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Christopher Quince

Job Title
Associate Professor
WMS - Biomedical Sciences
024 7652 2317
Research Interests

Metagenomics coupled to next generation sequencing has transformed our understanding of the microbial world. It has allowed us to directly determine community structure and function in situ from the DNA of the organisms present. This is revolutionising microbial ecology. My research consists of the development of improved statistical and bioinformatics tools for interpreting this sequence data. These tools exploit advanced methods from machine learning and Bayesian statistics. I work on both 16S rRNA gene amplicon data, having developed the AmpliconNoise algorithm for error removal from 454 pyrosequenced amplicons ( and shotgun metagenomics for example the CONCOCT algorithm for automated genome extraction from shotgun metagenome reads ( In addition, I also develop Bayesian statistical models for interpreting microbial community structure addressing questions such as are enterotypes real features of the human gut microbiome and are microbial communities neutrally assembled? In collaboration with numerous groups around the world I apply these methods to both environmental and host-associated microbial communities. For instance, with Dr Konstantinos Gerasimidis (Nutrition Group - University of Glasgow -- and Dr Nick Loman (University of Birmimgham - I have resolved the changes in gut microbiota composition of children with Crohn's disease during treatment with exclusive enteral nutrition. This could potentially lead to improved therapeutic strategies. With Dr Gavin Collins (University of Galway - I study the structure of anaerobic digestion reactor communities. More efficient AD digesters will provide more effective biogas production from wastewater, reducing pollution and providing a renewable energy resource. I am currently employed as an MRC Principal Research Fellow as part of the Cloud Computing for Microbial Bioinformatics (CLIMB) consortium (


View Christopher's publications on Google Scholar.

  • Quince, Christopher, Nurk, Sergey, Raguideau, Sébastien, James, Robert, Soyer, Orkun S., Summers, J. Kimberly, Limasset, Antoine, Eren, A. Murat, Chikhi, Rayan, Darling, Aaron E., 2021. STRONG : metagenomics strain resolution on assembly graphs. Genome Biology, 22 (1)
  • Lee, Kihyun, Kim, Dae-Wi, Lee, Do-Hoon, Kim, Yong-Seok, Bu, Ji-Hye, Cha, Ju-Hee, Thawng, Cung Nawl, Hwang, Eun-Mi, Seong, Hoon Je, Sul, Woo Jun, Wellington, Elizabeth M. H., Quince, Christopher, Cha, Chang-Jun, 2020. Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance. Microbiome, 8 (1)
  • Sagar, Nidhi M., Duboc, Henri, Kay, Gemma L., Alam, Mohammad T., Wicaksono, Alfian, Covington, James A., Quince, Christopher, Kokkorou, Margarita, Svolos, Vaios, Palmieri, Lola J., Gerasimidis, Konstantinos, Walters, Julian R. F., Arasaradnam, Ramesh P., 2020. The pathophysiology of bile acid diarrhoea : differences in the colonic microbiome, metabolome and bile acids. Scientific Reports, 10 (1)
  • Svolos, Vaios, Hansen, Richard, Nichols, Ben, Quince, Christopher, Ijaz, Umer Z., Papadopoulou, Rodanthi T., Edwards, Christine A., Watson, David, Alghamdi, Adel, Brejnrod, Asker, Ansalone, Cecilia, Duncan, Hazel, Gervais, Lisa, Tayler, Rachel, Salmond, Jonathan, Bolognini, Daniele, Klopfleisch, Robert, Gaya, Daniel R., Milling, Simon, Russell, Richard K. et al (Select to open full list), 2019. Treatment of active Crohn's disease with an ordinary food-based diet that replicates exclusive enteral nutrition. Gastroenterology, 156 (5), pp. 1354-1367.e6
  • Pasolli, Edoardo, Asnicar, Francesco, Manara, Serena, Zolfo, Moreno, Karcher, Nicolai, Armanini, Federica, Beghini, Francesco, Manghi, Paolo, Tett, Adrian, Ghensi, Paolo, Collado, Maria Carmen, Rice, Benjamin L., DuLong, Casey, Morgan, Xochitl C., Golden, Christopher D., Quince, Christopher, Huttenhower, Curtis, Segata, Nicola, 2019. Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. CELL, 176 (3), pp. 649-662.e20
  • Heidrich, E. S., Dolfing, J., Wade, M. J., Sloan, W. T., Quince, C., Curtis, T. P., 2018. Temperature, inocula and substrate : contrasting electroactive consortia, diversity and performance in microbial fuel cells. Bioelectrochemistry, 119, pp. 43-50
  • Zhou, Zhemin, Lundstrøm, Inge, Tran-Dien, Alicia, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Christophersen, Axel, Quince, Christopher, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon Y. W., Gilbert, M. Thomas P., Achtman, Mark, 2018. Pan-genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive Para C lineage for millennia. Current Biology, 28 (15), pp. 2420-2428
  • Quince, Christopher, Delmont, Tom O., Raguideau, Sébastien, Alneberg, Johannes, Darling, Aaron E., Collins, Gavin, Eren, A. Murat, 2017. DESMAN : a new tool for de novo extraction of strains from metagenomes. Genome Biology, 18 (1)
  • Fonseca, V. G., Sinniger, F., Gaspar, J. M., Quince, C., Creer, S., Power, Deborah M., Peck, Lloyd S., Clark, Melody S., 2017. Revealing higher than expected meiofaunal diversity in Antarctic sediments : a metabarcoding approach. Scientific Reports, 7 (1)
  • Connelly, Stephanie, Shin, Seung G., Dillon, Robert J., Ijaz, Umer Z., Quince, Christopher, Sloan, William T., Collins, Gavin, 2017. Bioreactor scalability : laboratory-scale bioreactor design influences performance, ecology, and community physiology in expanded granular sludge bed bioreactors. Frontiers in Microbiology, 8
  • Harris, Keith, Parsons, Todd L., Ijaz, Umer Z., Lahti, Leo, Holmes, Ian, Quince, Christopher, 2017. Linking statistical and ecological theory : Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process. Proceedings of the IEEE, 105 (3), pp. 516-529
  • Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Jørgensen, Tue Sparholt, Shapiro, Nicole, Blood, Philip D, Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z et al (Select to open full list), 2017. Critical assessment of metagenome interpretation - a benchmark of metagenomics software. Nature Methods, 14 (11), pp. 1063-1071
  • Quince, Christopher, Walker, Alan W., Simpson, Jared T., Loman, Nicholas J., Segata, Nicola, 2017. Shotgun metagenomics, from sampling to analysis. Nature Biotechnology, 35 (9), pp. 833-844
  • Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F. et al (Select to open full list), 2017. A communal catalogue reveals Earth's multiscale microbial diversity. Nature
  • Ijaz, Umer Zeeshan, Quince, Christopher, Hanske, Laura, Loman, Nick, Calus, Szymon T., Bertz, Martin, Edwards, Christine A., Gaya, Daniel R., Hansen, Richard, McGrogan, Paraic, Russell, Richard K., Gerasimidis, Konstantinos, 2017. The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically-linked kindred.. PLoS One, 12 (2)
  • D'Amore, Rosalinda, Ijaz, Umer Zeeshan, Schirmer, Melanie, Kenny, John G., Gregory, Richard, Darby, Alistair C., Shakya, Migun, Podar, Mircea, Quince, Christopher, Hall, Neil, 2016. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics, 17 (1)
  • Torondel, Belen, Ensink, Jeroen H.J., Gundogdu, Ozan, Ijaz, Umer Zeeshan, Parkhill, Julian, Abdelahi, Faraji, Nguyen, Viet-Anh, Sudgen, Steven, Gibson, Walter, Walker, Alan W., Quince, Christopher, 2016. Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines. Microbial Biotechnology, 9 (2), pp. 209-223
  • Haig, Sarah-Jane, Gauchotte-Lindsay, Caroline, Collins, Gavin, Quince, Christopher, 2016. Bioaugmentation mitigates the impact of estrogen on coliform-grazing protozoa in slow sand filters. Environmental Science & Technology, 50 (6), pp. 3101-3110
  • Widder, Stefanie, Allen, Rosalind, Pfeiffer, Thomas, Curtis, Thomas P., Wiuf, Carsten, Sloan, William T., Cordero, Otto X., Brown, Sam P., Momeni, Babak, Shou, Wenying, Kettle, Helen, Flint, Harry J., Haas, Andreas F., Laroche, Beatrice, Kreft, Jan-Ulrich, Rainey, Paul B., Freilich, Shiri, Schuster, Stefan, Milferstedt, Kim, van der Meer, Jan R. et al (Select to open full list), 2016. Challenges in microbial ecology : building predictive understanding of community function and dynamics. The ISME Journal, 2016 (10), pp. 2557-2568
  • Schirmer, Melanie, D'Amore, Rosalinda, Ijaz, Umer Z., Hall, Neil, Quince, Christopher, 2016. Illumina error profiles : resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics, 17 (1), pp. 1-15
  • Cho, Si-Kyung, Kim, Dong-Hoon, Quince, Christopher, Im, Wan-Taek, Oh, Sae-Eun, Shin, Seung Gu, 2016. Low-strength ultrasonication positively affects methanogenic granules toward higher AD performance : implications from microbial community shift. Ultrasonics Sonochemistry, 32, pp. 198-203
  • Ray, Jessica L., Althammer, Julia, Skaar, Katrine S., Simonelli, Paolo, Larsen, Aud, Stoecker, Diane, Sazhin, Andrey, Ijaz, Umer Z., Quince, Christopher, Nejstgaard, Jens C., Frischer, Marc, Pohnert, Georg, Troedsson, Christofer, 2016. Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities. Molecular Ecology, 25 (21), pp. 5585-5602
  • Oton, Eduard Vico, Quince, Christopher, Nicol, Graeme W., Prosser, James I., Gubry-Rangin, Cécile, 2016. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. The ISME Journal, 10 (1), pp. 85-96
  • Gregor, Ivan, Dröge, Johannes, Schirmer, Melanie, Quince, Christopher, McHardy, Alice C., 2016. PhyloPythiaS+ : a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes. PeerJ, 4
  • Sinclair, Lucas, Ijaz, Umer Z., Jensen, Lars Juhl, Coolen, Marco J.L., Gubry-Rangin, Cecile, Chronáková, Alica, Oulas, Anastasis, Pavloudi, Christina, Schnetzer, Julia, Weimann, Aaron, Ijaz, Ali, Eiler, Alexander, Quince, Christopher, Pafilis, Evangelos, 2016. Seqenv : linking sequences to environments through text mining. PeerJ, 4
  • Gerasimidis, Konstantinos, Bertz, Martin, Quince, Christopher, Brunner, Katja, Bruce, Alanna, Combet, Emilie, Calus, Szymon, Loman, Nick, Ijaz, Umer Zeeshan, 2016. The effect of DNA extraction methodology on gut microbiota research applications. BMC Research Notes, 9 (1)
  • Rognes, Torbjørn, Flouri, Tomá?, Nichols, Ben, Quince, Christopher, Mahé, Frédéric, 2016. VSEARCH : a versatile open source tool for metagenomics. PeerJ, 4
  • Haig, Sarah-Jane, Schirmer, Melanie, D'Amore, Rosalinda, Gibbs, Joseph, Davies, Robert L., Collins, Gavin, Quince, Christopher, 2015. Stable-isotope probing and metagenomics reveal predation by protozoa drives E. coli removal in slow sand filters. The ISME Journal, 9, pp. 797-808
  • Quince, Christopher, Ijaz, Umer Zeeshan, Loman, Nick, Eren, A. Murat, Saulnier, Delphine, Russell, Julie, Haig, Sarah J., Calus, Szymon T., Quick, Joshua, Barclay, Andrew, Bertz, Martin, Blaut, Michael, Hansen, Richard, McGrogan, Paraic, Russell, Richard K., Edwards, Christine A., Gerasimidis, Konstantinos, 2015. Extensive modulation of the fecal metagenome in children with Crohn's Disease during exclusive enteral nutrition. The American Journal of Gastroenterology, 110 (12), pp. 1718-1729
  • Alneberg, Johannes, Bjarnason, Brynjar Smári, de Bruijn, Ino, Schirmer, Melanie, Quick, Joshua, Ijaz, Umer Z., Lahti, Leo, Loman, Nicholas J., Andersson, Anders F., Quince, Christopher, 2014. Binning metagenomic contigs by coverage and composition. Nature Methods, 11, pp. 1144-1146
  • Loman, Nicholas J., Constantinidou, Chrystala, Christner, Martin, Rohde, Holger, Chan, Jacqueline, Quick, Joshua, Weir, Jacqueline C., Quince, Christopher, Smith, Geoffrey, Betley, Jason R., Aepfelbacher, Martin, Pallen, Mark J., 2013. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-Toxigenic Escherichia coli O104:H4. JAMA: The Journal of the American Medical Association, 309 (14), pp. 1502-1510
  • Quince, Christopher, Lundin, E. E., Andreasson, A. N., Greco, D., Rafter, J., Talley, N. J., Agreus, L., Andersson, A. F., Engstrand, L., D'Amato, M., 2013. The impact of Crohn's disease genes on healthy human gut microbiota : a pilot study. Gut, 62 (6), pp. 952-954
  • Holmes, Ian, Harris, Keith, Quince, Christopher, 2012. Dirichlet multinomial mixtures : generative models for microbial metagenomics. PLoS One, 7 (2)
  • Quince, Christopher, Lanzen, Anders, Davenport, Russell J., Turnbaugh, Peter J., 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics, 12 (1)
Title Funder Award start Award end
CLIMB 2 MRC 01 Apr 2020 31 Mar 2025
HPRU in Genomics and Enabling at University of Warwick National Institute for Health Research (DoH) 01 Apr 2020 31 Mar 2025
NIHR HPRU in Gastrointestinal Infections National Institute for Health Research (DoH) 01 Apr 2020 31 Mar 2025
Resolving the fate and studying the impact of pharmaceutical wastes on the environment and local community of a pharmaceutical manufacturing hub NERC 01 Oct 2020 30 Sep 2023
Health Data Research UK Health Data Research UK 02 Apr 2018 01 Apr 2023
Unravelling the diversity and function of the fine root endophyte NERC 02 Sep 2019 01 Sep 2022
Strain resolved metagenomics for medical microbiology MRC 01 Oct 2019 30 Sep 2021
BBSRC BBR - EBI Metagenomics - enabling the reconstruction of microbial populations (Warwick Component) BBSRC 03 Sep 2018 02 Sep 2021
LinkPI: Linking Phenotype function with Identity: a novel integrated single-cell technology and metagenomics approach - Nerc Global Partnership seedcorn fund NERC 01 Nov 2018 31 Aug 2021
Wellcome Trust Investigator Award - Deep evolutionary history of bacterial pathogens Wellcome Trust 01 Sep 2016 31 Aug 2021
The clinical effectiveness of CD-TREAT and its microbial mechanisms of action in patients with active Crohns disease Leona M. and Harry B. Helmsley Charitable Trust 15 Mar 2019 14 May 2021
New approaches to resolving community metaproteomes: ComProt NERC 01 Jan 2019 31 Dec 2019
MRC-KHIDI UK-KOREA PARTNERING AWARDS -Exploring the relationship between antibiotic persistence and antibiotic resistance in exposed bacteria in environmental locations MRC 31 May 2018 30 Apr 2019
Programme Integration Group (PIG) - Using next generation sequencing to reveal human impact on aquatic reservoirs of antibiotic resistant bacteria at the catchment scale NERC 01 Jul 2017 31 Dec 2018
MRC AMR Development Grant application - AMREPAK: Novel inter-disciplinary approaches for identifying and tackling the spread of AntiMicrobial Resistance through Environmental pathways in PAKistan MRC 01 Oct 2017 31 Mar 2018
Predictive Temporal Analysis of Functional Microbiomes in UK's Anerobic Digestion Reactors BBSRC 01 Jul 2016 07 Mar 2018
Newton fund via FIOCRUZ, Brazil: Leishmaniasis in the Brazilian Amazon: the role of accessory microbiota in disease progression, pathobiology and immunity RCUK 01 Jan 2015 31 Mar 2017