Next Generation Sequencing in Food Production

Within these years, we spend hundreds of Rupees to buy a box of Cookies, rather than making from scratch. In fact, it’s not just cookies but also, many other foods, like cakes, breads and fruit buns (you name it), are produced from food industries. Although it's quite durable to get foods and refreshment in no time but about its safety, can we guarantee it?
About a year or two, two kids died from food poisoning, after hours of ingesting newly prepared snacks, in Karachi. Again, it happened a few months back, when two kids died from food poisoning from a dish in a restaurant.
Speaking of food, something edible that starts with farm and ends on our plate. To get deeper, raw materials are harvested, stored, transported, processed, packed, distributed, sold to consumers, prepared and there we have, food ready to dive in. With a long journey of how food comes in our bowl, it’s better to be safe, such that it doesn’t cause us any harm. For such precautions, the quality control department analyses samples to ensure for further process or not, depending on food safety.
Certain traditional methods include isolation and culture of microorganisms, present in a sample, to
identify certain microbes that could cause diseases among consumers, upon ingestion (Kergourlay et. al.,2015). However, it doesn’t provide a complete picture of what’s present in the sample, as most microorganisms can’t be cultured (Kergourlay et. al., 2015). Another technique of routine use in food industry, i.e. Pulsed-Field Gel Electrophoresis (PFGE), doesn’t provide complete genomic information of microorganisms, present in food samples (Kergourlay et. al., 2015) Such processes risk time and money. Within the past few years, several studies reviewed the application of Next Generation Sequencing (NGS) in food industries. Being familiar with NGS , techniques that decipher sequences of large genomic structure (like of ourselves) which saves time and money. Currently, new techniques are still under development to make it cheaper and faster. Studies identified microbial communities within food samples, along with their functional capabilities, as well as, their current status by using NGS.
Studies highlighted three kinds of NGS for their applicability to monitor food quality and safety. Amplicon sequencing is a Polymerase Chain Reaction (PCR) based method which amplifies specific
genes that identifies species within microbial ecosystems (Bokulich et. al., 2016). Based on specificity of 16S rRNA, bacterial strains were identified within the microbial community (Bokulich et. al., 2016).
Another technique, metagenomics, doesn’t depend on PCR and requires direct implementation of
samples, providing functional capability of the microbial community by sequencing genomes of every microorganism present in the microbial community (Bokulich et. al., 2016; Vargas-Albores et. al., 2019). As it doesn’t require primer for sequence specificity, viral particles can be detected from edible goods (Bokulich et. al., 2016).
The next method, metatranscriptomics, identifies and quantifies total mRNA, being expressed within a microbial community of a sample, at a certain time period (Bokulich et. al., 2016). The mRNA needs to be converted to cDNA by reverse transcriptase and then proceeded for sequencing (Bokulich et. al.2016). The technique provides information about the current state of the microbial ecosystem within condition.
So, how is NGS useful in food production?

1. Agriculture: Each organism, like us, plants and livestocks, are surrounded by microorganisms. As a plant or animal goes through their development, microflora within them changes (Vargas-Albores et. al., 2019). So, it requires NGS to know of microbial communities, monitoring their health and development. Furthermore, NGS provides information about the presence of any antibiotic resistance genes within the microbial community, to treat plants with effective strategy (Vargas-Albores et. al., 2019). Also, soil communities provide insights about maintaining nutritional balance for crops to grow. As for livestock, knowing microbial ecosystems provides us with information to maintain the health of cattles (Vargas-Albores et. al., 2019). Also, drawing milk may affect the community within the milk, depending on the hygienic practice taken by a drawer, the storage and equipment where milk is contained.
2. Food processing: Monitoring the ecosystem during each process, gives us an insight about not just food spoilage, but also, maintaining food quality, like texture, color and flavors (Yeluri Jonnala et.al., 2018). Even, certain diversity can give a food its aroma (Yeluri Jonnala et. al., 2018). The abundance of some microorganisms after the initial stage, gives cheese its flavor by breaking casein and lipids (Yeluri Jonnala et. al., 2018). The diversity of the microbial community is different, depending on the portion of the edible product. For instance, The diversity of microbes on the surface of cheese is different from its core (Yeluri Jonnala et. al., 2018). The variation among microbial communities can be found within the same kind of food. A paper review of a cheese factory in Switzerland, manufacturing the same type of cheese as of Italy, but the variation among ecosystems were observed (Yeluri Jonnala et. al., 2018). Due to use of pasteurized milk that the former are now using to prepare the cheese (having an experience of harm that raw milk had caused, because of the presence of L. monocytogenes) (Yeluri Jonnala et. al., 2018). Furthermore, the quality depends on using starter culture for food processing. And it doesn’t mean that a specific microbe is a cause for the quality. The interaction among microorganisms affects one to grow and some to reduce. Also, it affects the activity of some of them. In short, the change in structure of the microbial community during food processing affects the texture, color, flavors and even aroma. By monitoring the microbial ecosystem, during each process with NGS, the change in microflora within the food product, can further aid us not just to find the current condition, but also, predict the structure and biochemical processes within the microbial community, to get our desired results.
To describe in brief, several studies have described the application of NGS in food industries. It not just identifies microorganisms, but also, helps in predicting the function of their own capability, with regards to affecting food quality. A study of Nigeria reported of Ugba production, which is a snack, native to their area (Olasupo et. al., 2016). It’s manually produced, requiring no control of parameters or of controlling microorganisms, while processing, resulting variation in quality among different batches (Olasupo et. al., 2016). Moreover, As per the article, a number of microorganisms enlisted out of which, pathogens were also identified (Olasupo et. al., 2016). A report stated of poor quality dates from Pakistan, which were exported to France in cheap price and on the other hand, France prepared improved dates quality to make a syrup and thereby, exporting to other countries with profitable amounts.. So, just by depending on culture based methods for food quality, it now needs rapid and accurate methods for early detection, although new methods are still under process.

By: Mohammad Irtaza Tafheem

REFERENCES:

1. Bokulich, N. A., Lewis, Z. T., Boundy-Mills, K., & Mills, D. A. (2016). A new perspective on microbial landscapes within food production. Current opinion in biotechnology, 37, 182-189.
2. Kergourlay, G., Taminiau, B., Daube, G., & Vergès, M. C. C. (2015). Metagenomic insights into the dynamics of microbial communities in food. International journal of food microbiology, 213, 31-39.
3. Olasupo, N. A., Okorie, C. P., & Oguntoyinbo, F. A. (2016). The biotechnology of ugba, a Nigerian traditional fermented food condiment. Frontiers in microbiology, 7, 1153.
4. Vargas-Albores, F., Martínez-Córdova, L. R., Martínez-Porchas, M., Calderón, K., & Lago-Lestón, A. (2019). Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences. Biotechnology and Genetic Engineering Reviews, 35(1), 69-91.
5. Yeluri Jonnala, B., McSweeney, P. L., Sheehan, J. J., & Cotter, P. D. (2018). Sequencing of the cheesemicrobiome and its relevance to industry. Frontiers in microbiology, 9, 1020.