The advantages of metagenomics over genome sequencing

Earlier this week, Neogen’s own Joe Heinzelmann was a special guest on Food Safety Magazine’s podcast, “Food Safety Matters.”

Heinzelmann dropped by to talk about metagenomics, next generation sequencing (NGS) and whole genome sequencing (WGS). This technology can help the food processing industry detect spoilage organisms within facilities, eliminate them, and reduce the possibility of spoiled products reaching consumers.

First up, Heinzelmann and Food Safety Magazine outlined what exactly this new technology is and where it comes from.

“As the cost of DNA testing decreases, its practical applications are increasing, with one of the most exciting applications available being the use of sequencing to identify microorganisms in samples,” said Heinzelmann. One of the handiest features: it works for microorganisms that traditionally can’t be cultured.

Food Safety Magazine asked Heinzelmann if he anticipated widespread adoption of WGS and metagenomics in the food processing industry.

“We think there are more applications with metagenomics, specifically because the information that people get from a metagenomics analysis is very different from what you would see from people using and interpreting WGS data,” he said. He compares WGS to a license plate; it provides a specific line of information for one particular organism, much like how a license plate is a code that identifies one particular car. “We’re using that information to compare against a lot of different microorganisms, either to rule them out, or to say they’re closely related.”

Metagenomics, however, has a less singular focus. It deals more closely with all of the microorganisms in a particular environment, based on environmental samples.

“Conversely, with metagenomics, what we’re really starting to do is look at the microbiome,” said Heinzelmann. “The microbiome is just a nice word to describe the microorganisms in the same location that are interacting with each other.”

NeoSeek is a service offered by Neogen that uses metagenomics to provide complete microbiological profiles of submitted samples, including environmental samples, raw material samples and others. NeoSeek uses 16s metagenomics.

“What that means is that we target the 16s gene of bacteria, which is a gene used to identify the genus of a bacteria,” said Heinzelmann. “Let’s look at, for example, a spoilage investigation. What we do is take in normal products and spoiled products and we do a microbiome comparison between the two groups of samples. Once we understand what’s not supposed to be there, we try and help those companies understand where those unwanted microorganisms could be coming from.”

There are several advantages to this method over traditional ones.

“Because this technology doesn’t rely on enrichment or isolation, we’re able to do analyses on environmental samples without any type of biases, and we’re also able to use organisms that are really hard to culture by traditional methods. We’re able to pull those out, identify them, and use that as part of the analysis.”

What’s the biggest surprise Heinzelmann and his team have found when looking at the data?

“The variety of microorganisms present, even in some of the clean surfaces that we’ve sampled — we’re surprised by the microbial diversity on a clean surface,” he said.

To listen to the entire interview and learn more about the future of NGS, WGS and metagenomics technology, click here.