ProfessorJulianMarchesi

• Microbiology of the gut
• The human microbiome and mucosal communties
• The Cancer Microbiome
• Host-microbes interactions in the gut
• Impact of bacterial produced metabolites in the gut
• Bioactive and biocatalytic agents from the gut using functional metagenomics

2019

Simon JC, Marchesi JR, Mougel C, Selosse MA. Host-microbiota interactions: from holobiont theory to analysis. Microbiome. 2019 Jan 11;7(1):5. doi: 10.1186/s40168-019-0619-4. PMID: 30635058

Ovadia C, Perdonnes-Montero A, Spagoue K, Smith A, Sarafin M, Gomez-Romer M, Bellafante E, Clarke L, Holmes E, Marchesi JR and Williamson C. Enhanced microbial bile acid deconjugation and impaired ileal uptake in pregnancy repress intestinal regulation of bile acid synthesis. Hepatology 2019 in press

Mullish BH, Ghani R, McDonald JAK, Marchesi JR. 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'. Clin Microbiol Infect. 2019 Jan 25. pii: S1198-743X(19)30030-8. doi: 10.1016/j.cmi.2019.01.010. [Epub ahead of print] No abstract available. PMID: 30685497

Hegade VS, Pechlivanis A, McDonald JAK, Rees D, Corrigan M, Hirschfield GM, Taylor-Robinson SD, Holmes E, Marchesi JR, Kendrick S, Jones DE. Autotaxin, bile acid profile and effect of ileal bile acid transporter inhibition in primary biliary cholangitis patients with pruritus. Liver Int. 2019 Feb 8. doi: 10.1111/liv.14069. [Epub ahead of print] PMID: 30735608

Brown RG, Al-Memar M, Marchesi JR, Lee YS, Smith A, Chan D, Lewis H, Kindinger L, Terzidou V, Bourne T, Bennett PR, MacIntyre DA. Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes. Transl Res. 2018 Dec 27. pii: S1931-5244(18)30238-X. doi: 10.1016/j.trsl.2018.12.005. PMID: 30633889

Allegretti JR, Kassam Z, Carrellas M, Mullish BH, Marchesi JR, Pechlivanis A, Smith M, Gerardin Y, Timberlake S, Pratt DS, Korzenik JR. Fecal Microbiota Transplantation in Patients With Primary Sclerosing Cholangitis: A Pilot Clinical Trial. Am J Gastroenterol. 2019 Jan 31. doi: 10.14309/ajg.0000000000000115. [Epub ahead of print] PMID: 30730351

Mullish BH, McDonald JAK, Pechlivanis A, Allegretti JR, Kao D, Barker GF, Kapila D, Petrof EO, Joyce SA, Gahan CGM, Williams HRT, Holmes E, Thursz MR & Marchesi JR. Bile-metabolising enzymes protect against Clostridioides difficile infection and mediate the efficacy of faecal microbiota transplant. Gut 2019 In press

2018

Pruski P, Lewis HV, Lee YS, Marchesi JR, Bennett PR, Takats Z, MacIntyre DA. Assessment of microbiota:host interactions at the vaginal mucosa interface. Methods. 2018 Oct 1;149:74-84. doi: 10.1016/j.ymeth.2018.04.022. Epub 2018 Apr 27. Review. PMID: 29705211.

Mullish BH, Pechlivanis A, Barker GF, Thursz MR, Marchesi JR, McDonald JAK. Functional microbiomics: Evaluation of gut microbiota-bile acid metabolism interactions in health and disease. Methods. 2018 Oct 1;149:49-58. doi: 10.1016/j.ymeth.2018.04.028. Epub 2018 Apr 26. PMID: 29704662

Mullish BH, Osborne LS, Marchesi JR, McDonald JA. The implementation of omics technologies in cancer microbiome research. Ecancermedicalscience. 2018 Sep 5;12:864. doi: 10.3332/ecancer.2018.864. eCollection 2018. Review. PMID: 30263055

Monaghan T, Mullish BH, Patterson J, Wong GK, Marchesi JR, Xu H, Jilani T, Kao D. 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. 2018 Sep 5:1-7. doi: 10.1080/19490976.2018.1506667. [Epub ahead of print] PMID: 30183484

McDonald J, Mullish B, Pechlivanis A, Liu Z, Li J, Holmes E, Gahan C, Joyce S, Thursz M and Marchesi JR. A novel route for controlling Clostridioides difficile germination and vegetative growth via valerate and bile acid modulation. Gastroentrology 2018. doi: 10.1053/j.gastro.2018.07.014. [Epub ahead of print]. PMID: 30025704

Moshkelgosha S, Masetti G, Berchner-Pfannschmidt U, Verhasselt HL, Horstmann M, Diaz-Cano S, Noble A, Edelman B, Covelli D, Plummer S, Marchesi JR, Ludgate M, Biscarini F, Eckstein A, Banga JP. Gut Microbiome in BALB/c and C57BL/6J Mice Undergoing Experimental Thyroid Autoimmunity Associate with Differences in Immunological Responses and Thyroid Function. Horm Metab Res. 2018 Aug 14. doi: 10.1055/a-0653-3766. [Epub ahead of print] PMID: 30107619

Naz I, Hodgson D, Smith A, Marchesi JR, Sehar S, Ahmed S, Lynch J, Avignone-Rossa C, Saroj DP. Investigation of the Active Biofilm Communities on Polypropylene Filter Media in a Fixed Biofilm Reactor for Wastewater Treatment. Journal of Chemical Technology and Biotechnology 2018 doi.org/10.1002/jctb.5686

Martin G, Kolida S, Marchesi JR, Want E, Sidaway J, Swann JR. In Vitro Modeling of Bile Acid Processing by the Human Fecal Microbiota. Frontiers in Microbiology, 2018 Jun 5;9:1153. doi: 10.3389/fmicb.2018.01153. eCollection 2018. PMID: 29922256

Masetti G, Moshkelgosha S, Kohling H, Covelli D, Banga P, Berchner-Pfannschmidt U, Horstmann M, Diaz-Cano S, Gortz G, Plummer S, Eckstein A, Ludgate M, Biscarini F and Marchesi JR, Gut microbiota in experimental murine model of Graves' orbitopathy established in different environments may modulate clinical presentation of disease. Microbiome 2018 May 25;6(1):97. doi: 10.1186/s40168-018-0478-4. PMID: 29801507

Brown RG, Marchesi JR, Lee YS, Smith A, Lehne B, Kindinger LM, Terzidou V, Holmes E, Nicholson JK, Bennett PR and MacIntyre DA. Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin. BMC Medicine, 2018 16(1):9. doi: 10.1186/s12916-017-0999-x.

Ding NS, Mullish BH, McLaughlin J, Hart A, Marchesi JR. Meeting update: faecal microbiota transplantation--bench, bedside, courtroom? Frontline Gastroenterol. 2018 Jan;9(1):45-48. doi: 10.1136/flgastro-2016-100752.

2017

Scott AJ, Merrifield CA, Alexander JL, Marchesi JR, Kinross JM. Highlights from the Inaugural International Cancer Microbiome Consortium Meeting (ICMC), 5-6 September 2017, London, UK. Ecancermedicalscience. 2017 Dec 20;11:791. doi: 10.3332/ecancer.2017.791

Lynch A, Crowley E, Casey ED, Cano R, McGlackan G, Marchesi JR and Clarke DJ. The Bacteriodales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolysin activity. Scientific Reports 2017 7(1):13270. doi: 10.1038/s41598-017-13774-6.

Mitra A, MacIntyre DA, Mahajan V, Lee YS, Smith A, Marchesi JR, Lyons D, Bennett PR, Kyrgiou M. Comparison of vaginal microbiota sampling techniques: cytobrush versus swab. Sci Rep. 2017 Aug 29;7(1):9802. doi: 10.1038/s41598-017-09844-4.

Mullish B, McDonald JAK, Thursz MR and Marchesi JR. Fecal Microbiota Transplant from a Rational Stool Donor Improves Hepatic Encephalopathy: A Randomized Clinical Trial. Hepatology. 2017 Jul 17. doi: 10.1002/hep.29369.

Kinross J, Mirnezami R, Alexander J, Veselkov K, Goldin R, Darzi A, Nicholson J, Marchesi JR. A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy. Scientific Reports. 2017 Aug 21;7(1):8979. doi: 10.1038/s41598-017-08150-3.

Innes A, Mullish B, Fernando F, Adams G, Marchesi JR, Apperley J, Brannigan E, Davies F, and Pavlu J. Fecal microbiota transplant: A novel biological approach to extensively drug-resistant organism-related non-relapse mortality. Bone Marrow Transplantation 2017 Jul 17. doi: 10.1038/bmt.2017.151.

O'Hagan C, Li J, Marchesi JR, Plummer S and Garaiova I. Long-term probiotic dietary supplement enhances memory and alters regional brain metabolites in aging rats. Neurobiology of Learning and Memory 2017, 144:36-47.

Michael DR, Davies TS, Moss We, Lama Calvente D, Ramji DP, Marchesi JR, Pechlivanis A, Plummer SF and Hughes TR. The anti-cholesterolemic effect of a consortium of probiotics: An acute study in C57BL/6 mice. Scientific Reports. 2017 Jun 6;7(1):2883. doi: 10.1038/s41598-017-02889-5.

Cobbold JFL, Atkinson S, Marchesi JR, Smith A, Nu Wai S, Stove J, Shojaee-Moradie F, Jackson N, Umpleby MA, Fitzpatrick J, Thomas LE, Bell JD, Holmes E, Taylor-Robinson SD, Goldin RD, Yee MS, Anstee QM and Thursz MR. Rifaximin in non-alcoholic steatohepatitis: an open-label pilot study. Hepatology Research 2017 Apr 20. doi: 10.1111/hepr.12904.

Marino PJ, Wise MP, Smith A, Marchesi JR, Riggio MP, Lewis MAO and Williams DW. Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients. J Critical Care. 2017 Feb 16;39:149-155. doi: 10.1016/j.jcrc.2017.02.020.

Kindinger LM; Bennett PR; Lee YS; Marchesi JR; Smith A; Cacciatore S; Holmes J; Nicholson JK; Teoh TG; MacIntyre DA. The interaction between vaginal microbiota, cervical length and vaginal progesterone treatment for preterm birth risk. Microbiome. 2017 Jan 19;5(1):6. doi: 10.1186/s40168-016-0223-9.

2016

Kindinger L, MacIntyre DA, Yun S Lee YS, Marchesi JR, Smith A, McDonald J, Vasso Terzidou V, Lees C, Holmes E, Nicholson J, Teoh TG and Bennett PR. Cervical cerclage using multifilament braided suture induces vaginal dysbiosis, inflammation and increased rates of preterm birth and intrauterine death. Science Trans Medicine 2016, 3;8(350):350ra102

Hodgson DM, Smith A, Dahale S, Stratford JP, Li JV, Grüning A, Bushell ME, Marchesi JR and Avignone Rossa C. Segregation of the Anodic Microbial Communities in a Microbial Fuel Cell Cascade. Frontiers in Microbiology. 2016. 11;7:699

Gratton J, Phetcharaburanin J, Mullish B, Williams HRT, Thursz M, Nicholson JK, Holmes E, Marchesi JR and Li JV. An optimized sampling strategy for metabolic profiling of human feces. Analytical Chemistry. 2016. 3;88(9):4661-8.

Phetcharaburanin J, Lees H, Marchesi JR, Nicholson JK, Holmes E, Seyfried F and Li JV. Systemic Characterization of an Obese Phenotype in the Zucker Rat Model Defining Metabolic Axes of Energy Metabolism and Host-Microbial Interactions. International J. Proteom Res.2016. 3;15(6):1897-906.

Sands K, Wilson M, Lewis M, Wise M, Marchesi JR, Smith A and Williams D. Microbial profiling of dental plaque from mechanically ventilated patients. J Microbiology Methods. 2016. 65(2):147-59.

2015

Marchesi JR and Ravel J. The vocabulary of microbiome research: a proposal. Microbiome 2015, 3:31

Mitra A, MacIntyre DA, Lee YS, Smith A, Marchesi JR, Holmes E, Nicholson JK, Bennett PR, Kyrgiou M.  Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity. Scientific Reports 2015, 17;5:16865.

2014

Progatzky F, Sangha NJ, Yoshida N, McBrien M, Cheung J, Shia A, Scott J, Marchesi JR, Lamb JR, Bugeon L and Dallman M. Dietary cholesterol directly induces acute inflammasome-dependent intestinal inflammation. Nature Communications 2014. 23;5:5864.

Mullish BH, Marchesi JR, Thursz MR and Williams HR. Microbiome manipulation with faecal microbiome transplantation as a therapeutic strategy in Clostridium difficile infection. QJM. 2014. Sep 4. pii: hcu182.

O'Mahony SM, Felice VD, Nally K, Savignac HM, Claesson MJ, Scully P, Woznicki J, Hyland NP, Shanahan F, Quigley EM, Marchesi JR, O'Toole PW, Dinan TG, Cryan JF. 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. 2014. pii: S0306-4522(14)00627-7.

Lees H, Swann J, Poucher SM, Nicholson JK, Holmes E, Wilson ID and Marchesi JR. Age and microenvironment outweigh genetic influence on the Zucker rat microbiome. 2014. PLoS ONE. 2014. 9(9):e100916.

Peng J, Narasimhan S, Marchesi JR, Benson A, Wong SF and Wen L. Long Term Effect of Gut Microbiota Transfer on Diabetes Development. 2014. J. Autoimmunity 53:85-94

2013

Lewis DA, Brown R, Williams J, White P, Jacobson SK, Marchesi JR, Drake MJ. The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. Front Cell Infect Microbiol. 2013 Aug 15;3:41. doi: 10.3389/fcimb.2013.00041. PMID: 23967406

Prorok-Hamon M, Friswell MK, Alswied A, Roberts CL, Song F, Flanagan PK, Knight P, Codling C,Marchesi JR, Winstanley C, Hall N, Rhodes JM, Campbell BJ. Colonic mucosa-associated diffusely adherent afaC Escherichia coli expressing lpfA and pks are increased in inflammatory bowel disease and colon cancer. Gut. 2013 Jul 11. [Epub ahead of print] PMID: 23846483

van Woerden HC, Gregory C, Brown R, Marchesi JR, Hoogendoorn B, Matthews IP. Differences in fungi present in induced sputum samples from asthma patients and non-atopic controls: a community based case control study. BMC Infect Dis. 2013 Feb 5;13:69. doi: 10.1186/1471-2334-13-69. PMID: 23384395

2012

Morris LS, Evans J, Marchesi JR. A robust plate assay for detection of extracellular microbial protease activity in metagenomic screens and pure cultures. J. Microbiol. Methods. 2012, 91(1):144-146

Claesson MJ, Jeffery IB, Conde S, Power SE, O'Connor EM, Cusack S, Harris HM, Coakley M, Lakshminarayanan B, O'Sullivan O, Fitzgerald GF, Deane J, O'Connor M, Harnedy N, O'Connor K, O'Mahony D, van Sinderen D, Wallace M, Brennan L, Stanton C, Marchesi JR, Fitzgerald AP, Shanahan F, Hill C, Ross RP, O'Toole PW. Diet drives gut microbiota variation in the elderly which correlates with health. Nature. 2012, 9;488(7410):178-84

Turroni F, Peano C, Pass DA, Foroni E, Severgnini M, Claesson MJ, Kerr C, Hourihane J, Murray D, Fuligni F, Gueimonde M, Margolles A, De Bellis G, O'Toole PW, van Sinderen D, Marchesi JR, Ventura M. Diversity of bifidobacteria within the infant gut microbiota. PLoS ONE, 2012, 7(5):e36957

Bull MJ, Marchesi JR, Vandamme P, Plummer S, Mahenthiralingam E. Minimum taxonomic criteria for bacterial genome sequence depositions and announcements. J. Microbiol Methods. 2012, 89:18-21

Culligan E, Sleator R, Marchesi JR and Hill C. Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome. ISME J. 2012, 6(10):1916-25

2011

Li JV, Reshat R, Wu Q, Ashrafian H, Bueter M, le Roux CW, Darzi A, Athanasiou T, Marchesi JR, Nicholson JK1,2, Elaine Holmes E, Gooderham N. Experimental Bariatric Surgery in Rats generates a cytotoxic chemical environment in the gut content. Frontiers in Microbiology. 2011; 2:183.

Brown R, Marchesi JR and Morby A. Functional characterisation of Lp_2714, an EAL-domain protein from Lactobacillus plantarum. Biochemical and Biophysical Research Communications. 2011;411(1):132-136.

Marchesi JR. Human distal gut microbiome. Env. Microbiol. 2011; 13(12):3088-3102.

Marchesi JR. Shifting from a gene-centric to metabolite-centric strategy to determine the core gut microbiome. Bioengineered Bugs Commentary. 2011; 2(6):309-314.

Li JV, Ashrafian H, Bueter M, Kinross J, Sands C, le Roux CW, Bloom SR, Darzi A, Athanasiou T,Marchesi JR, Nicholson JK and Elaine Holmes E Metabolic Surgery Profoundly Influences Gut Microbial-Host Metabolic Crosstalk. Gut. 2011; 60(9):1214-1223.

Twomey K, de Eulate A, Marchesi JR., Kolida S, Gibson G, Arrigan DWM, Ogurtsov VI. Characterisation of the electrochemical behavior of gastrointestinal fluids using a multi-electrode sensor probe. IEEE Transactions on Biomedical Engineering. 2011; 58(9):2521-2527.

Marchesi JR, Dutilh B, Hall N, Peters W, Roelofs R , Boleij A and Tjalsma H. Towards the Human Colorectal Cancer Tumour Microbiome. PloS ONE. 2011; 6(5):e20447

Swann J, Richards SE, Shen Q, Holmes E, Marchesi JR and Tuohy K. Culture independent analysis of the human gut microbiota and its activities. Molecular Microbial Ecology Manual. 2011

Lejon D, Kennedy J, Marchesi JR and Dobson A. Identification of Novel Bioactive Compounds from the Metagenome of the Marine Sponge Haliclona simulans. Handbook of Molecular Microbial Ecology II:  Metagenomics in Different Habitats, ISBN: 978-0-470-64719-6 2011, Wiley-Blackwell

2010

Marchesi JR. Prokaryotic and eukaryotic diversity of the human gut. . Adv Appl Microbiol. 2010;72:43-62. Review

Claesson MJ, Cusack S, O'Sullivan O, Greene-Diniz R, de Weerd H, Flannery E, Marchesi JR, Falush D, Dinan T, Fitzgerald G, Stanton C, van Sinderen D, O'Connor M, Harnedy N, O'Connor K, Henry C, O'Mahony D, Fitzgerald AP, Shanahan F, Twomey C, Hill C, Ross RP, O'Toole PW. Microbes and Health Sackler Colloquium: Composition, variability, and temporal stability of the intestinal microbiota of the elderly.  Proc Natl Acad Sci U S A. 2010 Aug 19.

Jones BV, Sun F and Marchesi JR. Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome. BMC genomics 2010 Jan 19;11:46.

Baker P, Kennedy J, Dobson ADW and Marchesi JR. Endoglucanase activities and growth of marine-derived fungi isolated from Haliclona simulans. J. Applied Microbiology. 2010 May;108(5):1668-1675.

Codling C, O’Mahony L, Shanahan F, Quigley EMM and Marchesi JR. A molecular analysis of fecal and mucosal bacterial communities in Irritable Bowel Syndrome. Digestive Diseases and Sciences. 2010 Feb;55(2):392-397

2009

Claesson MJ, O’Sullivan O, Wang Q, Nikkilä J, Marchesi JR, Smidt H, de Vos WM, Ross P, O’Toole P. Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine. PLoS ONE. 2009 Aug 20;4(8):e6669.

Forbes C, O’Leary N, Dobson ADW and Marchesi JR. The contribution of “omic” based approaches to the study of enhanced biological phosphorus removal microbiology. FEMS Microbiology Ecology 2009 Jul;69(1):1-15.

Scanlan P., Shanahan F and Marchesi JR. Culture-independent analysis of desulfovibrios in the human distal colon of healthy, colorectal and polypectomised individuals. FEMS Microbiology Ecology 2009 Aug;69(2):213-21.

Metagenomics and its application to human bacterial diseases. Marchesi JR. Invited chapter for book “Periodontal Medicine and Systems Biology” 2009.

Twomey K and Marchesi JR Swallowable Capsule Technology: current perspectives and future directions. Endoscopy 2009 41(4):357-362.

Turroni F, Marchesi JR, Foroni E, Gueimonde M, Shanahan F, Margolles A, van Sinderen D and Ventura M. Microbiomic analysis of the bifidobacterial population in the human distal gut. ISME Journal 2009 Jun;3(6):745-51.

Baker PW, Kennedy J, Dobson ADW and Marchesi JR. Phylogenetic diversity and antimicrobial activities of fungi associated with Haliclona simulans isolated from Irish coastal waters. Marine Biotechnology 2009 Jul-Aug;11(4):540-7.

Kennedy J, Baker P, Walsh M, Mooij M, Rea MC, O’Connor PM, Piper C, Cotter P, Hill C, O’Gara F,Marchesi JR and Dobson ADW. Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans isolated from Irish waters. Marine Biotechnology 2009 11(3):384-96.

2008

Kennedy J, Marchesi JR and Dobson ADW Marine Metagenomics: Strategies for the discovery of novel enzymes with Biotechnological applications from Marine Ecosystems. Microbial Cell Factories 2008. 7:27. http://dx.doi.org/10.1186/1475-2859-7-27

Jones BV, Begley M, Hill C, Gahan C, Marchesi JR. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proceedings of the National Academy of Science USA. 2008 http://dx.doi.org/10.1073/pnas.0804437105

Scanlan PD and Julian R. Marchesi JR. Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture dependent and independent analysis. International Society of Microbial Ecology Journal 2008. http://dx.doi.org/10.1038/ismej.2008.76

O' Mahony SM, Marchesi JR, Scully P, Codling C, Ceolho AM, Quigley EMM, Cryan J, and Dinan TG. Early life stress alters behaviour, immunity and microbiota: implications for irritable bowel syndrome and psychiatric illnesses. Biological Psychiatry. 2008. http://dx.doi.org/10.1016/j.biopsych.2008.06.026

Yap IKS, Li JV, Saric J, Martin F, Davies H, Wang Y, Wilson ID, Nicholson JK, Utzinger J, Marchesi JR, Holmes E. Metabonomic and Microbiological Analysis of the Dynamic Effect of Vancomycin-Induced Gut Microbiota Modification in the Mouse. J. Proteome Research 2008. http://dx.doi.org/10.1021/pr700864x

Scanlan PD, Shanahan F, Marchesi JR. Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiol. 2008 May 20;8:79.http://dx.doi.org/10.1186/1471-2180-8-79

Kennedy J, Codling CE, Jones BV, Dobson ADW and Marchesi JR (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. Env. Micro. 2008. epub.http://dx.doi.org/10.1111/j.1462-2920.2008.01614.x

Scanlan PD, Shanahan F, Clune Y, Collins JK, O'Sullivan GC, O'Riordan M, Holmes E, Wang Y,Marchesi JR. Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol. 2008 10(3):789-798. PMID: 18237311. http://dx.doi.org/10.1111/j.1462-2920.2007.01503.x

Saric J, Wang Y, Li J, Coen M, Utzinger J, Marchesi JR, Keiser J, Veselkov K, Lindon JC, Nicholson JK, Holmes E. Species variation in the fecal metabolome gives insight into differential gastrointestinal function. J Proteome Res. 2008 7(1):352-360. PMID: 18052033. http://dx.doi.org/10.1021/pr070340k 

2007

Jones BV, Marchesi JR. Accessing the mobile metagenome of the human gut microbiota. Mol Biosyst. 2007 3(11):749-758. PMID: 17940657. http://dx.doi.org/10.1039/b705657e

Jones BV, Sun F, Marchesi JR. Using skimmed milk agar to functionally screen a gut metagenomic library for proteases may lead to false positives. Lett Appl Microbiol. 2007 45(4):418-420. PMID: 17897385. http://dx.doi.org/10.1111/j.1472-765X.2007.02202.x

Kennedy J, Marchesi JR, Dobson AD. Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges. Appl Microbiol Biotechnol. 2007 75(1):11-20. PMID: 17318533. http://dx.doi.org/10.1007/s00253-007-0875-2

Moriarty J, Marchesi JR, Metcalfe A. 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. 2007 8:70. PMID: 17335566. http://dx.doi.org/10.1186/1471-2105-8-70

Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, Wilson ID, Wang Y. Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res. 2007 6(2):546-551. PMID: 17269711. http://dx.doi.org/10.1021/pr060470d

Jones BV, Marchesi JR. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods. 2007 4(1):55-61. PMID: 17128268.http://dx.doi.org/10.1038/NMETH964

2006 

Scanlan PD, Shanahan F, O'Mahony C, Marchesi JR. Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease. J Clin Microbiol. 2006 44(11):3980-3988. PMID: 16988018. http://dx.doi.org/10.1128/JCM.00312-06