• Actinomyces Produces Defensin-Like Bacteriocins (Actifensins) with a Highly Degenerate Structure and Broad Antimicrobial Activity

      Sugrue, Ivan; O’Connor, Paula M.; Hill, Colin; Stanton, Catherine; Ross, R. Paul; Teagasc Walsh Fellowship Programme; JPI; Science Foundation Ireland; SFI/12/RC/2273 (American Society for Microbiology, 2020-01-29)
      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.
    • Dietary Supplementation with a Magnesium-Rich Marine Mineral Blend Enhances the Diversity of Gastrointestinal Microbiota

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

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

      Bassett, Shalome A.; Young, Wayne; Fraser, Karl; Dalziel, Julie E.; Webster, Jim; Ryan, Leigh; Fitzgerald, Patrick; Stanton, Catherine; Dinan, Timothy G.; Cryan, John F.; et al. (Springer Science and Business Media LLC, 2019-10-01)
      Stress negatively impacts gut and brain health. Individual diferences in response to stress have been linked to genetic and environmental factors and more recently, a role for the gut microbiota in the regulation of stress-related changes has been demonstrated. However, the mechanisms by which these factors infuence each other are poorly understood, and there are currently no established robust biomarkers of stress susceptibility. To determine the metabolic and microbial signatures underpinning physiological stress responses, we compared stress-sensitive Wistar Kyoto (WKY) rats to the normoanxious Sprague Dawley (SD) strain. Here we report that acute stress-induced strain-specifc changes in brain lipid metabolites were a prominent feature in WKY rats. The relative abundance of Lactococcus correlated with the relative proportions of many brain lipids. In contrast, plasma lipids were signifcantly elevated in response to stress in SD rats, but not in WKY rats. Supporting these fndings, we found that the greatest diference between the SD and WKY microbiomes were the predicted relative abundance of microbial genes involved in lipid and energy metabolism. Our results provide potential insights for developing novel biomarkers of stress vulnerability, some of which appear genotype specifc.
    • Naturally Derived Polyphenols Protect Against Corticosterone-Induced Changes in Primary Cortical Neurons

      Donoso, Francisco; Ramírez, Valerie T; Golubeva, Anna V; Moloney, Gerard M; Stanton, Catherine; Dinan, Timothy G; Cryan, John F; Mead Johnson; Cremo; Suntory Wellness; et al. (Oxford University Press (OUP), 2019-12-08)
      Background: Polyphenols are phytochemicals that have been associated with therapeutic effects in stress-related disorders. Indeed, studies suggest that polyphenols exert significant neuroprotection against multiple neuronal injuries, including oxidative stress and neuroinflammation, but the mechanisms are unclear. Evidence indicates that polyphenol neuroprotection may be mediated by activation of Nrf2, a transcription factor associated with antioxidant and cell survival responses. On the other hand, in stress-linked disorders, Fkbp5 is a novel molecular target for treatment because of its capacity to regulate glucocorticoid receptor sensitivity. However, it is not clear the role Fkbp5 plays in polyphenol-mediated stress modulation. In this study, the neuroprotective effects and mechanisms of the naturally derived polyphenols xanthohumol and quercetin against cytotoxicity induced by corticosterone were investigated in primary cortical cells. Methods: Primary cortical cells containing both neurons and astrocytes were pre-incubated with different concentrations of quercetin and xanthohumol to examine the neuroprotective effects of polyphenols on cell viability, morphology, and gene expression following corticosterone insult. Results: Both polyphenols tested prevented the reduction of cell viability and alterations of neuronal/astrocytic numbers due to corticosterone exposure. Basal levels of Bdnf mRNA were also decreased after corticosterone insult; however, this was reversed by both polyphenol treatments. Interestingly, the Nrf2 inhibitor blocked xanthohumol but not quercetin-mediated neuroprotection. In contrast, we found that Fkbp5 expression is exclusively modulated by quercetin. Conclusions: These results suggest that naturally derived polyphenols protect cortical cells against corticosterone-induced cytotoxicity and enhance cell survival via modulation of the Nrf2 pathway and expression of Fkbp5.
    • Next-generation multiparameter flow cytometry assay improves the assessment of oxidative stress in probiotics

      Fallico, Vincenzo; Rea, Mary; Stanton, Catherine; Ilestam, Niclas; McKinney, Julie; Pfizer Consumer Healthcare (USA) (Elsevier, 2020-04-07)
      Stability of probiotic products’ potency throughout shelf life is essential to ensure systematic delivery of the dosages required to provide clinically-proven health benefits. Due to the oxygen sensitivity of gut-derived microorganisms, methods for the rapid and accurate monitoring of oxidative stress in probiotics are greatly needed as they can be instrumental to both bioprocess optimization and quality control. This study introduces a next-generation flow cytometry method multiplexing the CellROX® Green and Propidium Iodide probes for the simultaneous measurement of free total reactive oxygen species (ROS) and membrane integrity, respectively. The multiparameter method was compared to the single-parameter assays, measuring either ROS or membrane integrity, for the ability to evaluate the fitness of Lactobacillus rhamnosus GG (LGG) after freeze drying, spray drying and H2O2-mediated oxidative stress. Each stand-alone assay detected only three cell populations, showing either differential membrane integrity (Syto 24+/PI-, Syto 24+/PI+, Syto 24-/PI+) or ROS levels (ROS-, low-ROS, high-ROS), and no correlation could be drawn between these groups. Conversely, the multiparameter method detected up to five physiologically distinct cell populations and allowed the integrated assessment of their membrane integrity and oxidative stress. It also revealed a much larger fitness heterogeneity in LGG as each group of low-ROS and high-ROS cells was found to be formed by a healthier population with an intact membrane (L-ROS/PI-, H-ROS/PI-) and a population with damaged membrane (L-ROS/PI+, H-ROS/PI+). As the CRG probe only detects free unreacted ROS, these populations are suggested to reflect the dynamic lifecycle of ROS formation, accumulation and reactive depletion leading to oxidative damage of macromolecules and consequent cell death. With the stand-alone CRG assay being unable to detect ROS lifecycle, the multiparameter method here presented delivers a superior profiling of the heterogeneity generated by oxidative stress in bacteria and enables a more correct interpretation of CRG fluorescence data. We provide recent examples from literature where the use of a single-parameter fluorescence approach may have led to misinterpret oxidative stress data and eventually draw erroneous conclusions.
    • Precision Nutrition and the Microbiome, Part I: Current State of the Science

      Mills, Susan; Stanton, Catherine; Lane, Jonathan; Smith, Graeme; Ross, R. (MDPI AG, 2019-04-24)
      The gut microbiota is a highly complex community which evolves and adapts to its host over a lifetime. It has been described as a virtual organ owing to the myriad of functions it performs, including the production of bioactive metabolites, regulation of immunity, energy homeostasis and protection against pathogens. These activities are dependent on the quantity and quality of the microbiota alongside its metabolic potential, which are dictated by a number of factors, including diet and host genetics. In this regard, the gut microbiome is malleable and varies significantly from host to host. These two features render the gut microbiome a candidate ‘organ’ for the possibility of precision microbiomics—the use of the gut microbiome as a biomarker to predict responsiveness to specific dietary constituents to generate precision diets and interventions for optimal health. With this in mind, this two-part review investigates the current state of the science in terms of the influence of diet and specific dietary components on the gut microbiota and subsequent consequences for health status, along with opportunities to modulate the microbiota for improved health and the potential of the microbiome as a biomarker to predict responsiveness to dietary components. In particular, in Part I, we examine the development of the microbiota from birth and its role in health. We investigate the consequences of poor-quality diet in relation to infection and inflammation and discuss diet-derived microbial metabolites which negatively impact health. We look at the role of diet in shaping the microbiome and the influence of specific dietary components, namely protein, fat and carbohydrates, on gut microbiota composition.
    • Transcriptional control of central carbon metabolic flux in Bifidobacteria by two functionally similar, yet distinct LacI-type regulators

      Lanigan, Noreen; Kelly, Emer; Arzamasov, Aleksandr A.; Stanton, Catherine; Rodionov, Dmitry A.; van Sinderen, Douwe; Science Foundation Ireland; Department of Agriculture, Food and the Marine; Russian Science Foundation; SFI/12/RC/2273-P1; et al. (Springer Science and Business Media LLC, 2019-11-28)
      Bifdobacteria resident in the gastrointestinal tract (GIT) are subject to constantly changing environmental conditions, which require rapid adjustments in gene expression. Here, we show that two predicted LacI-type transcription factors (TFs), designated AraQ and MalR1, are involved in regulating the central, carbohydrate-associated metabolic pathway (the so-called phosphoketolase pathway or bifd shunt) of the gut commensal Bifdobacterium breve UCC2003. These TFs appear to not only control transcription of genes involved in the bifd shunt and each other, but also seem to commonly and directly afect transcription of other TF-encoding genes, as well as genes related to uptake and metabolism of various carbohydrates. This complex and interactive network of AraQ/MalR1-mediated gene regulation provides previously unknown insights into the governance of carbon metabolism in bifdobacteria.