Microbiota of Kefir Grains, Mljekarstvo 63 (1), 3-14 (2013) 3

T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013) 3

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 sometimes 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 possibilities 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

Introduction 1984; Farnworth, 2005). Also, the presence of certain microbial species within kefir grain is deter- Kefir is a specific dairy product from the group mined by the area of origin (Angulo et al., 1993; of fermented milks where lactose hydrolysis during Lin et al., 1999). Scientific researchers have, among fermentation occurs with the simultaneous action of others, tried to explain the interior and exterior bacteria and yeasts contained in kefir grains. Althou- physical structure of kefir grain which represents gh lactic acid is a main metabolite, due to yeast acti- the unique microbial ecosystem. However, due to vity kefir also contains significant quantities of CO2 numerous species and phenomenon of their associ- and variable alcohol quantity. Because of associative ations, microbiota of kefir grains has still not been growth of various microbial species in kefir, during completely elucidated (Leite et al., 2012; Wang et fermentation other organic compounds are formed, al., 2012). In investigation of kefir microbiota com- like bioactive peptides, exopolysaccharides, bacteri- position various microbiological and molecular met- ocins which are presumed to have a probiotic effect hods of isolate identification have been used, as well on human health (Kosikowski and Mistry, 1999; as new metagenomic molecular approaches based Stepaniak and Fetliński, 2003; Lopitz-Otsoa et on the identification of microbial population witho- al., 2006; Hong et al., 2010). ut the cultivation of microorganisms on a nutrient The microbial population of kefir grains con- medium (Unsal, 2008; Leite et al., 2012; Gao et sists of numerous species of lactic acid bacteria, al., 2013). The investigation of the unique eco sy- acetic acid bacteria, yeasts and filamentous moulds stem typical for kefir grains has a multiple scientific which develop a complex symbiotic relationship purpose. Apart from the description, these microbi- within a microbial community (Marshall et al., al species isolations can be used for composition of

*Corresponding author/Dopisni autor: Phone/Tel.: +385 (0)1 239 3646; E-mail: [email protected] 4 T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013) starter cultures. The purpose of the kefir grain in- traditional or industrial manufacturing process. The vestigation is based also on the isolate isolation with traditional way of manufacture is a direct inoculation potentially different probiotic and biochemical cha- of kefir grains into the milk, or the milk is inoculated racteristics (Hertzler and Clanci 2003; Santos by a technical culture prepared from the kefir grains. et al., 2003; Liu et al., 2005; Farnworth, 2005; Unlike this, the term industrial processes in kefir Lopitz-Otsoa et al., 2006; Powel, 2006; Ferreira manufacture, means the use of commercial, mostly et al., 2010; Hong et al., 2010; Magalhães et al., DVS cultures (Wszolek et al., 2006). Commercial 2011; Dimitreli and Antoniou, 2011; Purnomo cultures contain isolates of various lactic acid bac- and Muslimin, 2012). teria and/or yeasts species isolated from kefir gra- Based on the scientific researches carried out in ins. In comparison with kefir manufactured from past several last years, the purpose of this paper was kefir grains, kefir manufactured with a pure culture to give a review of research results of kefir grain mi- is significantly lacking its authenticity (Otles and crobial population. Also, because of the significance Caginidi, 2003; Farnworth, 2005; Garcia Fon- of kefir grains in technological and microbiological tán et al., 2006; Wszolek et al., 2006). The loss sense, the paper presents more details associated of authenticity is the most frequently connected to with microbiological and molecular experimental the comparatively small number of various microbial approaches used in investigation of microbial biodi- species contained in a pure culture. However, in Po- versity of kefir grains. 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 Kefir the traditional one and is characterised by creamier consistency, but with a significant improvement in Kefir is traditional fermented milk product the permanent quality, its authenticity has not been which has been produced and consumed for thou- significantly changed (Libudzizs and Piatkoiewi- sand years in the areas from Eastern Europe to cz, 1990; Muir et al., 1999). Mongolia. It is believed that the name kefir derives from the mountain areas of Caucas or Caucasia Regardless of the manufacturing method and where, according to the legend, the aboriginals got culture type according to Codex Allimentarius stan- it directly from the prophet Mohammed (Gaware dard (Codex Stan 243-2003) a typical microbial et al., 2011). The name kefir most likely derives population of kefir must contain Lb. kefiri as well from the Turkish word kefy or keif meaning hap- as species Leuconostoc, Lactococcus and Acetobacter piness, satisfaction (Kurman et al., 1992). Apart (prepared from kefir grains) and yeasts which fer- from the name kefir, the following names are used ment lactose (Kluyveromyces marxianus) as well as for the same product: kepyr, kephir, kefer, kiaphur, yeasts which do not ferment lactose (Saccharomyces knapson, kepi and kiipi (Rattray and O’Connell, cerevisiae and Saccharomyces exigous) when kefir 2011). grains are used for the culture. According to the same standard, a typical kefir must contain at least Industrial kefir is mostly produced in Russia 2.8 % proteins, less than 10 % fat, at least 0.6 % lactic and other countries of the ex Soviet Union, then in acid, while the alcohol percentage is not determi- Poland, Sweden, Hungary, Norway, Finland, Ger- ned. The total number of specified microorganisms many, The Czech Republic, Denmark and Switzer- from culture must be at least 107 cfu/mL, and the land. Kefir is also produced in Greece, Austria and number of yeasts not under 104 cfu/mL. Brazil (Saloff-Coste, 1996). Since it is considered as an ethnic product, the popularity of kefir incre- At the end of fermentation, which includes ased in the USA and Japan lately. According to the three days of cold ripening, the pH value of a typi- available data in Croatia, kefir is produced in Cro- cal kefir is between 4.2-4.7, it contains between atia in relatively small quantities by only few dairy, 0.8-1.2 % of lactic acid, 0.5-0.7 % of ethanol and exclusively by addition of a commercial culture. approximately 0.20 % of CO2. Apart from these compounds, kefir also contains various aromatic Various technologies are used in the producti- compounds like acetaldehyde, diacetyl and acetoin, on of kefir, but they can be basically described as a T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013) 5 other organic acids like formic, acetic and/or pro- and Lb. kefiranofaciens are differently placed within pionic and isoamyl alcohol in traces (Wszolek et a kefir grain. Lb. kefiranofaciens can be found in the al., 2006). Also, many scientific studies confirm that centre of a kefir grain where growth conditions are apart from nutritive value kefir also has a strong pro- anaerobic and where ethanol is present, and Lb. kefiri biotic effect (Farnworth, 2005; Lopitiz-Otsoa et at its peripheral part. Lactobacilli are also located at al., 2006; Rattray and O’Connell, 2011). 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 Kefir grains et al., 2007; Dimitreli et al., 2011). The bacteria Leuconostoc mesenteroides and yeast Kluyveromyces Kefir grains represent a unique ecosystem in marxianus are also dominant microbial species of a nature, formed by a symbiotic relation between bac- peripheral layer (Lin et al., 2007). So far, numerous teria and yeasts. A complex microbial community of species of lactococci, lactobacilli, streptococci, some kefir grains contains more than 50 various species type from acetobacter genus, yeasts and moulds have of bacteria and yeasts and, depending on their ori- been isolated from a kefir grain (FAO/WHO, 2001). gin, several species of filamentous moulds (Angu- lo et al., 1993; Garrote et al., 2001; Jukić et al., Some of the species like Lb. kefiri or Lb. kefi- 2001; Stepaniak and Fetliński, 2002; Sarkar et ranofaciens were named according to kefir. Regard- al., 2008; Wang et al., 2008). However, the ration ing the ratio of microbial species presence, depend- and number of individual microbial species within ing on the origin, a kefir grain contains approximately 9 7 8 a kefir grain depends significantly on the origin and 10 lactococci, between 10 -10 Leuconostoc species, 7 8 4 5 method of cultivation (Koroleva et al., 1988; Ta- 10 -10 thermophile lactobacilli, 10 -10 yeasts and 4 5 mime and Marshall, 1997; Ferreira et al., 2010). 10 -10 acetic acid bacteria, and among filamen- Apart from numerous microbial species, a kefir grain tous moulds Geotrichum candidum (Kurman et is made of a spongy fibrillated structure with reticular al., 1992). However, it should be emphasised that laminar matrix and fibrous cluster which, particularly neither the structure of microbial population nor a in the grain centre, branches and interconnects with single kefir grain is unequivocally determined. long chains. This complex structure is made of pro- The size of kefir grain is between 0.2-3 cm. They teins, polysaccharides, various cellular elements and are of irregular form looking like a cauliflower. They numerous other still undefined components. A wa- are slimy, but of firm consistence. By repeated inocu- ter-soluble substance kefiran makes a polysaccharide lation into milk, kefir grains increase their mass by component with approximately 25 % of dry grain we- approximately 25 % and have a characteristic scent. ight. Kefiran, which in its complex exopolysaccharide The colour of kefir grains is ivory or pale-yellowish structure contains D-glucose and D-galactose in 1:1 (Wszolek et al., 2006; Gaware et al., 2011). ratio is responsible for mutual connection of micro- Before their next use, kefir grains are conserved bial community of a kefir grain (La Rivière et al., by a conventional drying method at the temperature 1967; Kander and Kunath, 1983; Marshall et al., of 33 °C or by drying in a vacuum. In favourable and 1984; Micheli et al., 1999). Also, it is presumed stable conserving conditions, grains remain stable for that kefiran contains microbial community in a kefir several years without losing its activity (Wszolek et grain in symbiosis in a way that microbial population al., 2006). Re-activation of kefir grains is obtained by exists according to precisely determined pattern. A their repeated incubation in pasteurised or reconsti- peripheral part of a grain almost exclusively contains tuted milk (Sarkar et al., 2008). During incubation, bacteria, while yeasts dominate in the centre. Areas dried grains regain soft structure, first by slow and then between the centre and a peripheral part of a kefir by faster growth and the new kefir grains are formed. grain contain both bacteria and yeasts, but their ratio progressively changes depending on the distance from Biodiversity of microbial species the grain centre (Bottazzi and Bianchi, 1980; Lin et al., 1999). Thus, homofermentative Lactobacillus Due to complex microbial composition of kefir species which form kefiran like bacteria Lb. kefiri 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- subcultivation should be carried out in order to ob- bial composition of a kefir grain has been differently tain one “pure” isolate (Caprette, 2005), which is interpreted in the literature. Apart from different ori- used later for the isolation of genomic DNA for fur- gin of kefir grains, the choice of methods for microbial ther molecular identification. identification used in numerous studies is definitely Cultivation, purification and isolation of micro- one of the significant factors of mentioned diversity. organism are very sensitive and important microbiological techniques. The cultivation and/or isolation Cultivation and isolation of bacteria and yeasts itself can sometimes represent a much more serious problem problem than the molecular identification Various microbiological and molecular experi- which can sometimes be a routine analysis. It has mental approaches have been used for investigation to be emphasised since many autochthonous micro- of microbial population of kefir grains composition. bial species are very difficult to cultivate on standard The most represented and still most accepted expe- commercial nutrient media. Also, a routine use of rimental approach is a classical cultivation of micro- standard commercially available media developed in organisms on more or less selective nutrient media the last thirty years can be suitable for the growth (Jukić et al., 2001; Irigoyen et al., 2005; Wang et of always the same microbial species regardless of al., 2008; Chen et al., 2008; Chen et al., 2009) and the real number of species in the examined sample molecular identification of isolate. The identificati- (Neviani et al., 2009; Vartoukian et al., 2009), on without cultivation and isolation of isolates (me- presenting only a partial image of a microbial popula- tagenomic identification) has been used in the last tion which will be cultivated on a nutrient medium. few years in investigation of kefir grains microbial population (Leite et al., 2012; Gao et al., 2013). It Since molecular methods based on the isolated is based on the amplification of microbial DNA (cer- DNA and/or RNA are used mostly for the identi- tain gene or variable region) isolated directly from a fication of microorganisms, the basics of molecular sample (Juste et al., 2008; Ndoye et al., 2011). identification will be described. The most frequent media used for the classical cultivation of microbial species are standard co- Molecular identification mmercial media for the cultivation of lactobacillus (MRS agar, LAW agar, Rogosa agar, LamVab), lacto- Isolation of DNA from the isolate cocci (M17 agar), Leuconostoc species (MSE agar) The isolation of genomic microbial DNA from and yeasts (Sabouraud agar, potato dextrose agar) the isolate has experienced a significant development (Simova et al., 2006; Irigoyen et al., 2005; Gar- from the classic isolation procedure based on the use cía-Fontán et al., 2006., Wang et al., 2008). Also, of phenol-chloroform. Today, commercial kits of re- non-selective nutrient medium PCA (Plate count nowned manufacturers have been most frequently agar) is most frequently used for determination of used in routine DNA isolations and the isolation is aerobic mesophilic bacteria total number (García- carried out according to the manufacturer’s proto- Fontán et al., 2006, Wang, et al., 2012). col. Therefore, only a few general specificities of Isolate purification is a standard procedure DNA isolation from the isolate will be mentioned. which has to be carried out in order to be sure that a In order to isolate DNA from the isolate, a colony microorganism isolated from one colony represents (previously purified by 2-3 subcultivations) has to be only one isolate - one bacterial species, which very inoculated in a liquid medium, which ensures growth often is not the case after the first cultivation pro- of bacteria in the period from 12-24 hours. The in- cedure. Therefore, one, two or three subcultivations cubation period of isolates for 12-24 hours is usually have to be carried out on the same nutrient media sufficient to get a necessary cell density for DNA iso- under the same conditions (temperature, with or lation. However, for some isolates, it can be even 48 without the presence of oxygen). Also, after each hours to ensure a sufficient number of cells during cultivation, isolated colonies have to be examined incubation, or another inoculation (transplant) of the under the microscope in order to determine if it is isolate in a liquid medium is necessary. Namely, the a pure isolate or several morphotypes and if another existence of a specific feature of each isolate which T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013) 7 cannot be predicted in advance has to be taken into prepared in volumes of 25 or 50 μL. The very PCR account. The sample of 1-2 mL is taken from grown reaction consists of three main cycle steps: denatu- cells in a pure culture, for DNA isolation from the ration step of a two-strand DNA molecule, primer liquid medium, or the sample volume is determined annealing step and a strand extension step (Kuchta by an experienced estimation of medium turbidi- et al., 2006). PCR method is based on the activity ty or by measuring its optical density. Protocols for of Taq polymerase enzyme, isolated from the bacte- DNA isolation differ among themselves to a lesser or rium Thermus aquaticus which has natural habitats greater extent, i.e. there are numerous variations of as thermal sources and due to that does not lose the very similar protocols. These differences are usually ability of amplifying DNA on temperatures of PCR in concentration of certain reagents or the composi- reactions, generally 60-95 °C (Kuchta et al., 2006). tion of certain reagents is a manufacturing secret and The optimization of certain steps of PCR reac- the exact composition is not known. However, the tion (temperature, cycle repeating) and concentra- initial lysis of the bacterial cell wall with the additio- tion of certain reagents (primers, DNA, enzyme, nal enzyme of lysozyme and proteinase K is common deoxyribonucleotides) are the most frequent prob- in most protocols for the efficient DNA isolation. lems which can occur during an experiment. Also, After the isolation, DNA concentration (ng/μL) is potential problems could be contamination of prim- determined by spectrophotometry method or elec- ers or any other reagent or inactivity of Taq enzyme trophoretic methods (electrophoresis gel). This pro- polymerase. It is sometimes difficult to establish the cedure is important for determination of the exact causes of failure of an experiment and with some DNA microlitres that should be added for certain isolates they can never be established. The aim of DNA concentration (ng/μL) in the reaction mixtu- PCR reaction is to amplify a targeted gene or gene re, in the next step of PCR amplification (Kuchta region important for the identification of microor- et al., 2006). DNA concentration in PCR reactions ganisms. The most frequent target of amplification most frequently varies from 20 to 100 ng/μL, which in bacteria is 16S rRNA gene or one of variable re- depends on many factors. gions (V1-V9) of 16S rRNA gene (Cardenas and However, sometimes much simpler protocols Tiedje, 2008), for whose amplification universal for DNA isolation are implemented, based only on or genus specific primers are used. With yeasts, the the lysis of a cell wall and the lysed cell is used as a most frequent target of amplification is D1 region template DNA for PCR reaction (Juste et al., 2008; of 26S rRNA gene (Cocolin et al., 2002; Wang et Ndoye et al., 2011), or the whole colony is used for al., 2008). In cases when there are many isolates, for PCR reaction (colony-PCR) without DNA isolation certain isolates in order to get a valid result, either or previous cell lysis (Unsal, 2008). 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. Identification of isolates by PCR methods In further steps PCR product is purified and The identification of isolated microorganisms then mostly separately digested with the enzyme by methods based on PCR polymerase chain reacti- combinations (2, 3 or 4 enzymes). Every enzyme on has been applied since mid 1980-ies (Stefan et is specific for the digestion of the amplified PCR al., 1988). In that period, many variations of PCR product. Specific profiles for the exact species are method were developed and introduced by which obtained by the combination of various restriction a certain targeted gene or a variable gene region is enzymes (Mancini et al., 2012). Products obtained amplified in vitro (Bartlett and Stirling, 2003). by PCR reaction and enzyme digestion vary in the Primers are added to PCR reaction mixture (arti- number of base pairs and are separated by electrop- ficially synthesised oligonucleotides 5’-3’ and 3’-5’ horesis in agarose or polyacrylamide gel in order to direction), isolated DNA (DNA template), enzyme obtain specific profiles (Lushai et al., 1999; Kuch- Taq polymerase, deoxyribonucleotides (A,T,C,G), ta et al., 2006; Copola et al., 2008). The identifi- puffer and sterile water. Magnesium which is added cation of obtained profiles can be carried out in two can also be an integral part of the puffer or is added ways. The first one is the comparison of obtained separately. PCR reaction mixture is most frequently 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 manufacturers are used and the targeted region of the first one or as a supplement to the first one, is 16S rRNA gene in bacteria or 26S rRNA gene in ye- a sequencing of 16S rRNA gene from the represen- asts (which are the most frequent, but not the only tative profiles (Copola et al., 2008; Mancini et targets of the amplification) can be amplified by al., 2012). The obtained sequences are compared PCR reaction in order to get the insight in the struc- to some of available databases on the internet as ture of microbial community (Ünsal, 2008; Zhou BLAST. For some species the precise identification et al., 2009; Cruz et al., 2010; Gao et al., 2013). by comparison of the obtained profiles is possible by For investigation of kefir microbial population by the the use of only one restriction enzyme, but in some identification without cultivation, the most frequ- species which are genetically very close, 3 or 4 en- ently used methods are PCR-DGGE (Denaturing zymes have to be applied for the successful identifi- Gradient Gel Electrophoresis) and in the last few cation of an isolate, since profiles of genetically very years pyrosequencing (Wang et al., 2008; Ninane close microbial species, obtained by the use of one or et al. 2007; Chen et al., 2008; Miguel et al., 2010; two enzymes, can in some cases be identical, which Leite et al., 2012). Also, the method of cloning the prevents the unequiocal identification of species. amplified DNA (isolated directly from the kefir grain) was used in E. colli and sequencing of V1 and V2 One of the possible procedures of molecular region of 16S rRNA gene (Veronique et al., 2007). identification of isolates, independent of the enzyme digestion and sequencing of 16S rRNA gene is usage The totally isolated microbial DNA amplified of species-specific primers for proving the presence in PCR reaction is detected by PCR-DGGE method of a specified species. Such a molecular identification on the polyacrylic gel as fragments (of the same size is not used frequently because many species-specific regarding the number of base pairs, but of specific primers have to be used, i.e. as many as the number nucleotide sequence for each microbial species) whi- of expected species. However, this approach can be ch migrate in a gel to various positions (Muyzer and a final confirmation for the identification of species Smalla, 1998). The identification of DNA fragments or subspecies which cannot be identified by other is possible either by comparison of a fragment positi- methods and it can be used for the final confirmation on with the position of the reference strain fragment of the identification (Temmerman et al., 2004). or with sequencing of fragments cut from various po- Also, if the results of 16S rRNA gene sequencing sitions in a gel (Muyzer and Smalla, 1998; Copo- does not provide unequivocal identification, than it la et al., 2008; Jianzhong et al., 2009). In order to leaves the possibility that the result might be two compare fragment positions in a gel, gels are normali- or three genetically close species. The final confir- sed and analysed by bioinformatics programmes. mation of the identification can be carried out with However, one of the main drawbacks of investiinvesti-- species-specific primers (Temmerman et al., 2004) gating structures of complex microbial communities or DNA-DNA hybridisation (Goris et al., 2007). is that species which were present in small numbers, most frequently will not be amplified or their DNA Metagenomic identification will not be isolated at all (Ercolini, 2004). The The cultivation of microbial population gives a new method which has been used only recently in partial insight into the structure of microbial populati- microbial population of kefir investigation is pyrose- on of complex communities because many species are quencing (Dobson et al., 2011; Leite et al., 2012). either not cultivable or cultivation and isolation are Pyrosequencing is automated and sophisticated doubtful (Giraffa and Neviani, 2001; Copola et technique based on the synthesis of a single-strained al., 2008; Leite et al., 2012). Metagenomic identifi- DNA and detection of nucleotide sequences (Magra cation, without the cultivation and isolation of micro- et al., 2012). The main advantage of this method is organisms, represents a wide spectrum of structure that it gives the insight into the structure of minor investigation possibilities and dynamics of microbial microbial population present in the investigated mi- population of any microbial system (Huson et al., crobial system (Quigley et al., 2012). 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 T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013) 9

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 Magalhães 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 Magalhães 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 Magalhães 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 Magalhães 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 delbrueckii subsp. bulgaricus, Lactobacillus helveticus, Lactobacillus casei subsp. pseudoplantarum, Numerous microbial species in kefir grains and Lactobacillus brevis, Kluyveromyces marxianus var. kefir were identified by different microbiological lactis, Saccharomyces cerevisiae, Candida inconspi- and molecular techniques. The diversity of iden- cua, Candida maris. Wang et al., (2008) isolated tified species of bacteria and yeast confirms the and identified from the kefir grain yeasts Kluyvero- complex microbial structure of that natural micro- myces marxianus, Saccharomyces turicensis, Pichia bial system. According to recent scientific sources, fermentans and Saccharomyces unisporus. Jianz- the microbial population of the kefir grain includes hong et al. (2009) investigated the composition more than 50 various microorganism species (Table of the Tibetan kefir microbial population by PCR- 1). This number will probably be increased with the DGGE method without previous microorganism further development of metagenomic identification, cultivation. Primers 338F-GC and 518R were used but also with improving classical cultivation, since no for PCR reaction for bacterial DNA, and the target single approach is perfect and cannot give the com- of amplification was V3 region of 16S rRNA gene, plete insight into the structure of microbial popula- and for DNA of yeasts primers NL1GC and LS2 tion. were used. In the same way, the following bacteria Unsal (2008) isolated and identified by PCR- were identified: Pseudomonas sp., Leuconostoc me- DGGE method from the kefir grain Acetobacter senteroides, Lactobacillus helveticus, Lactobacillus syzygii, Leuconostoc mesenteroides, Enterococcus kefiranofaciens, Lactococcus lactis, Lactobacillus faecium, Lactobacillus kefiri/parabuchneri, and kefiri, Lactobacillus casei, and yeasts: Kazachstania Lactococcus lactis subsp. lactis, while the following unispora, Kluyveromyces marxianus, Saccharomyces were identified in kefir by metagenomic approach cerevisiae and Kazachstania exigua (Jianzhoung et without isolation: Lactococcus lactis subsp. lactis, al., 2009). Leite et al., (2012) amplified V3 region Lactobacillus kefiranofaciens, Lactobacillus helveti- of 16S rRNA gene with universal primers F357- GC cus, Acetobacter lovaniensis. In this paper the equal and R518, to explore microbiota of Brazilian kefir. number of microorganisms was identified by both Specific primers were also used for the identificati- approaches. However, Zhou et al. (2009) identified on of lactic acid bacteria: Lac1 and Lac2-GC for the by PCR-DGGE method without isolation 10 bacte- identification of bacteria from genera Lactobacillus, rial species in the kefir grain: Lactobacillus kefira- Pediococcus, Leuconostoc and Weissella, and primers nofaciens, Lactobacillus helveticus, Lactococcus lac- Lac3 for bacteria from genera Lactococcus, Streptoco- tis subsp. lactis, Lactococcus lactis subsp. cremoris, ccus, Enterococcus, Tetragenococcus and Vagococcus. Lactobacillus casei, Lactobacillus kefiri, Leuconostoc D1 domain of 26S of rRNA yeast gene was ampli- mesenteroides, Pseudomonas sp., Pseudomonas fluo- fied by primers NL1-GC and LS2. All GC primers rescens, Pseudomonas putida and seven species of ye- contained 39 bp GC nucleotides in order to prevent asts: Kazachstania unispora, Kazachstania exigua, total product denaturation (Leite et al., 2012). In- Kluyveromyces marxianus, Kluyveromyces lactis, vestigating the structure of microbial population of Saccharomyces cerevisiae, Saccharomyces martiniae, Brazilian kefir by pyrosequencing and DGGE met- Saccharomyces unisporus. These 17 microorganisms hod, the potential of both methods in metagenomic might have probably been so far the largest number identification of microbiota was compared (Leite et of identified microorganisms in one study. Gao et al. al., 2012). Only 5 species of microorganisms were (2012) isolated and identified 11 species of micro- identified by DGGE method: Lb. kefiranofaciens, organism from Tibetan kefir: Bacillus subtilis, Lacto- Lactococcus lactis, Lb. kefiri, Saccharomyces cere- coccus lactis, Lactobacillus kefiri, Leuconostoc lactis, visiae and Kazachstania unispora, while the same Lactobacillus plantarum, Kluyveromyces marxianus, microbe species which were identified by DGGE Saccharomyces cerevisiae, Pichia kudriavzevii, Ka- method were also identified by pyrosequencing, but zachstania unispora, Acetobacter fabarum, Pichia also representatives of Bifidobacterium, Leucono- guilliermondii. Simova et al., (2002) isolated and stoc, Streptococcus, Acetobacter, Pseudomonas, Halo- identified from the kefir grain Lactococcus lactis su- coccus, as well as numerous representatives of lacto- bsp. lactis, Streptococcus thermophilus, Lactobacillus bacilli which were not identified by DGGE method: T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013) 11

Lb. kefiranofaciens subsp. kefirgranum, Lb. kefira- for the detailed characterisation of microbial isolates nofaciens subsp. kefiranofaciens, Lb. parakefiri, Lb. and discovery of new strains. parabuchneri, Lb. amylovorus, Lb. crispatus, Lb. buchneri, and one representative of lactococcus Lc. lactis subsp. cremoris (Leite et al., 2012). It sho- Mikrobni sastav kefirnih zrna uld be emphasised that some of these species were represented with less of 1 % in the total populati- Sažetak on which emphasises the pyrosquencing potential in investigation of the structure of complex and in- Bakterije i kvasci, a ponekad i filamentozne completely investigated microbial communities like plijesni u kefirnim zrnima žive u složenom simbi- kefir (Leite et al., 2012). Also, Gao et al., (2013) otskom odnosu koji kefirna zrna čini jedinstvenom identified for the first time in Tibetan kefir grains mikrobnom zajednicom u prirodi. Složenost i kom- without cultivation species from genera Shewanella, pleksnost njihove fizičke i mikrobne strukture razl- Acinetobacter, Pelomonas, Dysgonomonas, Weissella ogom su što su kefirna zrna još uvijek mikrobiološki and Pseudomonas. Considering the fact that these nedovoljno i nepotpuno istražena. U istraživanju species were identified for the first time, their role mikrobnog sastava kefirnih zrna koriste se različiti and significance on specific characteristics of the ke- mikrobiološki i molekularni pristupi. Razvojem me- fir still remains to be elucidated. The mentioned tagenomike, bazirane na identifikaciji bez kultivacije, results of the investigation of the structure of kefir otvaraju se nove mogućnosti identifikacije do sada grain microbial population prove that the number of još neidentificiranih mikrobnih vrsta sadržanih u ke- identified microbial species is increased by the use firnom zrnu. Do sada je identificirano preko 50 vrsta of new molecular metagenomic methods in identi- mikroorganizama prisutnih u kefirnom zrnu. U radu fication and such a trend will be continued. It also su prikazane do danas identificirane mikrobne vrste indicates a smaller potential of identification based sadržane u kefirnim zrnima različitog podrijetla. on cultivation of microorganisms on media develo- Također, radi tehnološkog i mikrobiološkog značenja ped 30 or more years ago, since the fact is that the koja imaju kefirna zrna sama po sebi, u radu su de- development of new nutrient media has not been as taljnije prikazani molekularni eksperimentalni pris- intensive as the development of metagenomic iden- tupi koji se koriste u istraživanju njihove mikrobne tification (Huson et al., 2009; Vieites et al., 2010; bioraznolikosti. Quigley et al., 2011; Delmont et al., 2011). Ključne riječi: kefir, kefirna zrna, molekularne metode, mikrobne vrste Conclusion The studies of autochthonous microbial population of kefir grain by the use of contemporary microbiological and molecular methods give new ideas References on the complexity of the microbial system of the 1. Angulo, L., Lopez, E., Lema, C. (1993): Mikroflora pres- kefir grain which has so far resulted in more than ent in kefir grains of the galician region (North-West of 50 identified microbial species. The isolation of mi- Spain). Journal of Dairy Research 60, 263-267. croorganisms from kefir grains, due to their further 2. Bartlett, J.M.S., Stirling, D. (2003): A short history of the polymerase chain reaction. Methods in Molecular Bi- technological and probiotic characterisation can po- ology 226, 3-6. tentially result in strains with completely new cha- 3. Beshkova, D.M., Simova, E.D., Frengova, G.I., Simov, racteristics. Further development of metagenomics, Z.I., Dimitrov, Zh.P. (2003): Production of volatile aro- based on the identification of microbial communi- ma compounds by kefir starter cultures. International ties without cultivation, confirm that the microbial Dairy Journal 13, 529-535. culture isolated until now represent only one part 4. Bottazzi, M.S., Bianchi, F. (1980): A note on scanning electron microscopy of microorganisms associated with of the complex microbial system which influences the kefir granule. Journal of Applied Bacteriology 48, specific features of kefir. However, the classical cul- 265-268. tivation and isolation will still remain irreplaceable 12 T. POGAČIĆ et al.: Microbiota of kefir grains, Mljekarstvo 63 (1), 3-14 (2013)

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