In recent decades, scientific and clinical research has identified the intestinal microbial community (microbiota) as an essential ‘super organism’ pivotal to health and disease. There is great symbiosis between the human host and its gut microbiota. The enteric microbiota play a key role in immune function, are important in digestion and metabolism, affect and influence brain–gut communication, and are thus essential to normal gut physiology and health. Consequently, alteration or instability of the microbiota and changes in its biodiversity are characteristic of a number of gastrointestinal disorders and metabolic diseases. Understanding the complex host–microbiota relationship and how it may be modulated is of importance from a health and from a societal perspective.
The study of gut microbiota is a rapidly moving field of research. Knowledge about the various contributions of the microbiota to health is still in its infancy and much remains to be discovered. This article provides an overview of some of the recent hypotheses, theories, and research regarding the role of gut microbiota in health and disease, and provides thoughts and concepts for future areas of research. Specifically, this study focuses on five related topics:
The human gut microbiota ‘super organism’
The human gut is the habitat for a diverse and dynamic microbial ecosystem – a so-called ‘microbiota super-organism.’ Each individual has a unique signature gut flora, composed of some 100–1000 microbial species,1 made up of a common core, composed predominantly of bacterial species.2,3
Colonization of the gastrointestinal (GI) tract starts at birth and evolves and changes over a lifetime, such that the adult human GI tract is home to a unique ecosystem of several billion bacteria. The density of gut microbiota reaches its maximum in the distal colon with an estimated concentration of 1011 bacteria per gram of gut contents.4 While the gut microbiota evolves with age and varies in composition along the length of the GI tract, the microbiota is, in general, fairly resistant to environmental change, as illustrated by the remarkable stability of its species profile over time-scales spanning days to months and even years.1,5,6
A current goal is to characterize the human microbiota, enabling the study of its variation according to factors such as population, genotype, disease status and profile, age, nutrition, as well as exposure to various medications, and dietary factors. Worldwide, scientific and commercial interest in the cross-talk between microbes and their human hosts has also intensified – fueled by the recognition that the intestinal microbiota plays a pivotal role in many aspects of human disease,7–9 and by the expanding markets for probiotics and prebiotics, some of which have shown significant health benefits in clinical trial settings10,11 (see also section 3).
The make-up of the human gut microbiota – metagenomics
Advances in culture-independent techniques have spearheaded our knowledge of the complexity of this ecosystem. A detailed review of these techniques is beyond the scope of this article, but readers are referred to recent reviews by Fraher et al.12 and Simren et al.13 In summary, metagenomics involves the direct and complete assessment of the genomic content of an environmental sample or ecosystem, and has been crucial in characterizing and advancing our understanding of human gut microbiota. In Europe, the MetaHIT-integrated project (http://www.metahit.eu) has contributed immensely to this effort.
The most recent metagenomic explorations into the composition of human gut microbiota have employed direct shotgun sequencing of combined mixed genomes of gut microbiota, building on earlier studies involving comparative ribosomal DNA sequencing of complete or partial ribosomal DNA (16S rDNA).14,15 This sequencing has permitted a description of the complete repertoire of human gut microbial genes, highlighting the dominance of bacteria, and, strikingly, identifying that, despite the richness and high individual specificity of the human gut microbiota, there are some common and core patterns and features.3,15
Age-related changes in gut microbiome are now recognized. The microbiota of infants is seeded at birth with dominance of aerobes and factors such as mode of delivery, breast feeding, weaning, and antibiotic use influencing its composition which usually alters to a predominance of anaerobes within a few weeks of life.16 In adults, the human gut microbiota appears to have a dominant phylogenetic core.2 Initial 16S rDNA sequencing identified Gram-negative Bacteroidetes, Gram-positive Firmicutes, and Gram-positive Actinobacteria as the dominant phyla.14 Direct metagenomic sequencing of the gut microbiome has identified and defined three robust clusters – or enterotypes – each characterized by a specific set of networked bacterial genera.15 These are the Bacteroides-, the Prevotella- and the Ruminococcus-dominated enterotypes, profiles which may, in part, be determined by long-term nutritional habits.17 This ground-breaking research highlights this across the globe; although each individual’s microbiota profile is unique, all humans share a common pattern of gut microbiota in which three main bacterial phyla are likely to determine an individual’s response to diet or drug therapy. However, these observations may not apply to the elderly as with advancing age immune function declines with an increase in facultative anaerobes, shifts in ratios of bacteroides to firmicutes species, and marked decrease in bifidobacteria in those over 60 years.18 Furthermore, in the elderly, microbial diversity and composition is primarily driven by dietary factors and the microbiota, in turn, may significantly influence inflammatory tone and health status.19
Although the core nature of the human gut microbiota is fairly resistant to environmental changes,1,5,6,20 factors which predispose toward alterations in the make-up of the gut microbiota can precipitate specific disease states or, in contrast, be protective against disease, as will be described in later sections of this review (Fig. 1).
Summary and future directions: the human gut microbiota ‘super organism’
Alterations in the microbiota and gastrointestinal disorders
The human host and its indigenous microbiota have coevolved such that the normal interaction between gut bacteria and host is a symbiotic relationship in which the microbiota has become integral to host homeostasis,21 physiology, metabolism, and immune responses.22,23 The main functions of the microbiota can be broadly categorized into three groups – metabolic, protective, and trophic functions.21
In terms of their metabolic importance, the gut microbiota maximize calorific availability of ingested nutrients by extracting additional calories from indigestible oligosaccharides and by modulating the absorptive capacity of the intestinal epithelium to key nutrients and minerals.24 Bacteria contribute enzymes that are absent in humans and thus contribute to catabolism of dietary fibers and complex carbohydrates,25 and play a role in vitamin synthesis. The gut microbiota also ferment malabsorbed carbohydrates to provide energy for bacterial growth – a by-product of which is the production of short-chain fatty acids (SCFA) which have a trophic role in the GI tract (see below).
The protective functions of gut microbiota occur at several levels through mucosal adhesion and the ‘crowding out’ of potential pathogens, through the elaboration and secretion of anti-microbial peptides (such as bacteriocins), as well as through interactions with various components of the intestinal barrier26 and immune response. The disruption of this symbiotic equilibrium can be altered through the use of antibiotics and lead to the emergence of opportunistic enteric pathogens such as Clostridium difficile.
Gut microbiota can also have trophic functions – modulating and influencing gut epithelial cell differentiation and proliferation, affecting neuroendocrine pathways, and impacting on homeostatic regulation of the immune system. Extensive cross-talk between the gut bacteria and the immune system, contributes to the development of a healthy immune system. Gut commensals can also induce regulatory T cells, allowing the host to tolerate the massive burden of antigens presented to the gut, ensuring that innocuous antigens do not trigger inflammation; the phenomenon known as tolerance27–29
Among the gastrointestinal (GI) conditions linked with altered gut microbiota are acute diarrhea, irritable bowel syndrome (IBS), and inflammatory bowel diseases (IBDs).30 Certain malabsorption syndromes have been associated with an excess of colonic-type flora within the small intestine; small intestinal bacterial overgrowth (SIBO).31 Emerging evidence also suggests that intestinal bacterial may initiate colon cancer through the production of carcinogenic chemicals.32 Finally, antibiotics can have short-term effects on gut microbiota and cause diarrhea due to pathological overgrowth of, for example, C. difficile or vancomycin-resistant Enterococci,21 as well as long-lasting effects on certain species and strains.33
Irritable bowel syndrome
Irritable bowel syndrome is characterized by recurrent abdominal pain or discomfort, accompanied by abnormal bowel habits, in the absence of any discernible organic abnormality.34 Multiple pathological mechanisms are likely to be involved in IBS.35 A link between the intestinal microbiota and IBS has been suggested by differences between the microbiota of control groups vs that seen in groups of patients with IBS, where a relative reduction in lactobacilli and bifidobacteria, combined with increased numbers of enterobacteria, coliforms, bacteroides, and firmicutes species, have been noted.35–37 These modifications may constitute a primary or secondary phenomenon.13,38
Certain IBS symptoms, including those of abdominal pain, bloating, and flatulence may be related to excessive production of gas by bacterial fermentation in the distal bowel and colon. However, this mechanism is unlikely to explain symptoms in all patients, as overall gas volumes in IBS patients have been reported to be normal.39 Small intestinal bacterial overgrowth has also been controversially implicated in the pathophysiology of IBS40 as most studies describing this association have used breath tests41 which are not well validated as they can be influenced by rapid small intestinal transit, use of proton pump inhibitors, and differences in diet etc. Furthermore, postinfectious IBS has been associated with a subtle and persistent inflammatory process in the epithelium of the colon and it is increasingly thought that disturbances in gut microbiota, may occur and contribute to the symptomatology of IBS.47–49
Other hypotheses include the activation of mucosal adaptive and innate immune response by abnormal microbiota, leading to altered epithelial permeability, activation of nociceptive sensory pathways, and dysregulation of the enteric nervous system.13 In addition, epithelial defense mechanisms, including mucus secretion and host defense peptides (defensins), are dependent on the bidirectional signaling between microbiota and epithelium appear altered in IBS.42 Increased colonic mucosal expression of microbial recognition molecules such as Toll-like receptor 443 and increased circulating antibodies against components of indigenous microbiota have also been detected in IBS patients. Such abnormal microbial–host interactions could alter gut permeability, increase microbial antigenic load, and contribute to the sensory-motor dysfunction often observed in IBS. Furthermore, there is evidence for altered systemic immune response in IBS with an abnormal IL-10/IL-12 ratio in stimulated peripheral blood mononuclear cells which normalized after the use of proboitics.44,46
Evidence to support a role for microbiota–host interactions as important in IBS also comes from clinical trials demonstrating beneficial impacts for antibiotics,50 prebiotics,51 and probiotics in IBS.31,47 Recent meta-analysis of randomized controlled trials of probiotics in patients with IBS and related functional disorders found that, overall, these preparations were better than placebo at improving global IBS symptoms11 (Table 1). However, variations in trial design, poor quality of many of the studies, and a paucity of information on the potential mechanisms of actions of probiotics limit that interpretation of available data. Furthermore, benefits for probiotics over placebo in IBS have generally been modest and it is not yet known whether specific probiotics help to reduce specific symptoms and whether products with single strain are better than those with multiple strains. Further well-controlled studies are required.
Table 1. Meta-analyses and systematic reviews of probiotic therapy in irritable bowel syndrome
|Authors||Year||Number of studies (number of subjects)||Outcome||Ref.|
|Huertas-Ceballos et al.||2008||3 (168) children only||No benefit Pooled OR for improvement 1.17 (0.62–2.21)|| 89 |
|McFarland and Dublin||2008||20 (1414)||Less global IBS Symptoms: RR 0.77 (0.6–0.94) Less abdominal Pain: RR 0.78 (0.69–0.88)|| 90 |
|Nikfar et al.||2008||8 (922)||Clinical improvement : RR 1.22 (1.07–1.4)|| 91 |
|Moayyedi et al.||2010||20 (1628)||Outcomes as a dichotomous variable: 11 RCT’s (n = 936) RR of IBS not improving = 0.71; 95% CI = 0.57 to 0.87, NNT = 4 IBS score as a continuous outcome: 15 RCT’s (n = 1351) SMD = −0.34; 95% CI −0.60 to−0.07)|| 11 |
|Hoyveda et al.||2009||14||Outcomes as a dichotomous variable: 7 RCT’s (n = 895) OR for overall improvement = 1.6 (1.2–2.2) Continuous data: 6 RCT’s (n = 657) SMD for overall improvement = 0.23 (0.07–0.38)|| 92 |
|Brenner et al.||2009||16||Only Bifidobacterium infantis 35624 showed significant improvement over placebo in an appropriately designed study|| 93 |
|Horvath et al.||2011||3 (167) children only Lactobacillus rhamnosus GG (LGG) only||LGG associated with a significantly higher rate of treatment responders in children with IBS (RR 1.70, 95% CI 1.27–2.27, NNT 4)|| 94 |
Inflammatory bowel diseases – Crohn’s disease, ulcerative colitis, and pouchitis – are also thought to involve a degree of continuous microbial antigenic stimulation of pathogenic immune responses, due to host genetic defects in mucosal barrier function, innate bacterial killing, or immunoregulation.52,53 IBD susceptibility is associated with host polymorphisms in bacterial sensory genes such as nucleotide-binding oligomerization domain-containing 254 and TLR4.55 Early childhood exposure to antibiotics causing diminished microbial diversity has been linked to increased risk of Crohn’s disease.56
It has been suggested that a subset of Crohn’s disease and ulcerative colitis patients may have specific abnormalities in microbiota.57,58 For instance Enterobacteriaceae family may interact with a disordered microbiome to increase the risk of UC, whereas a deficiency of the anti-inflammatory bacterium Faecalibacterium prausnitzii59 and an over-representation of enterococcus faecium and protobacteria may occur in Crohn’s disease. To date, in vitro studies have shown that the proinflammatory effects of E Coli on inflamed mucosa in Crohn’s disease can be counteracted by probiotics,60 but, as yet, there have been relatively few clinical studies of probiotics in the IBD, and results have been mixed and indicate that further appropriately powered, high-quality randomized controlled trials are warranted.21 Putative mechanism of probiotic efficacy in IBD include production of bacteriocins (products that alter the growth of certain bacteria) to alter the composition of gut bacteria and reduce proinflammatory strains, altered epithelial barrier function by SCFA production, in particular butyrate which may enhance colonocyte function and repair of the mucosa, and activation of regulatory T cells may lead to downregulation of inflammation. In terms of therapy, the strongest evidence is in the area of pouchitis, whereas in Crohn’s and ulcerative colitis the best that can be said is that probiotics are adjunctive therapies61 (Fig. 2).
Summary box and future implications: alterations in the microbiota and gastrointestinal disorders
Microbiota and brain–gut communication in health and disease
The brain–gut axis is a recognized homeostatic construct that in recent years has been expanded to encompass the gut microbiota. The microbiota-gut–brain axis acknowledges an ability of gut microbiota to communicate with the gut and the brain and is emerging as an exciting concept in health, affording as it does, new opportunities for potential intervention in GI disease states and functional syndromes.78–80
Comprising the CNS, the neuroendocrine and neuroimmune systems, the autonomic nervous system, the enteric nervous system, and the intestinal microbiota, the microbiota-gut–brain axis is a bidirectional system. Signals from the brain can influence motor, sensory, and secretory modalities of the gastrointestinal tract and in turn, visceral messages from the gastrointestinal tract can influence brain function.81 In one direction, the brain can indirectly affect enteric microbiota by effecting changes in gastrointestinal motility, secretion, and/or intestinal permeability, or may directly influence microbiota via neuronally signaled release of molecules from enterochromaffin cells, neurons, and immune cells. In the other direction, enteric microbiota communicate with the brain via multiple mechanisms that may include direct stimulation of receptor-mediated signaling, enterochromaffin-cell signaling, through vagal afferents,81 and the recently described humoral route.45 This gut brain signaling can alter brain morphology, and neurochemistry such as GABA and serotonin levels.45,78,81 This microbiota-related brain communication is implicated in pain perception, and the modulation of immune responses and emotions.
Influence of gut microbiota on CNS signaling comes from various strands of evidence. For instance, studies in germ-free mice (GFM) have shown the importance of gut microbiota in the development of the hypothalamic pituitary adrenal (HPA) axis. For instance, restrained stress caused an increase in HPA response in GFM compared with controls, which was partially reversed after recolonization in GFM with fecal matter control mice and by administration of Bifidobacterium infantis in a time-dependent manner. This study suggested that gut microbial colonization must occur during a critical period in early life to ensure normal development of the HPA axis. Other influences of microbiota on CNS development include descriptions in GF animals of reduced brain-derived neurotrophic factor82; a key neurotrophin involved in neuronal growth and survival, and expression of the NMDA receptor subunit 2a in the cortex and hippocampus compared with specific pathogen free controls.
A role for the microbiota in anxiety-like behaviors is also suggested by the beneficial effects of probiotics in reducing these. For example, administration of a combination of Lactobacillus helveticus R0052 and B. longum R0175 reduced anxiety-like behavior in rats83; whereas chronic treatment with the probiotic L. rhamnosus (JB-1) reduced levels of stress-induced corticosterone and depressive behaviors in the forced swim test. The L. rhamnosus (JB-1)-treated animals also showed altered expression of GABAB1b and GABAA α2 mRNA in cortical and subcortical regions which may be mediated by the vagus nerve, as the vagotomized mice did not display the neurochemical and behavioral effects of this bacterium.81 The gut microbiota may also modulate pain perception, as specific Lactobacillus strains were shown to induce the expression of μ-opioid and cannabinoid receptors in intestinal epithelial cells and mimic the effects of morphine in promoting analgesia.84
The role of gut-microbiota–brain communication in functional disorders such as IBS is the subject of on-going research. It has been proposed that changes in gut flora influence behavior and provide a basis for a novel unifying hypothesis that accommodates both gut dysfunction and the behavioral changes that characterize many IBS patients. There are a number of animal studies that highlight the bidirectional relationship between gut microbiota and the brain in terms of the impact of each on behavior.85,86 Stress can change the composition of the microbiota and such changes are associated with increased vulnerability to inflammatory stimuli in the GI tract. In turn, experimental perturbation of the microbiota has been shown to alter behavior, with germ-free mice displaying Central neurochemistry and behavior suggestive of reduced anxiety compared with conventional mice.87 It has also been observed in animal models that administration of probiotic Lactobacillus and Bifidobacterium species confer antidepressant and anxiolytic effects that appear to be mediated via vagal pathways.81,83
These observations suggest that targeting the gut-microbiota–brain axis may provide a means of correcting stress-related disorders often comorbid with conditions such as IBS and inflammatory bowel disease87,88 (Fig. 4).
Summary and future implications: microbiota and brain–gut communication in health and disease
Gut microbiota: implications for future health care
Metagenomics has the potential to provide a tool to stratify individuals according to their gut microbiota profile and may help identify predictors of disease relapse and/or chronicity. In this way, metagenomics may play a future role in diagnosis, prognostication, and in the optimization of therapy – possibly being used to distinguish between closely related syndromes, or to predict or determine the intensity and type of medical care required. The potential marriage of culture-independent metagenomic methods with the field of gnotobiotics (rearing germ-free animals and assessing exposure to microbial species or consortia) may hold the key to improved understanding of the inter-relationships between diet, nutritional status, and gut microbial interactions and communication within the human host that extend beyond intestinal health to broader aspects of human health and well-being.
There is a need for continued focus on how manipulation of gut microbiota might offer a new approach to the prevention and management of a host of clinical symptoms, syndromes, and disorders. Rational deployment of antibiotics, probiotics, and prebiotics, alone or in synergy, may provide an effective means of sustaining changes in the human microbiome that would help in the management of conditions as diverse as acute gastroenteritis, antibiotic-associated diarrhea and colitis, constipation, inflammatory bowel disease, irritable bowel syndrome, necrotizing enterocolitis, diabetes, obesity, and a variety of other disorders and diseases.
Future studies will no doubt improve our understanding of the cause and effect relationship between diseases described above and the gut microbiome. Future areas of improved knowledge are likely to include: the identification of the implications of perturbations of the gut microbiome in early life to disease susceptibility in later life; whether the metagenome predicts risk for specific human diseases such as IBD or GI cancers; effects of the microbiome on the pharmacology of medicines, including whether microbiota influences pharmacokinetics and drug toxicity; implications of the microbiome in understanding altered brain gut signaling in health and disease, in particular whether manipulation of the gut microbiome may have therapeutic implications in stress-related disorders; harnessing of the microbiome to develop new narrow-spectrum antibiotics. These possibilities highlight the importance of understanding the impact of interactions between the gut microbiome and the host in terms of metabolic and immune functions and the potential to improve human health through disease management, risk reduction, stratified medicine, and thus providing a significant challenge for scientists in the 21st century.