How microbial profiling can aid food traceability and enhance taste

Microbiologist Greg Jones from Campden BRI explains how the technique can be used to change the flavour of milk and identify the origin of contaminated chicken.

22 November 2018
dairymeet the expertpoultryprovenancetechnology

Meet the Expert

Who: Greg Jones

What: Microbiologist

Where: Campden BRI


The term advanced microbial profiling (AMP) might sound complex, but it can be an incredibly useful tool in food manufacture. Essentially, it’s a way to examine a mixed population of bacteria – huge numbers of bacteria, in fact, at any one time, without having to resort to counting colonies on plates.

This is possible thanks to advances in DNA sequencing technology, which mean that a single DNA extract of a food sample can be used to identify the many different organisms present, allowing for more detailed analyses.

Okay, you might be thinking, but how is that helpful?

Well, it actually has implications in many areas of food manufacture where tracking the source of microbial populations is important, such as spoilage investigations and food chain traceability.

It can also be used to investigate the effect of changes in manufacturing practices and cleaning efficiency.

Below are three examples of how AMP can be used to investigate traceability in the food chain.

1. Tracing meat to where it was processed

Food factories inevitably build up a microflora (microscopic bacteria, algae and fungi) over time, despite the best efforts of hygiene teams. Recent research has shown that chicken from different cutting plants can be traced to its source by studying its microflora using AMP.

A poultry company provided us with 20 packs of pre-cut poultry portions from two of its processing plants. We used AMP to analyse the poultry samples. Swabs of machinery were also taken.

Figure 1: Sample composition at taxonomic level ‘genus’ (top 99% of genera across all samples)

Figure 1 shows the abundance of the different genus of bacteria identified in the chicken samples taken from the two plants. The bacterial composition of the samples suggests that the microflora from Site 1 originates from the chicken, whereas the microflora at Site 2 is more likely to originate from soil.

By comparing the populations, you can conclude that each site has produced chicken batches with very different microflora, and this can be used to identify the origin of a sample.

2. Tracing animal husbandry

AMP can be used to monitor the effects of changing the husbandry of cows on the microbial composition of the resulting raw milk.

Two farms producing raw milk cheese were compared using AMP. One farm kept cows exclusively in cubicles; however, their bedding was changed from straw to sand. The second farm kept cows exclusively on straw, with these cows moved from being held loose in a barn to cubicles. Raw milk samples were taken from the initial holding tank after two weeks on each bedding.

The results showed that milk flora was influenced mostly by whether the cows were kept loose or in cubicles; the bedding did not appear to have as big an influence.

The experiment shows that changing the husbandry of cows can affect the microflora of the milk produced. The dairy industry could design and test husbandry practices that result in a particular milk flora that could result in a preferred flavour.

3. Tracing authenticity

AMP can be used to explore the microbiology of fermented foods and drinks. All fermented foods share the common characteristic of using a microbial consortium to change ingredients into a final product. The organisms most often used in fermented products are lactic acid bacteria, yeasts and moulds.

Identification of most of these organisms to the level of genus or species is not currently possible with culture-based methods. However, profiling of fermented foods using AMP can be used as a tool to check the authenticity of products such as artisan cheeses.

Advanced microbial profiling can also be used for other applications in addition to authenticity and traceability. For example, it can be applied to spoilage investigations and shelf-life testing.

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