Mani Arumugam

Mani Arumugam

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 explaining your motivation and outlining your research ambitions.
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 explaining your motivation and outlining your research ambitions.

Primary fields of research

Human Microbiome, Systems Biology, Bioinformatics, Metagenomics, Machine Learning, Artificial Intelligence

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, C., 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. & 6 others, drb459, drb459, Hansen, Torben, Mande, S. S., Mohan, V., Arumugam, Mani & Pedersen, Oluf Borbye, 2021, In: Genome Medicine. 13, 37.

    Research output: Contribution to journalJournal articlepeer-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 journalReviewpeer-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. & 15 others, 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 journalJournal articlepeer-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 journalLetterpeer-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, T. & 4 others, 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 journalJournal articlepeer-review

  6. 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 journalJournal articlepeer-review

  7. 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. & 31 others, 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 journalJournal articlepeer-review

  8. 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 journalJournal articlepeer-review

Selected activities

  1. EMBO|EMBL Symposium: The Human Microbiome

    Arumugam, Mani (Organizer)

    20 Sep 202323 Sep 2023

    Activity: Participating in an event - typesOrganisation of and participation in conference

  2. EMBO|EMBL Symposium: The Human Microbiome

    Arumugam, Mani (Organizer)

    16 Sep 201819 Sep 2018

    Activity: Participating in an event - typesOrganisation of and participation in conference

  3. Pharmabiotics Conference 2018

    Arumugam, Mani (Invited speaker)

    15 Mar 2018

    Activity: Participating in an event - typesOrganisation of and participation in conference

  4. Gut Microbiota for Health World Summit 2018

    Arumugam, Mani (Invited speaker)

    10 Mar 2018

    Activity: Participating in an event - typesOrganisation of and participation in conference

  5. 25th United European Gastroenterology Week

    Arumugam, Mani (Invited speaker)

    30 Oct 2017

    Activity: Participating in an event - typesOrganisation of and participation in conference

  6. EMBL Conference: The Human Microbiome

    Arumugam, Mani (Organizer)

    10 Jun 201512 Jun 2015

    Activity: Participating in an event - typesOrganisation of and participation in conference

  7. Seminar: Human Microbiome

    Arumugam, Mani (Lecturer)

    14 Aug 201419 Aug 2014

    Activity: Talk or presentation typesLecture and oral contribution

ID: 41056735