Going to extremes – a metagenomic journey into the dark matter of life

Abstract

The Virus-X—Viral Metagenomics for Innovation Value—project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.

New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae

“…shibatae strains B12, S38A and BEU9 as described previously (Zaparty et al ., 2010). The DNA was sequenced in the framework of the Virus‐X project (Aevarsson et al ., 2021), using the Oxford Nanopore GridION Mk1 sequencer with FLO‐MIN106D flow cells and SQK‐RBK004 libraries, as well as the Illumina MiSeq and Nextera libraries. Both were carried out according to the manufacturer's instructions.…”

Bacteriophage Lytic Enzyme P9ly as an Alternative Antibacterial Agent Against Antibiotic-Resistant Shigella dysenteriae and Staphylococcus aureus

“…Bacteriophages are not only the most abundant biological particles in the world, but also play an important role in the environment, as lysis of host cells can promote organic matter cycling and reduction in the counts of specific bacteria can February 2022 | Volume 13 | Article 821989 Wang et al P9ly Combats Bacterial Pathogens regulate population equilibrium and biodiversity (Fernandez et al, 2021). In 2016, the Virus-X Consortium was established to explore genetic diversity and virions in extreme natural environments, further emphasizing essential roles of bacteriophages in bioprospecting and their importance as a source of new antimicrobial agents (Aevarsson et al, 2021).…”

Novel Lytic Enzyme of Prophage Origin from Clostridium botulinum E3 Strain Alaska E43 with Bactericidal Activity against Clostridial Cells

“…Recent studies in our laboratory resulted in the discovery of two thermostable endolysins, Ph2119 (GenBank accession no. AHF20915.1) and Ts2631 (AIM47292.1), with amino acid sequence similarity to eukaryotic peptidoglycan recognition proteins (PGRPs) [28][29][30]. Both enzymes, derived from Thermus scotoductus bacteriophages, Ph2119 and vB_Tsc2631, show strong muralytic activity against bacteria of genus Thermus.…”