2nd Young AMICI Symposium

September 11-12th, 2023


Book of abstracts



  • Nataliia Solntseva, PhD student, University of Vienna
  • Alexander Pfundner, PhD student, University of Vienna
  • Jessica Neubauer, PhD student, University of Vienna
  • Jasper Schierstaedt, PostDoc, University of Technology, Graz
  • Tea Movsesijan, PhD student, University of Veterinary Medicine, Vienna
  • Franz-Ferdinand Roch, PhD student, University of Veterinary Medicine, Vienna


The Young AMICI symposium on environmental and host-associated microbiomes is organized by and mainly intended for PhD students and early career researchers but everyone is welcome to join!
Registration is free but mandatory until September 7th, 2023.
Abstract submission until August 7th, 2023.
Register via amici.young.cemess@univie.ac.at, see flyer on how to apply and for more information.



Day 1 - September 11th

Food microbiology (13:30 - 15:30)

Liam Walsh, Teagasc, Agriculture and Food Development Authority, Ireland
Large Scale Metagenomic analysis of the Fermented Beverage Kefir

Lauren Alteio, FFoQSI, Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, Austria
Challenges and future perspectives on the persistence phenotype of food-associated Listeria monocytogenes

Vincenzo Valentino, University of Naples Federico II
Microbial communities in cheeses and their production environment explored through shotgun metagenomics

Bioinformatics in microbiology (15:30 - 18:00)

Olga Bochkareva, University of Vienna
Computational identification and biological interpretation of genome rearrangements in microbes

André Soares, University of Duisburg-Essen
A microbial oasis in extreme cave environments

Lovro Trgovec-Greif, University of Vienna
Annotating genomes in a custom way

Paolo Manghi, University of Trento
Large-scale meta-analytic approaches for systematic and reproducible associations between the human microbiome and host's conditions

Day 2 - September 12th

Microbe-microbe and microbe-host interactions (12:30 - 14:00)

Bidong Nguyen, ETH Zürich
The role of sugar substitutes in Salmonella Typhimurium virulence

Viktoriia Savchenko, University of Vienna
Biosynthetic flexibility of Pseudomonas aeruginosa leads to hydroxylated 2-Alkylquinolones with proinflammatory host response

Eeman Abbasi, University of Pennsylvania
Mathematical framework to elucidate the role of host immune response and its interaction with the microbiome community

Phages (14:00 - 16:00)

Xichuan Zhai, University of Copenhagen
The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analyses

Aryan Rahimi Midani, University of Würzburg
Phage-host interaction regulating skin microbiota

Weiwei Yang, New England Biolabs
Z-DNA containing phages and Z-DNA biosynthetic pathways using the concept of metaGPA

Sheetal Patpatia, University of Helsinki
Rapid hydrogel-based phage susceptibility test for pathogenic bacteria

Plant microbial ecology (16:00 - 18:00)

Samuel E. Barnett, Michigan State University
Functional resilience in the soil microbiome under long term anthropogenic disturbance: Insights from the seven-decade-old Centralia coal mine fire

Alexandros Mosca, University of Catania
Composition and functional profiles of soil bacterial communities in lemon groves of a dedicated production area

Gillian E. Bergmann, University of California-Davis
Overlap between stigma and seed bacterial communities of commercial watermelon and their effects on seedling vigor

Carolina Boto Courinha Lobato, University of Technology Graz
Exploring the Microbiome of Cannabis Seeds through Domestication and Breeding Stages