My research interest is to understand the role of the microbiome in stroke, with a focus on intestinal immune function and microbial metabolites.

I have been working on the topic of the gut microbiome-brain interaction in stroke for 8 years. I am fascinated by the interaction of these two highly complex super-organisms, particularly how commensal bacteria regulate the immune response and influence stroke outcome. I believe that a better understanding on how the gut interacts with the brain may provide new therapeutic avenues to protect the brain after stroke.

My scientific goal is to better understand how the gut microbiome may influence stroke outcome and post-stroke comorbidities. Modulation of the microbiome­–specially microbial metabolites–may have strong therapeutic implications in stroke by diet interventions.

Trainings & current position

2019 - Present

Principal investigator in Neuroimmunology

DFG-Deutsche Forschungsgemeinschaft
Lab of Dr. Arthur Liesz, LMU, Munich, Germany
Topic: Microglia – T cell interactions

2016 - 2019

Post-doc position in Neuroimmunology

European Marie Curie fellowship H2020
Lab of Dr. Arthur Liesz, LMU, Munich, Germany
Topic: Microbial metabolomics in stroke

2012 - 2016

Post-doc position in Neuroscience

Fellowship from the Swiss National Science Foundation
Lab of Prof. Costantino Iadecola
Weill Cornell University, New York
Topic: Microbiota and the immune system in stroke


PhD in Neuroscience


Master in Biochemistry, Geneva, Switzerland


Faculty of Science, University of Geneva, Switzerland

Grants & Fellowships


Deutsche Forschungsgemeinschaft grant


Marie Sklodowska-Curie European Individual Fellowships


Swiss National Science Foundation


Academic Society of Vaud, Post-doctoral research grant, Switzerland


Academic Society of Vaud, Doctoral research grant, Switzerland


Mobility Master scholarship, Ernest Boninchi Foundation, University of Geneva, Switzerland 

Mobility Master scholarship, Ernest Boninchi Foundation, University of Geneva, Switzerland 

My history

I am a neurobiologist with 7-years postdoc experience at the crossroad of neurobiology, immunology and microbiology. After my master degree in biochemistry in Geneva, Switzerland, I undertook my PhD in neuroscience at the university of Lausanne in the laboratory of Dr. Lorenz Hirt, Professor of Neurology. These first years of fundamental research in the cerebral ischemia field built my deep interest in seeking to understand the cellular mechanisms leading to neurodegenerative diseases. I specifically studied the role of a neuroprotective compound –a JNK inhibitor– on microglia activation and peripheral inflammation after stroke which leads to fruitful collaborations, in particular with a Swiss biopharmaceutical company, and had a well published record in this field (Benakis et al., Brain Behav. Immun., 2010; Benakis et al., J Neuroinflammation, 2012).

After graduating from my PhD in neuroscience in 2012, I obtained a competitive three-years post-doctoral fellowship from the Swiss National Research Foundation to join the Brain and Mind Research Institute of Weill Cornell Medicine in New York –headed by Prof. Costantino Iadecola, M.D., Anne Parrish Titzell Professor of Neurology. There, under the supervision of Dr. Josef Anrather, Professor of Neuroscience, I participated at first in studies tackling the molecular mechanisms of inflammatory preconditioning (Garcia-Bonilla et al., J. Neurosci., 2018) and on the role of SUMO and ubiquitin in ischemic brain injury (Hochrainer et al., JCBFM, 2015).

My main focus was then to investigate the mechanisms through which gut microbiota influence outcomes after an ischemic stroke. This innovative research project, of which I am the first author, was published in Nature Medicine in March 2016 (Benakis et al., Nat. Med., 2016). In this article, we shed new light on how gut microbiota have a remarkable impact on stroke outcome, with far-reaching and translationally relevant implications.

In July 2016, I joined the laboratory of Dr. Arthur Liesz at the Institute of Stroke and Dementia in Munich, with a Marie Sklodowska-Curie European fellowship to develop my own research topic on the specific role of gut metabolites, specifically tryptophan metabolites, on immune cell polarization in the context of brain injury.

In ongoing experiments, I am investigating the direct impact of intestinal T cells on the resident immune cells of the brain– the microglial cells. Specially, I am interested whether T cells primed by the gut microbiota may influence microglial function and further alter the neuroinflammation to stroke. For this project I recently obtained a DFG research grant as a Principal Investigator.

The last three years were very productive within the Liesz Lab, and I co-authored several publications: 1) the role of the choroid plexus as a route of T cell infiltration after stroke (Llovera at al., Acta Neuropathol., 2017), 2) the variation of the microbiota composition from different breeders in influencing the immune cell polarization (Sadler et al., Brain Behav. Immun., 2017), 3) an automated analysis of microglia morphology in a stroke context (Heindl et al., Front. Cell Neurosci., 2018), 4) characterization of a skull-meninges connections after stroke (Cai et al. Nat. Neurosci., 2019).

I am also involved in the supervision of master and medical students as well as teaching this year a practical course “Neuroimmunological methods in experimental stroke research” for students at the Graduate School of Systemic Neurosciences GSN-LMU.

I had the chance to give talks as invited speaker at several international conferences: “10th International Symposium on Neuroprotection and Neurorepair, Dresden October 9–11 208”, “International Stroke Conference, American Stroke Association, Honolulu February 6–8 2019”, and the up-coming “Brain & Brain PET Conference, International Society for Cerebral Blood Flow & Metabolism, Yokohama July 4–7 2019” and in October 2019 I will present my research at the SfN in Chicago (Neuroscience 2019, Society for Neuroscience, Chicago October 19–23).

My future plans is to lead my independent research group on “Stroke & Microbiome” investigating the critical role of the gut microbiome in stroke and to provide new therapeutic avenues to improve stroke recovery and dampen post-stroke comorbidities.

My publications

  1. Benakis C, Llovera G and Liesz A. The meningeal and choroidal infiltration routes for leukocytes in stroke. Therapeutics Advances in Neuroogical Disorders 2018, 11: 1–13 (IF:4.8)
  2. Heindl, S., Gesierich B, Benakis C, Llovera G, Duering M and Liesz A. Automated morphological analysis of microglia after stroke. Frontiers Cellular Neuroscience 2018; 12: 106 (IF:4.5)
  3. Llovera G, Benakis C, Enzmann G, Cai R, Arzberger T, Ghasemigharagoz A, Mao X, Malik R, Lazarevic I, Liebscher S, Ertürk A, Meissner L, Vivien D, Haffner C, Plesnila N, Montaner J, Engelhardt B and Liesz A. The choroid plexus is a key cerebral invasion route for T cells after stroke. Acta Neuropathologica 2017, 134: 1-18 (IF:12.2)
  4. Sadler R, Singh V, Benakis C, Garzetti D, Brea D, Stecher B, Anrather J and Liesz A. Microbiota differences between commercial breeders impacts the post-stroke immune response. Brain Behavior and Immunity Epub 2017 Mar 24 (IF:5.9)
  5. Benakis C, Brea D,Caballero S, Faraco G, Moore J, Murphy M, Sita G, Racchumi G, Ling L, Pamer EG, Iadecola C, Anrather J. Commensal microbiota affects ischemic stroke outcome by regulating intestinal T cells. Nature Medicine 2016, 22: 516-523, (IF:30.4)
  6. Benakis C, Vaslin A, Pasquali C, Hirt L. Neuroprotection by inhibiting the c-Jun N-terminal kinase pathway after cerebral ischemia occurs independently of Interleukin-6 and Keratinocyte-derived Chemokine (KC/CXCL1) secretion. Journal of Neuroinflammation 2012, 25: 76 (IF: 4.7)
  7. Benakis C, Bonny C, Hirt L. JNK inhibition and inflammation after cerebral ischemia. Brain Behavior and Immunity 2010, 24: 800-811 (IF: 5.9)
  8. Benakis C, Hirt L, Du Pasquier RA. Inflammation and Stroke. Cardiovascular Medicine 2009, 12: 143-150.