• HEK-293T cells infected with Chlamydia trachomatis expressing chlamydial deubiquitinase Cdu1-FLAG
Chair of Microbiology

Prof. Dr. Alexander Westermann

Contact information:

Tel.: +49 (0)931-31 83781
Room: C205

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Transcriptome data base

Research projects

RNA biology of anaerobic gut commensals​

Host-microbe interaction studies

Advanced cross-species RNA-seq approaches​​

Hypoxic tissue models for bacterial colonization

Dr. Lena Amend

Susanne Bauer

Room: C206

Elise Bornet

Dr. Thomas Guest

Gianlucca Prezza

Ann-Sophie Rüttiger

Dr. Daniel Ryan

Hannah Schlauch

Since 2023
W2-Professor at the Chair of Microbiology, Julius Maximilians University, Würzburg, Germany

2018 - 2023
Junior (W1) professor and leader of the group
“Dual RNA-seq” at the Institute of Molecular Infection Biology (IMIB)
Julius Maximilians University, Würzburg, Germany
Young Principal Investigator and leader of the group
“Host-pathogen-microbiota interactions” at the Helmholtz Institute for RNA-based Infection Research (HIRI)
Würzburg, Germany

EMBO Short-Term Fellow in the group of Prof. David Holden, Imperial College London, UK
Topic: “Molecular Aspects of Salmonella Pathogenesis”

Visiting researcher in the group of Prof. Andreas Bäumler, UC Davis, CA, USA
Topic: “Interplay of the Host and its Gut Microbiota with Enteric Pathogens”

2015 – 2017
Post-Doc in the group of Prof. Jörg Vogel (RNA Biology)
Institute of Molecular Infection Biology (IMIB)
Julius-Maximilians University, Würzburg, Germany
Topic: “The Role of Noncoding RNAs and RNA-binding Proteins in Bacterial Infections”

2010 – 2015
PhD student in the group of Prof. Jörg Vogel (RNA Biology)
Institute of Molecular Infection Biology (IMIB)
Julius-Maximilians University, Würzburg, Germany
Title of thesis: “Dual RNA-seq of Pathogen and Host”

Visiting scholar in the group of Prof. Ming C. Hammond
Department of Molecular and Cell Biology / Department of Chemistry, UC Berkeley, CA, USA
Topic: “Transgene regulation in plants by alternative splicing of a suicide exon”

2008 – 2010
Master’s program in Molecular Biosciences
"Molecular and Cellular Biology"
Ruprecht-Karls University, Heidelberg, Germany
Title of thesis: “Regulation of 3’ End Processing and its Impact on Differentiation in a Neuroblastoma Model”

*: equal contribution
+: co-correspondence

Däullary T*, Imdahl F*, Dietrich O, Hepp L, Krammer T, Fey C, Neuhaus W, Metzger M, Vogel J, Westermann AJ, Saliba A-E,
Zdzieblo D (2023) A primary cell-based in vitro model of the human small intestine reveals host Olfactomedin-4 induction in response to Salmonella
Typhimurium infection
Gut Microbes 15(1):2186109

Jiao C, Reckstadt C, König F, Homberger C, Yu J, Vogel J, Westermann AJ, Sharma CM, Beisel CL (2023) Programmable RNA recording in single living cells
Nature Biotechnology doi: 101038/s41587-022-01604-8 Online ahead of print

Schuster E-M, Epple MW, Bremser A, Lucht K, Zimmermann J, Polyzou A, Ballabio A, Trompouki E, Vogel J, Büscher J,
Westermann AJ, Rambold AS (2022) TFEB induces mitochondrial itaconate synthesis to suppress bacterial growth in macrophages
Nature Metabolism 4(7):856-866

Prezza G*, Ryan D*, Mädler G, Reichardt S, Barquist L +, Westermann AJ + (2022) Comparative genomics provides structural and functional insights into Bacteroides RNA biology
Molecular Microbiology 117(1):67-85

Fulde M*, van Vorst K*, Zhang K, Westermann AJ, Busche T, Huei YC, Welitschanski K, Froh I, Pägelow D, Plendl J, Pfarrer C,
Kalinowski J, Vogel J, Valentin-Weigand P, Hensel M, Tedin K, Repnik U, Hornef MW (2021) SPI2 T3SS effectors facilitate enterocyte apical to basolateral transmigration of Salmonella containing vacuoles in vivo
Gut Microbes 13(1):1973836

Santos SC, Bischler T, Westermann AJ +, Vogel J + (2021) MAPS integrates overlooked regulation of actin-targeting effector SteC into the virulence control network of Salmonella small RNA
Cell Reports 34(5):108722
Recommended in Faculty Opinions as being of special significance in its field

Venturini E, Svensson SL, Maaß S, Gelhausen R, Eggenhofer F, Li L, Cain AK, Parkhill J, Becher D, Backofen R, Barquist L +,
Sharma CM +, Westermann AJ +, Vogel J + (2020) A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence
microLife 1(1):uqaa002

Seelbinder B*, Wallstabe J*, Marischen L*, Weiss E, Wurster S, Page L, Löffler C, Bussemer L, Schmitt A-L, Wolf T, Linde J, Cicin-
Sain L, Becker J, Kalinke U, Vogel J, Panagiotou G, Einsele H, Westermann AJ*, Schäuble S*, Löffler J* (2020) Triple RNA-seq reveals synergy in a human virus-fungus co-infection model
Cell Reports 33(7):108389

Hennessen F, Miethke M, Zaburannyi N, Herrmann J, Loose M, Lukežič T, Hüttel S, Jansen R, Schmiedel J, Imirzalioglu C, Vogel
J, Westermann AJ, Hesterkamp T, Stadler M, Wagenlehner F, Petković H, Müller R (2020) Amidochelocardin overcomes resistance mechanisms exerted on tetracyclines and natural chelocardin
Antibiotics 9(9):E619

Ryan D, Jenniches L, Reichardt S, Barquist L, Westermann AJ (2020) A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron
Nature Communications 11(1):3557
HZI ‘Paper of the Month’ August 2020

Mika-Gospodorz B*, Giengkam S*, Westermann AJ, Wongsantichon J, Kion-Crosby W, Chuenklin S, Wang LC, Sunyakumthorn
P, Sobota RM, Subbian S, Vogel J, Barquist L, Salje J (2020) Dual RNA-seq provides insight into the biology of the neglected intracellular human pathogen Orientia tsutsugamushi
Nature Communications 11(1):3363

Prezza G, Heckel T, Dietrich S, Homberger C, Westermann AJ+, Vogel J + (2020) Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads
RNA 26(8):1069-1078

Schulte LN*, Schweinlin M*, Westermann AJ, Janga H, Santos SC, Appenzeller S, Walles H, Vogel J, Metzger M (2020) An advanced human intestinal co-culture model reveals compartmentalized host and pathogen strategies during Salmonella
mBio 11(1): e03348-19

Martins Gomes SF, Westermann AJ, Sauerwein T, Hertlein T, Förstner KU, Ohlsen K, Metzger M, Shusta EV, Kim BJ, Appelt-
Menzel A, Schubert-Unkmeir A (2019) Induced pluripotent stem cell-derived brain endothelial cells as a cellular model to study Neisseria meningitidis infection
Frontiers Microbiology 10:1181

Westermann AJ, Venturini E, Sellin ME, Förstner KU, Hardt W-D, Vogel J (2019) The major RNA-binding protein ProQ impacts virulence gene expression in Salmonella Typhimurium
mBio 10(1): e02504-18

Stapels DAC, Hill PWS, Westermann AJ, Fisher R, Thurston TL, Saliba A-E, Blommestein I, Vogel J, Helaine S (2018) Salmonella persisters undermine host immune defences during antibiotic treatment
Science 362(6419):1156-1160
Covered by In Brief in Nature Reviews Microbiology 17,65-65

Simon LM, Karg S, Westermann AJ, Engel M, Elbehery AHA, Hense B, Heinig M, Deng L, Theis FJ (2018) MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data
GigaScience 101093/gigascience/giy070

El Mouali Y, Gaviria-Cantin T, Sánchez-Romero MA, Gibert M, Westermann AJ, Vogel J, Balsalobre C (2018) CRP-cAMP mediates silencing of Salmonella virulence at the post-transcriptional level
PLoS Genetics 14(6):e1007401

Michaux C, Holmqvist E, Vasicek E, Sharan M, Barquist L, Westermann AJ, Gunn J, Vogel J (2017) RNA target profiles direct the discovery of virulence functions for the cold shock proteins CspC and CspE
PNAS 114(26):6824-6829

Westermann AJ, Förstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Müller L, Reinhardt R, Stadler PF, Vogel J (2016) Dual RNA-seq unveils noncoding RNA functions in Salmonella-host interplay
Nature 529(7587):496-501
Covered by News & Views in Nature 529(7587):472-3, Nature Reviews Genetics 17(3):126, Faculty 1000

Saliba A-E, Li L, Westermann AJ, Appenzeller S, Stapels DAC, Schulte L, Helaine S, Vogel J (2016) Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella
Nature Microbiology 2:16206
“Paper of the Month” December 2016 of the German Society for Hygiene and Microbiology (DGHM)

Müller AA, Dolowschiak T, Sellin ME, Felmy B, Verbree C, Gadient S, Westermann AJ, Vogel J, LeibundGut-Landmann S, Hardt
W-D (2016) An NK cell perforin response elicited via IL-18 controls mucosal inflammation kinetics during Salmonella gut infection
PLoS Pathogens 12(6):e1005723

Afonso-Grunz F, Hoffmeier K, Müller S, Westermann AJ, Rotter B, Vogel J, Winter P, Kahl G (2015) Dual 3’Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella Typhimurium and human host cells
BMC Genomics 16(1):323

Schulte LN, Westermann AJ, Vogel J (2013) Differential activation and functional specialization of miR-146 and miR-155 in innate immune sensing
Nucleic Acids Research 7;41(1):542-53

Hickey SF, Sridhar M, Westermann AJ, Qin Q, Vijayendra P, Liou G, Hammond MC (2012) Transgene regulation in plants by alternative splicing of a suicide exon
Nucleic Acids Research 40(10):4701-10

Stauffer E, Westermann A, Wagner G, Wachter A (2010) Polypyrimidine tract-binding protein homologues from Arabidopsis underlie regulatory circuits based on alternative splicing and
downstream control
Plant Journal 64(2):243-55