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Tackling a Microbial Mystery During Pandemic Times

spraying crops

When Sharon Pochron assembled a group of students and faculty to take on a project she was passionate about, she had high expectations for its success.

But Pochron, who is the faculty director of Ecosystems and Human Impact in Stony Brook University’s Sustainability Studies Program in the School of Marine and Atmospheric Sciences (SoMAS), underestimated the strength and energy of the team she brought together.

Sharon Pochron
Sharon Pochron (upper left) meets with URECA research team via Zoom.

Her project: Testing the hypothesis that dietary exposure to Roundup, a glyphosate-based herbicide manufactured by Monsanto, is driving inflammatory digestive disorders such as Crohn’s disease and colitis.

Before the project could launch, Pochron turned to Karen Kernan, director of the Undergraduate Research & Creative Activities (URECA) program, for assistance in funding dedicated students. URECA provided fellowships for senior biology majors Sultan Kaur and Ariel Shaddaie and sophomore biology ecosystems and human impact major Trinity Chen.

“I couldn’t have done this without URECA,” said Pochron.

Pochron’s daughter Clara Tucker was also available. The coronavirus pandemic prevented the Stony Brook graduate student from taking a gap year to study animal species in  Germany and the Dominican Republic, so she opted to begin her master’s program in ecology and evolution working in Professor Liliana Dávalos’ lab this fall.

Jackie Collier, an associate professor in SoMAS, whose research centers on phytoplankton physiological ecology and biocomplexity and microbial diversity, rounded out the team.

“Nobody else is studying this stuff,” said Pochron, referring to the fact that glyphosate (nonselective herbicides) could be driving changes in microbial communities and causing dysbiosis (microbial imbalance), affecting both human and soil health.

Pochron, Collier and Dávalos had been working on securing a grant that would research how worms and microbes together respond to glyphosate contamination, and Collier and Pochron came up with the idea for the project

The students took on very distinct roles. Kaur and Shaddaie were assigned to do a literature survey, combing through the published literature for relevant information. Tucker was skilled in coding, but Chen, who had already been working in Pochron’s and Dávalos’ labs, didn’t know how to code when recruited but became adept at it under the watchful eye of Tucker.  

“Trinity wanted to learn to code and is passionate about soil science,” said Pochron.

Due to the pandemic, it was Pochron’s first summer without access to a traditional wet lab, one in which chemicals are used rather than computational methods.

Pochron team meeting
The team shares a screen with background information on glyphosate.

“Most of us who run labs have wet and dry labs going on all of the time,” said Pochron. “My lab could be shut down for a year but I have a backlog of things I could analyze.”

Some unexpected difficulties arose during research. For example, Chen’s computer broke down and every member of the team lost electrical power as a result of Tropical Storm Isaias, so the project was put on hold for a week. And for Collier, who is conversant with code, teaching it online when she had never done so before was especially challenging.

Tucker sorted the microbes into groups, those sensitive to Roundup and those that are not. She also motivated Chen and Shaddaie to learn code and walked Pochron through it so she “gained an appreciation for it.”

One thing that wasn’t in short supply: Motivation.

“These kids were gung-ho,” said Pochron. “It was stunning how much they got done and how little input they needed. It was supposed to be a 10-week project, but they ran it for 12 weeks and they will keep goingThe pairing of grad students and undergrads gets so much done.”

Pochron said, however, that the project was “a little ambiguous” in terms of answering her original research questions.

“I was hoping we would find when looking at colitis and Crohn’s disease that Roundup would be driving it; instead we found that there were microbial changes, but not in the direction I had been predicting,” she said. “That’s how science goes.”

In the months ahead, team members know what they must do to find answers to those questions. They compiled a list of all of the microbes that change when a person develops Crohn’s disease or colitis.

Pochron explained that E. coli, which lives in the soil as well as in the human body, is an example of a possible variable microbe because it can kill a person, but it thrives in the intestines and produces important vitamins, such as Vitamin K.

Undergraduate students are not the only ones who benefit from a project of this scope. Graduate students often perform extensive research and share it with undergrads — and even their professors.

For example, Tucker introduced Pochron to the National Center for Biotechnology Information database, so she can now access “jillions of creatures” if she has the genus and species name using that database.

The team is looking to publish a paper on their research  in November.

— Glenn Jochum

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  • As a scientist that trains many undergraduates you will never hear me use a phrase like this:

    “I was hoping we would find when looking at colitis and Crohn’s disease that Roundup would be driving it”

    It shows that agenda was driving this quest, not a plausible hypothesis. In fact, when you do the math on glyphosate dietary exposure the levels are insignificant. The stoichometry just can’t work. Moreover, the body is moving the stuff out through the kidneys for the most part, so it is unclear what is hanging around the gut. Plus we did work with E.coli and glyphosate and found that it does not enter cells very easily without plenty of surfactant around, and the levels just do not exist as residues.

    The PIs should be commended on innovative projects that expose students to research environments. But it seems like this one was not to test a hypothesis as much as confirm a belief. I’m glad the team had the integrity to follow the data rather than the websites.

  • “I was hoping we would find when looking at colitis and Crohn’s disease that Roundup would be driving it; instead we found that there were microbial changes, but not in the direction I had been predicting,” she said. “That’s how science goes.”

    I hope this is not what she’s teaching her students. At least she did follow the data.