Low counts of Faecalibacterium prausnitzii in colitis microbiota

Increase in fecal primary bile acids and dysbiosis in patients with diarrhea-predominant irritable bowel syndrome

BACKGROUND

Irritable bowel syndrome (IBS) is a multifactorial disease for which a dysbiosis of the gut microbiota has been described. Bile acids (BA) could play a role as they are endogenous laxatives and are metabolized by gut microbiota. We compared fecal BA profiles and microbiota in healthy subjects (HS) and patients with diarrhea-predominant IBS (IBS-D), and we searched for an association with symptoms.

METHODS

Clinical features and stool samples were collected in IBS-D patients and HS. Fecal BA profiles were generated using HPLC coupled to tandem mass spectrometry. The fecal microbiota composition was assessed by q-PCR targeting dominant bacterial groups and species implicated in BA transformation.

KEY RESULTS

Fourteen IBS-D patients and 18 HS were included. The two groups were comparable in terms of age and sex. The percentage of fecal primary BA was significantly higher in IBS-D patients than in HS, and it was significantly correlated with stool consistency and frequency. Fecal counts of all bacteria, lactobacillus, coccoides, leptum and Faecalibacterium prausnitzii were similar. There was a significant increase of Escherichia coli and a significant decrease of leptum and bifidobacterium in IBS-D patients.

CONCLUSIONS & INFERENCES

We report an increase of primary BA in the feces of IBS-D patients compared to HS, correlated with stool consistency and frequency. A dysbiosis of different bacterial groups was detected, some of them involved in BA transformation. As the gut microbiota is the exclusive pathway to transform primary into secondary BA, this suggests a functional consequence of dysbiosis, leading to lower BA transformation.

Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome

BACKGROUND

The intestinal microbiota has been implicated in the pathophysiology of irritable bowel syndrome (IBS). Due to the variable resolutions of techniques used to characterize the intestinal microbiota, and the heterogeneity of IBS, the defined alterations of the IBS intestinal microbiota are inconsistent. We analyzed the composition of the intestinal microbiota in a defined subgroup of IBS patients (diarrhea-predominant IBS, D-IBS) using a technique that provides the deepest characterization available for complex microbial communities.

METHODS

Fecal DNA was isolated from 23 D-IBS patients and 23 healthy controls (HC). Variable regions V1-V3 and V6 of the 16S rRNA gene were amplified from all samples. PCR products were sequenced using 454 high throughput sequencing. The composition, diversity and richness of microbial communities were determined and compared between D-IBS and HC using the quantitative insights into microbial ecology pipeline.

KEY RESULTS

The contribution of bacterial groups to the composition of the intestinal microbiota differed between D-IBS and HC. D-IBS patients had significantly higher levels of Enterobacteriaceae (P = 0.03), and lower levels of Fecalibacterium genera (P = 0.04) compared to HC. β-Diversity values demonstrated significantly lower levels of UniFrac distances in HC compared to D-IBS patients. The richness of 16S rRNA sequences was significantly decreased in D-IBS patients (P < 0.04).

CONCLUSIONS & INFERENCES

Our 16S rRNA sequence data demonstrates a community-level dysbiosis in D-IBS. The altered composition of the intestinal microbiota in D-IBS is associated with significant increases in detrimental and decreases in beneficial bacterial groups, and a reduction in microbial richness.

454 pyrosequencing reveals a shift in fecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber

The relative contribution of novel fibers such as polydextrose and soluble corn fiber (SCF) to the human gut microbiome and its association with host physiology has not been well studied. This study was conducted to test the impact of polydextrose and SCF on the composition of the human gut microbiota using 454 pyrosequencing and to identify associations among fecal microbiota and fermentative end-products. Healthy adult men (n = 20) with a mean dietary fiber (DF) intake of 14 g/d were enrolled in a randomized, double-blind, placebo-controlled crossover study. Participants consumed 3 treatment snack bars/d during each 21-d period that contained no supplemental fiber (NFC), polydextrose (PDX; 21 g/d), or SCF (21 g/d) for 21 d. There were no washout periods. Fecal samples were collected on d 16-21 of each period; DNA was extracted, followed by amplification of the V4-V6 region of the 16S rRNA gene using barcoded primers. PDX and SCF significantly affected the relative abundance of bacteria at the class, genus, and species level. The consumption of PDX and SCF led to greater fecal Clostridiaceae and Veillonellaceae and lower Eubacteriaceae compared with a NFC. The abundance of Faecalibacterium, Phascolarctobacterium, and Dialister was greater (P < 0.05) in response to PDX and SCF intake, whereas Lactobacillus was greater (P < 0.05) only after SCF intake. Faecalibacterium prausnitzii, well known for its antiinflammatory properties, was greater (P < 0.05) after fiber consumption. Principal component analysis clearly indicated a distinct clustering of individuals consuming supplemental fibers. Our data demonstrate a beneficial shift in the gut microbiome of adults consuming PDX and SCF, with potential application as prebiotics.

'Omics' of the mammalian gut--new insights into function

To understand the role of gut microbes in host health, it is imperative to probe their genetic potential, expression, and ecological status. The current high-throughput sequencing revolution, in addition to advances in mass spectrometry-based proteomics, have recently enabled deep access to these complex environments, and are revealing important insights into the roles of the gastrointestinal (GI) microbiota in host physiology and health. This review discusses examples of how the integration of cutting-edge 'meta-omics' technologies are providing new knowledge about the relationships between host health status in mammals and the microbes inhabiting the GI tract. In addition, we address some promises that these techniques hold for future therapeutic and diagnostic applications.

Patients with inflammatory bowel disease exhibit dysregulated responses to microbial DNA

Background

A critical role for the gut epithelium lies in its ability to discriminate between pathogens and commensals and respond appropriately. Dysfunctional interactions between microbes and epithelia are believed to have a role in inflammatory bowel disease (IBD). In this study, we analyzed microbiota and gene expression in IBD patients and examined responses of mucosal biopsies to bacterial DNA.

Methods

Biopsies were taken from non-inflamed areas of the colon in healthy controls (HC) and Crohn's disease (CD) and ulcerative colitis (UC) patients in remission. Biopsies were snap-frozen or cultured with DNA from Lactobacillus plantarum (LP) or Salmonella dublin (SD). Gene expression was analyzed under basal conditions and in response to DNA. Gene networks were analyzed using Ingenuity Pathways software. Mucosal-associated microbiota was analyzed using terminal restriction fragment length polymorphism. Frequency of single nucleotide polymorphisms in NOD2 and TLR9 was assessed.

Results

Patients with IBD had altered microbiota, enhanced expression of inflammatory genes, and increased correlations between specific gene expression and microbes. Principle component analysis showed CD and UC patients to cluster independently from healthy controls in both gene expression and microbial analysis. DNA from LP stimulated anti-inflammatory pathways in controls and UC patients, but induced an upregulation of IL17A in CD patients. There were no differences in SNP frequencies of TLR9 or NOD2 in the groups.

Conclusions

Patients with Crohn's disease exhibit altered responses to bacterial DNA. These findings suggest that the gut response to bacterial DNA may depend not only on the specific type of bacterial DNA, but also on the host.

Comparative evaluation of establishing a human gut microbial community within rodent models

The structure of the human gut microbial community is determined by host genetics and environmental factors, where alterations in its structure have been associated with the onset of different diseases. Establishing a defined human gut microbial community within inbred rodent models provides a means to study microbial-related pathologies, however, an in-depth comparison of the established human gut microbiota in the different models is lacking. We compared the efficiency of establishing the bacterial component of a defined human microbial community within germ-free (GF) rats, GF mice, and antibiotic-treated specific pathogen-free mice. Remarkable differences were observed between the different rodent models. While the majority of abundant human-donor bacterial phylotypes were established in the GF rats, only a subset was present in the GF mice. Despite the fact that members of the phylum Bacteriodetes were well established in all rodent models, mice enriched for phylotypes related to species of Bacteroides. In contrary to the efficiency of Clostridiales to populate the GF rat in relative proportions to that of the human-donor, members of Clostridia cluster IV only poorly colonize the mouse gut. Thus, the genetic background of the different recipient rodent systems (that is, rats and mice) strongly influences the nature of the populating human gut microbiota, determining each model's biological suitability.

The human microbiome and its potential importance to pediatrics

The human body is home to more than 1 trillion microbes, with the gastrointestinal tract alone harboring a diverse array of commensal microbes that are believed to contribute to host nutrition, developmental regulation of intestinal angiogenesis, protection from pathogens, and development of the immune response. Recent advances in genome sequencing technologies and metagenomic analysis are providing a broader understanding of these resident microbes and highlighting differences between healthy and disease states. The aim of this review is to provide a detailed summary of current pediatric microbiome studies in the literature, in addition to highlighting recent findings and advancements in studies of the adult microbiome. This review also seeks to elucidate the development of, and factors that could lead to changes in, the composition and function of the human microbiome.

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

Background

The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis result from alterations in intestinal microbes and the immune system. However, the precise dysfunctions of microbial metabolism in the gastrointestinal microbiome during IBD remain unclear. We analyzed the microbiota of intestinal biopsies and stool samples from 231 IBD and healthy subjects by 16S gene pyrosequencing and followed up a subset using shotgun metagenomics. Gene and pathway composition were assessed, based on 16S data from phylogenetically-related reference genomes, and associated using sparse multivariate linear modeling with medications, environmental factors, and IBD status.

Results

Firmicutes and Enterobacteriaceae abundances were associated with disease status as expected, but also with treatment and subject characteristics. Microbial function, though, was more consistently perturbed than composition, with 12% of analyzed pathways changed compared with 2% of genera. We identified major shifts in oxidative stress pathways, as well as decreased carbohydrate metabolism and amino acid biosynthesis in favor of nutrient transport and uptake. The microbiome of ileal Crohn's disease was notable for increases in virulence and secretion pathways.

Conclusions

This inferred functional metagenomic information provides the first insights into community-wide microbial processes and pathways that underpin IBD pathogenesis.

Maintenance of small intestinal and colonic tolerance by IL-10-producing regulatory T cell subsets

The intestinal mucosa is continuously exposed to harmless exogenous antigens derived from food proteins and microbiota. Continuous surveillance by suppressive regulatory T cells prevents inflammatory responses to these antigens thereby maintaining intestinal homeostasis. The nature of the antigenic pressure varies at different locations of the intestinal tract. In agreement with this strong microenvironmental control, small intestinal and colonic regulatory T cell homeostasis varies considerably. In this review, we summarize the substantial advances that have been made in dissecting the phenotype and function of intestinal regulatory T cells, discuss how microbiota can modulate the intestinal regulatory T cell pool and review the crucial role of the immunoregulatory cytokine interleukin-10 (IL-10) in shaping and maintenance of mucosal tolerance.

Techniques used to characterize the gut microbiota: a guide for the clinician

The gut microbiota is a complex ecosystem that has a symbiotic relationship with its host. An association between the gut microbiota and disease was first postulated in the early 20(th) century. However, until the 1990s, knowledge of the gut microbiota was limited because bacteriological culture was the only technique available to characterize its composition. Only a fraction (estimated at <30%) of the gut microbiota has been cultured to date. Since the 1990s, advances in culture-independent techniques have spearheaded our knowledge of the complexity of this ecosystem. These techniques have elucidated the microbial diversity of the gut microbiota and have shown that alterations in the gut microbiota composition and function are associated with certain disease states, such as IBD and obesity. These new techniques are fast, facilitate high throughput, identify organisms that are uncultured to date and enable enumeration of organisms present in the gut microbiota. This Review discusses the techniques that can used to characterize the gut microbiota, when they can be applied to human studies and their relative advantages and limitations.

Microbes inside--from diversity to function: the case of Akkermansia

The human intestinal tract is colonized by a myriad of microbes that have developed intimate interactions with the host. In healthy individuals, this complex ecosystem remains stable and resilient to stressors. There is significant attention on the understanding of the composition and function of this intestinal microbiota in health and disease. Current developments in metaomics and systems biology approaches allow to probe the functional potential and activity of the intestinal microbiota. However, all these approaches inherently suffer from the fact that the information on macromolecules (DNA, RNA and protein) is collected at the ecosystem level. Similarly, all physiological and other information collected from isolated strains relates to pure cultures grown in vitro or in gnotobiotic systems. It is essential to integrate these two worlds of predominantly chemistry and biology by linking the molecules to the cells. Here, we will address the integration of omics- and culture-based approaches with the complexity of the human intestinal microbiota in mind and the mucus-degrading bacteria Akkermansia spp. as a paradigm.

Effect of the proton pump inhibitor omeprazole on the gastrointestinal bacterial microbiota of healthy dogs

The effect of a proton pump inhibitor on gastrointestinal (GI) microbiota was evaluated. Eight healthy 9-month-old dogs (four males and four females) received omeprazole (1.1 mg kg(-1) ) orally twice a day for 15 days. Fecal samples and endoscopic biopsies from the stomach and duodenum were obtained on days 30 and 15 before omeprazole administration, on day 15 (last day of administration), and 15 days after administration. The microbiota was evaluated using 16S rRNA gene 454-pyrosequencing, fluorescence in situ hybridization, and qPCR. In the stomach, pyrosequencing revealed a decrease in Helicobacter spp. during omeprazole (median 92% of sequences during administration compared to > 98% before and after administration; P = 0.0336), which was accompanied by higher proportions of Firmicutes and Fusobacteria. FISH confirmed this decrease in gastric Helicobacter (P < 0.0001) and showed an increase in total bacteria in the duodenum (P = 0.0033) during omeprazole. However, Unifrac analysis showed that omeprazole administration did not significantly alter the overall phylogenetic composition of the gastric and duodenal microbiota. In feces, qPCR showed an increase in Lactobacillus spp. during omeprazole (P < 0.0001), which was accompanied by a lower abundance of Faecalibacterium spp. and Bacteroides-Prevotella-Porphyromonas in the male dogs. This study suggests that omeprazole administration leads to quantitative changes in GI microbiota of healthy dogs.

Invited review: Application of omics tools to understanding probiotic functionality

The human gut microbiota comprises autochthonous species that colonize and reside at high levels permanently and allochthonous species that originate from another source and are transient residents of the human gut. The interactions between bacteria and the human host can be classified as a continuum from symbiosis and commensalism (mutualism) to pathogenesis. Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Recent advances in omics tools and sequencing techniques have furthered our understanding of probiotic functionality and the specific interactions between probiotics and their human hosts. Although it is known that not all probiotics use the same mechanisms to confer benefits on hosts, some specific mechanisms of action have been revealed through omic investigations. These include competitive exclusion, bacteriocin-mediated protection against intestinal pathogens, intimate interactions with mucin and the intestinal epithelium, and modulation of the immune system. The ability to examine fully sequenced and annotated genomes has greatly accelerated the application of genetic approaches to elucidate many important functional roles of probiotic microbes.

The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases

Faecalibacterium prausnitzii is one of the most abundant bacteria in the human gut ecosystem and it is an important supplier of butyrate to the colonic epithelium. Low numbers of faecalibacteria have been associated with inflammatory bowel disease. Despite being extremely oxygen sensitive, F. prausnitzii is found adherent to the gut mucosa where oxygen diffuses from epithelial cells. This paradox is now explained on the basis of gas tube experiments, flavin-dependent reduction of 5,5'-dithiobis-2-nitrobenzoate and microbial fuel cell experiments. The results show that F. prausnitzii employs an extracellular electron shuttle of flavins and thiols to transfer electrons to oxygen. Both compounds are present in the healthy human gut. Our observations may have important implications for the treatment of patients with Crohn's disease, for example, with flavin- or antioxidant rich diets, and they provide a novel key insight in host-microbe interactions at the gut barrier.

IBD-what role do Proteobacteria play?

The gastrointestinal microbiota has come to the fore in the search for the causes of IBD. This shift has largely been driven by the finding of genetic polymorphisms involved in gastrointestinal innate immunity (particularly polymorphisms in NOD2 and genes involved in autophagy) and alterations in the composition of the microbiota that might result in inflammation (so-called dysbiosis). Microbial diversity studies have continually demonstrated an expansion of the Proteobacteria phylum in patients with IBD. Individual Proteobacteria, in particular (adherent-invasive) Escherichia coli, Campylobacter concisus and enterohepatic Helicobacter, have all been associated with the pathogenesis of IBD. In this Review, we comprehensively describe the various associations of Proteobacteria and IBD. We also examine the importance of pattern recognition in the extracellular innate immune response of the host with particular reference to Proteobacteria, and postulate that Proteobacteria with adherent and invasive properties might exploit host defenses, drive proinflammatory change, alter the intestinal microbiota in favor of dysbiosis and ultimately lead to the development of IBD.

IBD-what role do Proteobacteria play?

The gastrointestinal microbiota has come to the fore in the search for the causes of IBD. This shift has largely been driven by the finding of genetic polymorphisms involved in gastrointestinal innate immunity (particularly polymorphisms in NOD2 and genes involved in autophagy) and alterations in the composition of the microbiota that might result in inflammation (so-called dysbiosis). Microbial diversity studies have continually demonstrated an expansion of the Proteobacteria phylum in patients with IBD. Individual Proteobacteria, in particular (adherent-invasive) Escherichia coli, Campylobacter concisus and enterohepatic Helicobacter, have all been associated with the pathogenesis of IBD. In this Review, we comprehensively describe the various associations of Proteobacteria and IBD. We also examine the importance of pattern recognition in the extracellular innate immune response of the host with particular reference to Proteobacteria, and postulate that Proteobacteria with adherent and invasive properties might exploit host defenses, drive proinflammatory change, alter the intestinal microbiota in favor of dysbiosis and ultimately lead to the development of IBD.

Crohn's disease patients have more IgG-binding fecal bacteria than controls

In Crohn's disease (CD), chronic gut inflammation leads to loss of mucosal barrier integrity. Subsequent leakage of IgG to the gut could produce an increase of IgG coating of intestinal bacteria. We investigated if there is more IgG coating in patients than in volunteers and whether this is dependent on the host IgG response or on the gut bacteria. Fecal and serum samples were obtained from 23 CD patients and 11 healthy volunteers. Both the in vivo IgG-coated fecal bacteria and in vitro IgG coating after serum addition were measured by flow cytometry and related to disease activity. The bacterial composition in feces was determined using fluorescence in situ hybridization. The IgG-binding capacities of Escherichia coli strains isolated from feces of patients and volunteers were assessed. The results showed that the in vivo IgG-coated fraction of fecal bacteria of patients was slightly larger than that of volunteers but significantly larger after incubation with either autologous or heterologous serum. This was dependent on the bacteria and independent of disease activity or the serum used. The presence of more Enterobacteriaceae and fewer faecalibacteria in patient feces was confirmed. E. coli isolates from patients bound more IgG than isolates from volunteers (P < 0.05) after the addition of autologous serum. Together, these results indicate that CD patients have more IgG-binding gut bacteria than healthy volunteers. We showed that the level of IgG coating depends on the bacteria and not on the serum used. Furthermore, CD patients have a strong specific immune response to their own E. coli bacteria.

Changes of gut bacteria and immune parameters in liver transplant recipients

BACKGROUND

Liver transplantation is one of the most effective therapeutic options for patients with end-stage liver diseases, and gut microbiota is actively involved in potential infections in pretransplant and posttransplant patients. However, the diversity of gut microbiota and its relationship with the immune parameter of liver transplantation recipients are not well understood.

METHODS

We collected fresh feces and blood samples from 190 participants in China from November 2004 to May 2008, including 28 healthy volunteers, 51 cirrhotic patients and 111 liver-transplanted patients. Six interesting gut bacteria, plasma endotoxin, serum cytokines (i.e., tumor necrosis factor alpha and interleukin-6) and fecal secretory IgA (SIgA) were investigated by real-time quantitative PCR, chromogenic limulus amoebocyte assay, sandwich-type enzyme-linked immunosorbent assay and radioimmunoassay, respectively.

RESULTS

All Eubacteria, Bifidobacterium spp., Faecalibacterium prausnitzii and Lactobacillus spp. were significantly lower in the liver transplantation recipients while Enterobacteriaceae and Enterococcus spp. were significantly higher (P<0.05). Except for Enterococcus spp., other bacteria showed a tendency to restore to normal level along with the time after liver transplantation. Plasma endotoxin, interleukin-6 and fecal SIgA in cirrhotic patients increased significantly, but not in liver transplantation recipients. Plasma endotoxin and interleukin-6 were negatively correlated with all Eubacteria and the Bacteroides-Prevotella group, while tumor necrosis factor alpha was not significantly correlated with these six gut bacteria in cirrhotic patients.

CONCLUSIONS

Our study demonstrates that abundant gut bacteria were altered significantly in both cirrhotic and liver transplantation patients, while plasma endotoxin and interleukin-6 increased remarkably in cirrhotic patients, showing significant correlations with gut microbiota. Interestingly, our data show a tendency for these gut bacteria to restore to normal levels in liver transplantation recipients.

Characterization of the gastrointestinal microbiota in health and inflammatory bowel disease

The enteric bacterial flora play a key role in maintaining health. Inflammatory bowel disease is associated with quantitative and qualitative alterations in the microbiota. Early characterization of the microbiota involved culture-dependent techniques. The advent of metagenomic techniques, however, allows for structural and functional characterization using culture-independent methods. Changes in diversity, together with quantitative alterations in specific bacterial species, have been identified. The functional significance of these changes, and their pathogenic role, remain to be elucidated.

Tumor necrosis factor alpha modulates the dynamics of the plasminogen-mediated early interaction between Bifidobacterium animalis subsp. lactis and human enterocytes

The capacity to intervene with the host plasminogen system has recently been considered an important component in the interaction process between Bifidobacterium animalis subsp. lactis and the human host. However, its significance in the bifidobacterial microecology within the human gastrointestinal tract is still an open question. Here we demonstrate that human plasminogen favors the B. animalis subsp. lactis BI07 adhesion to HT29 cells. Prompting the HT29 cell capacity to activate plasminogen, tumor necrosis factor alpha (TNF-α) modulated the plasminogen-mediated bacterium-enterocyte interaction, reducing the bacterial adhesion to the enterocytes and enhancing migration to the luminal compartment.

Prebiotic fiber modulation of the gut microbiota improves risk factors for obesity and the metabolic syndrome

Prebiotic fibers are non-digestible carbohydrates that promote the growth of beneficial bacteria in the gut. Prebiotic consumption may benefit obesity and associated co-morbidities by improving or normalizing the dysbiosis of the gut microbiota. We evaluated the dose response to a prebiotic diet on the gut microbiota, body composition and obesity associated risk factors in lean and genetically obese rats. Prebiotic fibers increased Firmicutes and decreased Bacteroidetes, a profile often associated with a leaner phenotype. Bifidobacteria and Lactobacillus numbers also increased. Changes in the gut microbiota correlated with energy intake, glucose, insulin, satiety hormones, and hepatic cholesterol and triglyceride accumulation. Here we provide a comprehensive analysis evaluating the results through the lens of the gut microbiota. Salient, new developments impacting the interpretation and significance of our data are discussed. We propose that prebiotic fibers have promise as a safe and cost-effective means of modulating the gut microbiota to promote improved host:bacterial interactions in obesity and insulin resistance. Human clinical trials should be undertaken to confirm these effects.

Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth

Faecalibacterium prausnitzii is one of the most abundant commensal bacteria in the healthy human large intestine, but information on genetic diversity and substrate utilization is limited. Here, we examine the phylogeny, phenotypic characteristics, and influence of gut environmental factors on growth of F. prausnitzii strains isolated from healthy subjects. Phylogenetic analysis based on the 16S rRNA sequences indicated that the cultured strains were representative of F. prausnitzii sequences detected by direct analysis of fecal DNA and separated the available isolates into two phylogroups. Most F. prausnitzii strains tested grew well under anaerobic conditions on apple pectin. Furthermore, F. prausnitzii strains competed successfully in coculture with two other abundant pectin-utilizing species, Bacteroides thetaiotaomicron and Eubacterium eligens, with apple pectin as substrate, suggesting that this species makes a contribution to pectin fermentation in the colon. Many F. prausnitzii isolates were able to utilize uronic acids for growth, an ability previously thought to be confined to Bacteroides spp. among human colonic anaerobes. Most strains grew on N-acetylglucosamine, demonstrating an ability to utilize host-derived substrates. All strains tested were bile sensitive, showing at least 80% growth inhibition in the presence of 0.5 μg/ml bile salts, while inhibition at mildly acidic pH was strain dependent. These attributes help to explain the abundance of F. prausnitzii in the colonic community but also suggest factors in the gut environment that may limit its distribution.

An analysis of the link between strokes and soils in the South Carolina coastal plains

The Stroke Belt is a geographical region of the Southeastern United States where resident individuals suffer a disproportionately higher rate of strokes than the rest of the population. While the "buckle" of this Stroke Belt coincides with the Southeastern Coastal Plain region of North and South Carolina and Georgia, there is a paucity of information pinpointing specific causes for this phenomenon. A number of studies posit that an exposure event-potentially microbial in nature-early in life, could be a risk factor. The most likely vector for such an exposure event would be the soils of the Southeastern Coastal Plain region. These soils may have chemical and physical properties which are conducive to the growth and survival of microorganisms which may predispose individuals to stroke. To this aim, we correlated SC stroke mortality data to soil characteristics found in the NRCS SSURGO database. In statewide comparisons, depth to water table (50 to 100 cm, R = 0.62) and soil drainage class (poorly drained, R = 0.59; well drained, R = -0.54) both showed statistically significant relationships with stroke rate. In a 20 county comparison, depth to water table, drainage class, hydric rating (hydric soils, R = 0.56), and pH (very strongly acid, R = 0.66) all showed statistically significant relationships with stroke rate. These data should help direct future research and epidemiology efforts to pinpoint the exact exposure events which predispose individuals to an increased stroke rate.

The murine caecal microRNA signature depends on the presence of the endogenous microbiota

The intestinal messenger RNA expression signature is affected by the presence and composition of the endogenous microbiota, with effects on host physiology. The intestine is also characterized by a distinctive micronome. However, it is not known if microbes also impact intestinal gene expression epigenetically. We investigated if the murine caecal microRNA expression signature depends on the presence of the microbiota, and the potential implications of this interaction on intestinal barrier function. Three hundred and thirty four microRNAs were detectable in the caecum of germ-free and conventional male mice and 16 were differentially expressed, with samples from the two groups clustering separately based on their expression patterns. Through a combination of computational and gene expression analyses, including the use of our curated list of 527 genes involved in intestinal barrier regulation, 2,755 putative targets of modulated microRNAs were identified, including 34 intestinal barrier-related genes encoding for junctional and mucus layer proteins and involved in immune regulation. This study shows that the endogenous microbiota influences the caecal microRNA expression signature, suggesting that microRNA modulation is another mechanism through which commensal bacteria impact the regulation of the barrier function and intestinal homeostasis. Through microRNAs, the gut microbiota may impinge a much larger number of genes than expected, particularly in diseases where its composition is altered. In this perspective, abnormally expressed microRNAs could be considered as novel therapeutic targets.

Induction of Treg cells in the mouse colonic mucosa: a central mechanism to maintain host-microbiota homeostasis

CD4+ regulatory T (Treg) cells expressing the transcription factor forkhead box P3 (Foxp3) play a critical role in maintaining immunological homeostasis. Treg cells are highly abundant in the mouse intestinal lamina propria, particularly in the colon. Recent studies using germ-free and gnotobiotic mice have revealed that specific components of the intestinal microbiota influence the number and function of Treg cells. Substantial changes in the composition of microbiota have been associated with inflammatory bowel disease. In this review, we will discuss recent findings that associate intestinal microbiota in mice with Treg responses and with the maintenance of intestinal immune homeostasis.

Assessment of the microbiota in microdissected tissues of Crohn's disease patients

The microbiota of the gastrointestinal tract is frequently mentioned as one of the key players in the etiopathogenesis of Crohn's disease (CD). Four hypotheses have been suggested: the single, still unknown bacterial pathogen, an abnormal overall composition of the bowel microbiota ("dysbiosis"), an abnormal immunological reaction to an essentially normally composed microbiota, and increased bacterial translocation. We propose that laser capture microdissection of selected microscopic structures, followed by broad-range 16S rRNA gene sequencing, is an excellent method to assess spatiotemporal alterations in the composition of the bowel microbiota in CD. Using this approach, we demonstrated significant changes of the composition, abundance, and location of the gut microbiome in this disease. Some of these abnormal findings persisted even after macroscopic mucosal healing. Further investigations along these lines may lead to a better understanding of the possible involvement of the bowel bacteria in the development of clinical Crohn's disease.

Decreased colonization of fecal Clostridium coccoides/Eubacterium rectale species from ulcerative colitis patients in an in vitro dynamic gut model with mucin environment

The mucus layer in the colon, acting as a barrier to prevent invasion of pathogens, is thinner and discontinuous in patients with ulcerative colitis (UC). A recent developed in vitro dynamic gut model, the M-SHIME, was used to compare long-term colonization of the mucin layer by the microbiota from six healthy volunteers (HV) and six UC patients and thus distinguish the mucin adhered from the luminal microbiota. Although under the same nutritional conditions, short-chain fatty acid production by the luminal communities from UC patients showed a tendency toward a lower butyrate production. A more in-depth community analysis of those microbial groups known to produce butyrate revealed that the diversity of the Clostridium coccoides/Eubacterium rectale and Clostridium leptum group, and counts of Faecalibacterium prausnitzii were lower in the luminal fractions of the UC samples. Counts of Roseburia spp. were lower in the mucosal fractions of the UC samples. qPCR analysis for butyryl-CoA:acetate CoA transferase, responsible for butyrate production, displayed a lower abundance in both the luminal and mucosal fractions of the UC samples. The M-SHIME model revealed depletion in butyrate producing microbial communities not restricted to the luminal but also in the mucosal samples from UC patients compared to HV.

An arabinoxylan-rich fraction from wheat enhances caecal fermentation and protects colonocyte DNA against diet-induced damage in pigs

Population studies show that greater red and processed meat consumption increases colorectal cancer risk, whereas dietary fibre is protective. In rats, resistant starches (a dietary fibre component) oppose colonocyte DNA strand breaks induced by high red meat diets, consistent with epidemiological data. Protection appears to be through SCFA, particularly butyrate, produced by large bowel carbohydrate fermentation. Arabinoxylans are important wheat fibre components and stimulate large bowel carbohydrate SCFA production. The present study aimed to determine whether an arabinoxylan-rich fraction (AXRF) from wheat protected colonocytes from DNA damage and changed colonic microbial composition in pigs fed with a diet high (30 %) in cooked red meat for 4 weeks. AXRF was primarily fermented in the caecum, as indicated by higher tissue and digesta weights and higher caecal (but not colonic) acetate, propionate and total SCFA concentrations. Protein fermentation product concentrations (caecal p-cresol and mid- and distal colonic phenol) were lower in pigs fed with AXRF. Colonocyte DNA damage was lower in pigs fed with AXRF. The microbial profiles of mid-colonic mucosa and adjacent digesta showed that bacteria affiliating with Prevotella spp. and Clostridial cluster IV were more abundant in both the mucosa and digesta fractions of pigs fed with AXRF. These data suggest that, although AXRF was primarily fermented in the caecum, DNA damage was reduced in the large bowel, occurring in conjunction with lower phenol concentrations and altered microbial populations. Further studies to determine the relationships between these changes and the lowering of colonocyte DNA damage are warranted.

Intestinal microecology in health and wellness

Intestinal microecology consists of 4 components-the luminal gastrointestinal tract, secretions of the tract, the epithelium, nutrients and foods that enter the tract, and the microbatome or microflora. This ecosystem is very dynamic. It is not possible to define a normal flora as it varies with geography, diet, and the dynamics of the microecology. A normal flora exists in a healthy human. The life cycle of the intestinal microbatome will vary with geography and feeding. Dysbiosis may occur in disease. At the present time, the flora is best determined from older biochemical techniques and newer genetic bacteriologic studies, but much more research is needed to define the makeup of the microbatome as it varies with diet and geography.

Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome

BACKGROUND & AIMS

Irritable bowel syndrome (IBS) has been associated with disruptions to the intestinal microbiota, but studies have had limited power, coverage, and depth of analysis. We aimed to define microbial populations that can be used discriminate the fecal microbiota of patients with IBS from that of healthy subjects and correlate these with IBS intestinal symptom scores.

METHODS

The microbiota composition was assessed by global and deep molecular analysis of fecal samples from 62 patients with IBS patients and 46 healthy individuals (controls). We used a comprehensive and highly reproducible phylogenetic microarray in combination with quantitative polymerase chain reaction.

RESULTS

The intestinal microbiota of IBS patients differed significantly (P = .0005) from that of controls. The microbiota of patients, compared with controls, had a 2-fold increased ratio of the Firmicutes to Bacteroidetes (P = .0002). This resulted from an approximately 1.5-fold increase in numbers of Dorea, Ruminococcus, and Clostridium spp (P < .005); a 2-fold decrease in the number of Bacteroidetes (P < .0001); a 1.5-fold decrease in numbers of Bifidobacterium and Faecalibacterium spp (P < .05); and, when present, a 4-fold lower average number of methanogens (3.50 × 10(7) vs 8.74 × 10(6) cells/g feces; P = .003). Correlation analysis of the microbial groups and IBS symptom scores indicated the involvement of several groups of Firmicutes and Proteobacteria in the pathogenesis of IBS.

CONCLUSIONS

Global and deep molecular analysis of fecal samples indicates that patients with IBS have a different composition of microbiota. This information might be used to develop better diagnostics and ultimately treatments for IBS.

The shifting interface between IBS and IBD

Recent data developing from the study of postinfectious IBS has challenged the belief that IBS is a purely psychological disorder. Distinct abnormalities of the gut mucosa have been reported including immune activation and increased release of inflammatory mediators with some overlap with IBD. New studies show that genetic factors which predispose to IBD are also associated with IBS. A common feature is impaired gut barrier function which appears to precede the development of IBD while in IBS it may be the result of either a preceding infection or psychosocial stress. Stress can activate mast cells which are a feature in most but not all IBS series. Anti-inflammatory treatments targeting activated mast cells may benefit IBS patients but currently the evidence is weak and larger trials are needed. Changes in the commensal microbiota have been recently described with a "dysbiosis" in CD characterised by reduced diversity. Inconsistent changes have also been described in IBS but studies controlling for antibiotic use and differences in diet and bowel habit are needed before definitive conclusions can be made.

In vitro fermentation of sugar beet arabino-oligosaccharides by fecal microbiota obtained from patients with ulcerative colitis to selectively stimulate the growth of Bifidobacterium spp. and Lactobacillus spp

The potential prebiotic properties of arabino-oligosaccharides (AOS) derived from sugar beet pulp was studied using mixed cultures of human fecal bacteria from patients with ulcerative colitis (UC), in remission or with active disease, and in healthy controls. These results were compared to those for fructo-oligosaccharides (FOS), which are known to have a prebiotic effect. Fermentation studies were carried out using a small-scale static batch system, and changes in the fecal microbial communities and metabolites were monitored after 24 h by quantitative real-time PCR and short-chain fatty acid analysis. With a few minor exceptions, AOS affected the communities similarly to what was seen for FOS. Quantitative real-time PCR revealed that Bifidobacterium spp. and Lactobacillus spp. were selectively increased after fermentation of AOS or FOS by fecal microbiota derived from UC patients. The stimulation of growth of Lactobacillus spp. and Bifidobacterium spp. was accompanied by a high production of acetate and hence a decrease of pH. The fermentation of AOS may help improve the inflammatory conditions in UC patients through stimulation of bacteria eliciting anti-inflammatory responses and through production of acetate. AOS may therefore represent a new prebiotic candidate for reduction of the risk of flare-ups in UC patients. However, human trials are needed to confirm a health-promoting effect.

Relationship between human intestinal dendritic cells, gut microbiota, and disease activity in Crohn's disease

BACKGROUND

Altered intestinal dendritic cell (DC) function underlies dysregulated T-cell responses to bacteria in Crohn's disease (CD) but it is unclear whether composition of the intestinal microbiota impacts local DC function. We assessed the relationship between DC function with disease activity and intestinal microbiota in patients with CD.

METHODS

Surface expression of Toll-like receptor (TLR)-2, TLR-4, and spontaneous intracellular interleukin (IL)-10, IL-12p40, IL-6 production by freshly isolated DC were analyzed by multicolor flow cytometry of cells extracted from rectal tissue of 10 controls and 28 CD patients. Myeloid DC were identified as CD11c(+) HLA-DR(+lin-/dim) cells (lin = anti-CD3, CD14, CD16, CD19, CD34). Intestinal microbiota were analyzed by fluorescent in situ hybridization of fecal samples with oligonucleotide probes targeting 16S rRNA of bifidobacteria, bacteroides-prevotella, C. coccoides-E. rectale, and Faecalibacterium prausnitzii.

RESULTS

DC from CD produced higher amounts of IL-12p40 and IL-6 than control DC. IL-6(+) DC were associated with the CD Activity Index (r = 0.425; P = 0.024) and serum C-reactive protein (CRP) (r = 0.643; P = 0.004). DC expression of TLR-4 correlated with disease activity. IL-12p40(+) DC correlated with ratio of bacteroides: bifidobacteria (r = 0.535, P = 0.003). IL-10(+) DC correlated with bifidobacteria, and IL-6(+) DC correlated negatively with F. prausnitzii (r = -0.50; P = 0.008). The amount of TLR-4 on DC correlated negatively with the concentration of F. prausnitzii.

CONCLUSIONS

IL-6 production by intestinal DC is increased in CD and correlates with disease activity and CRP. Bacterially driven local IL-6 production by intestinal DC may overcome regulatory activity, resulting in unopposed effector function and tissue damage. Intestinal DC function may be influenced by the composition of the commensal microbiota.

Role of microbiota in postnatal maturation of intestinal T-cell responses

PURPOSE OF REVIEW

Taking advantage of their rapid growth and capacity for continuous genetic adaptation, prokaryotes have colonized all possible ecological environments on earth, including the body surfaces of eukaryotes and their gastrointestinal tract. The mammalian gut contains a complex community of 10 bacteria with a meta-genome containing 1500-fold more genes than the human genome. The forces that control the relationships between eukaryotic hosts and their intestinal bacterial symbionts have, thus, become a major focus of interest.

RECENT FINDINGS

Recent data have highlighted how the dialogue between mammalian hosts and their microbiota stimulates the postnatal maturation of an efficient intestinal barrier that promotes niche colonization by symbiotic bacteria and opposes colonization by pathogens. Herein, we review microbiota-induced T-cell responses and discuss how individual bacteria may shape the balance between regulatory and inflammatory responses. We will also show how host factors might influence the outcome of gut immune responses and affect the structure of the microbiota.

SUMMARY

Deciphering host-microbiota reciprocal influence may not only help in understanding the recent outburst of intestinal inflammatory diseases but also point to strategies able to maintain or restore intestinal homeostasis.

New molecular insights into inflammatory bowel disease-induced diarrhea

Diarrhea is one of the common symptoms that significantly affects quality of life in patients with inflammatory bowel disease (IBD). The clinical manifestation of diarrhea is mainly dependant on the type of IBD and the location, extent and severity of intestinal inflammation. Understanding the pathophysiologic mechanisms of diarrhea in patients with IBD will be beneficial to developing effective treatments for IBD-associated diarrhea. In recent years, modern molecular techniques have been used intensively to dissect the role of the intestinal microbiota, epithelial barrier and the host immune system in the mechanisms of IBD-induced diarrhea. These studies have significantly advanced our knowledge of the mechanisms of IBD-induced diarrhea. In this article, we focus on the new and critical molecular insights into the contributions of the intestinal microbiota, epithelial tight junctions, proinflammatory cytokines and microRNA as potential mechanisms underlying to IBD-induced diarrhea.

High-level dietary fibre up-regulates colonic fermentation and relative abundance of saccharolytic bacteria within the human faecal microbiota in vitro

BACKGROUND

Health authorities around the world advise citizens to increase their intake of foods rich in dietary fibre because of its inverse association with chronic disease. However, a few studies have measured the impact of increasing mixed dietary fibres directly on the composition of the human gut microbiota.

AIMS OF THE STUDY

We studied the impact of high-level mixed dietary fibre intake on the human faecal microbiota using an in vitro three-stage colonic model.

METHODS

The colonic model was maintained on three levels of fibre, a basal level of dietary fibre, typical of a Western-style diet, a threefold increased level and back to normal level. Bacterial profiles and short chain fatty acids concentrations were measured.

RESULTS

High-level dietary fibre treatment significantly stimulated the growth of Bifidobacterium, Lactobacillus-Enterococcus group, and Ruminococcus group (p < 0.05) and significantly increased clostridial cluster XIVa and Faecalibacterium prausnitzii in vessel 1 mimicking the proximal colon (p < 0.05). Total short chain fatty acids concentrations increased significantly upon increased fibre fermentation, with acetate and butyrate increasing significantly in vessel 1 only (p < 0.05). Bacterial species richness changed upon increased fibre supplementation. The microbial community and fermentation output returned to initial levels once supplementation with high fibre ceased.

CONCLUSIONS

This study shows that high-level mixed dietary fibre intake can up-regulate both colonic fermentation and the relative abundance of saccharolytic bacteria within the human colonic microbiota. Considering the important role of short chain fatty acids in regulating human energy metabolism, this study has implications for the health-promoting potential of foods rich in dietary fibres.

The association of minocycline and the probiotic Escherichia coli Nissle 1917 results in an additive beneficial effect in a DSS model of reactivated colitis in mice

Antibiotics have been empirically used for human inflammatory bowel disease, being limited to short periods. Probiotics are able to attenuate intestinal inflammation due to its immunomodulatory properties, being considered as safe when chronically administered. The aim was to test the association of minocycline, a tetracycline with immunomodulatory properties, and the probiotic Escherichia coli Nissle 1917 (EcN) in a mouse model of reactivated colitis. For this purpose, female C57BL/6J mice were assigned to different groups: non-colitic and dextran sodium sulfate (DSS)-control groups (without treatment), minocycline (50 mg/kg/day; p.o.), EcN (5×10(8) CFU/day; p.o.), and minocycline plus EcN treated groups. Colitis was induced by adding DSS in the drinking water (3%) for 5 days; 2 weeks later, colitis was reactivated by subsequent exposure to DSS. The inflammatory status was evaluated daily by a disease activity index (DAI); colonic damage was assessed histologically and biochemically by evaluating mRNA relative expression of different mediators by qPCR. Finally, a microbiological analysis of the colonic contents was performed. Minocycline and EcN exerted intestinal anti-inflammatory effect and attenuated the reactivation of the colitis, as shown by the reduced DAI values, being these effects greater when combining both treatments. This was evidenced histologically and biochemically, by reduced expression of TNFα, IL-1β, IL-2, MIP-2, MCP-1, ICAM-1, iNOS and MMP-9, together with increased MUC-3 and ZO-1 expression. Finally, the altered microbiota composition of colitic mice was partially restored after the different treatments. In conclusion, EcN supplementation to minocycline treatment improves the recovery of the intestinal damage and prevents the reactivation of experimental colitis.

Correlation between protection against sepsis by probiotic therapy and stimulation of a novel bacterial phylotype

Prophylactic probiotic therapy has shown beneficial effects in an experimental rat model for acute pancreatitis on the health status of the animals. Mechanisms by which probiotic therapy interferes with severity of acute pancreatitis and associated sepsis, however, are poorly understood. The aims of this study were to identify the probiotic-induced changes in the gut microbiota and to correlate these changes to disease outcome. Duodenum and ileum samples were obtained from healthy and diseased rats subjected to pancreatitis for 7 days and prophylactically treated with either a multispecies probiotic mixture or a placebo. Intestinal microbiota was characterized by terminal-restriction fragment length polymorphism (T-RFLP) analyses of PCR-amplified 16S rRNA gene fragments. These analyses showed that during acute pancreatitis the host-specific ileal microbiota was replaced by an "acute pancreatitis-associated microbiota." This replacement was not reversed by administration of the probiotic mixture. An increase, however, was observed in the relative abundance of a novel bacterial phylotype most closely related to Clostridium lituseburense and referred to as commensal rat ileum bacterium (CRIB). Specific primers targeting the CRIB 16S rRNA gene sequence were developed to detect this phylotype by quantitative PCR. An ileal abundance of CRIB 16S rRNA genes of more than 7.5% of the total bacterial 16S rRNA gene pool was correlated with reduced duodenal bacterial overgrowth, reduced bacterial translocation to remote organs, improved pancreas pathology, and reduced proinflammatory cytokine levels in plasma. Our current findings and future studies involving this uncharacterized bacterial phylotype will contribute to unraveling one of the potential mechanisms of probiotic therapy.

Gut microbiota, immunity, and disease: a complex relationship

Our immune system has evolved to recognize and eradicate pathogenic microbes. However, we have a symbiotic relationship with multiple species of bacteria that occupy the gut and comprise the natural commensal flora or microbiota. The microbiota is critically important for the breakdown of nutrients, and also assists in preventing colonization by potentially pathogenic bacteria. In addition, the gut commensal bacteria appear to be critical for the development of an optimally functioning immune system. Various studies have shown that individual species of the microbiota can induce very different types of immune cells (e.g., Th17 cells, Foxp3(+) regulatory T cells) and responses, suggesting that the composition of the microbiota can have an important influence on the immune response. Although the microbiota resides in the gut, it appears to have a significant impact on the systemic immune response. Indeed, specific gut commensal bacteria have been shown to affect disease development in organs other than the gut, and depending on the species, have been found to have a wide range of effects on diseases from induction and exacerbation to inhibition and protection. In this review, we will focus on the role that the gut microbiota plays in the development and progression of inflammatory/autoimmune disease, and we will also touch upon its role in allergy and cancer.

Ectopic expression of blood type antigens in inflamed mucosa with higher incidence of FUT2 secretor status in colonic Crohn's disease

BACKGROUND

Host-intestinal microbial interaction plays an important role in the pathogenesis of inflammatory bowel diseases (IBDs). The surface molecules of the intestinal epithelium act as receptors for bacterial adhesion and regulate the intestinal bacteria. Some known receptors are the mucosal blood type antigens, which are regulated by the fucosyltransferase2 (FUT2) gene, and individuals who express these antigens in the gastrointestinal tract are called secretors. Recent research has revealed that the FUT2 gene is associated with Crohn's disease (CD) in western populations.

METHODS

To clarify the contribution of mucosal blood type antigens in IBD, we determined the incidence of five previously reported single-nucleotide polymorphisms of the FUT2 gene in Japanese patients. We also used immunohistochemistry to investigate the antigen expression in mucosal specimens from IBD patients and animal models.

RESULTS

Genetic analysis revealed that all of the patients with colonic CD were secretors, whereas the incidence of secretors was 80, 80, 67, and 80%, respectively, for the control, ileocolonic CD, ileal CD, and ulcerative colitis groups (P = 0.036). Abnormal expression of blood type antigens was observed only in colonic CD. Interleukin-10⁻/⁻ mice, but not dextran sulfate sodium colitis mice, had enhanced colonic expression of blood type antigens, and the expression of these antigens preceded the development of colitis in the interleukin-10⁻/⁻ mice.

CONCLUSIONS

FUT2 secretor status was associated with colonic-type CD. This finding, taken together with the immunohistochemistry data, suggests that the abnormal expression of blood type antigens in the colon may be a unique and essential factor for colonic CD.

Is metabolic stress a common denominator in inflammatory bowel disease?

The enteric epithelium represents the major boundary between the outside world and the body, and in the colon it is the interface between the host and a vast and diverse microbiota. A common feature of inflammatory bowel disease (IBD) is decreased epithelial barrier function, and while a cause-and-effect relationship can be debated, prolonged loss of epithelial barrier function (whether this means the ability to sense bacteria or exclude them) would contribute to inflammation. While there are undoubtedly individual nuances in IBD, we review data in support of metabolic stress--that is, perturbed mitochondrial function--in the enterocyte as a contributing factor to the initiation of inflammation and relapses in IBD. The postulate is presented that metabolic stress, which can arise as a consequence of a variety of stimuli (e.g., infection, bacterial dysbiosis, and inflammation also), will reduce epithelial barrier function and perturb the enterocyte-commensal flora relationship and suggest that means to negate enterocytic metabolic stress should be considered as a prophylactic or adjuvant therapy in IBD.

Intestinal microbiota in human health and disease: the impact of probiotics

The complex communities of microorganisms that colonise the human gastrointestinal tract play an important role in human health. The development of culture-independent molecular techniques has provided new insights in the composition and diversity of the intestinal microbiota. Here, we summarise the present state of the art on the intestinal microbiota with specific attention for the application of high-throughput functional microbiomic approaches to determine the contribution of the intestinal microbiota to human health. Moreover, we review the association between dysbiosis of the microbiota and both intestinal and extra-intestinal diseases. Finally, we discuss the potential of probiotic microorganism to modulate the intestinal microbiota and thereby contribute to health and well-being. The effects of probiotic consumption on the intestinal microbiota are addressed, as well as the development of tailor-made probiotics designed for specific aberrations that are associated with microbial dysbiosis.

Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms

Background

While our knowledge of the intestinal microbiota during disease is accumulating, basic information of the microbiota in healthy subjects is still scarce. The aim of this study was to characterize the intestinal microbiota of healthy adults and specifically address its temporal stability, core microbiota and relation with intestinal symptoms. We carried out a longitudinal study by following a set of 15 healthy Finnish subjects for seven weeks and regularly assessed their intestinal bacteria and archaea with the Human Intestinal Tract (HIT)Chip, a phylogenetic microarray, in conjunction with qPCR analyses. The health perception and occurrence of intestinal symptoms was recorded by questionnaire at each sampling point.

Principal Findings

A high overall temporal stability of the microbiota was observed. Five subjects showed transient microbiota destabilization, which correlated not only with the intake of antibiotics but also with overseas travelling and temporary illness, expanding the hitherto known factors affecting the intestinal microbiota. We identified significant correlations between the microbiota and common intestinal symptoms, including abdominal pain and bloating. The most striking finding was the inverse correlation between Bifidobacteria and abdominal pain: subjects who experienced pain had over five-fold less Bifidobacteria compared to those without pain. Finally, a novel computational approach was used to define the common core microbiota, highlighting the role of the analysis depth in finding the phylogenetic core and estimating its size. The in-depth analysis suggested that we share a substantial number of our intestinal phylotypes but as they represent highly variable proportions of the total community, many of them often remain undetected.

Conclusions/Significance

A global and high-resolution microbiota analysis was carried out to determine the temporal stability, the associations with intestinal symptoms, and the individual and common core microbiota in healthy adults. The findings provide new approaches to define intestinal health and to further characterize the microbial communities inhabiting the human gut.

Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis

BACKGROUND & AIMS

Interactions between genetic and environmental factors are believed to be involved in onset and initiation of inflammatory bowel disease. We analyzed the interaction between gastrointestinal mucosal microbiota and host genes in twin pairs discordant for ulcerative colitis (UC) to study the functional interaction between microbiota and mucosal epithelium.

METHODS

Biopsy were collected from sigmoid colon of UC patients and their healthy twins (discordant twin pairs) and from twins without UC. Microbiota profiles were determined from analysis of 16S ribosomal DNA libraries; messenger RNA profiles were determined by microarray analysis.

RESULTS

Patients with UC had dysbiotic microbiota, characterized by less bacterial diversity and more Actinobacteria and Proteobacteria than that of their healthy siblings; healthy siblings from discordant twins had more bacteria from the Lachnospiraceae and Ruminococcaceae families than twins who were both healthy. In twins who were both healthy, 34 mucosal transcripts correlated with bacterial genera, whereas only 25 and 11 correlated with bacteria genera in healthy individuals and their twins with UC, respectively. Transcripts related to oxidative and immune responses were differentially expressed between patients with UC and their healthy twins.

CONCLUSIONS

The transcriptional profile of the mucosa appears to interact with the colonic microbiota; this interaction appears to be lost in colon of patients with UC. Bacterial functions, such as butyrate production, might affect mucosal gene expression. Patients with UC had different gene expression profiles and lower levels of biodiversity than their healthy twins, as well as unusual aerobic bacteria. Patients with UC had lower percentages of potentially protective bacterial species than their healthy twins.

Metagenomic biomarker discovery and explanation

This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.

Towards the human colorectal cancer microbiome

Multiple factors drive the progression from healthy mucosa towards sporadic colorectal carcinomas and accumulating evidence associates intestinal bacteria with disease initiation and progression. Therefore, the aim of this study was to provide a first high-resolution map of colonic dysbiosis that is associated with human colorectal cancer (CRC). To this purpose, the microbiomes colonizing colon tumor tissue and adjacent non-malignant mucosa were compared by deep rRNA sequencing. The results revealed striking differences in microbial colonization patterns between these two sites. Although inter-individual colonization in CRC patients was variable, tumors consistently formed a niche for Coriobacteria and other proposed probiotic bacterial species, while potentially pathogenic Enterobacteria were underrepresented in tumor tissue. As the intestinal microbiota is generally stable during adult life, these findings suggest that CRC-associated physiological and metabolic changes recruit tumor-foraging commensal-like bacteria. These microbes thus have an apparent competitive advantage in the tumor microenvironment and thereby seem to replace pathogenic bacteria that may be implicated in CRC etiology. This first glimpse of the CRC microbiome provides an important step towards full understanding of the dynamic interplay between intestinal microbial ecology and sporadic CRC, which may provide important leads towards novel microbiome-related diagnostic tools and therapeutic interventions.

Towards the human colorectal cancer microbiome

Multiple factors drive the progression from healthy mucosa towards sporadic colorectal carcinomas and accumulating evidence associates intestinal bacteria with disease initiation and progression. Therefore, the aim of this study was to provide a first high-resolution map of colonic dysbiosis that is associated with human colorectal cancer (CRC). To this purpose, the microbiomes colonizing colon tumor tissue and adjacent non-malignant mucosa were compared by deep rRNA sequencing. The results revealed striking differences in microbial colonization patterns between these two sites. Although inter-individual colonization in CRC patients was variable, tumors consistently formed a niche for Coriobacteria and other proposed probiotic bacterial species, while potentially pathogenic Enterobacteria were underrepresented in tumor tissue. As the intestinal microbiota is generally stable during adult life, these findings suggest that CRC-associated physiological and metabolic changes recruit tumor-foraging commensal-like bacteria. These microbes thus have an apparent competitive advantage in the tumor microenvironment and thereby seem to replace pathogenic bacteria that may be implicated in CRC etiology. This first glimpse of the CRC microbiome provides an important step towards full understanding of the dynamic interplay between intestinal microbial ecology and sporadic CRC, which may provide important leads towards novel microbiome-related diagnostic tools and therapeutic interventions.

Degradation of the extracellular matrix components by bacterial-derived metalloproteases: implications for inflammatory bowel diseases

BACKGROUND

Proteolytic degradation of the extracellular matrix, a feature of mucosal homeostasis and tissue renewal, also contributes to the complications of intestinal inflammation. Whether this proteolytic activity is entirely host-derived, or, in part, produced by the gut microbiota, is unknown.

METHODS

We screened the bacterial colonies for gelatinolytic activity from fecal samples of 20 healthy controls, 23 patients with ulcerative colitis, and 18 with Crohn's disease (CD). In addition, the genes encoding metalloproteases were detected by conventional or real-time polymerase chain reaction (PCR).

RESULTS

Gelatinolytic activity was found in approximately one-quarter of samples regardless of the presence of inflammation and without any attempt to enhance the sensitivity of the culture-based screen. This was associated with a diversity of bacteria, particularly in CD, but was predominantly linked with Clostridium perfringens. Culture supernatants from C. perfringens degraded gelatin, azocoll, type I collagen, and basement membrane type IV collagen, but different isolates varied in the degree of proteolytic activity. Results were confirmed by detection of the C. perfringens colA gene (encoding collagenase) in fecal DNA, again regardless of the presence or absence of inflammation. However, the biologic significance and potential implications of microbial-derived proteolytic activity were confirmed by reduced transepithelial resistance (TER) after exposure of rat distal colon to culture supernatants of C. perfringens in Ussing chambers.

CONCLUSIONS

The study shows that microbial-derived proteolytic activity has the capacity to contribute to mucosal homeostasis and may participate in the pathogenesis of inflammatory bowel disease.

A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome

In the human gastrointestinal tract, bacterial β-D-glucuronidases (BG; E.C. 3.2.1.31) are involved both in xenobiotic metabolism and in some of the beneficial effects of dietary compounds. Despite their biological significance, investigations are hampered by the fact that only a few BGs have so far been studied. A functional metagenomic approach was therefore performed on intestinal metagenomic libraries using chromogenic glucuronides as probes. Using this strategy, 19 positive metagenomic clones were identified but only one exhibited strong β-D-glucuronidase activity when subcloned into an expression vector. The cloned gene encoded a β-D-glucuronidase (called H11G11-BG) that had distant amino acid sequence homologies and an additional C terminus domain compared with known β-D-glucuronidases. Fifteen homologs were identified in public bacterial genome databases (38-57% identity with H11G11-BG) in the Firmicutes phylum. The genomes identified derived from strains from Ruminococcaceae, Lachnospiraceae, and Clostridiaceae. The genetic context diversity, with closely related symporters and gene duplication, argued for functional diversity and contribution to adaptive mechanisms. In contrast to the previously known β-D-glucuronidases, this previously undescribed type was present in the published microbiome of each healthy adult/child investigated (n = 11) and was specific to the human gut ecosystem. In conclusion, our functional metagenomic approach revealed a class of BGs that may be part of a functional core specifically evolved to adapt to the human gut environment with major health implications. We propose consensus motifs for this unique Firmicutes β-D-glucuronidase subfamily and for the glycosyl hydrolase family 2.