Available online at www.sciencedirect.
com
Precision fermentation for improving the quality, flavor,
safety, and sustainability of foods
Karson Hilgendorf 1, Yirong Wang 2, Michael J Miller 1,3 and
Yong-Su Jin 1,3
Precision fermentation involves the rewiring of metabolic
pathways in generally recognized as safe microorganisms,
fermentation scale-up, and downstream processing to produce
food ingredients from abundant and inexpensive substrates.
Using precise genome editing of food-fermenting
microorganisms, precision fermentation can also produce
fermented foods with more desirable properties. These genetic
tools allow for the manipulation of flavors and nutritional
content in fermented foods, the economic production of
functional food ingredients, and the sustainable production of
otherwise-costly macronutrients. By introducing the metabolic
designs, genetic modifications, and resulting products of
engineered microorganisms developed through academic and
industrial research, this review aims to provide insights into the
potentials and challenges of precision fermentation for the
economic, safe, and sustainable production of foods.
Addresses
1
Department of Food Science and Human Nutrition, University of Illinois
at Urbana-Champaign, Urbana, IL, USA
2 Precision fermentation aims to produce food ingredients
Department of Energy, Environmental & Chemical Engineering,
Washington University in St. Louis, St. Louis, MO, USA
3
Carl R. Woese Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, IL, USA
Corresponding author: Jin, Y.-S. (ysjin@illinois.edu)
Current Opinion in Biotechnology 2024, 86:103084
This review comes from a themed issue on Food Biotechnology
Edited by Christoph Wittmann and Ken-ichi Yoshida
Available online xxxx
https://doi.org/10.1016/j.copbio.2024.103084
0958–1669/© 2024 Published by Elsevier Ltd.
Introduction
The food industry is unremittingly committed to im­
proving the quality of food. This includes efforts to in­
crease nutritional value, extend shelf life, improve colors
and flavors, and reduce safety risks. The industry is also
increasingly concerned with the sustainability of the
food production system. With the potential for the global
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population to reach ten billion by the year 2100, the
industry is expected to face a 50–80% surge in global
food demand as compared with current levels [1]. This
underscores the urgency of re-evaluating our food pro­
duction to ensure a sustainable and resilient future food
supply.
Microbial fermentation has been widely used to produce
fermented foods and food ingredients. In addition to
fermented foods, such as beer, wine, and cheese, mi­
crobial fermentation is currently used to produce various
other products, including chymosin for curd formation in
cheese manufacturing, monosodium glutamate (MSG)
for enhancing savory flavors, and citric acid for providing
the sour taste in soft drinks. With the recent technolo­
gical progress in metabolic engineering and synthetic
biology, microbial fermentation has evolved into preci­
sion fermentation.
from abundant and inexpensive substrates by using
precise genetic perturbations to rewire metabolic path­
ways in microorganisms. When traditional food-fer­
menting microorganisms are used as hosts, precision
fermentation can also produce fermented foods with
more desirable properties. To do this, the precise ge­
netic engineering tools developed for industrial bio­
technology to produce biofuels and biochemicals are
being adopted for precision fermentation. The in­
troduction of heterologous genes from Generally
Regarded as Safe (GRAS) microorganisms and/or dele­
tion of endogenous genes to redirect metabolic fluxes
toward a desired product can optimize production in
food-fermenting/GRAS microorganisms. Bioprocess en­
gineering strategies can then improve the titer, rate, and
yield (TRY) of target products. In addition, precision
fermentation encompasses broader research efforts for
downstream processing, regulatory approval, and gar­
nering consumer acceptance (Figure 1).
Numerous academic laboratories, startups, and estab­
lished food companies are increasingly adopting preci­
sion fermentation to produce food ingredients, nutrients,
and fermented foods economically and sustainably. It is
the opinion of the authors that the growth and devel­
opment of the precision fermentation industry are ex­
citing and will bring positive change to current food
Current Opinion in Biotechnology 2024, 86:103084
2 Food Biotechnology
Figure 1
Illustration of the research targets in precision fermentation.
systems. However, this sentiment is not shared by all. In
our experience, words such as ‘bioengineered’ and ‘ge­
netically modified (GM)’ tend to inspire negative reac­
tions among consumers. It is not within the scope of this
review to analyze the basis for these reactions. Instead,
we aim to provide examples that demonstrate the con­
sumer-focused improvements precision fermentation
can introduce to the industry and, at the end, to propose
a new system for categorizing genetically engineered
products that could refine the way we refer to, and label,
engineered food products.
Improving the quality of foods
Maintenance and enhancement of food quality con­
stitute the primary objectives of food science and tech­
nology research. While chemistry- and physics-based
approaches have traditionally played significant roles in
improving food quality, biotechnology-based methods
have emerged as innovative solutions to overcome the
limitations of conventional approaches.
Owing to the brief nature of this review, we have chosen to
focus on the potential for precision fermentation to im­
prove food flavor, safety, and sustainability. However, there
are other aspects of food quality, such as color and nutri­
tional value, and examples of exciting innovations that
cannot be fully explained within this review. For the cur­
ious reader, Table 1 lists precision fermentation endeavors
to improve the quality of food and beverage products in
peer-reviewed publications, and Table 2 lists the same in
GRAS FDA Notices (abbreviated GRN) and patents.
As demonstrated by the examples listed in these tables,
and the rest of this review, the precision fermentation
Current Opinion in Biotechnology 2024, 86:103084
Current Opinion in Biotechnology
industry is incredibly broad, even when confined to the
context of food science. This breadth demonstrates the
prospects for precision fermentation to be applied
widely across the food industry, but it also leads to
challenges regarding regulation, labeling, and main­
taining safe practices. As these tools move from aca­
demic research to commercial adoption (which is
happening now, as evidenced by an increase in precision
fermentation-related GRN applications), the proprietary
nature of industry research and development has the
potential to confuse consumers about the safety of the
tools being used to make their food. There is a current
lack of transparency or labeling for consumers to tell the
difference between, for example, food ingredients that
are purified from a fermentation broth of microorganisms
that are expressing heterologous genes [6,11,12], and
products that may have the engineered microorganisms
incorporated [4,9]. However, unlike the stereotypical
GM crop (Roundup Ready or Bt corn, for example), a
majority of these GM microorganisms are making im­
provements to the food industry that are benefitting the
consumer directly by providing tastier, safer, or new food
products.
Rather than focusing solely on reducing manufacturing
costs, the field of precision fermentation is making
consumer-driven innovations possible. This is why we
argue that precision fermentation is not only a positive
driving force for the food industry, but also that, al­
though proprietary research makes transparency a chal­
lenge, with proper regulations in place, companies
employing now-accessible genetic engineering tools to
benefit consumers may be the change GM organisms
need to be viewed in a more positive light. The rest of
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 Precision fermentation for improving food quality Hilgendorf et al. 3

Table 1
Recent research publications, which are not covered in the text, aim to improve the quality of food and beverage products.

Target Description Reference (s)

Antimicrobial activity against
nonpathogenic bacteria
Color production
Flavor improvement
Flavor compound production
Sustainable ingredient production
Vitamin and antioxidant production
Improved antimicrobial activity of Lactobacillus acidophilus by genome [2]
shuffling, inhibited growth of Alicyclobacillus acidoterrestris in apple juice
Production of red/purple cyanidin and delphinidin and orange/yellow [3•]
pyranoanthocyanidins using green tea as a substrate by Lactococcus lactis engineered
with heterologous pathway genes
Endogenous gene overexpression in yeast to increase NADH availability and glycerol [4]
production to improve beer aromas
Heterologous expression of methyl anthranilate (grape flavor) synthesis pathway and [5]
fine-tuning in E. coli and Corynebacterium glutamicum
Sustainable production of oleic acids by Yarrowia lipolytica through heterologous [6]
expression and a series of gene deletions and overexpressions
Heterologous expression of fusion enzyme for production of rebaudioside M from [7]
rebaudioside A by Pichia pastoris
Overexpression of genes in L. lactis to overproduce vitamin K2 [8]
Improved production of β-carotene by S. cerevisiae by insertion and deletion of relevant [9]
genes

this review will describe these prospects and challenges
regarding innovations aimed at improving specifically
the flavor, safety, and sustainability of food and beverage
products.
Improving the flavor of foods
While the major historical intention of making fer­
mented foods has been to preserve commodities, fer­
mentation has also contributed to more palatable flavors
or the introduction of new flavor profiles to foods. Many
flavor molecules in fermented foods are generated via
biochemical and metabolic reactions. As such, metabolic
engineering allows scientists to directly manipulate fla­
vors in fermented foods, and to produce flavor compo­
nents safely and economically.
In fermented foods, such as bread, cheese, wine, and
beer, fermenting microorganisms are part of the final
food products, and metabolic engineering of these mi­
croorganisms can directly modify the flavor profiles of
the final product. A seminal example is the Saccharomyces
cerevisiae ML01 expressing Schizosaccharomyces pombe
malate transporter (SpMAE) and Oenococcus oeni malic
enzyme (mleA) for simultaneous malolactic and ethanolic
fermentation in wine production [14]. The engineered
yeast decreased the acidity of wine and contributed to
softer wine tastes [14]. More recent examples are a yeast
expressing lactate dehydrogenase used for sour beer
production (GRN 841), and hoppy flavor yeasts expres­
sing linanool and geraniol synthases used to produce
hoppy beer without using hops [15••–17]. In these ex­
amples, even if the engineered yeasts are removed from
the products through filtration, the fermented beverages
can be unattractive to consumers because of the notion
that transgenic microorganisms were employed.
As such, it is more desirable to improve flavor by genetic
editing without involving any heterologous genes. For
example, S. cerevisiae has been genetically edited to
overexpress endogenous genes coding for the enzymes
that cleave thiols from the thiol precursors present in
musts and worts, resulting in more tropical fruit aromas
[18]. These volatile thiols can enhance the flavor of beer
and wine without introducing heterologous genes. More

Table 2
Recent GRAS notifications and patents, which are not covered in the text, aim to improve the quality of food and beverage products.

Target Description Reference (s)

Color improvement Peroxidase production by GM Aspergillus niger to bleach whey protein, DSM Food Specialties GRAS 402 [10]
reducing unwanted color changes
Flavor compound Gene encoding brazzein (a sweetener) heterologously expressed in Oobli Inc. (formerly Joywell Foods, Inc.)
production Komagataella phaffii (aka P. pastoris) GRN 1142 [11]
Sustainable ingredient β-lactoglobulin heterologously produced by K. phaffii (aka P. pastoris) Remilk Ltd. GRN 1056
production Pea protein fermented by shiitake mycelia MycoTechnology, Inc. GRN 1125
Production of oil rich in omega-3 fatty acids by microalgae Prototheca Corbion Biotech GRN 754
moriformis that has been modified by mutagenesis and gene editing
Production of human milk oligosaccharides by bacteria expressing Glycosyn LLC [12]
heterologous genes
Vitamin production Heterologous expression of cobalamin (vitamin B12) and transcobalamin ImaginDairy Ltd. [13]
(carrier protein of cobalamin) in dairy-like food products

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4 Food Biotechnology
recent genome editing examples in academic research
include enhancing fruity flavors in wines [19–21] and
synthesizing butter aromas in cheese [22••]. Notably,
the softer-tasting wines increased availability of hoppy
beers (because they no longer have to rely on growing
hops), and expanded flavor options for these fermented
foods are all direct benefits that consumers can enjoy
because of the GM microorganisms.
Outside of in situ flavor production in fermented foods,
there have been a variety of microorganisms developed
to produce flavors that are highly sought-after in the
industry but difficult to procure. Flavor-active molecules
can be purified from the fermentation broth, and, as
opposed to when microorganisms are incorporated into
the final product, inserting heterologous genes to pro­
duce them may not require special labeling on the end
product depending on local regulations. Using in­
dustrially robust strains such as S. cerevisiae to produce
high titers of these flavor compounds can be more eco­
nomically viable than extracting them from plant sources
and safer and more sustainable than chemical synthesis.
Vanillin (vanilla flavor [23,24]), methyl anthranilate
(grape flavor [25]), cinnamaldehyde (cinnamon
flavor [26]), and diacetyl (butter flavor [22••]) have been
produced by engineered yeast [23–26] and lactic acid
bacteria (LAB [22••]). A culminating example of flavor
production is the overproduction of soy leghemoglobin
by Pichia pastoris (GRN 737). Leghemoglobin contains
heme — a molecule that can make soy protein taste like
meat when it is cooked (GRN 737). The drawback to
producing these flavor molecules through precision fer­
mentation is that they are often toxic to the host cell or
produced at low titers, but cellular and bioprocess en­
gineering can alleviate the toxicity and improve pro­
duction TRY. For consumers, the sustainable production
of these flavor compounds prospectively increases access
to flavors that would otherwise be too costly to in­
corporate into foods.
Improving the safety of foods
Food safety is one of the primary concerns of the food
industry, with emphasis on reducing short-term (such as
foodborne pathogens that cause acute illness) and long-
term (such as carcinogen exposure) health risks.
Historically, one of the primary purposes of fermenting
food has been to prevent the growth of pathogenic or­
ganisms by promoting or introducing microorganisms
that compete for resources and contribute to inhibitory
conditions. One of the ways to inhibit the growth of food
pathogens is to allow the production of antimicrobials,
such as organic acids and bacteriocins, by fermenting
microorganisms in foods. Nisin is the most widely used
bacteriocin in food, and it is industrially produced by
batch fermentation of certain species of Lactococcus lactis
[27]. Genetic engineering allows for the improvement of
Current Opinion in Biotechnology 2024, 86:103084
nisin activity by identifying mutants with increased ac­
tivity for specific pathogens, as reviewed by Zhang and
colleagues [19]. Recent advances have included im­
proving the functionality of nisin in food [28] and im­
proving its specificity [29]. While nisin is the most-
studied bacteriocin, there is also exciting work being
done regarding other bacteriocins [30]. The prospect for
precision fermentation strategies to enhance its utility is
compelling because nisin is already accepted as an an­
timicrobial in food products.
Endolysins are another way to prevent pathogenic bac­
terial growth in food products. Derived from bacter­
iophages, endolysins are enzymes capable of
exogenously breaking down the peptidoglycan in the
cell walls of Gram (+) bacteria. This mechanism makes
them useful against Gram (+) food pathogens, such as
Listeria monocytogenes [31]. The use of endolysins for food
safety purposes has been recently reviewed by Khan and
colleagues [31]. To the authors’ knowledge, re­
combinant endolysins produced microbially have not yet
been used commercially in food. However, PlyP100, an
endolysin derived from a GRAS bacteriophage that tar­
gets L. monocytogenes, has been shown to inhibit L.
monocytogenes growth in fresh cheeses [32,33]. This could
be an easy first step to industrial endolysin production
and use in food, especially considering that recombinant
chymosin is usually included as ‘enzymes’ on the in­
gredient list of these products, so adding additional en­
zymes from GRAS sources may not require additional
labeling. Furthermore, precision fermentation of both
endolysins and bacteriocins is an interesting prospect
consistent with the current clean-label trend. While
consumers continue to favor clean-label products and
fermented foods continue to have a positive connotation,
labeling these antimicrobial compounds as ‘fermentation
broth’ or ‘enzymes’ could allow for the industry to pro­
duce safe, clean-label, and consumer-acceptable foods.
Along with preventing acute foodborne disease, pre­
venting chemical toxins in food products is important to
the food industry. Artificial colorants are an example, as
they are primarily derived from synthetic chemicals
proven to cause serious health consequences [34]. Re­
cently, the state of California in the United
States banned the use of food dyes that might cause
cancer in animals. Promising replacements for synthetic
food colors are bio-based colors, including carotenoids,
anthocyanins, indigoidine, violaceins, and betalains,
which can be produced from microbial fermentation
[35–38•]. These are considered natural food additives,
giving them a considerable consumer perception ad­
vantage over synthesized colorants.
Another prominent example of precision fermentation
for the reduction of chemical toxins in food is preventing
the formation of acrylamide, a known carcinogen [39]. A
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 Precision fermentation for improving food quality Hilgendorf et al.
working strategy to avoid acrylamide production is to
reduce the concentrations of asparagine (an amino acid
often present in foods, especially potatoes, which reacts
with sugars via the Maillard reaction to form acrylamide)
in foods that are fried or baked. For this purpose, the
asparaginase gene has been inserted into S. cerevisiae
(GRN 604, GRN 422), Bacillus subtilis (GRN 476), and
Aspergillus niger (GRN 428), and a metabolic pathway to
consume asparagine during fermentation has been in­
troduced to S. cerevisiae [40]. Treating raw food materials
with these engineered strains or the asparaginase they
produce has been shown to decrease acrylamide con­
centrations in cooked food products after frying and
baking, which is a promising way to increase food safety
for the benefit of the consumer.
Bacteriocins, endolysins, colorants, and asparaginase
produced by engineered microorganisms might readily
be incorporated into foods after purification. However,
food production where the fermenting microorganisms
are incorporated into the final composition of the food
requires thorough safety assessments for commerciali­
zation. If food-fermenting microorganisms contain no
heterologous genes but genome editing of endogenous
genes only, or if they only contain heterologous genes
from other food-fermenting or GRAS organisms, the
resulting engineered microorganisms are less likely to be
rejected for GRAS status by a regulatory agency. The
difference between these strategies of engineering mi­
croorganisms is currently not reflected in regulatory fra­
meworks, which means all engineered microorganisms,
whether edited with endogenous genes only or en­
gineered to express genes from non-GRAS organisms,
are currently treated the same way. This lack of dis­
tinction directly contributes to consumer hesitancy be­
cause there is a lack of transparency.
Improving the sustainability of foods
As the global population continues to increase and
consumer demand shifts toward sustainably sourced
food products, renewable and animal-free sources of
food are becoming more popular and necessary. Using
microorganisms as machinery for producing flavor-active
or antimicrobial molecules, as discussed in previous
sections, is a step in the right direction because the
microorganisms are self-replicating and produce minimal
unusable waste. To further improve the sustainability of
food production, precision fermentation also aims to re­
place or alleviate some of the environmental burdens of
traditional farming strategies.
Namely, animal-free protein sources are gaining atten­
tion rapidly. As mentioned previously, heme, the pre­
dominant molecule responsible for meaty color and
flavor, has been produced recombinantly and used to
make plant-based proteins that taste like meat (GRN
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5
737). This product, sold by Impossible Foods Inc., is the
embodiment of consumer-focused improvement to the
food industry. Because of these GM microorganisms,
consumers can buy a vegan soy product that tastes and
looks like meat.
While this innovation has been useful in shifting toward
more sustainable protein options, plant protein sources
often lack the functional properties (e.g., digestibility,
foaming ability, and emulsifying capacity) of animal
proteins. Consequently, replacing animal proteins with
plant proteins might be an incomplete solution [41]. To
fill this gap, GRAS filamentous fungi have been en­
gineered to heterologously express animal proteins,
specifically dairy and egg proteins, due to their post­
translational modification and protein secretion cap­
abilities [42••]. Many start-up precision fermentation
companies are using this method to make animal-free
animal proteins. Perfect Day, Inc. produces dairy-like
products that are dairy-free and fortified instead with
recombinant milk proteins, such as β-lactoglobulin pro­
duced by the fungus Trichoderma reesei (GRN 863 [43]).
ImaginDairy Ltd. has a similar business strategy. They
recently submitted a GRAS proposal for β-lactoglobulin
produced by Aspergillus oryzae (GRN 1145). The EVERY
Company (formerly Clara Foods Co.) also produces an­
imal-free egg proteins for the food industry ([44], GRN
967, GRN 1104). These sustainable food ingredient
production methods almost always necessitate the use of
heterologous genes, but they can meet regulations by
filtering out the microorganisms to yield only the final,
already- GRAS, product. The macromolecules being
produced are very similar, if not identical, to those found
in animals or plants, so the fact that they are produced by
microorganisms is more of a consumer acceptance con­
cern than a safety or regulatory concern.
Other companies, such as LanzaTech, Solar Foods, and
Air Protein Inc., are working toward using carbon di­
oxide as a substrate to produce food ingredients [45–47].
This subject has been reviewed by Bachleitner and
colleagues [48•], who provide an interesting perspective
on where the future of the industry may lie. While the
idea of using microorganisms to ferment proteins from
air is compelling, this is quite the leap from the current
state of biotechnology.
The consumer demand for clean-label products meets
an interesting dilemma when faced with microbially
produced egg and dairy products. However, these busi­
nesses are gaining public attention and popularity, sug­
gesting that there is demand for such products. Based on
the number of start-up companies in the animal-free
protein and sustainable ingredient production sectors of
the food industry, it can be inferred that innovation in
this field is being driven by consumer demand. It is the
perspective of the authors that this shift toward
Current Opinion in Biotechnology 2024, 86:103084
6 Food Biotechnology
Figure 2
Proposed categories of GM microorganisms depending on the safety of host strains and their degree of engineering.
benefitting the consumer may be able to shift consumer
attitudes about GM products from negative to positive,
especially when coupled with the regulatory framework
described in this review.
Conclusions and perspectives
As demonstrated by the examples presented here, pre­
cision fermentation shows incredible potential to im­
prove the flavor, safety, and sustainability of food
products across the industry, ultimately improving the
overall quality of the food supply for the sake of the
consumer. Producing valuable food ingredients from
abundant, renewable substrates by the metabolism of
self-replicating, programmable microorganisms is a sig­
nificant step in the right direction toward a sustainable
and resilient future food supply. There are many new
(not to mention successful) start-up companies taking
advantage of genome editing and metabolic engineering
to move the food industry toward safe, sustainable
Current Opinion in Biotechnology 2024, 86:103084
Current Opinion in Biotechnology
innovations; the field is not limited to academic research
anymore. However, as a new technology, two challenges
that the precision fermentation industry will continue to
face are consumer acceptance and maintaining safe
practices.
While we believe the consumer-focused nature of in­
novation is a first step toward gaining consumer accep­
tance, it is also imperative to keep the engineering itself
safe and transparent. In addition to using GRAS host
microorganisms, future microbial engineering should
attempt to minimize the use of heterologous genes. If
heterologous genes must be used, it is preferable to
source them from GRAS organisms. Avoiding hetero­
logous genes and organisms that are not GRAS is es­
sential to producing marketable food products, but it is
also necessary for ensuring long-term product safety. A
major reason for consumer hesitancy surrounding ge­
netic engineering, or broadly GM organisms, is the
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 Precision fermentation for improving food quality Hilgendorf et al.
potential for pathogenic or antibiotic-resistant genes
from engineered organisms to be incorporated into those
in the environment. In contrast to traditional GM or­
ganisms based on recombinant DNA technologies, cur­
rent precision fermentation technology is based on
precise genome editing without the need for selective
marker genes such as antibiotic resistance. Moreover,
precision fermentations to produce food ingredients take
place contained in bioreactors, with very little likelihood
for the engineered microorganisms to be released into
the environment. From our perspective, being able to
communicate these positive changes to consumers
would reduce consumer acceptance issues and provide
consumers the ability to choose what degree of genetic
engineering they are willing to accept. While the dis­
tinctive characteristics of precision fermentation render
it a safer production method than what industrial bio­
technology previously had access to, the importance of
robust regulation and surveillance remains paramount.
To streamline the regulatory process and offer guidance
for safe microbial engineering practices, we advocate for
the categorization of GM microorganisms into four ca­
tegories based on their safety and risk profiles. Like
biosafety levels utilized to determine protective mea­
sures in laboratory settings for safeguarding workers, the
environment, and the public, GM microorganisms in­
volved in precision fermentation could be designated
into four categories, ranging from GM Level 1 to GM
Level 4 (Figure 2). As with any new technology, it is
important that the proper regulations are put in place.
The introduction of this more transparent system of
characterizing GM microorganisms would likely drive
companies to prefer GM Level-1 modifications to appeal
to consumers, but it would also provide a good starting
point for understanding what kind of genetic modifica­
tions need to have stricter regulations. Because of the
broad potential for precision fermentation to improve
foods in diverse ways, the methods in which genetic
tools are used should be categorized and disclosed so
that the primary goal of the innovations remains to
produce better products for consumers and society rather
than to decrease manufacturing costs.
Data Availability
No data were used for the research described in the ar­
ticle.
Declaration of Competing Interest
The authors declare no conflict of interest.
Acknowledgements
The authors would like to thank Hyunjoon Oh and Christine Atkinson for
kindly proofreading and providing comments on this paper. This work was
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7
supported by the Investment for Growth Program from the University of
Illinois at Urbana-Champaign, Synthetic Biology for Food and Nutrition
Innovation (SynFoNI).
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•• of special interest
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8 Food Biotechnology
yeast engineered for the production of primary flavor
determinants in hopped beer. Nat Commun 2018, 9:965.
This is an excellent and thorough example of genetic engineering to
make beer production more sustainable. The authors used Golden Gate
cloning and Gibson assembly to introduce heterologous genes and edit
the metabolic pathway until they achieved a yeast strain that can pro­
duce the flavor determinants of hoppy beer without the addition of hops.
16. Zhou P, Du Y, Xu N, Yue C, Ye L: Improved linalool production in
Saccharomyces cerevisiae by combining directed evolution of
linalool synthase and overexpression of the complete
mevalonate pathway. Biochem Eng J 2020, 161:107655.
17. Zhou P, Du Y, Fang X, Xu N, Yue C, Ye L: Combinatorial
modulation of linalool synthase and farnesyl diphosphate
synthase for linalool overproduction in Saccharomyces
cerevisiae. J Agric Food Chem 2021, 69:1003-1010.
18. Holt S, Cordente AG, Williams SJ, Capone DL, Jitjaroen W, Menz
IR, Curtin C, Anderson PA: Engineering Saccharomyces
cerevisiae to release 3-mercaptohexan-1-ol during
fermentation through overexpression of an S. cerevisiae Gene,
STR3 , for improvement of wine aroma. Appl Environ Microbiol
2011, 77:3626-3632.
19. Zhang T, Zhang Y, Li L, Jiang X, Chen Z, Zhao F, Yi Y:
Biosynthesis and production of class II bacteriocins of food-
associated lactic acid bacteria. Fermentation 2022, 8:217.
20. Dong J, Wang P, Fu X, Dong S, Li X, Xiao D: Increase ethyl
acetate production in Saccharomyces cerevisiae by genetic
engineering of ethyl acetate metabolic pathway. J Ind Microbiol
Biotechnol 2019, 46:801-808.
21. Hong K-Q, Fu X-M, Dong S-S, Xiao D, Dong J: Modulating acetate
ester and higher alcohol production in Saccharomyces
cerevisiae through the cofactor engineering. J Ind Microbiol
Biotechnol 2019, 46:1003-1011.
22. Liu JM, Chen L, Jensen PR, Solem C: Food grade microbial
•• synthesis of the butter aroma compound butanedione using
engineered and non-engineered Lactococcus lactis. Metab Eng
2021, 67:443-452.
This paper is an outstanding example of the difference between genetic
engineering and genetic editing. The authors engineered an LAB strain
to enhance the butter-aroma compound butanedione, and then used
what they learned to make another strain to do the same without the use
of heterologous genes. These authors also emphasize the use of waste
streams as fermentation medium, increasing the process’ sustainability
and economic viability.
23. Hansen EH, Møller BL, Kock GR, Bünner CM, Kristensen C, Jensen
OR, Okkels FT, Olsen CE, Motawia MS, Hansen J: De novo
biosynthesis of vanillin in fission yeast (Schizosaccharomyces
pombe) and baker’s yeast (Saccharomyces cerevisiae). Appl
Environ Microbiol 2009, 75:2765-2774.
24. Brochado AR, Matos C, Møller BL, Hansen J, Mortensen UH, Patil
KR: Improved vanillin production in baker’s yeast through in
silico design. Micro Cell Fact 2010, 9:1-15, https://doi.org/10.
1186/1475-2859-9-84
25. Kuivanen J, Kannisto M, Mojzita D, Rischer H, Toivari M, Jäntti J:
Engineering of Saccharomyces cerevisiae for anthranilate and
methyl anthranilate production. Micro Cell Fact 2021, 20:1-12,
https://doi.org/10.1186/s12934-021-01532-3
26. Gottardi M, Knudsen JD, Prado L, Oreb M, Branduardi P, Boles E:
De novo biosynthesis of trans-cinnamic acid derivatives in
Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2017,
101:4883-4893.
27. Field D, Considine K, O’Connor PM, Ross RP, Hill C, Cotter PD:
Bio-engineered nisin with increased anti-Staphylococcus and
selectively reduced anti-Lactococcus activity for treatment of
bovine mastitis. Int J Mol Sci 2021, 22:3480.
28. Ibarra-Sánchez LA, Kong W, Lu T, Miller MJ: Efficacy of nisin
derivatives with improved biochemical characteristics, alone
and in combination with endolysin PlyP100 to control Listeria
monocytogenes in laboratory-scale Queso Fresco. Food
Microbiol 2021, 94:103668.
Current Opinion in Biotechnology 2024, 86:103084
29. Guo L, Wang C, Broos J, Kuipers OP: Lipidated variants of the
antimicrobial peptide nisin produced via incorporation of
methionine analogs for click chemistry show improved
bioactivity. J Biol Chem 2023, 299:104845.
30. Acuña L, Corbalán N, Quintela-Baluja M, Barros-Velázquez J,
Bellomio A: Expression of the hybrid bacteriocin Ent35-MccV in
Lactococcus lactis and its use for controlling Listeria
monocytogenes and Escherichia coli in milk. Int Dairy J 2020,
104:104650.
31. Khan FM, Chen J-H, Zhang R, Liu B: A comprehensive review of
the applications of bacteriophage-derived endolysins for
foodborne bacterial pathogens and food safety: recent
advances, challenges, and future perspective. Front Microbiol
2023, 14:1259210.
32. Van Tassell ML, Ibarra-Sánchez LA, Hoepker GP, Miller MJ: Hot
topic: antilisterial activity by endolysin PlyP100 in fresh cheese.
J Dairy Sci 2017, 100:2482-2487.
33. Ibarra-Sánchez LA, Van Tassell ML, Miller MJ: Antimicrobial
behavior of phage endolysin PlyP100 and its synergy with nisin
to control Listeria monocytogenes in Queso Fresco. Food
Microbiol 2018, 72:128-134.
34. Kobylewski S, Jacobson MF: Toxicology of food dyes. Int J
Occup Environ Health 2012, 18:220-246.
35. Yang D, Park SY, Lee SY: Production of rainbow colorants by
metabolically engineered Escherichia coli. Adv Sci 2021,
8:e2100743.
36. Seo S-O, Jin Y-S: Next-generation genetic and fermentation
technologies for safe and sustainable production of food
ingredients: colors and flavorings. Annu Rev Food Sci Technol
2022, 13:463-488.
37. Yang D, Jang WD, Lee SY: Production of carminic acid by
metabolically engineered Escherichia coli. J Am Chem Soc
2021, 143:5364-5377.
38. Thomsen PT, Meramo S, Ninivaggi L, Pasutto E, Babaei M, Avila-
• Neto PM, Pastor MC, Sabri P, Rago D, Parekh TU, et al.: Beet red
food colourant can be produced more sustainably with
engineered Yarrowia lipolytica. Nat Microbiol 2023, 8:2290-2303.
This paper is of interest because of the authors’ use of a ‘non-con­
ventional’ yeast strain to enhance production. In addition to strain en­
gineering, they describe different substrate sources that can be used,
and they performed a techno-economic analysis to evaluate the in­
dustrial potential of their strain.
39. NTP (National Toxicology Program). 2021. Report on Carcinogens,
Fifteenth Edition. Research Triangle Park, NC: U.S. Department of
Health and Human Services, Public Health Service. https://ntp.
niehs.nih.gov/go/roc15%20DOI:%20https:/doi.org/10.22427/NTP-
OTHER-1003.
40. Lee Y-G, Kim B-Y, Bae J-M, Wang Y, Jin Y-S: Genome-edited
Saccharomyces cerevisiae strains for improving quality, safety,
and flavor of fermented foods. Food Microbiol 2022, 104:103971.
41. Day L, Cakebread JA, Loveday SM: Food proteins from animals
and plants: differences in the nutritional and functional
properties. Trends Food Sci Technol 2022, 119:428-442.
42. Aro N, Ercili-Cura D, Andberg M, Silventoinen P, Lille M, Hosia W,
•• Nordlund E, Landowski CP: Production of bovine beta-
lactoglobulin and hen egg ovalbumin by Trichoderma reesei
using precision fermentation technology and testing of their
techno-functional properties. Food Res Int 2023, 163:112131.
This study is an excellent example of academic research regarding
expression of food proteins by filamentous fungi. Of special note is that
the authors conducted a comparison of functional properties between
the proteins from their engineered strain and those from animals.
43. Geistlinger T., Jhala R., Krueger K.P., Pamesh B.: Food products
comprising milk proteins and non-animal proteins, and methods of
producing the same. US Patent 11,771,104 B2; 2023.
44. Anchel D.: Methods and compositions for egg white protein
production. US Patent 11,518, 797 B2; 2022.
www.sciencedirect.com
 Precision fermentation for improving food quality Hilgendorf et al.
45. Conorado R.J., Gao A.H.: Integration of fermentation and
gasification. US Patent 11,097,967 B2; 2021.
46. Holmström S., Pitkänen J.-P.: Strains and processes for single cell
protein or biomass production. WO 2021/084159 A1; 2021.
47. Dyson L., Reed J., Geller J., Hande S.: Microbial conversion of CO2
and other C1 substrates to protein and meat substitute products.
US Patent 2020/0216797 A1; 2020.
www.sciencedirect.com
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48. Bachleitner S, Ata Ö, Mattanovich D: The potential of CO2-based
• production cycles in biotechnology to fight the climate crisis.
Nat Commun 2023, 14:6978.
This is an interesting review on the potential for carbon dioxide to be
used as a substrate for precision fermentation. The authors bring up
compelling examples of microorganisms fixing carbon dioxide and
provide thought-provoking commentary on where this technology might
take us.
Current Opinion in Biotechnology 2024, 86:103084