newly discovered bacteriophage found in fecal samples of Americans, Asians, and Europeans may have profound effects on the population of Bacteroides species in the human gut.  Bacteroides are infected with the bacteriophage called crAssphage, which may modify the cell’s behavior or kill the cell outright.


B. fragilis
Bacteroides fragilis gram stain/CDC

Bacteriophage populations are viruses that solely infect bacteria.  They are present everywhere in the world, and so far there is not a single bacterial species that is unsusceptible to at least one bacteriophage.  While they are detrimental to bacteria, bacteriophages are often used in biotechnology to aid in cell cultures and treatment.

The study authors, spread across nine departments at five universities on three continents, sought to begin the task of decoding the human virome by figuring out which virus is most common in human fecal samples.  Using data from the Human Microbiome Project (which is seeking to discover all bacterial species on and in the human body), the authors used a metagenomic approach to screen all the genes found in stored fecal samples.  Surprisingly, the most abundant viral genome not only did not infect humans, but had gone completely unnoticed until now.

The 97 kbp crAssphage genome is six times more abundant than all other human bacteriophage genomes combined, comprising 90% of the viral load and 1.68% of the entire genomic pool in the given fecal samples.  Based on gene characteristics, the authors concluded that crAssphage infects Bacteroides, one of the most common species of bacteria discovered in the Human Microbiome Project.

The implications for this discovery could be huge.  Bacteroides are a generally benign species, living comfortably with the host while secreting toxins to ward off invading pathogens.  Over- or undercolonization by Bacteroides though has been implicated in diabetes and obesity, and Bacteroides-associated bacteremia can be as fatal as cholera.  By identifying a control mechanism for Bacteroides survival, the researchers posit that a new mechanism exists for treating these pathologies.

This study could also pave the way for breakthroughs in using the human virome as a therapeutic weapon.  “The fact that the virome has been overlooked for 10 years is the elephant in the room in microbiome research,” said study author Bas Dutilh of Radboud University Medical Centre in the Netherlands. “Most people just focus on bacteria, but there are also viruses and even fungi. It’s the interaction between all of these things and the host gut that is really important.”