Beyond cells – The virome in the human holobiont

Abstract

Viromics, or viral metagenomics, is a relatively new and burgeoning field of research that studies the complete collection of viruses forming part of the microbiota in any given niche. It has strong foundations rooted in over a century of discoveries in the field of virology and recent advances in molecular biology and sequencing technologies. Historically, most studies have deconstructed the concept of viruses into a simplified perception of viral agents as mere pathogens, which demerits the scope of large-scale viromic analyses. Viruses are, in fact, much more than regular parasites. They are by far the most dynamic and abundant entity and the greatest killers on the planet, as well as the most effective geo-transforming genetic engineers and resource recyclers, acting on all life strata in any habitat. Yet, most of this uncanny viral world remains vastly unexplored to date, greatly hindered by the bewildering complexity inherent to such studies and the methodological and conceptual limitations. Viromic studies are just starting to address some of these issues but they still lag behind microbial metagenomics. In recent years, however, higher-throughput analysis and resequencing have rekindled interest in a field that is just starting to show its true potential. In this review, we take a look at the scientific and technological developments that led to the advent of viral and bacterial metagenomics with a particular, but not exclusive, focus on human viromics from an ecological perspective. We also address some of the most relevant challenges that current viral studies face and ponder on the future directions of the field.

Mimicking prophage induction in the body: induction in the lab with pH gradients

“…Exploration of the human microbiome has uncovered a vast diversity of viral species, particularly bacteriophages (see review García-López, Pérez-Brocal & Moya, 2019 ). Phages are vital members of microbiota; they can transform bacterial communities by predation ( Fuhrman, 1999 ; Suttle, 2005 ; Clokie et al, 2011 ) and drive bacterial diversity ( Buckling & Rainey, 2002 ; Rodriguez-Valera et al, 2009 ; Tellier, Moreno-Gámez & Stephan, 2014 ; Koskella & Brockhurst, 2014 ).…”

Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

“…The phages usually exhibit temperate lifestyle and integration into bacterial hosts as prophages, however, environmental stressors can induce the lytic cycle resulting in viral replication and destruction of host cells. Thus, the intestinal virome is closely linked to the prokaryotic microbial communities not just by sharing a common niche, but also by contributing to the ecosystem dynamics as well as by providing various genetic elements such as virulence factors or antibiotic resistance genes while integrated as a prophage [83]. Accordingly, there is mounting evidence that the community of phages in the gut is altered when dysbiosis-related disorders are considered, such as IBD and colorectal cancer.…”

Crossing the kingdom border: Human diseases caused by plant pathogens

“…Although plant viruses can enter animal cells and propagate within them, there is no clear evidence that these viruses can cause disease symptoms in animals. (Colson et al, 2010;Garcia-Lopez et al, 2019;Jiwaji et al, 2019). However, the possibility that plant viruses could elicit animal disease cannot be excluded and this eventuality should be reconsidered.…”