PhD Projects » ESR 13: Functional inferences from colinear crAssphage genomes

Mikhail Fofanov

I am Mikhail Fofanov and I come from Russia. I earned my master’s degree in molecular biology from Novosibirsk State University. During this period, I became passionate about combating antibiotic-resistant bacteria through the use of bacteriophages. My master’s project focused on the development of recombinant bacteriophages specific to Klebsiella, with an expanded spectrum of bacterial hosts.

My journey into bioinformatics began with the analysis, annotation, and deposition of bacteriophage genomes into Genbank — genomes that my colleagues had sequenced and assembled. It was during this work that I first encountered the crassphages discovered by Dr. Bas E. Dutilh and his colleagues. I actively contributed to the discovery and study of diversity-generating retroelements (DGRs) in the genomes of the Crassvirales. To further hone my skills in bioinformatics, I completed a one-year program at the Bioinformatics Institute in St. Petersburg.

Currently, as part of this project, I am studying the evolution of Crassvirales within the context of their hosts at Utrecht University in the Netherlands and Friedrich Schiller University Jena in Germany. My goal is to combine my knowledge of bioinformatics and Crassvirales biology for an in-depth exploration of their fascinating evolution and the reasons behind their remarkable diversity and abundance.

Outside of my academic pursuits, I find enjoyment in hiking, biking, and socializing with friends. I am also engaged in the development of several pet projects in Python. Previously, I actively participated in international student tournaments in the natural sciences for several years.

Daniel Carrillo (March 2021 – April 2022)

I am Daniel Carrillo and I come from Spain. It was during my BSc in Biotechnology that I discovered bioinformatics and knew that I wanted to dedicate to it, and thereby my bachelor thesis was about in silico development of antimicrobial compounds. After this, I did my MSc in Bioinformatics at the University of Valencia.

I got hired soon by a company to work as a bioinformatician. My four years there allowed me to gain sound knowledge about DNA sequencing and all the different kinds of analyses that can come after it. My main focuses there were metagenomics, bacterial genomics and transcriptomics. However, I had not the opportunity to work on any project involving phages, organisms that I always have found very intriguing.

For my PhD, I am excited to join Utrecht University to study the most prevalent phages in the human gut, the crAssphages. I am interested in understanding how these phages have evolved, how they relate to their bacterial hosts, and when they first became associated to the human lineage. Shedding light on these questions will contribute to understand which is the role of phages in the human gut virome.

If I am not coding, you will probably find me reading a Roman’s history book, painting miniatures, or playing the guitar. Except if it is sunny, then I am outside.

Field:
Bioinformatics
Host institution:
Utrecht University (UU), the Netherlands
Local supervisor:
Dr. Bas E. Dutilh (UU)
Local co-supervisor:
Dr. Pieter-Jan Haas (University Medical Center Utrecht)
Project partner:
Nikolas Basler (ESR 11)
Work packages:
WP 1.1 Virus identification
WP 1.3 Virus-host interactions

Project description

Viruses related to crAssphage, a bacteriophage discovered by us in 2014, are abundant in the intestinal tract of humans around the world. We computationally predicted that crAss-like phages infect Bacteroidetes hosts and this was confirmed when the virus was recently cultured. Strikingly, amplification of the virus did not impair the host, but the molecular mechanisms involved remain unknown because the proteins involved in host interaction remain unknown. ESR 13 will focus on identifying host-interaction proteins in crAssphage. We recently discovered that crAss-like phages have been genomically co-linear for millions of years yet encode different proteins in similar genomic contexts.

Significant host-association proteins will be validated at the KU Leuven viromics group by exploiting available human and insect-associated viromes (ESR 11). Thus, we will exploit signals from fundamental processes in genome evolution to predict host-interaction proteins and further our understanding of virus-host interactions.

@article{Piedade2024,

title = {Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape},

author = {Gonçalo J. Piedade and Max E. Schön and Cédric Lood and Mikhail V. Fofanov and Ella M. Wesdorp and Tristan E. G. Biggs and Lingyi Wu and Henk Bolhuis and Matthias G. Fischer and Natalya Yutin and Bas E. Dutilh and Corina P. D. Brussaard},

doi = {10.1038/s41467-024-53317-y},

year  = {2024},

date = {2024-10-24},

urldate = {2024-10-24},

journal = {Nature Communications},

volume = {15},

pages = {9192},

abstract = {The Southern Ocean microbial ecosystem, with its pronounced seasonal shifts, is vulnerable to the impacts of climate change. Since viruses are key modulators of microbial abundance, diversity, and evolution, we need a better understanding of the effects of seasonality on the viruses in this region. Our comprehensive exploration of DNA viral diversity in the Southern Ocean reveals a unique and largely uncharted viral landscape, of which 75% was previously unidentified in other oceanic areas. We uncover novel viral taxa at high taxonomic ranks, expanding our understanding of crassphage, polinton-like virus, and virophage diversity. Nucleocytoviricota viruses represent an abundant and diverse group of Antarctic viruses, highlighting their potential as important regulators of phytoplankton population dynamics. Our temporal analysis reveals complex seasonal patterns in marine viral communities (bacteriophages, eukaryotic viruses) which underscores the apparent interactions with their microbial hosts, whilst deepening our understanding of their roles in the world’s most sensitive and rapidly changing ecosystem.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}