Research interests

I am interested in the complex interactions between a host’s adaptive immune gene diversity (major histocompatibility complex), gut microbiota and pathogens. Further how these interactions might change due to anthropogenic habitat disturbance which in turn can have consequences for wild animal health. Thus, my research interests include:

  • Wildlife gut microbiome & health
  • Gut dysbiosis
  • Landscape ecology and genetics
  • Immune gene diversity (MHC)
  • Host-pathogen interactions

Scientific projects

Nowadays anthropogenic disturbance is ubiquitous and wild animal populations can be affected by these alterations in various respects, including changes in genetic diversity, gut microbiota and pathogen burden. In my PhD thesis, I investigate the effects of anthropogenic disturbance on wildlife microbiota and health. I study the effects of anthropogenic disturbance on genetic diversity at the functionally important regions of the MHC II and pathogen diversity in the widely distributed and generalistic rodent Proechimys semispinosus, which inhabits a wide range of habitats in the neotropics, including human-disturbed ones.

Further I am interested in the interactions between a host’s adaptive immune gene diversity (MHC), gut microbiota and pathogens, and how such interactions might change due to anthropogenic habitat disturbance. Since aside from direct involvement in providing the host’s adaptive immune response, MHC class II genes are also hypothesized to regulate the gut bacterial diversity and composition. Thus, they shape the production of immune-modulatory substances by microbes and also indirectly modulate host susceptibility. But despite initial evidence for the link between host MHC and the microbiota, associations among these factors remain largely unknown, especially in wild animal populations. To contribute to increase our understanding in MHC - microbiota – pathogen interactions in wildlife I study associations between MHC II and gut microbiota in Jamaican fruit bats challenged with Astrovirus infections.


Fleischer R, Jones C, Ledezma-Campos P, Czirják GÁ, Sommer S, Gillespie TR, Vicente-Santos A (2024) Gut microbial shifts in vampire bats linked to immunity due to changed diet in human disturbed landscapes. Science of the Total Environment, 907, 167815. (

Fleischer R, Eibner GJ, Schwensow NI, Paraskevopoulou S, Mayer G, Corman VM, Drosten C, Wilhelm K, Heni AC*, Sommer S*, Schmid DW* (2024) Hidden zoonotic risk: immunogenetic-pathogen networks shrink in a generalist rodent inhabiting disturbed landscapes. Communications Biology, in press.
* shared senior authors, contributed equally to the study.

Víquez RL, Fleischer R, Wilhelm K, Tschapka M & Sommer S (2020). Jumping the green wall: The use of PNA-DNA clamps to enhance microbiome sampling depth in wildlife microbiome research. Ecology and Evolution, 10(20), 11779-11786.

Fleischer R, Risely A, Hoeck PE, Keller LF & Sommer S (2020). Mechanisms governing avian phylosymbiosis: Genetic dissimilarity based on neutral and MHC regions exhibits little relationship with gut microbiome distributions of Galápagos mockingbirds. Ecology and Evolution, 10(23), 13345-13354.


  • Ramona Fleischer, MSc.
    Institute of Evolutionary Ecology
    and Conservation Genomics
    University of Ulm
    Albert-Einstein-Allee 11
    89081 Ulm
    Email: ramona.fleischer()