Employees overview – University of Copenhagen

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Novo Nordisk Foundation Center for Basic Metabolic Research > Employees

Manimozhiyan Arumugam

Manimozhiyan Arumugam

Associate Professor

  • Section for Metabolic Genetics

    Universitetsparken 1, 1st floor, DIKU, 2100 Copenhagen Ø, DIKU


    Phone: +45 35 33 75 81

Member of:

  • Novo Nordisk Foundation Center for Basic Metabolic Research

Dr. Manimozhiyan Arumugam is a Group Leader and Associate Professor at the Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen. Dr. Arumugam received his PhD in computational biology from the European Molecular Biology Laboratory (Heidelberg) in 2010. At the Metabolic Genetics section of the Center, 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. He believes that our health and diseases are strongly influenced by our genetics, by the environment we live in, and by our gut microbiome. His research is thus interdisciplinary, combining metagenomics (a technique to study the gut microbiome), (epi)genomics, (epi)genetics, (meta)transcriptomics, and metabolomics. Arumugam group investigates the role of gut microbiome in multiple sclerosis, type 2 diabetes and obesity. The group also 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!

Job Opportunities

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.

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. Published

    Human gut microbes impact host serum metabolome and insulin sensitivity

    Pedersen, H. K., Gudmundsdottir, V., Nielsen, H. B., Hyotylainen, T., Nielsen, T., Jensen, B. A. H., Forslund, K., Hildebrand, F., Prifti, E., Falony, G., Le Chatelier, E., Levenez, F., Doré, J., Mattila, I., Plichta, D. R., Pöhö, P., Hellgren, L. I., Arumugam, M., Sunagawa, S., Vieira-Silva, S., Jørgensen, T., Holm, J. B., Trošt, K., Kristiansen, K., Brix, S., Raes, J., Wang, J., Hansen, T., Bork, P., Brunak, S., Oresic, M., Ehrlich, S. D., Pedersen, O. B. & MetaHIT Consortium 2016 In : Nature. 535, 7612, p. 376-381 6 p.

    Publication: Research - peer-reviewJournal article

  2. 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

    Publication: Research - peer-reviewJournal article

  3. Published

    Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

    Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., Pedersen, H. K., Arumugam, M., Kristiansen, K., Yvonne Voigt, A., Vestergaard, H., Hercog, R., Igor Costea, P., Roat Kultima, J., Li, J., Jørgensen, T., Levenez, F., Dore, J., Nielsen, H. B., Brunak, S., Raes, J., Hansen, T., Wang, J., Dusko Ehrlich, S., Bork, P. & Pedersen, O. B. 2015 In : Nature. 528, 7581, p. 262-266 5 p.

    Publication: Research - peer-reviewJournal article

  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.

    Publication: Research - peer-reviewJournal article

  5. 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.

    Publication: Research - peer-reviewJournal article

  6. 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.

    Publication: Research - peer-reviewJournal article

  7. Published

    Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

    Nielsen, H. B., Almeida, M., Juncker, A., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D. R., Gautier, L., Pedersen, A. G., Le Chatelier, E., Pelletier, E., Bonde, I., Nielsen, T., Manichanh, C., Arumugam, M., Batto, J-M., dos Santos, M. B. Q., Blom, N., Borruel, N., Burgdorf, K. S., Boumezbeur, F., Casellas, F., Doré, J., Dworzynski, P., Guarner, F., Hansen, T., Hildebrand, F., Kaas, R. S., Kennedy, S., Kristiansen, K., Kultima, J. R., Léonard, P., Levenez, F., Lund, O., Moumen, B., Le Paslier, D., Pons, N., Pedersen, O. B., Prifti, E., Qin, J., Raes, J., Sørensen, S. J., Tap, J., Tims, S., Ussery, D., Yamada, T., Renault, P., Sicheritz-Pontén, T., Bork, P., Wang, J., Brunak, S., Ehrlich, S. D. & MetaHIT Consortium 2014 In : Nature Biotechnology. 32, 8, p. 822–828 7 p.

    Publication: Research - peer-reviewJournal article

  8. 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.

    Publication: Research - peer-reviewJournal article

  9. Published

    Metagenomic species profiling using universal phylogenetic marker genes

    Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., Rasmussen, S., Brunak, S., Pedersen, O. B., Guarner, F., de Vos, W. M., Wang, J., Li, J., Doré, J., Ehrlich, S. D., Stamatakis, A. & Bork, P. 2013 In : Nature Methods. 10, 12, p. 1196-1199 4 p.

    Publication: Research - peer-reviewJournal article

  10. Published

    Richness of human gut microbiome correlates with metabolic markers

    Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J-M., Kennedy, S., Leonard, P., Li, J., Burgdorf, K. S., Grarup, N., Jørgensen, T., Brandslund, I., Nielsen, H. B., Juncker, A., dos Santos, M. B. Q., Levenez, F., Pons, N., Rasmussen, S., Sunagawa, S., Tap, J., Tims, S., Zoetendal, E. G., Brunak, S., Clément, K., Doré, J., Kleerebezem, M., Kristiansen, K., Renault, P., Sicheritz-Ponten, T., de Vos, W. M., Zucker, J-D., Raes, J., Hansen, T., Bork, P., Wang, J., Ehrlich, S. D., Pedersen, O. B., Guedon, E., Delorme, C., Layec, S., Khaci, G., van de Guchte, M., Vandemeulebrouck, G., Jamet, A., Dervyn, R., Sanchez, N., Maguin, E., Haimet, F., Winogradski, Y., Cultrone, A., Leclerc, M., Juste, C., Blottière, H., Pelletier, E., LePaslier, D., Artiguenave, F., Bruls, T., Weissenbach, J., Turner, K., Parkhill, J., Antolin, M., Manichanh, C., Casellas, F., Boruel, N., Varela, E., Torrejon, A., Guarner, F., Denariaz, G., Derrien, M., van Hylckama Vlieg, J. E. T., Veiga, P., Oozeer, R., Knol, J., Rescigno, M., Brechot, C., Mérieux, A., M'Rini, C. & Yamada, T. 2013 In : Nature. 500, 7464, p. 541-546 6 p.

    Publication: Research - peer-reviewJournal article

  11. 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.

    Publication: Research - peer-reviewJournal article

  12. 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.

    Publication: Research - peer-reviewJournal article

  13. 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., Dervyn, R., Foerstner, K. U., Friss, C., van de Guchte, M., Guedon, E., Haimet, F., Huber, W., van Hylckama-Vlieg, J., Jamet, A., Juste, C., Kaci, G., Knol, J., Lakhdari, O., Layec, S., Le Roux, K., Maguin, E., Mérieux, A., Melo Minardi, R., M'rini, C., Muller, J., Oozeer, R., Parkhill, J., Renault, P., Rescigno, M., Sanchez, N., Sunagawa, S., Torrejon, A., Turner, K., Vandemeulebrouck, G., Varela, E., Winogradsky, Y., Zeller, G., Weissenbach, J., Ehrlich, S. D., Bork, P., Kristiansen, K. & MetaHIT Consortium 2011 In : Nature. 473, 7346, p. 174-180 7 p.

    Publication: Research - peer-reviewJournal article

  14. Published

    A human gut microbial gene catalogue established by metagenomic sequencing

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

    Publication: Research - peer-reviewJournal article

Selected activities

  1. EMBL Conference: The Human Microbiome

    Arumugam, M. (Organizer)
    10 Jun 201512 Jun 2015

    Activity: Participating in or organising an eventOrganisation of and participation in conference

  2. Seminar: Human Microbiome

    Arumugam, M. (Lecturer)
    14 Aug 201419 Aug 2014

    Activity: Talk or presentationLecture and oral contribution

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