Showing papers by "Fergus Shanahan published in 2011"

Composition, variability, and temporal stability of the intestinal microbiota of the elderly

Abstract: Alterations in the human intestinal microbiota are linked to conditions including inflammatory bowel disease, irritable bowel syndrome, and obesity. The microbiota also undergoes substantial changes at the extremes of life, in infants and older people, the ramifications of which are still being explored. We applied pyrosequencing of over 40,000 16S rRNA gene V4 region amplicons per subject to characterize the fecal microbiota in 161 subjects aged 65 y and older and 9 younger control subjects. The microbiota of each individual subject constituted a unique profile that was separable from all others. In 68% of the individuals, the microbiota was dominated by phylum Bacteroides, with an average proportion of 57% across all 161 baseline samples. Phylum Firmicutes had an average proportion of 40%. The proportions of some phyla and genera associated with disease or health also varied dramatically, including Proteobacteria, Actinobacteria, and Faecalibacteria. The core microbiota of elderly subjects was distinct from that previously established for younger adults, with a greater proportion of Bacteroides spp. and distinct abundance patterns of Clostridium groups. Analyses of 26 fecal microbiota datasets from 3-month follow-up samples indicated that in 85% of the subjects, the microbiota composition was more like the corresponding time-0 sample than any other dataset. We conclude that the fecal microbiota of the elderly shows temporal stability over limited time in the majority of subjects but is characterized by unusual phylum proportions and extreme variability.

Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor

Abstract: Development of the human gut microbiota commences at birth, with bifidobacteria being among the first colonizers of the sterile newborn gastrointestinal tract. To date, the genetic basis of Bifidobacterium colonization and persistence remains poorly understood. Transcriptome analysis of the Bifidobacterium breve UCC2003 2.42-Mb genome in a murine colonization model revealed differential expression of a type IVb tight adherence (Tad) pilus-encoding gene cluster designated "tad(2003)." Mutational analysis demonstrated that the tad(2003) gene cluster is essential for efficient in vivo murine gut colonization, and immunogold transmission electron microscopy confirmed the presence of Tad pili at the poles of B. breve UCC2003 cells. Conservation of the Tad pilus-encoding locus among other B. breve strains and among sequenced Bifidobacterium genomes supports the notion of a ubiquitous pili-mediated host colonization and persistence mechanism for bifidobacteria.

Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon

Abstract: Vancomycin, metronidazole, and the bacteriocin lacticin 3147 are active against a wide range of bacterial species, including Clostridium difficile. We demonstrate that, in a human distal colon model, the addition of each of the three antimicrobials resulted in a significant decrease in numbers of C. difficile. However, their therapeutic use in the gastrointestinal tract may be compromised by their broad spectrum of activity, which would be expected to significantly impact on other members of the human gut microbiota. We used high-throughput pyrosequencing to compare the effect of each antimicrobial on the composition of the microbiota. All three treatments resulted in a decrease in the proportion of sequences assigned to the phyla Firmicutes and Bacteroidetes, with a corresponding increase in those assigned to members of the Proteobacteria. One possible means of avoiding such “collateral damage” would involve the application of a narrow-spectrum antimicrobial with specific anti-C. difficile activity. We tested this hypothesis using thuricin CD, a narrow-spectrum bacteriocin produced by Bacillus thuringiensis, which is active against C. difficile. The results demonstrated that this bacteriocin was equally effective at killing C. difficile in the distal colon model but had no significant impact on the composition of the microbiota. This offers the possibility of developing a targeted approach to eliminating C. difficile in the colon, without collateral damage.

Small intestinal bacterial overgrowth in nonalcoholic steatohepatitis: Association with toll-like receptor 4 expression and plasma levels of interleukin 8

Abstract: Experimental and clinical studies suggest an association between small intestinal bacterial overgrowth (SIBO) and nonalcoholic steatohepatitis (NASH). Liver injury and fibrosis could be related to exposure to bacterial products of intestinal origin and, most notably, endotoxin, including lipopolysaccharide (LPS). To compare the prevalence of SIBO and its relationships to LPS receptor levels and systemic cytokines in NASH patients and healthy control subjects. Eighteen NASH patients (eight males) and 16 age-matched and gender-matched healthy volunteers were studied. SIBO was assessed by the lactulose breath hydrogen test (LHBT), plasma lipopolysaccharide binding protein (LBP) levels by ELISA, and expression (as a percentage) of TLR-2 and 4 on CD14-positive cells by flow cytometry. Pro-inflammatory cytokines (IL-1β, IL-6, IL-8, and TNF-α) were measured in plasma. SIBO was more common in NASH patients than control subjects (77.78% vs. 31.25%; P < 0.0001). LBP levels and TLR-2 expression were similar in both groups, TLR-4/MD-2 expression on CD14 positive cells was higher among NASH patients: expression, mean ± SEM, NASH vs. control: 20.95 ± 2.91% vs. 12.73 ± 2.29%, P < 0.05. Among the examined cytokines, only IL-8 levels were significantly higher in patients than control (P = 0.04) and correlated positively with TLR-4 expression (r = 0.5123, P = 0.036). NASH patients have a higher prevalence of small intestinal bacterial overgrowth which is associated with enhanced expression of TLR-4 and release of IL-8. SIBO may have an important role in NASH through interactions with TLR-4 and induction of the pro-inflammatory cytokine, IL-8.

Induction and Activation of Adaptive Immune Populations During Acute and Chronic Phases of a Murine Model of Experimental Colitis

Abstract: Background Dextran sodium sulphate (DSS) is commonly used to induce intestinal inflammation in rodents. Despite its continuing importance as a model system for examining IBD pathogenesis, the mucosal and systemic immune responses have not been comprehensively documented.

Biochemical and metabolomic phenotyping in the identification of a vitamin D responsive metabotype for markers of the metabolic syndrome.

Abstract: Scope: Metabolic phenotyping promises to be a useful tool in human intervention studies. This study examined whether metabolic phenotyping could identify responders to vitamin D supplementation in terms of the metabolic syndrome. Methods and results: In a double-blind, randomised placebo-controlled dietary intervention subjects were assigned to receive 15 μg vitamin D3 or placebo daily. Serum 25-hydroxyvitamin D (25(OH)D) and biochemical markers of the metabolic syndrome were measured at baseline and following the 4-wk intervention. k-means clustering and 1H-NMR metabolomic analysis were used to explore responsive phenotypes. Vitamin D supplementation significantly increased serum 25(OH)D to an endpoint concentration of 78.1±20.0 nmol/L (p<0.001). There was no effect of supplementation on the measured markers of the metabolic syndrome. k-means cluster analysis based on 13 biochemical markers of the metabolic syndrome and 25(OH)D concentrations revealed five discrete biomarker clusters. One of these clusters, characterised by lower serum 25(OH)D and higher levels of adipokines, showed significant responses in insulin (15% decrease), homestatic model assessment scores (19% decrease) and c-reactive protein (54% decrease). Metabolomic analysis revealed further changes and the extent of change in serum vitamin D correlated negatively with changes in glucose. Conclusion: Overall, metabolic phenotyping revealed a phenotype that was responsive to vitamin D supplementation.

Degradation of the extracellular matrix components by bacterial‐derived metalloproteases: Implications for inflammatory bowel diseases

Abstract: Background: Proteolytic degradation of the extracellular matrix, a feature of mucosal homeostasis and tissue renewal, also contributes to the complications of intestinal inflammation. Whether this proteolytic activity is entirely host-derived, or, in part, produced by the gut microbiota, is unknown. Methods: We screened the bacterial colonies for gelatinolytic activity from fecal samples of 20 healthy controls, 23 patients with ulcerative colitis, and 18 with Crohn's disease (CD). In addition, the genes encoding metalloproteases were detected by conventional or real-time polymerase chain reaction (PCR). Results: Gelatinolytic activity was found in approximately one-quarter of samples regardless of the presence of inflammation and without any attempt to enhance the sensitivity of the culture-based screen. This was associated with a diversity of bacteria, particularly in CD, but was predominantly linked with Clostridium perfringens. Culture supernatants from C. perfringens degraded gelatin, azocoll, type I collagen, and basement membrane type IV collagen, but different isolates varied in the degree of proteolytic activity. Results were confirmed by detection of the C. perfringens colA gene (encoding collagenase) in fecal DNA, again regardless of the presence or absence of inflammation. However, the biologic significance and potential implications of microbial-derived proteolytic activity were confirmed by reduced transepithelial resistance (TER) after exposure of rat distal colon to culture supernatants of C. perfringens in Ussing chambers. Conclusions: The study shows that microbial-derived proteolytic activity has the capacity to contribute to mucosal homeostasis and may participate in the pathogenesis of inflammatory bowel disease. (Inflamm Bowel Dis 2010)

Recombinant lactobacilli expressing linoleic acid isomerase can modulate the fatty acid composition of host adipose tissue in mice.

Abstract: We have previously demonstrated that oral administration of a metabolically active Bifidobacterium breve strain, with ability to form cis-9, trans-11 conjugated linoleic acid (CLA), resulted in modulation of the fatty acid composition of the host, including significantly elevated concentrations of c9, t11 CLA and omega-3 (n-3) fatty acids in liver and adipose tissue. In this study, we investigated whether a recombinant lactobacillus expressing linoleic acid isomerase (responsible for production of t10, c12 CLA) from Propionibacterium acnes (PAI) could influence the fatty acid composition of different tissues in a mouse model. Linoleic-acid-supplemented diets (2 %, w/w) were fed in combination with either a recombinant t10, c12 CLA-producing Lactobacillus paracasei NFBC 338 (Lb338), or an isogenic (vector-containing) control strain, to BALB/c mice for 8 weeks. A third group of mice received linoleic acid alone (2 %, w/w). Tissue fatty acid composition was assessed by GLC at the end of the trial. Ingestion of the strain expressing linoleic acid isomerase was associated with a 4-fold increase (P<0.001) in t10, c12 CLA in adipose tissues of the mice when compared with mice that received the isogenic non-CLA-producing strain. The livers of the mice that received the recombinant CLA-producing Lb338 also contained a 2.5-fold (albeit not significantly) higher concentration of t10, c12 CLA, compared to the control group. These data demonstrate that a single gene (encoding linoleic acid isomerase) expressed in an intestinal microbe can influence the fatty acid composition of host fat.

The colonic microflora and probiotic therapy in health and disease.

Abstract: PURPOSE OF REVIEW: Host-microbe dialogue is involved not only in maintenance of mucosal homeostasis but also in the pathogenesis of several infectious, inflammatory, and neoplastic disorders of the gut. This has led to a resurgence of interest in the colonic microbiota in health and disease. Recent landmark findings are addressed here. RECENT FINDINGS: Reciprocal signalling between the immune system and the microbiota plays a pivotal role in linking alterations in gut microbiota with risk of metabolic disease in the host, notably insulin resistance, obesity, and chronic low-grade inflammation. Loss of ancestral indigenous organisms consequent upon a modern lifestyle may contribute to an increased frequency of various metabolic and immuno-allergic diseases. The potential to address this underpins the science of pharmabiotics. SUMMARY: Advances in understanding host-microbe interactions within the gut can inform rational probiotic or pharmabiotic selection criteria. In addition, the gut microbiota may be a repository for drug discovery as well as a therapeutic target.

Molecular mechanisms of probiotic action: it's all in the strains!

Abstract: The influence of the commensal microbiota on intestinal and extra-intestinal development has been evident since the first studies of germ-free animals over a half-century ago. Microbial signals from the lumen of the gut are trophic for the digestive, immune and other systems, including the developing brain.1 2 In later life, reciprocal host–microbe interactions remain critical for mucosal homeostasis. Probiotic therapy is, in essence, an attempt to harness the beneficial effects of the commensal microbiota for the host.3 In most instances, the molecular underpinning of these exchanges remains to be defined but represents an intriguing strategy for identifying therapeutic targets and drug discovery.4 While the therapeutic potential of immunomodulatory molecules from pathogens is well recognised, the pursuit of bioactive molecules from the commensal gut microbiota is a more recent venture; examples include the discovery of bacteriocins with activity against Clostridium difficile and bacterial-derived immunomodulatory molecules.4 However, much more remains to be mined from the commensal microbiota. The study by Fernandez and colleagues published in this issue of Gut ( see page 1050 …

Clinical Dilemmas in Inflammatory Bowel Disease: New Challenges

Abstract: The second edition of Clinical Dilemmas in Inflammatory Bowel Disease: New Challenges, is a practical, up-to-date handbook providing expert guidance on specific clinical dilemmas and areas of difficulty that the gastroenterologist regularly faces in day-to-day practice. In this new edition, 75% of the “dilemmas” are brand new dilemmas facing the IBD specialist concerning emerging treatment therapies, such as the use of cannabinoids and Viagra for Crohn’s disease. The remaining 25% of the dilemmas are fully updated from the previous edition, incorporating the latest clinical thinking.

Increased health burden associated with Clostridium difficile diarrhoea in inflammatory bowel disease

Abstract: SIRS, In their recent study using UK Hospital Episode Statistics (HES), Jen et al. report a substantially increased risk of death and longer in-patient stays in patients with IBD complicated by hospital-acquired Clostridium difficile-associated diarrhoea (IBD-CDAD-HAI) than in those with IBD alone. The authors point out several major and largely unavoidable limitations of data obtained through HES or other nationwide datasets, which have not been designed primarily for research. These include miscoding, absence of case ascertainment and, in this instance, under-recording of C. difficile cases. We have some additional questions. First, is it possible that checking for, and thus finding, C. difficile might, at least in some patients, be a surrogate for severe disease and poor outcome, rather than its cause? Knowledge of the precise cause of death in the IBD-CDAD-HAI group would help confirm causality, but we imagine that it would be difficult to find using HES. Both the 2006 and 2008 UK National IBD audits showed that only about half of patients with acute severe ulcerative colitis had stools sent for C. difficile toxin, suggesting that the association between C. difficile and adverse outcome in IBD patients in this study might reflect selective targeting of C. difficile testing at the sickest patients, rather than those having an uncomplicated inpatient course. Indeed, C. difficile infection was identified most commonly in older patients (especially those over 70), and in those with more comorbidities. If this suggestion is correct, it implies that some IBD patients with undiagnosed C. difficile infection recover without its specific treatment, (although there is scant published evidence to this effect). Secondly, might a similar bias exist in relation to coding, with greater efforts being made by coders to identify C. difficile infection in IBD patients doing poorly than in those doing well? Thirdly, the authors excluded patients admitted with IBD who seemed to have acquired their CDAD in the community. Although these patients represented <10% of the total IBD-CDAD-HAI group, it would be interesting to know how they fared in comparison with those with hospital-acquired CDAD and with IBD alone. Lastly, what proportion of those admitted with a primary diagnosis of CDAD actually had IBD recorded as an historical, but possibly clinically irrelevant secondary diagnosis? D. S. Rampton* & F. Shanahan *Digestive Diseases Clinical Academic Unit, Barts and the London School of Medicine and Dentistry, London, UK. Department of Medicine, University College Cork, Cork, Ireland. E-mail: d.rampton@qmul.ac.uk

Perplexing plain abdominal x-ray

Abstract: A 62-year-old man presented with generalised abdominal pain of 4 h duration with associated cough and pyrexia for 2 days. He had developed nephrotic syndrome 17 years previously due to focal segmental glomerulosclerosis and progressed to end-stage kidney disease for which he required haemodialysis three times a week for 6 years. The patient had undergone resection of 10 cm of his distal small bowel due to obstruction secondary to a benign stricture 5 years previously. Oesophagogastroduodenoscopy, colonoscopy, barium meal and enema studies in the previous 2 years were normal apart from the detection of a small sliding hiatus hernia. Examination revealed diffuse abdominal tenderness without …

Who needs doctors? Staying fresh in changing times.

Abstract: As society changes, doctors must adapt. Despite remarkable advances in medicine, the pace of change--greater now than ever--is challenging doctors to define their role and relevance. Is medicine really facing a crisis? Are claims for a malaise in medicine overstated? Regardless, the profession has been called upon to respond collectively to change. However, clinicians as individuals will need to be equipped with a strategy for embracing and enjoying change. Approaches will vary but one constant should be a steadfast adherence to the scientific basis of medicine as a way of thinking. Engagement with the medical humanities will also help doctors stay fresh and deepen their understanding of what it feels like to be ill. In so doing, clinicians will find inspiration in the ordinary.