Microbiome and Metabolome Forensics

Swiss Population Genetics


Forensic Biogeographical Ancestry prediction


Genomic Epidemiology and Evolutionary History of the Treponematoses

 
 

Microbiome Forensics

Body fluid identification is of importance in many crime scene investigations as yields valuable information and evidence in court. Determining the body site/tissue of origin of a trace can be instrumental in pointing towards the nature of the crime, reconstruction of the crime scene and verifying testimonies.ais an important area of forensic case work as it aids in crime scene reconstruction. Nonetheless, accurate body fluid identification remains a challenge in forensic cases given the limitations of current identification methods. Recent human microbiome  studies have shown the tissue-specificity of microbial communities and their metabolites, highlighting their potential utilization to distinguish body sites.  In this project, we investigate the robustness and accuracy of an integrated microbiome and metabolome method microbial forensic methods for body fluid identification, utilizing next-generation sequencing methods as well as machine-learning algorithms. In addition, we also explore the potential of microbiome data for individual identification.

Project team ZIFM

  • Meghna Swayambhu, PhD candidate

  • Dr. Akos Dobay, Zurich Institute of Forensic Medicine, University of Zurich 

  • Prof. Dr. Thomas Krämer, Zurich Institute of Forensic Medicine, University of Zurich

Collaborations​​

  • Dr. Maria Anisimova Applied Computational Genomics group, ZHAW School of Life Sciences and Facility Management

  • Dr. Krzysztof Kryszczuk, ZHAW School of Life Sciences and Facility Management

  • Dr. João F. Matias Rodrigues, von Mehring Group, Dept. of Molecular Life Sciences 

  • Dr. Janko Tackmann, von Mehring Group, Dept. of Molecular Life Sciences 


Publications

  • Dobay A, Haas C, Fucile G, Downey N, Morrison HG, Kratzer A, and Arora N (2019). Microbiome-based body fluid identification of samples exposed to indoor conditions. Forensic Science International Genetics, doi: https://doi.org/10.1016/j.fsigen.2019.02.010

  • Tackmann J, Arora N, Benedikt Schmidt TS, Matias Rodrigues JF, and von Mering C (2018). Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites. BMC Microbiome 6: 192, https://doi.org/10.1186/s40168-018-0565-6

 
 

Swiss Population genetics

Studies on the genetic structure of human populations provide insights on the patterns of diversity and distribution, opening a window into the study of evolutionary history, and a better comprehension of the association between genes and disease. We explore fine scale structure of Alpine populations using uniparental and biparental markers, focusing on the Walser communities, in order to determine how historical and geographical factors have shaped genetic variation.


Project team UZH

  • Peter Rešutík, PhD candidate

  • PD Dr. Cordula Haas, Zurich Institute of Forensic Medicine, University of Zurich

  • Dr. Simon Aeschbacher, Department of Evolutionary Biology and Environmental Studies, University of Zurich

  • Prof. Dr. Michael Krützen, Anthropological Institute and Museum, University of Zurich

 
 

Prediction of Biogeographical Ancestry

Investigation of the markers and algorithms for accurate matching of individuals to one or more populations, for forensic phenotyping.


Project team UZH

  • Peter Rešutík, PhD candidate

  • Dr. Cordula Haas, Zurich Institute of Forensic Medicine, University of Zurich

  • Dr. Simon Aeschbacher, Department of Evolutionary Biology and Environmental Studies, University of Zurich

  • Prof. Dr. Michael Krützen, Anthropological Institute and Museum, University of Zurich

 
 

Genomic epidemiology and evolutionary history of the treponematoses

The surprising re-emergence of syphilis across the globe has prompted new genomic approaches to understand the epidemiology of the disease and its historical origins. By applying ancient DNA techniques to the study of a notoriously challenging and fragile bacterium, and through interdisciplinary collaborative efforts, we have been able to obtain whole genome data from clinical samples across numerous countries. Such data has provided new insights into the diversity of strains in current infections, as well as the rising incidence of antibiotic resistance. 


Project team UZH

  • Prof. Verena J. Schuenemann, Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.


Collaborations

  • Dr. Homayoun C. Bagheri, Repsol Chemie Deutschland GmbH, Frankfurt

  • PD Dr. Philipp P. Bosshard, Department of Dermatology, University Hospital of Zurich, Zurich, Switzerland.

  • Dr. Louis du Plessis, Department of Zoology, University of Oxford

  • Dr. Lorenzo Giacani, University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, and Department of Global Health, Seattle (WA), USA.

  • Prof. Fernando González-Candelas, Unidad Mixta Infección y Salud Pública FISABIO/Universidad de Valencia. CIBER in Epidemiology and Public Health, Spain.

  • Prof. Johannes Krause, Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.

  • Dr. Denise Kühnert, Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.

  • Prof. Kay Nieselt, Center for Bioinformatics, University of Tübingen, Tübingen, Germany. 

  • Prof. Steven J. Norris, Department of Pathology and Laboratory Medicine, UTHealth McGovern Medical School, Houston, TX USA.

  • Prof. David Šmajs, Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.


Articles


Publications

  • Grillová L, Oppelt J, Mikalová L, Nováková M, Giacani L, Niesnerová A, Noda A.A., Mechaly A.E, Pospíšilová P, Čejková D, Grange P.A, Dupin N, Strnadel R, Chen M, Denham I, Arora N, Picardeau M, Weston C, Forsyth R.A, Šmajs D (2019). Directly sequenced genomes of contemporary strains of syphilis reveal recombination-driven diversity in genes encoding predicted surface-exposed antigens. Frontiers in Microbiology, doi: https://doi.org/10.3389/fmicb.2019.01691

  • Grillova L, Bawa T, Mikalová L, Gayet-Ageron A., Nieselt K, Strouhal M, Sednaoui P, Ferry T, Cavassini M, Lautenschlager S, Dutly F, Pla-Díaz M, Krützen M, González-Candelas F, Bagheri HC, Smajs D*, Arora N*, and Bosshard PB* (2018). Molecular characterization of Treponema pallidum subsp. pallidum in Switzerland and France with a new multilocus sequence typing scheme. PLoS ONE 13(7): e0200773. 

  • Strouhal M, Oppelt J, Mikalová L, Arora N, Nieselt K, González-Candelas F, and Smajs D (2018). Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes. BMC Research Notes 11: 16.

  • Arora N, Schuenemann VJ, Jäger G, Peltzer A, Seitz A, Herbig A, Strouhal M, Grillová L, Sánchez-Busó L, Kühnert D, Bos KI, Rivero Davis L, Mikalová L, Bruisten S, Komericki P, French P, Grant PR, Pando MA, Gallo Vaulet L, Rodríguez Fermepin M, Martinez A, Centurion Lara A, Giacani L, Norris SJ, Šmajs D, Bosshard PB, González-Candelas F, Nieselt K, Krause J and Bagheri HC (2016). Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster. Nature Microbiology doi: 10.1038/nmicrobiol.2016.245

 

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