Gut phageome: challenges in research and impact on human microbiota

Abstract

The human gut microbiome plays a critical role in maintaining our health. Fluctuations in the diversity and structure of the gut microbiota have been implicated in the pathogenesis of several metabolic and inflammatory conditions. Dietary patterns, medication, smoking, alcohol consumption, and physical activity can all influence the abundance of different types of microbiota in the gut, which in turn can affect the health of individuals. Intestinal phages are an essential component of the gut microbiome, but most studies predominantly focus on the structure and dynamics of gut bacteria while neglecting the role of phages in shaping the gut microbiome. As bacteria-killing viruses, the distribution of bacteriophages in the intestine, their role in influencing the intestinal microbiota, and their mechanisms of action remain elusive. Herein, we present an overview of the current knowledge of gut phages, their lifestyles, identification, and potential impact on the gut microbiota.

Keywords: composition; gut microbiome; gut phages; interactions; lysogenic phages; phage identification.

Figure 1

Overview of phage life cycles and classification. (A) This section of the figure classifies phages into four primary groups based on their nucleic acid types. These include: (i) Double-stranded DNA (dsDNA) phages, incorporating families such as Siphoviridae, Myoviridae, and Podoviridae. (ii) Single-stranded DNA (ssDNA) phages, represented by families like Microviridae and Inoviridae. (iii) Double-stranded RNA (dsRNA) phages, which belong to the Cystoviridae family. (iv) Single-stranded RNA (ssRNA) phages, exemplified by the Leviviridae family. (B) The second part of the figure illustrates the two primary life cycles a phage may undertake after infecting a host cell: (i) The Lysis Cycle: Here, the phage’s DNA (or RNA) replicates, transcribes, and expresses its genes within the host cell. This leads to the assembly of new phage progeny, which eventually cause the host cell to lyse (rupture) for release, or exit through extrusion. (ii) The Lysogenic Cycle: Contrary to the lysis cycle, the phage integrates its genetic material into the host’s chromosome. This integration allows the phage to replicate along with the host cell’s DNA during cell division.

Figure 2

Illustration of phage research methodologies. This figure delineates the methodologies employed in isolating and studying phages. Initially, intestinal samples are extracted and amalgamated with bacterially sensitive strains. This combined specimen is then cultured in a liquid medium, a step crucial for fostering the growth and release of a large quantity of phages. For visualization, the figure shows how a meticulously measured mix of phage and sensitive bacteria is incorporated into soft agar, then layered onto a solid agar medium for incubation. The interaction between the phage and bacteria during this phase leads to the lysis of bacterial colonies, forming distinctive clear zones known as “phage plaques.” These plaques are pivotal for phage purification as, ideally, a single phage particle can produce one plaque. For advanced analysis, the figure further explains that phages are cultivated in significant numbers to extract phage DNA. This DNA undergoes high-throughput sequencing, followed by comprehensive bioinformatics analysis for deeper insights. Additionally, computational tools like PhiSpy, a marker gene-dependent phage detection algorithm, are depicted as instrumental in identifying phages directly within metagenomic datasets.