The Human Gut Phage Community and Its Implications for Health and Disease

Abstract

In this review, we assess our current understanding of the role of bacteriophages infecting the human gut bacterial community in health and disease. In general, bacteriophages contribute to the structure of their microbial communities by driving host and viral diversification, bacterial evolution, and by expanding the functional diversity of ecosystems. Gut bacteriophages are an ensemble of unique and shared phages in individuals, which encompass temperate phages found predominately as prophage in gut bacteria (prophage reservoir) and lytic phages. In healthy individuals, only a small fraction of the prophage reservoir is activated and found as extracellular phages. Phage community dysbiosis is characterized by a shift in the activated prophage community or an increase of lytic phages, and has been correlated with disease, suggesting that a proper balance between lysis and lysogeny is needed to maintain health. Consequently, the concept of microbial dysbiosis might be extended to the phage component of the microbiome as well. Understanding the dynamics and mechanisms to restore balance after dysbiosis is an active area of research. The use of phage transplants to re-establish health suggests that phages can be used as disease treatment. Such advances represent milestones in our understanding of gut phages in human health and should fuel research on their role in health and disease.

A century of bacteriophage research and applications: impacts on biotechnology, health, ecology and the economy!

“…In healthy individuals there is a dynamic equilibrium between the microbial and phage members. Gut phages tend to be an aggregate of unique and shared phages in individuals and encompass temperate phages that exist as prophages, their DNA being integrated in the host chromosome, and lytic phages . In addition, an absence of a balanced microbial ecology leads to a dysbiotic state that has been correlated with multiple diseases and conditions such as inflammatory bowel disease, obesity, allergic disorders, type 1 diabetes and colorectal cancer in human and animal models.…”

Introduction: The host‐associated microbiome: Pattern, process and function

“…Phage is hypothesized to underlie bacterial community dynamics, particularly in systems with high functional redundancy (Louca et al., ). Such effects can, in turn, impact the eukaryotic hosts of these bacteria (Manrique et al., ). To address phage impacts here, the authors isolated bacteria and phage from tomato plants.…”

“…Such effects can, in turn, impact the eukaryotic hosts of these bacteria (Manrique et al, 2017). To address phage impacts here, the authors isolated bacteria and phage from tomato plants.…”

“…Distinguishing between this possibility and a changing abiotic environment (i.e., habitat filtering due to factors such as changing host diet (Koenig et al., )) requires careful investigation (Levy & Borenstein, ). Furthermore, additional types of biotic interactions may play out among members of the microbiota, including interference competition (Scheuring & Yu, ), exploitation competition, cooperation (Faust et al., ) or predation by phage (Koskella, Hall, & Metcalf, ; Manrique, Dills, & Young, ). The lesson here is that the within‐host ecology of symbiotic microbes must be accounted for to fully make sense of the microbiome (Moran & Sloan, ).…”

Metabolic characterization and viable delivery of Akkermansia muciniphila for its future application

“…To obtain bacteriophages, we filtered faecal samples that were previously shown to have a high relative abundance of A. muciniphila, because a high relative abundance increases the chance of the presence of a bacteriophage for the target species (Manrique, et al, 2017, Weinbauer, 2004. Subsequent plaque assays and enrichment of potential bacteriophage in liquid medium resulted in the discovery of a potential bacteriophage for A. muciniphila, which was only observed using electron microscopy, see Figure 4.…”