• The Basic Concepts of Metabarcoding and Metagenomics

  • Metabarcoding Applications in the Food Industry

In the second part of our Next Generation Sequencing (NGS) blog series, we will take a deeper dive into NGS to explore metabarcoding. We will cover how metabarcoding works and how this technology can benefit the food industry, especially for fermentation in foods, spoilage investigations, and shelf life studies.

Metabarcoding and Metagenomics: Basic Concepts

Before diving into metabarcoding, it may be easier to start by explaining the concept of metagenomics. The term “metagenomics” refers to the study of the metagenome, which is the collective DNA content of all the organisms found in a given environment. Simply put, a metagenomics approach uses high-throughput sequencing (HTS) to capture all of the DNA present in a complex sample, whether it be food, environmental, or clinical. Those DNA sequences are then analyzed to identify which organisms (animals, plants, bacteria, fungi, virus, etc.) are present.

Metabarcoding is an identification (ID) method for organisms (e.g., microorganisms, plants, and animals) combining two technologies: DNA barcoding and HTS. DNA barcoding is a technique that targets certain existing genetic markers that carry ID information of organisms. HTS enables identification of numerous (micro)organisms from many samples at one time. Metabarcoding, thereby, can be used to profile or survey the microbial community, and other communities, present in a sample without needing to cultivate or isolate.

Common genetic markers for microbial ID include the 16S rRNA (16S) to determine the bacterial community composition, internal transcribed spacer 1/2 (ITS1/2) and 18S rRNA (18S) for the fungal community, and other gene targets like gyrB for speciation or subspeciation. Because the 16S and ITS1/2 regions are the most commonly used targets for surveying bacterial and fungal communities, metabarcoding is often referred to as 16S or ITS metagenomics.

Metabarcoding Applications for the Food Industry

Metabarcoding can be used to determine the community composition of bacteria, or fungi, present in a complex sample with high resolution. This is also referred to as “surveying” or “profiling” the microbial community. Profiling and tracking complex microbial communities are valuable tools for the food industry, especially in fermentation.

Numerous studies (1) have used metabarcoding to study the fermentations of drinks, vegetables, and dairy; answering questions like: What are the normal/favorable microbial communities for fermentation? What is the succession of microbes during fermentation? Which microbes may serve as indicators for product quality, flavor, or texture?

Another application for metabarcoding is spoilage investigation in foods (2-4). Studies have shown that metabarcoding reveals which microbes, including spore formers may be responsible for causing spoilage in foods like raw meat, ready-to-eat (RTE) meat, seafood, canned food, and perishable food. By extracting DNA from food samples, using HTS and bioinformatics, the trouble-making microbe(s) can be identified.

Metabarcoding is also a powerful tool for shelf life studies by determining the predominant microbes present at various stages and showing how the microbial communities may shift during shelf life (5).  For example, if a product is reformulated to remove a preservative, metabarcoding can be applied to determine the effect of that reformulation by understanding the changes in the bacterial or fungal community during product shelf life.

As sequencing and data analysis become more accessible and affordable, NGS emerges as a more attractive option for food producers and manufacturers. Application of metabarcoding to all parts of the food supply chain will only continue to grow, from authenticity of raw ingredients to product development to environmental monitoring.

See how Mérieux NutriSciences can help you learn more about metabarcoding, spoilage investigations, and shelf life studies.



Stay tuned for part 3 in our NGS blog series: Shotgun metagenomics

Click here to read part 1


  1. Bokulich, N.A., Lewis, Z.T., Boundy-Mills, K. and Mills, D.A., 2016. A new perspective on microbial landscapes within food production. Current opinion in biotechnology, 37, pp.182-189.
  2. Ioannidis, A.G., Kerckhof, F.M., Drif, Y.R., Vanderroost, M., Boon, N., Ragaert, P., De Meulenaer, B. and Devlieghere, F., 2018. Characterization of spoilage markers in modified atmosphere packaged iceberg lettuce. International journal of food microbiology, 279, pp.1-13.
  3. de Boer, P., Caspers, M., Sanders, J.W., Kemperman, R., Wijman, J., Lommerse, G., Roeselers, G., Montijn, R., Abee, T. and Kort, R., 2015. Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores. Microbiome, 3(1), p.30.
  4. Poirier, S., Rue, O., Peguilhan, R., Coeuret, G., Zagorec, M., Champomier-Verges, M.C., Loux, V. and Chaillou, S., 2018. Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing. PloS one, 13(9).
  5. Raimondi, S., Luciani, R., Sirangelo, T.M., Amaretti, A., Leonardi, A., Ulrici, A., Foca, G., D’Auria, G., Moya, A., Zuliani, V. and Seibert, T.M., 2019. Microbiota of sliced cooked ham packaged in modified atmosphere throughout the shelf life: Microbiota of sliced cooked ham in MAP. International journal of food microbiology, 289, pp.200-208.

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