Introduction: been possible using qualitative and quantitative techniques.

Introduction: Based on a meta-analysis covering severallarge Sanger-sequencing studies of human gut samples from different populationsthe most numerically dominant phyla within the intestinal microbial communityare the firmicutes and bacteroidetes that comprise more than 90% of the totalbacteria.

The levels and diversity of the microbial community within thegastrointestinal tract can differ according to the location as differentphysicochemical properties and substrate availability dictate the environmentalconditions. This enormous microbial community has been estimated to be in theregion of 1014 microorganisms, the collective gene set of which is termed the”microbiome” and is thought to contain approximately 100 times the number ofgenes in the human genome (Backhed et al. The distal large intestine is thearea of highest colonization with more than 500 differ- ent species (with someestimates suggesting up to 1,000 species) with potentially up to 100 billionmicrobial inhabitants (Boyle and Tang 2006. Other bacterial phyla that havebeen isolated include also actinobacteria, gammaproteobacteria, verrucomicrobia,and betaproteobacteria (Hamady and Knight 2009. The total area of the mucosalsurface of the human gastrointestinal tract is 300 m2 which makes it thelargest surface area in the body that inter- acts with the external environment(Bjorksten 2006. This has led to collaborative research projects the largest ofwhich is probably the Human Microbiome Project, which is a worldwide strategyaiming to further delineate the extent of both human and microbial diversity.For example, all humans possess several hundred species within each genus intheir gut, however the foremost species within that genus will differconsiderably between individuals (Simon and Gorbach 1984. More recently, use ofa culture-independent approach has revealed the complexity of the residentmicrobial communities; this was enabled by use of oligonucleotide probes basedon 16S rRNA gene sequences.

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Further classification of bacteria based uponphylogenetic comparisons of the 16S rRNA sequences has been possible usingqualitative and quantitative techniques. For example, PCR reactions andfluorescent in situ hybridization (FISH) use primers and probes respectivelywhich tar- get bacteria based on their 16S rRNA sequences. It is estimated thatthese specific probes have enabled identification of up to 80% of the totalmicrobial diversity within the intestinal. Differences in microbiotacomposition have been found between infants born in different countries andraised with different diets and even between hospital wards (Adlerberth et al.Probably the most important factors in determining the initial colonizationpattern are the type of delivery at birth (either vaginal or caesarean section)and the initial diet (whether the newborn is fed mother’s milk or infantformula. The composition of the adult microbiota is thought to be more stable,however acute effects can disrupt this homeostasis for example, duringantibiotic treatment, after gastrointestinal surgery, exposure to radiation,and in some infectious.

It can be thought of as a ‘microbial organ’ as theprocesses performed by this diverse population are extensive; it cancommunicate with itself (bacteria: bacteria) and with the host (bacteria:human. The presence of the gut microbiota has influenced human evolution inthat the human host cannot perform certain vital intestinal functions withoutthem. Maintenance of homeostasis is an interactive process between the bacteriaand host epithelia which influences both intestinal physiology and thederivation and distribution of energy. Germ-free animal models have provideduseful insights into the roles of the microbiota and the extent of interaction.The major source of energy from colonic fermentation is from carbohydrates,which include large polysaccharides (such as plant derived pectin,hemicellulose, cellulose, gums, and resistant starch) and also less complexcarbohydrates such as oligosaccharides and non-absorbed alcohols and sugars (Cummingset al.

This is an example of a symbiotic relationship as the human host bene-fits from a wide array of microbial enzymes which are outside the host’s ownbiochemical repertoire. This provides the host with a source of energy from thefood ingested and also to the micro flora which in turn is used to sustain themicrobial community. In contrast, the left side of the colon has lesscarbohydrate fermentation, the pH is less acidic, and it is associated with anincrease in proteolysis which has been linked to the production of harmfulnitrogenous products, which accounts for the recommendation to eat acarbohydrate and fiber enriched diet (Guarner and Malagelada 2003.

Fermentationactivity differs according to area within the gut, the most metabolicallyactive area is the caecum and right colon, consequently this is an area ofrapid bacterial growth, low pH (5–6) and rapid generation of SCFA as a resultof carbohydrate fermentation (Cummings et al. Fermentation can also occur withnoncarbohydrate substrates, therefore proteolytic fermentation (of proteins andpeptides) also generates potentially damaging compounds such as ammonia,amines, and phenolic compounds (Macfarlane et al. The main fermentation endproducts are short chain fatty acids (SCFA) which are small organic moleculesabsorbed. THE GUT MICROBIOTA AND AUGMENTATION OFHOST DEFENSE: Anti-pathogenicActivity: Bacteriocins A useful feature of probiotic bacteria is the ability ofsome strains to demonstrate a specific inhibitory activity towards otherorganisms which can sometimes be against pathogenic strains. It is thought thatthe gut microbiota can positively influence the immune system by maintaining asufficiently stimulated mucosal immune system, which can react quickly to anenvironmental antigen but which can also differentiate between pathogens andcom- mensal organisms, therefore not promoting an immune response un-necessarily. Bacteriocinogenic lactic acid bacteria (LAB) strains that areactive against food spoilage or pathogens are still the subject of researchinterest as they represent a source of natural food preservatives, aregenerally regarded as safe, and are well tolerated. More recently, this hasbeen redefined as “extracellularly released primary or modified products ofbacterial ribosomal synthesis, which can have a relatively narrow spectrum ofbactericidal activity, characterized by inclusion of at least some strains ofthe same species as the producer bacterium and against which the producerstrain has some mechanism(s) of self protection,” (Jack et al. This strategymakes it more difficult for pathogens to interact with epithelial cells; thismeans the pathogen can be competitively excluded from the epithelial surfacewhich can prevent adhesion of the pathogen and possibly subsequent infectionprocesses.

It can also be more specific due to production of bacteriocins whichare peptides defined as “antimicrobial proteins that are active againstbacteria, usually active against the producer organism and most often producedby Gram positive bacteria,” (Tagg 1976. The current model defined byKlaenhammer (1993) proposes four main classes; lantibiotics, nonlantibioticpeptides, nonlantibiotic large heat labile proteins, and complex bacteriocins(that contain essential lipid/protein residues in addition to protein.PROBIOTICS: Bifidobacteria and LactobacilliProbiotics are most commonly found within the genera Lactobacillus andBifidobacterium although exceptions do occur. The number of recognizedorganisms classified as Lactobacilli has in- creased, for example in 1984 therewere 44 reported Lactobacillus species, however in 2003 this reached 88 and in2007 reached 135 species (Bernardeau et al. This enzyme is also used as ataxonomic tool to identify Bifidobacterium species; however, it cannot be usedto discriminate between species (Lauer and Kandler 1983. Although sharing somephenotypic features with lactic acid bacteria, the genus Bifidobacterium isactually related to the Actinomycetes. Another common probiotic group includesthe bifidobacteria, the common human group isolates include B. This not onlyreflects the diversity of the Lac- tobacillus genus but also that with thecurrent progression of molecular techniques maybe other genera will also berevised.

Lactobacilli comprise a diverse group of Gram positive bacteria,typical features include: nonsporulation, catalase negative, devoid ofcytochromes, an- aerobic (sometimes aerotolerant) and acid tolerant cocci orrods which produce lactic acid as a major fermentation end product (Axelsson1998. Lactobacilli contain species with 33–53% chromosomal G+C content and havebeen classified according to phenotypic characteristics, fermentation/metabolic.A number of reasons could be influential including lack of standardization withstudy protocols or therapies (including antibiotics and probiotics used.

Therefore, probiotics are finding applications alongside modern medicine as itis thought that the incidence or severity of associated infections can bereduced during probiotic co- administration. boulardii and Lactobacillusspecies, however further studies were necessary to compensate for a lack ofplacebo design in studies already completed (Cremonini et al. ClostridiumDifficile Within the healthy population Clostridium difficile is considered tobe present at approximately 3%, however during hospital admissions it can riseto between 15% and 35%, which has recently been highlighted in the media.difficile is an opportunistic pathogen and recent figures in the United Statesshow it is the most common cause of nosocomial diarrhea with 15–25% of adultpatients suffering from it (Bartlett and Gerding, 2008. However, patients witha prior episode showed significant inhibition of reoccurrence (McFar- land etal. Diarrhea is a common side effect of the administration of antimicrobialtherapy such as antibiotic administration. Probiotics have been used as anantibiotic adjunct, for example S. 2009) however despite further research thereappears to be no definitive conclusions regarding probiotic efficiacy as anadjuvant therapy and in preventing patient relapse.

boulardii preparation, forexample 193 patients taking ?-lactam antibiotics were divided into two groups. Traveler’s Diarrhea with increasingworldwide travel, traveler’s diarrhea is a commonly reported complaint and itis estimated to affect 20–50% of travelers from industrialized countries whenvisiting tropical or semitropical countries (Fric 2002. There are severalpostulated antiviral mechanisms including competitive inhibition of the virusfrom binding to the epithelial surface, general immune enhancement (thus moreefficient virus inactivation), increased mucin gene expression (as glycosylatedmucins trap rotavirus), and production of antiviral sub- stances (found in someprobiotic supernatants. Acute childhood diarrhea worldwide is most commonlycaused by rotavirus and can be an important con- tributor to infant mortality,thus probiotics have been used to both treat and prevent the disease. A studyof 100 children admitted to a hospital with acute viral diarrhea demonstrated areduced duration of disease when the treatment group received Lactobacillus GGtherapy compared to a control, which received rehydration salts alone (Guarinoet al.

In fact, they con- cluded that Lactobacillus GG was effective atreducing the symptoms of not only rotavirus-positive subjects but also thosethat had diarrhea not caused by rotavirus. Viral Diarrhea A number of studieshave reported the efficacy of Lactobacillus GG in terms of its antiviraleffects. Although Lactobacillus GG is the most commonly reported probiotic inthis research, others have been used such as Bifidobacterium lactis BB-12 andLactobacillus reuteri SD2222 (Guarino et al. Several studies suggest thattravelers can expect a 20–50% reduction in the risk of illness if LactobacillusGG is con- sumed when entering an area of high risk (Hilton et al. An evenlarger study was conducted with 287 children with viral diarrhea.

The treatmentgroup received oral rehydration salts (standard therapy) with addition ofLactobacillus GG; the control group received oral rehydration salts with nolive bacteria.Probiotics have beenshown to boost host immune status via stimulation of specific and nonspecificimmune pathways involving modification and regulation of humoral, cellular, andnonspecific immunity (Cross et al. In summary, the immunomodulation process iscomplex and dependent on both host and the probiotic strain and could beinfluenced by host immune status, amount of probiotic administered, duration ofadministration, and strain viability. Inflammatory Conditions Inflammatorybowel disease (IBD) is a term for immune-mediated conditions which result inchronic intestinal inflammation and are not attributable to specific pathogens.

Some reported positive in vivo effects of probiotics including amplified mucusproduction, macrophage activation by Lactobacilli signaling, stimulation ofsecretory IgA, decreased proinflammatory cytokine production, and increasedperipheral immunoglobulin production. Probiotics can enhance barrier functionand stimulate specific and nonspecific immune responses in the host, thereforecould theoretically decrease the adherence of pathogens (and consequentinvasion. Allergic diseases such as asthma, atopic eczema, allergies, allergicrhinitis, coupled with inflammatory bowel disorders such as Crohn’s disease,chronic inflammatory bowel disease, and ulcerative colitis have all been linkedto impaired gut-barrier dysfunction (Sanderson and Walker 1993. The best clinicallydocumented effects of probiotics have been in treatment of acute diarrhea buthave been also documented for immune linked responses, for example in gutmucosal normalization and down-regulation of hypersensitivity reactions(Isolauri et al. Immunomodulation Inflammatory and allergic conditions aremajor problems to world health; they are thought to arise from a combination offactors including genetics and immunological disturbance (allergens andantigens. In animal models, age related decreased cytokine production has beenshown to be reversed with probiotic supplementation (Muscettola et al. Recentstudies have shown also the ability of probiotics to modulate the immune systemin the elderly, including activation of natural killer cells (Gill et al. A meta- analysis using data obtained from20 trials (with n = 1,404 subjects) concluded that probiotics did indeedprovide some quantifiable benefit in terms of overall symptom reduction whencompared to placebo, however comparison was hampered for several reasonsincluding pro- biotic species used, administration period, study sample size,and dos- age (McFarland and Dublin 2008.

One study found no beneficial effectof Lactobacillus GG on IBS symptoms in infants when compared to the control(Bausserman and Michail 2005. The first study found that patients successfullystayed in remission during the study (Cashman and Shanahan 2003. The secondstudy showed that the probiotics could have beneficial effects during periodsof active UC (Kato et al. Recent studies have compared the relapse rates of UCsufferers with two different treatments in a double-dummy blind double trialwhere patients received either mesalazine (3 × 500 mg/day) or E. Variousstudies have been conducted which look at easing symptoms or preventingreoccurrence of symptoms (Halpern et al. Cocktails of probiotics have been usedand found to be effective in maintenance of remission.

Studies inexperimentally-induced animal models of colitis have shown beneficial effectsof probiotics in terms of reduction of intestinalPREBIOTICS: Although prebiotic and probioticapproaches are likely to share common mechanisms of action since their effectis impacted through the increase of beneficial colonic bacteria in both cases,they differ in specific effects on microbiota composition and host metabolism.Selective Stimulation of Beneficial Bacteria In the GI tract, prebioticsselectively stimulate indigenous beneficial bacteria such as bifidobacteria andlactobacilli (Reid et al. Although the Prebiotics 35 effect of certainprebiotic-like inulin-type fructans on Bifidobacterium population is welldocumented, in vivo studies usually tend to consider the bifidobacterialcommunity as a whole, ignoring interspecies differences (Macfarlane et al.Prebiotic Effects The effects of prebiotics have been primarily directed towardthe colon, but an increased amount of evidence demonstrates that prebioticsexert their effect beyond the GI tract (Lenoir-Wijnkoop et al. PrebioticEffects The effects of prebiotics have been primarily directed toward thecolon, but an increased amount of evidence demonstrates that prebiotics exerttheir effect beyond the GI tract (Lenoir-Wijnkoop et al. The differentmechanisms of prebiotic action are complex and have been summarized in FigureSelective Stimulation of Beneficial Bacteria.

This definition has recently beenupdated as follows: ‘a prebiotic is a selectively fermented ingredient thatresults in specific changes in the composition and/or activity of the gastrointestinalmicrobiota, thus conferring benefit(s) upon host health’ (Gibson et al.Products of prebiotic fermentation by lactobacilli and bifidobacteria, such aslactic and acetic acid, can also be subsequently degraded by other members ofthe gut (Duncan et al. Prebiotics have been originally defined as’non-digestible food ingredients that beneficially affect the host byselectively stimulating the growth and/or activity of one or a limited numberof bacteria in the colon, and thus improve host health’ (Gibson and Roberfroid1995. This may impact their competition with other commensals. Impact of Prebiotics on Short Chain FattyAcid Production SCFAs (acetate, propionate, and butyrate) are the main productsof prebiotic fermentation in the gut. Close relationships between microbesusually explain an increase in butyrate production, often seen in the presenceof prebiotics, despite the fact that primary prebiotic utilizers (lactic acidbacteria) fail to produce this compound.

SCFAs may be important in hostmetabolism as these compounds provide energy to the host. Regulation of HostMetabolism Metabolomic studies that measure the impact of a single prebiotichave started to reveal the complexity of the changes induced by its ingestion.Using a multicompartmental modelling approach with metabolic signatures from 10tissue/fluid compartments to assess the effects of 5 g/day of galtactosyloligosaccharides,a significant reduction of lipogenesis, triacylglycerol incorporation intolipoproteins and triglyceride concentration in the liver and the kidney couldbe measured in mice (Martin et al. These different mechanisms illustrate thecomplexity of regulation of the host metabolism by prebiotics. This effect maybe partially due to the interaction of inulin type fructans with the Fok1 gene,a genetic modifier of calcium absorption, as well as due to the acidicenvironment caused by the production of SCFA, which may increase the solubilityof minerals and thus enhance their absorption (Abrams et al. MineralAbsorptionThe addition of prebiotics in food may offer other benefits by improving hostabsorption of minerals (like calcium or magnesium.

Crude fractions of chicory(a source of inulin) have shown improved bone parameters relative to native orreformulated inulin in rats, suggesting possible synergies between inulin-typefructans and other nutrients (Demigne et al. Re- cent advances in this fieldshow that inulin-type fructans enhanced calcium absorption primarily via thecolonic mucosa in humans (Abrams et al. Antiadhesive Prebiotics An extension tothe prebiotic concept is the use of oligosaccharides that selectively preventadhesion of certain bacterial species by mimicking their binding sites. Whilethis field of research is intriguing, no human trials have examined prebioticsin pro- phylactic studies and it warrants further investigation.  

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