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Gut phageome

Gut phageome

The community of bacteriophages, viruses that infect bacteria and archaea, that are associated with the gut microbiome.

Phage to bacteria ratios in the gut are thought to be about 1:1. The healthy gut phageome (HGP) is comprised of core and common bacteriophages and is thought to play a role in maintenance of a healthy functioning gut microbiome. It has been proposed that the phageome could shape microbial colonization, gut microbiome structure and function. The finding that sterile fecal filtrate has efficacy in treating C. difficile infection suggests gut phages could restrict the growth of pathogenic bacterial and promote a rich healthy gut microbiota. In healthy humans there are an estimated 35-2,800 viruses in the active phageome. The phageome has been reported to be stable within an individual. 



Microscopic methods of investigating the phageome include counting virus-like particles by transmission electron microscopy and epi-fluorescence microscopy. Individual bacteriophages that infect specific host strains have been isolated in bacteria culture but more than 95% if human gut bacteria are difficult to culture. High-throughput metagenomic sequencing has allowed a better appreciation of the complexity of gut bacteriophage populations. 



A deep DNA sequence dataset of active bacteriophages was analysed along with metagenomic datasets of the gut bacteriophage communities in healthy people. More than 23 shared bacteriophages were shared in more than half of the 64 individuals tested, who live in various locations in around the world. Researchers found a decrease in the HGP in ulcerative colitis and Crohn’s disease. Altered phageome compositions have also been associated with malnutrition, AIDS and type 2 diabetes.



Viruses have lytic and lysogenic cycles. The lytic cycle, also called virulent infection, is when the phage kills the host cell in order to produce many progeny. In the lysogenic cycle, the virus uses the host cell as a refuge and remains in a dormant state. In the lysogenic cycle the phage integrates into the host genome and is called a prophage and its genome is replicated along with the host genome. Phages can enter the lytic cycle and extract themselves from the host genome under certain stress conditions. It has been noted that gut bacteriophages generally interact with their host bacteria in the lysogenic cycle and persist for prolonged periods and have slower evolution rates than the less common, more virulent bacteriophages. This is in contrast to other ecological systems such as oceans where lytic cycles play a more central role in controlling bacterial populations. 

Software tools for phage and viral metagenomic analysis

Timmomatic

Bowtie 2

SPAdes and metaSPAdes

Sunbeam

VirSorter

vConTACT

PHASTER

Prokka

RASTtk

PhageTerm

iVIREONS

mauve

PyANI

Easyfig

GView

Vegan

ape

Databases

NCBI RefSeq Viral and Viral Genome Browser

IMG/VR

pVOGs





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