Medizinische Mikrobiologie & Krankenhaushygiene

Arbeitsgruppe Prof. Dr. Bärbel Stecher

The human gastrointestinal tract is an ecosystem of unsurpassed diversity. Microbial communities termed microbiota, including bacteria, archaea, eukaryotes and viruses colonize intestine. In particular, the bacterial members engage in a physiological network of cooperation and competition via their metabolic products, which has an enormous influence on human health. In otherwise healthy human individuals, the microbiota is mostly able to block colonization of enteric pathogens in a process termed colonization resistance. However, antibiotics, immunosuppression and inflammation can disrupt colonization resistance and introduce microbiota imbalances with increased susceptibility to pathogen infections. A disturbed microbiota is characterized by depletion of the obligate anaerobic species and a relative enrichment in facultative anaerobic bacteria, in particular members of the Enterobacteriaceae, leading to the term of “Enterobacterial blooming”. The mechanisms driving inflammation-induced blooms include generation of oxygen and alternative electron acceptors (e. g. NO3-), production of antimicrobials, iron depletion and intraluminal phagocyte-killing. Inflammation-induced Enterobacterial blooms are a potential threat to human health by increasing the risk of systemic infections, promoting horizontal spread of fitness- and virulence factors, as well as antibiotic resistances among potentially pathogenic species.

Due to the enormous complexity of the intestinal microbiota and the lack of appropriate animal models, the mechanisms governing colonization resistance, i. e. interaction between microbiota, host immune system and pathogens, remain largely unclear. We use synthetic microbial communities which we can study in vitro and in gnotobiotic mice. With a focus on infections with Gram-negative enteric pathogens including Salmonella enterica and pathogenic Escherichia coli, we aim for the following:

  1. Understanding interaction of commensal bacteria with each other and with enteric pathogens
  2. Elucidating how phages, inflammatory immune responses and antibiotics affect the microbiota and pathogens, their interaction and gene expression.
  3. Analysing how bacterial evolution and horizontal gene transfer in the intestinal ecosystem is shaped by microbial interactions, environmental factors and interaction with the host´s mucosa

Zur Arbeitsgruppe


Prof. Bärbel Stecher, Dr. rer. nat.

I am a microbiologist fascinated by the enormous complexity and functional flexibility of the mammalian microbiota (twitter:@baerboletta). My academic training started at LMU Munich where I studied microbiology, immunology and genetics. For my PhD I moved to the ETH Zürich, Switzerland where I focused on Salmonella pathogenesis. My academic career included positions at the ETH Zürich and the McMaster University, Canada. Since 2010, I´m leading an independent lab at the Max von Pettenkofer-Institute for Hygiene and Medical Microbiology, LMU Munich and I hold an Associate Professorship (tenured W2) since 2016. The central focus of my lab is on the gastrointestinal microbiome with a specific interest in molecular microbiology, microbial ecology and microbe-host interactions in infectious diseases.


© AG Stecher

Aktuelle Gruppenmitglieder

Bärbel Stecher, PhD, Professor
Phone: +49 89 2180 72948

Anna Burrichter, PhD, Dr. rer.nat.
Phone: +49 89 2180-72951

Éva Teréz de Hoog-Almási, Dr. rer.nat.
Phone: +49 89 2180 72951

Marla Gaissmaier, Master of Science
Phone: +49 89 2180 72871

Monica Matchado, Dr. rer.nat.
Phone: +49 89 2180 72951

Lisa Niedermeier, Master of Science
Phone: +49 89 2180 72861

Diana Ring, BTA
Phone: +49 89 2180 72871

Hussain Saib, CTA
Phone: +49 89 2180 72913

Marta Salvado Silva, Master of Science
Phone: +49 89 2180 72861

Simon Woelfel, Master of Science
Phone: +49 89 2180 72951


A synthetic community to study functions of the gut microbiome

A central challenge in gut microbiome research is to understand how interactions between the individual microorganisms affect community assembly, dynamics and functionality.  Gnotobiotic mice colonized with defined microbial communities have become essential tools to address this question. While a majority of studies uses human-derived bacteria, we have developed a model community consisting of twelve phylogenetically diverse bacteria isolated from mice (Brugiroux et al., 2016) (Fig. 3). In addition, we have developed a comprehensive set of protocols and analysis tools, allowing us to study this community in its native murine host. This Oligo-Mouse-Microbiota (OMM12) is unique because it recapitulates central physiologic and functional traits of a complex mouse microbiome. Furthermore, the OMM12 exhibits long-term stability in gnotobiotic mice and its composition is reproducible among different animal facilities. Hence, this model is used by an increasing number of research groups world-wide.

To provide an ecological context, we extensively studied the interaction network and metabolic capabilities of this synthetic bacterial community, both of which are factors that determine community assembly, dynamics and functionality (Weiss et al., ISME 2021). We employed a bottom-up approach connecting outcomes of mono- and pairwise co-culture experiments with observations from complex communities in in vitro batch culture. Furthermore, we combined metabolomics analysis of spent culture supernatants with genome-informed pathway reconstruction and generated metabolic models of the OMM12 consortium. Together, this work identified key interaction patterns among OMM12 strains relevant in community assembly and functionality.

Brugiroux, S., Beutler, M., Pfann, C., Garzetti, D., Ruscheweyh, H.J., Ring, D., Diehl, M., Herp, S., Lotscher, Y., Hussain, S., et al. (2016). Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat Microbiol. 2, 16215. DOI: 10.1038/nmicrobiol.2016.215.
Eberl C, Ring D, Münch PC, Beutler M, Basic M, Slack EC, Schwarzer M, Srutkova D, Lange A, Frick JS, Bleich A, Stecher B. Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities. Front Microbiol. 2020 Jan 10;10:2999.
Weiss, A.S., Burrichter, A., Durai Raj A.C., von Strempel A., Meng, C., Kleigrewe K., Münch P.C., Rössler L., Huber C., Eisenreich W., Jochum L.M., Göing S., Jung K., Lincetto C., Hübner J., Marinos G., Zimmermann, J., Kaleta C., Sanchez A., Stecher B. In vitro interaction network of a synthetic gut bacterial community. ISME (2021).


Phylogenetic tree of the OMM12 strains based on 16S rRNA gene sequences. The OMM12 consortium includes twelve strains of mouse origin, representing five bacterial phyla abundant in the mammalian gastrointestinal tract.

Identification of microbes providing colonization resistance against enteric infections

Work within the “Translational GI Microbiome Research Platform” funded by the German Center of Infection Research (DZIF) elucidates principles of microbiota-based intervention with virulence of intestinal pathogens (focus: EHEC and Salmonella). In the past, we identified different commensal bacteria that protect against enteric S. Tm infection using comparative microbiome analysis. The gnotobiotic OMM12 mouse model enabled us to demonstrate causality in protection and to uncover on the underlying mechanisms.

Commensal E. coli can block S. Tm colonization, a mechanism that is  microbial context dependent (Eberl et al., 2021). In an infection-permissive context (e.g. mice colonized with a low-diverse microbiota), a high diversity of carbon sources is available which enables growth of both, E. coli and S. Tm. In mice that were stably colonized with OMM12, establishing a protective context, E. coli depleted galactitol, a substrate otherwise fueling S. Tm colonization. Here, Lachnospiraceae, capable of consuming C5 and C6 sugars, critically contributed to colonization resistance. We propose that E. coli provides colonization resistance by depleting a limited carbon source when in a microbial community adept at removing simple sugars from the intestine.

Additionally, using a murine Salmonella infection model, we found that microbiota alterations and enrichment of Mucispirillum spp. correlated with protection against infection. This genus belongs to the phylum Deferribacteres and is a prevalent but low abundant member of the rodent, pig and human microbiota (Herp et al., 2021). Mucispirillum spp. is enriched under intestinal inflammatory conditions (Loy et al., 2017) and has recently also been causally linked to the development of Crohn’s disease-like colitis in immunodeficient mice (Herp et al., 2021). Using the OMM12 mouse model, we could show that Mucispirillum schaedleri also protects against S. Tm colitis by interfering with invasion gene expression and by competing for anaerobic electron acceptors like nitrate. Our study establishes M. schaedleri, a core member of the murine gut microbiota, as key antagonist of S. Tm virulence in the gut (Herp et al., 2019).

Eberl, C., Weiss, A.S., Jochum, L.M., Durai Raj, A.C., Ring, D., Hussain, S., Herp, S., Meng, C., Kleigrewe, K., Gigl, M., et al. (2021). E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source. Cell Host Microbe. 29(11), 1680-1692 e1687. Published online 2021/10/06 DOI: 10.1016/j.chom.2021.09.004.
Herp, S., Brugiroux, S., Garzetti, D., Ring, D., Jochum, L.M., Beutler, M., Eberl, C., Hussain, S., Walter, S., Gerlach, R.G., et al. (2019). Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis. Cell Host Microbe. Published online 2019/04/23 DOI: 10.1016/j.chom.2019.03.004.
Herp, S., Durai Raj, A.C., Salvado Silva, M., Woelfel, S., and Stecher, B. (2021). The human symbiont Mucispirillum schaedleri: causality in health and disease. Med Microbiol Immunol. 210(4), 173-179. Published online 2021/05/23 DOI: 10.1007/s00430-021-00702-9.
Loy, A., Pfann, C., Steinberger, M., Hanson, B., Herp, S., Brugiroux, S., Gomes Neto, J.C., Boekschoten, M.V., Schwab, C., Urich, T., et al. (2017). Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota. mSystems. 2(1). DOI: 10.1128/mSystems.00171-16.


EvoGutHealth: Functional relevance of within-host evolution

Microbial communities have co-speciated with their mammalian host over long-term evolutionary time scales. Estimates suggest that billions of mutations occur in the microbiome of individual persons on a daily basis. This indicates the potential for highly dynamic functional adaptations of the microbiome. Theoretical evidence suggests that the microbiota and its host co-evolve for mutual benefit, but the time range, over which reciprocal evolutionary adaptations occur, are unknown. Remarkably, bacterial lineages evolve in the mammalian gut on short, ecological time scales. The basis of short-term evolutionary changes includes immune evasion, drug-resistance and metabolic adaptation. In the EU-funded project EvoGutHealth, we explore the functional relevance of within-host evolution of microbial communities.

PhaStGut: Phage-Host interaction

An increasing number of human diseases is associated with an altered intestinal microbiota. The microbiota consists of trillions of microbes including viruses amongst which bacteriophages (phages) that predate on bacteria are the most abundant. Phages are important effectors and indicators of human health and disease by managing specific bacterial population structures and by interacting with the mucosal immune system. Although metagenome-based studies have addressed their abundance, diversity and stability over time in the gut, little is known on the role of phages in microbiome homeostasis and their impact on global microbiome functions. To overcome this limitation, we employ the OMM model and strain-specific phages in stably colonized gnotobiotic mice. We will conduct an in-depth characterization of phage ecology and study their influence on the microbiome and related functions in the gut. In addition, we study the mechanisms underlying stable coexistence of phages and their host bacteria in the gut. The final goal is to refine strategies for phage-based microbiome engineering. In PhaStGut, a DFG-ANR funded project, we collaborate in an interdisciplinary team of four partners combining meta-transcriptomics, meta-metabolomics and 3D DNA capture in gnotobiotic mice. Thereby, we will uncover mechanisms governing the dynamic interplay between phages and their host bacteria that shape the mammalian microbiota.

Project Partners

  • Laurent Débarbieux, Institut Pasteur, France (Coordinator)
  • Martial Marbouty, Institut Pasteur, France
  • Alesia Walker, Helmholtz Institute, Germany

MOB-TARGET: Interference with AMR Plasmid-spread

The most important cases of one-health antimicrobial resistance (AMR) are caused by dissemination of antibiotic resistance genes on mobile genetic elements. In the EU-funded consortium MOB-TARGET, we will develop novel interventions aimed at selectively eliminating mobile AMR from complex human and animal microbiomes. We will focus on two urgent AMR problems:

1. AMR poses a critical health risk to neonates. We will develop sequence specific antimicrobials (SSA) and conjugative delivery systems to eliminate AMR from the neonatal microbiome. These will include (1) CRISPR-Cas9 systems that will target AMR plasmids, (2) “killer cassettes” that will kill bacteria carrying mobile integrons that are key platforms for AMR, and (3) inducible toxin-intein antimicrobials that will kill cells carrying AMR plasmids. We will test the efficacy of these systems using in vitro and in vivo models of the neonatal human microbiome.

2. Chickens provide a key source of protein in low- and middle-income countries but the chicken gut microbiome acts as a reservoir of AMR that can be transmitted to humans. First, we will develop pilus-dependent lytic phages (PDB) as a tool to eliminate mobile ARGs. Second, we will test the ability of both SSAs and PDBs to control AMR in the chicken gut microbiome using in vivo experiments.
Our two-pronged approach will help eliminate AMR from a high-risk patient population and restrict the colonization of humans by decontaminating an important agricultural source of AMR.

Project Partners

  • Craig MacLean, University of Oxford, United Kingdom (Coordinator)
  • Michael Brockhurst, University of Manchester, United Kingdom
  • Alvaro San Millan, Centro Nacional de Biotecnología, Spain
  • Jose Antonio Escudero, Universidad Complutense, Spain
  • Didier Mazel, Institut Pasteur, France
  • Tao He, Jiangsu Academy of Agricultural Sciences, China

Current Funding



Top 10 Publikationen

Weiss AS, Niedermeier LS, von Strempel A, Burrichter AG, Ring D, Meng C, Kleigrewe K, Lincetto C, Hübner J, Stecher B. Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community. Nat Commun. 2023 Aug 8;14(1):4780. doi: 10.1038/s41467-023-40372-0.
Münch PC, Eberl C, Woelfel S, Ring D, Fritz A, Herp S, Lade I, Geffers R, Franzosa EA, Huttenhower C, McHardy AC, Stecher B. Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects. Cell Host Microbe. 2023 Jun 14;31(6):1007-1020.e4. doi: 10.1016/j.chom.2023.05.013. Epub 2023 Jun 5..
Weiss, A.S., Burrichter, A., Durai Raj A.C., von Strempel A., Meng, C., Kleigrewe K., Münch P.C., Rössler L., Huber C., Eisenreich W., Jochum L.M., Göing S., Jung K., Lincetto C., Hübner J., Marinos G., Zimmermann, J., Kaleta C., Sanchez A., Stecher B. In vitro interaction network of a synthetic gut bacterial community.ISME 2022. doi: 10.1038/s41396-021-01153-z
Eberl C, Weiss AS, Jochum LM, Durai Raj AC, Ring D, Hussain S, Herp S, Meng C, Kleigrewe K, Gigl M, Basic M, Stecher B. E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source. Cell Host Microbe 2021. Sep 29:S1931-3128(21)00420-0. doi: 10.1016/j.chom.2021.09.004.
Spriewald S, Stadler E, Hense BA, Münch PC, McHardy AC, Weiss AS, Obeng N, Müller J, Stecher B. Evolutionary Stabilization of Cooperative Toxin Production through a Bacterium-Plasmid-Phage Interplay. mBio. 2020 Jul 21;11(4):e00912-20. doi: 10.1128/mBio.00912-20.
Lourenço M, Chaffringeon L, Lamy-Besnier Q, Pédron T, Campagne P, Eberl C, Bérard M, Stecher B, Debarbieux L, De Sordi L. The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and BacteriophagesCell Host Microbe. 2020 Sep 9;28(3):390-401.e5. doi: 10.1016/j.chom.2020.06.002
Herp S, Brugiroux S, Garzetti D, Ring D, Jochum LM, Beutler M, Eberl C, Hussain S, Walter S, Gerlach RG, Ruscheweyh HJ, Huson D, Sellin ME, Slack E, Hanson B, Loy A, Baines JF, Rausch P, Basic M, Bleich A, Berry D, Stecher B. Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis. Cell Host Microbe. 2019 May 8;25(5):681-694. doi: 10.1016/j.chom.2019.03.004.
Brugiroux S., Beutler M., Pfann C., Garzetti D., Ruscheweyh H.J., Ring D., Diehl M., Herp S., Lötscher Y., Hussain S., Bunk B., Pukall R., Huson D.H., Münch P.C., McHardy A.C., McCoy K.D., Macpherson A.J., Loy A., Clavel T., Berry D., Stecher B. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat Microbiol. 2016 Nov 21;2:16215. doi: 10.1038/nmicrobiol.2016.215
Nedialkova L.P., Sidstedt M., Koeppel M.B., Spriewald S., Ring D., Gerlach R.G., Bossi L. and Stecher B.Temperate phages promote colicin-dependent fitness of Salmonella enterica serovar Typhimurium. Environmental Microbiology. 2015 Oct 6. doi: 10.1111/1462-2920.13077..
Nedialkova L, Denzler R., Koeppel M.B., Diehl M., Ring D., Gerlach R.G. and Stecher B. Inflammation fuels colicin Ib-dependent competition of Salmonella serovar Typhimurium and E. coli in Enterobacterial blooms. PLoS Pathogens. 2014 Jan;10(1):e1003844. doi: 10.1371/journal.ppat.1003844


Prof. Bärbel Stecher, Dr. rer. nat.

  • 2019 European Research Council (ERC), Consolidator Grant 2019
  • 2017 German Society for Hygiene and Microbiology (DGHM), Main Award 2017
  • 2011 Yakult-Prize ‘Science for Health’
  • 2009 Robert Koch Society ‘Postdoctoral Prize’
  • 2009 FEMS Travel Grant for the 3rd Congress of European Microbiologists
  • 2008 Swiss Society of Microbiology (SSM) Encouragement Award
  • 2008 Member of the TANDEM plus IDEA program