Klara Filek

Currently located in Zagreb, Croatia

Hi! I am a microbiome enthusiast/scientist with a PhD in microbial ecology. I am passionate about finding microbial solutions to global health challenges - microbes are full of potential! Currently, I am looking for a position where I can express all the microbial joy I have and contribute to finding microbial solutions through data analysis and visualization.

At this time I am undertaking an internship at Chr. Hansen in Denmark (they have the largest commercial bacterial strain collections in the world which I find immensely cool) learning more about the commercial use of microbes and their potential in production and growing healthier food.

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). 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

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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

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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.