The normal intestinal microbiota

Voices from within: gut microbes and the CNS

Recent advances in research have greatly increased our understanding of the importance of the gut microbiota. Bacterial colonization of the intestine is critical to the normal development of many aspects of physiology such as the immune and endocrine systems. It is emerging that the influence of the gut microbiota also extends to modulation of host neural development. Furthermore, the overall balance in composition of the microbiota, together with the influence of pivotal species that induce specific responses, can modulate adult neural function, peripherally and centrally. Effects of commensal gut bacteria in adult animals include protection from the central effects of infection and inflammation as well as modulation of normal behavioral responses. There is now robust evidence that gut bacteria influence the enteric nervous system, an effect that may contribute to afferent signaling to the brain. The vagus nerve has also emerged as an important means of communicating signals from gut bacteria to the CNS. Further understanding of the mechanisms underlying microbiome-gut-brain communication will provide us with new insight into the symbiotic relationship between gut microbiota and their mammalian hosts and help us identify the potential for microbial-based therapeutic strategies to aid in the treatment of mood disorders.

The intestinal microbiota dysbiosis and Clostridium difficile infection: is there a relationship with inflammatory bowel disease?

Gut microbiota is a compilation of microorganisms dwelling in the entire mammalian gastrointestinal tract. They display a symbiotic relationship with the host contributing to its intestinal health and disease. Even a slight fluctuation in this equipoise may be deleterious to the host, leading to many pathological conditions like Clostridium difficile infection or inflammatory bowel disease (IBD). In this review, we focus on the role of microbial dysbiosis in initiation of C. difficile infection and IBD, and we also touch upon the role of specific pathogens, particularly C. difficile, as causative agents of IBD. We also discuss the molecular mechanisms activated by C. difficile that contribute to the development and exacerbation of gastrointestinal disorders.

Movers and shakers: influence of bacteriophages in shaping the mammalian gut microbiota

The human intestinal microbiota is one of the most densely populated ecosystems on Earth, containing up to 10 ( 13) bacteria/g and in some respects can be considered an organ itself given its role in human health. Bacteriophages (phages) are the most abundant replicating entities on the planet and thrive wherever their bacterial hosts exist. They undoubtedly influence the dominant microbial populations in many ecosystems including the human intestine. Within this setting, lysogeny appears to be the preferred life cycle, presumably due to nutrient limitations and lack of suitable hosts protected in biofilms, hence the predator/prey dynamic observed in many ecosystems is absent. On the other hand, free virulent phages in the gut are more common among sufferers of intestinal diseases and have been shown to increase with antibiotic usage. Many of these phages evolve from prophages of intestinal bacteria and emerge under conditions where their bacterial hosts encounter stress suggesting that prophages can significantly alter the microbial community composition. Based on these observations, we propose the "community shuffling" model which hypothesizes that prophage induction contributes to intestinal dysbiosis by altering the ratio of symbionts to pathobionts, enabling pathobiont niche reoccupation. The consequences of the increased phage load on the mammalian immune system are also addressed. While this is an area of intestinal biology which has received little attention, this review assembles evidence from the literature which supports the role of phages as one of the biological drivers behind the composition of the gut microbiota.

Probiotics - do they have a role in the pig industry?

The delivery of certain living microorganisms in food has long been suggested as having positive health effects in humans. This practice has extended into food animal production, with a variety of microorganisms being used; lactic acid bacteria, various Bacillus species and the yeast Saccharomyces cerevisiae have been particularly used in the pig industry. The increased interest in probiotics is essentially due to the problem of microbial resistance to antibiotics and following the ban of the use of antibiotics in animal production, probiotics being considered an alternative means to reduce pathogen infection and improve animal health especially around the time of weaning. However, there is still a need to clarify the probiotic effectiveness in pigs, and the underlying mechanisms. When assessing the efficacy of probiotics one must consider the particular strain of organism being used and the production stage of the pigs being treated. The reproducible delivery of probiotics in industrial pig production is problematic as maintenance of viability is key to their beneficial activity, but difficult to achieve with commonly used feed processing technologies. One specific context where probiotics organisms may be reliably delivered is in systems utilising fermented liquid feeds. Liquid feed may be fermented by the activity of wild lactic acid bacteria or may be stimulated using specific isolates as 'starters'; the latter system has advantages in terms of reproducibility and speed of fermentation. The farm context in which the organism is used is likely to be critical; the use of probiotics is more likely to result in measurable economic gains in animals living in sub-optimal conditions rather than in those reared in the highest welfare and husbandry conditions. The establishment of a beneficial lactic acid bacteria population at birth may lead to healthier animals, this may be most effectively achieved by treating sows, which provide an amplification step and flood the neonatal pigs' environment with desirable bacterial strains. In contrast, it may be sufficient to provide a supportive, protective microbiota around the time of weaning as this is a time of major crisis with instability and loss of certain bacterial populations.

Reactive oxygen production induced by the gut microbiota: pharmacotherapeutic implications

The resident prokaryotic microbiota of the mammalian intestine influences diverse homeostatic functions, including regulation of cellular growth, maintenance of barrier function, and modulation of immune responses. However, it is unknown how commensal prokaryotic organisms mechanistically influence eukaryotic signaling networks. Recent data has demonstrated that gut epithelia contacted by enteric commensal bacteria rapidly generate reactive oxygen species (ROS). While the induced generation of ROS via stimulation of formyl peptide receptors is a cardinal feature of the cellular response of phagocytes to pathogenic or commensal bacteria, evidence is accumulating that ROS are also similarly elicited in other cell types, including intestinal epithelia, in response to microbial signals. Additionally, ROS have been shown to serve as critical second messengers in multiple signal transduction pathways stimulated by proinflammatory cytokines and growth factors. This physiologically-generated ROS is known to participate in cellular signaling via the rapid and transient oxidative inactivation of a defined class of sensor proteins bearing oxidant-sensitive thiol groups. These proteins include tyrosine phosphatases that serve as regulators of MAP kinase pathways, cytoskeletal dynamics, as well as components involved in control of ubiquitination-mediated NF-κB activation. Consistently, microbial-elicited ROS has been shown to mediate increased cellular proliferation and motility and to modulate innate immune signaling. These results demonstrate how enteric microbiota influence regulatory networks of the mammalian intestinal epithelia. We hypothesize that many of the known effects of the normal microbiota on intestinal physiology, and potential beneficial effects of candidate probiotic bacteria, may be at least partially mediated by this ROS-dependent mechanism.

Abdominal bloating and distension: what is the role of the microbiota

Most patients with irritable bowel syndrome complain of a sensation of an increase in pressure within their abdomen during the course of the day which is called bloating and, in approximately half of these individuals, this symptom is accompanied by an actual increase in abdominal girth, which is referred to as distension. The pathophysiology of these two phenomena is somewhat different and it is now recognised that a whole variety of overlapping mechanisms are involved. Some of these are potentially amenable to treatment by modification of the bacterial flora of the gut and this article reviews the evidence for this.

The rationale and clinical effectiveness of probiotics in irritable bowel syndrome

The pathophysiology of irritable bowel syndrome (IBS) is still unknown. However, several lines of epidemiological, physiological, and clinical data suggest a role for intestinal bacteria in the pathogenesis of the disorder. Recent microbiology studies demonstrated differences in the composition of the intestinal microbiota between patients with IBS and healthy individuals. In addition, physiological studies have shown that manipulation of the intestinal microbiota by antibiotics, prebiotics, or probiotics can affect intestinal functions (eg, motility and sensation) relevant in the pathogenesis of IBS. Several randomized control trials comparing the effects of probiotics versus placebo in IBS have been published. Despite considerable differences in study design, dosing regimens, probiotic species used, and reported clinical end points, the current data indicate improving IBS symptoms and reducing the risk of persistent IBS symptoms. The data on the use of probiotics in children with IBS is more limited but is also suggestive for beneficial effects. The inconsistencies between the studies underline the need to look at each probiotic product separately for specific conditions, symptoms, and patient populations. This review article discusses the rationale for targeting the intestinal microbiota in patient with IBS and provides an overview and a critical evaluation of the currently available clinical data on the use of probiotics in the treatment of patients with IBS.

The evolution of bacteriocin production in bacterial biofilms

Bacteriocin production is a spiteful behavior of bacteria that is central to the competitive dynamics of many human pathogens. Social evolution predicts that bacteriocin production is favored when bacteriocin-producing cells are mixed at intermediate frequency with their competitors and when competitive neighborhoods are localized. Both predictions are supported by biofilm experiments. However, the means by which physical and biological processes interact to produce conditions that favor the evolution of bacteriocin production remain to be investigated. Here we fill this gap using analytical and computational approaches. We identify and collapse key parameters into a single number, the critical bacteriocin range, that measures the threshold distance from a focal bacteriocin-producing cell within which its fitness is higher than that of a sensitive cell. We develop an agent-based model to test our predictions and confirm that bacteriocin production is most favored when relatedness is intermediate and competition is local. We then use invasion analysis to determine evolutionarily stable strategies for bacteriocin production. Finally, we perform long-term evolutionary simulations to analyze how the critical bacteriocin range and genetic lineage segregation affect biodiversity in multistrain biofilms. We find that biodiversity is maintained in highly segregated biofilms for a wide array of critical bacteriocin ranges. However, under conditions of high nutrient penetration leading to well-mixed biofilms, biodiversity rapidly decreases and becomes sensitive to the critical bacteriocin range.

Genome analysis of food grade lactic Acid-producing bacteria: from basics to applications

Whole-genome sequencing has revolutionized and accelerated scientific research that aims to study the genetics, biochemistry and molecular biology of bacteria. Lactic acid-producing bacteria, which include lactic acid bacteria (LAB) and bifidobacteria, are typically Gram-positive, catalase-negative organisms, which occupy a wide range of natural plant- and animal-associated environments. LAB species are frequently involved in the transformation of perishable raw materials into more stable, pleasant, palatable and safe fermented food products. LAB and bifidobacteria are also found among the resident microbiota of the gastrointestinal and/or genitourinary tracts of vertebrates, where they are believed to exert health-promoting effects. At present, the genomes of more than 20 LAB and bifidobacterial species have been completely sequenced. Their genome content reflects its specific metabolism, physiology, biosynthetic capabilities, and adaptability to varying conditions and environments. The typical LAB/bifidobacterial genome is relatively small (from 1.7 to 3.3 Mb) and thus harbors a limited assortment of genes (from around 1,600 to over 3,000). These small genomes code for a broad array of transporters for efficient carbon and nitrogen assimilation from the nutritionally-rich niches they usually inhabit, and specify a rather limited range of biosynthetic and degrading capabilities. The variation in the number of genes suggests that the genome evolution of each of these bacterial groups involved the processes of extensive gene loss from their particular ancestor, diversification of certain common biological activities through gene duplication, and acquisition of key functions via horizontal gene transfer. The availability of genome sequences is expected to revolutionize the exploitation of the metabolic potential of LAB and bifidobacteria, improving their use in bioprocessing and their utilization in biotechnological and health-related applications.

Inflammation, sanitation, and consternation: loss of contact with coevolved, tolerogenic microorganisms and the pathophysiology and treatment of major depression

CONTEXT

Inflammation is increasingly recognized as contributing to the pathogenesis of major depressive disorder (MDD), even in individuals who are otherwise medically healthy. Most studies in search of sources for this increased inflammation have focused on factors such as psychosocial stress and obesity that are known to activate inflammatory processes and increase the risk for depression. However, MDD may be so prevalent in the modern world not just because proinflammatory factors are widespread, but also because we have lost contact with previously available sources of anti-inflammatory, immunoregulatory signaling.

OBJECTIVE

To examine evidence that disruptions in coevolved relationships with a variety of tolerogenic microorganisms that were previously ubiquitous in soil, food, and the gut, but that are largely missing from industrialized societies, may contribute to increasing rates of MDD in the modern world.

DATA SOURCES

Relevant studies were identified using PubMed and Ovid MEDLINE.

STUDY SELECTION

Included were laboratory animal and human studies relevant to immune functioning, the hygiene hypothesis, and major depressive disorder identified via PubMed and Ovid MEDLINE searches.

DATA EXTRACTION

Studies were reviewed by all authors, and data considered to be potentially relevant to the contribution of hygiene-related immune variables to major depressive disorder were extracted.

DATA SYNTHESIS

Significant data suggest that a variety of microorganisms (frequently referred to as the "old friends") were tasked by coevolutionary processes with training the human immune system to tolerate a wide array of non-threatening but potentially proinflammatory stimuli. Lacking such immune training, vulnerable individuals in the modern world are at significantly increased risk of mounting inappropriate inflammatory attacks on harmless environmental antigens (leading to asthma), benign food contents and commensals in the gut (leading to inflammatory bowel disease), or self-antigens (leading to any of a host of autoimmune diseases). Loss of exposure to the old friends may promote MDD by increasing background levels of depressogenic cytokines and may predispose vulnerable individuals in industrialized societies to mount inappropriately aggressive inflammatory responses to psychosocial stressors, again leading to increased rates of depression.

CONCLUSION

Measured exposure to the old friends or their antigens may offer promise for the prevention and treatment of MDD in modern industrialized societies.

Recombinant lactobacilli expressing linoleic acid isomerase can modulate the fatty acid composition of host adipose tissue in mice

We have previously demonstrated that oral administration of a metabolically active Bifidobacterium breve strain, with ability to form cis-9, trans-11 conjugated linoleic acid (CLA), resulted in modulation of the fatty acid composition of the host, including significantly elevated concentrations of c9, t11 CLA and omega-3 (n-3) fatty acids in liver and adipose tissue. In this study, we investigated whether a recombinant lactobacillus expressing linoleic acid isomerase (responsible for production of t10, c12 CLA) from Propionibacterium acnes (PAI) could influence the fatty acid composition of different tissues in a mouse model. Linoleic-acid-supplemented diets (2 %, w/w) were fed in combination with either a recombinant t10, c12 CLA-producing Lactobacillus paracasei NFBC 338 (Lb338), or an isogenic (vector-containing) control strain, to BALB/c mice for 8 weeks. A third group of mice received linoleic acid alone (2 %, w/w). Tissue fatty acid composition was assessed by GLC at the end of the trial. Ingestion of the strain expressing linoleic acid isomerase was associated with a 4-fold increase (P<0.001) in t10, c12 CLA in adipose tissues of the mice when compared with mice that received the isogenic non-CLA-producing strain. The livers of the mice that received the recombinant CLA-producing Lb338 also contained a 2.5-fold (albeit not significantly) higher concentration of t10, c12 CLA, compared to the control group. These data demonstrate that a single gene (encoding linoleic acid isomerase) expressed in an intestinal microbe can influence the fatty acid composition of host fat.

Therapeutical use of probiotic formulations in clinical practice

BACKGROUND & AIMS

The spreading of gastrointestinal diseases is growing all over the world. Although for some of them an effective therapeutic approach has been found, palliation rather than cure is very frequent due to a partial knowledge of their aetiology and pathogenesis. This review, analyzing the main clinical studies, aims at being a state of the art update of the use of probiotic formulations in daily practice.

METHODS

In this review we include all the most significant clinical trials involving the use of probiotic formulations for the treatment of several pathologies.

RESULTS

Dysbiosis has been observed in irritable bowel syndrome patients. Probiotics may exert a beneficial effect on Crohn's disease affected patients who have shown gut microbiota antigens and altered wall permeability. Moreover some probiotic formulations seem to enhance the therapy for Helicobacter Pylori reducing its pathogenic potential. Intestinal ecology imbalance has been also linked to cancer induction, allergy, skin and urogenital diseases. In addition probiotics administration seems to be particularly useful to ease post-operative complications.

CONCLUSION

Further future clinical trials, involving large numbers of patients, will be mandatory to achieve definite evidence of the preventive and curative role of probiotics in medical practice.

Metabolism of a plant derived galactose-containing polysaccharide by Bifidobacterium breve UCC2003

In this study, we describe the functional characterization of the Bifidobacterium breve UCC2003 gal locus, which is dedicated to the utilization of galactan, a plant‐derived polysaccharide. Using a combination of molecular approaches we conclude that the galA gene of B. breve UCC2003 encodes a β‐1,4‐endogalactanase producing galacto‐oligosaccharides, which are specifically internalized by an ABC transport system, encoded by galBCDE, and which are then hydrolysed to galactose moieties by a dedicated intracellular β‐galactosidase, specified by galG. The generated galactose molecules are presumed to be fed into the fructose‐6‐phosphate phosphoketolase pathway via the Leloir pathway, thereby allowing B. breve UCC2003 to use galactan as its sole carbon and energy source. In addition to these findings we demonstrate that GalR is a LacI‐type DNA‐binding protein, which not only appears to control transcription of the galCDEGR operon, but also that of the galA gene.

Impact of administered bifidobacterium on murine host fatty acid composition

Recently, we reported that administration of Bifidobacteria resulted in increased concentrations of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in murine adipose tissue [1]. The objective of this study was to assess the impact of co-administration of Bifidobacterium breve NCIMB 702258 and the substrate for EPA, alpha-linolenic acid, on host fatty acid composition. alpha-Linolenic acid-supplemented diets (1%, wt/wt) were fed to mice (n = 8), with or without B. breve NCIMB 702258 (daily dose of 10(9) microorganisms) for 8 weeks. Two further groups received either supplement of B. breve alone or unsupplemented diet. Tissue fatty acid composition was assessed by gas liquid chromatography. Dietary supplementation of alpha-linolenic acid resulted in higher (P < 0.05) alpha-linolenic acid and EPA concentrations in liver and adipose tissue and lower (P < 0.05) arachidonic acid in liver, adipose tissue and brain compared with mice that did not receive alpha-linolenic acid. Supplementation with B. breve NCIMB 702258 in combination with alpha-linolenic acid resulted in elevated (P < 0.05) liver EPA concentrations compared with alpha-linolenic acid supplementation alone. Furthermore, the former group had higher (P < 0.05) DHA in brain compared with the latter group. These results suggest a role for interactions between fatty acids and commensals in the gastrointestinal tract. This interaction between administered microbes and fatty acids could result in a highly effective nutritional approach to the therapy of a variety of inflammatory and neurodegenerative conditions.

Molecular modulation of intestinal epithelial barrier: contribution of microbiota

The daunting task required of the gut-barrier to prevent luminal pathogens and harmful substances from entering into the internal milieu and yet promoting digestion and absorption of nutrients requires an exquisite degree of coordination between the different architectural units of this barrier. The complex integration and execution of these functions are superbly carried out by the intestinal mucosal (IM) surface. Exposed to trillions of luminal microbes, the IM averts threats by signaling to the innate immune system, through pattern recognition receptors (PRR), to respond to the commensal bacteria by developing tolerance (hyporesponsiveness) towards them. This system also acts by protecting against pathogens by elaborating and releasing protective peptides, cytokines, chemokines, and phagocytic cells. The IM is constantly sampling luminal contents and making molecular adjustments at its frontier. This article describes the topography of the IM and the mechanisms of molecular adjustments that protect the internal milieu, and also describes the role of the microbiota in achieving this goal.

Oral administration of Alequel, a mixture of autologous colon-extracted proteins for the treatment of Crohn's disease

The pathogenesis of Crohn's disease involves an immune-mediated damage to the gut mucosa. Current developed therapies are based on the use of immunosuppressive drugs that can lead to significant drug-related adverse responses. There is a need for a therapeutic strategy that is more specific and less global in its effect on the immune system. Oral tolerance is an active process wherein oral administration of antigens is associated with the induction of regulatory cells and the suppression of effector cells directed toward specific and nonspecific antigens. Studies in animal models of experimental colitis suggest that oral administration of proteins extracted from the gut can induce tolerance and alleviate the disease symptoms. Recent clinical trials showed that oral administration of Alequel, an autologous protein-containing colon extract, to patients with Crohn's disease is safe and may be effective as a therapeutic modality for treating the disease. This treatment was associated with disease-associated antigen alterations of the immune response in the patients. Oral administration of Alequel could provide a patient-tailored approach that is side-effect-free for the treatment of patients with Crohn's disease.

The role of the immune system in regulating the microbiota

A diverse population of bacteria, archaea and fungi, collectively known as the microbiota, abounds within the gastrointestinal tract of the mammalian host. This microbial population makes many important contributions to host physiology through inter-kingdom signalling and by providing nutrients that have both local and systemic effects. In a healthy state the overall host-microbial interaction is symbiotic; however, a growing number of diseases have been associated with a dysregulated microbiota. To avoid these consequences, the host exerts substantial effort to maintain proper regulation of the microbiota with respect to localization and composition. Although important to maintaining microbial balance, the host immune response can also be the cause of a disrupted microbiota, contributing to disease severity. Here, we discuss the role of the host in both maintaining and disrupting a balanced gastrointestinal microbiota.

Associations between dietary habits and body mass index with gut microbiota composition and fecal water genotoxicity: an observational study in African American and Caucasian American volunteers

Background

African Americans (AA) suffer from an increased incidence and mortality of colorectal cancer (CRC). Environmental exposures including dietary habits likely contribute to a high burden of CRC, however, data on the dietary habits of AA is sparse. Diet might change the composition and the activities of the intestinal microbiota, in turn affecting fecal genotoxicity/mutagenicity that is thought to be associated with carcinogenesis.

Methods

We assessed dietary habits by food frequency questionnaire and by food records in 52 AA and 46 CA residents of the Eastern Shore of MD. Fecal microbiota composition was determined using 16S rRNA based methods and fecal genotoxicity measured using the Comet assay.

Results

AA reported an increased intake of heterocyclic amines and a decreased dietary intake of vitamins including vitamin D (p < 0.05) that correlated with differences in fecal microbiota composition but not fecal genotoxicity. Intake of dietary fiber, calcium, total fat and heterocyclic amines correlated with differences in microbiota composition. Total bacterial counts/g of stool and raw counts of Bacteroides were increased in AA. In contrast to a previous study, BMI was not associated with proportions of Bacteroides.

Conclusion

Dietary habits of African Americans, including increased HCA intake and decreased vitamin D intake might at least partially contribute to CRC through modifications of gut microbiota composition that result in changes of the intestinal milieu.

The relationship between intestinal microbiota and the central nervous system in normal gastrointestinal function and disease

Although many people are aware of the communication that occurs between the gastrointestinal (GI) tract and the central nervous system, fewer know about the ability of the central nervous system to influence the microbiota or of the microbiota's influence on the brain and behavior. Within the GI tract, the microbiota have a mutually beneficial relationship with their host that maintains normal mucosal immune function, epithelial barrier integrity, motility, and nutrient absorption. Disruption of this relationship alters GI function and disease susceptibility. Animal studies suggest that perturbations of behavior, such as stress, can change the composition of the microbiota; these changes are associated with increased vulnerability to inflammatory stimuli in the GI tract. The mechanisms that underlie these alterations are likely to involve stress-induced changes in GI physiology that alter the habitat of enteric bacteria. Furthermore, experimental perturbation of the microbiota can alter behavior, and the behavior of germ-free mice differs from that of colonized mice. Gaining a better understanding of the relationship between behavior and the microbiota could provide insight into the pathogenesis of functional and inflammatory bowel disorders.

Metabolic activity of the enteric microbiota influences the fatty acid composition of murine and porcine liver and adipose tissues

BACKGROUND

Recent reports suggest that the metabolic activity of the gut microbiota may contribute to the pathogenesis of obesity and hepatic steatosis.

OBJECTIVE

The objective was to determine whether the fat composition of host tissues might be influenced by oral administration of commensal bifidobacteria previously shown by us to produce bioactive isomers of conjugated linoleic acid (CLA).

DESIGN

Murine trials were conducted in which linoleic acid-supplemented diets were fed with or without Bifidobacterium breve NCIMB 702258 (daily dose of 10(9) microorganisms) to healthy BALB/c mice and to severe combined immunodeficient mice for 8-10 wk. To ensure that the observations were not peculiar to mice, a similar trial was conducted in weanling pigs over 21 d. Tissue fatty acid composition was assessed by gas-liquid chromatography.

RESULTS

In comparison with controls, there was an increase in cis-9, trans-11 CLA in the livers of the mice and pigs after feeding with linoleic acid in combination with B. breve NCIMB 702258 (P < 0.05). In addition, an altered profile of polyunsaturated fatty acid composition was observed, including higher concentrations of the omega-3 (n-3) fatty acids eicosapentaenoic acid and docosahexaenoic acid in adipose tissue (P < 0.05). These changes were associated with reductions in the proinflammatory cytokines tumor necrosis factor-alpha and interferon-gamma (P < 0.05).

CONCLUSIONS

These results are consistent with the concept that the metabolome is a composite of host and microbe metabolic activity and that the influence of the microbiota on host fatty acid composition can be manipulated by oral administration of CLA-producing microorganisms.

Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle

The facultative intracellular bacterial pathogen Brucella infects a wide range of warm-blooded land and marine vertebrates and causes brucellosis. Currently, there are nine recognized Brucella species based on host preferences and phenotypic differences. The availability of 10 different genomes consisting of two chromosomes and representing six of the species allowed for a detailed comparison among themselves and relatives in the order Rhizobiales. Phylogenomic analysis of ortholog families shows limited divergence but distinct radiations, producing four clades as follows: Brucella abortus-Brucella melitensis, Brucella suis-Brucella canis, Brucella ovis, and Brucella ceti. In addition, Brucella phylogeny does not appear to reflect the phylogeny of Brucella species' preferred hosts. About 4.6% of protein-coding genes seem to be pseudogenes, which is a relatively large fraction. Only B. suis 1330 appears to have an intact beta-ketoadipate pathway, responsible for utilization of plant-derived compounds. In contrast, this pathway in the other species is highly pseudogenized and consistent with the "domino theory" of gene death. There are distinct shared anomalous regions (SARs) found in both chromosomes as the result of horizontal gene transfer unique to Brucella and not shared with its closest relative Ochrobactrum, a soil bacterium, suggesting their acquisition occurred in spite of a predominantly intracellular lifestyle. In particular, SAR 2-5 appears to have been acquired by Brucella after it became intracellular. The SARs contain many genes, including those involved in O-polysaccharide synthesis and type IV secretion, which if mutated or absent significantly affect the ability of Brucella to survive intracellularly in the infected host.

Metagenomics

The total number of prokaryotic cells on earth has been estimated to be approximately 4-6 x 10(30), with the majority of these being uncharacterized. This diversity represents a vast genetic bounty that may be exploited for the discovery of novel genes, entire metabolic pathways and potentially valuable end-products thereof. Metagenomics constitutes the functional and sequence-based analysis of the collective microbial genomes (microbiome) in a particular environment or environmental niche. Herein, we review the most recent sequence-based metagenomic analyses of some of the most microbiologically diverse locations on earth; including soil, marine water and the insect and human gut. Such studies have helped to uncover several previously unknown facts; from the true microbial diversity of extreme environments to the actual extent of symbiosis that exists in the insect and human gut. In this respect, metagenomics has and will continue to play an essential part in the new and evolving area of microbial systems biology.

Probiotics and gastrointestinal infections

Gastrointestinal infections are a major cause of morbidity and mortality worldwide, particularly in developing countries. The use of probiotics to prevent and treat a variety of diarrheal diseases has gained favor in recent years. Examples where probiotics have positively impacted gastroenteritis will be highlighted. However, the overall efficacy of these treatments and the mechanisms by which probiotics ameliorate gastrointestinal infections are mostly unknown. We will discuss possible mechanisms by which probiotics could have a beneficial impact by enhancing the prevention or treatment of diarrheal diseases.

Diagnosis of small intestinal bacterial overgrowth: the challenges persist!

Small intestinal bacterial overgrowth was originally defined in the context of an overt malabsorption syndrome and diagnostic tests were developed and validated accordingly. More recently, the concept of intestinal contamination with excessive numbers of bacteria, especially those of colonic type, has been extended beyond the bounds of frank maldigestion and malabsorption to explain symptomatology in disorders as diverse as irritable bowel syndrome, celiac sprue and nonalcoholic fatty liver disease. Owing to a lack of consensus with regard to the optimal diagnostic criteria (the 'gold standard') for the diagnosis of bacterial overgrowth, the status of these new concepts is unclear. This review sets out to critically appraise the various diagnostic approaches that have been taken and are currently employed to diagnose small intestinal bacterial overgrowth.

Microbes in gastrointestinal health and disease

Most, if not all, animals coexist with a complement of prokaryotic symbionts that confer a variety of physiologic benefits. In humans, the interaction between animal and bacterial cells is especially important in the gastrointestinal tract. Technical and conceptual advances have enabled rapid progress in characterizing the taxonomic composition, metabolic capacity, and immunomodulatory activity of the human gut microbiota, allowing us to establish its role in human health and disease. The human host coevolved with a normal microbiota over millennia and developed, deployed, and optimized complex immune mechanisms that monitor and control this microbial ecosystem. These cellular mechanisms have homeostatic roles beyond the traditional concept of defense against potential pathogens, suggesting these pathways contribute directly to the well-being of the gut. During their coevolution, the bacterial microbiota has established multiple mechanisms to influence the eukaryotic host, generally in a beneficial fashion, and maintain their stable niche. The prokaryotic genomes of the human microbiota encode a spectrum of metabolic capabilities beyond that of the host genome, making the microbiota an integral component of human physiology. Gaining a fuller understanding of both partners in the normal gut-microbiota interaction may shed light on how the relationship can go awry and contribute to a spectrum of immune, inflammatory, and metabolic disorders and may reveal mechanisms by which this relationship could be manipulated toward therapeutic ends.

Probiotic bacteria influence the composition and function of the intestinal microbiota

Probiotics have a range of proposed health benefits for the consumer, which may include modulating the levels of beneficial elements in the microbiota. Recent investigations using molecular approaches have revealed a human intestinal microbiota comprising over 1000 phylotypes. Mechanisms whereby probiotics impact on the intestinal microbiota include competition for substrates, direct antagonism by inhibitory substances, competitive exclusion, and potentially host-mediated effects such as improved barrier function and altered immune response. We now have the microbial inventories and genetic blueprints to begin tackling intestinal microbial ecology at an unprecedented level of detail, aided by the understanding that dietary components may be utilized differentially by individual phylotypes. Controlled intervention studies in humans, utilizing latest molecular technologies, are required to consolidate evidence for bacterial species that impact on the microbiota. Mechanistic insights should be provided by metabolomics and other analytical techniques for small molecules. Rigorous characterization of interactions between the diet, microbiota, and probiotic bacteria will provide new opportunities for modulating the microbiota towards improving human health.

Characterization of ApuB, an extracellular type II amylopullulanase from Bifidobacterium breve UCC2003

The apuB gene of Bifidobacterium breve UCC2003 was shown to encode an extracellular amylopullulanase. ApuB is composed of a distinct N-terminally located alpha-amylase-containing domain which hydrolyzes alpha-1,4-glucosidic linkages in starch and related polysaccharides and a C-terminally located pullulanase-containing domain which hydrolyzes alpha-1,6 linkages in pullulan, allowing the classification of this enzyme as a bifunctional class II pullulanase. A knockout mutation of the apuB gene in B. breve UCC2003 rendered the resulting mutant incapable of growth in medium containing starch, amylopectin, glycogen, or pullulan as the sole carbon and energy source, confirming the crucial physiological role of this gene in starch metabolism.

Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces

Molecular ecological surveys of the human gut microbiota to date have focused on the prokaryotic fraction of the community and have revealed a remarkable degree of bacterial diversity and functionality. However, there is a dearth of information on the eukaryotic composition of the microbiota, and no culture-independent sequence-based surveys of human faeces are available. Culture-independent analyses based on DNA extraction and polymerase chain reaction targeting both the total eukaryotic 18S rRNA genes and fungal internal transcribed regions (ITS), together with culture-dependent analyses of fungi, were performed on a group of healthy volunteers. Temporal analysis was also included wherever possible. Collectively, the data presented in this study indicate that eukaryotic diversity of the human gut is low, largely temporally stable and predominated by different subtypes of Blastocystis. Specific analyses of the fungal populations indicate that a disparity exists between the cultivable fraction, which is dominated by Candida sp, and culture-independent analysis, where sequences identical to members of the genera Gloeotinia/Paecilomyces and Galactomyces were most frequently retrieved from both fungal ITS profiles and subsequent clone libraries. Collectively, these results highlight the presence of unprecedented intestinal eukaryotic inhabitants whose functional roles are as yet unknown in healthy individuals. Furthermore, differences between results obtained from traditionally employed culture-based methods and those obtained from culture-independent techniques highlight similar anomalies to that encountered when first analysing the bacterial diversity of the human faecal microbiota using culture-independent surveys.

Host-bacteria homeostasis in the healthy and inflamed gut

PURPOSE OF REVIEW

We are currently entering an exciting transition period from studying the molecular and cellular bases of the virulence of bacterial pathogens to deciphering the mechanisms of tolerance of the gut commensal flora. This review attempts to delineate the (sometimes thin) border between these two situations that are at the heart of understanding gut homeostasis and its possible rupture.

RECENT FINDINGS

Essential issues are examined, such as metagenomic analysis of gut microbiota, the control of inflammation leading to tolerance, the molecular bases of regulation and rupture, and the way pathogens themselves regulate inflammation.

SUMMARY

Breakthroughs in understanding how gut homeostasis can be established, maintained or disrupted in the presence of microbes should be sources of new therapeutic targets and drugs (i.e. anti-inflammatory, immunomodulatory and anti-infectious molecules).