Posted on: March 31st, 2023


  • Advances in Sequencing Technology
  • Whole Genome Sequencing
  • How We Use Sequencing

Sequencing is a hot topic in the food industry, and many questions surround it. Is next-generation sequencing (NGS) the same as whole genome sequencing (WGS)? Why sequence a sample? What information can it provide compared to other analytical methods? This is the first of a blog trilogy that will cover the most recent sequencing technologies and applications in the food industry.

Sequencing Technologies

Frederick Sanger published the first commercialized DNA sequencing method in 1975. It became the most widely used tool to determine the sequence of nucleotides (genetic information) for decades and is still routinely used today. Sanger sequencing is a common application for bacterial and fungal identification in the food industry.

Since the late 1990s, newer technologies have been developed, enabling sequencing in a massively parallel fashion and generating large amounts of sequencing data; you may hear these referred to as high-throughput sequencing (HTS) or next-generation sequencing (NGS). One HTS approach, referred to as short-read sequencing, can simultaneously sequence thousands of small DNA pieces to get millions of data concurrently in an automated process. Sequencers made by Illumina (HiSeq, Miseq, and iSeq) and  Life Technologies (SOLiD4 and Ion Proton) are typical short-read sequencing platforms.

Long-read sequencing is differentiated from short-read sequencing by its ability to sequence longer lengths of DNA (> 100,000 base pairs is possible) at a single-molecule level with or without amplification and synthesis. Platforms using this type of HTS technology, Oxford Nanopore and PacBio, are receiving increasing attention. With appropriate analysis tools, these cutting-edge HTS technologies enable deeper insight into the relatedness and functions of microbes.

Whole Genome Sequencing

The first HTS application you may know is whole genome sequencing (WGS). WGS determines the order of all the nucleotides in an organism’s DNA. WGS can be done by Sanger sequencing, but HTS technology can drastically reduce the time and lower the price. The Human Genome Project spent over ten years and around  $300 million to sequence the entire human genome by Sanger sequencing. With today’s NGS technology, sequencing a human genome would require only a couple of days and could cost less than $1,000.

Because WGS captures all DNA information contained in a microorganism, any genetic variations of the organisms can be determined by comparing them to a reference genome or an established scheme. Federal agencies like the FDA and CDC utilize WGS to investigate foodborne illness outbreaks. Combined with metadata, the WGS results of clinical, environmental, and product isolates may help to identify the outbreak earlier, to infer the possible source of contamination faster, and to resolve the outbreak with better tracking ability. Today, WGS is recognized as the gold standard for bacteria fingerprinting. Because of that, some food companies have started applying WGS for internal contamination investigations.

WGS can be used for other applications beyond strain-to-strain comparison. For example, a dairy company may want to perform WGS of its proprietary starter cultures and understand which genes specifically contribute to fermentation quality or product flavor. WGS can also be used in a food company’s environmental monitoring program as another “tool” in their “toolbox” and complement other typing technologies to understand persistent strains in their facility better.

There are other NGS applications for food safety and quality. If you are interested to know more about them, such as using metabarcoding to solve spoilage issues, contact us – and subscribe to our blog.

Mérieux NutriSciences has NGS laboratories in North America, Europe, and Asia to provide WGS services worldwide. If you require WGS testing or NGS consulting, contact us for more information on how we can help.

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