Klara Filek

Currently located in Graz, Austria

Hi! I am a microbiome scientist with a PhD in microbial ecology from University of Zagreb in Croatia. I am passionate about finding microbial solutions to global health challenges - as microbes are full of potential! In 2024, I started working as a postdoctoral researcher at Medical University of Graz in Austria within the FWF funded project “Cluster of Excellence: Microbiomes Drive Planetary Health”. My research activites are spread across Diener lab, Moissl-Eichinger lab and Gorkiewicz lab.

My research so far, focused on internal and external microbial communities of loggerhead sea turtles: isolation, culturing and characterization of individual microbes (diatoms, bacteria), and DNA-based community surveys via amplicon sequencing (16S, 18S rRNA, and rbcL gene markers on Illumina MiSeq 250 or 300bp paired-end). Within my postdoctoral project I will be expanding my skillset towards metagenomic data analyses and microbial community metabolic models, along with isolation, cultivation and characterization of keystone taxa in gastrointestinal tract health disorders. Feel free to find out more by strolling through my projects, publications and CV.

selected publications

More than just hitchhikers: a survey of bacterial communities associated with diatoms originating from sea turtles

Klara Filek, Liesbeth Lebbe, Anne Willems, and 4 more authors

FEMS Microbiology Ecology, Sep 2022

Abs PDF

Diatoms and bacteria are known for being the first colonizers of submerged surfaces including the skin of marine reptiles. Sea turtle carapace and skin harbor diverse prokaryotic and eukaryotic microbes, including several epizoic diatoms. However, the importance of diatom-bacteria associations is hardly investigated in biofilms associated with animal hosts. This study provides an inventory of diatoms, bacteria and diatom-associated bacteria originating from loggerhead sea turtles using both metabarcoding and culturing approaches. Amplicon sequencing of the carapace and skin samples chloroplast gene rbcL and 16S rRNA gene detected, in total, 634 diatom amplicon sequence variants (ASVs) and 3661 bacterial ASVs, indicating high diversity. Cultures of putative epizoic and non-epizoic diatoms contained 458 bacterial ASVs and their bacterial assemblages reflected those of their host. Diatom strains allowed for enrichment and isolation of bacterial families rarely observed on turtles, such as Marinobacteraceae, Alteromonadaceae and Alcanivoracaceae. When accounting for phylogenetic relationships between bacterial ASVs, we observed that related diatom genera might retain similar microbial taxa in culture, regardless of the turtle’s skin or carapace source. These data provide deeper insights into the sea turtle-associated microbial communities, and reveal the potential of epizoic biofilms as a source of novel microbes and possibly important diatom-bacteria associations.
Characterization of oral and cloacal microbial communities of wild and rehabilitated loggerhead sea turtles (Caretta caretta)

Klara Filek, Adriana Trotta, Romana Gračan, and 3 more authors

Animal Microbiome, Sep 2021

Abs PDF

Microbial communities of wild animals are being increasingly investigated to provide information about the hosts’ biology and promote conservation. Loggerhead sea turtles (Caretta caretta) are a keystone species in marine ecosystems and are considered vulnerable in the IUCN Red List, which led to growing efforts in sea turtle conservation by rescue centers around the world. Understanding the microbial communities of sea turtles in the wild and how affected they are by captivity, is one of the stepping stones in improving the conservation efforts. Describing oral and cloacal microbiota of wild animals could shed light on the previously unknown aspects of sea turtle holobiont biology, ecology, and contribute to best practices for husbandry conditions.