MB4019 - Computational Biology
MB6300 - Computational systems biology
MB6301 - Genomic data analysis
I am also coordinating the MSc in Bioinformatics and Computational Biology.
Biography
Marcus Claesson did his BSc in Chemical Engineering and MSc in Bioinformatics at Chalmers University of Technology in Gothenburg, Sweden. After his MSc Thesis project at AstraZeneca Mölndal, he worked at the start-up biotechnology company AngioGenetics. This was interrupted by the opportunity to start a PhD at the Microbiology Department at University College Cork, where the main part of the project was dedicated to sequence and analyse a commensal Lactobacillus strain. Once completed in Oct 2006, Marcus worked for at the campus-based biotechnology company Alimentary Health, data mining bifidobacteria for beneficial probiotic traits. This was followed by a longer postdoctoral position in Prof. Paul O’Toole’s lab in the Microbiology Department, focusing on the bioinformatics involved in the ELDERMET metagenomics project aiming to sequence the gut-bacteria of hundreds of elderly Irish citizens. Since 2012 Marcus is a Principal Investigator at UCC, as well as a Funded Investigator at the Alimentary Pharmabiotic Center managing the BioIT platform. His main research interests in the role of microbiota in inflammatory bowel disease, and methods development for various 'omics' technologies. He is also coordinating the MSc programme in Bioinformatics and Computational Biology, and lectures on the subject to MSc and 4th year Microbiology and Genetics students. Between 2005-2015 Marcus has published 37 peer-reviewed papers, which as of Jan 1st 2015 resulted in over 2100 citations and an ISI H-index of 19.
Research Interests
My main research interests are the development of bioinformatics methods of “omics” technologies for application on particularly, but not exclusively, human microbiological systems. These technologies include compositional microbiota analysis, metagenomics and metatranscriptomics. I also have a particular interest in exploring the gut microbiomes involved in inflammatory bowel disease patients using the aforementioned methods. This work has been funded by both a Postdoctoral Fellowship award from the Health Research Board, and a Starting Investigator Research Granf from the Science Foundation Ireland.
My research focus up to recently has been on microbiota analysis as part of the ELDERMET project, which aims to use metagenomic and metabolomic approaches to determine the composition and function of the gut microbiome in elderly Irish subjects. I have analysed microbiota composition of over 300 subjects, as well as developed analysis methods to be applied on these systems. In our latest study we reveal novel relationships between microbiota, diet and health status within the elderly population.
Previous research included comparative analysis of sequenced genomes of beneficial commensal Lactobacillus and Bifidobacterium species. After sequencing the first genome in Ireland, that of Lactobacillus salivarius UCC118, I discovered a so-called mega-plasmid, which was the first one of its kind in Lactic Acid Bacteria. Although not essential for survival, it showed probiotic properties and appeared to increase the metabolic flexibility and competitiveness of the strain.
Publications
Peer Reviewed Journals
| Year | Publication | |
|---|---|---|
| (2014) | 'Metaphor: Finding Bi-directional Best Hit homology relationships in (meta)genomic datasets' van der Veen BE, Harris HM, O’Toole PW, Claesson MJ (2014) 'Metaphor: Finding Bi-directional Best Hit homology relationships in (meta)genomic datasets'. Genomics, [DOI] [Details] | |
| (2014) | 'Unusual genome complexity in Lactobacillus salivarius JCM1046' Raftis, EJ,Forde, BM,Claesson, MJ,O'Toole, PW (2014) 'Unusual genome complexity in Lactobacillus salivarius JCM1046'. BMC Genomics, 15 [DOI] [Details] | |
| (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' 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 (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, 277C :885-901 [DOI] [Details] | |
| (2013) | 'Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy' O'Sullivan, O,Coakley, M,Lakshminarayanan, B,Conde, S,Claesson, MJ,Cusack, S,Fitzgerald, AP,O'Toole, PW,Stanton, C,Ross, RP (2013) 'Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy'. Journal of Antimicrobial Chemotherapy, 68 :214-221 [DOI] [Details] | |
| (2013) | 'Pro-Inflammatory Flagellin Proteins of Prevalent Motile Commensal Bacteria Are Variably Abundant in the Intestinal Microbiome of Elderly Humans' Neville, BA,Sheridan, PO,Harris, HMB,Coughlan, S,Flint, HJ,Duncan, SH,Jeffery, IB,Claesson, MJ,Ross, RP,Scott, KP,O'Toole, PW (2013) 'Pro-Inflammatory Flagellin Proteins of Prevalent Motile Commensal Bacteria Are Variably Abundant in the Intestinal Microbiome of Elderly Humans'. Plos One, 8 [DOI] [Details] | |
| (2013) | 'The core faecal bacterial microbiome of Irish Thoroughbred racehorses' O' Donnell, MM,Harris, HMB,Jeffery, IB,Claesson, MJ,Younge, B,O' Toole, PW,Ross, RP (2013) 'The core faecal bacterial microbiome of Irish Thoroughbred racehorses'. Letters In Applied Microbiology, 57 :492-501 [DOI] [Details] | |
| (2013) | 'The Human Gut Chip HuGChip'', an Explorative Phylogenetic Microarray for Determining Gut Microbiome Diversity at Family Level' Tottey, W,Denonfoux, J,Jaziri, F,Parisot, N,Missaoui, M,Hill, D,Borrel, G,Peyretaillade, E,Alric, M,Harris, HMB,Jeffery, IB,Claesson, MJ,O'Toole, PW,Peyret, P,Brugere, JF (2013) 'The Human Gut Chip HuGChip'', an Explorative Phylogenetic Microarray for Determining Gut Microbiome Diversity at Family Level'. Plos One, 8 [DOI] [Details] | |
| (2012) | 'Categorization of the gut microbiota: enterotypes or gradients?' Jeffery, IB,Claesson, MJ,O'Toole, PW,Shanahan, F (2012) 'Categorization of the gut microbiota: enterotypes or gradients?'. Nature Reviews. Microbiology, 10 :591-592 [DOI] [Details] | |
| (2012) | 'Diet drives gut microbiota variation in the elderly which correlates with health' Claesson MJ, Jeffery IB, Conde S, Power SE, O’Connor EM, Cusack S, Harris H, Coakley M, Laks B, O’Sullivan O, Fitzgerald G, Deane J, 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, R Ross P, O’Toole PW (2012) 'Diet drives gut microbiota variation in the elderly which correlates with health'. Nature, [Details] | |
| (2012) | 'An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota' Jeffery, IB,O'Toole, PW,Ohman, L,Claesson, MJ,Deane, J,Quigley, EMM,Simren, M (2012) 'An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota'. Gut, 61 :997-1006 [DOI] [Details] | |
| (2012) | 'Characterization of Pro-Inflammatory Flagellin Proteins Produced by Lactobacillus ruminis and Related Motile Lactobacilli' Neville, BA,Forde, BM,Claesson, MJ,Darby, T,Coghlan, A,Nally, K,Ross, RP,O'Toole, PW (2012) 'Characterization of Pro-Inflammatory Flagellin Proteins Produced by Lactobacillus ruminis and Related Motile Lactobacilli'. Plos One, 7 [DOI] [Details] | |
| (2012) | 'Diversity of Bifidobacteria within the Infant Gut Microbiota' 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 (2012) 'Diversity of Bifidobacteria within the Infant Gut Microbiota'. Plos One, 7 [DOI] [Details] | |
| (2012) | 'Fibrinogen-binding and platelet-aggregation activities of a Lactobacillus salivarius septicaemia isolate are mediated by a novel fibrinogen-binding protein' Collins, J,van Pijkeren, JP,Svensson, L,Claesson, MJ,Sturme, M,Li, Y,Cooney, JC,van Sinderen, D,Walker, AW,Parkhill, J,Shannon, O,O'Toole, PW (2012) 'Fibrinogen-binding and platelet-aggregation activities of a Lactobacillus salivarius septicaemia isolate are mediated by a novel fibrinogen-binding protein'. Molecular Microbiology, 85 :862-877 [DOI] [Details] | |
| (2012) | 'Gut microbiota composition correlates with diet and health in the elderly' Claesson, MJ,Jeffery, IB,Conde, S,Power, SE,O'Connor, EM,Cusack, S,Harris, HMB,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 (2012) 'Gut microbiota composition correlates with diet and health in the elderly'. Nature, 488 [DOI] [Details] | |
| (2012) | 'Effect of Lactobacillus salivarius bacteriocin Abp118 on the mouse and pig intestinal microbiota' Riboulet-Bisson E, Sturme MH, Jeffery IB, O'Donnell MM, Neville BA, Forde BM, Claesson MJ, Harris H, Gardiner GE, Casey PG, Lawlor PG, O'Toole PW, Ross RP (2012) 'Effect of Lactobacillus salivarius bacteriocin Abp118 on the mouse and pig intestinal microbiota'. Plos One, 7 (2) [DOI] [CORA Link] [Details] | |
| (2011) | 'Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts' Forde, BM,Neville, BA,Donnell, MMO,Riboulet-Bisson, E,Claesson, MJ,Coghlan, A,Ross, RP,Toole, PWO (2011) 'Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts'. Microbial Cell Factories, 10 [DOI] [Details] | |
| (2011) | 'How beneficial is the use of probiotic supplements for the aging gut?' Cusack S, Claesson MJ, O'Toole MJ (2011) 'How beneficial is the use of probiotic supplements for the aging gut?'. Future Medicine, [Details] | |
| (2011) | 'Composition, variability, and temporal stability of the intestinal microbiota of the elderly' 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 (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 :4586-4591 [DOI] [Details] | |
| (2011) | 'Correlation of rRNA gene amplicon pyrosequencing and bacterial culture for microbial compositional analysis of faecal samples from elderly Irish subjects' O'Sullivan, O,Coakley, M,Lakshminarayanan, B,Claesson, MJ,Stanton, C,O'Toole, PW,Ross, RP,ELDERMET Consortium (2011) 'Correlation of rRNA gene amplicon pyrosequencing and bacterial culture for microbial compositional analysis of faecal samples from elderly Irish subjects'. Journal of Applied Microbiology, 111 :467-473 [DOI] [Details] | |
| (2011) | 'Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor' Motherway, MO,Zomer, A,Leahy, SC,Reunanen, J,Bottacini, F,Claesson, MJ,O'Brien, F,Flynn, K,Casey, PG,Munoz, JAM,Kearney, B,Houston, AM,O'Mahony, C,Higgins, DG,Shanahan, F,Palva, A,de Vos, WM,Fitzgerald, GF,Ventura, M,O'Toole, PW,van Sinderen, D (2011) 'Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor'. Proceedings of The National Academy of Sciences of The United States of America, 108 :11217-11222 [DOI] [Details] | |
| (2010) | 'Gut microbiota: Changes throughout the lifespan from infancy to elderly' O'Toole, PW,Claesson, MJ (2010) 'Gut microbiota: Changes throughout the lifespan from infancy to elderly'. International Dairy Journal, 20 :281-291 [DOI] [Details] | |
| (2010) | 'Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions' Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, Ross RP, O'Toole PW (2010) 'Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions'. Nucleic Acids Research, 38 (22) [DOI] [Details] | |
| (2010) | 'Evaluating the latest high-throughput molecular techniques for the exploration of microbial gut communities' Claesson MJ, O'Toole PW (2010) 'Evaluating the latest high-throughput molecular techniques for the exploration of microbial gut communities'. Gut, 1 (4):277-278 [DOI] [Details] | |
| (2009) | 'Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine' Claesson MJ, O'Sullivan O, Wang Q, Nikkilä J, Marchesi JR, Smidt H, de Vos WM, Ross RP, O'Toole PW (2009) 'Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine'. Plos One, [Details] | |
| (2009) | 'The Bifidobacterium dentium Bd1 Genome Sequence Reflects Its Genetic Adaptation to the Human Oral Cavity' Ventura, M,Turroni, F,Zomer, A,Foroni, E,Giubellini, V,Bottacini, F,Canchaya, C,Claesson, MJ,He, F,Mantzourani, M,Mulas, L,Ferrarini, A,Gao, BL,Delledonne, M,Henrissat, B,Coutinho, P,Oggioni, M,Gupta, RS,Zhang, ZD,Beighton, D,Fitzgerald, GF,O'Toole, PW,van Sinderen, D (2009) 'The Bifidobacterium dentium Bd1 Genome Sequence Reflects Its Genetic Adaptation to the Human Oral Cavity'. PLoS genetics, 5 [DOI] [Details] | |
| (2009) | 'Genome-scale analyses of health-promoting bacteria: probiogenomics' Ventura, M,O'Flaherty, S,Claesson, MJ,Turroni, F,Klaenhammer, TR,van Sinderen, D,O'Toole, PW (2009) 'Genome-scale analyses of health-promoting bacteria: probiogenomics'. Nature Reviews. Microbiology, 7 :61-77 [DOI] [Details] | |
| (2008) | 'Lactobacillus phylogenomics--towards a reclassification of the genus' Claesson MJ, van Sinderen D, O'Toole PW (2008) 'Lactobacillus phylogenomics--towards a reclassification of the genus'. International Journal of Systematic and Evolutionary Microbiology, [Details] | |
| (2008) | 'Characterization of endogenous plasmids from Lactobacillus salivarius UCC118' Fang F, Flynn S, Li Y, Claesson MJ, van Pijkeren JP, Collins JK, van Sinderen D, O'Toole PW (2008) 'Characterization of endogenous plasmids from Lactobacillus salivarius UCC118'. Applied Environmental Microbiology, [Details] | |
| (2007) | 'The genus Lactobacillus--a genomic basis for understanding its diversity' Claesson MJ, van Sinderen D, O'Toole PW (2007) 'The genus Lactobacillus--a genomic basis for understanding its diversity'. Fems Microbiology Letts, [Details] | |
| (2006) | 'Comparative and functional analysis of sortase-dependent proteins in the predicted secretome of Lactobacillus salivarius UCC118' Van Pijkeren, J-P., C. Canchaya, K. A. Ryan, Y. Li, M. J. Claesson, B. Sheil, L. Steidler, L. O¿Mahony, G. F. Fitzgerald, D. van Sinderen and P. W. O¿Toole. ; (2006) 'Comparative and functional analysis of sortase-dependent proteins in the predicted secretome of Lactobacillus salivarius UCC118'. Applied Environmental Microbiology, 72 :4143-4153 [Details] | |
| (2006) | 'Comparative genomics and transcriptional analysis of prophages identified in the genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei' Ventura M, Canchaya C, Bernini V, Altermann E, Barrangou R, McGrath S, Claesson MJ, Li Y, Leahy S, Walker CD, Zink R, Neviani E, Steele J, Broadbent J, Klaenhammer TR, Fitzgerald GF, O'toole PW, van Sinderen D (2006) 'Comparative genomics and transcriptional analysis of prophages identified in the genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei'. Applied and Environmental Microbiology, 72 (5):3130-3146 [DOI] [Details] | |
| (2006) | 'Genomic island identification in Vibrio vulnificus reveals significant genome plasticity in this human pathogen' Quirke AM, Reen FJ, Claesson MJ, Boyd EF (2006) 'Genomic island identification in Vibrio vulnificus reveals significant genome plasticity in this human pathogen'. Bioinformatics (Oxford, England), 22 (8):905-910 [DOI] [Details] | |
| (2006) | 'Multireplicon genome architecture of Lactobacillus salivarius' Claesson MJ, Li Y, Leahy S, Canchaya C, van Pijkeren JP, Cerdeño-Tárraga AM, Parkhill J, Flynn S, O'Sullivan GC, Collins JK, Higgins D, Shanahan F, Fitzgerald GF, van Sinderen D, O'Toole PW (2006) 'Multireplicon genome architecture of Lactobacillus salivarius'. Proceedings of The National Academy of Science Usa, [Details] | |
| (2006) | 'Diversity of the genus Lactobacillus revealed by comparative genomics of five species' Canchaya C, Claesson MJ, Fitzgerald GF, van Sinderen D, O'Toole PW (2006) 'Diversity of the genus Lactobacillus revealed by comparative genomics of five species'. Microbiology, [Details] | |
| (2005) | 'BlastXtract--a new way of exploring translated searches' Claesson MJ, van Sinderen D; (2005) 'BlastXtract--a new way of exploring translated searches'. Bioinformatics (Oxford, England), 21 (18):3667-3668 [DOI] [Details] | |
| (2005) | 'GI genomes' Cerdeno-Tarraga, A,Claesson, MJ,Sebaihia, M,Thomson, NR (2005) 'GI genomes'. Nature Reviews. Microbiology, 3 :368-369 [DOI] [Details] |
Book Chapters
| Year | Publication | |
|---|---|---|
| (2012) | 'Intestinal Microbiota, Alterations in Irritable Bowel Syndrome' Jeffery IB, Claesson MJ, O'Toole PW (2012) 'Intestinal Microbiota, Alterations in Irritable Bowel Syndrome' In: Encyclopedia of Metagenomics: SpringerReference. Heidelberg: Springer-Verlag. [DOI] [Details] | |
| (2012) | 'Intestinal Microbiota and Aging' Claesson MJ, Jeffery IB, O'Toole PW (2012) 'Intestinal Microbiota and Aging' In: Karen Nelson (eds). Encyclopedia of Metagenomics: SpringerReference. Heidelberg: Springer-Verlag. [DOI] [Details] |
Professional Activities
Honours and Awards
| Year | Title | Awarding Body | |
|---|---|---|---|
| 2012 | University College Cork Early Stage Researcher of the Year | University College Cork | |
| 2010 | Alimentary Pharmabiotic Centre Young Scientist of the Year | Alimentary Pharmabiotic Centre | |
| 2007 | Bioscience Institute Award for PhD Student of the Year | Bioscience Institute Award |
Committees
| Committee | Function | From / To | |
|---|---|---|---|
| International Education Committee | School of Microbiology representative | 2014 / |
Employment
| Employer | Position | From / To | |
|---|---|---|---|
| University College Cork | Lecturer | 01-SEP-12 / | |
| University College Cork | Research Fellow | 01-AUG-09 / 31-AUG-12 | |
| University College Cork | Postdoctoral Researcher | 01-AUG-07 / 31-JUL-09 | |
| Alimentary Health Ltd. | Bioinformatician | 01-OCT-06 / 01-JUL-07 | |
| AngioGenetics Ltd. | Bioinformatics software developer | 01-JAN-02 / 01-OCT-02 | |
| AstraZeneca | Pilot plant operator | 01-JUN-99 / 01-SEP-00 |
Education
| Year | Institution | Qualification | Subject | |
|---|---|---|---|---|
| 2006 | University College Cork | PHD | Bioinformatics | |
| 2001 | Chalmers University of Technology | MSc | Bioinformatics |
Teaching Activities
Teaching Interests
I currently teach the following modulesMB4019 - Computational Biology
MB6300 - Computational systems biology
MB6301 - Genomic data analysis
I am also coordinating the MSc in Bioinformatics and Computational Biology.
Current Postgraduate Students
| Student | Degree Type | |
|---|---|---|
| Ryan Feargal | Doctoral Degree | |
| Walsh Aaron Martin | Doctoral Degree | |
| Clooney Adam George | Doctoral Degree | |
| Harris Hugh | Doctoral Degree |
Modules Taught
| Term (ID)) | Title | Link | Subject | |
|---|---|---|---|---|
| 2015 | Computational Systems Biology | MB6300 | Computational Systems Biology | |
| 2015 | Genomic Data Analysis | MB6301 | Genomic Data Analysis | |
| 2015 | Research Dissertation | MB6303 | Research Dissertation | |
| 2015 | Research Frontiers in Microbiology | MB4027 | Research Frontiers in Microbiology | |
| 2015 | Computational Biology | MB4019 | Computational Biology |
Contact details
- Marcus Claesson
Lecturer - M.Claesson@ucc.ie
- Microbiology
University College Cork
Cork
Ireland - +353-21-490-3000