The host-microbe interface within the gut

Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes

The influence of resident gut microbes on xenobiotic metabolism has been investigated at different levels throughout the past five decades. However, with the advance in sequencing and pyrotagging technologies, addressing the influence of microbes on xenobiotics had to evolve from assessing direct metabolic effects on toxins and botanicals by conventional culture-based techniques to elucidating the role of community composition on drugs metabolic profiles through DNA sequence-based phylogeny and metagenomics. Following the completion of the Human Genome Project, the rapid, substantial growth of the Human Microbiome Project (HMP) opens new horizons for studying how microbiome compositional and functional variations affect drug action, fate, and toxicity (pharmacomicrobiomics), notably in the human gut. The HMP continues to characterize the microbial communities associated with the human gut, determine whether there is a common gut microbiome profile shared among healthy humans, and investigate the effect of its alterations on health. Here, we offer a glimpse into the known effects of the gut microbiota on xenobiotic metabolism, with emphasis on cases where microbiome variations lead to different therapeutic outcomes. We discuss a few examples representing how the microbiome interacts with human metabolic enzymes in the liver and intestine. In addition, we attempt to envisage a roadmap for the future implications of the HMP on therapeutics and personalized medicine.

Microbiota conservation and BMI signatures in adult monozygotic twins

The human gastrointestinal (GI) tract microbiota acts like a virtual organ and is suggested to be of great importance in human energy balance and weight control. This study included 40 monozygotic (MZ) twin pairs to investigate the influence of the human genotype on GI microbiota structure as well as microbial signatures for differences in body mass index (BMI). Phylogenetic microarraying based on 16S rRNA genes demonstrated that MZ twins have more similar microbiotas compared with unrelated subjects (P<0.001), which allowed the identification of 35 genus-like microbial groups that are more conserved between MZ twins. Half of the twin pairs were selected on discordance in terms of BMI, which revealed an inverse correlation between Clostridium cluster IV diversity and BMI. Furthermore, relatives of Eubacterium ventriosum and Roseburia intestinalis were positively correlated to BMI differences, and relatives of Oscillospira guillermondii were negatively correlated to BMI differences. Lower BMI was associated with a more abundant network of primary fiber degraders, while a network of butyrate producers was more prominent in subjects with higher BMI. Combined with higher butyrate and valerate contents in the fecal matter of higher BMI subjects, the difference in microbial networks suggests a shift in fermentation patterns at the end of the colon, which could affect human energy homeostasis.

Genomic approaches to studying the human microbiota

The human body is colonized by a vast array of microbes, which form communities of bacteria, viruses and microbial eukaryotes that are specific to each anatomical environment. Every community must be studied as a whole because many organisms have never been cultured independently, and this poses formidable challenges. The advent of next-generation DNA sequencing has allowed more sophisticated analysis and sampling of these complex systems by culture-independent methods. These methods are revealing differences in community structure between anatomical sites, between individuals, and between healthy and diseased states, and are transforming our view of human biology.

Probiotics for the treatment of inflammatory bowel disease

Probiotics are organisms which provide a desired and beneficial effect on human health. With recent evidence implicating a disruption in the balance of the gastrointestinal microbiome and intestinal immunity as a potential trigger for inflammatory bowel disease (IBD), there has been growing interest in using probiotics as an adjunct to standard anti-inflammatory and immune suppressing therapy. Animal models describe potential and plausible mechanisms of action for probiotics to counter inflammation of colonic mucosa. Although there are insufficient data to recommend probiotics in ulcerative colitis or Crohn's disease, good evidence supports the use of specific probiotics for maintenance of remission in pouchitis. Although there are limited regulatory standards for the agents, probiotics are relatively safe with minimal reported side effects or contraindications. More rigorous studies need to be published supporting efficacy and safety of these agents before they become a mainstay of IBD medical treatment.

The human gastrointestinal microbiota--an unexplored frontier for pharmaceutical discovery

The mammalian gastrointestinal tract (GIT) harbors microorganisms (the microbiota) of vast phylogentic, genomic, and metabolic diversity, and recent years have seen a rapid development in the techniques for studying these complex microbial ecosystems. It is increasingly apparent that the GIT microbiota plays an intricate role in host health and disease. Targeted strategies for modulating human health through the modification of the GIT microbiota, however, are developing and in their infancy. This perspective article discusses the rationale, benefits and limitations of using the GIT microbiota as a pharmacological and nutritional target in the treatment of various diseases and disorders linked to imbalances in our microbiota.

Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow

Development of an in vitro living cell-based model of the intestine that mimics the mechanical, structural, absorptive, transport and pathophysiological properties of the human gut along with its crucial microbial symbionts could accelerate pharmaceutical development, and potentially replace animal testing. Here, we describe a biomimetic 'human gut-on-a-chip' microdevice composed of two microfluidic channels separated by a porous flexible membrane coated with extracellular matrix (ECM) and lined by human intestinal epithelial (Caco-2) cells that mimics the complex structure and physiology of living intestine. The gut microenvironment is recreated by flowing fluid at a low rate (30 μL h(-1)) producing low shear stress (0.02 dyne cm(-2)) over the microchannels, and by exerting cyclic strain (10%; 0.15 Hz) that mimics physiological peristaltic motions. Under these conditions, a columnar epithelium develops that polarizes rapidly, spontaneously grows into folds that recapitulate the structure of intestinal villi, and forms a high integrity barrier to small molecules that better mimics whole intestine than cells in cultured in static Transwell models. In addition, a normal intestinal microbe (Lactobacillus rhamnosus GG) can be successfully co-cultured for extended periods (>1 week) on the luminal surface of the cultured epithelium without compromising epithelial cell viability, and this actually improves barrier function as previously observed in humans. Thus, this gut-on-a-chip recapitulates multiple dynamic physical and functional features of human intestine that are critical for its function within a controlled microfluidic environment that is amenable for transport, absorption, and toxicity studies, and hence it should have great value for drug testing as well as development of novel intestinal disease models.

Gut--liver axis: the impact of gut microbiota on non alcoholic fatty liver disease

AIM

To examine the impact of gut microbiota on non alcoholic fatty liver disease (NAFLD) pathogenesis.

DATA SYNTHESIS

Emerging evidence suggests a strong interaction between gut microbiota and liver. Receiving approximately 70% of its blood supply from the intestine, the liver represents the first line of defence against gut-derived antigens. Intestinal bacteria play a key role in the maintenance of gut-liver axis health. Disturbances in the homeostasis between bacteria- and host-derived signals at the epithelial level lead to a break in intestinal barrier function and may foster "bacterial translocation", defined as the migration of bacteria or bacterial products from the intestinal lumen to mesenteric lymph nodes or other extraintestinal organs and sites. While the full repertoire of gut-derived microbial products that reach the liver in health and disease has yet to be explored, the levels of bacterial lipopolysaccharide, a component of the outer membrane of Gram-negative bacteria, are increased in the portal and/or systemic circulation in several types of chronic liver diseases. Derangement of the gut flora, particularly small intestinal bacterial overgrowth, occurs in a large percentage (20-75%) of patients with chronic liver disease. In addition, evidence implicating the gut-liver axis in the pathogenesis of metabolic liver disorders has accumulated over the past ten years.

CONCLUSIONS

Complex metabolic diseases are the product of multiple perturbations under the influence of triggering factors such as gut microbiota and diet, thus, modulation of the gut microbiota may represent a new way to treat or prevent NAFLD.

Probiotics in the gastrointestinal diseases of the elderly

Changes of the gut microflora in elderly appear to involve a reduction in numbers of healthy bacteria (lactobacilli and bifidobacteria) and an increase in numbers of potentially pathogenic species. These changes are generally described as gastrointestinal disorders and infections. This review analyses benefits of probiotics in old people, with particular interesting for the latest researches relevant to elderly people, e.g. trials examining enteric infections, antibiotic-associated diarrhea and Clostridium difficile associated diarrhea, functional bowel problems (constipation and irritable bowel syndrome), inflammatory bowel diseases, stimulation of the immune system and prevention of cancer. A growing number of researches indicates that some probiotic strains may help to maintain the health in old people, suggesting both health and cost-saving benefits in offering fermented dairy products. These benefits include: establishment of balanced intestinal microflora; improving colonization resistance and or prevention of diarrhea; reduction of fecal enzymes; reduction of serum cholesterol; reduction of potential mutagenes; reduction of lactose intolerance; synthesis of vitamins; predigestion of proteins.

Gut Microbiota and Obesity

The current obesity epidemic clearly has many causes, including the impact of our modern world on both our diet and our lifestyle/physical activity. Although many interventions have been recommended, the prevalence of obesity continues to rise and has forced a re-evaluation of the potential interventions that could have an impact. In recent years it has been definitively shown that microbiota in the gastrointestinal tract are altered in obese individuals. Recent data provide a potential mechanistic understanding of the interactions between microbiota and obesity and allow potential new interventions to the control of obesity to be proposed.

Proteomics at the interface of psychology, gut physiology and dysfunction: an underexploited approach that deserves expansion

Gut functions such as digestion and absorption are essential to life and the emerging insights into the gut-brain axis - that is, the cross talk between the enteric and CNS - point towards critical links between (eating) behavior, psychology, whole body and gut physiology, and digestive and overall health. While proteomics is ideally positioned to shed more light on these interactions, be it applied to the periphery (e.g., blood) or the locus of action (i.e., the gut), it is to date largely underexploited, mainly because of challenging sampling and tissue complexity. In view of the contrast between potential and current delivery of proteomics in the context of intestinal health, this article briefs the reader on the state-of-the-art of molecular intestinal research, reviews current proteomic studies (explicitly focusing on the most recent ones that target inflammatory bowel disease patient samples) and argues for an expansion of this research field.

Review article: probiotics for the treatment of irritable bowel syndrome--focus on lactic acid bacteria

BACKGROUND

Irritable bowel syndrome (IBS) is a poorly understood, yet highly prevalent functional gastrointestinal disorder (FGID). The withdrawal, due to adverse events, of a number of pharmacological agents that were approved for the treatment of IBS has left a therapeutic vacuum for patients suffering from the disorder.

AIM

To review, summarise and critically evaluate current knowledge of lactic acid bacteria (LAB) used to treat IBS.

METHODS

We assessed a comprehensive range of relevant literature from Pubmed, Medline and online sources based on our definition of LAB which included both typical and atypical species, covering Lactobacilli, Bifidobacteria, Enterococci, Streptococci and Bacilli.

RESULTS

Of the 42 trials evaluated examining the efficacy of LAB in IBS, 34 reported beneficial effects in at least one of the endpoints or symptoms examined, albeit with tremendous variation in both the magnitude of effect and the choice of outcome under consideration. However, numerous concerns have been expressed over deficits of trial design and execution relating to strain selection, optimum dosage, mode of action, safety and long-term tolerability in a disorder that can persist throughout the lifetime of affected individuals.

CONCLUSIONS

Progress in the field will require an improved understanding of how the microbiota impacts on health and disease, adequately powered long-term multicentre trials and the embracing of bench to bedside approaches. Recent incremental advances suggest these areas are being addressed and that the future holds much promise for the use of lactic acid bacteria in the treatment of irritable bowel syndrome.

Microbial translocation across the GI tract

The lumen of the gastrointestinal (GI) tract is home to an enormous quantity of different bacterial species, our microbiota, that thrive in an often symbiotic relationship with the host. Given that the healthy host must regulate contact between the microbiota and its immune system to avoid overwhelming systemic immune activation, humans have evolved several mechanisms to attenuate systemic microbial translocation (MT) and its consequences. However, several diseases are associated with the failure of one or more of these mechanisms, with consequent immune activation and deleterious effects on health. Here, we discuss the mechanisms underlying MT, diseases associated with MT, and therapeutic interventions that aim to decrease it.

The intestinal microbiota and obesity

Obesity has been and continues to be an epidemic in the United States. Obesity has been addressed in multiple health initiatives, including Healthy People 2010, with no state meeting the proposed goal of a prevalence of obesity < 15% of the adult population. In contrast, obesity rates have continued to increase, with the self-reported prevalence of obesity among adults increasing by 1.1% from 2007 to the present. Indeed, since 2009, 33 states reported obesity prevalences of 25% or more with only 1 state reporting prevalence < 20%. There have been multiple approaches for the treatment of obesity, including fad diets, incentive-based exercise programs, and gastric bypass surgery; none of which have been optimal. In a murine model, it was shown that the majority of the intestinal microbiome consists of two bacterial phyla, the Bacteroidetes and the Firmicutes, and that the relative abundance of these two phyla differs among lean and obese mice; the obese mouse had a higher proportion of Firmicutes to Bacteroidetes (50% greater) than the lean mouse. The same results were appreciated in obese humans compared to lean subjects. The postulated explanation for this finding is that Firmicutes produce more complete metabolism of a given energy source than do Bacteroidetes, thus promoting more efficient absorption of calories and subsequent weight gain. Researchers were able to demonstrate that colonizing germ-free mice with the intestinal microbiome from obese mice led to an increased total body fat in the recipient mice despite a lack of change in diet. The converse, that, colonizing germ-free obese mice with the intestinal microbiome of thin mice causing a decreased total body fat in the recipient mice, has not yet been done. Other possible mechanisms by which the intestinal microbiome affects host obesity include induction of low-grade inflammation with lipopolysaccharide, regulation of host genes responsible for energy expenditure and storage, and hormonal communication between the intestinal microbiome and the host. The following review discusses the microbiome-obesity relationship and proposed mechanisms by which the intestinal microbiota is hypothesized to influence weight gain.

Brain-gut-microbe communication in health and disease

Bidirectional signalling between the gastrointestinal tract and the brain is regulated at neural, hormonal, and immunological levels. This construct is known as the brain–gut axis and is vital for maintaining homeostasis. Bacterial colonization of the intestine plays a major role in the post-natal development and maturation of the immune and endocrine systems. These processes are key factors underpinning central nervous system (CNS) signaling. Recent research advances have seen a tremendous improvement in our understanding of the scale, diversity, and importance of the gut microbiome. This has been reflected in the form of a revised nomenclature to the more inclusive brain–gut–enteric microbiota axis and a sustained research effort to establish how communication along this axis contributes to both normal and pathological conditions. In this review, we will briefly discuss the critical components of this axis and the methodological challenges that have been presented in attempts to define what constitutes a normal microbiota and chart its temporal development. Emphasis is placed on the new research narrative that confirms the critical influence of the microbiota on mood and behavior. Mechanistic insights are provided with examples of both neural and humoral routes through which these effects can be mediated. The evidence supporting a role for the enteric flora in brain–gut axis disorders is explored with the spotlight on the clinical relevance for irritable bowel syndrome, a stress-related functional gastrointestinal disorder. We also critically evaluate the therapeutic opportunities arising from this research and consider in particular whether targeting the microbiome might represent a valid strategy for the management of CNS disorders and ponder the pitfalls inherent in such an approach. Despite the considerable challenges that lie ahead, this is an exciting area of research and one that is destined to remain the center of focus for some time to come.

Prebiotics and probiotics: their role in the management of gastrointestinal disorders in adults

For decades, if not centuries, a variety of products with what would now be regarded as prebiotic and probiotic properties have been consumed by the general public and advocated for their benefits on health and, in particular, gastrointestinal well-being. More recently, medical science has taken a great interest in the population of micro-organisms, the gut microbiota that normally populates the human gut, and the range of important functions carried out by the microbiota in health is being progressively defined. As a corollary, the list of disorders and diseases that may result from disruption of the normal microbiota and/or its interaction with the host continues to grow. A scientific basis for the use of probiotics and prebiotics is, therefore, beginning to emerge. Unfortunately, although progress has been made, the clinical evidence to support the use of these preparations lags behind. Nevertheless, a number of human disease states may benefit from the use of probiotics, most notably, diarrheal illnesses, some inflammatory bowel diseases, certain infectious disorders, and irritable bowel syndrome. Prebiotics promote the growth of "good" bacteria, and although a variety of health benefits have been attributed to their use, prebiotics have been subjected to few large-scale clinical trials.

Distinct commensal bacteria associated with ingesta and mucosal epithelium in the gastrointestinal tracts of calves and chickens

The primary aim of this study was to determine whether distinct gastrointestinal tract (GIT) microbial communities are established within ingesta and on mucosal surfaces of dairy calves and chickens to evaluate whether the principle of microbial segregation is of broad biological significance. Multivariate analysis of the predominant bacterial PCR-denaturing gradient gel electrophoresis profiles and estimated bacterial populations were compared in rumen, jejunum, ileum, cecum, and colon ingesta and matching mucosal tissues. Samples collected from 3-week old (n = 8) and 6-month old (n = 8) calves revealed that the predominant mucosa-associated bacteria were distinct from those inhabiting ingesta, and bacterial diversity varied significantly among the GIT regions. The estimated bacterial populations displayed significant regional differences for bovine mucosal (P = 0.05) and for ingesta (P = 0.03) only at 6 months of age. This indicates an established segregation of the enteric bacterial population throughout the GIT in weaned calves. Analysis of ileal and cecal bacterial profiles in chickens confirmed that the segregation of commensal bacteria between ingesta and the mucosal tissue was a common biological phenomenon. Our study provides some fundamental understanding of the impact of sample type (mucosa vs. ingesta), region, and host age on commensal bacterial establishment and segregation throughout the GIT.

Gut microbiota and the role of probiotics in therapy

Thanks to rapid progress in the development and application of molecular techniques to the assessment of the human gut microbiome, the true nature, diversity and metabolic potential of this 'hidden organ' are being revealed. Simultaneously, the complex physiological, immunological and metabolic interactions between host and microbiome are being untangled. By contrast, the probiotic concept has been with us for decades and, while supported more by fad and folklore in the past, is now gaining support, not only from experimental work in animal models, but also by well-designed studies in human diseases, most notably infectious diarrheas, inflammatory bowel disease and the irritable bowel syndrome.

Xylo-oligosaccharides and the gut micro-ecosystem

The human gastrointestinal microbiota is a complex micro-ecosystem. It influences a variety of intestinal functions and plays a key role in nutrition regulation, in maintaining the integrity of the epithelial barrier, and in the development of mucosal immunity. In the normal gut the population structure of the microbiota is relatively stable and the relationship between the microbiota and the host is mutually beneficial. The complex network of host-microbe interactions is thought to prohibit colonization by intruding pathogens and any disruption of the net may lead to the loss of the microecological balance which will bring about the relevant diseases. Xylo-oligosaccharides (XOS), an emerging food additive, cause prebiotic effects when ingested as part of the diet through the modulation of colonic microflora. XOS affect the gut health and remedy diseases related to intestinal microbe dysbiosis by promoting the growth of good bacteria and diminishing the growth of deleterious microorganisms.

Therapies aimed at the gut microbiota and inflammation: antibiotics, prebiotics, probiotics, synbiotics, anti-inflammatory therapies

Several recent observations have raised the possibility that disturbances in the gut microbiota and/or a low-grade inflammatory state may contribute to symptomatology and the etiology of irritable bowel syndrome (IBS). Consequent on these hypotheses, several therapeutic categories have found their way into the armamentarium of those who care for IBS sufferers. These agents include probiotics, prebiotics, antibiotics, and anti-inflammatory agents.

Diversity and metabolic impact of intestinal Lactobacillus species in healthy adults and the elderly

The present study aimed at assessing the counts and species distribution of intestinal lactobacilli and exploring if the data are associated with BMI and blood glucose level in healthy adults and elderly persons. The BMI (P < 0·01), the level of fasting blood glucose (P < 0·001) and the total counts of lactobacilli (P < 0·01 by bacteriology; P < 0·001 by real-time PCR) were higher in the elderly. The number of species in adults was lower (P < 0·05), who were more often colonised with Lactobacillus acidophilus (P = 0·031) and L. helveticus (P < 0·001). In contrast, L. plantarum (P = 0·035), L. paracasei (P < 0·001) and L. reuteri (P = 0·031) were more prevalent in the elderly. L. rhamnosus was detected in adults (P < 0·001), but not in any elderly person. BMI was associated with counts of lactobacilli, adjusted for age and sex (P = 0·008). The higher BMI in both groups of persons was associated with the presence of obligate homofermentative lactobacilli and L. sakei, both adjusted for age and sex. Plasma glucose values were positively correlated with BMI and negatively correlated with colonisation with L. paracasei (P = 0·0238) in adults and on the borderline with L. fermentum (P = 0·052) in the elderly. Thus, the species-specific PCR analysis of Lactobacillus sp. combined with viable plating data indicates substantial age-related structural differences in the intestinal lactobacilli communities. The higher counts of intestinal Lactobacillus sp. are associated with higher BMI and blood glucose content, while their specific fermentative groups and species of lactobacilli appear at different glucose levels both in adults and in the elderly.

The enteric microbiota in the pathogenesis and management of constipation

For centuries, fiber has been recommended on an empirical basis for the management of constipation; it has only been in recent decades that the mechanisms whereby fiber and related products may influence colonic function have begun to be elucidated. The interaction between fiber and the microbiota of the human colon appears to play a major role in generating the beneficial effects of fiber. The microbiota is also the target for the other therapeutic interventions discussed in this chapter: prebiotics and probiotics. While a scientific basis for a role for these approaches in the management of constipation continues to develop, evidence from high-quality clinical trials to support their use in daily practice continues to lag far behind. While benefits for fiber and, perhaps, for certain prebiotic and probiotic preparations in constipation appear to be extant there is a real need for large well-conducted clinical trials in this important area of human medicine.

An iterative workflow for mining the human intestinal metaproteome

BACKGROUND

Peptide spectrum matching (PSM) is the standard method in shotgun proteomics data analysis. It relies on the availability of an accurate and complete sample proteome that is used to make interpretation of the spectra feasible. Although this procedure has proven to be effective in many proteomics studies, the approach has limitations when applied on complex samples of microbial communities, such as those found in the human intestinal tract. Metagenome studies have indicated that the human intestinal microbiome contains over 100 times more genes than the human genome and it has been estimated that this ecosystem contains over 5000 bacterial species. The genomes of the vast majority of these species have not yet been sequenced and hence their proteomes remain unknown. To enable data analysis of shotgun proteomics data using PSM, and circumvent the lack of a defined matched metaproteome, an iterative workflow was developed that is based on a synthetic metaproteome and the developing metagenomic databases that are both representative for but not necessarily originating from the sample of interest.

RESULTS

Two human fecal samples for which metagenomic data had been collected, were analyzed for their metaproteome using liquid chromatography-mass spectrometry and used to benchmark the developed iterative workflow to other methods. The results show that the developed method is able to detect over 3,000 peptides per fecal sample from the spectral data by circumventing the lack of a defined proteome without naive translation of matched metagenomes and cross-species peptide identification.

CONCLUSIONS

The developed iterative workflow achieved an approximate two-fold increase in the amount of identified spectra at a false discovery rate of 1% and can be applied in metaproteomic studies of the human intestinal tract or other complex ecosystems.

Right colon, left colon, and rectal surgeries are not similar for surgical site infection development. Analysis of 277 elective and urgent colorectal resections

PURPOSE

Surgical site infections (SSIs) are the most common infections in colorectal surgery. Although some studies suggest that rectal surgery differs from colon surgery for SSI incidence and risk factors, the National Nosocomial Infection Surveillance system categorizes all colorectal surgeries into only one group. The aim of this study was to determine incidence, characteristics, and risk factors of SSIs according to the subclassification of colorectal surgery into right colon surgery (RCS), left colon surgery (LCS), and rectum surgery (RS).

METHODS

From November 2005 to July 2009, all patients requiring colorectal resectioning were enrolled into our program. The outcome of interest was an SSI diagnosis. Univariate and multivariate analyses were performed to determine SSI predictors in each group.

RESULTS

Two hundred seventy-seven consecutive colorectal resections were analyzed. SSI rates were 8% in RCS, 18.4% in LCS, and 17.6% in RS. LCS and RS showed significantly higher SSI incidences (p = 0.022) and greater rates of organ/space infections compared to RCS (p = 0.029). Predictors of SSI were steroid use among RCS, age greater than 70 years, multiple comorbidities, steroid use, non-neoplastic colonic disease, urgent operation, ostomy creation, postoperative intensive care among LCS, preoperative chemoradiation, heart disease, and prolonged operation among RS patients. On multivariate analysis, the coupled LCS and RS groups showed an increased risk for SSI compared to RCS (OR, 2.57).

CONCLUSIONS

SSI incidences, characteristics, and risk factors seem to be different among RCS, LCS, and RS. A tailored SSI surveillance program should be applied for each of the three groups, leading to a more competent SSI recognition and reduction of SSI incidence and related costs.

Probiotics in gastrointestinal disorders

A new era in medical science has dawned with the realization of the critical role of the "forgotten organ," the enteric flora, in health and disease. Central to this beneficial interaction between the flora and humans is the manner in which the bacteria contained within the gut "talk" to the immune system and, in particular, the immune system that is widespread within the gut itself, the gut- (or mucosa-) associated lymphoid tissue (GALT or MALT). Into this landscape comes a new player: the probiotic. While many products have masqueraded as probiotics, only those that truly and reproducibly contain live organisms and have been shown, in high-quality human studies, to confer a health benefit can actually claim this title. Several human disease states have benefited from the use of probiotics, most notably diarrheal illnesses, some inflammatory bowel diseases, and certain infectious disorders. Irritable bowel syndrome can now be added to this list. Although this area holds much promise, more high-quality trials of probiotics in digestive disorders, as well as laboratory investigations of their mechanisms of action, are required.

Potential benefits of pro- and prebiotics on intestinal mucosal immunity and intestinal barrier in short bowel syndrome

The mechanism of impaired gut barrier function in patients with short bowel syndrome (SBS) is poorly understood and includes decreased intestinal motility leading to bacterial overgrowth, a reduction in gut-associated lymphoid tissue following the loss of intestinal length, inhibition of mucosal immunity of the small intestine by intravenous total parental nutrition, and changes in intestinal permeability to macromolecules. Novel therapeutic strategies (i.e. nutritive and surgical) have been introduced in order to prevent the establishment or improve the outcome of this prevalent disease. Pre- and probiotics as a nutritive supplement are already known to be very active in the intestinal tract (mainly in the colon) by maintaining a healthy gut microflora and influencing metabolic, trophic and protective mechanisms, such as the production of SCFA which influence epithelial cell metabolism, turnover and apoptosis. Probiotics have been recommended for patients suffering from SBS in order to decrease bacterial overgrowth and prevent bacterial translocation, two major mechanisms in the pathogenesis of SBS. The present review discusses the research available in the international literature, clinical and experimental, regarding probiotic supplementation for this complicated group of patients based on the clinical spectrum and pathophysiological aspects of the syndrome. The clinical data that were collected for the purposes of the present review suggest that it is difficult to correctly characterise probiotics as a preventive or therapeutic measure. It is very challenging after all to examine the relationship of the bacterial flora, the intestinal barrier and the probiotics as, according to the latest knowledge, demonstrate an interesting interaction.

Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon

Vancomycin, metronidazole, and the bacteriocin lacticin 3147 are active against a wide range of bacterial species, including Clostridium difficile. We demonstrate that, in a human distal colon model, the addition of each of the three antimicrobials resulted in a significant decrease in numbers of C. difficile. However, their therapeutic use in the gastrointestinal tract may be compromised by their broad spectrum of activity, which would be expected to significantly impact on other members of the human gut microbiota. We used high-throughput pyrosequencing to compare the effect of each antimicrobial on the composition of the microbiota. All three treatments resulted in a decrease in the proportion of sequences assigned to the phyla Firmicutes and Bacteroidetes, with a corresponding increase in those assigned to members of the Proteobacteria. One possible means of avoiding such "collateral damage" would involve the application of a narrow-spectrum antimicrobial with specific anti-C. difficile activity. We tested this hypothesis using thuricin CD, a narrow-spectrum bacteriocin produced by Bacillus thuringiensis, which is active against C. difficile. The results demonstrated that this bacteriocin was equally effective at killing C. difficile in the distal colon model but had no significant impact on the composition of the microbiota. This offers the possibility of developing a targeted approach to eliminating C. difficile in the colon, without collateral damage.

Cadmium chloride exhibits a profound toxic effect on bacterial microflora of the mice gastrointestinal tract

Cadmium (Cd²(+)), a naturally occurring heavy metal, is an important environmental pollutant and a potent toxicant to bacteria. The gastrointestinal (GI) tract microflora has a marked capacity to cope with the increased load of ingested metals. However, heavy metals may have harmful effects on GIT microflora. Under the conditions of experimental exposure to cadmium, changes in the population of intestinal microflora in healthy mice were examined. Five experimental groups received 23 to 50 mg kg⁻¹ cadmium in drinking water and control group was given water free from cadmium for 45 days. Intestinal contents and biopsy samples were aseptically collected and bacterial counts were performed. The microflora of the intestine in control group was represented by bacteria of the genera Bacillus cereus, Lactobacillus spp., Clostridium spp., Escherichia coli, Klebsiella spp., Pseudomonas spp., Enterococcus spp. and Proteus spp. As the result of dysbiosis induced by the introduction of cadmium, a sharp decrease in the population of all microbial species in the intestine was observed. The deleterious effect of cadmium appeared to be less in the large intestine and rectum than that of small intestine, suggesting a site-specific influence of cadmium. The gram-negative bacteria tested were less sensitive to cadmium compared to the gram-positive bacteria because of their possible different ability to uptake the metal ions.

Gut health: predictive biomarkers for preventive medicine and development of functional foods

There is an urgent need to develop and validate a series of biomarkers, which accurately measure and inform on how the human gut microbiota can affect human health. The human gut hosts a complex community of micro-organisms, with unique features in each individual. The functional role of this gut microbiota in health and disease is increasingly evident, but poorly understood. Comprehension of this ecosystem implies a significant challenge in the elucidation of interactions between all of its components, but promises a paradigm shift in preventive nutrition and medicine. ‘Omics’ technologies for the first time offer tools of sufficient subtlety to tackle this challenge. However, these techniques must be allied with traditional skills of the microbial physiologist, which are in danger of being lost. Targeting these efforts at the identification of biomarkers associated with gut health will require access to a ‘biobank’ from a pan-European or worldwide observation study, which would include samples taken with appropriate frequency from healthy individuals of different ages. This offers a pragmatic opportunity for a unique food and pharmaceutical industry collaboration.

Pharmacological management of constipation

The approach of this review is to give a pragmatic approach to using laxatives, based on a combination of what is known about mechanism of action and the available literature on evidence.

Panorganismal gut microbiome-host metabolic crosstalk

Coevolution shapes interorganismal crosstalk leading to profound and diverse cellular and metabolic changes as observed in gut dysbiosis in human diseases. Here, we modulated a simplified gut microbiota using pro-, pre-, and synbiotics to assess the depth of systemic metabolic exchanges in mice, using a multicompartmental modeling approach with metabolic signatures from 10 tissue/fluid compartments. The nutritionally induced microbial changes modulated host lipid, carbohydrate, and amino acid metabolism at a panorganismal scale. Galactosyl-oligosaccharides reduced lipogenesis, triacylglycerol incorporation into lipoproteins and triglyceride concentration in the liver and the kidney. Those changes were not correlated with decreased plasma lipoproteins that were specifically induced by L. rhamnosus supplementation. Additional alteration of transmethylation metabolic pathways (homocysteine-betaine) was observed in the liver and the pancreas following pre- and synbiotic microbial modulation, which may be of interest for control of glucose metabolism and insulin sensitivity. Probiotics also reduced hepatic glycogen and glutamine and adrenal ascorbate with inferred effects on energy homeostasis, antioxidation, and steroidogenesis. These studies show the breadth and the depth of gut microbiome modulations of host biochemistry and reveal that major mammalian metabolic processes are under symbiotic homeostatic control.

Alpha-defensins in enteric innate immunity: functional Paneth cell alpha-defensins in mouse colonic lumen

Paneth cells are a secretory epithelial lineage that release dense core granules rich in host defense peptides and proteins from the base of small intestinal crypts. Enteric alpha-defensins, termed cryptdins (Crps) in mice, are highly abundant in Paneth cell secretions and inherently resistant to proteolysis. Accordingly, we tested the hypothesis that enteric alpha-defensins of Paneth cell origin persist in a functional state in the mouse large bowel lumen. To test this idea, putative Crps purified from mouse distal colonic lumen were characterized biochemically and assayed in vitro for bactericidal peptide activities. The peptides comigrated with cryptdin control peptides in acid-urea-PAGE and SDS-PAGE, providing identification as putative Crps. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry experiments showed that the molecular masses of the putative alpha-defensins matched those of the six most abundant known Crps, as well as N-terminally truncated forms of each, and that the peptides contain six Cys residues, consistent with identities as alpha-defensins. N-terminal sequencing definitively revealed peptides with N termini corresponding to full-length, (des-Leu)-truncated, and (des-Leu-Arg)-truncated N termini of Crps 1-4 and 6. Crps from mouse large bowel lumen were bactericidal in the low micromolar range. Thus, Paneth cell alpha-defensins secreted into the small intestinal lumen persist as intact and functional forms throughout the intestinal tract, suggesting that the peptides may mediate enteric innate immunity in the colonic lumen, far from their upstream point of secretion in small intestinal crypts.

Enterovirulent E. coli in inflammatory and noninflammatory bowel diseases

We determined the incidence of enterovirulent E. coli (EVEC; which can to cause gastrointestinal infections) in strains isolated from patients with both of the major inflammatory bowel diseases (IBD), Crohn's disease (CD) and ulcerative colitis (UC) and from patients with noninflammatory bowel diseases (nonIBD). Cell detachment E. coli (CDEC) were detected in 14 % of all strains. A significant difference in the presence of CDEC was found between the groups of strains isolated from UC (24.1 %), nonIBD (11.9 %) and CD (4.7 %). Enteroaggregative E. coli (EAggEC) were detected in 2.5 %, typical enteropathogenic strains (EPEC) in 1.3 % and enterotoxigenic ones (ETEC) in 1.5 %. Enteroinvasive (EIEC) and shigatoxin producing E. coli (STEC) were not detected. Some strains showed a high invasion level in gentamicin-protection assay. These strains could therefore belong to adherent-invasive E. coli (AIEC) because they are free of genes encoding invasins (ipaH, ial) and are equipped with fimA gene. However, complete characterization of these strains and their classification as AIEC will require further tests.

Host-microbe communication within the GI tract

The gastrointestinal tract is a biologically diverse and complicated system which carries out essential physiological functions that support human health, while at the same time maintaining itself as an isolated environment to prevent infection and systemic disease. To maintain homeostasis in the gut, communication between the host and residing microbial communities must occur to identify and eliminate potential pathogens which could colonize and cause damage through aggressive pro-inflammatory responses by the mucosal immune system. To prevent such events, a number of host and bacterial-mediated mechanisms are utilized to monitor the environment and initiate appropriate immune responses to invading pathogens. An essential component of this communication process between gastrointestinal microflora and the host involves distinguishing indigenous species from pathogens through ligand-receptor interactions which lead to various signaling events in host cells. Such events generally result in the development of mucosal immunity and immunological tolerance. While these signaling pathways provide a highly effective means of communication between the gut microflora and the host, pathogens have developed mechanisms to manipulate these pathways to evade detection by the immune system to persist and cause disease. These adaptations include cell surface modifications and the expression of various virulence factors in response to different immunological and hormonal components produced by the host.

What is the evidence for the use of probiotics in functional disorders?

A rationale for the use of probiotics for a number of functional gastrointestinal symptoms and syndromes can be developed, and an experimental basis for their use continues to emerge, but data from well-conducted clinical trials of probiotics in this area remain scarce. Irritable bowel syndrome (IBS) has attracted the most attention; recent revelations regarding the potential pathogenic roles of the enteric flora and immune activation have led to reawakened interest in bacterio-therapy for this common and challenging disorder. Some recent randomized, controlled studies attest to the efficacy of some probiotics in alleviating individual IBS symptoms, and selected strains have a more global impact. Evidence for long-term efficacy is also beginning to emerge, though more studies are needed in this regard. In other functional syndromes, data are far from adequate to make recommendations, but there is evidence for efficacy of probiotics in treating individual symptoms such as diarrhea, constipation, and bloating. The interpretation of much of the literature in this area is complicated by lack of quality control, use of many different species and strains, and, above all, significant deficiencies in trial methodology.

Probiotics in the management of colonic disorders

Probiotics have been used in humans for almost a century and widely recommended for the treatment of a variety of ills assumed to be of colonic origin, including diarrhea, constipation, bloating, and flatulence. More recently, probiotics have been evaluated in the management of specific colonic disorders such as inflammatory bowel disease, irritable bowel syndrome, and Clostridium difficile colitis. It is evident that no two probiotics are exactly alike; why then should we expect reproducible results from studies that employ different species or strains, variable formulations, and diverse dosing schedules? When probiotics have been studied with the rigor appropriate to a new therapeutic modality, some coherent results have emerged: specific strains are effective in certain diarrheal states, irritable bowel syndrome, ulcerative colitis, and pouchitis, as well as in the prevention of C. difficile-related colitis. Even here, not to mention other colonic disorders, further adequately powered and appropriately designed trials are needed.

Nutrition and colonic health: the critical role of the microbiota

PURPOSE OF REVIEW

To highlight mechanisms whereby diet affects colonic function and disease patterns.

RECENT FINDINGS

Topical nutrients are preferentially used by the gut mucosa to maintain structure and function. With the colon, topical nutrients are generated by the colonic microbiota to maintain mucosal health. Most importantly, short chain fatty acids control proliferation and differentiation, thereby reducing colon cancer risk. In patients with massive loss of small intestine, short chain fatty acid production supports survival by releasing up to 1000 kcal energy/day. Human studies show that the microbiota synthesizes a large pool of utilizable folate which may support survival in impoverished populations. Unfortunately, the microbiota may also elaborate toxic products from food residues such as genotoxic hydrogen sulfide by sulfur-reducing bacteria in response to a high-meat diet. The employment of culture-free techniques based on 16S regions of DNA has revealed that our colons harbor over 800 bacterial species and 7000 different strains. Evidence suggests that the diet directly influences the diversity of the microbiota, providing the link between diet, colonic disease, and colon cancer. The microbiota, however, can determine the efficiency of food absorption and risk of obesity.

SUMMARY

Our investigations have focused on a small number of bacterial species: characterization of microbiota and its metabolism can be expected to provide the key to colonic health and disease.

Debugging how bacteria manipulate the immune response

Beyond the innate response that is elicited when tissues are infected, bacterial pathogens have evolved strategies to subvert the immune response and "recalibrate" it both qualitatively and quantitatively, thereby achieving a balance consistent with the survival of both the microbe and its infected host, a compromise that is likely the result of a long process of coevolution between pathogens and their hosts. By collaboratively studying the mechanisms employed, microbiologists and immunologists are fostering development of a renewed approach of infectious diseases that is expected to provide useful new concepts and applications for their control. In addition, the molecular strategies developed by bacteria to dampen immune mechanisms result from such strong and prolonged selective pressure for survival that they may point to original mechanisms and targets to conceive novel immunomodulatory, anti-inflammatory, and anti-infectious molecules.

'Bioengineered Bugs' - a patho-biotechnology approach to probiotic research and applications

Given the increasing commercial and clinical relevance of probiotic cultures, improving their stress tolerance profile and ability to overcome the physiochemical defences of the host is an important biological goal. Pathogenic bacteria have evolved sophisticated strategies to overcome host defences, interact with the immune system and modulate essential host systems. The 'Patho-biotechnology' concept promotes the exploitation of these valuable traits for the design of more technologically robust and effective probiotic cultures with potentially improved biotechnological and clinical applications, as well as the development of novel vaccine and drug delivery platforms.