Gastrointestinal Microbiome
In the human gut, microbial communities aid in digesting food, stimulate the immune system and protect against pathogens. As opposed to bacteria and archaea, bacteria-infecting viruses (phages) comprise a much less explored biodiversity with potentially high impact on microbial community composition. We build and apply bioinformatic tools to whole genome sequencing and metagenomics to explore biological processes occurring in human commensals and pathogens, and their influence on human health.
We are particularly interested in the following questions:
What is the natural within- and across-species genetic diversity of microbiome species?
How are key metabolic functions distributed in bacterial communities and how do they relate with host features?
How do mobile genetic elements (MGEs) shape the microbiome?
What is the genetic and functional diversity of pathogen surface antigens (collaboration with the Slack lab)?
Selected publications
High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains
Zünd M, Ruscheweyh HJ, Field CM, Meyer N, Cuenca M, Hoces D, Hardt WD, Sunagawa S✉
Microbiome: 9, 77, 2021. [external pageDOIcall_made]
Import of aspartate and malate by DcuABC drives H2/fumarate respiration to promote initial Salmonella gut-lumen colonization in mice
Nguyen BD, Cuenca M, Hartl J, Gul E, Bauer R, Meile S, Ruthi J, Margot C, Heeb L, Besser F, Perez Escriva P, Fetz C, Furter M, Laganenka L, Keller P, Fuchs LM, Christen M, Porwollik S, McClelland M, Vorholt JA, Sauer U, Sunagawa S✉, Christen B✉, Hardt WD✉
Cell Host Microbe: 27(6), 922-936, 2020. [external pageDOIcall_made]
Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Niewdorp M, Salojarvi J, Voigt AY, Zeller G, Sunagawa S✉, de Vos WM✉, Bork P✉
Science: 352(6285), 586-589, 2016. [external pageDOIcall_made]
Genomic variation landscape of the human gut microbiome.
Schloissnig S*, Arumugam M*, Sunagawa S*, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM✉, Bork P✉
Nature: 493(7430), 45-50, 2013. [external pageDOIcall_made]