Biotechnology applications in food processing: Can developing 
countries benefit?


1. Introduction
Biotechnology includes a wide range of diverse technologies and they may be applied in each of the different 
food and agriculture sectors. It includes technologies such as gene modification (manipulation) and transfer; 
the use of molecular markers; development of recombinant vaccines and DNA-based methods of disease 
characterisation/diagnosis; in-vitro vegetative propagation of plants; embryo transfer and other reproductive 
technologies in animals or triploidisation in fish. It also includes a range of technologies used to process the 
raw food materials produced by the crop, fishery and livestock sectors. This is the area that will be 
considered in this conference, the 11th one to be hosted by the FAO Biotechnology Forum since it was 
launched in March 2000. It is an area that receives relatively little attention from the media, but which is 
very important for food security in many developing countries.
Biotechnology in the food processing sector targets the selection and improvement of microorganisms with 
the objectives of improving proc ess control, yields and efficiency as well as the quality, safety and 
consistency of bioprocessed products. Microorganisms or microbes are generic terms for the group of living 
organisms which are microscopic in size, and include bacteria, yeasts and moulds.
Fermentation is the process of bioconversion of organic substances by microorganisms and/or enzymes 
(complex proteins) of microbial, plant or animal origin. It is one of the oldest forms of food preservation which 
is applied globally. Indigenous fermented foods such as bread, cheese and wine, have been prepared and 
consumed for thousands of years and are strongly linked to culture and tradition, especially in rural 
households and village communities. It is estimated that fermented foods contribute to about one-third of the 
diet worldwide.
During fermentation processes, microbial growth and metabolism (the biochemical processes whereby complex 
substances and food are broken down into simple substances) result in the production of a diversity of 
metabolites (products of the metabolism of these complex substances). These metabolites include enzymes 
which are capable of breaking down carbohydrates, proteins and lipids present within the substrate and/or 
fermentation medium; vitamins; antimicrobial compounds (e.g. bacteriocins and lysozyme); texture-forming 
agents (e.g. xanthan gum); amino acids; organic acids (e.g. citric acid, lactic acid) and flavour compounds 
(e.g. esters and aldehydes). Many of these microbial metabolites (e.g. flavour compounds, amino acids, 
organic acids, enzymes, xanthan gums, alcohol etc.) are produced at the industrial level in both developed 
and developing countries for use in food processing applications. A considerable volume of current research 
both in academia and industry targets the application of microbial biotechnology to improve the production, 
quality and yields of these metabolites.
Fermentation is globally applied in the preservation of a range of raw agricultural materials (cereals, roots, 
tubers, fruit and vegetables, milk, meat, fish etc.). Commercially produced fermented foods which are 
marketed globally include dairy products (cheese, yogurt, fermented milks), sausages and soy sauce. Certain 
microorganisms assoc iated with fermented foods, in particular strains of the Lactobacillus species, are 
probiotic i.e. used as live microbial dietary supplements or food ingredients that have a beneficial effect on 
the host by influencing the composition and/or metabolic activity of the flora of the gastrointestinal tract. 
Probiotic bacterial strains are also produced and commercially marketed in many developed countries.
In developing countries, fermented foods are produced primarily at the household and village level, where 
they find wide consumer acceptance. Food fermentations contribute substantially to food safety and food 
security, particularly in the rural areas of many developing countries. Traditional fermentation processes used 
in the production of these foods are uncontrolled and are dependent on microorganisms from the environment 
or the fermentation substrate for initiation of the fermentation processes. Such proc esses, therefore, result 
in products of low yield and variable quality. Microorganisms and metabolic pathways assoc iated with the 
production of fermented foods are the subject of considerable research, targeting strain isolation and 
identification; improvement of the efficiency of fermentation proc esses and the quality, safety and 
consistency of fermented foods. Much of this research incorporates the use of genetic technologies for strain 
development and improvement, and for diagnostic studies.
While microorganisms are beneficial in most fermentation proc esses, some may pose the risk of food 
contamination and can cause food-borne illness. Diagnostic methodologies which integrate the use of 
molecular genetic techniques, enhance the speed and sensitivity of microbial testing and are increasingly 
being applied in developing countries.
In conferences hosted by the FAO Biotechnology Forum, clearly defined topics of relevance to agricultural 
biotechnology in developing countries are discussed for a limited amount of time. The topic here is the 
application of biotechnology to the processing of food (including beverages) produced from 
agriculture. This e-mail conference discusses biotechnological tools and options that are applicable to the 
study and improvement of microorganisms which offer potential for improving the quality, safety and 
consistency of fermented foods; improving efficiency in the production of fermented foods, food ingredients, 
food additives and food processing aids (enzymes); diversifying the outputs of fermentation processes and, 
finally, improving diagnostic and identification systems applicable to foods. Applications of biotechnology to 
plants or animals to improve their food processing properties (e.g. development of the Flavr Savr tomato 
variety, genetically modified to reduce its ripening rate) or to produce proteins from genetically modified (GM) 
microorganisms to improve plant or animal production (e.g. production of bovine somatotropin (BST), a 
hormone increasing milk production in dairy cows, by GM bacteria) are not considered here. Finally, the 
conference topic covers applications of biotechnology to processing of food and not to processing of nonfood agricultural products (e.g. timber) or to applying biotechnology to microorganisms for environmental 
purposes (bioremediation, biofuels etc.).
2. Current Status of Biotechnology in Food Processing
2.1 Biotechnology in food fermentation
Microorganisms are an integral part of the processing system during the production of fermented foods. 
Microbial cultures can be genetically improved using both traditional and molecular approaches, and 
improvement of bacteria, yeasts and moulds is the subject of much academic and industrial research. Traits 
which have been considered for commercial food applications in both developed and developing countries 
include sensory quality (flavour, aroma, visual appearance, texture and consistency), virus (bacteriophage) 
resistance in the case of dairy fermentations, and the ability to produce antimicrobial compounds (e.g. 
bacteriocins, hydrogen peroxide) for the inhibition of undesirable microorganisms. In many developing 
countries, the foc us is on the degradation or inactivation of natural toxins (e.g. cyanogenic glucosides in 
cassava), mycotoxins (in cereal fermentations) and anti-nutritional factors (e.g. phytates).
2.1.1 Traditional approaches
Traditional methods of genetic improvement such as classical mutagenesis and conjugation have been the 
basis of industrial starter culture development in bacteria (a culture used to start a food fermentation is 
known as a starter culture), while hybridisation has been used in the improvement of yeast strains which are 
widely applied industrially in baking and brewing applications.
a) Classical mutagenesis
This involves the production of mutants by the exposure of microbial strains to mutagenic chemicals or 
ultraviolet rays to induce changes in their genomes. Improved strains thus produced are selected on the 
basis of specific properties such as improved flavour-producing ability or resistance to bacterial viruses. Such 
mutants may, however, show undesirable secondary mutations which can influence the behaviour of cultures 
during fermentation.
b) Conjugation
This is a natural process whereby genetic material is transferred among closely related microbial species as a 
result of physical contact between the donor and the recipient microorganism. Conjugational gene exchange 
allows both plasmid-loc alised and chromosomal gene transfer (a plasmid is a circular self-replicating nonchromosomal DNA molecule found in many bacteria, capable of transfer between bacterial cells of the same 
species, and oc casionally of different species).
c) Hybridisation (i.e. sexual breeding or mating)
Sexual reproduction in yeasts, and thus genetic recombination, has led to improvements in yeasts. For 
example, crossing of haploid yeast strains with excellent gassing properties and with good drying properties 
could yield a novel strain with both good gassing and drying properties.
2.1.2 Molecular approaches
a) Genetic modification
Recombinant DNA approaches have been used for genetic modification of bacterial, yeast and mould strains 
to promote expression of desirable genes, to hinder the expression of others, to alter specific genes or to 
inactivate genes so as to bloc k specific pathways. The successful application of genetic modification for food 
bioprocessing applications requires the development and use of food grade vectors, i.e. plasmids which do 
not contain antibiotic resistance genes as markers and which consist of DNA sequences from microorganisms 
which are generally recognised as safe (GRAS).
GM yeasts appropriate for brewing and baking applications have been approved for use (e.g. approval was 
granted in the United Kingdom for use of a GM yeast (Saccharomyces cerevisiae) in beer production, 
containing a transferred gene from the closely related Saccharomyces diastaticus, allowing it to better utilise 
the carbohydrate present in conventional feedstoc ks). None of these GM yeasts are, however, used 
commercially.
b) Genetic characterisation
The genetic characterisation of microbial strains through the use of molecular diagnostic techniques can 
contribute tremendously to the understanding of fermentation proc esses. Molecular diagnostics provide 
outstanding tools for the detection, identification and characterisation of microbial strains for bioprocessing 
applications and for the improvement of fermentation processes. The application of these and other related 
techniques, along with the development of molecular markers for bacterial strains, greatly facilitates 
understanding of the ecological interactions of microbial strains, their roles, succession, competition and 
prevalence in food fermentations and allows the correlation of these features to desirable quality attributes 
of the final product.
c) Genomics
In recent years, the genome sequences of many food-related microorganisms have been completed (e.g. 
Saccharomyces cerevisiae, commonly known as baker's or brewer's yeast, was the first eucaryote to have 
its genome sequenced - in 1996) and large numbers of microbial genome sequencing projects are also 
underway (see e.g. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome for an update). Functional 
genomics, a relatively new area of research, aims to determine patterns of gene expression and interaction in 
the genome, based on the knowledge of extensive or complete genomic sequence of an organism. It can 
provide an understanding of how microorganisms respond to environmental influences at the genetic level 
(i.e. by expressing specific genes) in different situations or ecologies, and should therefore allow adaptation 
of conditions to improve technological processes. For a range of microorganisms, it is now possible to observe 
the expression of many genes simultaneously, even those with unknown biological functions, as they are 
switched on and off during normal development or while an organism attempts to cope with pathogens or 
changing environmental conditions. For example, a recent paper by Cooper and colleagues (2003, available at 
(http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=298728) describes their use of DNA macroarrays 
to analyse expression of all 4,290 genes of the model bacterium Escherichia coli after 20,000 generations of 
evolution in a glucose-limited medium. Functional genomics can, for example, shed light on common genetic 
mechanisms which enable microorganisms to use certain sugars during fermentation, as well as on genetic 
differences allowing some strains to perform better than others. It holds great potential for defining and 
modifying elusive metabolic mechanisms used by microorganisms. Moving from the gene to the protein level, it 
should also be mentioned that proteomics, an approach aiming to identify and characterise complete sets of 
protein, and protein-protein interactions in a given species, is also a very active area of research which 
offers potential for improving fermentation technologies.
2.2 Biotechnology in the production of enzymes
Enzymes are biological catalysts used to facilitate and speed up metabolic reactions in living organisms. They 
are proteins and require a specific substrate on which to work. Their catalysing conditions are set within 
narrow limits, e.g. optimum temperature, pH conditions and oxygen concentration. Most enzymes are 
denatured at temperatures above 42°C. However, certain bacterial enzymes are tolerant to a broader 
temperature range. Enzymes are essential in the metabolism of all living organisms and are widely applied as 
processing aids in the food and beverage industry.
In the past, enzymes were isolated primarily from plant and animal sources, and thus a relatively limited 
number of enzymes were available to the food processor at a high cost. Today, bacteria and fungi are 
exploited and used for the commercial production of a diversity of enzymes. Several strains of microorganisms 
have been selected or genetically modified to increase the efficiency with which they produce enzymes. In 
most cases, the modified genes are of microbial origin, although they may also come from different kingdoms. 
For example, the DNA coding for chymosin, an enzyme found in the stomach of calves, that causes milk to 
curdle during the production of cheese, has been successfully cloned into yeasts (Kluyveromyces lactis), 
bacteria (Escherichia coli) and moulds (Aspergillus niger var. awamori). Chymosin produced by these 
recombinant microorganisms is currently commercially produced and is widely used in cheese manufacture.
The industrial production of enzymes from microorganisms involves culturing the microorganisms in huge tanks 
where enzymes are secreted into the fermentation medium as metabolites of microbial activity. Enzymes thus 
produced are extracted, purified and used as processing aids in the food industry and for other applications. 
Purified enzymes are cell free entities and do not contain any other macromolecules such as DNA.
Genetic technologies have not only improved the efficiency with which enzymes can be produced, but they 
have increased their availability, reduced their cost and improved their quality. This has had the beneficial 
impact of increasing efficiency and streamlining processes which employ the use of enzymes as proc essing 
aids in the food industry.
In addition, through protein engineering, it is possible to generate novel enzymes with modified structures 
that confer novel desired properties, such as improved activity or thermostability or the ability to work on a 
new substrate or at a higher pH. Directed evolution is one of the main methods currently used for protein 
engineering. This technique involves creating large numbers of new enzyme variants by random genetic 
mutation and subsequently screening them to identify the improved variants. This proc ess is carried out 
repeatedly, thus mimicking natural evolution processes.
2.3 Biotechnology in the production of food ingredients
As described in the Introduction, flavouring agents, organic acids, food additives and amino acids are all 
metabolites of microorganisms during fermentation processes. Microbial fermentation processes are therefore 
commercially exploited for production of these food ingredients. Metabolic engineering, a new approach 
involving the targeted and purposeful manipulation of the metabolic pathways of an organism, is being widely 
researched to improve the quality and yields of these food ingredients. It typically involves alteration of 
cellular activities by the manipulation of the enzymatic, transport and regulatory functions of the cell using 
recombinant DNA and other genetic techniques. Understanding the metabolic pathways assoc iated with these 
fermentation processes, and the ability to redirect metabolic pathways, can increase production of these 
metabolites and lead to production of novel metabolites and a diversified product base.
2.4 Biotechnology in diagnostics for food testing
Many of the classical food microbiological methods used in the past were culture-based, with microorganisms 
grown on agar plates and detected through biochemical identification. These methods are often tedious, 
labour-intensive and slow. Genetic based diagnostic and identification systems can greatly enhance the 
specificity, sensitivity and speed of microbial testing. Molecular typing methodologies, commonly involving the 
polymerase chain reaction (PCR), ribotyping (a method to determine homologies and differences between 
bacteria at the species or sub-species (strain) level, using restriction fragment length polymorphism (RFLP) 
analysis of ribosomal ribonucleic acids (rRNA) genes) and pulsed-field gel electrophoresis (PFGE, a method of 
separating large DNA molecules that can be used for typing microbial strains), can be used to characterise 
and monitor the presence of spoilage flora (microbes causing food to become unfit for eating), normal flora 
and microflora in foods. Random amplified polymorphic DNA (RAPD) or amplified fragment length polymorphism 
(AFLP) molecular marker systems can also be used for the comparison of genetic differences between 
species, subspecies and strains, depending on the reaction conditions used. The use of combinations of 
these technologies and other genetic tests allows the characterisation and identification of organisms at the 
genus, species, sub-species and even strain levels, thereby making it possible to pinpoint sources of food 
contamination, to trace microorganisms throughout the food chain or to identify the causal agents of 
foodborne illnesses. Monoclonal and polyclonal antibodies can also be used for diagnostics, e.g. in enzymelinked immunosorbent assay (ELISA) kits.
Microarrays are biosensors which consist of large numbers of parallel hybrid receptors (DNA, proteins, 
oligonucleotides). Microarrays are also referred to as bioc hip, DNA chip, DNA microarray or gene arrays and 
offer unprecedented opportunities and approaches to diagnostic and detection methods. They can be used 
for the detection of pathogens, pesticides and toxins and offer considerable potential for facilitating process 
control, the control of fermentation processes and monitoring the quality and safety of raw materials.
3. Some Issues Relevant to Developing Countries
This conference deals with the application of biotechnology to food processing in developing countries. 
Biotechnological research as applied to bioprocessing in the majority of developing countries, targets 
development and improvement of traditional fermentation processes. In this section, we consider some areas 
specifically relevant to developing countries and list some key issues that should be considered by 
participants in this conference. 
3.1 Socio-economic and cultural factors
Traditional fermentation processes employed in most developing countries are low input, appropriate food 
processing technologies with minimal investment requirements. They make use of loc ally produced raw 
materials and are an integral part of village life. These processes are, however, often uncontrolled, 
unhygienic and inefficient and generally result in products of variable quality and short shelf lives. Fermented 
foods, nevertheless, find wide consumer acceptance in developing countries and contribute substantially to 
food security and nutrition.
- How will applications of biotechnology to fermented foods impact on these socio-economic and cultural 
factors?
3.2 Infrastructural and logistical factors 
Physical infrastructural requirements for the manufacture, distribution and storage (e.g. by refrigeration) of 
microbial cultures or enzymes on a continuous basis is generally available in urban areas of many developing 
countries. However, this is not the case in most rural areas of developing countries.
- Should research be oriented to ensure that individuals at all levels can benefit from applications of 
biotechnology in food fermentation proc esses, i.e. should logistical arrangements for starter culture 
development be integrated into biotechnological research targeting improvement of traditional fermentations? 
What is required for the level of fermentation technologies and process controls to be upgraded in order to 
increase efficiency, yields and the quality and safety of fermented foods in developing countries?
3.3 Nutrition and food safety
Fermentation proc esses enhance the nutritional value of foods through the biosynthesis of vitamins, essential 
amino acids and proteins, through improving protein and fibre digestibility; enhancing micronutrient 
bioavailability and degrading antinutritional factors. Many bacteria in fermented foods also exhibit functional 
properties (probiotics).
The safety of fermented food products is enhanced through reduction of toxic compounds, such as 
mycotoxins and cyanogenic glucosides, and production of antimicrobial factors, such as bacteriocins, carbon 
dioxide, hydrogen peroxide and ethanol, which facilitate inhibition or elimination of food-borne pathogens.
- Are the nutritional characteristics (and safety aspects) of fermented foods adequately documented and 
appreciated in developing countries? Is there a need for consumer education about the benefits of fermented 
foods?
3.4 Intellectual property rights (IPRs)
The processes used in the more advanced areas of agricultural biotechnology tend to be covered by IPRs and 
these rights tend to be owned by parties in developed countries. This applies also to biotechnology proc esses 
used in food processing. On the other hand, many of the traditional fermentation processes applied in 
developing countries are based on traditional knowledge.
In addition to biotechnology processes, microbial strains may also be the object of IPRs. For example, an era 
of massive private investment in biotechnology was initiated when the United States Supreme Court ruled in 
1980 (in the Diamond versus Chakrabarty case) that a live GM bacterium (of the genus Pseudomonas, 
modified to degrade components of crude oil) could be patented. Many of the microorganisms assoc iated with 
traditional fermentation processes in developing countries are unique. Issues of ownership will become 
increasingly important as bacterial strains are characterised and starter cultures are developed in developing 
countries.
- How should food scientists, researchers, industry and governments in developing countries approach these 
issues?
- A considerable volume of research into the development and improvement of fermentation processes is 
currently taking place worldwide. Are the research results from developing countries adequately documented? 
Who owns this information? Are cell banks being developed to protect microbial strains characterised in 
developing countries?
3.5 Commercial opportunities
Biotechnological innovations have greatly assisted in industrialising production of certain indigenous fermented 
foods. Indonesian tempe and Oriental soy sauce are well known examples of indigenous fermented foods that 
have been industrialised and marketed globally. The results of biotechnology research will lead to fermented 
foods of improved quality, safety and consistency.
- Should biotechnology developments in developing countries target commercialisation? Should they target 
diversification into new value-added products? Should biotechnology development be linked to technological 
developments in food proc essing?
- Can the application of biotechnology to food processing allow farmers in developing countries to add value 
to their agricultural products (for export or for loc al consumption) and improve their revenues?
3.6 Appropriateness of food processing biotechnology in developing countries
As with any commitment of resources, investments in biotechnology for food processing should be weighed 
up against other potential uses of these resources in developing countries.
- How relevant and worthwhile can such investments be for developing countries?