Browse by Current Cardiff authors

Michael, D. R., John, D. A., Coates, N., Guschina, I., McDonald, J. A. K., Danckert, N. P., Valdivia-Garcı́a, M. A., Ramanathan, G., Plummer, S. F., Wang, D., Marchesi, J. R. ORCID: https://orcid.org/0000-0002-7994-5239 and Mullish, B. H. 2025. The impact of three distinct probiotic supplements on the gut microbiota and its metabolites in healthy adults. Beneficial Microbes 10.1163/18762891-bja00096

Lowe, John ORCID: https://orcid.org/0000-0003-4772-1879, Gillespie, David ORCID: https://orcid.org/0000-0002-6934-2928, Aboklaish, Ali, Lau, Tin Man Mandy ORCID: https://orcid.org/0000-0001-5894-570X, Consoli, Claudia, Babu, Malavika, Goddard, Mark, Hood, Kerenza ORCID: https://orcid.org/0000-0002-5268-8631, Klein, Nigel, Thomas-Jones, Emma ORCID: https://orcid.org/0000-0001-7716-2786, Turner, Mark, Hubbard, Marie, Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239, Berrington, Janet and Kotecha, Sailesh ORCID: https://orcid.org/0000-0003-3535-7627 2024. Azithromycin therapy for prevention of chronic lung disease of prematurity (AZTEC): a multicentre, double-blind, randomised, placebo-controlled trial. The Lancet Respiratory Medicine 12 (8) , pp. 608-618. 10.1016/S2213-2600(24)00079-1

Pinato, David J., D'Alessio, Antonio, Fulgenzi, Claudia Angela Maria., Schlaak, Alexandra Emilia, Celsa, Ciro, Killmer, Saskia, Blanco, Jesus Miguens., Ward, Caroline, Stikas, Charalampos-Vlasios, Openshaw, Mark R., Acuti, Nicole, Nteliopoulos, Georgios, Balcells, Cristina, Keun, Hector C., Goldin, Robert D., Ross, Paul J., Cortellini, Alessio, Thomas, Robert, Young, Anna Mary., Danckert, Nathan, Tait, Paul, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Bengsch, Bertram and Sharma, Rohini 2024. Safety and preliminary efficacy of pembrolizumab following trans-arterial chemoembolization for hepatocellular carcinoma: the PETAL phase Ib study. Clinical Cancer Research 30 (11) , pp. 2433-2443. 10.1158/1078-0432.CCR-24-0177

Gallacher, David J., Zhang, Lei ORCID: https://orcid.org/0000-0003-3536-8692, Aboklaish, Ali F., Mitchell, Emma, Wach, Richard, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Kotecha, Sailesh ORCID: https://orcid.org/0000-0003-3535-7627 2024. Baseline azithromycin resistance in the gut microbiota of preterm born infants. Pediatric Research 95 , pp. 205-212. 10.1038/s41390-023-02743-7

Biscarini, Filippo ORCID: https://orcid.org/0000-0002-3901-2354, Masetti, Giulia, Muller, Ilaria, Verhasselt, Hedda Luise, Covelli, Danila, Colucci, Giuseppe, Zhang, Lei ORCID: https://orcid.org/0000-0003-3536-8692, Draman, Mohd Shazli, Okosieme, Onyebuchi, Taylor, Pete ORCID: https://orcid.org/0000-0002-3436-422X, Daumerie, Chantal, Burlacu, Maria-Cristina, Marinò, Michele, Ezra, Daniel George, Perros, Petros, Plummer, Sue, Eckstein, Anja, Salvi, Mario, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Ludgate, Marian 2023. Gut microbiome associated with Graves disease and Graves orbitopathy: the INDIGO Multicenter European Study. The Journal of Clinical Endocrinology & Metabolism 108 (8) , pp. 2065-2077. 10.1210/clinem/dgad030

Michael, D. R., Kerry-Smith, J., Webberley, T. S., Murphy, K.R., Plummer, S. F., Parry, L. ORCID: https://orcid.org/0000-0002-4467-9196 and Marchesi, J. R. ORCID: https://orcid.org/0000-0002-7994-5239 2023. Does flow culture impact upon gut-probiotic interactions: a comparison with static culture. Journal of Functional Foods 104 , 105519. 10.1016/j.jff.2023.105519

Semertzidou, Anita, Grout-Smith, Harriet, Kalliala, Ilkka, Garg, Akanksha, Terzidou, Vasso, Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239, MacIntyre, David, Bennett, Phillip, Tsilidis, Konstantinos and Kyrgiou, Maria 2023. Diabetes and anti-diabetic interventions and the risk of gynaecological and obstetric morbidity: an umbrella review of the literature. BMC Medicine 21 , 152. 10.1186/s12916-023-02758-1

Whelan, Eilbhe, Kalliala, Ilkka, Semertzidou, Anysia, Raglan, Olivia, Bowden, Sarah, Kechagias, Konstantinos, Markozannes, Georgios, Cividini, Sofia, McNeish, Iain, Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239, MacIntyre, David, Bennett, Phillip, Tsilidis, Kostas and Kyrgiou, Maria 2022. Risk factors for ovarian cancer: An umbrella review of the literature. Cancers 14 (11) , e2708. 10.3390/cancers14112708

Webberley, Thomas S., Masetti, Giulia, Bevan, Ryan J., Kerry-Smith, Joshua, Jack, Alison A., Michael, Daryn R., Thomas, Sophie, Glymenaki, Maria, Li, Jia, McDonald, Julie A. K., John, Daniel, Morgan, James E., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Good, Mark A., Plummer, Sue F. and Hughes, Timothy R. ORCID: https://orcid.org/0000-0003-2348-3490 2022. The impact of probiotic supplementation on cognitive, pathological and metabolic markers in a transgenic mouse model of Alzheimer’s Disease. Frontiers in Neuroscience 16 , 843105. 10.3389/fnins.2022.843105

Allegretti, Jessica R., Kelly, Colleen R., Grinspan, Ari, Mullish, Benjamin H., Hurtado, Jonathan, Carrellas, Madeline, Marcus, Jenna, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, McDonald, Julie A.K., Gerardin, Ylaine, Silverstein, Michael, Pechlivanis, Alexandros, Barker, Grace F., Miguens Blanco, Jesus, Alexander, James L., Gallagher, Kate I., Pettee, Will, Phelps, Emmalee, Nemes, Sara, Sagi, Sashidhar V., Bohm, Matthew, Kassam, Zain and Fischer, Monika 2021. Inflammatory bowel disease outcomes following fecal microbiota transplantation for recurrent C. difficile infection. Inflammatory Bowel Diseases 27 (9) , 1371–1378. 10.1093/ibd/izaa283

Garaiova, I., Paduchová, Z., Nagyová, Z., Wang, D., Michael, D.R., Plummer, S.F., Marchesi, J.R. ORCID: https://orcid.org/0000-0002-7994-5239, Durackova, Z. and Muchová, J. 2021. Probiotics with vitamin C for the prevention of upper respiratory tract symptoms in children aged 3-10 years: randomised controlled trial. Beneficial Microbes 12 (5) , pp. 431-440. 10.3920/BM2020.0185

Li, Jia V., Ashrafian, Hutan, Sarafian, Magali, Homola, Daniel, Rushton, Laura, Barker, Grace, Cabrera, Paula Momo, Lewis, Matthew R., Darzi, Ara, Lin, Edward, Gletsu-Miller, Nana Adwoa, Atkin, Stephen L., Sathyapalan, Thozhukat, Gooderham, Nigel J., Nicholson, Jeremy K., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Athanasiou, Thanos and Holmes, Elaine 2021. Roux-en-Y gastric bypass-induced bacterial perturbation contributes to altered host-bacterial co-metabolic phenotype. Microbiome 9 (1) , 139. 10.1186/s40168-021-01086-x

O'Sullivan, Denise M., Doyle, Ronan M., Temisak, Sasithon, Redshaw, Nicholas, Whale, Alexandra S., Logan, Grace, Huang, Jiabin, Fischer, Nicole, Amos, Gregory C. A., Preston, Mark D., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Wagner, Josef, Parkhill, Julian, Motro, Yair, Denise, Hubert, Finn, Robert D., Harris, Kathryn A., Kay, Gemma L., O?Grady, Justin, Ransom-Jones, Emma, Wu, Huihai, Laing, Emma, Studholme, David J., Benavente, Ernest Diez, Phelan, Jody, Clark, Taane G., Moran-Gilad, Jacob and Huggett, Jim F. 2021. An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities. Scientific Reports 11 , 10590. 10.1038/s41598-021-89881-2

Ghani, Rohma, Mullish, Benjamin H, McDonald, Julie A K, Ghazy, Anan, Williams, Horace R T, Brannigan, Eimear T, Mookerjee, Siddharth, Satta, Giovanni, Gilchrist, Mark, Duncan, Neill, Corbett, Richard, Innes, Andrew J, Pavlů, Jiří, Thursz, Mark R, Davies, Frances and Marchesi, Julian R ORCID: https://orcid.org/0000-0002-7994-5239 2021. Disease prevention not decolonization: a model for fecal microbiota transplantation in patients colonized with multidrug-resistant organisms. Clinical Infectious Diseases 72 (8) , pp. 1444-1447. 10.1093/cid/ciaa948

Mullish, Benjamin H., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, McDonald, Julie A. K., Pass, Daniel A. ORCID: https://orcid.org/0000-0003-2799-8432, Masetti, Giulia, Michael, Daryn R., Plummer, Sue, Jack, Alison A., Davies, Thomas S., Hughes, Timothy R. ORCID: https://orcid.org/0000-0003-2348-3490 and Wang, Duolao 2021. Probiotics reduce self-reported symptoms of upper respiratory tract infection in overweight and obese adults: should we be considering probiotics during viral pandemics? Gut Microbes 13 (1) , pp. 1-9. 10.1080/19490976.2021.1900997

Moshkelgosha, Sajad, Verhasselt, Hedda Luise, Masetti, Giulia, Covelli, Danila, Biscarini, Filippo, Horstmann, Mareike, Daser, Anke, Westendorf, Astrid M., Jesenek, Christoph, Philipp, Svenja, Diaz-Cano, Salvador, Banga, J. Paul, Michael, Daryn, Plummer, Sue, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Eckstein, Anja, Ludgate, Marian and Berchner-Pfannschmidt, Utta 2021. Modulating gut microbiota in a mouse model of Graves' orbitopathy and its impact on induced disease. Microbiome 9 (1) , 45. 10.1186/s40168-020-00952-4

Short, Charlotte-Eve S., Brown, Richard G., Quinlan, Rachael, Lee, Yun S., Smith, Ann, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Shattock, Robin, Bennett, Phillip R., Taylor, Graham P. and MacIntyre, David A. 2021. Lactobacillus-depleted vaginal microbiota in pregnant women living with HIV-1 infection are associated with increased local inflammation and preterm birth. Frontiers in Cellular and Infection Microbiology 10 , 596917. 10.3389/fcimb.2020.596917

Seyfried, Florian, Phetcharaburanin, Jutarop, Glymenaki, Maria, Nordbeck, Arno, Hankir, Mohammed, Nicholson, Jeremy K., Holmes, Elaine, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Li, Jia V. 2021. Roux-en-Y gastric bypass surgery in Zucker rats induces bacterial and systemic metabolic changes independent of caloric restriction-induced weight loss. Gut Microbes 13 (1) , pp. 1-20. 10.1080/19490976.2021.1875108

Michael, D. R., Davies, T. S., Jack, A. A., Masetti, G., Marchesi, J. R. ORCID: https://orcid.org/0000-0002-7994-5239, Wang, D., Mullish, B. H. and Plummer, S. F. 2021. Daily supplementation with the Lab4P probiotic consortium induces significant weight loss in overweight adults. Scientific Reports 11 (1) , 5. 10.1038/s41598-020-78285-3

Huus, Kelsey E., Frankowski, Marcin, Pucic-Bakovic, Maja, Vuckovic, Frano, Lauc, Gordan, Mullish, Benjamin H., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Monaghan, Tanya M., Kao, Dina and Finlay, B. Brett 2021. Changes in IgA-targeted microbiota following fecal transplantation for recurrent Clostridioides difficile infection. Gut Microbes 13 (1) , pp. 1-12. 10.1080/19490976.2020.1862027

Baunwall, Simon Mark Dahl, Lee, Mads Ming, Eriksen, Marcel Kjærsgaard, Mullish, Benjamin H., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Dahlerup, Jens Frederik and Hvas, Christian Lodberg 2020. Faecal microbiota transplantation for recurrent Clostridioides difficile infection: An updated systematic review and meta-analysis. EClinicalMedicine 29 , 100642. 10.1016/j.eclinm.2020.100642

Taylor, Henry, Serrano-Contreras, Jose Ivan, McDonald, Julie A. K., Epstein, Jenny, Fell, JM, Seoane, Rocio C., Li, Jia V., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Hart, Ailsa L. 2020. Multiomic features associated with mucosal healing and inflammation in paediatric Crohn's disease. Alimentary Pharmacology and Therapeutics 52 (9) , pp. 1491-1502. 10.1111/apt.16086

Lowe, John ORCID: https://orcid.org/0000-0003-4772-1879, Gillespie, David ORCID: https://orcid.org/0000-0002-6934-2928, Hubbard, Marie, Zhang, Lei ORCID: https://orcid.org/0000-0003-3536-8692, Kirby, Nigel, Pickles, Timothy ORCID: https://orcid.org/0000-0001-7743-0234, Thomas-Jones, Emma, Turner, Mark A., Klein, Nigel, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Hood, Kerenza ORCID: https://orcid.org/0000-0002-5268-8631, Berrington, Janet and Kotecha, Sailesh ORCID: https://orcid.org/0000-0003-3535-7627 2020. Study protocol: azithromycin therapy for chronic lung disease of prematurity (AZTEC) - a randomised, placebo-controlled trial of azithromycin for the prevention of chronic lung disease of prematurity in preterm infants. BMJ Open 10 (10) , e041528. 10.1136/bmjopen-2020-041528

Skinner, Charlotte, Thompson, Alex J., Thursz, Mark R., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Vergis, Nikhil 2020. Intestinal permeability and bacterial translocation in patients with liver disease, focusing on alcoholic aetiology: methods of assessment and therapeutic intervention. Therapeutic Advances in Gastroenterology 13 , pp. 1-16. 10.1177/1756284820942616

Martinez-Gili, Laura, McDonald, Julie a K., Liu, Zhigang, Kao, Dina, Allegretti, Jessica R., Monaghan, Tanya M., Barker, Grace F., Miguéns Blanco, Jesús, Williams, Horace R. T., Holmes, Elaine, Thursz, Mark R., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Mullish, Benjamin H. 2020. Understanding the mechanisms of efficacy of fecal microbiota transplant in treating recurrent Clostridioides difficile infection and beyond: the contribution of gut microbial-derived metabolites. Gut Microbes 12 (1) , 1810531. 10.1080/19490976.2020.1810531

Pataia, Vanessa, McIlvride, Saraid, Papacleovoulou, Georgia, Ovadia, Caroline, McDonald, Julie A. K., Wahlström, Annika, Jansen, Eugène, Adorini, Luciano, Shapiro, David, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Marschall, Hanns-Ulrich and Williamson, Catherine 2020. Obeticholic acid improves fetal bile acid profile in a mouse model of gestational hypercholanemia. AJP - Gastrointestinal and Liver Physiology 319 (2) , G197-G211. 10.1152/ajpgi.00126.2020

Gallacher, David, Mitchell, Emma, Alber, Dagmar, Wach, Richard, Klein, Nigel, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Kotecha, Sailesh ORCID: https://orcid.org/0000-0003-3535-7627 2020. Dissimilarity of the gut-lung axis and dysbiosis of the lower airways in ventilated preterm infants. European Respiratory Journal 55 (5) , 1901909. 10.1183/13993003.01909-2019

Mitra, Anita, MacIntyre, David A., Ntritsos, George, Smith, Ann, Tsilidis, Konstantinos K., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Bennett, Phillip R., Moscicki, Anna-Barbara and Kyrgiou, Maria 2020. The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions. Nature Communications 11 (1) , 1999. 10.1038/s41467-020-15856-y

May, Stephanie, McDermott, Grace, Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239 and Parry, Lee ORCID: https://orcid.org/0000-0002-4467-9196 2020. Impact of black raspberries on the normal and malignant Apc deficient murine gut microbiome. Journal of Berry Research 10 (1) , pp. 61-76. 10.3233/JBR-180372

Michael, D. R., Jack, A. A., Masetti, G., Davies, T. S., Loxley, K. E., Kerry-Smith, J., Plummer, J. F., Marchesi, J. R. ORCID: https://orcid.org/0000-0002-7994-5239, Mullish, B. H., McDonald, J. A. K., Hughes, T. R. ORCID: https://orcid.org/0000-0003-2348-3490, Wang, D., Garaiova, I., Paduchová, Z., Muchová, J., Good, M. A. ORCID: https://orcid.org/0000-0002-1824-1203 and Plummer, S. F. 2020. A randomised controlled study shows supplementation of overweight and obese adults with lactobacilli and bifidobacteria reduces bodyweight and improves well-being. Scientific Reports 10 (1) , -. 10.1038/s41598-020-60991-7

Ovadia, Caroline, Perdones-Montero, Alvaro, Fan, Hei Man, Mullish, Benjamin H., McDonald, Julie A. K., Papacleovoulou, Georgia, Wahlström, Annika, Ståhlman, Marcus, Tsakmaki, Anastasia, Clarke, Louise C. D., Sklavounos, Alexandros, Dixon, Peter H., Bewick, Gavin A., Walters, Julian R. F., Marschall, Hanns-Ulrich, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Williamson, Catherine 2020. Ursodeoxycholic acid enriches intestinal bile salt hydrolase-expressing Bacteroidetes in cholestatic pregnancy. Scientific Reports 10 (1) , 3895. 10.1038/s41598-020-60821-w

Sequeira, Richard P., McDonald, Julie A. K., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Clarke, Thomas B. 2020. Commensal Bacteroidetes protect against Klebsiella pneumoniae colonization and transmission through IL-36 signalling. Nature Microbiology 5 (2) , pp. 304-313. 10.1038/s41564-019-0640-1

Al-Memar, M., Bobdiwala, S., Fourie, H., Manino, R., Lee, Y.S., Smith, Ashley, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Timmerman, D., Bourne, T., Bennett, P.R. and MacIntyre, D.A. 2020. The association between vaginal bacterial composition and miscarriage: a nested case-control study. BJOG: An International Journal of Obstetrics and Gynaecology 127 (2) , pp. 264-274. 10.1111/1471-0528.15972

Walters, Julian R.F. and Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 2020. Chronic diarrhea, bile acids, and Clostridia. Journal of Clinical Investigation 130 (1) , pp. 77-79. 10.1172/JCI133117

Segal, Jonathan P., Mullish, Benjamin H., Quraishi, Mohammed N., Iqbal, Tariq, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Sokol, Harry 2020. Mechanisms underpinning the efficacy of faecal microbiota transplantation in treating gastrointestinal disease. Therapeutic Advances in Gastroenterology 13 , pp. 1-14. 10.1177/1756284820946904

Segal, Jonathan P., Mak, Joyce W. Y., Mullish, Benjamin H., Alexander, James L., Ng, Siew C. and Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 2020. The gut microbiome: an under-recognised contributor to the COVID-19 pandemic? Therapeutic Advances in Gastroenterology 13 , 175628482097491. 10.1177/1756284820974914

Jukes, Caitlin A., Ijaz, Umer Zeeshan, Buckley, Anthony, Spencer, Janice, Irvine, June, Candlish, Denise, Li, Jia V., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Douce, Gillian 2020. Bile salt metabolism is not the only factor contributing to Clostridioides (Clostridium) difficile disease severity in the murine model of disease. Gut Microbes 11 (3) , pp. 481-496. 10.1080/19490976.2019.1678996

Yalchin, Mehmet, Segal, Jonathan P, Mullish, Benjamin H, Nabil Quraishi, Mohammed, Iqbal, Tariq H, Marchesi, Julian R ORCID: https://orcid.org/0000-0002-7994-5239 and Hart, Ailsa L 2019. Gaps in knowledge and future directions for the use of faecal microbiota transplant in the treatment of inflammatory bowel disease. Therapeutic Advances in Gastroenterology 12 , pp. 1-18. 10.1177/1756284819891038

Pinato, David J., Gramenitskaya, Daria, Altmann, Daniel M., Boyton, Rosemary J., Mullish, Benjamin H., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Bower, Mark 2019. Antibiotic therapy and outcome from immune-checkpoint inhibitors. Journal for ImmunoTherapy of Cancer 7 (1) , 287. 10.1186/s40425-019-0775-x

Salem, Fatouma, Kindt, Nadège, Marchesi, Julian R ORCID: https://orcid.org/0000-0002-7994-5239, Netter, Patrick, Lopez, Anthony, Kokten, Tunay, Danese, Silvio, Jouzeau, Jean-Yves, Peyrin-Biroulet, Laurent and Moulin, David 2019. Gut microbiome in chronic rheumatic and inflammatory bowel diseases: Similarities and differences. United European Gastroenterology Journal 7 (8) , pp. 1008-1032. 10.1177/2050640619867555

Mullish, Benjamin H, McDonald, Julie A K, Pechlivanis, Alexandros, Allegretti, Jessica R, Kao, Dina, Barker, Grace F, Kapila, Diya, Petrof, Elaine O, Joyce, Susan A, Gahan, Cormac G M, Glegola-Madejska, Izabela, Williams, Horace R T, Holmes, Elaine, Clarke, Thomas B, Thursz, Mark R and Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 2019. Microbial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent Clostridioides difficile infection. Gut 68 (10) , pp. 1791-1800. 10.1136/gutjnl-2018-317842

Scott, Alasdair J., Alexander, James L., Merrifield, Claire A., Cunningham, David, Jobin, Christian, Brown, Robert, Alverdy, John, O'Keefe, Stephen J., Gaskins, H. Rex, Teare, Julian, Yu, Jun, Hughes, David J, Verstraelen, Hans, Burton, Jeremy, O'Toole, Paul W., Rosenberg, Daniel W., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Kinross, James M. 2019. International Cancer Microbiome Consortium consensus statement on the role of the human microbiome in carcinogenesis. Gut 68 , pp. 1624-1632. 10.1136/gutjnl-2019-318556

McIlvride, Saraid, Nikolova, Vanya, Fan, Hei Man, McDonald, Julie A. K., Wahlström, Annika, Bellafante, Elena, Jansen, Eugene, Adorini, Luciano, Shapiro, David, Jones, Peter, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Marschall, Hanns-Ulrich and Williamson, Catherine 2019. Obeticholic acid ameliorates dyslipidemia but not glucose tolerance in mouse model of gestational diabetes. AJP - Endocrinology and Metabolism 317 (2) , E399-E410. 10.1152/ajpendo.00407.2018

Chambers, Edward S, Byrne, Claire S, Morrison, Douglas J, Murphy, Kevin G, Preston, Tom, Tedford, Catriona, Garcia-Perez, Isabel, Fountana, Sofia, Serrano-Contreras, Jose Ivan, Holmes, Elaine, Reynolds, Catherine J, Roberts, Jordie F, Boyton, Rosemary J, Altmann, Daniel M, McDonald, Julie A K, Marchesi, Julian R ORCID: https://orcid.org/0000-0002-7994-5239, Akbar, Arne N, Riddell, Natalie E, Wallis, Gareth A and Frost, Gary S 2019. Dietary supplementation with inulin-propionate ester or inulin improves insulin sensitivity in adults with overweight and obesity with distinct effects on the gut microbiota, plasma metabolome and systemic inflammatory responses: a randomised cross-over trial. Gut 68 (8) , pp. 1430-1438. 10.1136/gutjnl-2019-318424

Ovadia, Caroline, Perdones-Montero, Alvaro, Spagou, Konstantina, Smith, Ann, Sarafian, Magali H., Gomez-Romero, Maria, Bellafante, Elena, Clarke, Louise C.D., Sadiq, Fouzia, Nikolova, Vanya, Mitchell, Alice, Dixon, Peter H., Santa-Pinter, Natalie, Wahlström, Annika, Abu-Hayyeh, Shadi, Walters, Julian R.F., Marschall, Hanns-Ulrich, Holmes, Elaine, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Williamson, Catherine 2019. Enhanced microbial bile acid deconjugation and impaired ileal uptake in pregnancy repress intestinal regulation of bile acid synthesis. Hepatology 70 (1) , pp. 276-293. 10.1002/hep.30661

Mullish, B.H., Ghani, R., McDonald, J.A.K. and Marchesi, J.R. ORCID: https://orcid.org/0000-0002-7994-5239 2019. Faecal microbiota transplant for eradication of multidrug-resistant Enterobacteriaceae: a lesson in applying best practice? Re: 'a five-day course of oral antibiotics followed by faecal transplantation to eradicate carriage of multidrug-resistant Enterobacteriaceae: a randomized clinical trial'. Clinical Microbiology and Infection 25 (7) , pp. 912-913. 10.1016/j.cmi.2019.01.010

Brown, R.G., Chan, D., Terzidou, V., Lee, Y.S., Smith, A., Marchesi, J.R. ORCID: https://orcid.org/0000-0002-7994-5239, MacIntyre, D.A. and Bennett, P.R. 2019. Prospective observational study of vaginal microbiota pre- and post-rescue cervical cerclage. BJOG: An International Journal of Obstetrics and Gynaecology 126 (7) , pp. 916-925. 10.1111/1471-0528.15600

Brown, Richard G., Al-Memar, Maya, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Lee, Yun S, Smith, Ann, Chan, Denise, Lewis, Holly, Kindinger, Lindsay, Terzidou, Vasso, Bourne, Tom, Bennett, Phillip R. and MacIntyre, David A. 2019. Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes. Translational Research, The Journal of Laboratory and Clinical Medicine 207 , pp. 30-43. 10.1016/j.trsl.2018.12.005

Hegade, Vinod S., Pechlivanis, Alexandros, McDonald, Julie A. K., Rees, Douglas, Corrigan, Margaret, Hirschfield, Gideon M., Taylor-Robinson, Simon D., Holmes, Elaine, Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239, Kendrick, Stuart and Jones, David E. 2019. Autotaxin, bile acid profile and effect of ileal bile acid transporter inhibition in primary biliary cholangitis patients with pruritus. Liver International 39 (5) , pp. 967-975. 10.1111/liv.14069

Maurice, James B., Garvey, Lucy, Tsochatzis, Emmanuel A., Wiltshire, Matthew, Cooke, Graham, Guppy, Naomi, McDonald, Julie, Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239, Nelson, Mark, Kelleher, Peter, Goldin, Robert, Thursz, Mark and Lemoine, Maud 2019. Monocyte-macrophage activation is associated with nonalcoholic fatty liver disease and liver fibrosis in HIV monoinfection independently of the gut microbiome and bacterial translocation. AIDS 33 (5) , pp. 805-814. 10.1097/QAD.0000000000002133

Segal, Jonathan P., Mullish, Benjamin H., Quraishi, Mohammed Nabil, Acharjee, Animesh, Williams, Horace R. T., Iqbal, Tariq, Hart, Ailsa L. and Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 2019. The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease. Therapeutic Advances in Gastroenterology 12 , pp. 1-13. 10.1177/1756284818822250

Simon, Jean-Christophe, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Mougel, Christophe and Selosse, Marc-André 2019. Host-microbiota interactions: from holobiont theory to analysis. Microbiome 7 (1) , -. 10.1186/s40168-019-0619-4

Monaghan, Tanya, Mullish, Benjamin H, Patterson, Jordan, Wong, Gane K S, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Xu, Huiping, Jilani, Tahseen and Kao, Dina 2019. Effective fecal microbiota transplantation for recurrent Clostridioides difficile infection in humans is associated with increased signalling in the bile acid-farnesoid X receptor-fibroblast growth factor pathway. Gut Microbes 10 (2) , pp. 142-148. 10.1080/19490976.2018.1506667

Moshkelgosha, Sajad, Masetti, Giulia, Berchner-Pfannschmidt, Utta, Verhasselt, Hedda Luise, Horstmann, Mareike, Diaz-Cano, Salvador, Noble, Alistair, Edelman, Barbel, Covelli, Danila, Plummer, Sue, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Ludgate, Marian, Biscarini, Filippo ORCID: https://orcid.org/0000-0002-3901-2354, Eckstein, Anja and Banga, J. Paul 2018. Gut microbiome in BALB/c and C57BL/6J mice undergoing experimental thyroid autoimmunity associate with differences in immunological responses and thyroid function. Hormone and Metabolic Research 50 (12) , pp. 932-941. 10.1055/a-0653-3766

McDonald, Julie A.K., Mullish, Benjamin H., Pechlivanis, Alexandros, Liu, Zhigang, Brignardello, Jerusa, Kao, Dina, Holmes, Elaine, Li, Jia V., Clarke, Thomas B., Thursz, Mark R. and Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 2018. Inhibiting growth of Clostridioides difficile by restoring valerate, produced by the intestinal microbiota. Gastroenterology 155 (5) , pp. 1495-1507. 10.1053/j.gastro.2018.07.014

Naz, Iffat, Hodgson, Douglas, Smith, Ann, Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239, Sehar, Shama, Ahmed, Safia, Lynch, Jim, Avignone-Rossa, Claudio and Saroj, Devendra P 2018. Investigation of the active biofilm communities on polypropylene filter media in a fixed biofilm reactor for wastewater treatment. Journal of Chemical Technology and Biotechnology 93 (11) , pp. 3264-3275. 10.1002/jctb.5686

Mullish, Benjamin H., Pechlivanis, Alexandros, Barker, Grace F., Thursz, Mark R., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and McDonald, Julie A.K. 2018. Functional microbiomics: Evaluation of gut microbiota-bile acid metabolism interactions in health and disease. Methods 149 , pp. 49-58. 10.1016/j.ymeth.2018.04.028

Pruski, Pamela, Lewis, Holly V., Lee, Yun S., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Bennett, Phillip R., Takats, Zoltan and MacIntyre, David A. 2018. Assessment of microbiota:host interactions at the vaginal mucosa interface. Methods 149 , pp. 74-84. 10.1016/j.ymeth.2018.04.022

Pouncey, Anna Louise, Scott, Alasdair James, Alexander, James Leslie, Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239 and Kinross, James 2018. Gut microbiota, chemotherapy and the host: the influence of the gut microbiota on cancer treatment. ecancermedicalscience 12 , 868. 10.3332/ecancer.2018.868

Alexander, James L, Scott, Alasdair J, Pouncey, Anna L, Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239, Kinross, James and Teare, Julian 2018. Colorectal carcinogenesis: an archetype of gut microbiota-host interaction. ecancermedicalscience 12 , 865. 10.3332/ecancer.2018.865

Mullish, Benjamin H, Osborne, Laura S, Marchesi, Julian R ORCID: https://orcid.org/0000-0002-7994-5239 and McDonald, Julie AK 2018. The implementation of omics technologies in cancer microbiome research. ecancermedicalscience 12 , 864. 10.3332/ecancer.2018.864

Mullish, Benjamin H., McDonald, Julie A.K., Thursz, Mark R. and Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 2018. Antibiotic-associated disruption of microbiota composition and function in cirrhosis is restored by fecal transplant. Hepatology 68 (3) , p. 1205. 10.1002/hep.30090

Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 2018. Advancing microbiome research. Microbiology 164 (8) , pp. 1005-1006. 10.1099/mic.0.000688

Martin, Glynn, Kolida, Sofia, Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239, Want, Elizabeth, Sidaway, James E. and Swann, Jonathan R. 2018. In vitro modeling of bile acid processing by the human fecal microbiota. Frontiers in Microbiology 9 , 1153. 10.3389/fmicb.2018.01153

Masetti, Giulia, Moshkelgosha, Sajad, Kohling, Hedda-Luise, Covelli, Danila, Banga, Jasvinder Paul, Berchner-Pfannschmidt, Utta, Horstmann, Mareike, Diaz-Cano, Salvador, Goertz, Gina-Eva, Plummer, Sue, Eckstein, Anja, Ludgate, Marian, Biscarini, Filippo ORCID: https://orcid.org/0000-0002-3901-2354 and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2018. Gut microbiota in experimental murine model of Graves' orbitopathy established in different environments may modulate clinical presentation of disease. Microbiome 6 , 97. 10.1186/s40168-018-0478-4

Brown, Richard G., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Lee, Yun S., Smith, Ann, Lehne, Benjamin, Kindinger, Lindsay M., Terzidou, Vasso, Holmes, Elaine, Nicholson, Jeremy K., Bennett, Phillip R. and MacIntyre, David A. 2018. Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin. BMC Medicine 16 , 9. 10.1186/s12916-017-0999-x

Cobbold, Jeremy F.L., Atkinson, Stephen, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Smith, Ann, Wai, Sann N., Stove, Julie, Shojaee-Moradie, Fariba, Jackson, Nicola, Umpleby, A. Margot, Fitzpatrick, Julie, Thomas, E. Louise, Bell, Jimmy D., Holmes, Elaine, Taylor-Robinson, Simon D., Goldin, Robert D., Yee, Michael S., Anstee, Quentin M. and Thursz, Mark R. 2018. Rifaximin in non-alcoholic steatohepatitis: an open-label pilot study. Hepatology Research 48 (1) , pp. 69-77. 10.1111/hepr.12904

Ding, Nik Sheng, Mullish, Benjamin H., McLaughlin, John, Hart, Ailsa and Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 2018. Meeting update: faecal microbiota transplantation-bench, bedside, courtroom? Frontline Gastroenterology 9 (1) , pp. 45-48. 10.1136/flgastro-2016-100752

Pascoe, Emily L. ORCID: https://orcid.org/0000-0003-3493-3485, Hauffe, Heidi C., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Perkins, Sarah E. ORCID: https://orcid.org/0000-0002-7457-2699 2017. Network analysis of gut microbiota literature: an overview of the research landscape in non-human animal studies. ISME Journal 11 (12) , pp. 2644-2651. 10.1038/ismej.2017.133

Scott, Alasdair, Merrifield, Claire, Alexander, James, Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239 and Kinross, James 2017. Highlights from the Inaugural International Cancer Microbiome Consortium Meeting (ICMC), 5-6 September 2017, London, UK. ecancermedicalscience 11 10.3332/ecancer.2017.791

O'Hagan, Caroline, Li, Jia V., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Plummer, Sue, Garaiova, Iveta and Good, Mark A. ORCID: https://orcid.org/0000-0002-1824-1203 2017. Long-term multi-species Lactobacillus and Bifidobacterium dietary supplement enhances memory and changes regional brain metabolites in middle-aged rats. Neurobiology of Learning and Memory 144 , pp. 36-47. 10.1016/j.nlm.2017.05.015

Köhling, Hedda L., Plummer, Sue F., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Davidge, Kelly S. and Ludgate, Marian 2017. The microbiota and autoimmunity: their role in thyroid autoimmune diseases. Clinical Immunology 183 , pp. 63-74. 10.1016/j.clim.2017.07.001

Mullish, Benjamin H., McDonald, Julie A. K., Thursz, Mark R. and Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 2017. Fecal microbiota transplant from a rational stool donor improves hepatic encephalopathy: a randomized clinical trial. Hepatology 66 (4) , pp. 1354-1355. 10.1002/hep.29369

Mitra, Anita, MacIntyre, David A., Mahajan, Vishakha, Lee, Yun S., Smith, Ann, Marchesi, Julian r. ORCID: https://orcid.org/0000-0002-7994-5239, Lyons, Deirdre, Bennett, Phillip R. and Kyrgiou, Maria 2017. Comparison of vaginal microbiota sampling techniques: cytobrush versus swab. Scientific Reports 7 (1) , 9802. 10.1038/s41598-017-09844-4

Kinross, James, Mirnezami, Reza, Alexander, James, Brown, Richard, Scott, Alasdair, Galea, Dieter, Veselkov, Kirill, Goldin, Rob, Darzi, Ara, Nicholson, Jeremy and Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 2017. A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy. Scientific Reports 7 (1) , 8979. 10.1038/s41598-017-08150-3

Marino, Paola J., Wise, Matt P., Smith, Ann, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Riggio, Marcello P, Lewis, Michael A O ORCID: https://orcid.org/0000-0003-1917-0651 and Williams, David W. ORCID: https://orcid.org/0000-0002-7351-5131 2017. Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients. Journal of Critical Care 39 , pp. 149-155. 10.1016/j.jcrc.2017.02.020

Michael, D. R., Davies, T. S., Moss, J. W. E., Calvente, D. Lama, Ramji, D. P. ORCID: https://orcid.org/0000-0002-6419-5578, Marchesi, J. R. ORCID: https://orcid.org/0000-0002-7994-5239, Pechlivanis, A., Plummer, S. F. and Hughes, T. R. ORCID: https://orcid.org/0000-0003-2348-3490 2017. The anti-cholesterolaemic effect of a consortium of probiotics: An acute study in C57BL/6J mice. Scientific Reports 7 , 2883. 10.1038/s41598-017-02889-5

Drake, Marcus J., Morris, Nicola, Apostolidis, Apostolos, Rahnama'i, Mohammad S. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2017. The urinary microbiome and its contribution to lower urinary tract symptoms; ICI-RS 2015. Neurourology and Urodynamics 36 (4) , pp. 850-853. 10.1002/nau.23006

O'Toole, Paul W., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Hill, Colin 2017. Next-generation probiotics: the spectrum from probiotics to live biotherapeutics. Nature Microbiology 2 (5) , 17057. 10.1038/nmicrobiol.2017.57

Alexander, James L., Wilson, Ian D., Teare, Julian, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Nicholson, Jeremy K. and Kinross, James M. 2017. Gut microbiota modulation of chemotherapy efficacy and toxicity. Nature Reviews Gastroenterology & Hepatology 14 (6) , pp. 356-365. 10.1038/nrgastro.2017.20

Li, Jia V., Swann, Jonathan and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2017. Biology of the microbiome 2: metabolic role. Gastroenterology Clinics of North America 46 (1) , pp. 37-47. 10.1016/j.gtc.2016.09.006

Kindinger, Lindsay M., Bennett, Phillip R., Lee, Yun S, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Smith, Ann, Cacciatore, Stefano, Holmes, Elaine, Nicholson, Jeremy K., Teoh, T. G. and MacIntyre, David A. 2017. The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk. Microbiome 5 , 6. 10.1186/s40168-016-0223-9

Lynch, Alli, Crowley, Elaine, Casey, Eoghan, Cano, Rafael, Shanahan, Rachel, McGlacken, Ger, Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239 and Clarke, David J. 2017. The Bacteroidales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolytic activity. Scientific Reports 7 (1) , 13270. 10.1038/s41598-017-13774-6

Innes, Andrew J., Mullish, Benjamin H., Fernando, Fiona, Adams, George, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Apperley, Jane F., Brannigan, Eimear, Davies, Frances and Pavlu, Jiri 2017. Faecal microbiota transplant: a novel biological approach to extensively drug-resistant organism-related non-relapse mortality [Letter to the Editor]. Bone Marrow Transplantation 52 (10) , pp. 1452-1454. 10.1038/bmt.2017.151

Mitra, Anita, MacIntyre, David A., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Lee, Yun S., Bennett, Phillip R. and Kyrgiou, Maria 2016. The vaginal microbiota, human papillomavirus infection and cervical intraepithelial neoplasia: what do we know and where are we going next? Microbiome 4 , 58. 10.1186/s40168-016-0203-0

Kindinger, Lindsay M., MacIntyre, David A., Lee, Yun S., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Smith, Ann, McDonald, Julie A. K., Terzidou, Vasso, Cook, Joanna R., Lees, Christoph, Israfil-Bayli, Fidan, Faiza, Yazmin, Toozs-Hobson, Philip, Slack, Mark, Cacciatore, Stefano, Holmes, Elaine, Nicholson, Jeremy K., Teoh, T. G. and Bennett, Phillip R. 2016. Relationship between vaginal microbial dysbiosis, inflammation, and pregnancy outcomes in cervical cerclage. Science Translational Medicine 8 (350) , 350ra102. 10.1126/scitranslmed.aag1026

Hodgson, Douglas M., Smith, Ann, Dahale, Sonal, Stratford, James P., Li, Jia V., Grüning, Andre, Bushell, Michael E., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Avignone Rossa, C. 2016. Segregation of the anodic microbial communities in a microbial fuel cell cascade. Frontiers in Microbiology 7 , 699. 10.3389/fmicb.2016.00699

Gratton, Jasmine, Phetcharaburanin, Jutarop, Mullish, Benjamin H., Williams, Horace R. T., Thursz, Mark, Nicholson, Jeremy K., Holmes, Elaine, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Li, Jia V. 2016. Optimized sample handling strategy for metabolic profiling of human feces. Analytical Chemistry 88 (9) , pp. 4661-4668. 10.1021/acs.analchem.5b04159

Phetcharaburanin, Jutarop, Lees, Hannah, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Nicholson, Jeremy K., Holmes, Elaine, Seyfried, Florian and Li, Jia V. 2016. Systemic characterization of an obese phenotype in the Zucker rat model defining metabolic axes of energy metabolism and host-microbial interactions. Journal of Proteome Research 15 (6) , pp. 1897-1906. 10.1021/acs.jproteome.6b00090

Morris, Laura S. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2016. Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity. Journal of Microbiological Methods 123 , pp. 31-38. 10.1016/j.mimet.2016.02.001

Broaders, Eileen, O'Brien, Ciarán, Gahan, Cormac G. M. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2016. Evidence for plasmid mediated salt tolerance in the human gut microbiome and potential mechanisms. FEMS Microbiology Ecology 92 (3) , fiw019. 10.1093/femsec/fiw019

Holmes, Elaine, MacIntyre, David, Modi, Neena and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2016. Handing on health to the next generation. Holmes, Elaine, Nicholson, Jeremy K., Darzi, Ara W. and Lindon, John C., eds. Metabolic Phenotyping in Personalized and Public Healthcare, Academic Press, pp. 213-264. (10.1016/B978-0-12-800344-2.00008-2)

Kinross, James and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2016. The aging superorganism. Holmes, Elaine, Nicholson, Jeremy K., Darzi, Ara W. and Lindon, John C., eds. Metabolic Phenotyping in Personalized and Public Healthcare, Academic Press, pp. 265-290. (10.1016/B978-0-12-800344-2.00009-4)

Sands, Kirsty M., Twigg, Joshua A. ORCID: https://orcid.org/0000-0002-4567-7854, Lewis, Michael A. O. ORCID: https://orcid.org/0000-0003-1917-0651, Wise, Matt P., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Smith, Ann, Wilson, Melanie ORCID: https://orcid.org/0000-0002-8834-8268 and Williams, David W. ORCID: https://orcid.org/0000-0002-7351-5131 2016. Microbial profiling of dental plaque from mechanically ventilated patients. Journal of Medical Microbiology 65 (2) , pp. 147-159. 10.1099/jmm.0.000212

Naz, Iffat, Hodgson, Douglas, Smith, Ann, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Ahmed, Safia, Avignone-Rossa, Claudio and Saroj, Devendra P. 2016. Effect of the chemical composition of filter media on the microbial community in wastewater biofilms at different temperatures. RSC Advances 6 (106) , pp. 104345-104353. 10.1039/C6RA21040F

Mitra, A., MacIntyre, D. A., Lee, Y. S., Smith, A., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Lehne, B., Bhatia, R., Lyons, D., Paraskevaidis, E., Li, J. V., Holmes, E., Nicholson, J. K., Bennett, P. R. and Kyrgiou, M. 2015. Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity. Scientific Reports 5 , 16865. 10.1038/srep16865

Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Adams, David H., Fava, Francesca, Hermes, Gerben D. A., Hirschfield, Gideon M., Hold, Georgina, Quraishi, Mohammed Nabil, Kinross, James, Smidt, Hauke, Tuohy, Kieran M., Thomas, Linda V., Zoetendal, Erwin G. and Hart, Ailsa 2015. The gut microbiota and host health: a new clinical frontier. Gut 65 (2) , pp. 330-339. 10.1136/gutjnl-2015-309990

Kreisinger, Jakub, Bastien, Géraldine, Hauffe, Heidi C., Marchesi, Julian ORCID: https://orcid.org/0000-0002-7994-5239 and Perkins, Sarah E. ORCID: https://orcid.org/0000-0002-7457-2699 2015. Interactions between multiple helminths and the gut microbiota in wild rodents. Philosophical Transactions B: Biological Sciences 370 (1675) , 20140295. 10.1098/rstb.2014.0295

Flight, William G., Smith, Ann, Paisey, Christopher, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Bull, Matthew J., Norville, Phillip J., Mutton, Ken J., Webb, A. Kevin, Bright-Thomas, Rowland J., Jones, Andrew M., Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 and McAdam, A. J. 2015. Rapid detection of emerging pathogens and loss of microbial diversity associated with severe lung disease in cystic fibrosis. Journal of Clinical Microbiology 53 (7) , pp. 2022-2029. 10.1128/JCM.00432-15

Mullish, B. H., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Thursz, M. R. and Williams, H. R. T. 2015. Microbiome manipulation with faecal microbiome transplantation as a therapeutic strategy in Clostridium difficile infection. QJM: An International Journal of Medicine 108 (5) , pp. 355-359. 10.1093/qjmed/hcu182

MacIntyre, David A., Chandiramani, Manju, Lee, Yun S., Kindinger, Lindsay, Smith, Ann, Angelopoulos, Nicos ORCID: https://orcid.org/0000-0002-7507-9177, Lehne, Benjamin, Arulkumaran, Shankari, Brown, Richard, Teoh, Tiong Ghee, Holmes, Elaine, Nicoholson, Jeremy K., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Bennett, Phillip R. 2015. The vaginal microbiome during pregnancy and the postpartum period in a European population. Scientific Reports 5 , 8988. 10.1038/srep08988

O'Mahony, Mark M., Henneberger, Ruth, Selvin, Joseph, Kennedy, Jonathan, Doohan, Fiona, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Dobson, Alan D. W. 2015. Inhibition of the growth of Bacillus subtilis DSM10 by a newly discovered antibacterial protein from the soil metagenome. Bioengineered 6 (2) , pp. 89-98. 10.1080/21655979.2015.1018493

Morris, Laura S. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2015. Current functional metagenomic approaches only expand the existing protease sequence space, but does not presently add any novelty to it. Current Microbiology 70 (1) , pp. 19-26. 10.1007/s00284-014-0677-6

Lamour, Sabrina D., Veselkov, Kirill A., Posma, Joram M., Giraud, Emilie, Rogers, Matthew E., Croft, Simon, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Holmes, Elaine, Seifert, Karin and Saric, Jasmina 2015. Metabolic, immune, and gut microbial signals mount a systems response to Leishmania major infection. Journal of Proteome Research 14 (1) , pp. 318-329. 10.1021/pr5008202

Progatzky, Fränze, Sangha, Navjyot J., Yoshida, Nagisa, McBrien, Marie, Cheung, Jackie, Shia, Alice, Scott, James, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Lamb, Jonathan R., Bugeon, Laurence and Dallman, Margaret J. 2014. Dietary cholesterol directly induces acute inflammasome-dependent intestinal inflammation. Nature Communications 5 , 5864. 10.1038/ncomms6864

Bull, Matthew J., Jolley, Keith A., Bray, James E., Aerts, Maarten, Vandamme, Peter, Maiden, Martin C. J., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 2014. The domestication of the probiotic bacterium Lactobacillus acidophilus. Scientific Reports 4 , 7202. 10.1038/srep07202

O'Mahony, S. M., Felice, V. D., Nally, K., Savignac, H. M., Claesson, M. J., Scully, P., Woznicki, J., Hyland, N. P., Shanahan, F., Quigley, E. M., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, O'Toole, P. W., Dinan, T. L. and Cryan, J. F. 2014. Disturbance of the gut microbiota in early-life selectively affects visceral pain in adulthood without impacting cognitive or anxiety-related behaviors in male rats. Neuroscience 277 , pp. 885-901. 10.1016/j.neuroscience.2014.07.054

Lees, Hannah, Swann, Jonathan, Poucher, Simon M., Nicholson, Jeremy K., Holmes, Elaine, Wilson, Ian D. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2014. Age and microenvironment outweigh genetic influence on the zucker rat microbiome. PLoS ONE 9 (9) , e100916. 10.1371/journal.pone.0100916

Peng, Jian, Narasimhan, Sukanya, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Benson, Andrew, Wong, Florence Susan ORCID: https://orcid.org/0000-0002-2812-8845 and Wen, Li 2014. Long term effect of gut microbiota transfer on diabetes development. Journal of Autoimmunity 53 , pp. 85-94. 10.1016/j.jaut.2014.03.005

Culligan, Eamonn P., Sleator, Roy D., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Hill, Colin 2014. Metagenomic identification of a novel salt tolerance gene from the human gut microbiome which encodes a membrane protein with homology to a brp/blh-family β-Carotene 15,15′-Monooxygenase. PLoS ONE 9 (7) , e103318. 10.1371/journal.pone.0103318

Culligan, Eamonn P., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Hill, Colin and Sleator, Roy D. 2014. Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome. Frontiers in Microbiology 5 , 189. 10.3389/fmicb.2014.00189

Culligan, Eamonn P., Sleator, Roy D., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Hill, Colin 2014. Metagenomics and novel gene discovery: promise and potential for novel therapeutics. Virulence 5 (3) , pp. 1-14. 10.4161/viru.27208

Bull, Matthew J., Plummer, Sue, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 2013. The life history of 'Lactobacillus acidophilus' as a probiotic: a tale of revisionary taxonomy, misidentification and commercial success. FEMS Microbiology Letters 349 (2) , pp. 77-87. 10.1111/1574-6968.12293

Lewis, Debbie A., Brown, Richard C., Williams, Jon, White, Paul, Jacobsen, S. Kim, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Drake, Marcus J. 2013. The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. Frontiers in Cellular and Infection Microbiology 3 , p. 41. 10.3389/fcimb.2013.00041

Broaders, Eileen, Gahan, Cormac and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2013. Mobile genetic elements of the human gastrointestinal tract: Potential for spread of antibiotic resistance genes. Gut Microbes 4 (4) , pp. 271-280. 10.4161/gmic.24627

Van Woerden, Hugo C., Gregory, Clive James ORCID: https://orcid.org/0000-0003-4876-3982, Brown, Richard C., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Hoogendoorn, Bastiaan ORCID: https://orcid.org/0000-0001-9753-169X and Matthews, Ian Price 2013. Differences in fungi present in induced sputum samples from asthma patients and non-atopic controls: a community based case control study. BMC Infectious Diseases 13 , 69. 10.1186/1471-2334-13-69

Moreno-Hagelsieb, Gabriel, Culligan, Eamonn P., Sleator, Roy D., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Hill, Colin 2013. Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome. PLoS ONE 8 (12) , e82985. 10.1371/journal.pone.0082985

Prorok-Hamon, M., Friswell, M. K., Alswied, A., Roberts, C. L., Song, F., Flanagan, P. K., Knight, P., Codling, C., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Winstanley, C., Hall, N., Rhodes, J. M. and Campbell, B. J. 2013. Colonic mucosa-associated diffusely adherent afaC+ Escherichia coli expressing lpfA and pks are increased in inflammatory bowel disease and colon cancer. Gut 63 (5) , pp. 761-770. 10.1136/gutjnl-2013-304739

Culligan, Eamonn P., Sleator, Roy D., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Hill, Colin 2012. Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome. ISME Journal 6 (10) , pp. 1916-1925. 10.1038/ismej.2012.38

Tjalsma, Harold, Boleij, Annemarie, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Dutilh, Bas E. 2012. A bacterial driver-passenger model for colorectal cancer: beyond the usual suspects. Nature Reviews. Microbiology 10 (8) , pp. 575-582. 10.1038/nrmicro2819

Tilg, Herbert and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2012. Too much fat for the gut's microbiota. Gut 61 (4) , pp. 474-475. 10.1136/gutjnl-2011-301918

Bull, Matthew J., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Vandamme, Peter, Plummer, Sue and Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 2012. Minimum taxonomic criteria for bacterial genome sequence depositions and announcements. Journal of Microbiological Methods 89 (1) , pp. 18-21. 10.1016/j.mimet.2012.02.008

Turroni, Francesca, Peano, Clelia, Pass, Daniel A. ORCID: https://orcid.org/0000-0003-2799-8432, Foroni, Elena, Severgnini, Marco, Claesson, Marcus J., Kerr, Colm, Hourihane, Jonathan, Murray, Deirdre, Fuligni, Fabio, Gueimonde, Miguel, Margolles, Abelardo, De Bellis, Gianluca, O'Toole, Paul W., van Sinderen, Douwe, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Ventura, Marco 2012. Diversity of bifidobacteria within the infant gut microbiota. PLoS ONE 7 (5) , e36957. 10.1371/journal.pone.0036957

Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Li, Jia, Holmes, Elaine, Ashrafian, Hutan, Athanasiou, Thanos, Darzi, Ara and Nicholson, Jeremy K. 2012. Reply [to Eileen F. Murphy, Eamonn M.M. Quigley: The Microbiota and Bariatric Surgery: It's a Bug's Life. Gastroenterology, Volume 142, Issue 2, February 2012, Pages 399-401]. Gastroenterology 142 (2) , pp. 401-402. 10.1053/j.gastro.2011.12.024

Claesson, Marcus J., Jeffery, Ian B., Conde, Susana, Power, Susan E., O'Connor, Eibhlís M., Cusack, Siobhán, Harris, Hugh M. B., Coakley, Mairead, Lakshminarayanan, Bhuvaneswari, O'Sullivan, Orla, Fitzgerald, Gerald F., Deane, Jennifer, O'Connor, Michael, Harnedy, Norma, O'Connor, Kieran, O'Mahony, Denis, van Sinderen, Douwe, Wallace, Martina, Brennan, Lorraine, Stanton, Catherine, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Fitzgerald, Anthony P., Shanahan, Fergus, Hill, Colin, Ross, R. Paul and O'Toole, Paul W. 2012. Gut microbiota composition correlates with diet and health in the elderly. Nature 488 (7410) , pp. 178-184. 10.1038/nature11319

Morris, Laura, Evans, James and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2012. A robust plate assay for detection of extracellular microbial protease activity in metagenomic screens and pure cultures. Journal of Microbiological Methods 91 (1) , pp. 144-146. 10.1016/j.mimet.2012.08.006

Baker, Paul W., Dobson, Alan D. W. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2012. In situ extraction of RNA from marine-derived fungi associated with the marine sponge, Haliclona simulans. Mycological Progress 11 (4) , pp. 953-956. 10.1007/s11557-011-0796-4

Holmes, Elaine, Li, Jia V., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Nicholson, Jeremy K. 2012. Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk. Cell Metabolism 16 (5) , pp. 559-564. 10.1016/j.cmet.2012.10.007

Marchesi, Julian Robert ORCID: https://orcid.org/0000-0002-7994-5239 2011. Human distal gut microbiome. Environmental Microbiology 13 (12) , pp. 3088-3102. 10.1111/j.1462-2920.2011.02574.x

Twomey, K., Alvarez de Eulate, E., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Kolida, S., Gibson, G., Arrigan, D. W. M. and Ogurtsov, V. I. 2011. Characterization of the electrochemical behavior of gastrointestinal fluids using a multielectrode sensor probe. IEEE Transactions on Biomedical Engineering 58 (9) , pp. 2521-2527. 10.1109/TBME.2011.2158543

Brown, Richard C., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Morby, Andrew P. 2011. Functional characterisation of Lp_2714, an EAL-domain protein from Lactobacillus plantarum. Biochemical and Biophysical Research Communications 411 (1) , pp. 132-136. 10.1016/j.bbrc.2011.06.112

Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Dutilh, Bas, Hall, Neil, Peters, Wilbert, Roelofs, Rian, Boleij, Annemarie and Tjalsma, Harold 2011. Towards the human colorectal cancer microbiome. PLoS ONE 6 (5) , e20447. 10.1371/journal.pone.0020447

Claesson, Marcus J., Cusack, Siobhán, O'Sullivan, Orla, Greene-Diniz, Rachel, de Weerd, Heleen, Flannery, Edel, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Falush, Daniel, Dinan, Timothy, Fitzgerald, Gerald, Stanton, Catherine, van Sinderen, Douwe, O'Connor, Michael, Harnedy, Norma, O'Connor, Kieran, Henry, Colm, O'Mahony, Denis, Fitzgerald, Anthony P., Shanahan, Fergus, Twomey, Cillian, Hill, Colin, Ross, R. Paul and O'Toole, Paul W. 2011. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proceedings of the National Academy of Sciences of the United States of America 108 (S1) , pp. 4586-4591. 10.1073/pnas.1000097107

Li, J. V., Ashrafian, H., Bueter, M., Kinross, J., Sands, C., le Roux, C. W., Bloom, S. R., Darzi, A., Athanasiou, T., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Nicholson, J. K. and Holmes, E. 2011. Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk. Gut 60 (9) , pp. 1214-1223. 10.1136/gut.2010.234708

Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2011. Shifting from a gene-centric to metabolite-centric strategy to determine the core gut microbiome. Bioengineered Bugs 2 (6) , pp. 309-314. 10.4161/bbug.2.6.17235

Baker, P. W., Kennedy, J., Morrissey, J., O'Gara, F., Dobson, A. D. W. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2010. Endoglucanase activities and growth of marine-derived fungi isolated from the sponge Haliclona simulans. Journal of Applied Microbiology 108 (5) , 1668 -1675. 10.1111/j.1365-2672.2009.04563.x

Friswell, M. K., Roberts, C. L., Winstanley, C., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Rhodes, J. M. and Campbell, B. J. 2010. Increased mucosa-associated diffusely adherent E coli in Crohn's and colon cancer: possible role in pathogenesis [Abstract]. Gut 59 (S1) , A110. 10.1136/gut.2009.208983h

Jones, Brian, Sun, Funing and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2010. Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome. BMC Genomics 11 (1) , 46. 10.1186/1471-2164-11-46

Codling, C, O'Mahony, L, Shanahan, F, Quigley, E. M. M. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2010. A Molecular Analysis of Fecal and Mucosal Bacterial Communities in Irritable Bowel Syndrome. Digestive Diseases and Sciences 55 (2) , pp. 392-397. 10.1007/s10620-009-0934-x

Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2010. Prokaryotic and Eukaryotic Diversity of the Human Gut. Advances in Applied Microbiology 72 , pp. 43-62. 10.1016/S0065-2164(10)72002-5

Scanlan, Pauline, Shanahan, Fergus and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2009. Culture-independent analysis of desulfovibrios in the human distal colon of healthy, colorectal cancer and polypectomized individuals. FEMS Microbiology Ecology 69 (2) , pp. 213-221. 10.1111/j.1574-6941.2009.00709.x

Forbes, Christina, O'Leary, Niall, Dobson, Alan and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2009. The contribution of ‘omic’-based approaches to the study of enhanced biological phosphorus removal microbiology. FEMS Microbiology Ecology 69 (1) , pp. 1-15. 10.1111/j.1574-6941.2009.00698.x

Claesson, M. J., O'Sullivan, O., Wang, Q., Nikkila, J., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Smidt, H., De Vos, W. M., Ross, R. P. and O'Toole, P. W. 2009. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 4 (8) , e6669. 10.1371/journal.pone.0006669

O'Mahony, S. M., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Scully, P., Codling, C. E., Ceolho, A M., Quigley, E. M. M., Cryan, J. F. and Dinan, T. G. 2009. Early Life Stress Alters Behavior, Immunity, and Microbiota in Rats: Implications for Irritable Bowel Syndrome and Psychiatric Illnesses. Biological Psychiatry 65 (3) , pp. 263-267. 10.1016/j.biopsych.2008.06.026

Kennedy, J., Baker, P. W., Piper, C., Cotter, P. D., Walsh, M., Mooij, M. J., Bourke, M. B., Rea, M. C, O'Connor, P. M., Ross, R. P., Hill, C., O'Gara, F., Marchesi, Julain Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Dobson, A. D. W. 2009. Isolation and analysis of bacteria with antimicrobial activities from the marine sponge haliclona simulans collected from irish waters. Marine Biotechnology 11 (3) , pp. 384-396. 10.1007/s10126-008-9154-1

Turroni, F., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Foroni, E., Gueimonds, M., Shanahan, F., Margolles, A., Van Sinderen, D. and Ventura, M. 2009. Microbiomic analysis of the bifidobacterial population in the human distal gut. ISME Journal 3 (6) , pp. 745-751. 10.1038/ismej.2009.19

Baker, P. W., Kennedy, J., Dobson, A. D. W. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2009. Phylogenetic diversity and antimicrobial activities of fungi associated with haliclona simulans isolated from irish coastal waters. Marine Biotechnology 11 (4) , pp. 540-547. 10.1007/s10126-008-9169-7

Twomey, K. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2009. Swallowable capsule technology: current perspectives and future directions. Endoscopy 41 (4) , pp. 357-362. 10.1055/s-0028-1119640

Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Prosser, James 2008. Gut microbiology: the black box and beyond [Editorial]. FEMS Microbiology Ecology 66 (3) , pp. 485-486. 10.1111/j.1574-6941.2008.00607.x

Kennedy, Jonathan, Codling, Caroline, Jones, Brian, Dobson, Alan and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2008. Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome. Environmental Microbiology 10 (7) , pp. 1888-1902. 10.1111/j.1462-2920.2008.01614.x

Scanlan, Pauline, Shanahan, Fergus, Clune, Yvonne, Collins, John, O'Sullivan, Gerald, O'Riordan, Micheal, Holmes, Elaine, Wang, Yulan and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2008. Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environmental Microbiology 10 (3) , pp. 789-798. 10.1111/j.1462-2920.2007.01503.x

Scanlan, PD, Shanahan, F, Clune, Y, Collins, JK, O'Sullivan, GC, O'Riordan, M, Holmes, E, Wang, Y and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2008. Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Corrects article in Vol 10 (3) pages 789-798. Environmental Microbiology 10 (5) , p. 1382. 10.1111/j.1462-2920.2008.01622.x

Jones, B. V., Begley, M., Hill, C., Gahan, C. G. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2008. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proceedings of the National Academy of Sciences of the United States of America 105 (36) , pp. 13580-13585. 10.1073/pnas.0804437105

Scanlan, P. D., Shanahan, F and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2008. Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiology 8 :79 10.1186/1471-2180-8-79

Kennedy, J., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Dobson, A. D. 2008. Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microbial Cell Factories 7:27 10.1186/1475-2859-7-27

Scanlan, Pauline D. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2008. Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. ISME Journal 2 (12) , pp. 1183-1193. 10.1038/ismej.2008.76

Yap, I. K., Li, J. V., Saric, J., Martin, F. P., Davies, H., Wang, Y., Wilson, I. D., Nicholson, J. K., Utzinger, J., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Holmes, E. 2008. Metabonomic and microbiological analysis of the dynamic effect of vancomycin-induced gut microbiota modification in the mouse. Journal of Proteome Research 7 (9) , pp. 3718-28. 10.1021/pr700864x

Saric, J., Wang, Y., Li, J., Coen, M., Utzinger, J., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Keiser, J., Veselkov, K., Lindon, J. C., Nicholson, J. K. and Holmes, E. 2008. Species variation in the fecal metabolome gives insight into differential gastrointestinal function. Journal of Proteome Research 7 (1) , pp. 352-360. 10.1021/pr070340k

Scanlan, P. D. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2008. Application of TRACA to the human intestinal microbiota: insights into tetracycline resistant genes of the mobile metagenome using PCR based screen [Abstract]. FEBS Journal 275 (S1) , p. 284. 10.1111/j.1742-4658.2008.06448.x

Ferreira, Maria Isabelle M., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Janssen, Dick B. 2008. Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1. Applied Microbiology and Biotechnology 78 (4) , pp. 709-717. 10.1007/s00253-008-1343-3

Jones, B. V., Sun, F. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2007. Using skimmed milk agar to functionally screen a gut metagenomic library for proteases may lead to false positives. Letters In Applied Microbiology 45 (4) , pp. 418-420. 10.1111/j.1472-765X.2007.02202.x

Scanlan, Pauline D., Shanahan, Fergus, O'Mahony, Caitlin and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2007. Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease [Erratum]. Journal of Clinical Microbiology 45 (5) , p. 1671. 10.1128/JCM.00398-07

Kennedy, Jonathan, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Dobson, Alan D. W. 2007. Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges. Applied Microbiology and Biotechnology 75 (1) , pp. 11-20. 10.1007/s00253-007-0875-2

Moriarty, John, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Metcalfe, Anthony 2007. Bounds on the distribution of the number of gaps when circles and lines are covered by fragments: Theory and practical application to genomic and metagenomic projects. BMC Bioinformatics 8 , 70. 10.1186/1471-2105-8-70

Jones, Brian V. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2007. Accessing the mobile metagenome of the human gut microbiota. Molecular Biosystems 3 (11) , pp. 749-758. 10.1039/b705657e

Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Shanahan, Fergus 2007. The normal intestinal microbiota. Current Opinion in Infectious Diseases 20 (5) , pp. 508-513. 10.1097/QCO.0b013e3282a56a99

Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Holmes, Elaine, Khan, Fatima, Kochhar, Sunil, Scanlan, Pauline, Shanahan, Fergus, Wilson, Ian D. and Wang, Yulan 2007. Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. Journal of Proteome Research 6 (2) , pp. 546-551. 10.1021/pr060470d

Jones, Brian V. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2007. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nature Methods 4 (1) , pp. 55-61. 10.1038/nmeth964

Scanlan, Pauline D., Shanahan, Fergus, O'Mahony, Caitlin and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2006. Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease. Journal of Clinical Microbiology 44 (11) , pp. 3980-3988. 10.1128/JCM.00312-06

Kerr, Linda M. and Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2006. Isolation of novel bacteria able to degrade α-halocarboxylic acids by enrichment from environmental samples. Chemosphere 64 (5) , pp. 848-855. 10.1016/j.chemosphere.2005.10.042

O'Connor, Kevin E., O'Leary, Niall P., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Dobson, Alan D. W. and Duetz, Wouter 2005. Isolation and characterization of a diverse group of phenylacetic acid degrading microorganisms from pristine soil. Chemosphere 61 (7) , pp. 965-973. 10.1016/j.chemosphere.2005.03.017

Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 2003. A microplate fluorimetric assay for measuring dehalogenase activity. Journal of Microbiological Methods 55 (1) , pp. 325-329. 10.1016/S0167-7012(03)00132-5

Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Weightman, Andrew John ORCID: https://orcid.org/0000-0002-6671-2209 2003. Comparing the Dehalogenase Gene Pool in Cultivated  -Halocarboxylic Acid-Degrading Bacteria with the Environmental Metagene Pool. Applied and Environmental Microbiology 69 (8) , pp. 4375-4382. 10.1128/AEM.69.8.4375-4382.2003

Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Weightman, Andrew John ORCID: https://orcid.org/0000-0002-6671-2209 2003. Diversity of alpha-halocarboxylic acid dehalogenases in bacteria isolated from a pristine soil after enrichment and selection on the herbicide 2,2-dichloropropionic acid (Dalapon). Environmental Microbiology 5 (1) , pp. 48-54. 10.1046/j.1462-2920.2003.00384.x

Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Weightman, Andrew John ORCID: https://orcid.org/0000-0002-6671-2209, Cragg, Barry Andrew, Parkes, Ronald John and Fry, John Christopher 2001. Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiology Ecology 34 (3) , pp. 221-228. 10.1111/j.1574-6941.2001.tb00773.x

Poelarends, G. J., Zandstra, M., Bosma, T., Kulakov, L. A., Larkin, M. J., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Weightman, Andrew John ORCID: https://orcid.org/0000-0002-6671-2209 and Janssen, D. B. 2000. Haloalkane-Utilizing Rhodococcus Strains Isolated from Geographically Distinct Locations Possess a Highly Conserved Gene Cluster Encoding Haloalkane Catabolism. Journal of Bacteriology 182 (10) , pp. 2725-2731. 10.1128/JB.182.10.2725-2731.2000

Hill, Katja E. ORCID: https://orcid.org/0000-0002-8590-0117, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Weightman, Andrew J. ORCID: https://orcid.org/0000-0002-6671-2209 1999. Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families. Journal of Bacteriology 181 (9) , pp. 2535-2547. 10.1128/JB.181.8.2535-2547.1999

Ashelford, Kevin E. ORCID: https://orcid.org/0000-0003-3217-2811, Fry, John C., Day, Martin J., Hill, Katja E. ORCID: https://orcid.org/0000-0002-8590-0117, Learner, Michael A., Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239, Perkins, Caroline D. and Weightman, Andrew J. ORCID: https://orcid.org/0000-0002-6671-2209 1997. Using microcosms to study gene transfer in aquatic habitats. FEMS Microbiology Ecology 23 (2) , pp. 81-94. 10.1111/j.1574-6941.1997.tb00393.x

Bale, S. J., Goodman, K., Rochelle, Paul A., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Fry, John Christopher, Weightman, Andrew John ORCID: https://orcid.org/0000-0002-6671-2209 and Parkes, Ronald John 1997. Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. International Journal of Systematic Bacteriology 47 (2) , pp. 515-521. 10.1099/00207713-47-2-515

Hill, Katja E. ORCID: https://orcid.org/0000-0002-8590-0117, Marchesi, Julian R. ORCID: https://orcid.org/0000-0002-7994-5239 and Fry, John C.. 1996. Conjugation in the epilithon. Akkermans, Antoon D. L., Van Elsas, Jan Dirk and de Bruijn, Frans J., eds. Molecular Microbial Ecology Manual, Kluwer Academic Publishers, Dortrecht, The Netherlands, pp. 125-152. (10.1007/978-94-009-0215-2_9)