Key publications

Shoaie, P. Ghaffari, P. Kovatcheva-Datchary, A. Mardinoglu, P. Sen, E. Pujos-Guillot, T. de Wouters, C. Juste, S. Rizkalla, J. Chilloux, L. Hoyles, J. K. Nicholson, MICRO-Obes Consortium, J. Dore, M. E. Dumas, K. Clement, F. Bäckhed, and J. Nielsen, Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome, Cell Metabolism, 22, 320-331, 2015.

Mardinoglu*, S. Shoaie*, M. Bergentall, P. Ghaffari, C. Zhang, E. Larsson, F. Bäckhed, J. Nielsen, Revealing the metabolic differences between germ free and conventionally raised mice through metabolic modeling of gut microbiota and its host, Molecular Systems Biology, 11: 834, 2015. *Equal contribution.

A Witherden, D. L Moyes, K. D Bruce, S. D Ehrlich, S. Shoaie*, Using systems biology approaches to elucidate cause and effect in host-microbiome interactions, Current Opinion in Systems Biology, 2017.

Babaei, S. Shoaie, B. Ji and J. Nielsen. Challenges in modeling the human gut microbiome, Nature biotechnology, 36, 8, 682, 2018.

Kovatcheva-Datchary*, S. Shoaie*, S. Lee, J. Nielsen, F. Bäckhed, Simplified intestinal microbiota to study microbe-diet-host interactions in a mouse model, Cell Reports 26, 3772–3783 2019. *Equal contribution.

Saeed Shoaie

Research interests

We are investigating the global and temporal changes of human microbiome in health and diseases. We develop computational and quantitative systems biology tools and models to understand the role of microbiome in host physiology and propose an improved microbiome-based personalized medicine pathway for future therapy. Construction of atlas of human microbiome and metagenome species is the main goal in the lab.  We are updating different microbial gene catalogues together with metagenome species, including bacteria, fungi and phage to achieve better representation of uncultured genomes in the human microbiome. We characterize the metagenome species and gene catalogues with several functional annotations such antimicrobial resistance, virulence factors, mobile genetic elements, and secondary metabolites. Understanding the global relation between the human microbiome and antimicrobial resistance is one of the key questions we try to answer within the latest initiative of One Million Microbiome Project. 

Group members

We are opening soon for postdoctoral research associate positions.


Last updated: 2022-11-30

Content Responsible: David Gotthold(