• Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort.

      Hill, Cian J; Lynch, Denise B; Murphy, Kiera; Ulaszewska, Marynka; Jeffery, Ian B; O'Shea, Carol Anne; Watkins, Claire; Dempsey, Eugene; Mattivi, Fulvio; Tuohy, Kieran; et al. (2017-01-17)
      The gut is the most extensively studied niche of the human microbiome. The aim of this study was to characterise the initial gut microbiota development of a cohort of breastfed infants (n = 192) from 1 to 24 weeks of age.
    • Modulation of pathogen-induced CCL20 secretion from HT-29 human intestinal epithelial cells by commensal bacteria.

      Sibartie, Shomik; O'Hara, Ann M; Ryan, Jude; Fanning, Aine; O'Mahony, Jim; O'Neill, Shaun; Sheil, Barbara; O'Mahony, Liam; Shanahan, Fergus; Alimentary Pharmabiotic Centre, University College Cork, National University of Ireland, Cork, Ireland. shomiksibartie@gmail.com (2009)
      BACKGROUND: Human intestinal epithelial cells (IECs) secrete the chemokine CCL20 in response to infection by various enteropathogenic bacteria or exposure to bacterial flagellin. CCL20 recruits immature dendritic cells and lymphocytes to target sites. Here we investigated IEC responses to various pathogenic and commensal bacteria as well as the modulatory effects of commensal bacteria on pathogen-induced CCL20 secretion. HT-29 human IECs were incubated with commensal bacteria (Bifidobacterium infantis or Lactobacillus salivarius), or with Salmonella typhimurium, its flagellin, Clostridium difficile, Mycobacterium paratuberculosis, or Mycobacterium smegmatis for varying times. In some studies, HT-29 cells were pre-treated with a commensal strain for 2 hr prior to infection or flagellin stimulation. CCL20 and interleukin (IL)-8 secretion and nuclear factor (NF)-kappaB activation were measured using enzyme-linked immunosorbent assays. RESULTS: Compared to untreated cells, S. typhimurium, C. difficile, M. paratuberculosis, and flagellin activated NF-kappaB and stimulated significant secretion of CCL20 and IL-8 by HT-29 cells. Conversely, B. infantis, L. salivarius or M. smegmatis did not activate NF-kappaB or augment CCL20 or IL-8 production. Treatment with B. infantis, but not L. salivarius, dose-dependently inhibited the baseline secretion of CCL20. In cells pre-treated with B. infantis, C. difficile-, S. typhimurium-, and flagellin-induced CCL20 were significantly attenuated. B. infantis did not limit M. Paratuberculosis-induced CCL20 secretion. CONCLUSION: This study is the first to demonstrate that a commensal strain can attenuate CCL20 secretion in HT-29 IECs. Collectively, the data indicate that M. paratuberculosis may mediate mucosal damage and that B. infantis can exert immunomodulatory effects on IECs that mediate host responses to flagellin and flagellated enteric pathogens.
    • Plant-associated bacterial degradation of toxic organic compounds in soil.

      McGuinness, Martina; Dowling, David; Department of Science and Health, Institute of Technology Carlow, Kilkenny Road, Carlow, Ireland. Martina.McGuinness@itcarlow.ie (2009-08)
      A number of toxic synthetic organic compounds can contaminate environmental soil through either local (e.g., industrial) or diffuse (e.g., agricultural) contamination. Increased levels of these toxic organic compounds in the environment have been associated with human health risks including cancer. Plant-associated bacteria, such as endophytic bacteria (non-pathogenic bacteria that occur naturally in plants) and rhizospheric bacteria (bacteria that live on and near the roots of plants), have been shown to contribute to biodegradation of toxic organic compounds in contaminated soil and could have potential for improving phytoremediation. Endophytic and rhizospheric bacterial degradation of toxic organic compounds (either naturally occurring or genetically enhanced) in contaminated soil in the environment could have positive implications for human health worldwide and is the subject of this review.
    • Skin microbiome before development of atopic dermatitis: Early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year.

      Kennedy, Elizabeth A; Connolly, Jennifer; Hourihane, Jonathan O'B; Fallon, Padraic G; McLean, W H Irwin; Murray, Deirdre; Jo, Jay-Hyun; Segre, Julia A; Kong, Heidi H; Irvine, Alan D (Journal of Allergy and Clinical Immunology, 2017-01)
      Disease flares of established atopic dermatitis (AD) are generally associated with a low-diversity skin microbiota and Staphylococcus aureus dominance. The temporal transition of the skin microbiome between early infancy and the dysbiosis of established AD is unknown.
    • Toward the use of genomics to study microevolutionary change in bacteria.

      Falush, Daniel; Department of Microbiology, University College Cork, Environmental Research Institute, Lee Road, Cork, Ireland. d.falush@ucc.ie (2009-10)
      Bacteria evolve rapidly in response to the environment they encounter. Some environmental changes are experienced numerous times by bacteria from the same population, providing an opportunity to dissect the genetic basis of adaptive evolution. Here I discuss two examples in which the patterns of rapid change provide insight into medically important bacterial phenotypes, namely immune escape by Neisseria meningitidis and host specificity of Campylobacter jejuni. Genomic analysis of populations of bacteria from these species holds great promise but requires appropriate concepts and statistical tools.