What is Food Microbiology?

Over the next 30 years, the world population is predicted to increase up to 9.7 billion people. Accordingly, there is a pressing need to understand how best to produce, supply, and maintain food requirements for such a rapidly growing population.

Food Science

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The emerging issue of food security is also further compounded by the advent of global climate change, threatening the stability of food production for future societies.

To date, efforts have focused on assuring food safety by continuously monitoring food contaminants as well as identifying risk factors concerning human health, sanitation, and nutrition. These issues are particularly prevalent in developing countries, further increasing the importance of research in food security.

Studying microorganisms in food

In recent decades, considerable attention has been given to understanding the different facets related to food production, quality, and supply. In particular, the emergence of more powerful, precise, and affordable molecular technology has provided essential tools for increasing our knowledge of food security.  

Specifically, the study of microorganisms associated with food, or food microbiology, has emerged as an exciting and valuable field of research, fundamental in manipulating and improving elements of food biology. Microorganisms are necessary agents for the creation, processing, and digestion of food. Although microorganisms found in food have many beneficial effects for humans, such as producing probiotic properties, many are known to cause food contamination leading to the occurrence of toxic and lethal pathogens.

Within the human body, microorganisms are well recognized to influence food digestion, immune system function and are commonly linked with a range of conditions such as obesity. And yet, despite such considerable importance, scientific interest in the association between microorganisms found in food and the ones found in the human body has gained traction only in recent years.

Food microbiology is of common practice, albeit unknowingly, even in the distant past. For instance, the use of fermented food dates back at least 3500 years, and continues its relevancy today, with the widespread consumption of beer, wine, and dairy products. These products alone may have contributed to genetic differences in human populations on evolutionary timescales, indicating the extent of effects microbes may have had.

The molecular tools used for studying food microbiology

More recently, the use of molecular tools has provided an ideal platform for studying food microbiology and has become integral in the identification and quantification of microorganisms.

An article by Italian researchers describes the most common trends in food microbiology. Findings revealed some of the most studied microorganisms over the past decade, including 227 studies investigating effects of Escherichia coli and 167 studies considering Salmonella spp., demonstrating an abundance of specialized research.

Additionally, food microbiology has focused on several key topics, including risk factors associated with pathogens, the use of improving quality of fermented foods, and how best to maintain microbial integrity.

Such trends are directly applicable across human populations since these microorganisms and emerging issues are so pervasive and central to human health and nutrition. The widespread applicability and increased use of genomic tools have therefore provided key improvements to ensure global food security.

These tools are also expected to play even greater roles in securing food availability in the future. Such implications were further discussed in a comprehensive review of contemporary literature developed by an international expert group (Jagadeesan et al., 2019).

The review presents the implications of genomics in food microbiology research, providing a robust foundation for the use of next-generation sequencing tools in food microbiology. In particular, the team discusses the extensive information that may be provided by applying techniques such as metagenomics as well as whole-genome sequencing to quantify, identify and control microbial populations and strains in food.

Interestingly, several next-generation sequencing platforms are reviewed in detail, encompassing tools such as Ion Torrent and Nanopore, and their applications to public safety and food security.  

Despite the considerable potential of molecular tools and abundance of food microbiology studies, clear challenges need to be addressed as presented in this review. Research procedures, practices, and results require harmonization and standardization to make them more accessible to the wider community. These improvements will act in conjunction with technological progress, eventually broadening the application of genomic tools and leading to more effective applications in maintaining food security.

Nonetheless, more deep-rooted issues also remain when examining differences in research across geographic regions. Many regions already documenting higher levels of food deprivation are predicted to experience even more frequent issues relating to environmental factors as well as the pervasiveness of pathogens, exacerbating the disparity in research and potential solutions.

As genomic tools are already cheaper, and sometimes more effective (e.g. Franz et al., 2016), in comparison to other methods of microbial identification, further cost-effectiveness may help bridge the gap in socioeconomic disparity evident in food microbiology research.

Salmonella Bacteria

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Food microbiology provides compelling tools beneficial for human health and nutrition. Not only do genomic techniques provide cheaper, more accurate, and faster methods of examining microorganisms in food biology, but they also broaden the horizon of food biology research.

Exciting prospects such as the improvement of crop resistance and the development of microbiological supplements may be particularly valuable in a world-changing so rapidly, both socioeconomically and environmentally.


  • Jagadeesan, B. et al. (2019) ‘The use of next-generation sequencing for improving food safety: Translation into practice’, Food Microbiology, 79, pp. 96–115. doi: doi.org/10.1016/j.fm.2018.11.005.
  • Suzzi, G. and Corsetti, A. (2020) ‘Food Microbiology: The Past and the New Challenges for the Next 10 Years’, Frontiers in microbiology. Frontiers Media S.A., 11, p. 237. doi: 10.3389/fmicb.2020.00237.
  • Franz, E., Gras, L. M. and Dallman, T. (2016) ‘Significance of whole-genome sequencing for surveillance, source attribution and microbial risk assessment of foodborne pathogens’, Current Opinion in Food Science, 8, pp. 74–79. doi: doi.org/10.1016/j.cofs.2016.04.004.

Further Reading

Last Updated: Nov 20, 2020

James Ducker

Written by

James Ducker

James completed his bachelor in Science studying Zoology at the University of Manchester, with his undergraduate work culminating in the study of the physiological impacts of ocean warming and hypoxia on catsharks. He then pursued a Masters in Research (MRes) in Marine Biology at the University of Plymouth focusing on the urbanization of coastlines and its consequences for biodiversity.  


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