Hungry researchers have hard time replicating “Subway” microbiome study

YORK, UNITED KINGDOM — After hearing about a new scientific study that found bubonic plague DNA in the subway microbiome, a group of intrigued researchers led by Dr. Patty Mayonnaise and Dr. Herbert Hoagie at the University of York rushed out to do a metagenomics study of their own.

Admittedly they had not read the methods of the paper in detail, but they figured that the Subway restaurant that just opened on Hamsandwichshire Road would be a good starting point. Thus began the “new York Subway” study.

In order to get help with sample collection, the study leads emailed an advertisement for free food to the graduate student listserv. This proved to be highly successful for recruiting volunteers and saved a lot of money on labor as graduate students seemed to be totally satisfied being paid in sandwiches.

Figure showing the diversity of subway samples tested

 

“I was aware that others had found bubonic plague, anthrax, and microscopic particles of pizza in connection to Subway,” one graduate student said, “but sometimes one must take risks in the name of scientific progress. Plus, I couldn’t say no to the sweet, sweaty smell of the Sweet Onion Chicken Teriyaki sandwich.”

Graduate student wearing proper PPE warily examines one of the Subway samples

Before devouring the samples, each student took a representative cross-section of each Subway and stuffed it into a tube to send off for DNA extraction and sequencing.

Sequencing results indicated that the food contained lots and lots of DNA. Most of the resulting sequences could be traced to the wheat genome, with others mapping to chicken, pig, cow,  lettuce, and tomato. “One of the biggest surprises for me personally,” said Dr. Hoagie, “was the presence of Arabidopsis DNA in my sandwich when I specifically asked for no mustard”.

Many bacterial sequences were also found in the Subways. Unfortunately none of them shared similarity to Yersinia pestis, the bacteria responsible for the bubonic plague. Scientists plan to repeat the study the next week around lunchtime to see if they can’t find something else historical or cool sounding for the media to pick up on when describing their study.

Critics worry that by following a DNA trail in their pursuit of the plague, York researchers may be headed down the wrong road to knowledge. Even if DNA that matched the plague was to be found in the new York Subway, it could come from a totally harmless related bacteria that we’ve never sequenced before. So rest assured that you can continue to eat sandwiches and ride the subway in peace without having to wear one of those freaky crow masks.

 

About Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

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