[Today's post is courtesy of Laura Sisk-Hackworth, SDSU/UCSD JDP student and previously a rotation student in the Roach Lab. Thanks Laura!!! 😊]
At February’s iPATH seminar we were lucky enough to hear from Rob Edwards, the most cited researcher at San Diego State University! You may know him as the man behind the discovery of widely abundant and intriguingly-named crASSphage; we got to hear that story in person, including recent developments and new directions.
The discovery of crASSphage may not have happened without a software Rob’s lab came up with called crAss (cross assembly of metagenomes). crAss analyzes metagenomes to find common contigs (long assembled sequences) between samples. The idea was that the number of shared contigs between samples could give us a good idea of similarity between samples. However, when they analyzed large numbers of fecal metagenomes, they found something strange: there was one group of contigs that was always correlated with each other in different samples. As it turned out, these co-occurring sequences were a population of similar phages- crASSphage- named for the software that facilitated its discovery- and were present in most published human fecal metagenomes!
Dr. Edwards then went on to invite researchers all over the world to participate in an unprecedented phage study: checking local wastewater for crASSphage to determine the biogeography and phylogeny of the virus. crASSphage was sampled in over a third of the world’s countries, and when Dr. Edwards and his team analyzed the sequences of these phages, they found that the viral sequences had signatures specific to countries and even cities within the same country!
However, when they sampled and sequenced phages from our local area, San Diego, they found that even through phages were gathered from different cities that were geographically close, they found that the phage sequence signal was specific to the time of collection, rather than the location of collection. This led them to think that somehow the different strains of crASSphage were cycling through the population and being replaced by new strains of crASSphage. Some of the most intriguing next questions for exploration are: how does crASSphage cycle through population? At what distance does the city signal of the crASSphage become a better identifier than the time the sample was collected?
Then, of course, the million-dollar question: does crASSphage effect our health, for better or for worse? In short, we don’t know. It appears that crASSphage is part of a healthy gut virome, and has been evolving with us for a long time. So far, however, there is no clear link between the presence of crASSphage and any health conditions. Clearly, we still have much to learn about the human gut virome and its impact on human health. We can’t wait to see what Rob discovers next!
~Laura Sisk-Hackworth, Roach Lab alumni