Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes

Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa

Probiotic bacteria can modulate immune responses in the host gastrointestinal tract to promote health. The genomics era has provided novel opportunities for the discovery and characterization of bacterial probiotic effector molecules that elicit specific responses in the intestinal system. Furthermore, nutrigenomic analyses of the response to probiotics have unravelled the signalling and immune response pathways which are modulated by probiotic bacteria. Together, these genomic approaches and nutrigenomic analyses have identified several bacterial factors that are involved in modulation of the immune system and the mucosal barrier, and have revealed that a molecular 'bandwidth of human health' could represent a key determinant in an individual's physiological responsiveness to probiotics. These approaches may lead to improved stratification of consumers and to subpopulation-level probiotic supplementation to maintain or improve health, or to reduce the risk of disease.

Genome sequence of the probiotic strain Bifidobacterium animalis subsp. lactis CNCM I-2494

Bifidobacterium animalis subsp. lactis CNCM I-2494 is part of a commercialized fermented dairy product with documented health benefits revealed by multiple randomized placebo-controlled clinical trials. Here we report the complete genome sequence of this strain, which has a circular genome of 1,943,113 bp with 1,660 open reading frames and 4 ribosomal operons.

Impact of probiotics on colonizing microbiota of the gut

Although precise mechanisms responsible for all demonstrations of probiotic health benefits are not known, many lines of evidence suggest that probiotics function through direct or indirect impact on colonizing microbiota of the gut. Probiotics can directly influence colonizing microbes through multiple mechanisms, including the production of inhibitory compounds (bacteriocins, short chain fatty acids, and others), by producing substrates that might promote the growth of colonizing microbes (secreted exopolysaccharides, vitamins, fatty acids, sugars from undigested carbohydrates and others), and by promoting immune responses against specific microbes. Indirectly, probiotics can influence colonizing microbes by inhibiting attachment through stimulated mucin production, reinforcing gut barrier effects, and downregulation of gut inflammation, thereby promoting microbes that are associated with a healthier gut physiology. Although the value of targeted changes in populations of gut bacteria is a matter of debate, increased levels of Bifidobacterium and Lactobacillus in the gut correlate with numerous health endpoints. Microbiota changes due to probiotic intake include increased numbers of related phylotypes, decreasing pathogens and their toxins, altering bacterial community structure to enhance evenness, stabilizing bacterial communities when perturbed (eg, with antibiotics), or promoting a more rapid recovery from a perturbation. Further research will provide insight into the degree of permanence of probiotic-induced changes, although research to date suggests that continued probiotic consumption is needed for sustained impact.

Gut microbiota and probiotics in colon tumorigenesis

The human gastrointestinal tract harbors a complex and abundant microbial community reaching as high as 10(13)-10(14) microorganisms in the colon. This endogenous microbiota forms a symbiotic relationship with their eukaryotic host and this close partnership helps maintain homeostasis by performing essential and non-redundant tasks (e.g. nutrition/energy and, immune system balance, pathogen exclusion). Although this relationship is essential and beneficial to the host, various events (e.g. infection, diet, stress, inflammation) may impact microbial composition, leading to the formation of a dysbiotic microbiota, further impacting on health and disease states. For example, Crohn's disease and ulcerative colitis, collectively termed inflammatory bowel diseases (IBD), have been associated with the establishment of a dysbiotic microbiota. In addition, extra-intestinal disorders such as obesity and metabolic syndrome are also associated with the development of a dysbiotic microbiota. Consequently, there is an increasing interest in harnessing the power of the microbiome and modulating its composition as a means to alleviate intestinal pathologies/disorders and maintain health status. In this review, we will discuss the emerging relationship between the microbiota and development of colorectal cancer as well as present evidence that microbial manipulation (probiotic, prebiotic) impacts disease development.

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.

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.

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.

Lessons from probiotic-host interaction studies in murine models of experimental colitis

In inflammatory bowel diseases (IBD), it is known that besides genetic and environmental factors (e.g. diet, drugs, stress), the microbiota play an important role in the pathogenesis. Patients with IBD have an altered microbiota (dysbiosis) and therefore, probiotics, defined as 'live micro-organisms that when administered in adequate amounts can confer a health benefit on the host', have been suggested as nutritional supplements to restore these imbalances. The best response on probiotics among the different types of IBD appears to be in the case of ulcerative colitis. Although probiotics show promise in IBD in both clinical and animal studies, further mechanistic studies are necessary to optimize the use of probiotics as supporting therapy in IBD. Murine models of experimental colitis have been used for decades to study this pathology, and these models have been proven useful to search for new therapeutic approaches. The purpose of this review is to summarize probiotic-host interaction studies in murine models of experimental colitis and to evaluate how these models can further help in understanding these complex interactions. Unraveling the molecular mechanisms behind the beneficial effects will assist in better and possibly more efficient probiotic formulations.

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/.

T-bet in disease

The activation of immune-defense mechanisms in response to a microbial attack must be robust and appropriately tailored to fight particular types of pathogens. Infection with intracellular microorganisms elicits a type 1 inflammatory response characterized by mobilization of T helper type 1 (T(H)1) cells to the site of infection, where they are responsible for the recruitment and activation of macrophages. At the center of the type 1 inflammatory response is the transcription factor T-bet, a critical regulator of the T(H)1 differentiation program. T-bet induces the production of interferon-γ (IFN-γ) and orchestrates the T(H)1 cell-migratory program by regulating the expression of chemokines and chemokine receptors. However, tight regulation of the type 1 inflammatory response is essential for the prevention of immunopathology and the development of organ-specific autoimmunity. In this review, we discuss how T-bet expression drives autoaggressive and inflammatory processes and how its function in vivo must be delicately balanced to avoid disease.

Regulation of innate and adaptive immunity by the commensal microbiota

The microbial communities that inhabit the intestinal tract are essential for mammalian health. Communication between the microbiota and the host establishes and maintains immune homeostasis, enabling protective immune responses against pathogens while preventing adverse inflammatory responses to harmless commensal microbes. Specific bacteria, such as segmented filamentous bacteria, Clostridium species, and Bacteroides fragilis, are key contributors to immune homeostasis in the gut. The cellular and molecular interactions between intestinal microbes and the immune system are rapidly being elucidated. Here, we review advances in our understanding of the microbial populations that shape the mucosal immune system and create a protective defense that prevents infection while tolerating friendly commensals.

Key questions to guide a better understanding of host-commensal microbiota interactions in intestinal inflammation

Co-evolution with an extremely complex commensal enteric microbiota has helped shape mammalian mucosal immune responses. A yet incompletely defined subset of intestinal bacteria is required to stimulate chronic, immune-mediated intestinal inflammation, including human Crohn's disease, and intestinal microbiota composition is altered in a characteristic manner by the inflammatory response to create a dysbiotic relationship of protective vs. aggressive bacteria. We pose a number of questions regarding host interactions with the enteric microbiota, including influences of inflammation, host genetics, early environmental exposure, and diet on microbial composition and function, and conversely, the effect of bacterial metabolism, enteric fungi and viruses, and endogenous protective bacterial species on host immune and inflammatory responses. These questions are designed to stimulate research that will promote a better understanding of host-microbial interactions in the intestine and promote targeted novel therapeutic interventions.

Impact of microbial transformation of food on health - from fermented foods to fermentation in the gastro-intestinal tract

Fermentation of food components by microbes occurs both during certain food production processes and in the gastro-intestinal tract. In these processes specific compounds are produced that originate from either biotransformation reactions or biosynthesis, and that can affect the health of the consumer. In this review, we summarize recent advances highlighting the potential to improve the nutritional status of a fermented food by rational choice of food-fermenting microbes. The vast numbers of microbes residing in the human gut, the gut microbiota, also give rise to a broad array of health-active molecules. Diet and functional foods are important modulators of the gut microbiota activity that can be applied to improve host health. A truly multidisciplinary approach is required to increase our understanding of the molecular mechanisms underlying health beneficial effects that arise from the interaction of diet, microbes and the human body.

Impact of the metabolic activity of Streptococcus thermophilus on the colon epithelium of gnotobiotic rats

The thermophilic lactic acid bacterium Streptococcus thermophilus is widely and traditionally used in the dairy industry. Despite the vast level of consumption of S. thermophilus through yogurt or probiotic functional food, very few data are available about its physiology in the gastrointestinal tract (GIT). The objective of the present work was to explore both the metabolic activity and host response of S. thermophilus in vivo. Our study profiles the protein expression of S. thermophilus after its adaptation to the GIT of gnotobiotic rats and describes the impact of S. thermophilus colonization on the colonic epithelium. S. thermophilus colonized progressively the GIT of germ-free rats to reach a stable population in 30 days (10(8) cfu/g of feces). This progressive colonization suggested that S. thermophilus undergoes an adaptation process within GIT. Indeed, we showed that the main response of S. thermophilus in the rat's GIT was the massive induction of the glycolysis pathway, leading to formation of lactate in the cecum. At the level of the colonic epithelium, the abundance of monocarboxylic acid transporter mRNAs (SLC16A1 and SLC5A8) and a protein involved in the cell cycle arrest (p27(kip1)) increased in the presence of S. thermophilus compared with germ-free rats. Based on different mono-associated rats harboring two different strains of S. thermophilus (LMD-9 or LMG18311) or weak lactate-producing commensal bacteria (Bacteroides thetaiotaomicron and Ruminococcus gnavus), we propose that lactate could be a signal produced by S. thermophilus and modulating the colon epithelium.

Modulation of immune homeostasis by commensal bacteria

Intestinal bacteria form a resident community that has co-evolved with the mammalian host. In addition to playing important roles in digestion and harvesting energy, commensal bacteria are crucial for the proper functioning of mucosal immune defenses. Most of these functions have been attributed to the presence of large numbers of 'innocuous' resident bacteria that dilute or occupy niches for intestinal pathogens or induce innate immune responses that sequester bacteria in the lumen, thus quenching excessive activation of the mucosal immune system. However it has recently become obvious that commensal bacteria are not simply beneficial bystanders, but are important modulators of intestinal immune homeostasis and that the composition of the microbiota is a major factor in pre-determining the type and robustness of mucosal immune responses. Here we review specific examples of individual members of the microbiota that modify innate and adaptive immune responses, and we focus on potential mechanisms by which such species-specific signals are generated and transmitted to the host immune system.