On Wednesday, October 22, 2025, at 11:00, Ms. Maria Chasapia of the postgraduate program “Data Science and Information Technologies”, track on “Bioinformatics – Biomedical Data Science”, will present her MSc thesis titled:
Analysis of Rhizosphere at a protein family level through global metagenomics
Abstract:
The plant root microbiome plays a vital role in plant health, nutrient uptake, and environmental resilience. Over millions of years, plants and microbes have developed various associations ranging from mutualistic to parasitic. Plants and their associated microbes can be considered holobionts, in which the host relies on its microbiome for specific functions and traits. To explore and harness this diversity, this thesis presents metagRoot, a specialized and enriched database, that is focused on the protein families of the plant root microbiome. This database holds a massive collection of over 71,000 protein families, each one of them containing at least 100 sequences. This resource was created by integrating data from 1,199 metagenomic studies, 327 metatranscriptomic datasets, and 2,978 reference genomes. The families are annotated with multiple sequence alignments, CRISPR elements, Hidden Markov Models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context.
The plant root microbiome plays a vital role in plant health, nutrient uptake, and environmental resilience. Over millions of years, plants and microbes have developed various associations ranging from mutualistic to parasitic. Plants and their associated microbes can be considered holobionts, in which the host relies on its microbiome for specific functions and traits. To explore and harness this diversity, this thesis presents metagRoot, a specialized and enriched database, that is focused on the protein families of the plant root microbiome. This database holds a massive collection of over 71,000 protein families, each one of them containing at least 100 sequences. This resource was created by integrating data from 1,199 metagenomic studies, 327 metatranscriptomic datasets, and 2,978 reference genomes. The families are annotated with multiple sequence alignments, CRISPR elements, Hidden Markov Models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context.
EXAMINATION COMMITTEE:
Georgios A. Pavlopoulos, Research Director, IFBR – BSRC Alexander Fleming
Dimitrios J. Stravopodis, Associate Professor, Department of Biology, NKUA
Ioannis Z. Emiris, President & Director General, Athena Research Center & Professor, Department of Informatics and Telecommunications, National and Kapodistrian University of Athens.22 October 2025
11:00 – 12:00 (GTB)
Join Zoom Meeting
https://us05web.zoom.us/j/83982941566?pwd=uMkHSlPaIvgsDyhhTqI3R3f0uEVA1b.1
Meeting ID: 839 8294 1566
Passcode: hh4smK
Georgios A. Pavlopoulos, Research Director, IFBR – BSRC Alexander Fleming
Dimitrios J. Stravopodis, Associate Professor, Department of Biology, NKUA
Ioannis Z. Emiris, President & Director General, Athena Research Center & Professor, Department of Informatics and Telecommunications, National and Kapodistrian University of Athens.22 October 2025
11:00 – 12:00 (GTB)
Join Zoom Meeting
https://us05web.zoom.us/j/83982941566?pwd=uMkHSlPaIvgsDyhhTqI3R3f0uEVA1b.1
Meeting ID: 839 8294 1566
Passcode: hh4smK
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