Translational Microbiome Research and Clinical Application of Next-Generation Sequencing of Pathogens

The advent of next-generation sequencing (NGS) technology has revolutionized scientific approaches also in the field of microbiology. In order to translate the scientific discoveries of the past years into clinical practice, we are working on ways to implement and use NGS to inform healthcare practitioners at the bedside. We have performed NGS in several nosocomial infectious disease scenarios. In addition, NGS is used as a means to genetically characterize novel, emerging, and non-model microorganisms in a clinical context. Within the framework of a multidisciplinary study with the acronym IMAGINE (Identification of microbial antibiotics to protect the physiologic microbiota at body surfaces), we analyze microbiomes of a variety of body compartments, such as skin, gut, conjunctiva, gall bladder and the oral cavities. The aim is to compare the microbiomes of healthy individuals with those of diseased patients, thereby uncovering pathogens that prolong or worsen a certain common disease, and treat those specifically. On the other hand, we aim to detect beneficial commensal microbiota. Many commensal bacteria are known to produce secondary metabolites, that have a protective effect on the human host. In the course of this study, we strive to detect these microbiota and analyze the potential of novel antibiotic compounds, which they might harbor. If you are interested to learn more about this part of IMMH research, please feel free to contact us. 

Univ.-Prof. Dr. med. Dr. phil. Sören Becker

Tel.: +49 (0) 6841 16-23900
Fax: +49 (0) 6841 16-23985


M.Sc. Jacqueline Rehner

Tel.: +49 (0) 6841 16-23962
Fax: +49 (0) 6841 16-23985


Selected publications by members of the research group covering this topic:

The Effect of a Planetary Health Diet on the Human Gut Microbiome: A Descriptive Analysis


Rehner J, Schmartz GP, Kramer T, Keller V, Keller A, Becker SL (2023)

Nutrients 15(8):1924

DOI: 10.3390/nu15081924

Characteristics of the Skin Microbiome in Selected Dermatological Conditions: A Narrative Review

Olunoiki E, Rehner J, Bischoff M, Koshel E, Vogt T, Reichrath J, Becker SL (2022)

Life (Basel) 12(9):1420.

DOI: 10.3390/life12091420

WGS for infection prevention and control in Africa

Becker SL (2020)

Lancet Microbe 1(3):e95-e96

DOI: 10.1016/S2666-5247(20)30067-7

Occurrence, resistance patterns, and management of carbapenemase-producing bacteria in war-wounded refugees from Ukraine

Berger FK, Schmartz GP, Fritz T, Veith N, Alhussein F, Roth S, Schneitler S, Gilcher T, Gärtner BC, Pirpilashvili V, Pohlemann T, Keller A, Rehner J, Becker SL (2023)

Int J Infect Dis. 132:89-92

DOI: 10.1016/j.ijid.2023.04.394

Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies

Rehner J, Schmartz GP, Groeger L, Dastbaz J, Ludwig N, Hannig M, Rupf S, Seitz B, Flockerzi E, Berger T, Reichert MC, Krawczyk M, Meese E, Herr C, Bals R, Becker SL, Keller A, Müller R; IMAGINE Consortium. (2022)

Genomics Proteomics Bioinformatics 20(2):405-417

DOI: 10.1016/j.gpb.2022.05.006

Qualitative microbiome profiling along a wastewater system in Kampala, Uganda

Schneeberger PHH, Fuhrimann S, Becker SL, Pothier JF, Duffy B, Beuret C, Frey JE, Utzinger J (2019)

Sci Rep. 9:17334.

DOI: 10.1038/s41598-019-53569-5


  • Marie Skłodowska-Curie Actions (MSCA)
  • UdS/HIPS Tandem