Storify of the IFAL Roundtable on Microbiomes in Food and Agriculture

Here is a quick roundup of the Roundtable discussion I was involved in on Microbiomes in Food and Agriculture run by the IFAL at UC Davis.

10/19 in #DavisCA: 1st Quarterly Food and Agriculture Roundtable

For those in or near Davis, CA

Block the date – this will be awesome

October 19, 2015

1:00 to 3:00pm

Student Community Center, Multipurpose Room

Jonathan Eisen

1st Quarterly Food and Agriculture Roundtable

Discussion of Microbes in Food and Agriculture
including a discussion of glyphosate and microbiomes

Eisen Roundtable Flyer .pdf

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.


New lab paper: The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

A new paper out from my lab (with Jenna Lang as the 1st author and in collaboration with Angela Zivcovic from the UC Davis Food For Health Initiative and the Department of Nutrition):  The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types.  The work in the paper focuses on characterizing the abundance and taxonomy of microbes in food from three model diets.

Basically, Angela prepared meals for these three diets

Food was purchased and prepared in a standard American home kitchen by the same individual using typical kitchen cleaning practices including hand washing with non-antibacterial soap between food preparation steps, washing of dishes and cooking instruments with non-antibacterial dish washing detergent, and kitchen clean-up with a combination of anti-bacterial and non-antibacterial cleaning products. Anti-bacterial products had specific anti-bacterial molecules added to them whereas “non-antibacterial” products were simple surfactant-based formulations. The goal was to simulate a typical home kitchen rather than to artificially introduce sterile practices that would be atypical of how the average American prepares their meals at home. All meals were prepared according to specific recipes (from raw ingredient preparation such as washing and chopping, to cooking and mixing).

And then she blended them and we characterzied the microbial communities in the blended samples:

After food preparation, meals were plated on a clean plate, weighed on a digital scale (model 157W; Escali, Minneapolis, MN), and then transferred to a blender (model 5,200; Vita-Mix Corporation, Cleveland, OH) and processed until completely blended (approximately 1–3 min). Prepared, ready to eat foods that were purchased outside the home were simply weighed in their original packaging and then transferred to the blender. 4 mL aliquots of the blended meal composite were extracted from the blender, transported on dry ice and then stored at −80 °C until analysis. The following analyses were completed using these meal composite samples: (1) total aerobic bacterial plate counts, (2) total anaerobic bacterial plate counts, (3) yeast plate counts, (4) fungal plate counts, and (5) 16S rDNA analysis for microbial ecology.

And Jenna Lang coordainted the sequence analysis and then Angela and Jenna (with some help here and there from me) coordianted the analysis of the different microbial data and the writing of the paper.

Figure 5: Biplot of taxa in sample PCoA space.

Lots of interesting things reported in the paper (read it, I insist).  I note – this is a demonstration project in a way – trying to get the community and others to think about the source pools of microbes that come into our system from our food.  It is by no means comprehensive or conclusive (read the caveats section of the paper).  Congrats to Jenna and Angela for all their hard work. Anyway – the paper is Open Access in PeerJ.  Eat it up.

UPDATE: Some press and blog coverage

Hidden Gem in Davis – Farmer’s Kitchen Cafe

The Farmer’s Kitchen Cafe, which is part of the Natural FoodWorks Store, is possibly the biggest hidden gem of a restaurant in Davis. They specialize in :

delicious, homemade bioregional foods, free of gluten and casein. Your food is made with locally grown and organic fruits and vegetables, free range meats and wild fish. No aluminum pans, no hydrogenated fats, no microwaved foods, no unnatural additives.

Although the service there can be a little slow, that is part of the point. This is not a fast food restaurant. It is fresh, in season, homemade, and usually organic or at least local. Last time I went I had the chicken noodle soup, which was, I have to say, even better than mom used to make. It has a nice simple clear broth, a smattering of flavorful veggies and chicken, and a good helping of clearly top of the line noodles. I also had an organic eggplant sandwich with pesto and feta cheese that was nearly perfect. The eggplant was creamy and intermixed with the pesto into a spread with no hint of the bad eggplant flavors one can get sometime. Plus, there is a great basket of miscellaneous crayons and toys that our daughter spent much of the time playing with.

This is one of my favorite places in Davis and definitely worth a visit, especially if you are into sustainable, organic or local foods. Check it out at 624 4th Street or at their website.

Viruses as food additives

I find it sad that the world has come to this. The FDA announced that it has approved the use of viruses as a food additive. The particular viruses (known as phage in this case) target and kill common bacterial pathogens found in meat. It is entirely possible that this treatment will lead to reduction in deaths and illnesses. However, it is also possible that there will be unexpected consequences of this treatment and thus anything like this should be done with caution. What saddens me about this whole thing is that it is the wrong way to go about solving the problem. Most of the problem comes from the fact that our meat today in this country does not come to us in reasonable condition. The animals are usually kept in unsanitary conditions where diseases and nasty pathogens are prevalent.

The best way to think about this in my opinion is what I read in The Omnivore’s Dilemma, the new book by Michael Pollan. In this book he talks about how animals now frequently live in what can be considered the equivalent of the slums of the industrial revolution. Cities of animals, frequently wallowing in excrement, is not the best way to prevent bad microbes from getting in our food.

So in recent years all sorts of practices have been developed to kill these microbes in food products. Irradiation, for example. And now, viruses, sprinkled on your meat, to keep the bacteria from growing too much. Give me meat from animals that have not been swimming in their own shit and piss and I will be happy to take my risks without dumping viruses on top.