Impact of exclusive enteral nutrition on microbiome signatures and function in pediatric Crohn’s disease

Principal Investigators:
Haller, Dirk, TUM
Schwerd, Tobias, LMU

Crohn’s disease (CD) is one of the two main entities of idiopathic inflammatory bowel disease (IBD). In the second funding phase, the tandem will specify the diet-induced changes in the intestinal microbiome for therapeutic efficacy of exclusive enteral nutrition (EEN) in pediatric Crohn’s disease. EEN-associated signatures will be characterized using the combined approach of continuous culture, gnotobiotic mice and pig models. In this context, the role of dietary fiber in provoking disease relapse will be evaluated. Longitudinal bacterial- and metabolite-profiling of treatment responsive and refractory patients will be implemented to identify functionally relevant microbiome targets in response to EEN, leading to the development of protective synthetic bacterial consortia. The perspective of this project is to develop a microbiome-based maintenance therapy for pediatric CD patients.

Microbial triggers of intestinal inflammation in hosts deficient in X-linked inhibitor of apoptosis protein

Principal Investigators:
Zeissig, Sebastian,TUD   
Yabal, Monica, MRI TUM

Host-microbial interactions play critical roles in the pathogenesis of inflammatory bowel disease (IBD). We have recently demonstrated that loss-of-function variants in the gene encoding X-linked inhibitor of apoptosis protein (XIAP) provide the basis for a prevalent Mendelian form of IBD. Further, we observed that mice deficient in XIAP can develop spontaneous, microbiota-induced intestinal inflammation. Here, we aim to study XIAP-deficient mice as a model system to identify specific microbial triggers of intestinal inflammation in a genetically susceptible host and to delineate host pathways involved in this process. 

T cell skewing in relation to intestinal dysbiosis and GvHD in allogeneic stem cell transplantation

Principal Investigators:
Busch, Dirk, TUM
Meedt, Elisabeth, UKR

The key hypothesis of this project is that microbiota dysbiosis skews the reconstitution of a regulatory immune response in the gut and both contribute to development of graft-versus-host disease (GvHD) after allogeneic stem cell transplantation. This connection provides the rationale for reverting dysbiosis and the loss of regulatory T cells as a potent treatment of GvHD. We aim to identify changes in microbiota signatures in both, stool and mucosa, mucosal lymphocyte populations, T cell receptor repertoire composition and target antigens of clonally expanding T cells associated with clinical outcome, taking advantage of a unique collection of gut biopsies longitudinally collected over the course of GvHD onset and development, including patients with and without antibiotic therapy (ABX) as well as before and after fecal transplantation (FMT).

Impact of microbiota-derived metabolites on tissue homeostasis and immune function in graft-versus-host disease

Principal Investigators:
Poeck, Hendrik, TUM & UKR
Ruland, Jürgen, TUM

Besides bacteria, microbiota-derived metabolites play a pivotal role in modulating innate and T cell mediated immunity in graft-versus-host disease (GvHD). In fecal samples of allo-SCT recipients, we identified a microbiome signature consisting of bacteria and their associated immunomodulatory metabolites that associate with clinical outcomes and can engage a specific innate immune pathway to mediate protection from GvHD. Led by these discoveries, we will investigate the microbiota/metabolomic profile in intestinal tissue samples of patients with or without GvHD (Aim 1), analyze the functional role of identified metabolites/consortia on GvHD (Aim 2) and test the influence of metabolite cocktails or bacterial consortia on human GvHD in preclinical model systems (Aim 3). Our goal is to develop microbial-based interventions that minimize GvHD for more effective cancer treatment.

Defining intestinal microbiota orchestrating immune tolerance to intervene with allergic reactions to food and beyond

Principal Investigators:
Biedermann, Tilo, TUM
Fischer, Konrad, TUM

 The aim of this tandem is to create minimal consortia with which food allergy can be prevented or treated. We could already show that susceptibility to food allergy mediated by exposure to alpha-gal is efficiently modulated by different microbiota compositions. In the second funding phase, we will further characterize our identified bacteria and further select those capable to induce resilience to alpha-gal allergy. We will establish murine and human minimal consortia to induce this resilience in germfree mice. Since the pig more closely resembles humans in terms of physiology and diet, we will establish FMT in pigs and finally investigate the therapeutic potential of the human resilience associated minimal consortia as `bacterial therapeutics’ to prevent or treat food allergies and even allergic inflammation in general.

Microbiota-mediated modulation of protective immunity and immunopathology

Principal Investigators:
Ohnmacht, Caspar, TUM
Zehn, Dietmar, TUM

Acute and chronic viral infections remain a major public health concern yet most external factors affecting efficacy of anti-viral immunity remain poorly understood. Based on our previous results demonstrating enhanced immunopathology and impaired virus control in germfree and in mice with limited bacterial diversity (OligoMM¹²-colonized mice) after chronic LCMV infection, we will now assess particularities of OligoMM¹² consortia and derivatives thereof during the course of the infection and investigate mechanistic links of these particularities to the regulation of virus-specific cytotoxic and T helper cell responses in different tissues. These mechanistic insights may be highly useful for the rational design of more efficient and personalized vaccination regimens and anti-cancer therapies including checkpoint inhibition.

The role of primary metabolites in the intestinal ecosystem under normal and inflamed conditions

Principal Investigators:
Jung, Kirsten, LMU
Stecher, Barbara, LMU

 Inflammatory processes create metabolic and trophic niches in the gut which, in turn, affect the composition and function of the microbial ecosystem. Project P08 will investigate the role of primary luminal metabolites, specifically organic acids and polyamines and characterize the impact of sensing, uptake and metabolic interactions on the fitness and growth of disease-relevant Salmonella, Desulfovibrio, Enterococcus and the individual species of the microbiota. Analyses will be done in vitro and in gnotobiotic mice colonized with the minimal bacterial consortium Oligo-MM and other mouse models of gut inflammation.

Deciphering the role of the gut microbiota in the success of radiation therapy for colorectal cancer

Principal Investigator:
Tschurtschenthaler, Markus, TUM
Fischer, Julius Clemens, TUM

Radiation therapy (RT) plays a crucial role in the treatment of advanced rectal cancer. However, the influence of the intestinal microbiome in this context is largely unknown. In the next funding period, this project will examine the intestinal microbiome of study patients with advanced rectal cancer during their RT in order to link microbial signatures and specific microbial signals to therapy outcomes. In parallel, the mechanisms of these observations are investigated using novel in vitro and in vivo models, such as by experimental RT of rectally transplanted tumor organoids into mice with different microbial interventions. The aim of this clinical-experimental project is to pave the way for the clinical application of innovative microbiome-based treatment concepts (e.g. fecal microbiota transfer) to improve the therapy of advanced colorectal cancer.

Identifying microbiome-related mechanisms of polyp progression and regression in a porcine model for colorectal cancer

Principal Investigators:
Flisikowska, Tatiana, TUM
Saur, Dieter, TUM

We have generated a novel translational pig model of inflammatory bowel disease (IBD), which is based on the TNF^ΔΑRE/+ mouse. The model closely reflects the human disease. We have also characterised temporal and spatial changes of the microbiota in both the IBD and APC¹³¹¹ mutant colorectal cancer (CRC) pig models. The APC¹³¹¹ pigs show high incidence of polyps accompanied by regression of adenomas. Preliminary results suggest that the microbiome impacts the natural immune surveillance of polyps. In the next funding period, the tumour-immune cell- microbiome interactions in pro-/regressing polyps will be investigated. Further, the impact of high/low fat and high/low protein diets on immune surveillance will be studied. Finally, we will model subtypes of CRC by introducing further oncogenic mutations and analyse their effect on bacterial composition and the polyp pro-/regressing phenotype

Impact of gut microbiota on colorectal cancer lipid metabolism

Principal Investigators:
Ecker, Josef, UKR
Janssen, Klaus-Peter, TUM

Cancer cells feature a high demand for lipids as fuel for energy metabolism or membrane synthesis during cell proliferation. We could show that an altered lipid metabolism in colorectal cancer has clinical significance and is essentially recapitulated in genetic mouse models. Moreover, gut microbiota interferes decisively with the lipid metabolism of the host. The tandem project focuses on the interactions between gut microbiota, lipid metabolism and cancer formation, also with regards to their putative therapeutical relevance. Stable isotope labelled precursors and quantitative lipidomic analysis will be used on patient-derived organoids and genetic cancer mouse models to define the role of dietary versus de novo synthesized lipids in tumorigenesis. The functional contribution of gut microbiota for intestinal lipid uptake, lipid synthesis and desaturation in the context of colorectal cancer will be dissected with germfree and gnotobiotic mouse models.

Targeted design and manipulation of minimal bacterial consortia for strain replacement within microbiomes

Principal Investigators:
Clavel, Thomas, RWTH
Stecher, Barbara, LMU

In P14 we will work on the targeted modulation of synthetic communities (SYNs) by developing personalized strategies for strain-level replacement within mouse and human complex communities. This will be achieved by using combinations of phage treatment and targeted colonization with specific niche competitor strains. The work will focus on Enterobacteriaceae and enterococci as clinically relevant taxa related to infections, antimicrobial resistances, and chronic inflammation. We will also extend the concept to the commensal species Phocaeicola (formerly Bacteroides) vulgatus, a prevalent and genetically modifiable member of the core microbiota in the mouse and human gut, to study bacterial factors that facilitate strain engraftment and to modulate specific ecosystem functions such as complex carbohydrate conversion and proinflammatory functions.

Functional characterization of carcinogenic and inflammatory secondary metabolites from the intestinal microbiota

Principal Investigators:
Gulder, Tobias, (HIPS)
Sieber, Stephan, TUM
Zeller, Georg, EMBL (left the consortium)

P16 will systematically identify biosynthetic gene clusters (BGCs) in gut microbiota through in silico mining of genomic and metagenomic resources. To infer pro-inflammatory or carcinogenic effects of the encoded metabolites, we will determine statistical enrichment in metagenomes of colorectal cancer and inflammatory bowel disease patients. Promising candidate BGCs will be cloned, heterologously expressed and the produced metabolites isolated and structurally as well as functionally characterized. Particular emphasis will be on compounds with heterocyclic structural elements, as these often possess significant cytotoxic activity. We will focus on the elucidation of their cellular targets as well as the corresponding modes of action via chemical proteomics. The impact of the identified biologically relevant metabolites on the host will be evaluated in animal models collaborating with partners of the CRC 1371. Ultimately, this project will elucidate new links between gut microbial metabolism and disease development in the host.

Impact of Desulfovibrio spp. and sulfur metabolism on the pathogenesis of chronic intestinal inflammation and colitis-associated cancer

Principal Investigators:
Schirmer, Melanie (TUM)
Haller, Dirk (TUM)

Persistent inflammation increases the risk of developing colorectal cancer. In this newly established project, the tandem will characterize the impact of sulfate-reducing bacteria, explicitly focusing on newly compiled human Desulfovibrio isolates, and the production of H2S on the development of chronic inflammation and colitis-associated cancer. Comparative genomic analysis of bacterial strains and the use of naturally occurring minimal consortia in germ-free mouse models provide the basis to study bacteria and host functions at the edge of inflammation and tumorigenesis. Dietary substrate- and disease-related regulation of Desulfovibrio spp. gene expression and metabolite production will be characterized in vitro and in gnotobiotic mice. Furthermore, the impact of H2S on epithelial cell functions will be determined in primary organoid cultures from mouse models and patients.

Microbiome-based Strategies for Biocontrol of Preterm Necrotizing Enterocolitis

Principal Investigators:
Hall, Lindsay, TUM (left the consortium)
Deng, Li, TUM

Necrotising enterocolitis (NEC) is a serious condition affecting between 5-15% of preterm infants, and is associated with overgrowth of multi-drug resistant pathogenic microbiota members. There is a clear need for new treatment approaches that circumvent the threat of antimicrobial resistance, and (bacterio)phages represent an attractive therapeutic target. This new project will explore the main bacterial species that are associated with NEC through a combination of metagenomics, culturing and whole genome sequencing studies, as well as to define strain level relationships. Using cutting-edge phage isolation and characterisation approaches we will identify phage isolates and optimal phage combinations against the main NEC-causing pathogens, and delineate how phage(s) impact the wider preterm microbiota, including probiotic genera using model gut systems. Finally, after pre-screening a wide range of phage-pathogen combinations in the wax moth in vivo model, we will determine efficacy of key phage cocktails against NEC pathogens using clinically relevant pig models, and thus define optimal therapeutic products that could be tested in the clinic within the next funding phase.

Integration and analysis of clinical and multi-omics data

Principal Investigators:
List, Markus, TUM
Boeker, Martin, TUM
Schirmer, Melanie, TUM
Sharma, Sapna, TUM (left the consortium)

INF01 is responsible for uniform processing and integration of data across CRC 1371 projects. In the second funding phase, we will extend the existing software platform for processing and integration of metagenomic and metatranscriptomic sequencing data as well as untargeted metabolomics data. We further seek to establish tools for the joint analysis of 16S rRNA and metagenomic sequencing data and a better clinical integration through the development of suitable reporting tools.

Gnotobiotic mouse models and minimal bacterial consortia

Principal Investigators:
Basic, Marijana, MHH
Clavel, Thomas, RWTH
Haller, Dirk, TUM

Germ-free animals can be utilized to unravel the functionality of individual murine or human bacterial species, synthetic consortia or human fecal transplants in health and disease, implementing highly defined experimental conditions. In this core project, the two well-established facilities at TUM (PI Haller) and Hanover (PI Basic) generate and maintain gnotobiotic mice. This expertise will be complemented by high-throughput anaerobic bacterial cultivation techniques (PI Clavel) with the aim of tailoring novel bacterial consortia that are adapted to the specific needs of consortium members and to their implementation in gnotobiotic models.

Clinical integration of microbiome research

Principal Investigators:
Gessner, André, UKR
Middelhoff, Moritz, TUM
Steiger, Katja, TUM

The clinical service unit Z02 provides unique access for all members of the CRC 1371 consortium to well-annotated human material as well as associated multi-dimensional datasets. We aim to develop and translate microbiome-based clinical decision making and therapy selection. In the second funding period, we aim to promote translational research approaches with the continuation of tailored patient recruitment and biobanking in addition to the establishment of an organoid biobank from endoscopic biopsies. Collected specimens will undergo standardized structured histopathological reporting, and integration of a state-of-the-art high dimensional, multiplex tissue analysis platform (CODEX technology) will enable in-depth analysis of host-microbiome interactions on the tissue-level. Microbiome-derived therapeutics for disease-adapted strategies will be further developed (disease adapted fecal microbiota transfer (FMT) Aim 3). Molecular methods have been established allowing live/dead assessment, determination of replication activity, and metabolic capacities of FMT products. The legal authorization of quality and safety measures as well as the lyophilization technology established to produce and apply GMP certified-FMT products will allow to develop precisely defined personalized bacterial consortia.

Integrated Research Training Group

Principal investigator:
Tschurtschenthaler, Markus, TUM
Hall, Lindsay, TUM (left the consortium)

The Integrated Research Training Group (IRTG) will provide PhD students with a project-related qualification program dedicated to the integration of knowledge and methodologies from multiple disciplines. It will offer training opportunities to enable cross-disciplinary approaches and promote rapid progress of the individual research projects. The IRTG will foster interaction and collaboration of CRC 1371 teams at local or distant sites. Our diverse agenda of excellent academic and hands-on training will promote self-reliance in experimental and clinical research, originality in thinking, and innovation in research.

Central tasks of the Collaborative Research Centre

Principal Investigator:
Haller, Dirk, TUM

Central tasks of the CRC 1371 are coordinated and supervised by Dirk Haller in agreement with the CRC 1371 executive board. Tasks in Z04 include administrative coordination of the scientific consortia and IRTG, including the organization of CRC 1371 office, retreats, symposia, summer school, and guest lectures as well as all public relations and dissemination activities. An important task is ensuring gender equality, family and early career support. The CRC 1371 office closely interacts with the CRC 1371-specific Gender Equality Team. Finally, Z04 coordinates scientific services for microbiome and metabolite profiling.