Alongside bacterial members of the gut microbiota, scientists have now started exploring archaea, microbial eukaryotes (fungi and protozoa) and viruses present in the gut. Among them, the community of viruses (also called the human gut phageome) offers a promising area of research. Even though phages were first identified 100 years ago by Félix d’Herelle, it was not until recently that reproducible protocols for analyzing fecal phageomes using metagenomics analysis emerged.
A new review, led by Dr. Andrey N. Shkoporov and Dr. Colin Hill from APC Microbiome Ireland and the School of Microbiology at University College Cork (Ireland), updates the composition and physiological relevance of diverse and complex communities of bacterial viruses that colonize the human gastrointestinal tract.
It has been estimated that phages achieve concentrations up to 1010/g of fecal material compared to 1011 bacteria/g of fecal material (the estimated phage-bacterial ratio in the human gut is 1:1), thus representing more than 1012 viruses residing in the human gut.
The human gut phage community has been described as a complex ecosystem of different species with different genome sizes, including tailed viruses with icosahedral capsids belonging to the Siphoviridae, Podoviridae, and Myoviridae families. Furthermore, other viral communities present in lower levels include single-stranded deoxyribonucleic acid (DNA) eukaryotic viruses, human Herpesviridae and Papillomaviridae and ribonucleic acid plant viruses acquired through diet.
In one example, the same research group previously explored the most abundant virus in the human gut, called crAssphage. Although crAssphage was unknown until recently, we now know that it infects Bacteroidetes, constitutes 90% of fecal DNA and shows differences in health and disease.
When it comes to studying and characterizing the phageome, some challenges may arise and are mainly due to the high individual variability of bacterial viruses in the human gut and the heterogeneity of methods for studying them. Phages were initially studied through direct observation and counting via microscopic and culture-based methods. The recent incorporation of metagenomic and proteomic techniques has provided better knowledge on the diversity and richness of human gut bacteriophages, especially those that are unculturable.
As the vast majority of bacterial viruses in the gut are unknown and do not usually overlap between people, this incomplete picture of taxonomic composition and population structure of the gut phageome has been termed “viral dark matter”.
Shkoporov and Hill highlight that assembling, mapping, and classifying phages is one of the greatest challenges when bioinformaticians try to study them in the lab. In the review, the authors provide detailed coverage of the most significant and unsolved problems associated with studying gut viral populations through metagenomics. They include:
- The determination of total viral counts in the human gut, which may be underestimated especially in densely colonized areas.
- A significant distortion in gut virome diversity and insufficient detection of rare viral groups due to whole-genome amplification techniques.
- A lack of correspondence between existing gut viruses and gut-associated viral sequences in databases.
- The contamination of virome samples with residual bacterial DNA due to the filtration step used in metagenomic approaches.
Non-pathogenic viruses that colonize the gut are new actors in the human gut microbiome and they interact both with the host and other gut microbes. Specifically, the gut phageome may vary from one individual to the next and can be shaped not only by early-life factors such as birth mode, but also by aging.
Bacteriophage populations have been widely studied in natural environments and scientists have recently focused on bacteriophages cohabiting in the human gut, which have long been enigmatic given the lack of available genome sequences for comparison.
Within the human gut, it seems that phage density is increased in the luminal content and is propelled in the distal direction due to gut peristalsis. Furthermore, the dynamics of lytic and lysogenic phage cycles become more apparent in the distal colon and especially when close to the mucin layer, where commensal bacteria are almost absent. A tight regulation of the balance between temperate—leading to either lysogenic or lytic cycles—and virulent phages—leading to lytic cycles—also appears to be crucial in maintaining gut homeostasis in the thick mucin layer.
Meanwhile, different stages of the bacteriophage life cycle can interact with gut bacterial communities. Changes in phageome composition have been detected in gut-related and systemic conditions, including inflammatory bowel disease, malnutrition and acquired immunodeficiency syndrome. According to the authors, these interactions between known bacterial communities and bacteriophages should be considered in microbiome research.
In conclusion, this review takes an in-depth look at what we know about viral gut communities. Despite the current challenges in analyzing and characterizing gut phage populations, considering them to be important actors that shape the gut ecosystem can provide scientists with clues for a better understanding of how bacteriophages interact with the host and, most importantly, with other gut microbes that are equally as important as bacteria.
An in-depth and comprehensive analysis of phageome interactions with the host gut ecosystem and immune system, and subsequent implications for health and disease, can be scrutinized in other reviews recently published in this issue of Cell Host & Microbe.
Shkoporov AN, Hill C. Bacteriophages of the human gut: the “known unknown” of the microbiome. Cell Host Microbe. 2019; 25(2):195-209. doi: 10.1016/j.chom.2019.01.017.