Microbial Interactions (Faber lab)
Enteric infections and their clinical outcome are often associated with underlying microbial dysbiosis. Clostridioides difficile – being a leading cause of antibiotic-associated diarrhea – is a prime example. Therefore, a mechanistic understanding of virulence regulation in the context of pathogen-commensal interactions is paramount for the development of novel therapeutics.
The production of toxins and the ability to form antibiotic-resistant spores are the major virulence factors in C. difficile that contribute to significant morbidity and mortality and to high recurrence rates in patients. Their production is tightly regulated by metabolic signals whose abundance and composition throughout the infection cycle is shaped by the gut microbial community.
In our lab, we combine deep RNA-sequencing based approaches with biochemical, genetic and microbiology techniques to discover and mechanistically characterize non-coding RNAs and their RNA-binding protein partners involved in virulence gene regulation.
We are also interested in how the activities of these regulators is shaped by microbial and host signals. To better understand this cross-talk, we take a bottom-up approach by studying individual pathogen-commensal interactions using microbiology, genetic, intestinal organoids/advanced tissue culture and metabolomics approaches.
Pubmed Link: https://pubmed.ncbi.nlm.nih.gov/?term=Faber%2C%20Franziska%5BAuthor%5D&sort=date
Experimental work
- Schumacher J, Müller P, Sulzer J, Faber F, Molitor B, Maier L. Proton-pump inhibitors increase C. difficile infection risk by altering pH rather than by affecting the gut microbiome based on a bioreactor model.
Gut microbes 2025 doi: 10.1080/19490976.2025.2519697 - Rüttiger AS, Ryan D, Spiga L, Lamm-Schmidt V, Prezza G, Reichardt S, Langford M, Barquist L, Faber F, Zhu W, Westermann AJ. The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron.
Nature Communications 2025 doi: 10.1038/s41467-024-55383-8. - Lenče T, Sulzer J, Andress K, Gribling-Burrer A-S, Lamm-Schmidt V, Barquist L, Smyth RP, Faber F. The conserved noncoding RNA ModT coordinates growth and virulence in Clostridioides difficile.
PLoS Biology 2024 doi: 10.1371/journal.pbio.3002948. - Velasco-Gomariz M, Sulzer J, Faber F, Fröhlich KS. An sRNA overexpression library reveals AbnZ as a negative regulator of an essential translocation module in Caulobacter crescentus.
Nucleic Acids Research 2025 doi: 10.1093/nar/gkae1139. - Fuchs M, Lamm-Schmidt V, Lenče T, Sulzer J, Bublitz A, Wackenreuter J, Gerovac M, Strowig T, Faber F. A network of small RNAs regulates sporulation initiation in C. difficile.
EMBO Journal 2023 doi: 10.15252/embj.2022112858 - Tiffany CR, Lee JY, Rogers AWL, Olsan EE, Morales P, Faber F*, Bäumler A* The metabolic footprint of Clostridia and Erysipelotrichia reveals their role in depleting sugar alcohols in the cecum.
Microbiome 2021 doi: 10.1186/s40168-021-01123-9 - Ponath F, Tawk C, Zhu Y, Barquist L, Faber F, Vogel J. RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum.
Nature Microbiology 2021 doi: 10.1038/s41564-021-00927-7 - Fuchs M*, Lamm-Schmidt V*, Sulzer J, Ponath F, Jenniches L, Kirk JA, Fagan RP, Barquist L, Vogel J, Faber F. An RNA-centric global view of the clinically important bacterium Clostridioides difficile reveals broad activity of Hfq in a Gram-positive species.
PNAS 2021 doi: 10.1073/pnas.2103579118 - Walker GT, Yang G, Tsai JY, Rodriguez JL, English BC, Faber F, Souvannaseng L, Butler BP, Tsolis RM. Malaria parasite infection compromises colonization resistance to an enteric pathogen by reducing gastric acidity.
Science Advances 2021 doi: 10.1126/sciadv.abd6232 - Lamm-Schmidt V, Fuchs M, Sulzer J, Gerovac M, Hör J, Dersch P, Vogel J, Faber F. Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production.
microLife 2021 doi: 10.1093/femsml/uqab004 - Saedtler M, Förtig N, Ohlsen K, Faber F, Masota N, Kowalick K, Holzgrabe U, Meinel L. Anti-bacterial anacardic acid derivatives.
ACS Infectious Diseases 2020 doi: 10.1021/acsinfecdis.9b00378 - Velazquez EM, Nguyen H, Heasley KT, Seachao CH, Gil LM, Rogers AWL, Miller BM, Rolston MR, Lopez CA, Litvak Y, Liou MJ, Faber F, Bronner DN, Tiffany CR, Byndloss MX, Byndloss AJ, Bäumler AJ. Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection.
Nature Microbiology 2019 doi: 10.1038/s41564-019-0407-8 - An S, Ding Y, Faber F, Hobley L, Sá-Pessoa J. Social behaviour and making attachments: a report from the fifth ‘Young Microbiologists Symposium on Microbe Signalling, Organisation and Pathogenesis’.
Microbiology 2018 doi: 10.1099/mic.0.000746 - Litvak Y, Mon KKZ, Nguyen H, Chanthavixay G, Liou M, Velazquez EM, Kutter L, Alcantara MA, Byndloss MX, Tiffany CR, Walker GT, Faber F, Zhu Y, Bronner DN, Byndloss AJ, Tsolis RM, Zhou H, Bäumler AJ. Commensal Enterobacteriaceae protect against Salmonella colonization by competing for oxygen.
Cell Host & Microbe 2018 doi: 10.1016/j.chom.2018.12.003
Selected for Nature Milestones in Human Microbiota Research - Bronner DN, Faber F, Olsan EE, Byndloss MX, Sayed NA, Xu G, Yoo W, Kim K, Ryu S, Lebrilla CB, Bäumler AJ Genetic ablation of butyrate utilization attenuates gastrointestinal Salmonella disease.
Cell Host & Microbe 2018 doi: 10.1016/j.chom.2018.01.004 - Byndloss MX, Olsan EE, Rivera-Chávez F, Tiffany CR, Cevallos SA, Lokken KL, Torres TP, Byndloss AJ, Faber F, Gao Y, Litvak Y, Lopez CA, Xu G, Napoli E, Giulivi C, Tsolis RM, Revzin A, Lebrilla CB, Bäumler AJ. Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion.
Science 2017 doi: 10.1126/science.aam9949
Covered by News&Views in Nature
Selected for Nature Milestones in Human Microbiota Research - Faber F, Thiennimitr P, Spiga L, Byndloss MX, Litvak Y, Lawhon S, Andrews-Polymenis HL, Winter SE, Bäumler AJ. Respiration of microbiota-derived 1,2-propanediol drives Salmonella expansion during colitis.
PLoS Pathogens 2017 doi: 10.1371/journal.ppat.1006129 - Elfenbein JR, Knodler LA, Schaeffer AR, Faber F, Bäumler AJ, Andrews-Polymenis HL A Salmonella Regulator Modulates Intestinal Colonization and Use of Phosphonoacetic Acid.
Front in Cellular and Infection Microbiology 2017 doi: 10.3389/fcimb.2017.00069 - Faber F, Tran L, Byndloss MX, Lopez CA, Velazquez EM, Kerrinnes T, Nuccio SP, Wangdi T, Fiehn O, Tsolis RM, Bäumler AJ. Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion.
Nature 2016 doi: 10.1038/nature18597
Selected for Nature Milestones in Human Microbiota Research - Rivera-Chávez F, Zhang LF, Faber F, Lopez CA, Byndloss MX, Olsen EE, Xu G, Velazquez EM, Lebrilla CB, Winter SE, Bäumler AJ. Depletion of Clostridia from the gut microbiota drives an aerobic luminal expansion of Salmonella.
Cell Host & Microbe 2016 doi: 10.1016/j.chom.2016.03.004
Commentary in Cell Host & Microbe
Selected for Nature Milestones in Human Microbiota Research - Mooney JP, Lokken KL, Byndloss MX, George MD, Velazquez EM, Faber F, Butler BP, Walker GT, Ali MM, Potts R, Tiffany C, Ahmer BM, Luckhart S, Tsolis RM. Inflammation-associated alterations to the intestinal microbiota reduce colonization resistance against non-typhoidal Salmonella during concurrent malaria parasite infection.
Scientific Reports 2015 doi: 10.1038/srep14603 - Winter SE, Winter MG, Poon V, Keestra AM, Sterzenbach T, Faber F, Costa LF, Cassou F, Costa EA, Alves GE, Paixão TA, Santos RL, Bäumler AJ. Salmonella enterica Serovar Typhi conceals the invasion-associated type three secretion system from the innate immune system by gene regulation.
PLoS Pathogens 2014 doi: 10.1371/journal.ppat.1004207 - Skiebe E, de Berardinis V, Morczinek P, Kerrinnes T, Faber F, Lepka D, Hammer B, … Pfeifer Y, Wilharm G. Surface-associated motility, a common trait of clinical isolates of Acinetobacter baumannii, depends on 1,3-diaminopropane.
International Journal of Medical Microbiology 2012 302(3):117-28 - Volkmann M, Skiebe E, Kerrinnes T, Faber F, Lepka D, Pfeifer Y, Holland G, Bannert N, Wilharm G Orbus hercynius gen. nov., sp. nov., isolated from faeces of wild boar, is most closely related to members of the orders Enterobacteriales and Pasteurellales.
International Journal of Systematic and Evolutionary Microbiology 2010 60(Pt 11):2601-5 - Wilharm G, Lepka D, Faber F, Hofmann J, Kerrinnes T, Skiebe E A simple and rapid method of bacterial transformation.
Journal of Microbiological Methods 2010 80(2):215-6 - Kerrinnes T, Zelas Z, Streckel W, Faber F, Tietze E, Tschäpe H, Yaron S CsrA and CsrB are required for the post-ranscriptional control of the virulence-associated effector protein AvrA of Salmonella enterica.
International Journal of Medical Microbiology 2009 299(5):333-41 - Forster G, Schwieger C, Faber F, Weber T, Blume A Influence of poly(L:-lysine) on the structure of dipalmitoylphosphatidylglycerol/water studied by X-ray scattering.
European Biophysics Journal 2007 36(4-5):425-35 - Faber F, Gembardt F, Sun X, Mizutani S, Siems WE, Walther T Lack of angiotensin II conversion to angiotensin III increases water but not alcohol consumption in aminopeptidase A-deficient mice.
Regulatory Peptides. 2006 136(1-3):130-7
Reviews
- Clavel T, Faber F, Groussin M, Haller D, Overmann J, Pauvert C, Poyet M, Selkrig J, Stecher B, Typas A, Vehreschild MJGT, Westermann AJ, Wylensek D, Lisa Maier L. Enabling next-generation anaerobic cultivation through biotechnological innovation to advance functional microbiome research.
Nature Biotechnology 2025 doi:10.1038/s41587-025-02660-6
- Vogel J, Faber F, Barquist L, Sparmann A, Popella L, Ghosh C. Meeting report ASOBIOTICS 2024: an interdisciplinary symposium on antisense-based programmable RNA antibiotics.
RNA 2025 doi:10.1261/rna.080347.124
- Winter SE, Faber F, Bäumler AJ. Durchfallerreger und die Homöostase der Mikrobiota
Biospektrum 2023 doi: 10.1007/s12268-023-1901-3
- Olsen E, Byndloss MX, Faber F, Rivera-Chávez F, Tsolis RM, Bäumler AJ Colonization resistance: the deconvolution of a complex trait.
Journal of Biological Chemistry 2017 292(21):8577-8581
- Faber F, Bäumler AJ The impact of intestinal inflammation on the nutritional environment of the gut microbiota.
Immunology Letters. 2014 162(2 Pt A):48-53
Preprints
- Spiga L, Winter MG, Muramatsu MK, Rojas VK, Chanin RB, Zhu W, Hughes ER, Taylor SJ, Faber F, Porwollik S, Carvalho TF, Qin T, Santos RL, Andrews-Polymenis H, McClelland M, Winter SE. Byproducts of inflammatory radical metabolism provide transient nutrient niches for microbes in the inflamed gut.
bioRxiv 2023 doi: 10.1101/2023.12.08.570695
