The MET-FLAM Faculty

Vanessa STADLBAUER-KÖLLNER

Scientific Interests:

We also described factors that influence microbiome composition in liver cirrhosis (liver disease etiology, severity, drug intake, inflammation and nutritional status). We found a strong association of proton pump inhibitor use and “oralization” (the occurrence of oral bacteria Veillonella parvula and Streptococcus salivarius in the gut microbiome) with inflammation, complications and mortality. Besides medical acid suppression, also reduction of stomach acid production due to surgical resection causes this oralization. We investigated the effect of microbiome modulation via probiotics as possible strategy to improve microbiome composition in cirrhosis. [9–12] We further demonstrated interactions between disease, drug intake and the composition and function on the gut microbiome in patients with liver cirrhosis, dementia, chronic kidney disease, polycystic ovary syndrome and secondary sclerosing cholangitis in critically ill patients. [11, 13–16] We further discovered that alcohol intake is associated with a steep and rapid increase in FGF21 levels and contributed to the understanding the role of FGF21 in the regulation of water intake [17, 18].

We currently have a strong research interest in sarcopenia (muscle loss) in liver cirrhosis and we recently described the role of secondary bile acids, which are transformed from primary bile acids by the gut microbiome in sarcopenia in cirrhosis. We also work on clinical sarcopenia projects where we aim to improve diagnostics by using machine learning tools and to predict prognosis with a variety of traditional and non-traditional biomarkers [19, 20]. We aim to deepen the knowledge on the pathophysiology of the disease as well as the peculiarities of sarcopenia in liver diseases and to identify novel therapeutic targets. We currently perform the first interventional study treat muscle loss with a microbiome modulating strategies.

Proposed Dissertation Topic:

Background: The loss of muscle mass, quality and strength (sarcopenia) is a common problem of older age, especially in people with chronic diseases such as liver cirrhosis. Sarcopenia impairs quality of life and increases mortality. Decreased protein synthesis and increased protein degradation mediated by inflammation contribute to sarcopenia in cirrhosis. However, the starting point of this negative cascade of events has not been fully elucidated and therefore, to date, no specific therapy is available to treat or prevent sarcopenia. We have recently identified distinct changes in secondary bile acid abundance and composition being associated with sarcopenia. Furthermore, we have shown that bile acids induce neutrophil ROS production ex vivo, indicating a link between the gut microbiome, bile acids, and inflammation in cirrhosis.

Hypothesis and objectives: We hypothesize that changes in microbial bile acid metabolism play a key role in the development of sarcopenia in cirrhosis. The PhD student will dissect the effects of cirrhosis and sarcopenia on the transformation of primary to secondary bile acids in the gut microbiome using a patient-derived in vitro cultivated microbiome model and will identify in silico and in vitro differences in bile acid transformation pathways in stool microbiomes of cirrhotic patients with and without sarcopenia. Furthermore, the student will investigate the effects of altered bile acid composition on gut permeability and inflammation as well as muscle cell function in ex vivo / in vitro cell culture model systems.

Methods and approaches: The PhD candidate will learn to use an anaerobic bioreactor system developed for long-term culture of the human stool microbiome. The student will evaluate bile acid profiles by LC-MS-MS and perform metagenomics analysis (1st year). The student will use an in vitro model of the intestinal barrier (Caco-2 cells, assessment of transepithelial resistance, expression of tight junction and adherens junction proteins) and an ex vivo innate immune model, in which neutrophils and peripheral blood mononuclear cells will be challenged with different bile acid compositions or the supernatant of in vitro anaerobic microbiome cultures to assess the production of reactive oxygen species, calprotectin, and cytokines (2nd and 3rd year). Adult human skeletal muscle cells will be cultivated by the student and challenged with different bile acid compositions, and a comprehensive cell biology qPCR array for human skeletal muscles will be performed to characterize muscle-cell contractility, development and proliferation, differentiation, muscle atrophy and dystrophy (4th year). The student will be trained to apply advanced biostatistical and bioinformatics tools to analyze complex multi-omics datasets obtained from the experimental work.

Pitfalls and alternative approaches: The followings are the estimated risk of the proposed project and the contingency plans for them:
 

Risk description:	Mitigation:
Unavailability of patient material (low risk)	Established clinical network and clinical study coordination structure within the research unit of the PI
No differences are detectable in bile acid transformation between cirrhosis and sarcopenia (medium risk)	Metagenomics analysis beyond bile acid metabolism, identification of additional pathways of interest, analysis of potential additional microbial metabolites on muscle cells and innate immune cells
Unavailability of adult human skeletal muscle cells (medium risk)	Training of the PhD candidate at the “Center of Myology” in Paris, France, in the group of Professor Trollet and Professor Mouly (contact established), use of established cell lines or use of rodent muscle cells

Involved Faculty members: Vanessa Stadlbauer-Köllner (PI), Julia Kargl (innate immune model), Aitak Farzi (intestinal permeability).

International Collaborations: Paul O'Toole School of Microbiology, APC Microbiome Ireland, University College Cork (microbiome modulation).

Facilities: Our lab has developed and fully established the in vitro models for neutrophil function, the in vitro model of the gut microbiome (Figure 1) and an in vitro model of the gut barrier (Figure 2). The lab is located at the Zentrum für Medizinische Grundlagenforschung (ZMF). At ZMF the team has also access to cell culture facilities, flow cytometry, imaging, and all general lab methods (e. g. western blot, photometry, qPCR). Access to LC-MS/MS and untargeted metabolomics techniques as well as microbiome sequencing is available through the ZMF core facilities and our collaboration partners. For translational research, access to patient data and clinical samples is crucial, which is available at the Department of Gastroenterology and Hepatology and through the study coordination team of the research group.

Preparatory Findings:

Figure 1. Setup of the in vitro gut microbiome model.
 

Figure 2. Setup of the gut barrier model.
 

Figure 3. Preliminary data on differences in bile acid composition in patients with liver cirrhosis with and without sarcopenia.
Altered secondary and primary BAs between cirrhotic patients with and without sarcopenia (A–C). Shift from classical to the alternative pathway between cirrhotic patients with and without sarcopenia (D). Altered BAs transformation from primary to secondary BAs between cirrhotic patients with and without sarcopenia (E–H). Altered BAs pool hydrophilicity status between the cirrhotic patients with and without sarcopenia (I). Altered BA 12α-hydroxylation between cirrhotic patients with and without sarcopenia (J). Altered gut microbiome-derived metabolites, BCAA, and SCFA between cirrhotic patients with and without sarcopenia (K–L).

1. Balazs I, Horvath A, Leber B, Feldbacher N, Sattler W, Rainer F, Fauler G, Vermeren S, Stadlbauer V: Serum bile acids in liver cirrhosis promote neutrophil dysfunction. Clin Transl Med, 2022; 12(2):​e735.
   
2. Leber B, Balázs I, Horvath A, Posch A, Streit A, Spindelböck W, Feldbacher N, Stiegler P, Stauber RE, Rechberger GN, Kollroser M, Sattler W, Nusshold C, Stadlbauer V: Direct acting antiviral therapy rescues neutrophil dysfunction and reduces hemolysis in hepatitis C infection. Transl Res, 2021; 232:​103–114.
   
3. Horvath A, Leber B, Feldbacher N, Tripolt N, Rainer F, Blesl A, Trieb M, Marsche G, Sourij H, Stadlbauer V: Effects of a multispecies synbiotic on glucose metabolism, lipid marker, gut microbiome composition, gut permeability, and quality of life in diabesity: a randomized, double-blind, placebo-controlled pilot study. Eur J Nutr, 2020; 59(7):​2969–2983.
   
4. Tritto G, Bechlis Z, Stadlbauer V, Davies N, Francés R, Shah N, Mookerjee RP, Such J, Jalan R: Evidence of neutrophil functional defect despite inflammation in stable cirrhosis . J Hepatol, 2011; 55(3):​574–581.
   
5. Stadlbauer V, Mookerjee RP, Wright GA, Davies NA, Jürgens G, Hallström S, Jalan R: Role of Toll-like receptors 2, 4, and 9 in mediating neutrophil dysfunction in alcoholic hepatitis. Am J Physiol Gastrointest Liver Physiol, 2009; 296(1):​G15–G22.
   
6. Shawcross DL, Wright GA, Stadlbauer V, Hodges SJ, Davies NA, Wheeler-Jones C, Pitsillides AA, Jalan R: Ammonia impairs neutrophil phagocytic function in liver disease. Hepatology, 2008; 48(4):​1202–1212.
   
7. Stadlbauer V, Mookerjee RP, Hodges S, Wright GA, Davies NA, Jalan R: Effect of probiotic treatment on deranged neutrophil function and cytokine responses in patients with compensated alcoholic cirrhosis. J Hepatol, 2008; 48(6):​945–951.
   
8. Mookerjee RP, Stadlbauer V, Lidder S, Wright GA, Hodges SJ, Davies NA, Jalan R: Neutrophil dysfunction in alcoholic hepatitis superimposed on cirrhosis is reversible and predicts the outcome. Hepatology, 2007; 46(3):​831–840.
   
9. Horvath A, Bausys A, Sabaliauskaite R, Stratilatovas E, Jarmalaite S, Schuetz B, Stiegler P, Bausys R, Stadlbauer V, Strupas K: Distal Gastrectomy with Billroth II Reconstruction is Associated with Oralization of Gut Microbiome and Intestinal Inflammation: A Proof-of-Concept Study. Ann Surg Oncol, 2021; 28(2):​1198–1208.
   
10. Horvath A, Leber B, Feldbacher N, Steinwender M, Komarova I, Rainer F, Blesl A, Stadlbauer V: The effects of a multispecies synbiotic on microbiome-related side effects of long-term proton pump inhibitor use: A pilot study. Sci Rep, 2020; 10(1):​2723.
    
11. Stadlbauer V, Komarova I, Klymiuk I, Durdevic M, Reisinger A, Blesl A, Rainer F, Horvath A: Disease severity and proton pump inhibitor use impact strongest on faecal microbiome composition in liver cirrhosis. Liver Int, 2020; 40(4):​866–877.
    
12. Horvath A, Rainer F, Bashir M, Leber B, Schmerboeck B, Klymiuk I, Groselj-Strele A, Durdevic M, Freedberg DE, Abrams JA, Fickert P, Stiegler P, Stadlbauer V: Biomarkers for oralization during long-term proton pump inhibitor therapy predict survival in cirrhosis. Sci Rep, 2019; 9(1):​12000.
    
13. Blesl A, Jüngst C, Lammert F, Fauler G, Rainer F, Leber B, Feldbacher N, Stromberger S, Wildburger R, Spindelböck W, Fickert P, Horvath A, Stadlbauer V: Secondary Sclerosing Cholangitis in Critically Ill Patients Alters the Gut-Liver Axis: A Case Control Study. Nutrients, 2020; 12(9):​2728.
    
14. Stadlbauer V, Engertsberger L, Komarova I, Feldbacher N, Leber B, Pichler G, Fink N, Scarpatetti M, Schippinger W, Schmidt R, Horvath A: Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study. BMC Geriatr, 2020; 20(1):248.
    
15. Stadlbauer V, Horvath A, Ribitsch W, Schmerböck B, Schilcher G, Lemesch S, Stiegler P, Rosenkranz AR, Fickert P, Leber B: Structural and functional differences in gut microbiome composition in patients undergoing haemodialysis or peritoneal dialysis. Sci Rep, 2017; 7(1):​15601.
    
16. Lindheim L, Bashir M, Münzker J, Trummer C, Zachhuber V, Leber B, Horvath A, Pieber TR, Gorkiewicz G, Stadlbauer V, Obermayer-Pietsch B: Alterations in Gut Microbiome Composition and Barrier Function Are Associated with Reproductive and Metabolic Defects in Women with Polycystic Ovary Syndrome (PCOS): A Pilot Study. PLoS One, 2017; 3;12(1):​e0168390.
    
17. Wagner-Skacel J, Horvath A, Grande P, Wenninger J, Matzer F, Fazekas C, Mörkl S, Meinitzer A, Stadlbauer V: Association of fibroblast growth factor 21 with alcohol consumption and alcohol liver cirrhosis. Neuropsychiatr, 2021; 35(3):​140–146.
    
18. Song P, Zechner C, Hernandez G, Cánovas J, Xie Y, Sondhi V, Wagner M, Stadlbauer V, Horvath A, Leber B, Hu MC, Moe OW, Mangelsdorf DJ, Kliewer SA: The Hormone FGF21 Stimulates Water Drinking in Response to Ketogenic Diet and Alcohol. Cell Metab, 2018; 27(6):​1338–1347.e4.
    
19. Schweighofer N, Colantonio C, Haudum CW, Hutz B, Kolesnik E, Mursic I, Pilz S, Schmidt A, Stadlbauer V, Zirlik A, Pieber TR, Verheyen N, Obermayer-Pietsch B: DXA-Derived Indices in the Characterisation of Sarcopenia. Nutrients, 2021; 14(1):186.
    
20. Traub J, Bergheim I, Eibisberger M, Stadlbauer V: Sarcopenia and Liver Cirrhosis-Comparison of the European Working Group on Sarcopenia Criteria 2010 and 2019. Nutrients, 2020; 12(2):547.