Trends in Food Science & Technology 16 (2005) 4–11

Review

Microbial ecology of
cereal fermentations Introduction
When considering the multitude of foods made from
cereals one has to recognise that their greater part has been
Walter P. Hammes*, Markus subjected to fermentation processes taking place at least at
one step of their generation. In general, fermentation is a
J. Brandt, Kerstin L. Francis, process that proceeds under the influence of activities
exerted by enzymes and/or microorganisms. In fact, both
Julia Rosenheim, Michael activities are important in cereal fermentation (Hammes &
Gänzle, 1998), but in the context of this treatise neither plain
F.H. Seitter and Stephanie enzymatic processes are considered, nor those numerous
A. Vogelmann &
fermentations in which cereals are mixed with substantial
amounts of additional substrates, such as legumes or milk
Institut für Lebensmitteltechnologie, Fachgebiet (e.g. soy sauce and miso in south-east Asia; idli and dosa in
Allgemeine Lebensmitteltechnologie India; kishk in the Middle East (Campbell-Platt, 1987)).
und-Mikrobiologie, Universität Hohenheim, Like with any other fermentation process the understanding
Garbenstr. 28, 70599 Stuttgart, Germany of the microbial ecology of cereal fermentations needs the
(Tel.: C49 711 459 2305; fax: C49 711 459 4199; knowledge of the fermentation substrates, i.e. the grains or
e-mail: hammeswp@uni-hohenheim.de) seeds of the various cereal plants, as well as the products
obtained thereof. This framework includes the characteris-
Cereals are globally number one as food crops as well as ation of the microbial associations and ecological factors,
substrates for fermentation. Well known products are which govern the fermentation process and arise from the
beer, sake, spirits, malt vinegar, and baked goods made nature of the cereal substrate. In cereal fermentations
from doughs leavened by yeasts or sourdough. Fermenta- endogenous enzymes, bacteria, yeast and moulds play roles
tion processes are enabled by technological measures that either singularly or in combination, and contribute to the
act on the metabolically resting grains and direct creation of a great variety of products.
ecological factors controlling the activity of lactic acid In Table 1 the phylogenetic position and relationship
bacteria and yeasts. Fermentable substrates originate from between cereals are depicted.
endogenous or added hydrolytic enzyme activities. Included in this group of crops are species that belong to
Examples of their management are malting, koji technol- the family of Poaceae (formerly Gramineae). In addition
ogy, addition of enzymes from external sources and so-named pseudo-cereals are of more or less importance in
sourdough, which stands on the origin of all fermentation. certain geographic regions. Their composition is similar to
When sourdough is continuously propagated under the that of cereals especially with regard to the starch content.
conditions applied in bakery practice, a stable association
The knowledge of the phylogenetic relationship is not only
of only few species of lactic acid bacteria (LAB) and
important for breeders but also for selecting appropriate
cereals for fabrication of foods for persons that suffer from
yeasts achieve dominance and ensure a controlled
food component intolerance, such as allergy or celiac
process. The variation of the ecological parameters acting
disease. The bioactive compound responsible for the latter
on the microbial association such as the nature of cereal,
disease is exclusively found in the subfamily Poideae.
temperature, size of inoculum, and length of propagation
Cereals have been, and still are, the most important food
intervals leads in each case to a characteristic species
crop. Their cultivation dates back to 7000 B.C. for wheat
association, thus explaining that altogether 46 LAB
and barley, 4500 B.C. for rice and maize, 4000 B.C. for
species and 13 yeast species have been identified as
millet and sorghum, 400 B.C. for rye, and 100 B.C. for oats.
sourdough specific.
Triticale is the only cereal (since 1930) of our time (McGee,
1984). At present (FAO, 2002) the total global production of
food crops amounts to roughly 3.6 billion tonnes, and 60%
* Corresponding author. thereof are cereals. In developed countries up to 70% of
0924-2244/$ - see front matter q 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tifs.2004.02.010
 W.P. Hammes et al. / Trends in Food Science & Technology 16 (2005) 4–11 5

Table 1. Phylogenetic relationship between cereals and pseudo-cereals

the cereal harvest is used as animal feed. The remaining part – Saccharification by use of koji (Yoshizawa, 1977) prior
plus nearly all cereals in developing countries are used for to alcoholic fermentation or producing sweetened rice
human nutrition. The greater part thereof is subjected to (Wang & Hesseltine, 1970).
fermentation and its volume surpasses by far that of all other – Preservation, which relies mainly on acidification and/or
fermented foods such as those made from milk (cheese and alcohol production (Hammes & Tichaczek, 1994).
yoghurt), meat (fermented sausages), fish (fish sauce), soy – Enhancing food safety by inhibition of pathogens,
(soy sauce), olives (fermented), or cabbage (sauerkraut). e.g. Burkholderia gladioli that had caused Bongkrek
It is assumed that initially porridges were consumed that poisoning in products made from pre-soaked corn (Meng
were made of pounded or ground grains, which were later et al., 1988), Staphylococcus aureus and Bacillus cereus
baked, yielding still unfermented flat bread. These products causing enterotoxicoses.
have long been, and still are, in use. Porridges, more or less – Improving the nutritive value by removing antinutritive
liquid, had also a tradition as fermented food in Europe compounds (e.g. phytate, enzyme inhibitors, polyphe-
(Fenton, 1974), and numerous examples can still be found nols, tannins), and enhancing the bioavailability of
outside of the western world (Nout & Rombouts, 2000). It is components by, e.g. affecting physio-chemical properties
just a short way to boiling or baking these fermented of starch and associations of fibre constituents with
products and, thus, already at the fourth millennium B.C. vitamins, minerals or proteins (Chavan & Kadam, 1989).
leavened bread was produced in Egypt. Remarkably, this – Removal of undesired compounds such as mycotoxins
first use of cereal fermentation for bread making was tightly (FAO, 1999; Nakazato et al., 1990; Nout, 1994),
related to alcohol production, as leftovers of gruels, endogenous toxins, cyanogenic compounds, flatulence
porridge, dough, or bread after suspending in water will producing carbohydrates.
spontaneously undergo lactic acid and alcoholic fermenta- – Reducing energy required for cooking.
tion. In such a way the history of beer production runs – Achieving the condition of bakeability as it is
parallel of that of leavened bread. required for producing leavened rye bread. (Hammes &
Gänzle, 1998).
Aims of cereal fermentations
A multitude of fermented products made from cereals In the course of the fermentation process the arising
have been created in the history of human nutrition. In their products are characterised by quite different properties and
production, the fermentation steps aim to achieve the uses. They serve for example to the following:
following:
– Leavened baked goods obtained from sourdough and/or
– Conditioning for wet milling by steeping of maize yeast leavened dough.
(Johnson, 2000) and wild rice (Oelke & Boedicker, – African lactic acid fermented gruels such as ogi obtained
2000). from cereals or fufu from cassava, which are further heat
– Affecting sensory properties (aroma, taste, colour, processed to obtain porridges and dumplings,
texture). respectively.
6 W.P. Hammes et al. / Trends in Food Science & Technology 16 (2005) 4–11

– Alcoholic drinks such as beer, sake and spirits. carbohydrates, microorganisms are initially well supplied.
– Acid fermented drinks such as boza (Turkey), Berliner The concentrations of free total sugars in cereal grains range
Weibe (Germany), kwass (Russia), or mahewu (South between 0.5 and 3%. Therein sucrose is the major
Africa). These processes occur commonly in compound (Shelton & Lee, 2000), representing a percentage
combination with alcoholic fermentation. of O50%. Especially through the activities of b-amylase
– Vinegar, obtained through a secondary aerobic fermenta- present in the endosperm, the maltose generation in dough
tion of, e.g. alcoholic fermented rice (East Asia), or from proceeds efficiently after the addition of water to flour. The
beer without added hops (Europe). endogenous hydrolytic activities provide a more or less
– Colorants such as Angkak obtained by fermenting rice strong continuous further supply with free sugars.
grains with Monascus purpureus. Similarly, peptides and amino acids become available
through proteolytic activities. As shown by Prieto, Collar,
and Benedito de Barber (1990), the content of total free
amino acids increases by 64% in the course of 15 min
Basics of cereal fermentations
mixing of an unfermented wheat dough.
The stored grains of cereals are metabolically in a resting
state, which is primarily controlled by low water activity The mineral content of grains is generally sufficient for
(aw%0.6, 14% moisture). In this state the constituents are microbial growth but differs in the various fractions
not available for microorganisms, and the endogenous obtained after milling (Betschart, 1988). It is strongly
enzymes are inactive. Fermentation processes will be decreased in the white flour and increased in the germ and
enabled under the influence of technological measures bran fractions. For example, manganese as an important
including addition of water, comminution by milling, and growth factor of LAB occurs in whole wheat, white flour,
controlled management of microorganisms and enzyme wheat germ, and wheat bran at concentrations of 4.6, 0.7,
activities. It is especially the addition of water that affects 13.7, and 6.4–11.9 mg/100 g, respectively. The minerals of
the ecological factors dramatically. After the water activity the grain are not readily available for microorganisms as
increases by water absorption, a reduction of the redox they are complexed with phytate. However, at pH values of
potential takes place by respiration, as well as a drop of pH !5.5 the endogenous grain phytase hydrolyses phytate and
by respiration and fermentation, whereupon substrates minerals are released from the complex. Therefore, a
become available from (i) endogenous hydrolytic activities limitation in minerals may occur only at starting a
(e.g. amylolysis, proteolysis and lipolysis) and (ii) physio- spontaneous fermentation. In processes as exemplified by
logical activities of deliberately added or contaminating sourdough propagation, the addition of sourdough to the
microorganisms. These events cause a continuous change of bread dough lowers the pH and, thus, ensures that
the ecological state in the cereal matrix, which is evident, phytase activity is sufficient and no need for physiological
e.g. in sourdough (Hammes & Gänzle, 1998). microbial activity exists (Fretzdorff & Brümmer, 1993;
Cereal fermentation processes are affected by character- Tangkongchitr, Seib, & Hoseney, 1982). The concentration
istic variables, the control of which is the basis of all of phytate in the various cereals ranges between 0.2 and
technological measures that are used to obtain the various 1.35%, and again is strongly increased in the bran fraction.
products at a defined quality. These variables include the As phytate develops a high buffering capacity, the degree of
following (Hammes & Gänzle, 1998): flour extraction affects the metabolic activity of LAB in
substrates such as doughs. Therein the formation of titrable
– Type of cereal determining the fermentable substrates, acids correlates with the phytate content.
nutrients, growth factors, minerals, buffering capacity,
Inhibitors in cereals exert a selective effect on microbial
and efficacy of growth inhibiting principles.
growth. Known compounds are purothionins and complex-
– Water content.
ing compounds that interfere with the hydrolytic activities
– Degree and moment of comminution of the grains,
of the organisms or the availability of growth factors
i.e. before or after soaking or fermentation.
(Wrigley & Bietz, 1988). Little is known to what extent
– Duration and temperature of fermentation.
these factors determine the development of a specific
– Components added to the fermenting substrate, such as
sugar, salt, hops and oxygen. fermentation association, which can be shown to become
– Source of amylolytic activities that are required to gain established, for example, in sourdoughs prepared from
fermentable sugars from starch or even other different types or fractions of cereals (see below).
polysaccharides. The addition of water to cereals usually ensures optimum
water activity for fermenting microorganisms. The ‘driest’
Among these variables, the type of cereal plays a key fermenting substrates are traditional sourdoughs, which
role. It affects the amount and quality of carbohydrates as are commonly adjusted to dough yields [(mass(water)C
primary fermentation substrates, nitrogen sources, growth mass(flour))/mass(flour)!100] ranging between 160 and
factors such as vitamins, minerals, buffering capacity, and 220, corresponding to aw values of 0.965 and 0.980,
the efficacy of growth inhibitors. With regard to fermentable respectively. Clearly, the lower value is already in
 W.P. Hammes et al. / Trends in Food Science & Technology 16 (2005) 4–11 7

the stress range for LAB, and optimum values are a beneficial effect on whisky flavour. The LAB species
approached with increasing dough yields. involved are compiled in Fig. 1.
A LAB-yeast mixed fermentation takes also place in
certain types of acid beers, such as the Belgian Gueuze
Categories of fermentation technologies (Verachtert & Debourg, 1995) or Rodenbach-types or
The management of hydrolytic activities needed to the Berliner Weibbier. Of more general importance is the
obtain the fermentable carbohydrates requires specific controlled use of thermophilic lactobacilli to perform a
technologies, which have evolved in history and have biological acidification, which has technological advantages
different regional importance. Four basic technologies can as it improves the sensory quality of beer with regard to
be identified, namely flavour, colour and foam stability. One modern method is
the acidification of an aliquot of wort. It is then used to
(i) Malting, i.e. the management of endogenous activities.
lower the pH of the wort to 5.2 before boiling and/or that of
(ii) Koji technology, i.e. the use of physiological fungal
the mash to pH 5.5–5.6.
activities.
In the packaged beer microbial growth means spoilage
(iii) Use of hydrolytic activities originating from external
and, therefore, contamination has to be prevented. In
enzyme sources, e.g. from fungi, bacteria, plants or
addition the hop added to mash before boiling exerts an
human saliva.
antibacterial effect. Certain resistant organisms however
(iv) Dough (batter or gruel) fermentation.
exist and may cause spoilage. Among these LAB are of
special importance (Back, 1994).

Products from malt

In Fig. 1, the scheme of production of beer and whisky Products from koji
from grains subjected to a malting process is shown. Whisky The use of the physiological hydrolytic activities of
is one example of a great variety of spirits, which are molds to achieve the saccharification of starch has
obtained by distillation of a yeast-fermented wort (or mash). evolved in East Asia and is known as koji technology.
In addition to distillation, specific differences between From there it spread also to the western world and is
whisky and beer production exist in the process design and used for production of soy sauce and condiments on a
in the fermentation events. Whereas in beer brewing wort is cereal basis. The fermentation is a solid phase process
boiled and, thus, microorganisms are killed, for whisky and well-known products are sweet rice in China and
production yeasts (Saccharomyces cerevisiae) are added to rice wine. One example is the Japanese sake, whose
the unboiled wort. Therefore, the soluble hydrolytic production process is shown in Fig. 2. This scheme
activities are retained and contribute to a maximized provides also an example for a process involving starch
ethanol yield. Furthermore, LAB grow spontaneously and gelatinisation before fermentation. Steamed polished rice
acidify the wort during that ‘mixed’ fermentation step is used to prepare the inoculum, called tane koji. In
(van Beek & Priest, 2002). This practice is said to have Japanese industrial practice selected strains of Aspergillus

Fig. 1. Use of malt for production of beer and whisky. Modifications specific of the whiskey production are shown in the shadowed area and the
process flow is indicated by dotted lines.
8 W.P. Hammes et al. / Trends in Food Science & Technology 16 (2005) 4–11

Fig. 2. Application of koji in the production of sake (Yoshizawa & Ishikawa, 1989).

oryzae are propagated, whereas in other countries such as Products from use of hydrolytic enzymes originating
China, various indigenous Mucorales are in use. A seed from external sources
mash, called moto, is then prepared by inoculation of The use of hydrolytic enzymes from external sources is
steamed rice with tane koji. Upon diluting with water, common practice in industrial ethanol production (Senn &
sake yeast (S. cerevisiae) is added and lactic acid, or Pieper, 1996), and has also a tradition in brewing chicha,
traditionally LAB, are used to achieve controlled which is a type of South American beer produced by making
acidification. Katagiri, Kitahara, and Fukami (1934) use of diastase originating from human saliva (FAO, 1999).
identified in moto Lactobacillus sakei, Lactobacillus
plantarum, and Leuconostoc mesenteroides. In this Products from fermented dough
environment the yeast is especially protected and is The concerted activity of hydrolytic activities of the
able to form ethanol up to a concentration of 20%. Moto grain and microorganisms (LAB and yeasts) is the origin of
is used to inoculate the main mash, called moromi, all cereal fermentations and is best represented by the
which ferments over three succeeding steps by feeding traditional sourdough fermentation. A basic scheme of
steamed rice as new substrate. The finally resulting sake dough fermentation for production of baked goods is
may spoil and turns then in so called hiochi. From this depicted in Fig. 3. The process requires comminuted grains
spoiled product Kitahara, Kaneko, and Goto (1957) or fractions thereof that have not been heat treated before
isolated Leuconostoc mesenteroides, Lactobacillus and still possess the hydrolytic activities. By addition of
fermentum, Lactobacillus homohiochii, and, most abun- water, contaminating microorganisms will become
dant, Lactobacillus heterohiochii, which is identical with metabolically active, multiply and, at extended incubation,
Lactobacillus fructivorans. the most competitive organisms will inevitably dominate

Fig. 3. Basic scheme of dough fermentation for the production of baked goods.
 W.P. Hammes et al. / Trends in Food Science & Technology 16 (2005) 4–11 9

the process. These will always be LAB and yeasts. This type Table 2. Yeasts isolated from and adapted to doughs
of processing is still the basic practice for preparing
Species Synonyms
so-named predoughs. The only modification rests in
addition of baker’s yeast when preparing the dough. The Candida boidinii
Candida glabrata Torulopsis glabrata
more often the fermented product is used as an inoculum for Candida humilis Candida milleri
a succeeding fermentation run the greater becomes the Candida parapsilosis
adaptation of the microbial association to the process. Candida stellata Torulopsis stellata
Indeed, in continuously propagated doughs a few strains Debaryomyces hansenii Torulopsis candida, Candida
may prevail for years (Böcker, Vogel, & Hammes, 1990). famata
Dekkera bruxellensis Brettanomyces custersii
The continuous propagation results in so-called type I Galactomyces geotrichum Geotrichum candidum
doughs, which fulfil all requirements needed to obtain baked Issatchenkia orientalis Candida krusei
goods such as bread when added in the appropriate ratio to Kluyveromyces marxianus
the bread dough. They recieve the acidity from the Pichia anomala Candida pelliculosa, Hansenula
metabolism of LAB, and LAB and yeasts together provide anomala
Pichia fermentans Candida lambica
the gas formation capacity, development of flavour, and Pichia ohmeri
principles acting on texture of the crumb and the Pichia subpelliculosa Hansenula subpelliculosa
nutritional value. Pichia minuta var. minuta Hansenula minuta
A disadvantage of this traditional sourdough propagation Saccharomyces bayanus Saccharomyces inusitatus
process is, that they are time and labour consuming (e.g. in Saccharomyces cerevisiae Saccharomyces fructuum
Saccharomyces exiguus Torulopsis holmii, Candida
rye bread 24 h, up to three propagation steps), and therefore, holmii, Saccharomyces minor
more convenient one-stage processes have been established. Saccharomyces kluyveri
These ensure that all ingredients can be mixed together, and Saccharomyces servazzi
within a short time the baking condition of the dough is Saccharomycopsis fibuligera Endomyces fibuliger
achieved. In these so-called type II doughs the leavening Saturnispora saitoi Pichia saitoi
Torulaspora delbrueckii Torulopsis colliculosa, Candida
capacity needs, however, to be achieved by addition of colliculosa, Saccharomyces
baker’s yeast. The ecological conditions of the production rosei, Saccharomyces del-
of inocula differ greatly from those described for type I brueckii, Saccharomyces incon-
doughs and, therefore, usually species of different taxons are spicuous
employed that are adapted to high acid tolerance and often Torulaspora pretoriensis Saccharomyces pretoriensis
affect the sensory profile of the baked goods recognisable The fermenting sourdough specific species are printed in bold.
for the gourmet.
goods when occurring at high numbers. In Table 2 well
Microbial associations in sourdough adapted and frequently isolated sourdough specific species
The LAB species characteristic for the various types of are printed in bold and synonyms are indicated. Yeasts in
sourdough are subject of the papers of Ehrmann and Vogel doughs may originate from the flour or the environment in
and De Vuyst and Neysens of this issue. We counted from the bakery. Truly adapted species are characteristic for type
published work a number of 46 LAB species, the majority of I doughs, and Candida humilis (originally described by
which belongs to the genus Lactobacillus (30 species). Sugihara, Kline, and Miller (1971) as Candida holmii) is of
When all types of cereal fermentations are considered more superior importance therein. The predominant occurrence of
than half of the 80 recognised Lactobacillus species other species depends strongly on the condition of dough
(Hammes & Hertel, 2004) occur in association with cereal propagation. It was shown by Meroth, Hammes, and Hertel
fermentation. Furthermore it is of interest that 15 Lacto- (2003) and Meroth, Walter, Hertel, Brandt, and Hammes
bacillus species known to occur in sourdough are also (2003) that, under otherwise identical conditions, at 25 8C
known as inhabitants of the intestines of humans and and propagation cycles of 12 h (Batch A), C. humilis
animals. For example L. acidophilus was found in humans, (together with L. sanfranciscensis and L. mindensis)
swine, poultry, cattle and horse and L. reuteri in the same becomes a dominant yeast in sourdough, whereas at 30 8C
organisms, as well as in mouse and hamster. Remarkably, and 24 h cycles (Batch B) S. cerevisiae (together with
no other habitat is known for Lactobacillus sanfranciscensis Lactobacillus crispatus, Lactobacillus frumenti and
as the most characteristic sourdough LAB. As LAB in type I Lactobcillus pontis) achieved dominance. Furthermore, at
doughs are obligately heterofermentative they contribute 40 8C (Batch C), a shift to the more thermophilic species
decisively to gas production (Hammes & Gänzle, 1998). Candida glabrata and Issatchenkia orientalis (but also S.
Numerous yeasts have been isolated from sourdoughs cerevisiae) was observed.
(see Table 2) but only part of them can be considered to play In addition to the effects on the ecological factors con-
a substantial role in fermentation processes. For example, trolled by the process conditions, the nature of the cereals
non-fermenting species may be just ubiquitous contami- has a profound effect on the establishment of a charac-
nants although they may affect the flavour of the baked teristic fermentation association. We have propagated
10 W.P. Hammes et al. / Trends in Food Science & Technology 16 (2005) 4–11

(unpublished results) according to the conditions described Hammes, W. P., & Tichaczek, P. S. (1994). The potential of lactic
above (Batch B) doughs from seven cereals and three acid bacteria for the production of safe and wholesome food.
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Katagiri, H., Kitahara, K., & Fukami, K. (1934). The characteristics of
Conclusion the lactic acid bacteria isolated from moto, yeast mashes for sake
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156–157.
associations in the fermentation of the various cereals. Kitahara, K., Kaneko, T., & Goto, O. (1957). Taxonomic studies on
It can be expected that better-controlled processes and the hiochi-bacteria, specific saprophytes of sake II. Identification
greater sensory variety or standardization of baked goods and classification of hiochi-bacteria. The Journal of General and
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