Celebrating World Microbiome Day 2023: Microbes and Food

Julie MacKinnon, Microbiome Services Manager

We always like to mark world microbiome day here at NCIMB, and this year the theme is “Microbes and Food”. It’s an important topic and one that NCIMB has been involved in for decades, through the culture collection that we maintain, the services we provide and the research and development products that have been involved in.

Microbes and food are interwoven in so many ways its difficult to know where to start – from the soil in which crops are grown, to fermented foods, the gut microbiome and how the food we eat can impact on that, this is fascinating and highly important area for research and development activity.

Perhaps the key message is that while some microbes undoubtedly cause harm in the food production system, others play an essential part in food and nutrition – from farm to fork, and beyond! As the pressure on food production increases, it is vital that we continue to develop our understanding of the microbes that play an important role.

A good starting point in considering the topic of “microbes and food” is the role of soil microorganisms in agricultural production. A healthy soil microbiome is essential for food production, but as it has been estimated that a teaspoon of soil includes a billion individual microbial cells, from up to 10,000 species, building an understanding the full complexity of the microbial life within the soil has been a hugely challenging task, and one to which many microbiologists have dedicated their careers.

Historically, one of the major challenges has been around how to study organisms that cannot be grown under laboratory conditions. However, the availability of next generation sequencing and 16S metagenomics analysis has transformed our ability to “see” organisms within environmental samples.  At NCIMB we are increasingly called on to undertake 16S metagenomic analysis for our customers, and when it comes to studying complex environmental samples, this technique is almost like turning on a light to reveal the groups of organisms present.

16S metagenomics analysis generates results in the form of a simple bar chart that indicates the relative abundance of each organism in the sample, and this can be very useful for comparing diversity of different samples or tracking changes in bacterial diversity over time. This can be applied to the study of soil health, microbial communities in sediments and aquatic environments, or even the bacterial strains involved in the spontaneous fermentation process that are essential for some food and drink products such as chocolate and coffee manufacturing processes.

It is also the method used in studies of the human microbiome – 16S metagenomic studies of faecal samples have been essential in developing understanding of the gut microbiome and at NCIMB we have undertaken this kind of work for both companies and academic researchers.

While 16S metagenomics analysis is an increasingly popular analysis amongst our customers NCIMB supports research into the topic of “Microbes and Food” in other ways as well. 

For example, we are currently involved in an EU funded project “Aristo”. Aristo is the European Industry-Academia Network for Revising and Advancing the Assessment of the Soil Microbial Toxicity of Pesticides. It is an International Training Network (ITN) funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement. The network includes 9 PhD projects, 7 academic and 9 industrial beneficiaries, and five partner organisations from nine different countries, and NCIMB is one of the industrial beneficiaries. The project aims to develop tools to assess the toxicity of pesticides on soil microorganisms.

As microorganisms are essential to soil health and crop performance it is vital that pesticides are adequately assessed for their impact on soil microbes. However, within the EU the assessment of pesticide toxicity on soil microbes lags behind the assessment for aquatic organisms, and the European Food Safety Authority has identified soil microorganisms as an attribute to monitor during pesticides environmental risk assessment.

Novel tests will be required to achieve this, and recent studies have indicated that ammonia-oxidizing microbes, which perform the first and typically rate-limiting step of the important nitrogen cycling process nitrification, are ideal microbial indicators of agrochemical toxicity because of their key functional role, their sensitivity to xenobiotic compounds, and the availability of established tools to measure activity and abundance both in vitro and in situ.

NCIMB is hosting a PhD student who is working on the in vitro assessment of the toxicity of pesticides on nitrifying microorganisms and as part of her project she is working with NCIMB’s microbial ecotoxicity assay MARA – a multispecies microbial ecotoxicity test that includes 11 microbial strains to provide a more genetically diverse alternative to single species bacterial tests.

Of course, another contribution that NCIMB makes to the topic of microbes and food is through our culture collection – the National Collection of Industrial, Food and Marine Bacteria. This unique and important collection includes strains isolated from spoiled foods as well as a large collection of lactic acid bacteria, including strains isolated from fermented foods from around the world. The collection also includes bacteria that have been studied for their plant protection potential and their role in nutrient cycling within the soil.  Culture collections play a vital role in preserving and storing strains isolated by researchers and making them available to others for research or commercial use. They are an important genetic resource and so It is essential that culture collections develop their holdings in line with the direction of current research – it is an important part of our role and recent additions to the collection have included human gut microbes as well as strains isolated from breast milk.

In conclusion, a microbiome is the community of microorganisms living in any given habitat and so many different microbiomes each play an essential part in food production and nutrition. At NCIMB we are committed to working collaboratively with, and providing supporting services to, the scientists in industry and academia that are involved in microbiome research and the application of that knowledge to food production and nutrition, for the benefit of society.  

Julie MacKinnon, Microbiome Services Manager, NCIMB

At NCIMB we are increasingly called on to undertake 16S metagenomic analysis for our customers, and when it comes to studying complex environmental samples, this technique is almost like turning on a light to reveal the groups of organisms present.