Novel perspectives on therapeutic modulation of the gut microbiota

Abstract

The gut microbiota contributes to the maintenance of health and, when disrupted, may drive gastrointestinal and extragastrointestinal disease. This can occur through direct pathways such as interaction with the epithelial barrier and mucosal immune system or indirectly via production of metabolites. There is no current curative therapy for chronic inflammatory conditions such as inflammatory bowel disease, which are complex multifactorial disorders involving genetic predisposition, and environmental triggers. Therapies are directed to suppress inflammation rather than the driver, and these approaches are not devoid of adverse effects. Therefore, there is great interest in modulation of the gut microbiota to provide protection from disease. Interventions that modulate the microbiota include diet, probiotics and more recently the emergence of experimental therapies such as fecal microbiota transplant or phage therapy. Emerging data indicate that certain bacteria can induce protective immune responses and enhance intestinal barrier function, which could be potential therapeutic targets. However, mechanistic links and specific therapeutic recommendations are still lacking. Here we provide a pathophysiological overview of potential therapeutic applications of the gut microbiota.

Keywords

fecal microbiota transplant inflammatory bowel disease irritable bowel syndrome microbiota prebiotics probiotics

Introduction

During birth we are colonized with a plethora of microorganisms that will play a crucial role in defining our future physiology and immunity, impacting health and disease. The key role of bacteria in shaping immunity and gut structure emerged over the last decades [Logan et al. 1991; Shroff and Cebra, 1995; Round and Mazmanian, 2009; El Aidy et al. 2012]. These studies have provided the rationale to develop procedures that reconstitute the microbiota to a state that would prevent or treat disease [Carding et al. 2015]. Gut dysbiosis can be defined as a stable, perturbed ecosystem that has reduced capacity for protection and is associated with disease. The most studied gastrointestinal clinical condition in association with dysbiosis is inflammatory bowel disease (IBD) [Dalal and Chang, 2014], although meta-analyses, studies that combine multiple trials and provide the highest clinical evidence, have not been able to reproduce consistently the alterations that are described within single studies [Walters et al. 2014]. One of the key questions relates to causality of these associations. Some animal models have shown a primary role of dysbiosis in models of IBD [Natividad et al. 2015; Schaubeck et al. 2015; Seo et al. 2015], but it has been difficult to translate this to the clinical setting [Abraham and Cho, 2009; Kaser et al. 2010]. Another common gut disorder is celiac disease, a chronic autoimmune enteropathy, genetically linked to human leucocyte antigen (HLA) DQ2/8 and triggered by dietary gluten. Additional environmental factors to gluten are believed to play a role in disease progression, given the fact that 30% of the population carry genetic risk but about 3–4% will develop the disease. Some studies have demonstrated dysbiosis in patients with celiac disease [De Palma et al. 2010], with increases in bacteria with virulence factors [Sanchez et al. 2008] and persistence of dysbiosis after treatment with the gluten-free diet in association with clinical symptoms [Wacklin et al. 2014]. More recently, evidence for a modulatory role of gut microbiota in host responses to gluten has been described in animal models of gluten sensitivity [Galipeau et al. 2015]. The microbiota has also been implicated in one of the most common categories of gastrointestinal disease, functional bowel disorders, and its prototype irritable bowel syndrome (IBS) as well as its psychiatric comorbidities [Bercik et al. 2011; Collins, 2014; De Palma et al. 2015]. In addition to gut disorders, studies are beginning to show how the microbiota can influence systemic diseases such as arthritis and psoriasis [Scher et al. 2015a], type 1 diabetes [Sun et al. 2015a], cardiovascular disease [Koeth et al. 2013] and conditions such as obesity [Cox et al. 2015]. Overall, studies in both animals and humans suggest that the microbiota could constitute a worthy target for preventative or therapeutic modulation (overviewed in Figure 1). Many studies have demonstrated the roles of specific microbes in contributing to either protection or exacerbation of disease. However, harnessing the power of these microbes has not yet been fully elucidated.

Figure 1.

Proposed homeostatic and dysbiotic mechanisms of the microbiota and possible therapeutic interventions. AMP, antimicrobial peptides; FMT, fecal microbiota transplant; HDAC, histone deacetylase; IFN, interferon; IL, interleukin; ILC, innate lymphoid cell; NLRP6, NOD-like receptor family pyrin domain containing 6; SCFA, short chain fatty acid; Treg, T-regulatory cell.

Potential targets of microbiota modulation

T-cell modulation

The development and maintenance of T cells is directly influenced by the microbiota as demonstrated in seminal studies investigating CD4⁺ T-cell induction in germ-free mice colonized by commensal microbes [Macpherson and Harris, 2004]. Indirect interactions through changes in microbiota induced by diet have been demonstrated. A diet high in milk-derived saturated fats led to blooming of the pathobiont, Bilophila wadsworthia, and enhanced colonic T helper 1 (Th1) responses [interferon (IFN)-γ-producing CD4⁺ cells] in interleukin (IL)-10^–/– mice [Devkota et al. 2012]. Targeting the expansion of a pathobiont that induces proinflammatory responses could be one approach to treat disease. Indeed, antibiotics decrease both IFNγ and IL-17 producing CD4⁺ cells [Hill et al. 2010] and studies using genetic models of IBD have demonstrated that treatment of mice with antibiotics decreases disease severity [Gkouskou et al. 2014]. However, antibiotics have also been linked to the development of disease later in life [Vangay et al. 2015]. But as recently shown, mice colonized with human bacteria rich in Firmicutes, specifically Lachnospiricheae and Ruminocaceae, were less susceptible to colitis, and had reduced pathogenic Th17 cells [Natividad et al. 2015]. Thus, expansion of beneficial bacteria that decrease proinflammatory responses may also constitute a viable approach to treat IBD. This may also apply to extraintestinal disorders that involve the proinflammatory Th17 pathway [Horai et al. 2015], which could be driven by gut dysbiosis.

T-regulatory cells (Tregs) are essential for homeostasis in the gastrointestinal tract for suppression of responses to nonpathogenic bacteria [Sun et al. 2015b] and food antigens [Pabst and Mowat, 2012]. Induction of Tregs improves colitis in animal models of IBD [Mayne and Williams, 2013], autoimmune diseases [Wing and Sakaguchi, 2010] and allergy [Palomares et al. 2010]. Specific microbial inducers of Tregs have been identified, such as those belonging to Clostridia [Atarashi et al. 2011, 2013] and possibly Parabacteroides [Kverka et al. 2011]. The mechanism likely depends on the production of the short-chain fatty acid (SCFA) butyrate [Furusawa et al. 2013], as it has been shown to expand Tregs in vivo [Arpaia et al. 2013] via an epigenetic mechanism; acetylation of Foxp3 locus. Demonstrating this in the context of disease is a recent study indicating protection of offspring from allergic airway disease via Treg induction by supplementing a maternal diet with high fiber that increases acetate production [Thorburn et al. 2015]. Additionally, polysaccharide A from Bacteroides fragilis has been shown to induce IL-10-producing Tregs, likely through a different mechanism [Round and Mazmanian, 2009], protecting against experimental autoimmune encephalomyelitis [Ochoa-Reparaz et al. 2009]. More recently, a distinct Treg population, expressing Rorγ (defined as Rorγ⁺ Helios^– FoxP3⁺ CD4⁺ TCRβ⁺) has been shown to be controlled by microbiota, specifically Clostridium ramosum, Bacteroides thetaiotaomicron, Peptostreptococcus magnus and Bacteroides fragilis. This Treg subset was shown to improve 2, 4, 6 trinitrobenzenesulfonic acid model of colitis [Sefik et al. 2015]. Thus, mechanisms of Treg induction could be targeted to prevent of disease.

Dendritic cell modulation

Dendritic cells (DCs) control downstream T-cell responses, and thus are potential targets of therapeutic manipulation. The mechanisms by which microbiota affects DC subsets has been less explored than those of T cells. However, a few studies have demonstrated a microbiota–DC axis. For instance, mice colonized with segmented filamentous bacteria produce more serum amyloid A (SAA) which act on DCs to skew toward a Th17 phenotype [Ivanov et al. 2009]. Microbiota can induce SAA, leading to neutrophil migration, which may also be partly mediated by DC activity [Kanther et al. 2014]. Further, it has been demonstrated that induction of SAA is mediated by bacterial adhesion to epithelial cells, leading to downstream Th17 cell responses via CD11c⁺ cells, which were critical for the response [Atarashi et al. 2015]. Recent data suggest that manipulating the microbiota may modulate cancer immunotherapy through DCs. Intestinal microbes, such as Bifidobacterium, may cause DCs to enhance CD8⁺ T-cell responsiveness to checkpoint blockade therapies, although the mechanism of this effect remains to be elucidated [Sivan et al. 2015]. More research is needed to identify how pro- and anti-inflammatory DC subsets interact with the microbiota and their metabolites.

Intestinal barrier function

Many diseases of the gastrointestinal tract and extraintestinal conditions are associated with intestinal barrier alterations. This includes both functionality (permeability) and immune or structural parameters of the barrier such as secretion of antimicrobial peptides and mucins, in which the microbiota can play a central role [Vaishnava et al. 2008; Natividad and Verdu, 2013]. Alterations in barrier function by bacteria has been associated in animal studies with increases in translocation of bacteria, uptake of microbial products and dietary antigens, and it has been proposed that this could promote a proinflammatory state. Clinically, small intestinal bacterial overgrowth is associated with changes in barrier function in humans, however mechanisms and bacterial culprits or constituents are unknown [Bures et al. 2010]. It has been previously shown that mice fed a high-fat diet have increased paracellular permeability in the ileum. This change correlated with a decrease in the class Clostridia [Hamilton et al. 2015]. The class Clostridia was also implicated in the development of allergy. Stefka and colleagues demonstrated that mice colonized with Clostridia are protected from allergy due to IL-22-mediated enhanced barrier function [Stefka et al. 2014] and induction of innate lymphoid cells (ILCs). Although, the implications of supplementing Clostridia for enhancement of barrier function have not been explored, the same group has recently found that supplementing children with a probiotic Lactobacillus rhamnosus GG induced members of the Clostridia class, Lachnospiraceae, which are butyrate producers [Berni Canani et al. 2016]. Low-dose SCFAs have also been shown to enhance barrier function in vitro [Peng et al. 2007], reduce translocation of bacteria [Lewis et al. 2010] and affect tight junction assembly [Peng et al. 2009], and be protective in animal models of colitis via regulation of barrier function [Macia et al. 2015]. Specifically, in animal models, butyrate is critical for many aspects of barrier function including permeability, mucin and antimicrobial peptide production, by inducing HIF1α [Kelly et al. 2015]. Barrier function is controlled epigenetically and butyrate, being a histone deacetylase inhibitor via suppression of histone deacetylases, can increase tight junction proteins [Bordin et al. 2004]. The bacterium Faecalibacterium prausnitzii has also demonstrated the ability to increase barrier function in dextran sodium sulfate (DSS) colitis, which may be mediated through butyrate [Carlsson et al. 2013]. These studies suggest that a diet targeting the expansion or the introduction of butyrate-producing bacteria, such as Clostridia, may enhance barrier function. Antimicrobial production is also important in shaping barrier function in the gut. Bacterial metabolites and constituents have a critical role in induction of antimicrobials. It has been recently demonstrated by Levy and colleagues that microbial-derived taurine, histamine and spermine are important in NOD-like receptor family pyrin domain containing 6 (NLRP6) inflammasome activation, critical for antimicrobial production in the epithelia of the colon and protective in DSS-induced colitis [Levy et al. 2015]. Utilizing these metabolites in the clinic may be a future therapy for restoring microbial homeostasis in the gut of diseased individuals.

New players

Interest in the role of ILCs has emerged in the past few years since their populations are regulated by the microbiota [Sonnenberg and Artis, 2015]. ILCs play a role in an array of inflammatory and autoimmune conditions, including asthma, psoriasis and IBD [McKenzie et al. 2014; Marafini et al. 2015]. ILC3s have been shown to be affected by the microbiota and to modify the microbiota in turn. The expansion and maintenance of ILC3s is dependent on the aryl hydrocarbon receptor (AHR) [Qiu et al. 2013]. It has been demonstrated in vitro that indole, tryptamine and indole-3-acetate modulated AHR-mediated responses in Caco-2 cells, and indole is produced by the microbiota [Jin et al. 2014]. Specifically, it has been shown that Lactobacillus reuteri and L. acidophilus can produce indole-3-aldehyde from dietary tryptophan, inducing the production of IL-22 from ILC3s [Zelante et al. 2013]. This may have implications for allergy [Leung and Loke, 2013] and IBD [Zenewicz et al. 2008, 2013], thus more research is needed on the role of specific microbes that induce ILCs in mammalian hosts.

Manipulation of the gut microbiota

Basic research studies have demonstrated important roles of the gut microbiota in the development of immune, metabolic and host function, as well as provided evidence that disruptions in host–microbiota interactions may impact disease. Strategies to manipulate the gut microbiota with the aim to treat inflammatory disorders, such as probiotics, prebiotics and FMT have therefore been proposed.

Diet as a strategy to modulate microbiota and prevent or treat disease

Diet is considered one of the main driving forces shaping intestinal bacterial communities. Several studies highlight the effects of diet on gut microbiota composition and repertoire of microbial metabolites [Wu et al. 2011; David et al. 2014]. Sonnenburg and colleagues have shown that a modern diet low in fiber contributes to the loss of taxa over generations, and may be responsible for the lower-diversity microbiota observed in the industrialized world. Humans have experienced major dietary changes from gathered to farmed foods during the agricultural revolution, and more recently to the mass consumption of processed foods in the industrialized world. Each dietary shift was most likely accompanied by a concomitant adjustment in the microbiota [Sonnenburg et al. 2016]. This could explain the increasing rate of intestinal disorders in western countries. Altered diet–intestinal microbiota interactions may play a role in IBD, IBS and metabolic disorders such as obesity, type 2 diabetes, insulin resistance, and nonalcoholic fatty liver disease. Despite many unsubstantiated claims, the exact characteristics of what the ideal ‘healthy microbiota’ constitutes, or the ‘ideal diet’ promoting it, have not been completely elucidated. Several studies support the concept that diet should be viewed as a means to prevent alteration of symbiosis (beneficial host–bacteria interactions) observed in some intestinal and extraintestinal diseases [Thorburn et al. 2014; Cani and Everard, 2016; Lee et al. 2015].

Human intervention studies have demonstrated that dietary consumption of certain food products can result in changes in the composition of the gut microbiota in line with the prebiotic concept [Roberfroid et al. 2010]. Prebiotics typically refer to selectively fermented nondigestible food ingredients or substances that specifically support the growth and activity of health-promoting bacteria that colonize the gastrointestinal tract [Bindels et al. 2015]. The general consensus is that low bacterial richness is associated with IBD and altered host metabolic markers such as increased body weight fat mass, insulin resistance and inflammation [Hansen et al. 2010; Le Chatelier et al. 2013]. Microbiota gene richness was predictive of a reduced response to low-caloric diet intervention in terms of weight loss and improvement of metabolism and inflammatory traits [Le Chatelier et al. 2013]. Cotillard and colleagues showed that energy restrictions and supplementation with dietary fibers may increase microbial diversity up to 25% in people with low diversity [Cotillard et al. 2013]. It has also been shown that resistant starches affect the composition of the microbiota and enhance metabolic health, as assessed by circulating inflammatory mediators, innate immune cells, and the bile acid cycle [Bindels et al. 2015]. Dietary components such as fructo-oligosaccharides, galacto-oligosaccharides, soya-oligosaccharides, xylo-oligosaccharides, and pyrodextrins have also been proposed to increase bacterial diversity in the gut [Gibson and Roberfroid, 1995; Bindels et al. 2015]. Independently of an increase in bacterial richness, nondigestible foods are fermented by bacteria producing important metabolites in gut homeostasis such as SCFAs, ω-3 fatty acids or tryptophan derivate metabolites [Furusawa et al. 2013; Thorburn et al. 2014]. Dietary metabolites have a key role in gut homeostasis: promoting epithelial integrity, regulatory T cell responses and tissue repair, as discussed previously. Faecalibacterium prausnitzii and Akkermansia muciniphila have been associated with SCFA production, bacterial richness, metabolic markers and anti-inflammatory effects. Specific prebiotic feeding increases the abundance of these bacteria and improves metabolic markers of disease [Dewulf et al. 2013; Everard et al. 2013]. However, recent observations suggest that this concept may be too simplistic due the strong individuality of responses to nutritional modulation and its dependence on the initial microbiota composition [Dore and Blottiere, 2015]. Moreover, advances in our understanding of diet–microbiome–host interactions challenge important aspects of the current concept of prebiotics, and especially the requirement for effects to be ‘selective’ or ‘specific’ [Bindels et al. 2015]. With this in mind, Bindels and colleagues proposed a new definition of prebiotic as a nondigestible compound that, through its metabolization by microorganisms in the gut, modulates composition and activity of the gut microbiota, thus conferring a beneficial physiological effect on the host [Bindels et al. 2015].

Gut function parameters such as intestinal motility, visceral perception, permeability or low-grade inflammation have also been linked to bacteria–diet interactions [Verdu et al. 2006; Kau et al. 2011; Dey et al. 2015]. A recent study in a novel murine model reported that malnutrition changes the small intestinal microbiota composition and their metabolites, intraepithelial lymphocyte phenotype, and the susceptibility to enteric infection [Brown et al. 2015]. Observational studies have attempted to identify dietary patterns that contribute to the risk of specific diseases. Diets high in red meat and fat, particularly polyunsaturated fatty acids, induce large-scale changes in the microbiota composition and bacterial metabolites that may be involved in the pathogenesis of metabolic disorders, IBD or cancer [Daniel et al. 2014; Lee et al. 2015]. For instance, bacteria can metabolize meat proteins and produce nitrosamines, which may be linked to carcinogenesis [Hughes et al. 2001; Paul et al. 2015]. Consumption of red meat delivers L-carnitine to certain gut bacteria converting it to trimethylamine-N-oxide which has been shown to cause atherosclerosis in mice [Koeth et al. 2013]. In contrast, cruciferous vegetables such as cabbage, broccoli, kale, and cauliflower are rich sources of fiber, lutein, flavonoids, phytosterols, folic acid, sulphur-containing glucosinolates, and vitamin C, each of which have been associated with reduced risk of various kinds of cancer [Paul et al. 2015]. Sulphur-containing glucosinolates can be converted to biologically active compounds such as indoles, nitriles, and isothiocyanates by β thioglucosidases produced by the gut microbiome. Epidemiological studies suggest a lower risk of IBD among people with diets high in fiber, fruits and vegetables. Specifically, the Mediterranean diet has been suggested to beneficially impact the gut microbiota and associated metabolome [De Filippis et al. 2015]. Some dietary nutrients have been shown to help regulate mucosal immune functions, such as vitamins, amino acids, and SCFAs, many of which are influenced by the gut microbiota [Brestoff and Artis, 2013]. Thus, defined diets may become attractive tools in the personalized treatment of inflammatory and metabolic disorders, but more research is needed to characterize this. Dietary intervention studies and their effects on the microbiota and health, in humans, are limited by the difficulty in accurately capturing dietary intake, as well as the potential for complex interactions between foods and bacteria, which are characteristic of each individual. However, studies are beginning to emerge, as recently demonstrated by Dey and colleagues showing how a single food ingredient interacts with a functional microbiota trait to regulate host physiology [Dey et al. 2015].

Some diets have also been proposed to worsen symptoms in patients with IBS, which is a functional gastrointestinal disorder characterized by abdominal pain or discomfort in conjunction with altered bowel habits, in the absence of organic pathology [Longstreth et al. 2006; Drossman et al. 2011]. Approximately 60% of patients with IBS identify food as a trigger for their symptoms, and there has been interest in exclusion diets for the management of IBS. However, no specific food item has conclusively been implicated in the overall IBS population, and these patients improve modestly to a variety of food restrictions as well as traditional dietary advice [Bohn et al. 2015]. IBS is a heterogeneous condition and multifactorial and thus many dietary components may trigger symptoms, and not all necessarily through alterations in the microbiota. Dietary components which stimulate bacterial fermentation in the colon have been related to IBS symptoms such as bloating. Foods high in fermentable oligosaccharides, disaccharides and polyols (FODMAPs), which are poorly digested carbohydrates, may cause IBS symptoms in a subgroup of patients with IBS through their osmotic effect and fermentation by colonic bacteria, leading to gas production, as well as their direct effects on gastrointestinal motility [Halmos et al. 2014; Bohn et al. 2015; Halland and Saito, 2015]. It has been shown that diets differing in FODMAP content can affect gut microbiota composition [Halmos et al. 2015]. It is important to remember that IBS is a complex syndrome, multifactorial, and that recent studies have shown that traditional dietary advice is as effective as selective restrictive diets to improve symptoms [Bohn et al. 2015]. Microbiota and dietary manipulation in IBS may be one of many options of treatment, and not necessarily effective in all IBS subtypes.

Probiotics in the treatment of intestinal disorders

Probiotics are live microorganisms which, when administered in sufficient quantity, provide a health beneﬁt to the host. There are numerous probiotic strains commercially available currently, many of which lack strong clinical evidence to support their use in specific diseases. It has been suggested that probiotic bacteria should be preferably isolated from the human intestine, proven to be safe for the host, genetically stable and capable of surviving passage through the gastrointestinal tract. Among the many health claims for probiotics, beneficial immunomodulation, restoration of barrier function, modulation of metabolic parameters, and modification of intestinal microbiota have been proposed [Wolvers et al. 2010; Rijkers et al. 2011]. The growing skepticism regarding the use of probiotics in clinics is based on poorly substantiated health claims, lack of reproducibility and standardization of probiotic strains, doses and delivery methods in the different studies. However, a few studies have been well conducted and powered, suggesting we may be able to separate wheat from chaff and some probiotic intervention strategies may become an important element to prevent or attenuate intestinal disorders.

Meta-analyses suggest the use of probiotic formulations in different diseases such as IBS or necrotizing enterocolitis [Moayyedi et al. 2010; Wang et al. 2012]. Some Bifidobacteria strains have beneficial effects on global IBS, abdominal pain, bloating, and flatulence [O’Mahony et al. 2005]. Some patients with IBS display altered composition of the gut microbiota and the use of probiotics would be beneficial at the gastrointestinal and psychological levels via gut–brain axis [De Palma et al. 2014]. In the specific case of necrotizing enterocolitis, oral supplementation of Bifidobacterium breve and Lactobacillus casei reduced the occurrence of the disease while there was no evidence of benefit for other specific probiotics such as B. breve BBG-001 [Braga et al. 2011; Costeloe et al. 2016].

Although several probiotic formulations have been proposed as a treatment for IBD, results are controversial. Studies in animal models of colitis have been promising. Lactobacillus strains such as L. plantarum 299v, L. reuteri (R2LC), L. salivarius UCC118 or formulations like VSL#3 prevented onset of colitis [Mao et al. 1996; Madsen, 2001; O’Mahony et al. 2001; Schultz et al. 2002]. Unfortunately, there has been poor clinical correlation. One confounding factor relates to the fact that clinical studies have been performed combining drugs with different probiotics such as L. casei GG, L. salivarius UCC118, Saccharomyces boulardii, Escherichia coli Nissle 1917 [Malchow, 1997; Venturi et al. 1999; Gupta et al. 2000; Guslandi et al. 2000; Prantera et al. 2002]. Therefore, no clear recommendation on dose or probiotic strain can be given for patients with active IBD, and more research is needed. A different paradigm in the search for anti-inflammatory strains emerged with the identification of Faecalibacterium praustnizii depletion, a core member of the intestinal microbiota, in IBD. This bacterium may protect the host from mucosal inflammation by several mechanisms, including the downregulation of inflammatory cytokines or stimulation of IL-10 [Sokol et al. 2008]. Specific mechanisms of action of probiotic strains, relevant to IBD pathophysiology, will need to be identified and then these strains tested in patients with IBD before formal recommendations can be made. Prevention, maintenance of remission, versus active therapy will be important aspects of future research.

Intestinal bacteria play a dual role in the response to dietary components, either generating harmful or beneficial metabolites for the host. Some bacteria are implicated in the production of nutrients and metabolites such as the previously mentioned SCFAs. Intestinal microbiota can also synthesize several vitamins and affect the absorption of key minerals, such as iron [Kau et al. 2011]. However, observational studies have reported greater abundance of Firmicutes and lower abundance of Bacteroidetes in people with obesity compared with their lean counterparts. The basis for this may relate to the capacity of gut microbiota components to harvest energy differentially for the host through microbial fermentation of dietary polysaccharides that cannot be digested by the host, and by microbial regulation of host genes that promote deposition of the lipids in adipocytes [Backhed et al. 2004; Turnbaugh et al. 2006]. In this context, certain bacteria could be used as probiotics with targeted pathways to restore health in metabolic disorders. Intestinal bacteria such as Akkermansia muciniphila, several Lactobacillus strains and probiotic formulations as VSL#3 have been proposed as modulators of metabolism [Le Barz et al. 2015], but more research is needed to understand what subsets will benefit from these strains and the short- and long-term benefits, as well as cost–benefit of such supplementation.

Fecal microbiota transplant

Fecal microbiota transplants (FMTs) have been used in the last decade for severe cases of Clostridium difficile. For mild cases, specific antibiotics are the primary care, particularly vancomycin and metronidazole [Rohlke and Stollman, 2012], however the rates of success for FMT in C. difficile infection are thought to be greater, roughly 90% [Gough et al. 2011]. Although FMT has been shown to be an effective option for C. difficile, the mechanisms as to why exactly it works are unknown. The leading hypothesis being that certain bacteria in the microbiota of healthy individuals contribute to colonization resistance, inhibiting the growth or outcompeting C. difficile for space and nutrients. To support this notion, there are taxa which have been shown to be protective or provide resistance to C. difficile infection and antibiotics can make an individual more susceptible to C. difficile infection [Buffie et al. 2012, 2015; Deshpande et al. 2013; Theriot et al. 2014; Collins et al. 2015]. Bacteria that provide resistance include, but are not limited to, B. longum, and species belonging to Lachnospiraceae and Porphyromonadaceae. Lawley and colleagues found that treating mice infected with C. difficile with healthy stool resolved the infection and they further created a therapeutic synthetic mixture of six strains of bacteria (novel Bacteroidetes species, Lactobacillus reuteri, Enterococcus hirae, novel Anaerostipes species, Straphylococcus warneri and a novel Enterorhabdus species) [Lawley et al. 2012]. More recently, Buffie and colleagues demonstrated that Clostridium scindens provides resistance to mice from C. difficile. The mechanism being that this bacterium is 7-dehydroxylating, producing secondary bile acids that inhibit C. difficile expansion and can treat already present C. difficile infection [Buffie et al. 2015]. Due to the high success of treating C. difficile infection with FMT, there is great interest in evaluating FMT in other gastrointestinal disorders where the microbiota has a key role in disease development or severity. Particularly in ulcerative colitis (UC), a recent trial suggests success of treatment [Moayyedi et al. 2015]. One of the suggested mechanisms include the abundance of the butyrate producer Lachnospiraceae in the donor microbiota [Moayyedi et al. 2015; Natividad et al. 2015]. However, due to the rates of success in UC compared with treating C. difficile, it is likely that the underlying mechanism of success of FMT is different. Thus far FMT also seems safe as studies have not reported serious adverse effects even in immunocompromised patients [Kelly et al. 2015]. One important regulatory issue for the future relates to transmission of pathogens or other morbidity phenotypes by FMT, given the bulk of animal work indicating effects of microbiota in the gut–brain axis [Bercik et al. 2011; De Palma et al. 2015]. Additionally, there is a documented case of a female patient with C. difficile infection receiving a FMT from an obese individual and subsequently becoming obese herself [Alang and Kelly, 2015]. Thus, there are concerns that need to be addressed before this form of therapy is approved in clinical management of IBD.

Phage therapy for microbiota manipulation

Bacteriophage are the most abundant organic entities on the planet, intimately controlling microbial populations. Therefore, their role in modulating microbial communities in the gut has arisen. Until recently, the role of phage in the gastrointestinal tract had been greatly understudied. It was only in 2003, when an estimated 1200 viral genotypes in fecal contents were reported in healthy humans [Mills et al. 2013]. Most studies investigating bacteriophage in the gut have utilized healthy individuals, and their role in diseases has not been investigated in depth. A few studies have demonstrated that individuals with Crohn’s disease or UC have increased bacteriophage quantities, some suggesting decreased diversity overall [Lepage et al. 2008; Perez-Brocal et al. 2013; Wagner et al. 2013] and another suggesting increases in diversity [Norman et al. 2015]. The changes occurring in the virome during disease seem to be disease specific, however increases in Caudovirales have been demonstrated in both Crohn’s disease and UC [Norman et al. 2015]. The same large-scale study also provided data supporting the notion that increases in phage populations were not due to decreased bacterial diversity, suggesting phage may contribute to dysbiosis in IBD and therefore inflammation. The potential application of phage is vast, from developing communities of phage to skew whole microbial dysbiosis to phage-bacterial-specific therapies or mining for compounds that block phage induction. For instance, specific bacteria have shown to contribute to IBD in animal models, such as adherent-invasive E. coli [Rolhion and Darfeuille-Michaud, 2007], which could be targeted by a specific single phage therapy. In addition, certain bacteria use phage to remain viable in a niche (including some pathobionts) [Duerkop et al. 2012], blocking phage induction could be an alternative to modulating whole microbiota. An additional noteworthy role of phage is that the interactions of phage with mammalian hosts is greatly understudied, but it has been demonstrated that phage are capable of inducing immune responses, having documented anti-inflammatory and proinflammatory attributes [Mills et al. 2013]. The dynamics of phage in the gut is intriguing and holds great potential. Currently, therapeutic applications using phage therapy remain exploratory and at a discovery phase.

Conclusion

The role of a perturbed microbiota in triggering inflammation and disease progression has been proposed largely based on animal studies. Clinical studies have and continue to be conducted to test the hypotheses generated in basic research studies. Several clinical studies have confirmed an association between chronic gut inflammatory, functional disorders, and metabolic conditions with an altered microbiome. Also some, but not all studies, have identified specific probiotic interventions with beneficial effects in particular clinical conditions. The results using a given probiotic are not applicable to all disease conditions or to all probiotic products. Basic studies are performed in controlled environments that include defined microbiota, dietary control, and genetic background. They are key to provide mechanistic insight and hypothesis generation, but their results are not always directly translatable to humans. There is growing interest to manipulate the gut microbiome for preventative and therapeutic purpose. The area shows great promise, however more research is needed before conclusive clinical recommendations can be given. Specifically, we need to understand how certain microbiota components or metabolic activities influence specific disease conditions, and decipher the complex interactions between microbes and dietary components. Combined basic and clinical research will continue to provide insight for the ultimate strategies on how to manipulate the microbiota to protect against onset and progression of disease.

Footnotes

Acknowledgements

EFV holds a Canada Research Chair in inflammation, nutrition and the microbiota. AC holds a PDF scholarship from CAG/CIHR. JLM received a new investigator award from the Canadian Celiac Association.

Funding

This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.

Conflict of interest statement

EFV receives funding from Nestle.

References

Abraham

Cho

(2009) Inflammatory bowel disease. N Engl J Med 361: 2066–2078.

Alang

Kelly

(2015) Weight gain after fecal microbiota transplantation. Open Forum Infect Dis 2: ofv004.

Arpaia

Campbell

Fan

Dikiy

Van Der Veeken

Deroos

. (2013) Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 504: 451–455.

Atarashi

Tanoue

Ando

Kamada

Nagano

Narushima

. (2015) Th17 cell induction by adhesion of microbes to intestinal epithelial cells. Cell 163: 367–380.

Atarashi

Tanoue

Oshima

Suda

Nagano

Nishikawa

. (2013) Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 500: 232–236.

Atarashi

Tanoue

Shima

Imaoka

Kuwahara

Momose

. (2011) Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331: 337–341.

Backhed

Ding

Wang

Hooper

Koh

Nagy

. (2004) The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 101: 15718–15723.

Bercik

Denou

Collins

Jackson

Jury

. (2011) The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology 141: 599–609.e3.

Berni Canani

Sangwan

Stefka

A.T.

Nocerino

Paparo

Aitoro

. (2016) Lactobacillus rhamnosus Gg-supplemented formula expands butyrate-producing bacterial strains in food allergic infants. ISME J 10: 742–750.

10.

Bindels

Delzenne

Cani

Walter

(2015) Towards a more comprehensive concept for prebiotics. Nat Rev Gastroenterol Hepatol 12: 303–310.

11.

Bindels

Walter

Ramer-Tait

(2015) Resistant starches for the management of metabolic diseases. Curr Opin Clin Nutr Metab Care 18: 559–565.

12.

Bohn

Storsrud

Liljebo

Collin

Lindfors

Tornblom

. (2015) Diet low in FODMAPs reduces symptoms of irritable bowel syndrome as well as traditional dietary advice: a randomized controlled trial. Gastroenterology 149: 1399–1407.e2.

13.

Bordin

D’Atri

Guillemot

Citi

(2004) Histone deacetylase inhibitors up-regulate the expression of tight junction proteins. Mol Cancer Res 2: 692–701.

14.

Braga

Da Silva

De Lira

De Carvalho Lima

(2011) Efficacy of Bifidobacterium breve and Lactobacillus casei oral supplementation on necrotizing enterocolitis in very-low-birth-weight preterm infants: a double-blind, randomized, controlled trial. Am J Clin Nutr 93: 81–86.

15.

Brestoff

Artis

(2013) Commensal bacteria at the interface of host metabolism and the immune system. Nat Immunol 14: 676–684.

16.

Brown

Wlodarska

Willing

Vonaesch

Han

Reynolds

. (2015) Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model. Nat Commun 6: 7806.

17.

Buffie

Bucci

Stein

McKenney

Ling

Gobourne

. (2015) Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517: 205–208.

18.

Buffie

Jarchum

Equinda

Lipuma

Gobourne

Viale

. (2012) Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect Immun 80: 62–73.

19.

Bures

Cyrany

Kohoutova

Forstl

Rejchrt

Kvetina

. (2010) Small intestinal bacterial overgrowth syndrome. World J Gastroenterol 16: 2978–2990.

20.

Cani

Everard

(2016) Talking microbes: when gut bacteria interact with diet and host organs. Mol Nutr Food Res 60: 58–66.

21.

Carding

Verbeke

Vipond

Corfe

Owen

(2015) Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis 26: 26191.

22.

Carlsson

Yakymenko

Olivier

Hakansson

Postma

Keita

. (2013) Faecalibacterium prausnitzii supernatant improves intestinal barrier function in mice DSS colitis. Scand J Gastroenterol 48: 1136–1144.

23.

Collins

Auchtung

Schaefer

Eaton

Britton

(2015) Humanized microbiota mice as a model of recurrent Clostridium difficile disease. Microbiome 3: 35.

24.

Collins

(2014) A role for the gut microbiota in IBS. Nat Rev Gastroenterol Hepatol 11: 497–505.

25.

Costeloe

Hardy

Juszczak

Wilks

Millar

(2016) Bifidobacterium breve BBG-001 in very preterm infants: a randomised controlled phase 3 trial. Lancet 387: 649–660.

26.

Cotillard

Kennedy

Kong

Prifti

Pons

Le Chatelier

. (2013) Dietary intervention impact on gut microbial gene richness. Nature 500: 585–588.

27.

Cox

West

Cripps

(2015) Obesity, inflammation, and the gut microbiota. Lancet Diabetes Endocrinol 3: 207–215.

28.

Dalal

Chang

(2014) The microbial basis of inflammatory bowel diseases. J Clin Invest 124: 4190–4196.

29.

Daniel

Moghaddas Gholami

Berry

Desmarchelier

Hahne

Loh

. (2014) High-fat diet alters gut microbiota physiology in mice. ISME J 8: 295–308.

30.

David

Maurice

Carmody

Gootenberg

Button

Wolfe

. (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505: 559–563.

31.

De Filippis

Pellegrini

Vannini

Jeffery

La Storia

Laghi

. (2015) High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut 28 September (Epub ahead of print).

32.

De Palma

Blennerhassett

Deng

Park

Green

. (2015) Microbiota and host determinants of behavioural phenotype in maternally separated mice. Nat Commun 6: 7735.

33.

De Palma

Collins

Bercik

(2014) The microbiota–gut–brain axis in functional gastrointestinal disorders. Gut Microbes 5: 419–429.

34.

De Palma

Nadal

Medina

Donat

Ribes-Koninckx

Calabuig

. (2010) Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children. BMC Microbiol 10: 63.

35.

Deshpande

Pasupuleti

Thota

Pant

Rolston

Sferra

. (2013) Community-associated Clostridium difficile infection and antibiotics: a meta-analysis. J Antimicrob Chemother 68: 1951–1961.

36.

Devkota

Wang

Musch

Leone

Fehlner-Peach

Nadimpalli

. (2012) Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in IL10-/- mice. Nature 487: 104–108.

37.

Dewulf

Cani

Claus

Fuentes

Puylaert

Neyrinck

. (2013) Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women. Gut 62: 1112–1121.

38.

Dey

Wagner

Blanton

Cheng

Fontana

Haque

. (2015) Regulators of gut motility revealed by a gnotobiotic model of diet-microbiome interactions related to travel. Cell 163: 95–107.

39.

Dore

Blottiere

(2015) The influence of diet on the gut microbiota and its consequences for health. Curr Opin Biotechnol 32: 195–199.

40.

Drossman

Chang

Bellamy

Gallo-Torres

Lembo

Mearin

. (2011) Severity in irritable bowel syndrome: a Rome Foundation Working Team report. Am J Gastroenterol 106: 1749–1759; quiz 1760.

41.

Duerkop

Clements

Rollins

Rodrigues

Hooper

(2012) A composite bacteriophage alters colonization by an intestinal commensal bacterium. Proc Natl Acad Sci U S A 109: 17621–17626.

42.

El Aidy

Van Baarlen

Derrien

Lindenbergh-Kortleve

Hooiveld

Levenez

. (2012) Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice. Mucosal Immunol 5: 567–579.

43.

Everard

Belzer

Geurts

Ouwerkerk

Druart

Bindels

. (2013) Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci U S A 110: 9066–9071.

44.

Furusawa

Obata

Fukuda

Endo

Nakato

Takahashi

. (2013) Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 504: 446–450.

45.

Galipeau

McCarville

Huebener

Litwin

Meisel

Jabri

. (2015) Intestinal microbiota modulates gluten-induced immunopathology in humanized mice. Am J Pathol 185: 2969–2982.

46.

Gibson

Roberfroid

(1995) Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr 125: 1401–1412.

47.

Gkouskou

Deligianni

Tsatsanis

Eliopoulos

(2014) The gut microbiota in mouse models of inflammatory bowel disease. Front Cell Infect Microbiol 4: 28.

48.

Gough

Shaikh

Manges

(2011) Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin Infect Dis 53: 994–1002.

49.

Gupta

Andrew

Kirschner

Guandalini

(2000) Is Lactobacillus GG helpful in children with Crohn’s disease? Results of a preliminary, open-label study. J Pediatr Gastroenterol Nutr 31: 453–457.

50.

Guslandi

Mezzi

Sorghi

Testoni

(2000) Saccharomyces boulardii in maintenance treatment of Crohn’s disease. Dig Dis Sci 45: 1462–1464.

51.

Halland

Saito

(2015) Irritable bowel syndrome: new and emerging treatments. BMJ 350: h1622.

52.

Halmos

Christophersen

Bird

Shepherd

Gibson

Muir

(2015) Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut 64: 93–100.

53.

Halmos

Power

Shepherd

Gibson

Muir

(2014) A diet low in fodmaps reduces symptoms of irritable bowel syndrome. Gastroenterology 146: 67–75.e65.

54.

Hamilton

Boudry

Lemay

Raybould

(2015) Changes in intestinal barrier function and gut microbiota in high-fat diet-fed rats are dynamic and region dependent. Am J Physiol Gastrointest Liver Physiol 308: G840–G851.

55.

Hansen

Gulati

Sartor

(2010) The role of mucosal immunity and host genetics in defining intestinal commensal bacteria. Curr Opin Gastroenterol 26: 564–571.

56.

Hill

Hoffmann

Abt

Kobuley

Kirn

. (2010) Metagenomic analyses lreveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunol 3: 148–158.

57.

Horai

Zarate-Blades

Dillenburg-Pilla

Chen

Kielczewski

Silver

. (2015) Microbiota-dependent activation of an autoreactive T cell receptor provokes autoimmunity in an immunologically privileged site. Immunity 43: 343–353.

58.

Hughes

Cross

Pollock

Bingham

(2001) Dose-dependent effect of dietary meat on endogenous colonic N-nitrosation. Carcinogenesis 22: 199–202.

59.

Ivanov

Atarashi

Manel

Brodie

Shima

Karaoz

. (2009) Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139: 485–498.

60.

Jin

Lee

Sridharan

Lee

Davidson

Jayaraman

. (2014) Microbiome-derived tryptophan metabolites and their aryl hydrocarbon receptor-dependent agonist and antagonist activities. Mol Pharmacol 85: 777–788.

61.

Kanther

Tomkovich

Xiaolun

Grosser

Koo

Flynn

3rd . (2014) Commensal microbiota stimulate systemic neutrophil migration through induction of serum amyloid A. Cell Microbiol 16: 1053–1067.

62.

Kaser

Zeissig

Blumberg

(2010) Inflammatory bowel disease. Annu Rev Immunol 28: 573–621.

63.

Kau

Ahern

Griffin

Goodman

Gordon

(2011) Human nutrition, the gut microbiome and the immune system. Nature 474: 327–336.

64.

Kelly

Zheng

Campbell

Saeedi

Scholz

Bayless

. (2015) Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function. Cell Host Microbe 17: 662–671.

65.

Koeth

Wang

Levison

Buffa

Org

Sheehy

. (2013) Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med 19: 576–585.

66.

Kverka

Zakostelska

Klimesova

Sokol

Hudcovic

Hrncir

. (2011) Oral administration of Parabacteroides distasonis antigens attenuates experimental murine colitis through Modulation of Immunity and Microbiota Composition. Clin Exp Immunol 163: 250–259.

67.

Lawley

Clare

Walker

Stares

Connor

Raisen

. (2012) Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog 8: e1002995.

68.

Le Barz

Anhe

Varin

Desjardins

Levy

Roy

. (2015) Probiotics as complementary treatment for metabolic disorders. Diabetes Metab J 39: 291–303.

69.

Le Chatelier

Nielsen

Qin

Prifti

Hildebrand

Falony

. (2013) Richness of human gut microbiome correlates with metabolic markers. Nature 500: 541–546.

70.

Lee

Albenberg

Compher

Baldassano

Piccoli

Lewis

. (2015) Diet in the pathogenesis and treatment of inflammatory bowel diseases. Gastroenterology 148: 1087–1106.

71.

Lepage

Colombet

Marteau

Sime-Ngando

Dore

Leclerc

(2008) Dysbiosis in inflammatory bowel disease: a role for bacteriophages? Gut 57: 424–425.

72.

Leung

Loke

(2013) A role for IL-22 in the relationship between intestinal helminths, gut microbiota and mucosal immunity. Int J Parasitol 43: 253–257.

73.

Levy

Thaiss

Zeevi

Dohnalova

Zilberman-Schapira

Mahdi

. (2015) Microbiota-modulated metabolites shape the intestinal microenvironment by regulating NLRP6 inflammasome signaling. Cell 163: 1428–1443.

74.

Lewis

Lutgendorff

Phan

Soderholm

Sherman

McKay

(2010) Enhanced translocation of bacteria across metabolically stressed epithelia is reduced by butyrate. Inflamm Bowel Dis 16: 1138–1148.

75.

Logan

Chow

George

Weinstein

Cebra

(1991) Use of Peyer’s patch and lymph node fragment cultures to compare local immune responses to Morganella morganii. Infect Immun 59: 1024–1031.

76.

Longstreth

Thompson

Chey

Houghton

Mearin

Spiller

(2006) Functional bowel disorders. Gastroenterology 130: 1480–1491.

77.

Macia

Tan

Vieira

Leach

Stanley

Luong

. (2015) Metabolite-sensing receptors GPR43 and GPR109a facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome. Nat Commun 6: 6734.

78.

Macpherson

Harris

(2004) Interactions between commensal intestinal bacteria and the immune system. Nat Rev Immunol 4: 478–485.

79.

Madsen

(2001) Inflammatory bowel disease: lessons from the IL-10 gene-deficient mouse. Clin Invest Med 24: 250–257.

80.

Malchow

(1997) Crohn’s disease and Escherichia coli. A new approach in therapy to maintain remission of colonic Crohn’s disease? J Clin Gastroenterol 25: 653–658.

81.

Mao

Nobaek

Kasravi

Adawi

Stenram

Molin

. (1996) The effects of Lactobacillus strains and oat fiber on methotrexate-induced enterocolitis in rats. Gastroenterology 111: 334–344.

82.

Marafini

Monteleone

Di Fusco

Cupi

Paoluzi

Colantoni

. (2015) TNF-alpha producing innate lymphoid cells (ILCs) are increased in active celiac disease and contribute to promote intestinal atrophy in mice. PLoS One 10: e0126291.

83.

Mayne

Williams

(2013) Induced and natural regulatory T cells in the development of inflammatory bowel disease. Inflamm Bowel Dis 19: 1772–1788.

84.

McKenzie

Spits

Eberl

(2014) Innate lymphoid cells in inflammation and immunity. Immunity 41: 366–374.

85.

Mills

Shanahan

Stanton

Hill

Coffey

Ross

(2013) Movers and shakers: influence of bacteriophages in shaping the mammalian gut microbiota. Gut Microbes 4: 4–16.

86.

Moayyedi

Ford

Talley

Cremonini

Foxx-Orenstein

Brandt

. (2010) The efficacy of probiotics in the treatment of irritable bowel syndrome: a systematic review. Gut 59: 325–332.

87.

Moayyedi

Surette

Kim

Libertucci

Wolfe

Onischi

. (2015) Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology 149: 102–109.e6.

88.

Natividad

Pinto-Sanchez

Galipeau

Jury

Jordana

Reinisch

. (2015) Ecobiotherapy rich in Firmicutes decreases susceptibility to colitis in a humanized gnotobiotic mouse model. Inflamm Bowel Dis 21: 1883–1893.

89.

Natividad

Verdu

(2013) Modulation of intestinal barrier by intestinal microbiota: pathological and therapeutic implications. Pharmacol Res 69: 42–51.

90.

Norman

Handley

Baldridge

Droit

Liu

Keller

. (2015) Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 160: 447–460.

91.

Ochoa-Reparaz

Mielcarz

Ditrio

Burroughs

Foureau

Haque-Begum

. (2009) Role of gut commensal microflora in the development of experimental autoimmune encephalomyelitis. J Immunol 183: 6041–6050.

92.

O’Mahony

Feeney

O’Halloran

Murphy

Kiely

Fitzgibbon

. (2001) Probiotic impact on microbial flora, inflammation and tumour development in IL-10 knockout mice. Aliment Pharmacol Ther 15: 1219–1225.

93.

O’Mahony

McCarthy

Kelly

Hurley

Luo

Chen

. (2005) Lactobacillus and bifidobacterium in irritable bowel syndrome: symptom responses and relationship to cytokine profiles. Gastroenterology 128: 541–551.

94.

Pabst

Mowat

(2012) Oral tolerance to food protein. Mucosal Immunol 5: 232–239.

95.

Palomares

Yaman

Azkur

Akkoc

Akdis

(2010) Role of Treg in immune regulation of allergic diseases. Eur J Immunol 40: 1232–1240.

96.

Paul

Barnes

Demark-Wahnefried

Morrow

Salvador

Skibola

. (2015) Influences of diet and the gut microbiome on epigenetic modulation in cancer and other diseases. Clin Epigenetics 7: 112.

97.

Peng

Chen

Holzman

Lin

(2007) Effects of butyrate on intestinal barrier function in a Caco-2 cell monolayer model of intestinal barrier. Pediatr Res 61: 37–41.

98.

Peng

Green

Holzman

Lin

(2009) Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers. J Nutr 139: 1619–1625.

99.

Perez-Brocal

Garcia-Lopez

Vazquez-Castellanos

Nos

Beltran

Latorre

. (2013) Study of the viral and microbial communities associated with Crohn’s disease: a metagenomic approach. Clin Transl Gastroenterol 4: e36.

100.

Prantera

Scribano

Falasco

Andreoli

Luzi

(2002) Ineffectiveness of probiotics in preventing recurrence after curative resection for Crohn’s disease: a randomised controlled trial with Lactobacillus GG. Gut 51: 405–409.

101.

Qiu

Guo

Chen

Sonnenberg

Artis

. (2013) Group 3 innate lymphoid cells inhibit T-cell-mediated intestinal inflammation through aryl hydrocarbon receptor signaling and regulation of microflora. Immunity 39: 386–399.

102.

Rijkers

De Vos

Brummer

Morelli

Corthier

Marteau

(2011) Health benefits and health claims of probiotics: bridging science and marketing. Br J Nutr 106: 1291–1296.

103.

Roberfroid

Gibson

Hoyles

McCartney

Rastall

Rowland

. (2010) Prebiotic effects: metabolic and health benefits. Br J Nutr 104(Suppl. 2): S1–S63.

104.

Rohlke

Stollman

(2012) Fecal microbiota transplantation in relapsing Clostridium difficile infection. Therap Adv Gastroenterol 5: 403–420.

105.

Rolhion

Darfeuille-Michaud

(2007) Adherent-invasive Escherichia coli in inflammatory bowel disease. Inflamm Bowel Dis 13: 1277–1283.

106.

Round

Mazmanian

(2009) The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 9: 313–323.

107.

Sanchez

Nadal

Donat

Ribes-Koninckx

Calabuig

Sanz

(2008) Reduced diversity and increased virulence-gene carriage in intestinal enterobacteria of coeliac children. BMC Gastroenterol 8: 50.

108.

Schaubeck

Clavel

Calasan

Lagkouvardos

Haange

Jehmlich

. (2015) Dysbiotic gut microbiota causes transmissible Crohn’s disease-like ileitis independent of failure in antimicrobial defence. Gut 65: 225–237.

109.

Scher

Ubeda

Artacho

Attur

Isaac

Reddy

. (2015) Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease. Arthritis Rheumatol 67: 128–139.

110.

Schultz

Veltkamp

Dieleman

Grenther

Wyrick

Tonkonogy

. (2002) Lactobacillus plantarum 299V in the treatment and prevention of spontaneous colitis in interleukin-10-deficient mice. Inflamm Bowel Dis 8: 71–80.

111.

Sefik

Geva-Zatorsky

Konnikova

Zemmour

McGuire

. (2015) Mucosal immunology. Individual intestinal symbionts induce a distinct population of RORgamma(+) regulatory T cells. Science 349: 993–997.

112.

Seo

Kamada

Munoz-Planillo

Kim

Koizumi

. (2015) Distinct commensals induce interleukin-1beta via NLRP3 inflammasome in inflammatory monocytes to promote intestinal inflammation in response to injury. Immunity 42: 744–755.

113.

Shroff

Cebra

(1995) Development of mucosal humoral immune responses in germ-free (GF) mice. Adv Exp Med Biol 371A: 441–446.

114.

Sivan

Corrales

Hubert

Williams

Aquino-Michaels

Earley

. (2015) Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 350: 1084–1089.

115.

Sokol

Pigneur

Watterlot

Lakhdari

Bermudez-Humaran

Gratadoux

. (2008) Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 105: 16731–16736.

116.

Sonnenberg

Artis

(2015) Innate lymphoid cells in the initiation, regulation and resolution of inflammation. Nat Med 21: 698–708.

117.

Sonnenburg

Smits

Tikhonov

Higginbottom

Wingreen

Sonnenburg

(2016) Diet-induced extinctions in the gut microbiota compound over generations. Nature 529: 212–215.

118.

Stefka

Feehley

Tripathi

Qiu

McCoy

Mazmanian

. (2014) Commensal bacteria protect against food allergen sensitization. Proc Natl Acad Sci U S A 111: 13145–13150.

119.

Sun

Furio

Mecheri

Van Der Does

Lundeberg

Saveanu

. (2015a) Pancreatic beta-cells limit autoimmune diabetes via an immunoregulatory antimicrobial peptide expressed under the influence of the gut microbiota. Immunity 43: 304–317.

120.

Sun

Cong

Liu

(2015b) Regulatory immune cells in regulation of intestinal inflammatory response to microbiota. Mucosal Immunol 8: 969–978.

121.

Theriot

Koenigsknecht

Carlson

Jr Hatton

Nelson

. (2014) Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat Commun 5: 3114.

122.

Thorburn

Macia

Mackay

(2014) Diet, metabolites, and ‘western-lifestyle’ inflammatory diseases. Immunity 40: 833–842.

123.

Thorburn

McKenzie

Shen

Stanley

Macia

Mason

. (2015) Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites. Nat Commun 6: 7320.

124.

Turnbaugh

Ley

Mahowald

Magrini

Mardis

Gordon

(2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027–1031.

125.

Vaishnava

Behrendt

Ismail

Eckmann

Hooper

(2008) Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host–microbial interface. Proc Natl Acad Sci U S A 105: 20858–20863.

126.

Vangay

Ward

Gerber

Knights

(2015) Antibiotics, pediatric dysbiosis, and disease. Cell Host Microbe 17: 553–564.

127.

Venturi

Gionchetti

Rizzello

Johansson

Zucconi

Brigidi

. (1999) Impact on the composition of the faecal flora by a new probiotic preparation: preliminary data on maintenance treatment of patients with ulcerative colitis. Aliment Pharmacol Ther 13: 1103–1108.

128.

Verdu

Bercik

Verma-Gandhu

Huang

Blennerhassett

Jackson

. (2006) Specific probiotic therapy attenuates antibiotic induced visceral hypersensitivity in mice. Gut 55: 182–190.

129.

Wacklin

Laurikka

Lindfors

Collin

Salmi

Lahdeaho

. (2014) Altered duodenal microbiota composition in celiac disease patients suffering from persistent symptoms on a long-term gluten-free diet. Am J Gastroenterol 108: 1933–1941.

130.

Wagner

Maksimovic

Farries

Sim

Bishop

Cameron

. (2013) Bacteriophages in gut samples from pediatric Crohn’s disease patients: metagenomic analysis using 454 pyrosequencing. Inflamm Bowel Dis 19: 1598–1608.

131.

Walters

Knight

(2014) Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett 588: 4223–4233.

132.

Wang

Dong

Zhu

(2012) Probiotic supplement reduces risk of necrotizing enterocolitis and mortality in preterm very low-birth-weight infants: an updated meta-analysis of 20 randomized, controlled trials. J Pediatr Surg 47: 241–248.

133.

Wing

Sakaguchi

(2010) Regulatory T cells exert checks and balances on self tolerance and autoimmunity. Nat Immunol 11: 7–13.

134.

Wolvers

Antoine

Myllyluoma

Schrezenmeir

Szajewska

Rijkers

(2010) Guidance for substantiating the evidence for beneficial effects of probiotics: prevention and management of infections by probiotics. J Nutr 140: 698S–712S.

135.

Chen

Hoffmann

Bittinger

Chen

Keilbaugh

. (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334: 105–108.

136.

Zelante

Iannitti

Cunha

De Luca

Giovannini

Pieraccini

. (2013) Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 39: 372–385.

137.

Zenewicz

Yancopoulos

Valenzuela

Murphy

Stevens

Flavell

(2008) Innate and adaptive interleukin-22 protects mice from inflammatory bowel disease. Immunity 29: 947–957.

138.

Zenewicz

Yin

Wang

Elinav

Hao

Zhao

. (2013) IL-22 deficiency alters colonic microbiota to be transmissible and colitogenic. J Immunol 190: 5306–5312.