Biodiversity of Yeasts in the Gastrointestinal Ecosystem with Emphasis on Its Importance for the Host

Thinking of the diversity of the microbial world most readers will focus their attention to the bacteria and archea. However, among most of the ecosystems present on Earth, such as soil or intestine of animals, another microbial group has established: the yeasts. Their biodiversity has been hardly investigated although they possess probably as much adaptation potential as bacteria, considering the enormous differences between the habitats and the challenges the different ecosystems must face. In the chapter the authors would like to provide to the reader the state of the art in the field of intestinal yeast research, with focus on the diversity of the yeasts in the gastrointestinal tract of animals – insects and mammals. Up to date there are about 1,500 yeast species known, belonging to two phyla Ascomycota (Suh et al., 2006a) and Basidiomycota (Fell et al., 2000; Scorzetti et al., 2002) of the Dikarya subkingdom (Kurtzman & Fell, 2006). These unicellular fungi are considered as ubiquitous microorganisms, which can be found in a vast variety of different ecological systems associated with terrestrial and underwater flora and fauna (Rosa & Peter, 2006). Nevertheless, based on the currently researches it could be suggested that only 1% of the diversity of yeast species has been described yet (Kurtzman & Fell, 2006). The gastrointestinal tract (GIT) of animals remains a largely unexplored habitat. Most of the yeasts were isolated from the GIT of beetles and other insects. The current knowledge about yeasts’ diversity in the digestive tract of vertebrates, especially of farm animals, is still based generally on the findings from 50’s and 70’s of the XXth Century. Furthermore, the taxonomy of yeasts undergoes continuous revision, e.g., variety of yeasts has double names or even many synonyms. This came off due to the fact that sometimes the same yeasts have been described by different scientists (Kurtzman & Fell, 1998) or several yeasts were invalidly classified, e.g., species assigned to genus Torulopsis were reclassified to the genus Candida (Yarrow & Meyer, 1978). Moreover, it transpires frequently when yeast species previously described based on its phenotypic characteristics has been later phylogenetically analysed and on that basis reclassified into another genus, consequently obtained a new name (Kurtzman & Fell, 2006). Therefore, few yeast species will be mentioned in the further sections with a double name. Furthermore, in this review we will provide some consideration to the importance of the yeasts for the host. Advantages and disadvantages of the contemporary methods used for diversity studies will also be pointed.


Introduction
Thinking of the diversity of the microbial world most readers will focus their attention to the bacteria and archea. However, among most of the ecosystems present on Earth, such as soil or intestine of animals, another microbial group has established: the yeasts. Their biodiversity has been hardly investigated although they possess probably as much adaptation potential as bacteria, considering the enormous differences between the habitats and the challenges the different ecosystems must face. In the chapter the authors would like to provide to the reader the state of the art in the field of intestinal yeast research, with focus on the diversity of the yeasts in the gastrointestinal tract of animals -insects and mammals. Up to date there are about 1,500 yeast species known, belonging to two phyla Ascomycota (Suh et al., 2006a) and Basidiomycota (Fell et al., 2000;Scorzetti et al., 2002) of the Dikarya subkingdom (Kurtzman & Fell, 2006). These unicellular fungi are considered as ubiquitous microorganisms, which can be found in a vast variety of different ecological systems associated with terrestrial and underwater flora and fauna (Rosa & Peter, 2006). Nevertheless, based on the currently researches it could be suggested that only 1% of the diversity of yeast species has been described yet (Kurtzman & Fell, 2006). The gastrointestinal tract (GIT) of animals remains a largely unexplored habitat. Most of the yeasts were isolated from the GIT of beetles and other insects. The current knowledge about yeasts' diversity in the digestive tract of vertebrates, especially of farm animals, is still based generally on the findings from 50's and 70's of the XX th Century. Furthermore, the taxonomy of yeasts undergoes continuous revision, e.g., variety of yeasts has double names or even many synonyms. This came off due to the fact that sometimes the same yeasts have been described by different scientists (Kurtzman & Fell, 1998) or several yeasts were invalidly classified, e.g., species assigned to genus Torulopsis were reclassified to the genus Candida (Yarrow & Meyer, 1978). Moreover, it transpires frequently when yeast species previously described based on its phenotypic characteristics has been later phylogenetically analysed and on that basis reclassified into another genus, consequently obtained a new name (Kurtzman & Fell, 2006). Therefore, few yeast species will be mentioned in the further sections with a double name. Furthermore, in this review we will provide some consideration to the importance of the yeasts for the host. Advantages and disadvantages of the contemporary methods used for diversity studies will also be pointed.

Yeasts associated with the gut of some pests
In the gut of some maize' pests (Diabrotica virgifera, Helicoverpa armigera and Ostrina nubialalis), Molnar et al. (2008) isolated 97 yeast strains; furthermore they detected yeasts as well as other fungi of the genera: Acremonium, Aspergillus, Cladosporium and Fusarium by means of cloning and denaturing gradient gel electrophoresis (DGGE). The occurence of clones was given in percents. All methods reveald that Metschnikowia spp., closely related to Metschnikowia pulcherrima, Cryptococcus spp. (Cr. luteolus, Cr. zeae and Cr. flavescens) as well as Candida spp., bearing close similarity to C. xestobii or C. sake, and Pseudozyma s p p . w e r e t h e m o s t f r e q u e n t l y i d e n t i f i e d y e a s t s . Pichia guiliermondii and Rhodotorula species were less common. Some of occassionaly found yeasts e.g. Aureobasidium pullulans, Candida quercitrusa, Hanseniaspora uvarum, Sprobolomyces coprosmae, Tilletiopsis washingtonensis were detected however only via culturing. There are some publications reporting presence of the yeasts in the gut of mosquitos (Diptera: Culicidae), which are known to be vectors of many diseases in humans. Gusmão et al. (2007; identified Pichia caribbica, Pichia guilliermondii, Pichia (syn. Kodamaea) ohmeri, Candida fermentati and Candida nodaensis in the diverticulum of Aedes aegypti. Ricci et al. (2011a) investigated yeasts in the gut of Anopheles stephensi using molecular and cultivation-dependent methods. Forty six clones that expressed fragments of the 18S rRNA gene retrieved from the gut samples of 6 adults were sequenced. Eleven clones were identified as Wickerhamomyces anomalus, known also as Pichia anomala, while others could be assigned either to genus Candida or Pichia or to unidentified fungus. Moreover, 100 colonies were cultured from 10 insect speciemens, classified based on their morphology and identified as Candida intermedia, Hanseniaspora uvarum and W. anomalus (77%, 15% and 8% respectively) by sequencing analysis of 18S and 26S rRNA genes and ITS fragments. W. anomalus was detectable using both approaches. Furthermore, Ricci et al. (2011a;2011b) observed the presence of W. anomalus in the midgut of different mosquitos species Anopheles stephensi, Anopheles gambiae, Aedes albopictus and Aedes aegypti of both sexes as well as on larvae, pupae and gonads, thereby supposed close relationship between this yeast species and mosquitos.

Yeasts in the digestive tract of lacewings
Lacewings (Neuroptera: Chrysopidae) are one of the predators admitted as biological control agents of pests. During the scanning and transmission electron microscopical studies, a large numbers of yeast cells were observed within lacewings' alimentary tract Chen et al., 2006).  investigated yeasts in the different parts: diverticulum, foregut, midgut, and hindgut of digestive tract of 24 lacewing adults (Chrysoperla rufilabris) collected at two field locations in Mississippi. With the exception of 7 insects that were yeasts-free, lacewings harboured a high concentration (≈ 10 3 colony forming units; CFU) of yeasts distributed in the all analysed gut sections; however the highest (5.4x10 5 CFU/g) density was in diverticulum. In total 752 yeasts were isolated in the study and arranged in five groups based on their phenotypic properties; some specimens were randomly chosen from each group for further genotyping analysis. Interestingly, 89% of the isolates were identified as Metschnikowia pulcherrima and the remaining 11% involved either Cryptococcus victoriae or Cryptococcus luteolus or strains that could not be assigned by the authors to any known species. Sometimes, closely related yeast species could be separated only according to the genotypic characterization, while they were showing similar physiological properties (Kurtzman & Fell, 2006) as it was the case in the study of Suh et al. (2004a).  1) were discovered in the gut of other members of the Neuroptera, too .

Yeasts in the digestive tract of beetles
At the present time, the most yeasts were isolated from the digestive tract of beetles (Coleoptera). Shifrine & Phaff (1956)  ernobii and the strains related to the one Candida sp. were prevalent in all parts of gut and frass and P. guilliermondii and C. ernobii were cultured most frequently from the posterior midgut.
In relation to high number of the yeast isolates (richness) described above, comparatively low yeast diversity was found in the assemblage of Dendroctonus beetles. It thereby underlined the impact of the host and/or environmental factors on the yeasts diversity. Nevertheless, examination of yeasts harbouring the GIT of beetles from 27 families reviled a huge variety of yeasts (Suh et al., 2005a).  During three-years-period, Suh et al. (2005a) isolated about 650 yeasts from the gut of diverse beetles collected from the south-eastern USA and Panama. Sequence analyses of the D1&D2 domains of LSU rRNA gene revealed 290 single species belonging to at least 27 taxa (Fig. 1.); the great majority of which were ascomycetous and some basidiomycetous yeasts. It is noteworthy that nearly 200 yeasts determined throughout the study were considered by the authors to represent new, not yet described species. In the meantime, some of them (table 1) were characterized by Suh, Nguyen, Blackwell and their co-workers. Based on their observation Suh et al. (2005a) suggested that almost each beetle species may be a host for at least one unknown yeast species. In the last decades, describing of many novel species of yeasts isolated from the gut of insects corroborates this supposition.

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The Dynamical Processes of Biodiversity -Case Studies of Evolution and Spatial Distribution 288 Nowadays, there are over one million of accepted insect species; however, their number has yearly increased and is still largely undiscovered (Chapman, 2009). Thus, it can be supposed that the number of yeasts would tremendously rise, even if only the intestinal tracts of the currently known insects were explored.

Yeasts' diversity in the GIT of vertebrates with focus on farm animals
The more intensive investigations of the yeast population present in the GIT of vertebrates, based on various cultivation procedures, began in the fifties of the XX th Century. Van Uden et al. (1958) and Van Uden & Carmo Sousa (1957b) examined yeasts in the caecal samples of large number of animals: 252 cattle, 252 horses, 503 sheep, 250 goats and 250 pigs. Yeasts were also studied by Parle (1957) in the digestive tract of cows, rabbits, sheep, guinea pigs, opossums, monkeys, cats, dogs, hedgehogs, mice, pigs and rats. Lund (1974) explored yeasts and moulds in the bovine rumen. Lately, yeasts were also described in the intestinal tract of reptiles (Kostka et al., 1997), birds (Cafarchia et al., 2006;Brilhante et al., 2010;Costa et al., 2010), mice (Scupham et al., 2006), dogs (Brito et al., 2009) and fish (Gatesoupe, 2007). In these studies, the scientists have detected various ascomycetous and basidiomycetous yeasts chiefly representing the genera Candida, Trichosporon, Pichia, Rhodotorula, Debaryomyces, Kluyveromyces and Saccharomyces. In general, the diversity of the yeast population depended on the host; but many species occurred at diverse, also not intestinal ecosystems; and several exhibited direct relationship to the individual animal. It should be noticed, however, that yeasts could not be always isolated from the investigated GIT and often they were present in small numbers. Nevertheless, taking into consideration the scarce information existing on yeasts in the gastrointestinal ecosystems of vertebrates, it is well known that relatively high variety as well as quantity of yeasts can be found in the GIT of pigs. Here, the yeasts diversity in the GIT of farm animals representing diverse nutritional types: omnivores (pig), monogastric herbivores (horse) and ruminants will stay in focus and will be compared.

Yeasts in the GIT of pigs
Comparatively to all animals investigated in the study of Van Uden et al. (1958), the most frequent occurrence (88.8%) of yeasts was detected in the caecum of pigs (horses 52.4%, cattle 46.8%, sheep 6.8%, and goats 6.4%). The yeasts Candida slooffiae, Candida krusei, Saccharomyces telluris, Candida albicans, Candida (Torulopsis) glabrata, were commonly found in the porcine gut. However, C. slooffiae was isolated most frequently (48.4%). A few other yeasts such as Saccharomyces spp., Pichia membranifaciens, Pichia farinose and Candida mycoderma could also be identified. Roughly the same situation has been confirmed in the following studies (Van Uden & Carmo-Sousa, 1962;Mehnert & Koch, 1963), where the scientists isolated almost the same variety of yeasts from the different parts of porcine GIT. After investigation of digesta samples collected from stomach, three parts of small intestine as well as caecum and rectum of healthy 57 pigs, Van Uden & Carmo Sousa (1962) reported high animal-individual qualitative and quantitative variability if the yeast occupation. In total 15 yeast species were identified; while C. slooffiae was present in 27 pigs, many other species mentioned above occurred only sporadically. Moreover, C. slooffiae was highly abundant, from 10 2 to 10 3 CFU/g of chyme in the stomach and up to 10 6 CFU/g intestine contents in the rectum. A still higher occurrence of yeasts in the gut of pigs was detected by Mehnert & Koch (1963), up to 10 7 CFU/g in rectum. They isolated 292 yeasts from 200 digesta samples collected from stomach and rectum from 98 (of 100 examined) pigs. Apart from the C. slooffiae which was detectable in 75% of pigs, yeast species such as C. krusei, S. telluris, C. albicans, C. glabrata, C. tropicalis, C. parapsilosis and C. pintolopesii (60%, 26%, 9%, 4%, 3%, 3% and 2% respectively) were isolated, too. Also in this study the appearance of yeasts was variable within a part of the GIT and among examined animals. Thus, stomach was generally colonized by yeasts at lesser intense than rectum. In most animals, C. slooffiae and C. krusei were detected both in stomach and rectum, while just in a few cases the yeasts could be found only in a single part of the GIT. C. slooffiae and its closely related species: S. telluris and C. pintolopesii have been newly molecularly investigated and based on multigene sequence analyses they were assigned to the teleomorphic genus Kazachstania (Kurtzman et al., 2005). Recently, Urubschurov et al. (2008) described yeasts' diversity in the gut of piglets around weaning which were reared at two facilities: at experimental farm (EF) with improved husbandry conditions than at commercial farm (CF). Most piglets, 33 at CF and 35 at EF, were weaned at 28 days (d) of age and fed with the same diet until 39 d in both farms. A number of piglets, namely 18 at CF and 9 at EF, were left by the sows without additional feeding. All piglets were sacrificed at 39 d of age and digesta samples from GIT were collected. D1&D2 domains of 26S rRNA gene from 173 yeast isolates obtained from 95 piglets were sequenced. The alignment to known sequences revealed close relationship to 17 species, of which the most dominated are presented in figure 2. Urubschurov et al. (2008) observed distinction of yeasts variety between both facilities that were proven by calculation of different similarity and diversity indices. In piglets from CF Galactomyces geotrichum, Kazachstania slooffiae and Candida catenulata were the most abundant ones and the other were present only at low abundances. Unlike at CF, at EF two species, namely K. slooffiae and C. glabrata were found to be the most dominating ones and the others were rarely isolated. Some of the other species could be found in piglets either only at the EF (P. fermentans, C. tropicalis, C. oleophila, C. parapsilosis, P. guilliermondii, Rh. mucillaginosa, T. montevideense) or at the CF (C. silvae and P. farinose). This study provided evidence for association of K. slooffiae with the porcine GIT. K (C.) slooffiae was found for the first time in 6 of 252 examined horses (Van Uden & Carmo-Sousa, 1957a), however, due to frequent occurrence and high concentration in the porcine digestive tract it can be considered to be specific for pigs. Furthermore, compared to other yeasts occurring in the porcine GIT, which can survive also in other ecological niches outside the animals, K (C.) slooffiae seems to be well adapted to the porcine gastrointestinal habitat, as this species is one of those that need high temperature to grow, comparable to the temperature of animal body, being characterized as thermophilic or psychrophobic (Travassos & Cury, 1971).

Yeasts in the equine GIT
Several investigators focused on the effect of yeast, Saccharomyces cerevisiae, on intestinal microbiota of horses and on the digestibility of different diets (e.g. Medina et al., 2002;Jouany et al., 2008;. But little is known about the yeasts naturally occurring in the equine gut. Van Uden et al., (1958) studied yeasts in the caecal contents of 252 horses, and these authors revealed presence of yeasts in over half (52.4%) of the investigated animals.

Yeasts in the GIT of ruminants
As reported by Lund (1974), a different number of yeasts has been observed in the ruminal contents from cows and sheep depending on the culture conditions and incubation temperature. After at 39°C incubation of the rumen contents collected at different times from five cows, Clarke & Menna (1961) Lund (1974) examined fungal microbiota in rumen liquid of 10 fistulated and 2 non fistulated cows fed different diets. Forty nine collected samples were plated and incubated simultaneously at 25°C and at 39°C. A considerably larger number of yeast colonies, up to 1000 fold and about 20 fold on average, were observed after incubation at 25°C, while sometimes even none could be obtain after incubation at 39°C. Nevertheless, only 67 yeast isolates growing at 39°C, as it is the temperature proper to the rumen environment, were used for further identification. The largest share (77.6%) of them was identified as C. krusei, T. cutaneum and T. capitatum and the rest were C. valida, C. ingens, C. pintolepesii, Klyveromyces bulgaricus, Saccharomycopsis lipolytica and Hansenula fabianii. Other fungi (molds) belonging to the order Mucorales have been also found in the study. Additionally, Lund (1974) observed two yeast species C. krusei and T. capitatum in faeces of the cattle. However, their counts were lower than in the rumen samples of corresponding host. Later, Lund (1980) conducted a similar study where the researcher investigated yeasts microbiota in 16 rumen samples of musk oxen. Only 6 strains of one species, C. parapsilosis were identified after incubation at 37°C, while 41 yeast strains belonging to Candida spp., Cryptococcus spp., Trichosporon spp., Rhodotorula spp., Torulopsis spp. and Pichia spp. were characterized after growing at 25°C. But, the authors indicated that the rumen contents were kept frozen for a long period (more than 7 weeks), what could have had considerable effects on yeast colonization. As mentioned above, Van Uden et al. (1958) (503) and goats (250). Among the investigated animals, cattle showed the highest (46.8%) occurrence of yeasts, whereas just a few yeasts could be found in sheep and goats, 6.8% and 6.4% of the animals, respectively. The most frequently isolated yeasts were C. tropicalis and C. krusei in cattle, and C. albicans in sheep. These species were also isolated from the goats, but just two times each; and C. glabrata four times. A few other yeasts identified as members of Saccharomyces spp., Candida spp. and Pichia spp. have been found only occasionally. Quite similar results regarding yeast colonization have been obtained in the cultivation dependent studies (Clarke & Menna 1961;Lund 1974;1980;Van Uden et al. 1958) from different geographical regions. Shin et al. (2004) explored different rumen samples (fluid, solid and epithelium) from one cow, examined for yeasts population using molecular approaches. Shin et al. (2004) have succeeded to obtain 97 clones containing 26S rRNA gene fragments from the three types of samples and to assign them to the different phylogenetic groups. Compared to 4 phylotypes from the rumen epithelium showing the closest relatedness to Geotrichum silvicola, Acremonium alternatum, Pseudozyma rugulosa (up to 99%) and Galactomyces sp. (97%), and 2 phylotypes (Geotrichum silvicola, 99% and Galactomyces sp., 97%) from the rumen solid, the highest yeast' diversity was observed in the samples of rumen fluid revealing presence of 15 various phylotypes. Only 5 (Setosphaeria monoceras, Raciborskiomyces longisetosum, Magnaporthe grisea, Ustilago affinis and Pseudozyma rugulosa) of the 15 phylotypes showed 99% identity with the sequences deposited at the NCBI GenBank. The identification rate of the others belonging also to the classes Pezizomycotina, Urediniomycetes, Saccharomycotina and Hymenomycetes ranged from 91 to 98%. These phylotypes could represent new species, because in yeasts more than 1% of the nucleotide divergence in D1&D2 domains of the 26S rRNA gene may represent a separate species (Kurtzman & Fell, 2006). In spite of the lack of inter-individual comparison, this study showed a potential existence of the other yeasts that have not been discovered yet.

Methods for investigating biodiversity of the yeasts from GIT
From the cited references it is obvious, the biodiversity studies depend very much on the applied method. However, this is beyond the scope of this chapter to provide very detailed description of all possible methods that could be used for studies on yeasts' diversity. Nor calculation of the different biodiversity indices is in the focus of the paragraph. This paragraph is meant to provide short discussion on the existing possibilities, their limitations and advantages, and provide the reader with some input for consideration which methods he or she would choose for his/her studies. Any application of either method mentioned below requires correct sampling of the material. Studying the biodiversity of the yeasts harbouring the GIT the dominating yeasts are in focus of most studies, as well as their abundance and changes of the abundance in time and in relation to the diet. For these purposes faecal or digesta samples have been collected from large animals (Urubschurov et al., 2008; or whole intestines from e.g. insects have been dissected (Suh et al., 2004b;2005a;Nguyen et al., 2007). Whereas rain worms, termites or other small animals can provide the whole GIT for the studies, only part of contents of wall of the GIT can be studied in large animals. Therefore the choice of sampling is the first bottle neck in the studies on yeasts biodiversity in the GIT. Following proceedings such as homogenization, concentration or dilution of the samples must be hereby additionally considered.
Among the methods applied for investigating the biodiversity of yeasts harbouring the GIT of animals, cultivation and morphological and/or biochemical identification have been the most often used for more than 150 years. However, these methods bear limitations such as the choice of the right cultivation medium, pH, temperature and moisture. Furthermore the yeast species that need more time for growth and are at lower abundance in the community cannot be identified in this way. It has been accepted that every ecosystem consists, next to cultivable organisms, also of viable but non-cultivable (VBNC) microorganisms, that contemporarily cannot be cultivated in laboratory because of nutrient limitation or lack of optimal living conditions (Edwards, 2000). This is why only approximately 1% of yeast species could be described so far (Kurtzman & Fell, 2006). Sabouraud agar is the medium most commonly used for cultivation of yeasts from clinical or ecological samples (Odds, 1991), however many others have been used for industrial purposes, providing alternatives for cultivation of more demanding species (King et al., 1986;Jarvis & Williams, 1987;Fleet, 1990;Deak, 1991). It is to remember, that various species can give similar colonies, and the same species can grow in a different way under different conditions. Cultivated species can be however observed under microscope, what helps for identification of the isolates. Spectrophotometric methods such as MALDI-TOF could also provide fast and good tool for identification of the isolates. Molecular methods can be also applied for identification of isolates, e.g. pyrosequencing of target genes (Borman et al., 2009;. Further development of modified media and combinations of temperature, pH, aerobic/anaerobic conditions and moisture would probably increase the number of isolated yeasts, it is however laborious and very time consuming. Cultivation-independent methods which have been used for the last two decades provided the researches with fast and specific tools for the biodiversity studies. Polymerase chain reaction (PCR), DNA-DNA hybridization or fluorescence in situ hybridization (FISH) applying probes targeting the RNA allow in theory detection of 1 single colony present in a sample population. Further separation of the specific DNA fragments performing denaturing or temperature gradient gel electrophoresis (DGGE / TGGE) allows studying the diversity of the complex community (Cocolin et al., 2002;Prakitchaiwattana et al., 2004;Molnar et al., 2008). Other molecular methods could be also applied for identification of members of a community, e.g. terminal restriction fragment length polymorphism (T-RFLP), amplified fragment length polymorphism (AFLP), multiple-locus variable number tandem repeat analysis (MLVA) (e.g. Tiedje et al., 1999;Gemmer et al., 2002). These methods are very specific, allowing targeting of specified species and thus quantification of the yeasts and calculating the biodiversity. The largest limitation for methods based on PCR is the low sensitivity, as the practice shows only 1-2% of the community can be detected in this way (Macnaughton et al., 1999). Furthermore, fingerprint methods have the bias combined to the fact that amplicons form different species with sequences of similar energetic profile may migrate to the same positions; multiple gene copies with slight sequence differences may give multiple bands for one strain or species; finally some species are phylogeneticaly very similar (Lachance et al., 2003;Janczyk et al., 2006;Borman et al., 2010). The design of probes for direct targeting needs knowledge on the sequence of the target gene and differences between species. Pyrosequencing and other high-throughput methods provide a fast and very efficient tool for identification of the members of the complex populations. Metagenome analyses targeting the D1/D2 domain of the 26S rRNA gene or the internal transcribed regions (ITSs) allow distinction of the yeasts (Kurtzman & Fell, 2006) and seem to be very suitable methods

Biodiversity of Yeasts in the Gastrointestinal
Ecosystem with Emphasis on Its Importance for the Host 293 for studying the yeast biodiversity in the GIT of animals. Pyrosequencing is a rapid method providing up to several thousands of sequences per sample in just few days. Followed by bioinformatics processing, alignment to known species is performed resulting not only in a phylogenetic tree but also in description of the species diversity. Unknown species can be also detected in this way. The high cost provides the limitation for the wide application of this method; however it is to expect that in the near future the high-throughput sequencing will be as expensive as the other commonly used molecular tools. A microarray has been recently developed allowing characterization of pig GIT bacterial community, targeting over 800 phylotypes (Pérez Gutiérrez, 2010). Microarrays for yeasts would need to be developed to provide further molecular tool for studying the biodiversity and its changes caused by different extrinsic factors.

Role of yeasts in GIT
Studying diversity of yeasts harbouring the GIT of animals would be incomplete without consideration of the role that these microorganisms play for the host. For years the yeasts harbouring the GIT of animals and humans have been considered rather as harmful to the host's health. Indeed, there are some species belonging to Candida, Cryptococcus, Malassezia, Trichosporon and Geotrichum that could be pathogenic to members of the Animal kingdom (Fidel et al., 1999;Girmenia et al., 2005;Cabañes, 2010). Furthermore, many researchers have evaluated yeasts in association with various diseases and if they found representatives of this group they acted against them applying medical treatment (Schulze & Sonnenborn, 2009). However, there is just as little known about yeasts harbouring the GIT of healthy animals to understand their importance there, and growing evidences appear for their role in the proper function and survival of the host. In fact, the current knowledge about yeasts in the digestive tract of vertebrates is still based on the findings from 50's and 70's of the XX th Century; therefore there is a great demand for the scientific evaluation in this field. As enough reports exist concerning pathogenic yeasts, in this paragraph a possible positive impact of yeasts on the gut ecology and host health will be discussed. There are nice reviews (e.g. Phaff & Starmer, 1987;Ganter, 2006) pronouncing a yeast-insect relationship. Gatesoupe (2007) gave an insight into the ecology of yeasts naturally occurring in the intestinal tract of fish, and thereby emphasized a possible importance of yeasts to the host.
Similarily to the probiotic strains of Saccharomyces cerevisiae (Buts, 2009), the cells of some intestinal yeasts could have a trophic effects since they provide a source of B vitamins, proteins, trace minerals and essential amino acids. Besides, the major portion (> 90%) of the yeast cell walls comprise of polysaccharides such as β-glucans, mannans and chitin, which composition and structure are specific for individual yeast (Latgé, 2007). In many human and animals studies, β-glucans and mannans have been comprehensively investigated; they may play important diverse roles for the host immune system and exhibit antimicrobial activity against bacteria thereby influencing the establishment of the intestinal microbiota and promising to promote host's health. Therefore, several studies concentrated on use of the live or dead yeast cells in human and animal nutrition as supplements or as a remedy for acute diarrhoea in humans (Bekatorou et al., 2006;Buts & De Keyser, 2006;Fleet, 2007;Buts, 2009). Furthermore, due to production of several enzymes, some yeast species, e.g. found in the gut of termites (Schäfer et al., 1996;Molnar et al., 2004) and beetles (Suh et al., 2003), are able to degrade hemicelluloses that are being the main carbohydrates of herbivorous diet, and also detoxify toxins that can appear in the feed. The possibility cannot b e e x c l u d e d t h a t s o m e y e a s t s h a r b o u r i n g GIT of herbivorous animals may produce extracellular enzymes (e.g. exohemicellulases, exocellulases) or show endocellulolytic activity, and thereby contribute to their digestion by braking down complex, indigestible fibre into simple carbohydrates. It is still a prevalent opinion, that yeasts harbouring the digestive tract of animals have only minor importance for the host. The main scientific argument up to date is the negligible quantity of yeasts. Nevertheless, yeasts may be of physiological relevance, even though they are present to a much lesser extent than bacteria. In fact, yeasts could provide a relevant biomass, as their have a cell volume 30-to 100-fold higher than bacteria (Gatesoupe, 2007). Commensal yeasts may interact with intestinal bacteria and due to this interplay affect microbial diversity and host organism. An example of such yeasts-bacteria interrelationship provides the study of Urubschurov et al. (2011) who examined changes of yeasts and major bacterial groups (lactobacilli, enterobacteria and enterococci) in the faeces of piglets after weaning. They observed that the increase of yeasts number, where the dominating species was Kazachstania slooffiae, significantly correlated with the increase of lactobacilli and decrease of enterobacteria numbers. Other studies hypothesized that specific yeasts frequently occurred in high quantity at the digestive tract of lacewings  and mosquitoes (Ricci et al., 2011a;2011b) and were symbiotically related to the host. These first indications need further confirmation but they already show that the yeasts cannot be considered negligible any more.

Conclusions
Yeasts belong to gastrointestinal microbiota even though they are not as frequent as the bacteria or archea. However, it does not disclude their importance for the host and for the members of the complex microbial community. Despite long time of research, whereas our knowledge on bacterial intestinal communities has increased dramatically during last decade, still only little is known on the intestinal yeasts. This review provides an overview on what has been done in the field of intestinal yeast research up till now, and the reader surely agrees that much more work needs to be done. Not only the diversity of the intestinal yeasts and its changes depending on different conditions shall be further uncovered. The importance of yeasts for the host and the interplay between yeasts and other members of the intestinal milieu is also waiting to be explored. New cultivation techniques; cultivation combined with molecular techniques will need to be further developed to overcome the existing limitations. Driven by the increasing necessity to define the biological diversity frame of widespread, endemic and threatened species, as well as by the stimulating chance to describe new species, the study of the evolutive and spatial dynamics is in constant execution. Systematic overviews, biogeographic and phylogenic backgrounds, species composition and distribution in restricted areas are focal topics of the 15 interesting independent chapters collected in this book, chosen to offer to the reader an overall view of the present condition in which our planet is.

How to reference
In order to correctly reference this scholarly work, feel free to copy and paste the following: Vladimir Urubschurov and Pawel Janczyk (2011). Biodiversity of Yeasts in the Gastrointestinal Ecosystem with Emphasis on Its Importance for the Host, The Dynamical Processes of Biodiversity -Case Studies of Evolution and Spatial Distribution, PhD. Oscar Grillo (Ed.), ISBN: 978-953-307-772-7, InTech, Available from: http://www.intechopen.com/books/the-dynamical-processes-of-biodiversity-case-studies-of-evolution-andspatial-distribution/biodiversity-of-yeasts-in-the-gastrointestinal-ecosystem-with-emphasis-on-its-importancefor-the-hos