Yeasts in foods and beverages: impact on product quality
and safety
Graham H Fleet
The role of yeasts in food and beverage production extends
beyond the well-known bread, beer and wine fermentations.
Molecular analytical technologies have led to a major revision of
yeast taxonomy, and have facilitated the ecological study of
yeasts in many other products. The mechanisms by which yeasts
grow in these ecosystems and impact on product quality can
now be studied at the level of gene expression. Their growth and
metabolic activities are moderated by a network of strain and
species interactions, including interactions with bacteria and
other fungi. Some yeasts have been developed as agents for the
biocontrol of food spoilage fungi, and others are being
considered as novel probiotic organisms. The association of
yeasts with opportunistic infections and other adverse
responses in humans raises new issues in the field of food safety.
Addresses
School of Chemical Sciences and Engineering, The University of
New South Wales, Sydney, New South Wales, Australia
Corresponding author: Fleet, Graham H (g.fleet@unsw.edu.au)
Current Opinion in Biotechnology 2007, 18:170–175
This review comes from a themed issue on
Food biotechnology
Edited by Christophe Lacroix and Beat Mollet
Available online 1st February 2007
0958-1669/$ – see front matter
# 2007 Elsevier Ltd. All rights reserved.
DOI 10.1016/j.copbio.2007.01.010
Introduction
The impact of yeasts on the production, quality and safety
of foods and beverages is intimately linked to their
ecology and biological activities. Recent advances in
understanding the taxonomy, ecology, physiology, bio-
chemistry and molecular biology of yeasts have stimu-
lated increased interest in their presence and significance
in foods and beverages. This has led to a deeper under-
standing of their roles in the fermentation of established
products, such as bread, beer and wine, and greater
awareness of their roles in the fermentation processes
associated with many other products. As the food industry
develops new products and processes, yeasts present new
challenges for their control and exploitation. Food safety
and the linkage between diet and health are issues of
major concern to the modern consumer, and yeasts have
emerging consequences in this context. On the positive
side, there is increasing interest in using yeasts as novel
Current Opinion in Biotechnology 2007, 18:170–175
probiotic and biocontrol agents, and for the nutrient for-
tification of foods. On the negative side, food-associated
yeasts could be an under-estimated source of infections
and other adverse health responses in humans.
Two books, entirely devoted to the occurrence and
significance of yeasts in foods and beverages, have
recently been published [1,2] and another includes
several chapters on food spoilage yeasts [3]. These pub-
lications demonstrate the expanding academic and indus-
trial interest in the field. This article reviews recent
developments in understanding the ecology and biology
of yeasts in foods and beverages and discusses how these
impact on product quality and safety.
New analytical tools
The ability to isolate, enumerate and identify yeasts to
genus, species and strain levels is fundamental to under-
standing their occurrence and significance in foods and
beverages. Although cultural procedures remain basic to
these needs, molecular methods are making the study of
yeast ecology much more attractive and convenient than
ever before [4,5].
Yeast taxonomy and species identification
Whereas the identification of new yeast isolates once
required the laborious completion of 80 to 100 morpho-
logical, biochemical and physiological analyses, this task is
now quickly achieved by DNA sequencing. The DNA
sequences of the genes encoding the D1/D2 domain of the
large (26S) subunit of ribosomal RNA are known for all
yeast species, and the sequence of the ITS1-ITS2 region of
rRNA, as well as other genes, is known for many. These
sequence–phylogenetic data have led to a complete revi-
sion of yeast taxonomy, and the description of many new
genera and species [6]. Although sequencing of ribosomal
genes is now the accepted method for yeast identification,
restriction fragment length polymorphism (RFLP) analysis
of the ITS1-ITS2 region is a less expensive, faster alterna-
tive, and databases containing the results of such analyses
have been established for food yeasts [5].
Nucleic acid probes and real-time PCR detection methods
have been described for some species, such as Saccharo-
myces cerevisiae, Brettanomyces bruxellensis and Zygosacchar-
omyces bailii [4,5,7], and a novel probe-flow cytometric
assay has been reported for various Candida species [8].
Strain differentiation
The distinctive character of many breads, beers and wines
can be linked to particular strains of S. cerevisiae used in
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the fermentation [9]. Consequently, differentiation of
yeasts at the subspecies level is an important require-
ment. Molecular methods developed for this purpose
include pulsed-field gel electrophoresis (PFGE) of chro-
mosomal DNA and PCR-based methods such as random
amplification of polymorphic DNA (RAPD), amplified
fragment length polymorphism (AFLP), RFLP, and pro-
filing of microsatellite DNA. A simpler, faster method is
based on RFLP analysis of mitochondrial DNA, where no
PCR amplification of DNA is required [4,5,10]. These
methods are not only useful for quality assurance typing
of yeast starter cultures and spoilage species, but they
have been used to reveal the ecological complexity of the
yeast flora associated with many food and beverage fer-
mentations. For example, it is now known that the
fermentation of wine, cheese, meat sausages and other
products not only involves the successional contributions
from many different species of yeast, but successional
growth of numerous strains within each species also
occurs [11,12].
Culture-independent analysis
Most branches of microbial ecology now accept that viable
but non-culturable species occur in many habitats, includ-
ing foods and beverages. Detection of these organisms
requires extraction and analysis of the habitat DNA. One
approach that is finding increasing application is PCR in
conjunction with denaturing gradient gel electrophoresis
(DGGE) or temperature gradient gel electrophoresis
(TGGE). Total DNA is extracted from the food, and yeast
DNA is specifically amplified using PCR and primers
targeting regions of rDNA. The yeast DNA is then
resolved into amplicons for individual species by DGGE
or TGGE. These amplicons are extracted from the gel and
their species identity determined through sequence
analysis. PCR-DGGE/TGGE has been applied to analyse
the yeast communities associated with grapes, wine, sour-
dough, cocoa bean, coffee bean and meat sausage fermen-
tations [4,5,13,14,15]. There is good agreement in the
results obtained by cultural and PCR-DGGE/TGGE
methods, although in some cases species that were not
identified by agar culture were recovered by PCR-DGGE
— suggesting the presence of non-culturable flora. How-
ever, the reverse also occurs, where PCR-DGGE has not
detected yeasts that were isolated by culture. Many factors
affect the performance of PCR-DGGE/TGGE analyses
and further research is required to understand and optimize
the assay conditions [4,13].
Molecular understanding of the yeast
response
As yeasts grow in foods and beverages, they utilize carbon
and nitrogen substrates and generate a vast array of
volatile and non-volatile metabolites that determine
the chemosensory properties of the product and its appeal
to the consumer. Some yeasts produce extracellular pro-
teases, lipases, amylases and pectinases that also impact
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Yeasts in foods and beverages Fleet 171
on product flavour and texture. The biochemistry of these
reactions and their linkage to product quality are gener-
ally well known [16]. Now, genomic studies using
sequence, DNA array, and proteomic analyses enable
the linkage of these responses to the expression and
regulation of individual genes [17]. Only a few such
studies have been performed with food and beverage
yeasts, and these have yielded interesting new insights.
For example, during wine and beer fermentations,
S. cerevisiae exhibits sequential expression and regulation
of many genes associated with carbon, nitrogen and sulfur
metabolism, as well as other genes required to tolerate
stresses such as high sugar concentration, low pH, ethanol
and nutrient deficiency [17,18,19]. Genomic analyses
also give molecular explanations of the remarkable
tolerance of some yeasts to the extremes of high salt and
sugar contents in some foods (e.g. Debaryomyces hansenii in
cheese brines, Zygosaccharomyces rouxii in sugar syrups and
fruit juice concentrates), and to organic acid preservatives
in other foods (e.g. Z. bailii in salad dressings and soft
drinks) [20].
Beyond brewing, baking and wine yeasts
Although research on the contribution of S. cerevisiae to
beer, bread and wine fermentations continues to be a
focus, there is expanding interest in the role of yeasts in
other products [12].
It is now well recognized that yeasts make important
contributions to the process of cheese maturation, where
various strains of D. hansenii, Yarrowia lipolytica, Kluyver-
omyces marxianus and S. cerevisiae frequently grow to high
populations. They contribute to the development of
cheese flavour and texture through proteolysis, lipolysis,
utilization of lactic acid, fermentation of lactose and auto-
lysis of their biomass [21]. In a similar way, D. hansenii,
Y. lipolytica and various Candida species affect flavour,
texture and colour development in fermented salami style
sausages and country cured hams [15,22]. Many breads,
especially sour dough varieties, are still produced by
traditional fermentation processes where no commercial
strains of baker’s yeast are added. Although indigenous
strains of S. cerevisiae are prominent in many of these
fermentations, other yeasts are significant and include
Saccharomyces exiguus, Candida milleri, Candida humilis,
Candida krusei (Issatchenkia orientalis), Pichia anomala, Pichia
membranifaciens and Y. lipolyitica. These yeasts grow in
cooperation with lactic acid bacteria, giving distinctive
flavours to the final product [23].
High-value cash crops such as cocoa beans and coffee
beans also undergo processes that involve the action of
yeasts [24]. Coca beans must be fermented to generate
the precursors of chocolate flavour, and various species of
Saccharomyces, Hanseniaspora, Candida, Issatchenkia and
Pichia contribute to the process [14,25]. Coffee beans
are processed to remove pulp and other mucilaginous
Current Opinion in Biotechnology 2007, 18:170–175
172 Food biotechnology
materials that surround the seeds, and species of Candida,
Saccharomyces, Kluyveromyces, Saccharomycopsis, Hansenias-
pora, Pichia and Arxula have been associated with these
fermentations [26]. A vast array of traditional fermented
foods and beverages are produced in African, Asian and
South American countries from raw materials such as
maize, wheat, cassava, rice, soy beans and fruit. Fermen-
tation is essential in contributing to the quality, safety and
nutritional value of these products. Aspects of their
microbial ecology are just starting to emerge, and demon-
strate important contributions from numerous yeast
species [27,28].
Collectively, the ecological studies of yeasts in products
other than beer, bread and wine are providing the knowl-
edge base for developing a new generation of yeast starter
cultures, beyond S. cerevisiae.
Microbial interactions and biocontrol
Yeasts rarely occur in food and beverage ecosystems as
single cultures. Exceptions occur in highly processed
products where spoilage outbreaks by single, well-
adapted species are known: for example, Z. rouxii in high
sugar products [29].
Generally, most habitats are comprised of a mixture of
yeasts, bacteria, filamentous fungi and their viruses, and
product quality is determined by the interactive growth
and metabolic activity of the total microflora. Even within
yeasts themselves, there can be significant species and
strain interactions that impact on the population dynamics
of the ecosystem. The diversity and complexity of these
microbial interactions is just beginning to emerge
[11,30,31].
A network of yeast–yeast interactions occurs in most
ecosystems, and is observed in fermentations of wine,
cheese, meat, and cocoa beans. These interactions mani-
fest themselves as the successive growth and death of
different yeast species and strains within each species, as
the fermentation progresses. The mechanisms under-
lying these ecological shifts are numerous. Explanations
include the different rates of nutrient transport and
uptake by the different species and strains, their sensi-
tivities to metabolic end products (e.g. ethanol), and
responses to killer toxins [11]. Cell–cell interactions
might also occur through the production of quorum sen-
sing molecules [32] and unexplained spatial phenomena
[33]. Defining the metabolic outcomes of these inter-
actions and their impact on product quality remains a
greater challenge, as demonstrated by the interactive
effects of S. cerevisiae and Saccharomyces bayanus strains
on the chemical composition and flavour of wines [34].
Interactions between yeast and bacteria are often seen as
the inhibitory effects of yeasts on bacteria through etha-
nol production; however, the relationships are much
Current Opinion in Biotechnology 2007, 18:170–175
broader than this. The death and autolysis of yeast cells
releases vitamins and other nutrients that stimulate the
growth of important flavour-enhancing bacteria, such as
the malolactic bacteria in wine fermentations [11,31],
staphylolcocci, micrococci and brevibacteria during
cheese maturation [21], and lactic acid bacteria during
sour dough fermentations [23]. Ethanol, produced by
yeasts during cocoa bean fermentations, stimulates the
growth of acetic acid bacteria that oxidize the ethanol to
acetic acid. This acid is essential for killing the cocoa
beans (seeds) and triggering endogenous bean metab-
olism that generates the precursors of chocolate flavour
[24,25]. Some yeasts utilize the organic acids that occur in
cheeses, fruit products and salad dressings, causing an
increase in product pH and growth of spoilage and patho-
genic bacteria [30]. Some bacteria are antagonistic
towards yeasts. Excessive growth of lactic acid bacteria
and acetic acid bacteria on grapes produces acetic acid and
other substances that inhibit the growth of yeasts in grape
juice, causing stuck or sluggish wine fermentations and
loss of process efficiency [11,31].
Interactions between yeast and fungi have not been
widely studied, except in the context of biocontrol. Fun-
gal growth on wine grapes produces substances that
inhibit the growth of yeasts during grape juice fermenta-
tion [11]. By contrast, some yeasts improve the growth of
Penicillium spp. during the maturation of cheeses [35].
Several species within the genera Candida, Pichia, Metsch-
nikowia, Cryptococcus and Pseudozyma have strong antifun-
gal properties mediated through the production of lytic
enzymes, toxic proteins, toxic fatty acids and ethyl
acetate, and have potential for the biocontrol of fungi.
Commercial preparations of some species are now avail-
able for the pre- and post-harvest control of fruit, veg-
etable and grain spoilage fungi [36,37].
Yeasts and food safety
As part of daily life, humans consume large populations of
yeasts without adverse impact on their health. Unlike
bacteria and viruses, yeasts are rarely associated with
outbreaks of foodborne gastroenteritis, intoxications or
other infections. Nevertheless, caution is needed, and
further research on this topic is required [38].
Significant ‘lay’ literature connects the dietary intake of
yeasts with a range of gastrointestinal, respiratory, skin,
migraine and even psychiatric disorders. Overgrowth of
yeasts in the gastrointestinal tract might contribute to the
development of these disorders, but immune reactions to
yeast cell wall polysaccharides and responses to yeast-
produced amines and sulfur dioxide could also occur. The
connection between yeast, the human response and food
is largely based on dietary observations. If foods sus-
pected to contain yeasts or their products are removed
from the diet, the adverse responses disappear, but return
when such foods are reintroduced [38,39].
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Yeasts are not aggressive, infectious organisms, but some
species such as Candida albicans and Cryptococcus neoformans
are opportunistic pathogens that cause a range of muco-
cutaneous, cutaneous, respiratory, central nervous system
and organ infections, as well as general fungemia [40].
Individuals with weakened health and immune systems
are at greatest risk, and include cancer, AIDS and hospi-
talized patients, and those undergoing treatment with
immunosuppressive drugs, broad spectrum antibiotics
and radio- chemotherapies. The greater frequency of such
individuals in the community has led to increased reporting
of yeast infections. Moreover, an increasing number of
yeast species has been implicated, including many found in
foods (e.g. S. cerevisiae, C. krusei, C. famata, P. anomola,
Rhodotorula spp. [38,41]. Infections caused by S. cerevisiae
are notable because of its extensive use in the food indus-
try, and infections with this yeast have been reported in
immunocompetent individuals [42,43]. It is thought that
hospitalized patients become exposed to high levels of
yeasts through the biofilms they form on catheters and
other invasive devices, and that these yeasts probably
originate from the hands of hospital workers and the foods
brought into the hospital environment [38]. More research
is needed to establish stronger linkages between the role of
foods in contributing to yeast infections. Information is
needed on the survival and growth of yeasts throughout the
gastrointestinal system, the potential for yeasts to translo-
cate from the gastrointestinal tract to the blood system, and
the general occurrence of yeasts ‘in the hospital and health
care environments. The circumstances whereby a non-
pathogenic yeast, such as S. cerevisiae, becomes pathogenic
also require investigation.
Probiotic and other health benefits
Probiotics are viable microorganisms that are beneficial to
consumers when ingested in appropriate quantities.
Although certain species of lactic acid bacteria are pro-
minent as probiotic organisms, there is increasing interest
in yeasts as probiotics [38,44,45]. S. cerevisiae var bou-
lardii has been used for many years as an oral biother-
apeutic agent for treating a range of diarrheal disorders.
This species colonizes the intestinal tract where, in a
probiotic function, it combats diarrhoea-causing bacteria
[44,46]. Food carrier systems for this yeast need to be
developed for its commercial application as a probiotic,
but technical obstacles have been encountered. When
incorporated into some products, it caused gassy, etha-
nolic spoilage and off-flavours [47,48]. Of greater concern,
are reports of fungemia infections caused by S. boulardii
[42,43]. Other yeasts mentioned as potential probiotics
include D. hansenii, Kluy. marxianus, Y. lipolytica, I. orien-
talis, P. farinosa and P. anomala, but further research is
required [38]. Yeasts are increasingly used as probiotics
in the livestock and aquaculture industries [38].
Yeast products, principally derived from S. cerevisiae, have
been used for many years as ingredients and additives in
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Yeasts in foods and beverages Fleet 173
food processing. These products include flavourants,
enzymes, antioxidants, vitamins, colourants and polysac-
charides [49,50]. Three points are worthy of mention.
First, many of these products are prepared from yeast
cells after they have been processed by autolysis. Despite
its commercial significance, molecular understanding of
yeast autolysis is still very limited and more research is
needed to optimize this process [51,52]. Second, most
products are derived from S. cerevisiae. The yield and
range of products could be increased by screening for
their presence in other yeast species and strains, as
demonstrated for the vitamin folic acid [53], cell wall
polysaccharides [54] and autolysates [55]. Finally, there
remains undiscovered bioactivity and functionality in
yeast products. Whereas the glucan polysaccharides from
the walls of S. cerevisiae were originally valued for their
water-binding and rheological functionalities, it is now
recognized that they can stimulate the immune system,
lower serum cholesterol, exhibit antitumour activity, and
adsorb substances such as mycotoxins [38,49].
Conclusions
Advances in molecular technologies have provided new
analytical tools for studying the diversity and biological
activities of yeasts associated with food and beverage
production, although more research is still required on
the ecology and activities of yeasts in products other than
beer, bread and wine. The interactions between yeasts and
the ecosystems in which they occur provide another area
for future study; yeasts form interactions with other species
and strains, along with bacteria, other fungi, protozoans and
their viruses, but as yet these relationships remain poorly
described and understood. Interest in the public health
significance of yeasts in foods and beverages is also increas-
ing, in both positive and negative contexts. Again, we are
likely to see future developments in this regard.
Update
Debaryomyces hansenii is one of the most significant yeasts in
food and beverage production, and this is highlighted in a
recent review of its phylogeny, ecology, physiology, mol-
ecular biology and its biotechnological potential [56]. As
mentioned in the conclusion, yeast interactions between
themselves and with other organisms have implications for
food quality and safety, and further research is needed on
these topics. Aspects of yeast cell interactions have been
considered in a recent review that discusses their under-
lying molecular mechanisms, how they impact on growth
and survival and how they affect pathogenicity [57].
References and recommended reading
Papers of particular interest, published within the annual period of
review, have been highlighted as:
 of special interest
 of outstanding interest
1. Boekhout T, Robert V (Eds): Yeasts in Food. Beneficial and
 Detrimental Aspects. Behr’s Verlag; 2003.
Current Opinion in Biotechnology 2007, 18:170–175
174 Food biotechnology
Comprenhensive discussions of yeasts in foods and beverages — an
emphasis is placed on commodities.
2. Querol A, Fleet GH (Eds): Yeasts in Food and Beverages. Springer;
 2006.
Comprehensive discussions of yeasts in foods and beverages – emphasis
on ecology and biology of yeasts.
3. Blackburn C (Ed): Food Spoilage Microorganisms. CRC Press;
2006.
4. Beh AL, Fleet GH, Prakitchaiwattana C, Heard GM: Evaluation of
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Reviews and lists recent literature on molecular methods used for the
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Outlines the most recent changes to yeast classification and taxonomy,
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Good, basic introduction to yeast genomics and its applications in food
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Good, general review of the biology and practical significance of the
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