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  • Journal article
    Cardenas PA, Cooper PJ, Cox MJ, Chico M, Arias C, Moffatt MF, Cookson WOet al., 2012,

    Upper Airways Microbiota in Antibiotic-Naive Wheezing and Healthy Infants from the Tropics of Rural Ecuador

    , PLOS ONE, Vol: 7, ISSN: 1932-6203
  • Journal article
    Merrifield CA, Lewis MC, Claus SP, Pearce JTM, Cloarec O, Duncker S, Heinzmann SS, Dumas M, Kochhar S, Rezzi S, Mercenier A, Nicholson JK, Bailey M, Holmes Eet al., 2012,

    Weaning diet induces sustained metabolic phenotype shift in the pig and influences host response to Bifidobacterium lactis NCC2818

    , Gut

    Background The process of weaning causes a major shift in intestinal microbiota and is a critical period for developing appropriate immune responses in young mammals.Objective To use a new systems approach to provide an overview of host metabolism and the developing immune system in response to nutritional intervention around the weaning period.Design Piglets (n=14) were weaned onto either an egg-based or soya-based diet at 3 weeks until 7 weeks, when all piglets were switched onto a fish-based diet. Half the animals on each weaning diet received Bifidobacterium lactis NCC2818 supplementation from weaning onwards. Immunoglobulin production from immunologically relevant intestinal sites was quantified and the urinary 1H NMR metabolic profile was obtained from each animal at post mortem (11 weeks).Results Different weaning diets induced divergent and sustained shifts in the metabolic phenotype, which resulted in the alteration of urinary gut microbial co-metabolites, even after 4 weeks of dietary standardisation. B lactis NCC2818 supplementation affected the systemic metabolism of the different weaning diet groups over and above the effects of diet. Additionally, production of gut mucosa-associated IgA and IgM was found to depend upon the weaning diet and on B lactis NCC2818 supplementation.Conclusion The correlation of urinary 1H NMR metabolic profile with mucosal immunoglobulin production was demonstrated, thus confirming the value of this multi-platform approach in uncovering non-invasive biomarkers of immunity. This has clear potential for translation into human healthcare with the development of urine testing as a means of assessing mucosal immune status. This might lead to early diagnosis of intestinal dysbiosis and with subsequent intervention, arrest disease development. This system enhances our overall understanding of pathologies under supra-organismal control.
  • Journal article
    Sim K, Cox MJ, Wopereis H, Martin R, Knol J, Li MS, Cookson WO, Moffatt MF, Kroll JSet al., 2012,

    Improved Detection of Bifidobacteria with Optimised 16S rRNA-Gene Based Pyrosequencing

    , PLoS One, Vol: 7, Pages: e32543-e32543

    The 16S rRNA gene is conserved across all bacteria and as such is routinely targeted in PCR surveys of bacterial diversity. PCR primer design aims to amplify as many different 16S rRNA gene sequences from as wide a range of organisms as possible, though there are no suitable 100% conserved regions of the gene, leading to bias. In the gastrointestinal tract, bifidobacteria are a key genus, but are often under-represented in 16S rRNA surveys of diversity. We have designed modified, 'bifidobacteria-optimised' universal primers, which we have demonstrated detection of bifidobacterial sequence present in DNA mixtures at 2% abundance, the lowest proportion tested. Optimisation did not compromise the detection of other organisms in infant faecal samples. Separate validation using fluorescence in situ hybridisation (FISH) shows that the proportions of bifidobacteria detected in faecal samples were in agreement with those obtained using 16S rRNA based pyrosequencing. For future studies looking at faecal microbiota, careful selection of primers will be key in order to ensure effective detection of bifidobacteria.
  • Journal article
    Mestdagh R, Dumas M-E, Rezzi S, Kochhar S, Holmes E, Claus SP, Nicholson JKet al., 2012,

    Gut Microbiota Modulate the Metabolism of Brown Adipose Tissue in Mice

    , JOURNAL OF PROTEOME RESEARCH, Vol: 11, Pages: 620-630, ISSN: 1535-3893
  • Journal article
    Dumas M-E, 2011,

    The Microbial-Mammalian Metabolic Axis: Beyond Simple Metabolism

    , CELL METABOLISM, Vol: 13, Pages: 489-490, ISSN: 1550-4131
  • Conference paper
    Molyneaux PL, Mallia P, Duff RM, Moffatt MF, Cookson WO, Johnston SLet al., 2011,

    Investigating The Role Of Rhinovirus Infection In Precipitating Bacterial Infections In COPD Using Culture Independent Molecular Microbiology

    , Publisher: AMER THORACIC SOC, ISSN: 1073-449X
  • Journal article
    Rezzonico E, Mestdagh R, Delley M, Combremont S, Dumas M-E, Holmes E, Nicholson J, Bibiloni Ret al., 2011,

    Bacterial adaptation to the gut environment favors successful colonization Microbial and metabonomic characterization of a simplified microbiota mouse model

    , GUT MICROBES, Vol: 2, Pages: 307-318, ISSN: 1949-0976
  • Journal article
    Hilty M, Burke C, Pedro H, Cardenas P, Bush A, Bossley C, Davies J, Ervine A, Poulter L, Pachter L, Moffatt MF, Cookson WOCet al., 2010,

    Disordered Microbial Communities in Asthmatic Airways

    , PLOS ONE, Vol: 5, ISSN: 1932-6203
  • Journal article
    Dumas ME, Wilder SP, Bihoreau MT, Barton RH, Fearnside JF, Argoud K, D'Amato L, Wallis RH, Blancher C, Keun HC, Baunsgaard D, Scott J, Sidelmann UG, Nicholson JK, Gauguier Det al., 2007,

    Direct quantitative trait locus mapping of mammalian metabolic phenotypes in diabetic and normoglycemic rat models

    , Nat Genet, Vol: 39, Pages: 666-672, ISSN: 1061-4036
  • Journal article
    Dumas M-E, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, Fearnside J, Tatoud R, Blanc V, Lindon JC, Mitchell SC, Holmes E, McCarthy MI, Scott J, Gauguier D, Nicholson Jet al., 2006,

    Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice

    , Proc Natl Acad Sci, Vol: 103, Pages: 12511-12516, ISSN: 0027-8424

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