Staff overview – University of Copenhagen

Manimozhiyan Arumugam

Manimozhiyan Arumugam

Associate Professor

Dr. Manimozhiyan Arumugam is a Group Leader and Associate Professor at the Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark. He received his PhD in computational biology from the European Molecular Biology Laboratory (Heidelberg) in 2010. He studies the trillions of microbes that inhabit the human gut, collectively called the human gut microbiota. As part of the European MetaHIT consortium, he has contributed to major advances in understanding the human gut microbiome (collective genomes of the human gut microbiota), including the establishment of the first human gut microbial gene catalog and the discovery of enterotypes.

Dr. Arumugam leads the “Microbiome Systems Biology” research group that investigates how our health and diseases are influenced by our gut microbiome. His research is interdisciplinary, combining metagenomics (a technique to study gut microbiome), genomics, genetics, (meta)transcriptomics, and metabolomics to study host-microbial cross-talk. He is the principal investigator in several externally funded studies investigating the role of gut microbiome in multiple sclerosis (Lundbeck Foundation), obesity (Novo Nordisk Foundation), alcoholic liver fibrosis (EU Horizon 2020), ageing (Danish Independent Research Council) and producing antimicrobial peptides (Danish Independent Research Council). His group has international collaborations studying the interaction between the gut microbiome and the host in the context of several other diseases, including cardiometabolic diseases, chronic liver diseases and cancer.

Masters Thesis Opportunities in Bioinformatics

Highly motivated Masters students are invited to perform their thesis or project work in our group. We prefer students with experience in programming and/or high performance computing. Background in biology is not necessary! Please check out this flyer!


We are always looking for excellent researchers to join our group

1.Postdoctoral fellows in bioinformatics or microbiome research:
 Postdoctoral opportunities are available for outstanding candidates with experience and background in bioinformatics and human gut microbiome. If you like our research and are interested in joining our group, please send me an email.
2.PhD fellows in bioinformatics or microbiome research:
 We are always looking for highly motivated PhD students to join us. If you like our research and are interested in joining our group, please send me an email. International students can also apply to the Copenhagen Bioscience PhD Program where I am a participating supervisor.

Primary fields of research

Human Microbiome, Bioinformatics, Metagenomics

Current research

Obesity, diabetes and several other metabolic disorders are increasing at an alarming rate across the globe. Although lifestyle changes and lack of physical activity are widely being blamed for this trend, the true cause for these diseases is more likely the interactions between human genetics, environmental factors and the human microbiome. For the past several years, researchers around the world have only been focusing on the interactions between two of these three factors, and ignoring the microbiome. The human gut microbiome plays an important role in our health, nutrition and well-being. Its imbalance may signify an unhealthy state of the host (like in Inflammatory Bowel Diseases), or worse, might be the reason for an ailment (like in Clostridium difficile infections). We aim to study the interactions between all three factors – human genetics, environmental factors and human microbiome – in order to understand the molecular mechanisms underlying metabolic disorders. To this end, we use (i) an array of clinical measurement data, (ii) next-generation sequencing of human genome, transcriptome, gut metagenome, and epigenome, and (iii) SNP and DNA microarrays. The Metabolic Genetics section has established a genotyping and sequencing facility to generate most of these data. For analyzing the vast amount of such data, we have acquired a brand-new high-performance computing cluster with more than 500 CPUs. We also have a strong research partnership with BGI-Shenzhen, the largest sequencing centre in the world.

Fields of interest

Systems Biology, Human Diseases, Genomics, Machine Learning

Selected publications

  1. E-pub ahead of print

    Circulating microbiome in blood of different circulatory compartments

    Schierwagen, R., Alvarez-Silva, C., Madsen, M. S. A., Kolbe, C. C., Meyer, C., Thomas, D., Uschner, F. E., Magdaleno, F., Jansen, C., Pohlmann, A., Praktiknjo, M., Hischebeth, G. T., Molitor, E., Latz, E., Lelouvier, B., Trebicka, J. & Arumugam, M., 26 Mar 2018, In : Gut.

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Published

    Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer

    Yu, J., Feng, Q., Wong, S. H., Zhang, D., Liang, Q. Y., Qin, Y., Tang, L., Zhao, H., Stenvang, J., Li, Y., Wang, X., Xu, X., Chen, N., Wu, W. K. K., Al-Aama, J., Nielsen, H. J., Kiilerich, P., Jensen, B. A. H., Yau, T. O., Lan, Z., Jia, H., Li, J., Xiao, L., Lam, T. Y. T., Ng, S. C., Cheng, A. S-L., Wong, V. W-S., Chan, F. K. L., Xu, X., Yang, H., Madsen, L., Datz, C., Tilg, H., Wang, J., Brünner, N., Kristiansen, K., Arumugam, M., Sung, J. J-Y. & Wang, J., 2017, In : Gut. 66, p. 70-78 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota

    Palleja, A., Kashani, A., Allin, K. H., Nielsen, T., Zhang, C., Li, Y., Brach, T., Liang, S., Feng, Q., Jørgensen, N. B., Bojsen-Møller, K. N., Dirksen, C., Burgdorf, K. S., Holst, J. J., Madsbad, S., Wang, J., Pedersen, O. B., Hansen, T. & Arumugam, M., 2016, In : Genome Medicine. 8, 13 p., 67.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    A catalog of the mouse gut metagenome

    Xiao, L., Feng, Q., Liang, S., Sonne, S. B., Xia, Z., Qiu, X., Li, X., Long, H., Zhang, J., Zhang, D., Liu, C., Fang, Z., Chou, J., Glanville, J., Hao, Q., Kotowska, D. E., Colding, C. S., Licht, T. R., Wu, D., Yu, J., Sung, J. J. Y., Liang, Q., Li, J., Jia, H., Lan, Z., Tremaroli, V., Dworzynski, P., Nielsen, H. B., Bäckhed, G. F., Dore, J., Le Chatelier, E., Ehrlich, S. D., Lin, J. C., Arumugam, M., Wang, J., Madsen, L. & Kristiansen, K., 2015, In : Nature Biotechnology. 33, 10, p. 1103-1108 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    An integrated catalog of reference genes in the human gut microbiome

    Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J. R., Prifti, E., Nielsen, T., Juncker, A., Manichanh, C., Chen, B., Zhang, W., Levenez, F., Wang, J., Xu, X., Xiao, L., Liang, S., Zhang, D., Zhang, Z., Chen, W., Zhao, H., Al-Aama, J. Y., Edris, S., Yang, H., Wang, J., Hansen, T., Nielsen, H. B., Brunak, S., Kristiansen, K., Guarner, F., Pedersen, O., Doré, J., Ehrlich, S. D., Bork, P. & Wang, J., 2014, In : Nature Biotechnology. 32, 8, p. 834-845 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Interplay between FGF21 and insulin action in the liver regulates metabolism

    Emanuelli, B., Vienberg, S. G., Smyth, G., Cheng, C., Stanford, K. I., Arumugam, M., Michael, M. D., Adams, A. C., Kharitonenkov, A. & Kahn, C. R., 3 Feb 2014, In : The Journal of Clinical Investigation. 124, 2, p. 515-27 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Country-specific antibiotic use practices impact the human gut resistome

    Forslund, K., Sunagawa, S., Kultima, J. R., Mende, D. R., Arumugam, M., Typas, A. & Bork, P., Jul 2013, In : Genome Research. 23, 7, p. 1163-9 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    Genomic variation landscape of the human gut microbiome

    Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., Kota, K., Sunyaev, S. R., Weinstock, G. M. & Bork, P., 2013, In : Nature. 493, 7430, p. 45-50 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Enterotypes of the human gut microbiome: [Plus]Corrigendum [Plus]Addendum

    Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., Batto, J-M., dos Santos, M. B. Q., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H. B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E. G., Wang, J., Guarner, F., Pedersen, O., de Vos, W. M., Brunak, S., Doré, J., Antolín, M., Artiguenave, F., Blottiere, H. M., Almeida, M., Brechot, C., Cara, C., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Kristiansen, K. & MetaHIT Consortium, 2011, In : Nature. 473, 7346, p. 174-180 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    A human gut microbial gene catalogue established by metagenomic sequencing

    MetaHIT Consortium, 2010, In : Nature. 464, 7285, p. 59-65 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

Selected activities

  1. Pharmabiotics Conference 2018

    Manimozhiyan Arumugam (Invited speaker)
    15 Mar 2018

    Activity: Participating in or organising an event typesOrganisation of and participation in conference

  2. Gut Microbiota for Health World Summit 2018

    Manimozhiyan Arumugam (Invited speaker)
    10 Mar 2018

    Activity: Participating in or organising an event typesOrganisation of and participation in conference

  3. 25th United European Gastroenterology Week

    Manimozhiyan Arumugam (Invited speaker)
    30 Oct 2017

    Activity: Participating in or organising an event typesOrganisation of and participation in conference

  4. 25th United European Gastroenterology Week

    Manimozhiyan Arumugam (Organizer)
    30 Oct 2017

    Activity: Participating in or organising an event typesOrganisation of and participation in conference

  5. 53rd Congress of the European Societies of Toxicology

    Manimozhiyan Arumugam (Invited speaker)
    11 Sep 2017

    Activity: Participating in or organising an event typesOrganisation of and participation in conference

  6. 12th Copenhagen Bioscience Conference

    Manimozhiyan Arumugam (Organizer)
    1 Oct 20175 Oct 2017

    Activity: Participating in or organising an event typesOrganisation of and participation in conference

  7. European Microbiome Congress

    Manimozhiyan Arumugam (Invited speaker)
    1 Dec 2016

    Activity: Participating in or organising an event typesParticipation in workshop, seminar, course

  8. Wenner-Gren Foundation Symposium

    Manimozhiyan Arumugam (Invited speaker)
    16 Jun 2016

    Activity: Participating in or organising an event typesParticipation in workshop, seminar, course

  9. EMBL Conference: The Human Microbiome

    Manimozhiyan Arumugam (Organizer)
    10 Jun 201512 Jun 2015

    Activity: Participating in or organising an event typesOrganisation of and participation in conference

  10. Seminar: Human Microbiome

    Manimozhiyan Arumugam (Lecturer)
    14 Aug 201419 Aug 2014

    Activity: Talk or presentation typesLecture and oral contribution

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