FDA details progress of next-gen sequencing tool at Probiota Americas

FDA details progress of next-gen sequencing tool at Probiota Americas

On Wednesday the Food Drug Administration presented a detailed look at its next gen sequencing tool for probiotic products at the IPA World Congress + Probiota Americas event in Chicago.

The event, hosted by NutraIngredients-USA's parent company William Reed, brought together more than 200 scientists, regulators, formulators, marketers and brand holders in Chicago. It featured a first for the probiotics space, a presentation by regulators from five national and international bodies: FDA, Health Canada, EFSA, Food Standards Australia New Zealand (a joint standards-development body) and ANVISA, Brazil’s supplement and foods regulatory body. It is the second iteration of the event in North America. Next’s year’s event is scheduled to be held in San Francisco on June 7-9.

FDA’s project is led by Dr Christopher Elkins, Director of the Division of Molecular Biology at the FDA’s Center for Food Safety and Applied Nutrition (CFSAN).  Up to now, FDA’s effort has been focused on food borne enteric pathogens, he said. 

Dr Elkins seemed to take note that attendees were perhaps particularly sensitive on the subject of regulation, as Dr Valeriu Curtui of EFSA had made an appearance the night before.  At the moment the regulatory climate for probiotics in Europe is restrictive enough that the word can no longer be used on packages.

“I’m a scientist, first and foremost,” Elkins told the attendees. “Safety is our primary concern. We are not interested in efficacy at this point. And I want you to note that I used the word ‘probiotics’ in the title of my talk.”

Building a database

Elkins said the sequencing effort uses a DNA microarray called GutProbe, a custom DNA microarray that provides a ‘quick, more accurate, and inexpensive’ method for identifying microbials and probiotics in dietary supplements. The microarray is able to identify specific strains in supplements containing a mixture of probiotics, and extensive details about it were published in the Journal of Applied Microbiology last year.

The microarray was described as “a valuable addition to QC” by the scientific advisory board of the International Probiotics Association (IPA). 

FDA is also developing a whole genome database of beneficial microbes, and is initially focusing on things that are on the market to give its scientists an idea of what is currently commercially available.

“The goal is to provide better understanding of the contents of foods that contain microbials,” Dr Elkins said. “We want to create a genotypic and phenotypic database of microbials commonly found in dietary supplements.”

Dr Elkins said that the tool could be especially useful in answering some of the questions that swirl around probiotics in supplements such as if they need to have a New Dietary Ingredient notification on file.

“If we have a good enough database we can start to answer some of those questions such as history of use. Is it the same strain we’ve seen before?” he said.

Dr Elkins said the information could also potentially be used to look at claims verification. Products that make specific claims often are (and ought to be) linked to a specific strain, but many probiotics are on the market with only genus and species identifiers on the label.

“Generalized health claims are generally OK. However, we know that there are underpinnings and in some cases very specific underpinnings of these health claims that in some cases are strain specific,” he said.

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