for establishing appropriate communication along the axis throughout the life span. In other words, the microbiota is hypothesized to act like an expected input to calibrate the development of the microbiota–gut–brain axis. The absence or disruption of the microbiota during specific developmental windows would therefore be expected to have a disproportionate effect on specific functions or potentially for regulation of the system as a whole. Evidence for microbial modulation of neurocognitive development and neurodevelopmental risk is discussed in light of this hypothesis, finishing with a focus on the challenges that lay ahead for the future study of the microbiota–gut–brain axis during development.
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.
Anti-yeast activity and characterisation of synthetic radish peptides Rs-AFP1 and Rs-AFP2 against food spoilage yeast: Synthetic radish peptides against food spoilage yeast
(Elsevier Ltd., 2020-02-22) Shwaiki, Laila N.; Arendt, Elke K.; Lynch, Kieran M.; Department of Agriculture, Food and the Marine, Ireland
Food spoilage resulting from the presence of yeast is a common problem in the food industry. The development of natural food preservatives is a growing area of interest for the food industry. The application of antimicrobial peptides derived from plants can be a simple and natural method of preserving food. This study looked at the antiyeast activity of two chemically synthesised radish antimicrobial peptides, Rs-AFP1 and Rs-AFP2, for their inhibitory effect against different yeast species. The minimum inhibitory concentration (MIC) of both peptides was generated. Two mechanisms of action were studied (membrane permeabilisation and the overproduction of reactive oxygen species (ROS)) and both were found to occur with Rs-AFP2, while only the overproduction of ROS was detected for Rs-AFP1. The effect of the peptides on the yeast cells was also visualised by scanning electron microscopy. Their safety in terms of human consumption was studied and no adverse effects were found. Lastly, the stability of the peptides in different conditions, such as high salt, heat and a range of pH were studied in addition to their antiyeast activity in different food matrices such as soft drink, fruit juices and salad dressing, further supporting the peptides' potential for use in food preservation.
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.
Antibiotic treatment-induced dysbiosis differently affects BDNF and TrkB expression in the brain and in the gut of juvenile mice
(PLoS, 2019-02-22) Bistoletti, Michela; Caputi, Valentina; Baranzini, Nicolò; Marchesi, Nicoletta; Filpa, Viviana; Marsilio, Ilaria; Cerantola, Silvia; Terova, Genciana; Baj, Andreina; Grimaldi, Annalisa; Pascale, Alessia; Frigo, Gianmario; Crema, Francesca; Giron, Maria Cecilia; Giaroni, Cristina; Università degli Studi dell'Insubria; Università degli Studi di Pavia; Università degli Studi di Padova
Antibiotic use during adolescence may result in dysbiosis-induced neuronal vulnerability both in the enteric nervous system (ENS) and central nervous system (CNS) contributing to the onset of chronic gastrointestinal disorders, such as irritable bowel syndrome (IBS), showing significant psychiatric comorbidity. Intestinal microbiota alterations during adolescence influence the expression of molecular factors involved in neuronal development in both the ENS and CNS. In this study, we have evaluated the expression of brain-derived neurotrophic factor (BDNF) and its high-affinity receptor tropomyosin-related kinase B (TrkB) in juvenile mice ENS and CNS, after a 2-week antibiotic (ABX) treatment. In both mucosa and mucosa-deprived whole-wall small intestine segments of ABX-treated animals, BDNF and TrKB mRNA and protein levels significantly increased. In longitudinal muscle-myenteric plexus preparations of ABX-treated mice the percentage of myenteric neurons staining for BDNF and TrkB was significantly higher than in controls. After ABX treatment, a consistent population of BDNF- and TrkB-immunoreactive neurons costained with SP and CGRP, suggesting up-regulation of BDNF signaling in both motor and sensory myenteric neurons. BDNF and TrkB protein levels were downregulated in the hippocampus and remained unchanged in the prefrontal cortex of ABX-treated animals. Immunostaining for BDNF and TrkB decreased in the hippocampus CA3 and dentate gyrus subregions, respectively, and remained unchanged in the prefrontal cortex. These data suggest that dysbiosis differentially influences the expression of BDNF-TrkB in the juvenile mice ENS and CNS. Such changes may potentially contribute later to the development of functional gut disorders, such as IBS, showing psychiatric comorbidity.

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