Probiotics in Perspective

Abstract

“… words are signals, counters. They are not immortal …”—Brian Friel (Translations) Medicine is beset by a tyranny of terminology. Words and labels outlive their usefulness when rendered inaccurate by new discoveries or if they become an impediment in the face of changing concepts. The term antibiotic was once restricted to metabolites of microbial origin, but modern usage demanded that it embrace sulfonamides and synthetic antimicrobials. Similarly, probiotics are “live microorganisms, which, when consumed in adequate amounts, confer a health benefit on the host,”1Preidis G.A. Versalovic J. Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era.Gastroenterology. 2009; 136: 2015-2031Abstract Full Text Full Text PDF PubMed Scopus (361) Google Scholar but this fails to account for usage of dead organisms or bioactive bacterial constituents, including proteins, polysaccharides, and DNA, or genetically modified organisms. Therefore, a less restrictive definition or a more inclusive term, such as alimentary pharmabiotic, seems desirable to encompass all forms of manipulation or mining of host–microbe–dietary interactions in the gut. Regardless of terminology, the concept of harnessing the benefits of the gut microbiota is an old story, part of a bigger story of mankind in a microbial world. Comprehensive reviews of the microbiota and probiotics may be found elsewhere.1Preidis G.A. Versalovic J. Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era.Gastroenterology. 2009; 136: 2015-2031Abstract Full Text Full Text PDF PubMed Scopus (361) Google Scholar, 2Garrett W.S. Gordon J.I. Glimcher L.H. Homeostasis and inflammation in the intestine.Cell. 2010; 140: 859-870Abstract Full Text Full Text PDF PubMed Scopus (559) Google Scholar, 3Sekirov I. Russell S.L. Anunes C.M. et al.Gut microbiota in health and disease.Physiol Rev. 2010; 90: 859-904Crossref PubMed Scopus (2664) Google Scholar, 4Lebeer S. Vanderleyden J. De Keersmaecker S.C.J. Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens.Nat Rev Microbiology. 2010; 8: 171-184Crossref PubMed Scopus (697) Google Scholar Here is a perspective on promising aspects of this rapidly developing area, where intrigue and controversy should be anticipated. We evolved in a microbial world, and our activities profoundly influence the biodiversity of that world. No longer neglected or considered esoteric, the commensal microbiota is now center stage in human biology. This has been driven by several factors including the lessons of Helicobacteri pylori and peptic ulcer disease, escalating frequency of antibiotic-associated disease, and discoveries that genetic risk factors for Crohn's disease code for proteins that either sense the microbial environment or that regulate the host response to the environment, or in the case of ulcerative colitis, regulate the mucosal barrier to the microbial environment.5Kaser A. Zeissig S. Blumberg R.S. Inflammatory bowel disease.Annu Rev Immunol. 2010; 28 (573–562)Crossref PubMed Scopus (1487) Google Scholar In addition, there is emerging evidence linking modern lifestyle with changes in the colonizing microbiota in early life, and the influence of the latter on the developing immune system and hence with risk of immunoallergic diseases.6Bernstein C.N. Shanahan F. Disorders of a modern lifestyle: reconciling the epidemiology of inflammatory bowel diseases.Gut. 2008; 57: 1185-1191Crossref PubMed Scopus (215) Google Scholar Among features of a modern lifestyle in developed societies (including sanitation, hygiene, urbanization, birth delivery, and antibiotic exposure), diet has a predominant influence on the gut microbiota.7De Filippo C. Cavalieri D. Di Paola M. et al.Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.Proc Natl Acad Sci USA. 2010; 107: 14691-14696Crossref PubMed Scopus (3741) Google Scholar, 8Hildebrandt M.A. Hoffmann C. Sherrill-Mix S.A. et al.High-fat diet determines the composition of the murine gut microbiome independently of obesity.Gastroenterology. 2009; 137: 1716-1724Abstract Full Text Full Text PDF PubMed Scopus (1140) Google Scholar Loss of biodiversity within the gut in developed societies might have arisen because of reduced acquisition of environmental microbes from soil, water, and food, as implied by the hygiene hypothesis. Alternatively, it may reflect progressive loss of ancestral microorganisms (“old friends”) that co-evolved with humans, striking examples being the decline in endemic helminthic parasitism and the progressive loss of H pylori over the last century, both of which have been linked with increased risk of immunoallergic disorders.9Rook G.A.W. 99th Dahlem conference on infection, inflammation and chronic inflammatory disorders: Darwinian medicine and the ‘hygiene’ or ‘old friends’ hypothesis.Clin Exp Immunol. 2010; 160: 70-79Crossref PubMed Scopus (208) Google Scholar, 10Atherton J.C. Blaser M.J. Coadaptation of Helicobacter pylori and humans: ancient history, modern implications.J Clin Invest. 2009; 119: 2475-2487Crossref PubMed Scopus (407) Google Scholar Molecular profiling of the normal microbiota using metagenomics has also shown that loss of biodiversity with reductions of specific organisms, such as Faecalibacterium prausnitzii, have been linked with inflammatory disease.11Peterson D.A. Frank D.N. Pace N.R. et al.Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases.Cell Host Microbe. 2008; 3: 417-427Abstract Full Text Full Text PDF PubMed Scopus (392) Google Scholar, 12Sokol H. Pigneur B. Watterlot L. et al.Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients.Proc Natl Acad Sci U S A. 2008; 105: 16731-16736Crossref PubMed Scopus (2930) Google Scholar Indeed, recruitment of “old friends” to protect against new problems is one of the promises of pharmabiotic therapy. The changing risk of disease associated with a changing microbiota should be considered in light of the fact that the human genome does not contain enough information for full mucosal and extraintestinal development, the required information being derived from the environment. Our dependency on environmental information is easily appreciated in the case of sensory development, including immunosensory function. Although sensory organs are present at birth, they are dysfunctional without environmental stimulation. In the gut, the required input is derived from our other genome—the microbiome. Collectively, this exceeds the host genome by about 100-fold. At birth, the colonizing microbiota is a source of trophic signals for the developing immune and digestive systems, is a rich repository of metabolic activity including provision of vitamins and nutrients, and serves a protective role by competition with pathogens, enhancement of barrier function, and immune stimulation. Throughout life, continual host–microbe interactions remain critical for mucosal homeostasis.2Garrett W.S. Gordon J.I. Glimcher L.H. Homeostasis and inflammation in the intestine.Cell. 2010; 140: 859-870Abstract Full Text Full Text PDF PubMed Scopus (559) Google Scholar, 3Sekirov I. Russell S.L. Anunes C.M. et al.Gut microbiota in health and disease.Physiol Rev. 2010; 90: 859-904Crossref PubMed Scopus (2664) Google Scholar The molecular basis of such host–microbe signaling has been defined in only a few instances, but promises to provide a platform for novel drug design.13Shanahan F. Gut microbes: from bugs to drugs.Am J Gastroenterol. 2010; 105: 275-279Crossref PubMed Scopus (41) Google Scholar The relationship between the microbiota and disease within the host extends beyond classical infectious or immunoinflammatory disorders. Perhaps the most intriguing discovery has been the role of the microbiota as an environmental modifier of adipose tissue in the host, not only in terms of fat quantity,14Bäckhed F. Ding H. Wang T. et al.The gut microbiota as an environmental factor that regulates fat storage.Proc Natl Acad Sci U S A. 2004; 101: 15718-15723Crossref PubMed Scopus (4362) Google Scholar but also composition,15Wall R. Ross R.P. Shanahan F. et al.The metabolic activity of the enteric microbiota influences the fatty acid composition of murine and porcine liver and adipose tissues.Am J Clin Nutr. 2009; 89: 1393-1401Crossref PubMed Scopus (156) Google Scholar and as a contributor to the risk of obesity, fatty liver phenotype, the metabolic syndrome, and diabetes.16Vrieze A. Holleman F. Zoetendal E.G. et al.The environment within: how gut microbiota may influence metabolism and body composition.Diabetologia. 2010; 53: 606-613Crossref PubMed Scopus (242) Google Scholar The development of metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5 is consistent with the reciprocal nature of host–microbe interactions in the gut and striking evidence for a direct link between a disturbance of innate immunity with changes in the microbiota and development of metabolic disease in the host.17Vijay-Kumar M. Aitken J.D. Carvalho F.A. et al.Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5.Science. 2010; 328: 228-231Crossref PubMed Scopus (1534) Google Scholar The microbiota is primarily a health asset, and shaped by human activities. However, depending on context, it may become a risk factor for disease. Enhancement of microbial assets or offsetting liabilities is, in essence, the rationale of probiotic consumption. Probiotics mimic the commensal microbiota.4Lebeer S. Vanderleyden J. De Keersmaecker S.C.J. Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens.Nat Rev Microbiology. 2010; 8: 171-184Crossref PubMed Scopus (697) Google Scholar However, as with all biodiverse communities, probiotics exhibit considerable inter-strain diversity. Properties of one probiotic should not be extrapolated to another. In addition, it should not be assumed that probiotic actions in vitro reflect mechanisms of action in vivo. There are numerous reports of probiotics eliciting various responses in vitro when exposed to mammalian cells. Such phenomena, although insightful, are neither surprising nor proof of mechanism of action. Experiments demonstrating probiotic action in vivo are more convincing. Different probiotics exert their predominant action either in the lumen, at the mucosal surface, by engagement with the mucosal innate immune response, or by action beyond the gut with stimulation of the acquired immune response (Figure 1). One of the clearest demonstrations of probiotic action has been in a murine model of listeria infection. Of several probiotic candidates, one (L salivarius UCC118) was shown to be particularly effective in protecting against L monocytogenes and the mechanism of action was shown conclusively to be due to production of an antimicrobial bacteriocin.18Corr S.C. Li Y. Riedel C.U. et al.Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118.Proc Natl Acad Sci U S A. 2007; 104: 7617-7621Crossref PubMed Scopus (617) Google Scholar This was visualized directly in live animals by tracking a luciferase-tagged inoculum of L monocytogenes in controls and probiotic-fed animals. The same probiotic was also protective against salmonella infection, but by a different mechanism, because a bacteriocin-negative mutant retained its protective effect. Thus, probiotics differ from each other and a given probiotic may have different mechanism of action in different settings. In addition to production of antimicrobials, probiotics may modify the metabolic behavior of the indigenous microbiota. Skeptics have claimed that the average daily dose of probiotic (109–1012) is such a tiny fraction of the total resident bacteria in the gut and, therefore, unlikely to have a meaningful impact on the intestinal ecosystem, but it has been demonstrated that the introduction of probiotic bacteria to gnotobiotic animals elicits marked changes in gene expression within the resident bacterial community.19Sonnenburg J.L. Chen C.T.L. Gordon J.I. Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host.PLoS Biology. 2006; 4: 2213-2226Crossref Scopus (333) Google Scholar Because most probiotics are harnessed commensals, it should be anticipated that they engage in dialogue with the host. Diverse effects include induction of mucins and defensins, enhanced barrier function by action at tight junctions and subcellularly within enterocytes.4Lebeer S. Vanderleyden J. De Keersmaecker S.C.J. Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens.Nat Rev Microbiology. 2010; 8: 171-184Crossref PubMed Scopus (697) Google Scholar That such phenomena may occur in vivo has been supported by direct visualization of mucus-binding pili on probiotic lactobacilli, which enhance the potential for colonization and interaction with the host.20Kankainen M. Paulin L. Tynkkynen S. et al.Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein.Proc Natl Acad Sci U S A. 2009; 106: 17193-17198Crossref PubMed Scopus (569) Google Scholar Furthermore, because probiotics express microorganism-associated molecular patterns capable of engaging with the same pattern recognition receptors as do pathogens, they have the molecular means of protecting the mucosal surface by competitive exclusion.4Lebeer S. Vanderleyden J. De Keersmaecker S.C.J. Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens.Nat Rev Microbiology. 2010; 8: 171-184Crossref PubMed Scopus (697) Google Scholar Some probiotics protect against pathogen-induced tissue injury by stimulation of innate and acquired immunity, notably induction of regulatory T-cell function. This was the dominant mechanism whereby the probiotic, B infantis, down-regulated the inflammatory response induced either by salmonella infection or by injection of lipopolysaccharide in mice.21O'Mahony C. Scully P. O'Mahony D. et al.Commensal-induced regulatory T cells mediate protection against pathogen-stimulated NF-κB activation.PLoS Pathogens. 2008; 4: e1000112Crossref PubMed Scopus (305) Google Scholar This probiotic effect was shown in live animals by imaging the attenuation of nuclear factor-κB activation in inflamed tissues, and the regulatory T-cell mechanism was confirmed by reproducing the anti-inflammatory effect in naïve recipients after adoptive transfer of these. Although the efficacy of probiotics has been consistent in several animal models, results in humans have, with notable exceptions, been less impressive. The most promising results have been in protection against infection, particularly in those most vulnerable at the extremes of life. Because reduced microbial diversity may be associated with reduced competitive defense against pathogens and less environmental stimulation of the developing immune and digestive systems (Figure 2),22Kitano H. Oda K. Robustness trade-offs and host-microbial symbiosis in the immune system.Mol Syst Biol. 2006; 2 (2006.0022)Crossref Scopus (130) Google Scholar it follows that premature, low-birth-weight neonates who are vulnerable to necrotizing enterocolitis might be particularly suited to probiotic usage. So it is; probiotics not only reduce the risk of necrotizing enterocolitis, but also reduce all causes of mortality.23Deshpande G. Rao S. Patole S. et al.Updated meta-analysis of probiotics for preventing necrotizing enterocolitis in preterm neonates.Pediatrics. 2010; 125: 921-930Crossref PubMed Scopus (443) Google Scholar Indeed, the weight of evidence has been sufficient for pediatricians to debate whether it remains appropriate to deny such vulnerable babies the protection of probiotics, and it seems likely that future trials will focus on optimal regimens.24Tarnow-Mordi W.O. Wilkinson D. Trivedi A. et al.Probiotics reduce all-cause mortality and necrotizing enterocolitis: it is time to change practice.Pediatrics. 2010; 125: 1068-1070Crossref PubMed Scopus (80) Google Scholar, 25Soll R.F. Probiotics: are we ready for routine use?.Pediatrics. 2010; 125: 1071-1072Crossref PubMed Scopus (74) Google Scholar Another vulnerable group includes those with natural defenses overwhelmed by a high burden of water-borne pathogens. Acute diarrheal infections are still a worldwide public health problem, and although there has been support for probiotic prophylaxis, trials in developing countries are sparse. The positive results of a recent large community-based trial in children in India are particularly welcome.26Sur D. Manna B. Niyogi S.K. et al.Role of probiotics in preventing acute diarrhoea in children: a community-based, randomized, double-blind placebo-controlled field trial in an urban slum.Epidemiol Infect. 2010 Jul; 30 ([Epub ahead of print]): 1-8Google Scholar At the other end of the age spectrum, particularly where the protective influence of the indigenous microbiota has been depleted by antibiotics, protection against C difficile-associated disease using probiotics is conceptually appealing. In the largest randomized, controlled trial for this indication, a beneficial effect was found using a blend of L acidophilus and L casei.27Gao X.W. Mubasher M. Fang C.Y. et al.Dose-response efficacy of a proprietary probiotic formula of Lactobacillus acidophilus CL1285 and Lactobacillus casei LBC80R for antibiotic-associated diarrhea and Clostridium difficile-associated diarrhea prophylaxis in adult patients.Am J Gastroenterol. 2010; 105: 1636-1641Crossref PubMed Scopus (255) Google Scholar The role of probiotics in inflammatory bowel disease is more complex.1Preidis G.A. Versalovic J. Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era.Gastroenterology. 2009; 136: 2015-2031Abstract Full Text Full Text PDF PubMed Scopus (361) Google Scholar, 28Haller D. Antoine J.M. Bengmark S. et al.Guidance for substantiating the evidence for beneficial effects of probiotics: probiotics in chronic inflammatory bowel disease and the functional disorder irritable bowel syndrome.J Nutr. 2010; 140: 690S-697SCrossref PubMed Scopus (80) Google Scholar Despite strong rationale and promising results in animal models, controlled trials in Crohn's disease provide no encouragement, whereas the evidence for probiotics in ulcerative colitis and pouchitis is more favorable. E coli Nissle 1917 seems to be equivalent in efficacy to mesalamine for maintenance of remission of ulcerative colitis. For patients with pouchitis, trials with a cocktail of 8 different bacteria (VSL#3), have shown both therapeutic and prophylactic efficacy, although experience in clinical practice seems to be inconsistent. Perhaps unexpectedly, the efficacy for probiotics in irritable bowel syndrome has been more evident than in inflammatory bowel disease, albeit with less a priori rationale.28Haller D. Antoine J.M. Bengmark S. et al.Guidance for substantiating the evidence for beneficial effects of probiotics: probiotics in chronic inflammatory bowel disease and the functional disorder irritable bowel syndrome.J Nutr. 2010; 140: 690S-697SCrossref PubMed Scopus (80) Google Scholar, 29Brenner D.M. Moeller M.J. Chey W.D. et al.The utility of probiotics in the treatment of irritable bowel syndrome: a systematic review.Am J Gastroenterol. 2009; 104: 1033-1049Crossref PubMed Scopus (303) Google Scholar This is true of some, but not all, probiotic strains, with efficacy linked with bifidobacteria more than with lactobacilli. Although additional controlled trials of different agents and dosing regimens are desirable, probing mechanisms of action may provide novel insights into this complex syndrome. Potential mechanisms of probiotic action in irritable bowel syndrome include an anti-inflammatory effect, reduction in visceral hyperalgesia, or modulation of the resident microbiota. It seems likely that other disorders stem from abnormal host–microbe–dietary interactions in the gut, but at present, clinical studies of probiotics are too sparse or limited in design to be conclusive. Probiotics have a long and impressive record of safety, but there is no such thing as zero risk. The distinction between a commensal or probiotic and a pathogen is dependent on context. Unexpected hazards are rare, and some are unexplained.30Editors of LancetExpressions of concern—probiotic prophylaxis in predicted severe acute pancreatitis: a randomized, double-blind, placebo-controlled trial.Lancet. 2010; 375: 875-876Abstract Full Text Full Text PDF PubMed Scopus (22) Google Scholar Perhaps of greater concern is product quality control, for which vigilance is critical. Despite unsubstantiated or exaggerated claims by some enthusiasts, the science of probiotics is well grounded and has delivered important successes. This is part of a bigger story, which is the role of the inner microbial environment in health and disease. Restrictive definitions of probiotics have already outlived their usefulness with the discovery of molecular mechanisms of action and deployment of probiotic metabolites. For now, the best clinical evidence for probiotic efficacy is in protection against infection, particularly in vulnerable neonatal or elderly groups, but encouraging results in other settings, such as irritable bowel syndrome, will focus more attention on host–microbe interactions in these conditions. Probiotics are supplementary to conventional therapy and are not substitutes. Their efficacy is modest but not uniform; results with one strain cannot be extrapolated to another or to a different clinical indication. In addition, combinations may be antagonistic as well as additive. Clinicians recommending a probiotic should retain the same principles and evidence-based standards that apply to other forms of therapeutics. This includes selection from a reputable supplier and scientific evidence for the specific indication. Although the desirability of large trials in different clinical indications is self-evident, funding for such trials is doubtful. In contrast with big pharma, which has had limited interest in probiotics, the food industry focuses primarily on biomarkers of risk rather than tackling established disease. In addition, the food industry struggles with lower profit margins, smaller research budgets, and increasing regulatory constraints on health claims. However, the future requires greater specificity of probiotic selection, matched for the precise clinical indication. In some instances, specificity of action may be determined by engineering probiotics for delivery of vaccines or other bioactive molecules to the gut. This has already been accomplished, but routine use in humans requires not only robust trials, but also a public receptive to genetically modified microbes. The scope of manipulating the microbiota will extend beyond probiotics to include other forms of pharmabiotics, such as topically active, narrow-spectrum antibiotics and even phage viruses. Finally, with greater clarification of molecular mechanisms, there is the prospect of new therapeutic targets at the host–microbe interface and the very real promise of “drugs from bugs.”13Shanahan F. Gut microbes: from bugs to drugs.Am J Gastroenterol. 2010; 105: 275-279Crossref PubMed Scopus (41) Google Scholar