Going viral: next-generation sequencing applied to phage populations in the human gut

Abstract

Over the past decade, researchers have begun to characterize viral diversity using metagenomic methods. These studies have shown that viruses, the majority of which infect bacteria, are probably the most genetically diverse components of the biosphere. Here, we briefly review the incipient rise of a phage biology renaissance, which has been catalysed by advances in next-generation sequencing. We explore how work characterizing phage diversity and lifestyles in the human gut is changing our view of ourselves as supra-organisms. Finally, we discuss how a renewed appreciation of phage dynamics may yield new applications for phage therapies designed to manipulate the structure and functions of our gut microbiomes.

Figure 1. Experimental and computational methods for characterization of phage populations present in the human gut microbiota

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Figure 2. Potential consequences of a temperate phage lifecycle in the human gut

Viral metagenomic show that the phage population associated with the adult human gut microbiota is characterized by a relatively low number of virotypes compared to other ecosystems (e.g., soils, sediments, marine environments). These gut populations also exhibit high temporal stability of virotypes with respect to both viral community structure and nucleotide sequence conservation, and a high prevalence of temperate phages. These characteristics suggest that a temperate lifestyle is dominant in the distal human gut versus the lytic lifestyle observed in open oceans. (a–c) Illustration of the benefits of this temperate lifestyle on phage-host dynamics. (a) Integration as a prophage protects the host from superinfection, effectively ‘immunizing’ the bacterial host against infection from the same or closely related phages. Furthermore, the genes encoded by the viral genome may expand the niche of the bacterial host by enabling metabolism of new nutrient sources (e.g., carbohydrates), providing antibiotic resistance, conveying virulence factors, or altering host gene expression. This temperate lifecycle allows viral expansion in a 1:1 ratio with the bacterial host. If the integrated virus conveys increased fitness to its bacterial host, there will be increased prevalence of the host and phage in the microbiota. (b) Induction of a lytic cycle may follow a lysogenic state and can be triggered by environmental stress. As a consequence, bacterial turnover is accelerated and energy utilization optimized through ‘phage shunts’, where the debris remaining after lysis is used as a nutrient source by the surviving population. Furthermore, a subpopulation of bacteria that undergoes lytic induction sweeps away other sensitive species and increases the niche for survivors (i.e., bacteria that already have an integrated phage). Periodic induction of prophages can also lead to a constant diversity dynamic , which helps maintain community structure and functional efficiency. (c) Novel infections or infections of novel bacterial hosts by phages bring the benefit of horizontally transferred genes, and create selective pressure on the hosts for diversification of their phage receptors, which are often involved in carbohydrate utilization.

Figure 3. Potential strategies for phage therapy

(a) The traditional strategy has been to use a lytic phage against pathogenic bacteria. While transiently useful, this approach can lead to rapid resistance given positive selection for subpopulations (‘clones’) that are resistant to the lytic phage. Note that this is an antiquated approach to phage therapy that can be trivially improved by using multiple phages with non-overlapping host resistance patterns, or by selecting for phage mutants that overcome host resistance. (b) More recently, synergistic relationships between phage and antibiotics have been exploited, where lysogenic phages are introduced that alone do not kill the pathogen, but instead decrease its survival when used in concert with antibiotics. An example is a phage that inhibits a DNA damage repair system (SOS), which makes bacteria exquisitely sensitive to quinolone-class antibiotics . (c) With our growing understanding of the human microbiome, it may be possible to take a more nuanced approach - selectively manipulating (enhancing) microbial community functions or clearing the way for invasion by probiotic consortia. Strategies can be envisioned to benefit both microbes and their host; for example, introducing genes into phage genomes that are involved in nutrient biosynthesis (with direct benefits to the bacterial and potentially human host), or degradation of nutrients (which may stabilize the representation and niches of beneficial microbes, especially during times of acute stress).