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3
T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013)
Introduction
Kefir is a specific dairy product from the group
of fermented milks where lactose hydrolysis during
fermentation occurs with the simultaneous action of
bacteria and yeasts contained in kefir grains. Althou-
gh lactic acid is a main metabolite, due to yeast acti-
vity kefir also contains significant quantities of CO
2
and variable alcohol quantity. Because of associative
growth of various microbial species in kefir, during
fermentation other organic compounds are formed,
like bioactive peptides, exopolysaccharides, bacteri-
ocins which are presumed to have a probiotic effect
on human health (Kosikowski and Mistry, 1999;
Stepaniak and Fetliński, 2003; Lopitz-Otsoa et
al., 2006; Hong et al., 2010).
The microbial population of kefir grains con-
sists of numerous species of lactic acid bacteria,
acetic acid bacteria, yeasts and filamentous moulds
which develop a complex symbiotic relationship
within a microbial community (Marshall et al.,
*Corresponding author/Dopisni autor: Phone/Tel.: +385 (0)1 239 3646; E-mail: tpogacic@agr.hr
Review - Pregledni rad UDK: 637.146.21
Microbiota of kefir grains
Tomislav Pogačić*, Sanja Šinko, Šimun Zamberlin, Dubravka Samaržija
Department of Dairy Science, Faculty of Agriculture University of Zagreb,
Svetošimunska 25, 10000 Zagreb, Croatia
Received - Prispjelo: 07.12.2012.
Accepted - Prihvaćeno: 15.02.2013.
Summary
Kefir grains represent the unique microbial community consisting of bacteria, yeasts, and some-
times filamentous moulds creating complex symbiotic community. The complexity of their physical
and microbial structures is the reason that kefir grains are still not unequivocally elucidated. Micro-
biota of kefir grains has been studied using many microbiological and molecular approaches. The
development of metagenomics, based on the identification without cultivation, is opening new pos-
sibilities for identification of previously non-isolated and non-identified microbial species from kefir
grains. According to recent studies, there are over 50 microbial species associated with kefir grains.
The aim of this review is to summarize the microbiota structure of kefir grains. Moreover, because
of technological and microbiological significance of kefir grains, the paper provides an insight into
microbiological and molecular methods applied to study microbial biodiversity of kefir grains.
Key words: kefir, kefir grains, molecular methods, microbiota
1984; Farnworth, 2005). Also, the presence of
certain microbial species within kefir grain is deter-
mined by the area of origin (Angulo et al., 1993;
Lin et al., 1999). Scientific researchers have, among
others, tried to explain the interior and exterior
physical structure of kefir grain which represents
the unique microbial ecosystem. However, due to
numerous species and phenomenon of their associ-
ations, microbiota of kefir grains has still not been
completely elucidated (Leite et al., 2012; Wang et
al., 2012). In investigation of kefir microbiota com-
position various microbiological and molecular met-
hods of isolate identification have been used, as well
as new metagenomic molecular approaches based
on the identification of microbial population witho-
ut the cultivation of microorganisms on a nutrient
medium (Unsal, 2008; Leite et al., 2012; Gao et
al., 2013). The investigation of the unique eco sy-
stem typical for kefir grains has a multiple scientific
purpose. Apart from the description, these microbi-
al species isolations can be used for composition of
4
T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013)
starter cultures. The purpose of the kefir grain in-
vestigation is based also on the isolate isolation with
potentially different probiotic and biochemical cha-
racteristics (Hertzler and Clanci 2003; Santos
et al., 2003; Liu et al., 2005; Farnworth, 2005;
Lopitz-Otsoa et al., 2006; Powel, 2006; Ferreira
et al., 2010; Hong et al., 2010; Magalhães et al.,
2011; Dimitreli and Antoniou, 2011; Purnomo
and Muslimin, 2012).
Based on the scientific researches carried out in
past several last years, the purpose of this paper was
to give a review of research results of kefir grain mi-
crobial population. Also, because of the significance
of kefir grains in technological and microbiological
sense, the paper presents more details associated
with microbiological and molecular experimental
approaches used in investigation of microbial biodi-
versity of kefir grains.
Kefir
Kefir is traditional fermented milk product
which has been produced and consumed for thou-
sand years in the areas from Eastern Europe to
Mongolia. It is believed that the name kefir derives
from the mountain areas of Caucas or Caucasia
where, according to the legend, the aboriginals got
it directly from the prophet Mohammed (Gaware
et al., 2011). The name kefir most likely derives
from the Turkish word kefy or keif meaning hap-
piness, satisfaction (Kurman et al., 1992). Apart
from the name kefir, the following names are used
for the same product: kepyr, kephir, kefer, kiaphur,
knapson, kepi and kiipi (Rattray and O’Connell,
2011).
Industrial kefir is mostly produced in Russia
and other countries of the ex Soviet Union, then in
Poland, Sweden, Hungary, Norway, Finland, Ger-
many, The Czech Republic, Denmark and Switzer-
land. Kefir is also produced in Greece, Austria and
Brazil (Saloff-Coste, 1996). Since it is considered
as an ethnic product, the popularity of kefir incre-
ased in the USA and Japan lately. According to the
available data in Croatia, kefir is produced in Cro-
atia in relatively small quantities by only few dairy,
exclusively by addition of a commercial culture.
Various technologies are used in the producti-
on of kefir, but they can be basically described as a
traditional or industrial manufacturing process. The
traditional way of manufacture is a direct inoculation
of kefir grains into the milk, or the milk is inoculated
by a technical culture prepared from the kefir grains.
Unlike this, the term industrial processes in kefir
manufacture, means the use of commercial, mostly
DVS cultures (Wszolek et al., 2006). Commercial
cultures contain isolates of various lactic acid bac-
teria and/or yeasts species isolated from kefir gra-
ins. In comparison with kefir manufactured from
kefir grains, kefir manufactured with a pure culture
is significantly lacking its authenticity (Otles and
Caginidi, 2003; Farnworth, 2005; Garcia Fon-
tán et al., 2006; Wszolek et al., 2006). The loss
of authenticity is the most frequently connected to
the comparatively small number of various microbial
species contained in a pure culture. However, in Po-
land, kefir is produced by milk inoculation with its
own lyophilised culture produced from kefir grains.
Using this method “modified” kefir is less sour than
the traditional one and is characterised by creamier
consistency, but with a significant improvement in
the permanent quality, its authenticity has not been
significantly changed (Libudzizs and Piatkoiewi-
cz, 1990; Muir et al., 1999).
Regardless of the manufacturing method and
culture type according to Codex Allimentarius stan-
dard (Codex Stan 243-2003) a typical microbial
population of kefir must contain Lb. kefiri as well
as species Leuconostoc, Lactococcus and Acetobacter
(prepared from kefir grains) and yeasts which fer-
ment lactose (Kluyveromyces marxianus) as well as
yeasts which do not ferment lactose (Saccharomyces
cerevisiae and Saccharomyces exigous) when kefir
grains are used for the culture. According to the
same standard, a typical kefir must contain at least
2.8 % proteins, less than 10 % fat, at least 0.6 % lactic
acid, while the alcohol percentage is not determi-
ned. The total number of specified microorganisms
from culture must be at least 10
7
cfu/mL, and the
number of yeasts not under 10
4
cfu/mL.
At the end of fermentation, which includes
three days of cold ripening, the pH value of a typi-
cal kefir is between 4.2-4.7, it contains between
0.8-1.2 % of lactic acid, 0.5-0.7 % of ethanol and
approximately 0.20 % of CO2. Apart from these
compounds, kefir also contains various aromatic
compounds like acetaldehyde, diacetyl and acetoin,
5
T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013)
other organic acids like formic, acetic and/or pro-
pionic and isoamyl alcohol in traces (Wszolek et
al., 2006). Also, many scientific studies confirm that
apart from nutritive value kefir also has a strong pro-
biotic effect (Farnworth, 2005; Lopitiz-Otsoa et
al., 2006; Rattray and O’Connell, 2011).
Kefir grains
Kefir grains represent a unique ecosystem in
nature, formed by a symbiotic relation between bac-
teria and yeasts. A complex microbial community of
kefir grains contains more than 50 various species
of bacteria and yeasts and, depending on their ori-
gin, several species of filamentous moulds (Angu-
lo et al., 1993; Garrote et al., 2001; Jukić et al.,
2001; Stepaniak and Fetliński, 2002; Sarkar et
al., 2008; Wang et al., 2008). However, the ration
and number of individual microbial species within
a kefir grain depends significantly on the origin and
method of cultivation (Koroleva et al., 1988; Ta-
mime and Marshall, 1997; Ferreira et al., 2010).
Apart from numerous microbial species, a kefir grain
is made of a spongy fibrillated structure with reticular
laminar matrix and fibrous cluster which, particularly
in the grain centre, branches and interconnects with
long chains. This complex structure is made of pro-
teins, polysaccharides, various cellular elements and
numerous other still undefined components. A wa-
ter-soluble substance kefiran makes a polysaccharide
component with approximately 25 % of dry grain we-
ight. Kefiran, which in its complex exopolysaccharide
structure contains D-glucose and D-galactose in 1:1
ratio is responsible for mutual connection of micro-
bial community of a kefir grain (La Rivi ère et al.,
1967; Kander and Kunath, 1983; Marshall et al.,
1984; Micheli et al., 1999). Also, it is presumed
that kefiran contains microbial community in a kefir
grain in symbiosis in a way that microbial population
exists according to precisely determined pattern. A
peripheral part of a grain almost exclusively contains
bacteria, while yeasts dominate in the centre. Areas
between the centre and a peripheral part of a kefir
grain contain both bacteria and yeasts, but their ratio
progressively changes depending on the distance from
the grain centre (Bottazzi and Bianchi, 1980; Lin
et al., 1999). Thus, homofermentative Lactobacillus
species which form kefiran like bacteria Lb. kefiri
and Lb. kefiranofaciens are differently placed within
a kefir grain. Lb. kefiranofaciens can be found in the
centre of a kefir grain where growth conditions are
anaerobic and where ethanol is present, and Lb. kefiri
at its peripheral part. Lactobacilli are also located at
the peripheral part of a matrix, as well as yeasts which
do not form kefiran and which usually cannot pass
through a polysaccharide part into its interior (Zhou
et al., 2007; Dimitreli et al., 2011). The bacteria
Leuconostoc mesenteroides and yeast Kluyveromyces
marxianus are also dominant microbial species of a
peripheral layer (Lin et al., 2007). So far, numerous
species of lactococci, lactobacilli, streptococci, some
type from acetobacter genus, yeasts and moulds have
been isolated from a kefir grain (FAO/WHO, 2001).
Some of the species like Lb. kefiri or Lb. kefi-
ranofaciens were named according to kefir. Regard-
ing the ratio of microbial species presence, depend-
ing on the origin, a kefir grain contains approximately
10
9
lactococci, between 10
7
-10
8
Leuconostoc species,
10
7
-10
8
thermophile lactobacilli, 10
4
-10
5
yeasts and
10
4
-10
5
acetic acid bacteria, and among filamen-
tous moulds Geotrichum candidum (Kurman et
al., 1992). However, it should be emphasised that
neither the structure of microbial population nor a
single kefir grain is unequivocally determined.
The size of kefir grain is between 0.2-3 cm. They
are of irregular form looking like a cauliflower. They
are slimy, but of firm consistence. By repeated inocu-
lation into milk, kefir grains increase their mass by
approximately 25 % and have a characteristic scent.
The colour of kefir grains is ivory or pale-yellowish
(Wszolek et al., 2006; Gaware et al., 2011).
Before their next use, kefir grains are conserved
by a conventional drying method at the temperature
of 33 °C or by drying in a vacuum. In favourable and
stable conserving conditions, grains remain stable for
several years without losing its activity (Wszolek et
al., 2006). Re-activation of kefir grains is obtained by
their repeated incubation in pasteurised or reconsti-
tuted milk (Sarkar et al., 2008). During incubation,
dried grains regain soft structure, first by slow and then
by faster growth and the new kefir grains are formed.
Biodiversity of microbial species
Due to complex microbial composition of kefir
grains, the isolation and identification of individual
species have been methodologically demanding and
6
T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013)
complex. Therefore, it is not surprising that the micro-
bial composition of a kefir grain has been differently
interpreted in the literature. Apart from different ori-
gin of kefir grains, the choice of methods for microbial
identification used in numerous studies is definitely
one of the significant factors of mentioned diversity.
Cultivation and isolation of bacteria and yeasts
Various microbiological and molecular experi-
mental approaches have been used for investigation
of microbial population of kefir grains composition.
The most represented and still most accepted expe-
rimental approach is a classical cultivation of micro-
organisms on more or less selective nutrient media
(Jukić et al., 2001; Irigoyen et al., 2005; Wang et
al., 2008; Chen et al., 2008; Chen et al., 2009) and
molecular identification of isolate. The identificati-
on without cultivation and isolation of isolates (me-
tagenomic identification) has been used in the last
few years in investigation of kefir grains microbial
population (Leite et al., 2012; Gao et al., 2013). It
is based on the amplification of microbial DNA (cer-
tain gene or variable region) isolated directly from a
sample (Juste et al., 2008; Ndoye et al., 2011).
The most frequent media used for the classi-
cal cultivation of microbial species are standard co-
mmercial media for the cultivation of lactobacillus
(MRS agar, LAW agar, Rogosa agar, LamVab), lacto-
cocci (M17 agar), Leuconostoc species (MSE agar)
and yeasts (Sabouraud agar, potato dextrose agar)
(Simova et al., 2006; Irigoyen et al., 2005; Gar-
cía-Fontán et al., 2006., Wang et al., 2008). Also,
non-selective nutrient medium PCA (Plate count
agar) is most frequently used for determination of
aerobic mesophilic bacteria total number (García-
Fontán et al., 2006, Wang, et al., 2012).
Isolate purification is a standard procedure
which has to be carried out in order to be sure that a
microorganism isolated from one colony represents
only one isolate - one bacterial species, which very
often is not the case after the first cultivation pro-
cedure. Therefore, one, two or three subcultivations
have to be carried out on the same nutrient media
under the same conditions (temperature, with or
without the presence of oxygen). Also, after each
cultivation, isolated colonies have to be examined
under the microscope in order to determine if it is
a pure isolate or several morphotypes and if another
subcultivation should be carried out in order to ob-
tain one “pure” isolate (Caprette, 2005), which is
used later for the isolation of genomic DNA for fur-
ther molecular identification.
Cultivation, purification and isolation of micro-
organism are very sensitive and important microbio-
logical techniques. The cultivation and/or isolation
itself can sometimes represent a much more serious
problem problem than the molecular identification
which can sometimes be a routine analysis. It has
to be emphasised since many autochthonous micro-
bial species are very difficult to cultivate on standard
commercial nutrient media. Also, a routine use of
standard commercially available media developed in
the last thirty years can be suitable for the growth
of always the same microbial species regardless of
the real number of species in the examined sample
(Neviani et al., 2009; Vartoukian et al., 2009),
presenting only a partial image of a microbial popula-
tion which will be cultivated on a nutrient medium.
Since molecular methods based on the isolated
DNA and/or RNA are used mostly for the identi-
fication of microorganisms, the basics of molecular
identification will be described.
Molecular identification
Isolation of DNA from the isolate
The isolation of genomic microbial DNA from
the isolate has experienced a significant development
from the classic isolation procedure based on the use
of phenol-chloroform. Today, commercial kits of re-
nowned manufacturers have been most frequently
used in routine DNA isolations and the isolation is
carried out according to the manufacturer’s proto-
col. Therefore, only a few general specificities of
DNA isolation from the isolate will be mentioned.
In order to isolate DNA from the isolate, a colony
(previously purified by 2-3 subcultivations) has to be
inoculated in a liquid medium, which ensures growth
of bacteria in the period from 12-24 hours. The in-
cubation period of isolates for 12-24 hours is usually
sufficient to get a necessary cell density for DNA iso-
lation. However, for some isolates, it can be even 48
hours to ensure a sufficient number of cells during
incubation, or another inoculation (transplant) of the
isolate in a liquid medium is necessary. Namely, the
existence of a specific feature of each isolate which
7
T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013)
cannot be predicted in advance has to be taken into
account. The sample of 1-2 mL is taken from grown
cells in a pure culture, for DNA isolation from the
liquid medium, or the sample volume is determined
by an experienced estimation of medium turbidi-
ty or by measuring its optical density. Protocols for
DNA isolation differ among themselves to a lesser or
greater extent, i.e. there are numerous variations of
very similar protocols. These differences are usually
in concentration of certain reagents or the composi-
tion of certain reagents is a manufacturing secret and
the exact composition is not known. However, the
initial lysis of the bacterial cell wall with the additio-
nal enzyme of lysozyme and proteinase K is common
in most protocols for the efficient DNA isolation.
After the isolation, DNA concentration (ng/μL) is
determined by spectrophotometry method or elec-
trophoretic methods (electrophoresis gel). This pro-
cedure is important for determination of the exact
DNA microlitres that should be added for certain
DNA concentration (ng/μL) in the reaction mixtu-
re, in the next step of PCR amplification (Kuchta
et al., 2006). DNA concentration in PCR reactions
most frequently varies from 20 to 100 ng/μL, which
depends on many factors.
However, sometimes much simpler protocols
for DNA isolation are implemented, based only on
the lysis of a cell wall and the lysed cell is used as a
template DNA for PCR reaction (Juste et al., 2008;
Ndoye et al., 2011), or the whole colony is used for
PCR reaction (colony-PCR) without DNA isolation
or previous cell lysis (Unsal, 2008).
Identification of isolates by PCR methods
The identification of isolated microorganisms
by methods based on PCR polymerase chain reacti-
on has been applied since mid 1980-ies (Stefan et
al., 1988). In that period, many variations of PCR
method were developed and introduced by which
a certain targeted gene or a variable gene region is
amplified in vitro (Bartlett and Stirling, 2003).
Primers are added to PCR reaction mixture (arti-
ficially synthesised oligonucleotides 5’-3’ and 3’-5’
direction), isolated DNA (DNA template), enzyme
Taq polymerase, deoxyribonucleotides (A,T,C,G),
puffer and sterile water. Magnesium which is added
can also be an integral part of the puffer or is added
separately. PCR reaction mixture is most frequently
prepared in volumes of 25 or 50 μL. The very PCR
reaction consists of three main cycle steps: denatu-
ration step of a two-strand DNA molecule, primer
annealing step and a strand extension step (Kuchta
et al., 2006). PCR method is based on the activity
of Taq polymerase enzyme, isolated from the bacte-
rium Thermus aquaticus which has natural habitats
as thermal sources and due to that does not lose the
ability of amplifying DNA on temperatures of PCR
reactions, generally 60-95 °C (Kuchta et al., 2006).
The optimization of certain steps of PCR reac-
tion (temperature, cycle repeating) and concentra-
tion of certain reagents (primers, DNA, enzyme,
deoxyribonucleotides) are the most frequent prob-
lems which can occur during an experiment. Also,
potential problems could be contamination of prim-
ers or any other reagent or inactivity of Taq enzyme
polymerase. It is sometimes difficult to establish the
causes of failure of an experiment and with some
isolates they can never be established. The aim of
PCR reaction is to amplify a targeted gene or gene
region important for the identification of microor-
ganisms. The most frequent target of amplification
in bacteria is 16S rRNA gene or one of variable re-
gions (V1-V9) of 16S rRNA gene (Cardenas and
Tiedje, 2008), for whose amplification universal
or genus specific primers are used. With yeasts, the
most frequent target of amplification is D1 region
of 26S rRNA gene (Cocolin et al., 2002; Wang et
al., 2008). In cases when there are many isolates, for
certain isolates in order to get a valid result, either
the conditions of PCR reaction or primers should be
changed, since the applied protocol does not have to
be equally efficient for all the isolates.
In further steps PCR product is purified and
then mostly separately digested with the enzyme
combinations (2, 3 or 4 enzymes). Every enzyme
is specific for the digestion of the amplified PCR
product. Specific profiles for the exact species are
obtained by the combination of various restriction
enzymes (Mancini et al., 2012). Products obtained
by PCR reaction and enzyme digestion vary in the
number of base pairs and are separated by electrop-
horesis in agarose or polyacrylamide gel in order to
obtain specific profiles (Lushai et al., 1999; Kuch-
ta et al., 2006; Copola et al., 2008). The identifi-
cation of obtained profiles can be carried out in two
ways. The first one is the comparison of obtained
profiles with profiles of reference strains and the
8
T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013)
other can be carried out either independently from
the first one or as a supplement to the first one, is
a sequencing of 16S rRNA gene from the represen-
tative profiles (Copola et al., 2008; Mancini et
al., 2012). The obtained sequences are compared
to some of available databases on the internet as
BLAST. For some species the precise identification
by comparison of the obtained profiles is possible by
the use of only one restriction enzyme, but in some
species which are genetically very close, 3 or 4 en-
zymes have to be applied for the successful identifi-
cation of an isolate, since profiles of genetically very
close microbial species, obtained by the use of one or
two enzymes, can in some cases be identical, which
prevents the unequiocal identification of species.
One of the possible procedures of molecular
identification of isolates, independent of the enzyme
digestion and sequencing of 16S rRNA gene is usage
of species-specific primers for proving the presence
of a specified species. Such a molecular identification
is not used frequently because many species-specific
primers have to be used, i.e. as many as the number
of expected species. However, this approach can be
a final confirmation for the identification of species
or subspecies which cannot be identified by other
methods and it can be used for the final confirmation
of the identification (Temmerman et al., 2004).
Also, if the results of 16S rRNA gene sequencing
does not provide unequivocal identification, than it
leaves the possibility that the result might be two
or three genetically close species. The final confir-
mation of the identification can be carried out with
species-specific primers (Temmerman et al., 2004)
or DNA-DNA hybridisation (Goris et al., 2007).
Metagenomic identification
The cultivation of microbial population gives a
partial insight into the structure of microbial populati-
on of complex communities because many species are
either not cultivable or cultivation and isolation are
doubtful (Giraffa and Neviani, 2001; Copola et
al., 2008; Leite et al., 2012). Metagenomic identifi-
cation, without the cultivation and isolation of micro-
organisms, represents a wide spectrum of structure
investigation possibilities and dynamics of microbial
population of any microbial system (Huson et al.,
2009). By such a molecular approach it is possible to
isolate the total microbial DNA (or RNA) from kefir
or kefir grain, for which commercial kits of various
manufacturers are used and the targeted region of
16S rRNA gene in bacteria or 26S rRNA gene in ye-
asts (which are the most frequent, but not the only
targets of the amplification) can be amplified by
PCR reaction in order to get the insight in the struc-
ture of microbial community (Ünsal, 2008; Zhou
et al., 2009; Cruz et al., 2010; Gao et al., 2013).
For investigation of kefir microbial population by the
identification without cultivation, the most frequ-
ently used methods are PCR-DGGE (Denaturing
Gradient Gel Electrophoresis) and in the last few
years pyrosequencing (Wang et al., 2008; Ninane
et al. 2007; Chen et al., 2008; Miguel et al., 2010;
Leite et al., 2012). Also, the method of cloning the
amplified DNA (isolated directly from the kefir gra-
in) was used in E. colli and sequencing of V1 and V2
region of 16S rRNA gene (Veronique et al., 2007).
The totally isolated microbial DNA amplified
in PCR reaction is detected by PCR-DGGE method
on the polyacrylic gel as fragments (of the same size
regarding the number of base pairs, but of specific
nucleotide sequence for each microbial species) whi-
ch migrate in a gel to various positions (Muyzer and
Smalla, 1998). The identification of DNA fragments
is possible either by comparison of a fragment positi-
on with the position of the reference strain fragment
or with sequencing of fragments cut from various po-
sitions in a gel (Muyzer and Smalla, 1998; Copo-
la et al., 2008; Jianzhong et al., 2009). In order to
compare fragment positions in a gel, gels are normali-
sed and analysed by bioinformatics programmes.
However, one of the main drawbacks of investi- However, one of the main drawbacks of investi-
gating structures of complex microbial communities
is that species which were present in small numbers,
most frequently will not be amplified or their DNA
will not be isolated at all (Ercolini, 2004). The
new method which has been used only recently in
microbial population of kefir investigation is pyrose-
quencing (Dobson et al., 2011; Leite et al., 2012).
Pyrosequencing is automated and sophisticated
technique based on the synthesis of a single-strained
DNA and detection of nucleotide sequences (Magra
et al., 2012). The main advantage of this method is
that it gives the insight into the structure of minor
microbial population present in the investigated mi-
crobial system (Quigley et al., 2012).
9
T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013)
Table 1. Microbiota of kefir grains
Microorganism Reference*
1
Acetobacter fabarum Gao i sur., 2012
2
Acetobacter lovaniensis Unsal, 2008
3
Acetobacter syzygii Unsal, 2008
4
Acinetobacter Gao i sur., 2013
5
Bifidobacterium spp Leite i sur., 2012
6
Candida inconspicua Simova i sur., 2002
7
Dysgonomonas Gao i sur., 2013
8
Enterococcus faecium Unsal, 2008
9
Geotrichum candidum Timara, 2010
10
Gluconobacter japonicus Miguel i sur., 2012
11
Halococcus spp. Leite i sur., 2012
12
Kazachstania aerobia Magalhã es i sur., 2011
13
Kazachstania exigua Zhou i sur., 2009
14
Kazachstania unispora Zhou i sur., 2009
15
Kluyveromyces lactis
Zhou i sur., 2009
16
Kluyveromyces marxianus Zhou i sur., 2009
17
Kluyveromyces marxianus var. lactis Simova i sur., 2002
18
Lachancea meyersii Magalhã es i sur., 2011
19
Lactobacillus amylovorus Leite i sur., 2012
20
Lactobacillus brevis Simova i sur., 2002
21
Lactobacillus buchneri Leite i sur., 2012
22
Lactobacillus casei Zhou i sur., 2009
23
Lactobacillus paracasei Magalhã es i sur., 2011
24
Lactobacillus casei subsp. pseudoplantarum Simova i sur., 2002
25
Lactobacillus crispatus Leite i sur., 2012
26
Lactobacillus delbrueckii subsp. bulgaricus Simova i sur., 2002
27
Lactobacillus helveticus Unsal, 2008
28
Lactobacillus kefiranofaciens Unsal, 2008
29
Lactobacillus kefiranofaciens subsp. kefiranofaciens Leite i sur., 2012
30
Lactobacillus kefiranofaciens subsp. kefirgranum Leite i sur., 2012
31
Lactobacillus kefiri Unsal, 2008
32
Lactobacillus parabuchneri Magalhã es i sur., 2011
33
Lactobacillus parakefiri Leite i sur., 2012
34
Lactobacillus plantarum Gao i sur., 2012
35
Lactobacillus satsumensis Miguel i sur., 2012
36
Lactobacillus uvarum Miguel i sur., 2012
37
Lactococcus lactis subsp. cremoris Zhou i sur., 2009
38
Lactococcus lactis subsp. lactis Unsal, 2008
39
Leuconostoc lactis Gao i sur., 2012
40
Leuconostoc mesenteroides Unsal, 2008
41
Pelomonas Gao i sur., 2013
42
Pichia fermentans Wang i sur., 2008
43
Pichia guilliermondii Gao i sur., 2012
44
Pichia kudriavzevii Gao i sur., 2012
45
Pseudomonas putida Zhou i sur., 2009
46
Saccharomyces cerevisiae Zhou i sur., 2009
47
Saccharomyces martiniae Zhou i sur., 2009
48
Saccharomyces turicensis Wang i sur., 2008
49
Saccharomyces unisporus Zhou i sur., 2009
50
Shewanella Gao i sur., 2013
51
Streptococcus thermophilus Simova i sur., 2002
52
Weissella Gao i sur., 2013
*The table gives the review of identified kefir grain microorganisms, not mentioning whether the microorganism was identified in
that reference for the first time, or if it was only identified in that reference
10
T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013)
Microbial species of kefir grains
Numerous microbial species in kefir grains and
kefir were identified by different microbiological
and molecular techniques. The diversity of iden-
tified species of bacteria and yeast confirms the
complex microbial structure of that natural micro-
bial system. According to recent scientific sources,
the microbial population of the kefir grain includes
more than 50 various microorganism species (Table
1). This number will probably be increased with the
further development of metagenomic identification,
but also with improving classical cultivation, since no
single approach is perfect and cannot give the com-
plete insight into the structure of microbial popula-
tion.
Unsal (2008) isolated and identified by PCR-
DGGE method from the kefir grain Acetobacter
syzygii, Leuconostoc mesenteroides, Enterococcus
faecium, Lactobacillus kefiri/parabuchneri, and
Lactococcus lactis subsp. lactis, while the following
were identified in kefir by metagenomic approach
without isolation: Lactococcus lactis subsp. lactis,
Lactobacillus kefiranofaciens, Lactobacillus helveti-
cus, Acetobacter lovaniensis. In this paper the equal
number of microorganisms was identified by both
approaches. However, Zhou et al. (2009) identified
by PCR-DGGE method without isolation 10 bacte-
rial species in the kefir grain: Lactobacillus kefira-
nofaciens, Lactobacillus helveticus, Lactococcus lac-
tis subsp. lactis, Lactococcus lactis subsp. cremoris,
Lactobacillus casei, Lactobacillus kefiri, Leuconostoc
mesenteroides, Pseudomonas sp., Pseudomonas fluo-
rescens, Pseudomonas putida and seven species of ye-
asts: Kazachstania unispora, Kazachstania exigua,
Kluyveromyces marxianus, Kluyveromyces lactis,
Saccharomyces cerevisiae, Saccharomyces martiniae,
Saccharomyces unisporus. These 17 microorganisms
might have probably been so far the largest number
of identified microorganisms in one study. Gao et al.
(2012) isolated and identified 11 species of micro-
organism from Tibetan kefir: Bacillus subtilis, Lacto-
coccus lactis, Lactobacillus kefiri, Leuconostoc lactis,
Lactobacillus plantarum, Kluyveromyces marxianus,
Saccharomyces cerevisiae, Pichia kudriavzevii, Ka-
zachstania unispora, Acetobacter fabarum, Pichia
guilliermondii. Simova et al., (2002) isolated and
identified from the kefir grain Lactococcus lactis su-
bsp. lactis, Streptococcus thermophilus, Lactobacillus
delbrueckii subsp. bulgaricus, Lactobacillus helve-
ticus, Lactobacillus casei subsp. pseudoplantarum,
Lactobacillus brevis, Kluyveromyces marxianus var.
lactis, Saccharomyces cerevisiae, Candida inconspi-
cua, Candida maris. Wang et al., (2008) isolated
and identified from the kefir grain yeasts Kluyvero-
myces marxianus, Saccharomyces turicensis, Pichia
fermentans and Saccharomyces unisporus. Jianz-
hong et al. (2009) investigated the composition
of the Tibetan kefir microbial population by PCR-
DGGE method without previous microorganism
cultivation. Primers 338F-GC and 518R were used
for PCR reaction for bacterial DNA, and the target
of amplification was V3 region of 16S rRNA gene,
and for DNA of yeasts primers NL1GC and LS2
were used. In the same way, the following bacteria
were identified: Pseudomonas sp., Leuconostoc me-
senteroides, Lactobacillus helveticus, Lactobacillus
kefiranofaciens, Lactococcus lactis, Lactobacillus
kefiri, Lactobacillus casei, and yeasts: Kazachstania
unispora, Kluyveromyces marxianus, Saccharomyces
cerevisiae and Kazachstania exigua (Jianzhoung et
al., 2009). Leite et al., (2012) amplified V3 region
of 16S rRNA gene with universal primers F357- GC
and R518, to explore microbiota of Brazilian kefir.
Specific primers were also used for the identificati-
on of lactic acid bacteria: Lac1 and Lac2-GC for the
identification of bacteria from genera Lactobacillus,
Pediococcus, Leuconostoc and Weissella, and primers
Lac3 for bacteria from genera Lactococcus, Streptoco-
ccus, Enterococcus, Tetragenococcus and Vagococcus.
D1 domain of 26S of rRNA yeast gene was ampli-
fied by primers NL1-GC and LS2. All GC primers
contained 39 bp GC nucleotides in order to prevent
total product denaturation (Leite et al., 2012). In-
vestigating the structure of microbial population of
Brazilian kefir by pyrosequencing and DGGE met-
hod, the potential of both methods in metagenomic
identification of microbiota was compared (Leite et
al., 2012). Only 5 species of microorganisms were
identified by DGGE method: Lb. kefiranofaciens,
Lactococcus lactis, Lb. kefiri, Saccharomyces cere-
visiae and Kazachstania unispora, while the same
microbe species which were identified by DGGE
method were also identified by pyrosequencing, but
also representatives of Bifidobacterium, Leucono-
stoc, Streptococcus, Acetobacter, Pseudomonas, Halo-
coccus, as well as numerous representatives of lacto-
bacilli which were not identified by DGGE method:
11
T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013)
Lb. kefiranofaciens subsp. kefirgranum, Lb. kefira-
nofaciens subsp. kefiranofaciens, Lb. parakefiri, Lb.
parabuchneri, Lb. amylovorus, Lb. crispatus, Lb.
buchneri, and one representative of lactococcus Lc.
lactis subsp. cremoris (Leite et al., 2012). It sho-
uld be emphasised that some of these species were
represented with less of 1 % in the total populati-
on which emphasises the pyrosquencing potential
in investigation of the structure of complex and in-
completely investigated microbial communities like
kefir (Leite et al., 2012). Also, Gao et al., (2013)
identified for the first time in Tibetan kefir grains
without cultivation species from genera Shewanella,
Acinetobacter, Pelomonas, Dysgonomonas, Weissella
and Pseudomonas. Considering the fact that these
species were identified for the first time, their role
and significance on specific characteristics of the ke-
fir still remains to be elucidated. The mentioned
results of the investigation of the structure of kefir
grain microbial population prove that the number of
identified microbial species is increased by the use
of new molecular metagenomic methods in identi-
fication and such a trend will be continued. It also
indicates a smaller potential of identification based
on cultivation of microorganisms on media develo-
ped 30 or more years ago, since the fact is that the
development of new nutrient media has not been as
intensive as the development of metagenomic iden-
tification (Huson et al., 2009; Vieites et al., 2010;
Quigley et al., 2011; Delmont et al., 2011).
Conclusion
The studies of autochthonous microbial popu-
lation of kefir grain by the use of contemporary mi-
crobiological and molecular methods give new ideas
on the complexity of the microbial system of the
kefir grain which has so far resulted in more than
50 identified microbial species. The isolation of mi-
croorganisms from kefir grains, due to their further
technological and probiotic characterisation can po-
tentially result in strains with completely new cha-
racteristics. Further development of metagenomics,
based on the identification of microbial communi-
ties without cultivation, confirm that the microbial
culture isolated until now represent only one part
of the complex microbial system which influences
specific features of kefir. However, the classical cul-
tivation and isolation will still remain irreplaceable
for the detailed characterisation of microbial isolates
and discovery of new strains.
Mikrobni sastav kefirnih zrna
Sažetak
Bakterije i kvasci, a ponekad i filamentozne
plijesni u kefirnim zrnima žive u složenom simbi-
otskom odnosu koji kefirna zrna čini jedinstvenom
mikrobnom zajednicom u prirodi. Složenost i kom-
pleksnost njihove fizičke i mikrobne strukture razl-
ogom su što su kefirna zrna još uvijek mikrobiološki
nedovoljno i nepotpuno istražena. U istraživanju
mikrobnog sastava kefirnih zrna koriste se različiti
mikrobiološki i molekularni pristupi. Razvojem me-
tagenomike, bazirane na identifikaciji bez kultivacije,
otvaraju se nove mogućnosti identifikacije do sada
još neidentificiranih mikrobnih vrsta sadržanih u ke-
firnom zrnu. Do sada je identificirano preko 50 vrsta
mikroorganizama prisutnih u kefirnom zrnu. U radu
su prikazane do danas identificirane mikrobne vrste
sadržane u kefirnim zrnima različitog podrijetla.
Također, radi tehnološkog i mikrobiološkog značenja
koja imaju kefirna zrna sama po sebi, u radu su de-
taljnije prikazani molekularni eksperimentalni pris-
tupi koji se koriste u istraživanju njihove mikrobne
bioraznolikosti.
Ključne riječi: kefir, kefirna zrna,
molekularne metode, mikrobne vrste
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