Unit:
Κατεύθυνση ΒιοπληροφορικήΠληροφορική
Author:
Kardaras Filippos
Supervisors info:
Άρτεμις Χατζηγεωργίου, Καθηγήτρια, Τμήμα Πληροφορικής με Εφαρμογές στη Βιοϊατρική, Πανεπιστήμιο Θεσσαλίας
Original Title:
Εκτίμηση της μικροβιακής κατάστασης germ-free ποντικιών με τη χρήση RNA-Seq δεδομένων
Translated title:
Assessment of the microbiome status of germ-free mice using RNA Sequencing datasets
Summary:
In the ongoing attempt to investigate the role of microbes in human physiology and their associations with pathological conditions, researchers have turned to using mouse models with known microbiota (gnotobiotic mice) or without microbiota (germ-free mice), maintained in well-controlled conditions.
The purpose of the present study was the evaluation of the microbial status of germ-free and gnotobiotic mice using data from RNA Sequencing (RNA-Seq) experiments. Thus, it is examined whether data from expression profiling with high throughput sequencing on mouse tissue samples can also be used to detect infections of germ-free or gnotobiotic mice with unwanted microorganisms. The RNA-Seq data were derived from the NCBI GEO database and were analyzed with three metagenomic programs: Kraken 2, CLARK and AGAMEMNON.
Eventually, we detected presence of microbial sequences in this type of data and attempted to identify the microbes and their expressed genes. In this way we propose an additional method for testing or confirming the sterility of germ-free and gnotobiotic mice.
In addition, we collected 995 experimentally supported microbe-disease associations, by manually curating 101 scientific papers, that will appear useful for the creation of a microbe-disease associations database.
Main subject category:
Science
Keywords:
microbiome, metagenomics, germ-free, gnotobiotic, RNA-Seq
