A

argiri, a., Zoumpopoulou, g., Karatzas, K.-A., Tsakalidou, e., Nychas, G.-J., Panagou, E. and Tassou, C. (2013) Selection of potential probiotic lactic acid bacteria from fermented olives by in vitro tests. Food Microbiology, 33 (2). pp. 282-291. ISSN 0740-0020

B

Bienestock, J., Gibson, G. ORCID: https://orcid.org/0000-0002-0566-0476, Klaenhammer, T. R., Walker, W. A. and Neish, A. (2013) New insights into probiotic mechanisms: a harvest from functional and metagenomic studies. Gut Microbes, 4 (2). pp. 94-100. ISSN 1949-0984 doi: https://doi.org/10.4161/gmic.23283

Boulange, C. L., Claus, S. P., Chou, C. J., Collino, S., Montoliu, I., Kochhar, S., Holmes, E., Rezzi, S., Nicholson, J. K., Dumas, M. E. and Martin, F.-P. J. (2013) Early metabolic adaptation in C57BL/6 mice resistant to high fat diet induced weight gain involves an activation of mitochondrial oxidative pathways. Journal of Proteome Research, 12 (4). pp. 1956-1968. ISSN 1535-3907 doi: https://doi.org/10.1021/pr400051s

C

Chapman, C.M.C., Gibson, G.R. ORCID: https://orcid.org/0000-0002-0566-0476, Todd, S. ORCID: https://orcid.org/0000-0002-9981-923X and Rowland, I. (2013) Comparative in vitro inhibition of urinary tract pathogens by single- and multi-strain probiotics. European Journal of Nutrition, 52 (6). pp. 1669-1677. ISSN 1436-6215 doi: https://doi.org/10.1007/s00394-013-0501-2

Claus, S. P. (2013) Fighting undernutrition: don't forget the bugs. Cell Host and Microbe, 13 (3). pp. 239-240. ISSN 1931-3128 doi: https://doi.org/10.1016/j.chom.2013.02.015

Claus, S. P. and Swann, J. R. (2013) Nutrimetabonomics: applications for nutritional sciences, with specific reference to gut microbial interactions. Annual Review of Food Science and Technology, 4. pp. 381-399. ISSN 1941-1413 doi: https://doi.org/10.1146/annurev-food-030212-182612

Connolly, J., Valdramidis, V. P., Byrne, E., Karatzas, K.-A., Cullen, P. J., Keener, K. M. and Mosnier, J. P. (2013) Characterization and antimicrobial efficacy against E. coli of a helium/air plasma at atmospheric pressure created in a plastic package. Journal of Physics D: Applied Physics, 46 (3). 035401. ISSN 1361-6463 doi: https://doi.org/10.1088/0022-3727/46/3/035401

Cueva, C., Sánchez-Patán, F., Monagas, M., Walton, G. E. ORCID: https://orcid.org/0000-0001-5426-5635, Gibson, G. R. ORCID: https://orcid.org/0000-0002-0566-0476, Martín-Álvarez, P. J., Bartolomé, B. and Moreno-Arribas, M. V. (2013) In vitro fermentation of grape seed flavan-3-ol fractions by human faecal microbiota: changes in microbial groups and phenolic metabolites. FEMS Microbiology Ecology, 83 (3). pp. 792-805. ISSN 1574-6941 doi: https://doi.org/10.1111/1574-6941.12037

D

De Castro, N. M., Yaqoob, P. ORCID: https://orcid.org/0000-0002-6716-7599, De la Fuente, M., Baeza, I. and Claus, S. P. (2013) Premature impairment of methylation pathway and cardiac metabolic dysfunction in fa/fa obese Zucker rats. Journal of Proteome Research, 12 (4). pp. 1935-1945. ISSN 1535-3907 doi: https://doi.org/10.1021/pr400025y

Dewulf, E. M., Cani, P. D., Claus, S. P., Fuentes, S., Puylaert, P. G. B., Neyrinck, A. M., Bindels, L. B., de Vos, W. M., Gibson, G. R. ORCID: https://orcid.org/0000-0002-0566-0476, Thissen, J.-P. and Delzenne, N. M. (2013) Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women. Gut, 32 (8). pp. 1112-1121. ISSN 1468-3288 doi: https://doi.org/10.1136/gutjnl-2012-303304

E

El Aidy, S., Derrien, M., Merrifield, C. A., Levenez, F., Dore, J., Boekschoten, M. V., Dekker, J., Holmes, E., Zoetendal, E. G., van Baarlen, P., Claus, S. P. and Kleerbezem, M. (2013) Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon. ISME Journal, 7. pp. 743-755. ISSN 1751-7370 doi: https://doi.org/10.1038/ismej.2012.142

El Aidy, S., Merrifield, C. A., Derrien, M., van Baarlen, P., Hooiveld, G., Levenez, F., Doré, J., Dekker, J., Holmes, E., Claus, S. P., Reijngoud, D. J. and Kleerebezem, M. (2013) The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalisation. Gut, 62 (9). pp. 1306-1314. ISSN 1468-3288 doi: https://doi.org/10.1136/gutjnl-2011-301955

F

Feehily, C., O'Byrne, C.P. and Karatzas, K. A. G. (2013) Functional γ-aminobutyrate shunt in Listeria monocytogenes: role in acid tolerance and succinate biosynthesis. Applied and Environmental Microbiology, 79 (1). pp. 74-80. ISSN 0099-2240 doi: https://doi.org/10.1128/AEM.02184-12

G

Guerra-Ordaz, A. A., Molist, F., Hermes, R. G., Gómez de Segura, A., La Ragione, R. M., Woodward, M. J., Tchorzewska, M. A., Collins, J. W., Pérez, J. F. and Martin-Orúe, S. M. (2013) Effect of inclusion of lactulose and Lactobacillus plantarum on the intestinal environment and performance of piglets at weaning. Animal Feed Science and Technology, 185 (3-4). pp. 160-168. ISSN 0377-8401 doi: https://doi.org/10.1016/j.anifeedsci.2013.07.009

H

Hayward, M. R., Jansen, V. A. A. and Woodward, M. J. (2013) Comparative genomics of Salmonella enterica serovars Derby and Mbandaka, two prevalent serovars associated with different livestock species in the UK. BMC Genomics, 14 (1). p. 365. ISSN 1471-2164 doi: https://doi.org/10.1186/1471-2164-14-365

Hobden, M. R., Martin-Morales, A., Guerin-Deremaux, L., Wils, D., Costabile, A., Walton, G. E. ORCID: https://orcid.org/0000-0001-5426-5635, Rowland, I., Kennedy, O. B. ORCID: https://orcid.org/0000-0003-3885-4872 and Gibson, G. R. ORCID: https://orcid.org/0000-0002-0566-0476 (2013) In Vitro Fermentation of NUTRIOSE® FB06, a wheat dextrin soluble fibre, in a continuous culture human colonic model system. PLoS ONE, 8 (10). e77128. doi: https://doi.org/10.1371/journal.pone.0077128

Hoyles, L., Clear, J. A. and McCartney, A. L. (2013) Use of denaturing gradient gel electrophoresis to detect Actinobacteria associated with the human faecal microbiota. Anaerobe, 22. pp. 90-96. ISSN 1075-9964 doi: https://doi.org/10.1016/j.anaerobe.2013.06.001

Hoyles, L., Ortman, K., Cardew, S., Foster, G., Rogerson, F. and Falsen, E. (2013) Corynebacterium uterequi sp. nov., a non-lipophilic bacterium isolated from urogenital samples from horses. Veterinary Microbiology, 165 (3-4). pp. 469-474. ISSN 0378-1135 doi: https://doi.org/10.1016/j.vetmic.2013.03.025

I

Inness, V.L., Khoo, C., Gross, K.L., Hoyles, L., Gibson, G. R. ORCID: https://orcid.org/0000-0002-0566-0476 and McCartney, A. L. (2013) An assessment of the prebiotic potential of single and blended substrates in anaerobic in vitro batch culture fermentations using canine faecal samples as inocula. International Journal of Probiotics and Prebiotics, 8 (4). p. 133. ISSN 1555-1431

J

Jarvis, B. (2013) 15. Statistical approaches to the analysis of microbiological data. In: Granato, D. and Ares, G. (eds.) Mathematical and Statistical Methods in Food Science and Technology. John Wiley & Sons, Inc., Hoboken, USA, pp. 249-284, Chapter 15. ISBN 9781118433683 doi: https://doi.org/10.1002/9781118434635.ch15

K

Kok, M. G. M., Ruijken, M. A., Swann, J. R., Wilson, I. D., Somsen, G. W. and de Jong, G. J. (2013) Anionic metabolic profiling of urine from antibiotic-treated rats by capillary electrophoresis–mass spectrometry. Analytical and Bioanalytical Chemistry, 405 (8). pp. 2585-2594. ISSN 1618-2650 doi: https://doi.org/10.1007/s00216-012-6701-4

L

La Ragione, R. M., Woodward, M. J., Kumar, M., Rodenberg, J., Fan, H., Wales, A. D. and Karaca, K. (2013) Efficacy of a live attenuated Escherichia coli O78:K80 vaccine in chickens and turkeys. Avian Diseases, 57 (2). pp. 273-279. ISSN 0005-2086 doi: https://doi.org/10.1637/10326-081512-Reg.1

Lees, H. J., Swann, J. R., Wilson, I. D., Nicholson, J. K. and Holmes, E. (2013) Hippurate: the natural history of a mammalian-microbial co-metabolite. Journal of Proteome Research, 12 (4). pp. 1527-1546. ISSN 1535-3907 doi: https://doi.org/10.1021/pr300900b

Lewis, M. (2013) A pig’s microbiota – a result of many factors. Pig Progress, 29 (8). pp. 24-26.

Lewis, M. C., Patel, D. V., Fowler, J., Duncker, S., Zuercher, A. W., Mercenier, A. and Bailey, M. (2013) Dietary supplementation with Bifidobacterium lactis NCC2818 from weaning reduces local immunoglobulin production in lymphoid-associated tissues but increases systemic antibodies in healthy neonates. British Journal of Nutrition, 110 (7). pp. 1243-1252. ISSN 1475-2662 doi: https://doi.org/10.1017/S0007114513000251

Likotraftiti, E., Tuohy, K. M., Gibson, G. R. ORCID: https://orcid.org/0000-0002-0566-0476 and Rastall, R. A. (2013) Development of antimicrobial synbiotics using potentially-probiotic faecal isolates of Lactobacillus fermentum and Bifidobacterium longum. Anaerobe, 20. pp. 5-13. ISSN 1075-9964

Lopez-Andres , P., Luciano, G., Vasta, V., Gibson, T. M., Biondi, L., Priolo, A. and Mueller-Harvey, I. (2013) Dietary quebracho tannins are not absorbed, but increase the antioxidant capacity of liver and plasma in sheep. British Journal of Nutrition, 110 (4). pp. 632-639. ISSN 1475-2662 doi: https://doi.org/10.1017/S0007114512005703

M

Mann, E. R., You, J., Horneffer-van der Sluis, V., Bernardo, D., Omar Al-Hassi, H., Landy, J., Peake, S. T., Thomas, L. V., Tee, C. T., Lee, G. H., Hart, A. L., Yaqoob, P. ORCID: https://orcid.org/0000-0002-6716-7599 and Knight, S. C. (2013) Dysregulated circulating dendritic cell function in ulcerative colitis is partially restored by probiotic strain Lactobacillus casei Shirota. Mediators of inflammation, 2013. 573576. ISSN 0962-9351 doi: https://doi.org/10.1155/2013/573576

Mappley, L. J., Tchórzewska, M. A., Nunez, A., Woodward, M. and La Ragione, R. M. (2013) Evidence for systemic spread of the potentially zoonotic intestinal spirochaete Brachyspira pilosicoli in experimentally challenged laying chickens. Journal of Medical Microbiology, 62 (2). pp. 297-302. ISSN 0022-2615 doi: https://doi.org/10.1099/jmm.0.052126-0

Mappley, L. J., Tchórzewska, M. A., Nunez, A., Woodward, M. J., Bramley, P. M. and La Ragione, R. M. (2013) Oral treatment of chickens with Lactobacillus reuteri LM1 reduces Brachyspira pilosicoli-induced pathology. Journal of Medical Microbiology, 62 (2). pp. 287-296. ISSN 0022-2615 doi: https://doi.org/10.1099/jmm.0.051862-0

Merrifield, C. A., Lewis, M. C., Claus, S. P., Pearce, J. T. M., Cloarec, O., Duncker, S., Heinzmann, S. S., Dumas, M.-E., Kochar, S., Rezzi, S., Mercenier, A., Nicholson, J. K., Bailey, M. and Holmes, E. (2013) Weaning diet induces sustained metabolic phenotype shift in the pig and influences host response to Bifidobacterium lactis NCC2818. Gut, 62 (6). pp. 842-851. ISSN 1468-3288 doi: https://doi.org/10.1136/gutjnl-2011-301656

Merrifield, C. A., Lewis, M. C., Claus, S., Pearce, J. T. M., Cloarec, O., Duncker, S., Heinzmann, S. S., Dumas, M., Kochhar, S., Rezzi, S., Mercenier, A., Nicholson, J. K., Bailey, M. and Holmes, E. (2013) Weaning diet induces sustained metabolic phenotype shift in the pig and influences host response to Bifidobacterium lactis NCC2818. Gut, 62 (6). pp. 842-851. ISSN 1468-3288 doi: https://doi.org/10.1136/gutjnl-2011-301656

Mills, C. ORCID: https://orcid.org/0000-0002-8313-3700, Oruna-Concha, M. J. ORCID: https://orcid.org/0000-0001-7916-1592, Mottram, D. S., Gibson, G. R. ORCID: https://orcid.org/0000-0002-0566-0476 and Spencer, J. P. E. ORCID: https://orcid.org/0000-0003-2931-7274 (2013) The effect of processing on chlorogenic acid content of commercially available coffee. Food Chemistry, 141 (4). pp. 3335-3340. ISSN 0308-8146 doi: https://doi.org/10.1016/j.foodchem.2013.06.014

P

Petschow, B., Dore, J., Hibberd, P., Dinan, T., Reid, G., Blaser, M., Cani, P. D., Degnan, F. H., Foster, J., Gibson, G. ORCID: https://orcid.org/0000-0002-0566-0476, Hutton, J., Klaenhammer, T. R., Ley, R., Nieuwdorp, M., Pot, B., Relman, D., Serazin, A. and Sanders, M. E. (2013) Probiotics, prebiotics, and the host microbiome: the science of translation. Annals of the New York Academy of Sciences, 1306. pp. 1-17. ISSN 1749-6632 doi: https://doi.org/10.1111/nyas.12303

R

Richards, S. E., Wang, Y., Claus, S. P., Lawler, D., Kochhar, S., Holmes, E. and Nicholson, J. K. (2013) Metabolic phenotype modulation by caloric restriction in a lifelong dog study. Journal of Proteome Research, 12 (7). pp. 3117-3127. ISSN 1535-3907 doi: https://doi.org/10.1021/pr301097k

S

Sarbini, S. R., Kolida, S., Gibson, G. R. ORCID: https://orcid.org/0000-0002-0566-0476 and Rastall, R. A. (2013) In vitro fermentation of commercial α-gluco-oligosaccharide by faecal microbiota from lean and obese human subjects. British Journal of Nutrition, 109 (11). pp. 1980-1989. ISSN 0007-1145 doi: https://doi.org/10.1017/S0007114512004205

Swann, J. R., Spagou, K., Lewis, M., Nicholson, J. K., Glei, D. A., Seeman, T. E., Coe, C. L., Goldman, N., Ryff, C. D., Weinstein, M. and Holmes, E. (2013) Microbial−mammalian cometabolites dominate the age-associated urinary metabolic phenotype in Taiwanese and American populations. Journal of Proteome Research, 12 (7). pp. 3166-3180. ISSN 1535-3907 doi: https://doi.org/10.1021/pr4000152

T

Tejero-Sarinena, S., Barlow, J., Costabile, A., Gibson, G. R. ORCID: https://orcid.org/0000-0002-0566-0476 and Rowland, I. (2013) Antipathogenic activity of probiotics against Salmonella Typhimurium and Clostridium difficile in anaerobic batch culture systems: is it due to synergies in probiotic mixtures or the specificity of single strains? Anaerobe, 24. pp. 60-65. ISSN 1075-9964 doi: https://doi.org/10.1016/j.anaerobe.2013.09.011

V

Vulevic, J., Juric, A., Tzortzis, G. and Gibson, G. R. ORCID: https://orcid.org/0000-0002-0566-0476 (2013) A mixture of trans-galactooligosaccharides reduces markers of metabolic syndrome and modulates the fecal microbiota and immune function of overweight adults. Journal of Nutrition, 143 (3). pp. 324-331. ISSN 1541-6100 doi: https://doi.org/10.3945/jn.112.166132

W

Wu, G., Day, M. J., Mafura, M. T., Nunez-Garcia, J., Fenner, J. J., Sharma, M., van Essen-Zandbergen, A., Rodríguez, I., Dierikx, C., Kadlec, K., Schink, A.-K., Wain, J., Helmuth, R., Guerra, B., Schwarz, S., Threlfall, J., Woodward, M. J.,, Woodford, N., Coldham, N. and Mevius, D. (2013) Comparative Analysis of ESBL-Positive Escherichia coli isolates from Animals and Humans from the UK, the Netherlands and Germany. PLoS ONE, 8 (9). ISSN 1932-6203 doi: https://doi.org/10.1371/journal.pone.0075392