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Sampling research sets stage for ascent into emerging microbiome field

October 25, 2018
 
Key Take-Aways
   
* Project examines potential biases of packinghouse
or food processing plant swabbing as it relates to emerging
field of microbiomes - or microbial communities.
 
* Researchers will look at whether material from which swabs
are made affects collection of microbial communities.
 
* They also will study whether duration of swabbing, surface
composition and sampling proximity influence outcome.
 
* Results could lead to sampling protocols for microbial communities
and easier "apples-to-apples" comparison of research results.
October 26, 2018 -  Does the material from which swabs are made, such as polyurethane, polypropylene or cellulose, bias the recovery of microbial communities?  As basic as that question may seem, Edward Dudley, Ph.D, and associate professor of food safety at The Pennsylvania State University, said he found no literature references about how it might apply to collecting microbiome samples from food processing facilities.
 
As the leader of the one-year proof-of-concept project, "Identifying optimal methods of recovering bacteria from food processing plants for downstream microbiome analyses,"  he is taking the question of potential biases even further. Dudley also wants to examine how the length of time spent swabbing surfaces, ranging from 5 to 30 seconds, may influence the microbial communities collected as well as how non-porous stainless steel and porous concrete surface areas may affect results. In addition, he plans to look at how collecting samples with different proximities to one another within a packinghouse may affect the outcome.

Joining Dudley is co-principal investigator Luke LaBorde, Ph.D ., who  shares a research and extension appointment at Penn State. In that role,  he travels the state, working with growers, packers and food processors  on  food safety issues. "Luke brings a practical knowledge of the produce industry and advises on practical applications," Dudley said.  Unlike  many previous research projects that focused on one or a few individual  pathogen species, such as Salmonella or Listeria, Dudley and LaBorde's project will deal with microbiomes-communities of  numerous microbial species that  inhabit a specific environment.  
 
Research into microbiomes, particularly in the human gut, has developed rapidly in the past decade and has the potential to be applied to food safety, Dudley said. Researchers have found that shifts in the hundreds of microbial species comprising the human gut microbiome  may be responsible for several diseases such as obesity. 

"There's been a growing interest, not only in the produce industry but the food industry in general, about how we can apply this emerging field of microbiomes and techniques we can use to look at the microbiome organization," Dudley said. "Can this be applied to the food industry to predict 
the presence of pathogens?"

"If we're swabbing the same spots in our processing facility and the studies are consistent over several months and all of a sudden, six or seven months later, we pick up different communities, did something happen in that processing plant? Was there a change in the process or a new ingredient? We're just trying to understand by observing shifts in the microbial community in a food processing plant, does that mean anything?"  To get to that point, Dudley said basic research, such as the type he and LaBorde are conducting, must first be done to identify inherent biases.
 
Depending on the results of their project, Dudley said he'd like to eventually see a protocol developed that addresses sampling of food processing facilities for microbial communities. He cited as an example the ongoing Earth Microbiome Project, an initiative to collect samples from around the globe to analyze and compare different microbiomes. All of the researchers are following the same protocol, down to the materials used to collect samples. "I'd like to see some similar recommendations to the community of researchers who study food processing facilities," Dudley said. "That way, we can directly compare data collected for a research project in California to a similar study that was done on the East Coast."
 
The same benefits also would apply to those responsible for produce industry quality assurance who want to compare test or research results from multiple sources.  Currently, food safety specialists typically start sample collection by swabbing surfaces within a food processing facility or packinghouse with a pre-wetted swab or sponge, followed by DNA extraction. "Certainly in the past, there's been a lot of interest in developing sampling standards for say Listeria," he said. "There's been a lot of work on the type of material and technique. If you follow the instructions, you will maximize the chances of collecting Listeria if it's there."
 
"Does that plant, which has a lot of Listeria, have a distinctive microbiome footprint that favors Listeria?" Dudley questioned. Another one of the questions that Dudley and LaBorde hope to answer is "Does this also apply to the much larger community of microbes found in a packinghouse or food processing facility?" The two will conduct their sampling research in a Pennsylvania apple packinghouse routinely positive for Listeria monocytogenes. LaBorde is interested in determining how the microbial community within that packinghouse may differ from one without the recurring pathogen problem.
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