Mani Arumugam

Mani Arumugam

ORCID: 0000-0002-0886-9101

Dr. Manimozhiyan Arumugam leads the Microbiome Systems Biology research group, investigating how health and diseases are influenced by our gut microbiome; how the gut microbiome interacts with the host and environmental factors; and how we can therapeutically modulate the gut microbiome to improve health. His research is interdisciplinary, combining metagenomics (a technique to study gut microbiome) and other host-microbial multi-omics readouts 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), liver diseases (EU Horizon 2020), ageing (Danish Independent Research Council) and producing antimicrobial peptides (Danish Independent Research Council).

Dr. Arumugam received his PhD in computational biology from the European Molecular Biology Laboratory (Heidelberg) in 2010.

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, Systems Biology, Bioinformatics, Metagenomics

Current research

Lifestyle changes and lack of physical activity are important factors involved in metabolic disorders. However, emerging evidence suggests that our gut microbiome and their interactions with us play an important role in our health and well-being. An imbalance in the gut microbiome may signify an unhealthy state of the host and contribute to obesity and diabetes pathogenesis.

The Arumugam Group aims to study the interactions between the host and the gut microbiome in order to understand the molecular mechanisms underlying metabolic disorders. The Group takes interdisciplinary approaches combining multi-omics microbiome data to study host-microbial cross-talk. The Group also investigates therapeutic approaches to modulate the gut microbiome towards improving human health.

Fields of interest

Systems Biology, Human Diseases, Genomics, Machine Learning

Selected publications

  1. Published

    Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India

    Alvarez Silva, Maria Camila, Kashani, A., Hansen, T. H., Pinna, N. K., Anjana, R. M., Dutta, A., Saxena, S., Støy, J., Kampmann, U., Nielsen, T., Jørgensen, T., Gnanaprakash, V., Gnanavadivel, R., Sukumaran, A., Rani, C. S. S., Færch, K., Radha, V., Balasubramanyam, M., Nair, G. B., Das, B., drb459, drb459, Hansen, Torben, Mande, S. S., Mohan, V., Arumugam, Mani & Pedersen, Oluf Borbye, 2021, In: Genome Medicine. 13, 37.

    Research output: Contribution to journal › Journal article › Research › peer-review

  2. Published

    Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure

    Trebicka, J., Bork, P., Krag, A. & Arumugam, Mani, 2021, In: Nature Reviews Gastroenterology & Hepatology. 18, p. 167-180 14 p.

    Research output: Contribution to journal › Review › Research › peer-review

  3. Published

    Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

    Wirbel, J., Pyl, P. T., Kartal, E., Zych, K., Kashani, A., Milanese, A., Fleck, J. S., Voigt, A. Y., Palleja, A., Ponnudurai, R., Sunagawa, S., Coelho, L. P., Schrotz-King, P., Vogtmann, E., Habermann, N., Niméus, E., Thomas, A. M., Manghi, P., Gandini, S., Serrano, D., Mizutani, S., Shiroma, H., Shiba, S., Shibata, T., Yachida, S., Yamada, T., Waldron, L., Naccarati, A., Segata, N., Sinha, R., Ulrich, C. M., Brenner, H., Arumugam, Mani, Bork, P. & Zeller, G., 2019, In: Nature Medicine. 25, 4, p. 679-689 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    Circulating microbiome in blood of different circulatory compartments

    Schierwagen, R., Alvarez Silva, Maria Camila, 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, Mani, 2019, In: Gut. 68, 3, p. 578-580

    Research output: Contribution to journal › Letter › Research › peer-review

  5. Published

    Recovery of gut microbiota of healthy adults following antibiotic exposure

    Palleja, A., Mikkelsen, K. H., Forslund, S. K., Kashani, A., Allin, K. H., Nielsen, T., Hansen, T. H., Liang, S., Feng, Q., Zhang, C., Pyl, P. T., Coelho, L. P., Yang, H., Wang, J., Typas, A., Nielsen, M. F., Nielsen, H. B., Bork, P., Wang, J., Vilsbøll, Tina, Hansen, Torben, Knop, Filip Krag, Arumugam, Mani & Pedersen, Oluf Borbye, Nov 2018, In: Nature Microbiology. 3, 11, p. 1255-1265 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  6. 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, Jan, Li, Y., Wang, X., Xu, X., Chen, N., Wu, W. K. K., Al-Aama, J., Nielsen, H. J., Kiilerich, P., Jensen, Benjamin Anderschou Holbech, Yau, T. O., Lan, Z., Jia, H., Li, J., Xiao, L., Lam, T. Y. T., Ng, S. C., Cheng, A. S., Wong, V. W., Chan, F. K. L., Xu, X., Yang, H., Madsen, L., Datz, C., Tilg, H., Wang, J., Brünner, N., Kristiansen, Karsten, Arumugam, Mani, Sung, J. J. & Wang, J., 2017, In: Gut. 66, p. 70-78 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. 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, Thorsten, Liang, S., Feng, Q., Jørgensen, N. B., Bojsen-Møller, K. N., Dirksen, C., Burgdorf, Kristoffer Sølvsten, Holst, Jens Juul, Madsbad, Sten, Wang, J., Pedersen, Oluf Borbye, Hansen, Torben & Arumugam, Mani, 2016, In: Genome Medicine. 8, 13 p., 67.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    A catalog of the mouse gut metagenome

    Xiao, L., Feng, Q., Liang, S., Sonne, Si Brask, 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., S.Colding-Christensen, Camilla, 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, Mani, Wang, J., Madsen, L. & Kristiansen, Karsten, 2015, In: Nature Biotechnology. 33, 10, p. 1103-1108 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    Genomic variation landscape of the human gut microbiome

    Schloissnig, S., Arumugam, Mani, 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 journal › Journal article › Research › peer-review

  10. Published

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

    Arumugam, Mani, Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., Batto, J., dos Santos, M. B. Q., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, Torben, 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, Oluf Borbye, de Vos, W. M., Brunak, Søren, Doré, J., Antolín, M., Artiguenave, F., Blottiere, H. M., Almeida, M., Brechot, C., Cara, C., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Kristiansen, Karsten & MetaHIT Consortium, M. C., 2011, In: Nature. 473, 7346, p. 174-180 7 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. Published

    A human gut microbial gene catalogue established by metagenomic sequencing

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

    Research output: Contribution to journal › Journal article › Research › peer-review

Selected activities

  1. Pharmabiotics Conference 2018

    Arumugam, Mani (Invited speaker)

    15 Mar 2018

    Activity: Participating in an event - types › Organisation of and participation in conference

  2. Gut Microbiota for Health World Summit 2018

    Arumugam, Mani (Invited speaker)

    10 Mar 2018

    Activity: Participating in an event - types › Organisation of and participation in conference

  3. 25th United European Gastroenterology Week

    Arumugam, Mani (Invited speaker)

    30 Oct 2017

    Activity: Participating in an event - types › Organisation of and participation in conference

  4. 25th United European Gastroenterology Week

    Arumugam, Mani (Organizer)

    30 Oct 2017

    Activity: Participating in an event - types › Organisation of and participation in conference

  5. 53rd Congress of the European Societies of Toxicology

    Arumugam, Mani (Invited speaker)

    11 Sep 2017

    Activity: Participating in an event - types › Organisation of and participation in conference

  6. 12th Copenhagen Bioscience Conference

    Arumugam, Mani (Organizer)

    1 Oct 2017 → 5 Oct 2017

    Activity: Participating in an event - types › Organisation of and participation in conference

  7. European Microbiome Congress

    Arumugam, Mani (Invited speaker)

    1 Dec 2016

    Activity: Participating in an event - types › Participation in workshop, seminar, course

  8. Wenner-Gren Foundation Symposium

    Arumugam, Mani (Invited speaker)

    16 Jun 2016

    Activity: Participating in an event - types › Participation in workshop, seminar, course

  9. EMBL Conference: The Human Microbiome

    Arumugam, Mani (Organizer)

    10 Jun 2015 → 12 Jun 2015

    Activity: Participating in an event - types › Organisation of and participation in conference

  10. Seminar: Human Microbiome

    Arumugam, Mani (Lecturer)

    14 Aug 2014 → 19 Aug 2014

    Activity: Talk or presentation types › Lecture and oral contribution

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