Review Article

The Gut Microbiome in Inflammatory Bowel Disease—Avenues for Microbial Management

J. McIlroy; G. Ianiro; I. Mukhopadhya; R. Hansen; G. L. Hold


Aliment Pharmacol Ther. 2018;47(1):26-42. 

In This Article

Microbiota as a Therapeutic Target in Inflammatory Bowel Disease


Generally, antimicrobial drugs are known to influence the natural history of several disorders, including inflammatory bowel disease, by modulating the host microbiota, which in turn drives beneficial or harmful consequences in clinical practice.[62,63] Antibiotics can potentially ameliorate the microbial environment of patients with inflammatory bowel disease, both by decreasing proinflammatory bacteria and by increasing beneficial ones, throughout the intestinal lumen.[64] Several antimicrobial drugs have been investigated in patients with ulcerative colitis for the induction and/or maintenance of disease remission. Long-term ciprofloxacin usage was found to improve clinical outcomes, when given as adjuvant therapy to steroids and salicylates, for the induction and maintenance of disease remission,[65] without any advantage in ulcerative colitis as short-term therapy.[66] Metronidazole did not show any benefit in the induction of remission,[67] despite achieving similar results to salicylates in the remission maintenance of mildly-to-moderately active ulcerative colitis.[68] Alternate results come from the use of oral tobramycin, as this drug was shown to be effective in achieving clinical remission[69] but not in maintaining it.[70] Rifaximin has been shown to be capable of improving symptoms, but not activity of disease, in patients with moderate-severe ulcerative colitis.[71] Finally, a combination of different antibiotics (metronidazole, amoxicillin, doxycycline and vancomycin) achieved promising results in children with moderate-severe refractory ulcerative colitis.[72]

According to several systematic reviews and meta-analyses of randomised placebo-controlled trials, antibiotics appear to be effective in the induction of remission in patients with ulcerative colitis.[73–76] However, these meta-analyses pooled together studies that investigated different antibiotics, which is arguably not appropriate for amalgamated analysis, therefore their conclusions should be considered carefully. Based on available evidence, the use of antibiotics for patients with ulcerative colitis has only been approved in clinical practice for a limited number of specific indications, including Clostridioides (formerly Clostridium) difficile superinfection, before surgical intervention, toxic megacolon, and if an infection is suspected.[77] There is no evidence to support a routine role for antibiotics in the induction and/or maintenance of remission.[78]

Although antibiotics have a well-defined role in the management of complicated CD, mainly in perianal disease and septic complications,[79] their value in uncomplicated disease has not yet been established. Several antibiotic classes have been investigated in inducing or maintaining disease remission in patients with CD. Rifaximin, metronidazole, ciprofloxacin and anti-mycobacterial drugs have been investigated more extensively than other antibiotics, mainly in RCTs against placebo or active comparators. Rifaximin has been shown to be more effective than placebo in achieving clinical remission of mild-to-moderately active CD.[80,81] Metronidazole was shown to improve CD activity index (CDAI), and to prevent disease recurrence after surgery,[82] if combined with azathioprine, but not to achieve clinical remission.[83] Moreover, data show that when used in combination with azithromycin, metronidazole was effective in inducing remission in paediatric CD.[63] Ciprofloxacin has been shown to reduce CDAI significantly,[84] but not to prevent post-surgical recurrence.[85] There has been long-standing interest in Mycobacterium avium subsp. paratuberculosis as a potential trigger of CD. Consequently, many studies have addressed the role of anti-mycobacterial drugs—such as rifampicin, clofazimine, ethambutol, isoniazid, sulphadoxine-pyrimethamine, dapsone—alone or in combination, in several clinical settings, including induction of remission (either alone or as adjuvant therapy to steroid)[86–89] and maintenance of remission.[87] However, in a large randomised control trial (RCT) of patients with active CD, a 2-year combination therapy of clarithromycin, rifabutin and clofazimine did not provide any clinical benefit.[90] This suggests that M. avium subsp. paratuberculosis does not have a role as a chronic infection in CD.

In a meta-analysis of RCTs, antibiotics showed an overall significant advantage over placebo in the induction of disease remission, although, at sub-analysis, only rifaximin and anti-mycobacterial drugs achieved significant success in induction of remission (RR = 0.78; 95% CI = 0.76–0.91) and in maintenance (RR = 0.62; 95% CI = 0.46–0.84) respectively.[74] The inconsistencies of these results mean that antibiotics are still not considered a standard treatment option for CD. To date, antibiotics are not recommended for the management of uncomplicated CD because of possible side effects. Their use is recommended only in particular situations, including sepsis, perianal disease and bacterial overgrowth.[79]

As well as being a potentially useful therapeutic intervention, there is evidence that suggests antibiotics play a role in the pathogenesis of inflammatory bowel disease, in particular CD, through development of dysbiosis. In the RISK study, an assessment of treatment-naïve microbiomes of children with CD showed that the use of antibiotics increased the microbial dysbiosis associated with the background disease.[34] In a recent meta-analysis, antibiotic therapy was identified as a significant risk factor for the development of CD (odd ratio [OR] 1.74, 95% CI 1.35–2.23), mainly in childhood (OR 2.75, 95% CI 1.72–4.38), without being significant for ulcerative colitis (OR 1.08, 95% CI 0.91–1.27).[91]

Probiotics and Prebiotics

Many probiotic strains, administered as single strains or probiotic combinations, have been investigated in inflammatory bowel disease, with the aim of modulating the microbiota and reversing intestinal dysbiosis. Escherichia coli Nissle (ECN) 1917, a nonpathogenic strain, is the most frequently investigated. ECN 1917 achieved comparable efficacy and safety outcomes to salicylates in maintenance of remission in subjects with quiescent ulcerative colitis.[92–94] In the same population setting, another single strain, Lactobacillus rhamnosus GG, achieved a longer time free from relapse than salicylates.[95]

In few pilot studies, the probiotic yeast S. boulardii was effective both in inducing and in maintaining remission in subjects with mild-to-moderately active ulcerative colitis.[96,97] VSL#3, a probiotic mix of 4 Lactobacilli, 3 Bifidobacteria and a Streptococcus, is the product with the most available evidence to date. In a small sample of patients with ulcerative colitis unsuitable for salicylates, VSL#3 was found to be effective in maintenance of remission.[98] Moreover, VSL#3 has been shown to be effective in inducing remission in subjects with mild-to-moderately active ulcerative colitis, either combined with standard treatment[99] or alone.[100] In a meta-analysis, VSL#3, added as adjuvant to standard treatment, achieved better results than standard treatment alone in the induction of clinical remission (OR = 2.4) and clinical response (OR = 3.03; NNT: 3–4).[101] Other combinations of probiotic strains have not achieved results as consistent as those of VSL#3.[102–104]

Several systematic reviews and meta-analyses tried to address the role of probiotics in the management of ulcerative colitis, without conclusive results. A Cochrane review showed probiotics were not more effective than placebo or active comparators in inducing the remission of active ulcerative colitis.[105] However, when only RCTs were pooled, probiotics were shown to be effective in the induction of remission (RR 1.80), although only VSL#3 was confirmed to achieve a significant advantage over placebo (RR 1.74) after analysis of strain subgroups.[106] A further Cochrane review found that probiotics were ineffective in the maintenance of remission in ulcerative colitis,[107] although a meta-analysis of RCTs showed their efficacy in the prevention of pouchitis.[108] Overall, these meta-analyses suffer from several biases, as the authors pooled together studies that included different species and strains, therapeutic dosages and periods of treatment. In the light of this, probiotics are not currently recommended for the induction of remission in adults patients with ulcerative colitis, although the value of VSL#3 has been highlighted. Moreover, ECN 1917 has been shown to be as effective as salicylates in maintenance of remission.[77] ECN 1917 and VSL#3 have been suggested, with caution, to be useful alone for the induction of remission of mild ulcerative colitis in children not tolerating salicylates, or as an adjunct to standard treatment in patients not completely achieving remission.[78] Finally, probiotics have also been shown to cause sepsis in patients with ulcerative colitis.[109] This finding suggests that probiotics are not always free from side effects, especially in high-risk patients (such as immunosuppressed subjects with severely active inflammatory bowel disease); therefore, their administration should be approached with caution, particularly in severe disease.

Only limited data are available for probiotic application in CD. A number of probiotic strains have been used; however, none of them have shown efficacy in different outcomes of CD (induction of remission, maintenance of remission, prevention of relapse after surgery) either in single studies or meta-analysis of RCTs.[110–113] Moreover, Lactobacilli did not show any effect on the maintenance of remission as an adjunct to standard treatment.[80,114] Other probiotic strains have not achieved better results. ECN 1917 may have an advantage over placebo in achieving a faster induction of remission, but without any effect on remission rates.[115]Saccharomyces boulardi has shown some efficacy in decreasing recurrence rates after clinical remission is achieved;[116] however, it did not improve remission rates in subjects with active disease.[117]

Finally, 2 Cochrane reviews found that probiotics conferred no advantage over placebo in maintaining or inducing remission of CD.[118,119] Therefore, probiotics are not suggested in the routine maintenance of remission in patients with CD.[79] The available evidence on the efficacy of prebiotics in CD is still poor. As suggested in a systematic review of RCTs,[120] further high-quality studies are needed to address the role of probiotics and prebiotics in the management of CD.

The disappointing results from probiotics to date are perhaps not surprising given that they were generally studied during a period with limited comprehension of, or ability to monitor, the microbiota in inflammatory bowel disease. Moreover, currently available probiotics were not rationally designed to correct the dysbiosis which can underlie the disease; therefore, any therapeutic effect from a single strain is a chance finding. Further study of targeted, specific probiotics informed by the modern microbial pathogenesis paradigm of inflammatory bowel disease is badly needed. The application of metagenomics may help to identify specific strains with biologically plausible efficacy in inflammatory bowel disease.

Faecal Microbial Transplantation

Faecal microbiota transplantation is a medical treatment that involves the administration of faecal microbiota into the intestinal tract of a recipient. Various methods have been utilised for delivery of FMT, such as nasogastric tube, nasoduodenal tube, rectal enema, the biopsy channel of a colonoscope and more recently via enteric-coated capsules.[121,122] The optimal method of delivery remains unclear. The most researched and widely practiced form of FMT is allogenic and involves the transfer of faecal microbiota from a healthy donor into a patient. However, it should be noted that FMT can also be autologous in nature,[123] where faecal material is banked by a patient and reinstated a later date.

In modern medicine, FMT was first described in the literature in 1958 as a treatment for fulminant pseudomembranous colitis, where Eiseman et al reported the successful treatment of 4 patients using FMT enemas.[124] Over the subsequent decades, there were several scattered case reports and case series of FMT for C. difficile infection (CDI), the majority of which were successful; however, there was still a lack of controlled clinical trial data for clinicians to reference.[125] In a landmark paper, van Nood et al published the first randomised control trial of FMT in C. difficile infection.[126] The effects were dramatic, with 81% of patients cured after a single FMT, given through nasoduodenal tube, compared with a cure rate of <31% in control groups. Since then, a large body of controlled and noncontrolled evidence has accumulated that reports a primary cure rate of 85%-90% in recurrent C. difficile infection where antibiotic treatment has failed.[127,128] Although the mechanism of action of FMT in the treatment of C. difficile infection has yet to be fully defined, several theories have been put forward. These include direct activity against C. difficile by the bacteria in the donated sample and restoration of secondary bile acid metabolism.[129] Interestingly, the notion that the bacteria in the donated sample play an indispensable role in the efficacy of FMT recently came into question in the light of a clinical case series that reported that sterile faecal filtrate was also effective in treating patients with C. difficile infection.[130]

The success of FMT as a treatment for recurrent C. difficile infection has prompted a surge of interest in evaluating its efficacy as a treatment intervention in other diseases and disorders where perturbations to the microbiota are thought to play a role in pathogenesis and severity, including inflammatory bowel disease, where the first case report was published in 1989.[131] Since then, some authors have reported positive results,[132–141] others have reported variable results or no observed clinical improvement.[142–145] The strongest evidence for FMT in inflammatory bowel disease comes from 4 double-blind randomised control trials,[136,137,142,146] all of which were performed on patients with ulcerative colitis. A recent systematic review and meta-analysis published by Costello et al, in this journal, found that in cohort studies, 24% of patients achieved clinical remission.[147] In the 4 published randomised control trials, clinical remission was achieved in 28% of patients who received FMT from healthy donors and 9% of patients in the placebo groups. These results indicate that FMT appears to be a moderately effective treatment for patients with active ulcerative colitis. There are, however, several methodological differences between the studies that make the results challenging to translate into clinical practice. These differences, along with the reported microbiome changes associated with FMT in inflammatory bowel disease, are explored below.

Rossen et al randomised 50 patients suffering from ulcerative colitis to undergo 2 FMTs via nasoduodenal tube, containing faeces from either a healthy donor or patients own stool.[142] The authors reported that there was no statistically significant difference in clinical or endoscopic remission between the 2 arms of the study. Moayyedi et al allocated 75 patients to 6 FMT s, using stool prepared from a healthy donor or drinking water (placebo) via retention enema.[136] Patients who received FMT met the robust primary endpoint (clinical and endoscopic remission Mayo <3 with endoscopic Mayo 0) in a higher percentage of patients than placebo (24% vs 5%; P = .03). An interesting observation is that stool from 1 out of the 6 donors induced remission in 39% of patients, which was remarkably higher than the other donors (10%), suggesting that there may be a donor-patient compatibility effect for FMT in inflammatory bowel disease. Moayyedi et al reported that disease <1 year was also more associated with remission. However, the systematic review and meta-analysis performed by Costello et al found no association between disease duration and remission. Paramsothy et al randomly allocated 85 patients with active ulcerative colitis to receive either FMT or placebo (isotonic saline with added brown food colourant and odorant) administered once by colonoscopy, followed by 39 self-administered enemas over 8 weeks.[137] The faecal microbiota administered to patients was prepared from a mix of between 3 and 7 donors. The authors noted that this was a deliberate attempt to increase microbial diversity in each infusion and indeed increased diversity was confirmed using 16S amplicon sequencing. However, clearly this approach makes identifying microbial signals of efficacy more challenging and concurrently runs the risk of inadvertent "friendly fire" between the combined donor microbial ecosystems in the pooled FMT. Furthermore, the risk of infection transmission is theoretically higher in multi-donor FMT. The primary outcome (steroid-free clinical remission and endoscopic improvement of Mayo ≤2) was achieved in 27% of patients allocated to FMT with only 8% of the 40 patients allocated the placebo achieving the primary outcome. Costello et al allocated 73 patients with active ulcerative colitis to receive multi-donor faecal microbiota or autologous FMT (placebo) via colonoscopy on day 0 followed by 2 enemas on day 7.[146] The authors reported that in the intention-to-treat analysis, 32% of patients that received FMT achieved the primary endpoint (steroid-free remission, Mayo ≤2 and endoscopic subscore ≤1), as compared to 9% who received autologous FMT. In contrast to all prior FMT in inflammatory bowel disease studies, Costello et al processed the faecal microbiota in anaerobic conditions, which could theoretically influence the efficacy of the FMT. Some bacteria such as F. prausnitzii, which have anti-inflammatory effects, are known to only survive in strictly anaerobic conditions and therefore may be lost over the course of aerobic processing.[148]

There are several methodological differences between each trial that make it challenging to recommend an optimal protocol. However, taken collectively, the data from the randomised control trials that have been published to date suggest that distal administration, frequent dosing and use of diverse faecal microbiota could all be factors that could influence a positive response in ulcerative colitis. Interestingly, a recent study of FMT in CD reported that frequent dosing was associated with increased efficacy.[149] Future research should investigate the efficacy and safety of capsule-delivered FMT in inflammatory bowel disease as this would be more suitable for frequent dosing and would simplify the design of placebo-controlled trials, though dose limitation may become a factor.[150]

Across all studies FMT appear to be safe in the short term, with the majority of reported adverse events being mild, self-limiting and gastrointestinal in nature.[151] However, serious adverse events such as bacteraemia, perforations and death have been reported. Furthermore, there have been reported instances of flares, significant escalation of therapy and development of perianal disease in patients with concomitant inflammatory bowel disease and C. difficile infection treated with FMT.[152–154] Overall, the rate of serious adverse events appears to be higher in recipients of FMT through the upper gastrointestinal tract as a result of procedure-induced aspiration pneumonia.[151] The causality between nonprocedural adverse events and FMT has yet to be fully delineated and therefore further research from controlled trials is necessary to establish the factors involved.[151,155] The long-term effects of FMT are yet to be established. However, as FMT involves the infusion of a largely uncharacterised active microbial suspension, there is a theoretical possibility that diseases linked to gut bacteria could be transferred.

Faecal microbiota transplantation is known to elicit significant changes to the structure and function of the microbiome of the recipient. Paramsothy et al reported that the presence of several taxa in the donor were associated significantly with the primary endpoint. In particular, Barnesiella spp., Parabacteroides spp., Clostridium cluster IV, Ruminococcus spp., Blautia spp., Dorea spp. and Clostridium cluster XVIII. These results are broadly consistent with Moayyedi et al, who reported that donor B was enriched with Ruminococcus and Lachanospiraceae (Clostridium cluster IV and XIVa). Interestingly, Rossen et al reported that remission was associated with donor enrichment in IV, XIVa and XVIII, which contain known butyrate-producing species. Taken collectively, it appears that Clostridium clusters IV, XIVa and XVIII are consistently associated with remission. Remarkably, these observations are supported by animal models showing that cocktails of Clostridial species belonging to clusters XIVa, IV and XVIII promote an anti-inflammatory immune responses by activating regulatory T (Treg) cells[156] as well as data that show that inoculation of clostridia during early life reared mice resistant to colitis.[157] Cluster XIVa contains highly oxygen-sensitive organisms of clinical importance in UC pathogenesis, particularly Roseburia hominis. Interestingly, this renewed focus on cluster XIVa also reinvigorates interest in the role of butyrate in ulcerative colitis pathogenesis. FMT is a relatively crude approach to treating inflammatory bowel disease, which is likely a complex continuum of disorders. However, these results suggest that when combined with robust microbial analysis of both the donor and the recipient, FMT can be an efficacious treatment option and a powerful research tool which may facilitate patient stratification and personalised microbial therapeutics.

Nutritional Therapy in Inflammatory Bowel Disease

The use of supportive nutrition in inflammatory bowel disease is outside the scope of this review, which will instead focus on the use of nutrition as therapy in inflammatory bowel disease and the microbial signals that emerge from its use. The role of particular foods in driving inflammation and triggering flare in inflammatory bowel disease is also of huge interest; however, while research in this area may well point to microbial mechanisms of action, insufficient targeted microbial research has been undertaken in this area for us to develop specific microbial arguments further. Such food/microbiome research, particularly coupled with disease activity/flare data, represents an important unmet need in inflammatory bowel disease.

The potential utility of nutrition as therapy in inflammatory bowel disease was first demonstrated in an observational study by Voitk et al who recognised that use of an elemental diet prevented the need for surgery in some patients where operative management was planned.[158] While this observation prompted an initial interest in elemental and semi-elemental protein sources in early trials of exclusive enteral nutrition, including the seminal control trials from O'Moráin et al and from Sanderson et al. subsequent meta-analysis has highlighted that whole protein approaches are equally effective.[159–161] Similarly, although the initial observation was not disease phenotype-specific, very limited work has looked at the role of enteral nutrition in ulcerative colitis, although anecdotally it is thought to be ineffective. The focus has therefore fallen on enteral nutrition in CD, with recognition that exclusive liquid diets for periods of 6–8 weeks are highly effective in inducing remission in ~80% of paediatric patients with active luminal CD, leading to exclusive enteral nutrition being promoted as first-line therapy in paediatric CD by the European and North American Societies of Paediatric Gastroenterology, Hepatology and Nutrition and the European Crohn's and Colitis Organisation.[162,163] The ethics of repeat colonoscopy limits studies of mucosal healing (and mucosal microbial change) in paediatric CD; however, small series support mucosal healing rates comparable to described rates of remission (75% vs 81% at week 8 in Rubio et al[164]). The lack of before/after mucosal microbiota studies impacts our understanding of the fundamental biological mechanism of action of exclusive enteral nutrition, with most work to date relying on serial faecal samples instead. Exclusive enteral nutrition also helps with nutritional rehabilitation and lean body mass, hence is an obvious choice in paediatric inflammatory bowel disease practice where weight loss is a common feature at presentation.[165,166] Use of exclusive enteral nutrition within adult practice remains limited and probably relates to the cumbersome social aspects of a liquid-only diet.

A description of the efficacy of exclusive enteral nutrition preceded any meaningful understanding of its mechanism of action, which has only recently begun to be understood with the advent of high-throughput, culture-free, microbial ecology tools. One early microbial study of exclusive enteral nutrition suggested either the low residue nature or potential prebiotic properties of the diet as potential modulators of the microbiome.[167] Recent data, however, demonstrate that the mechanism of action is paradoxical when compared to our understanding of CD pathogenesis. Exclusive enteral nutrition appears to reduce bacterial diversity further and reduces the proportion of key species, including F. prausnitzii, suggesting that its main mechanism of action is a reduction in the availability of bacterial substrate in the gut lumen (Figure 1).[168–171] This offers the tantalising prospect of potentially identifiable key pathogenic organisms, which might be amenable to long-term remission by directed microbial therapy.

Limited data support the use of partial enteral nutrition as maintenance therapy for CD, with only 1 randomised control trial published to date describing a 35% relapse rate on half enteral nutrition vs 64% on free diet, over nearly 12-month follow-up, after induction of remission with exclusive enteral nutrition in 92%.[172] Unsurprisingly, the message of larger volumes of enteral formula being associated with higher rates of remission emerges from published work.[173] Although partial enteral nutrition is not thought to be effective as an induction agent in CD,[174] interest has turned recently to solid food alternatives to the socially challenging liquid-only exclusive enteral nutrition currently in use. Exploration of such strategies has the support of patients and their families.[175] Exciting work from Sigall-Boneh et al in Israel demonstrates proof-of-principle of this approach, where a structured specific food elimination diet was used in children and adults with active CD, supplemented with 50% polymeric formula.[176] Remission rates were encouragingly high at ~70%. The exact constituents of the diet were not reported, but it involved reduced exposure to animal fat, dairy, gluten and emulsifiers while allowing fruit- and vegetable-derived fibre sources. It is difficult to comment on the potential mechanism of action without further dietary data, specifically regarding the substrate availability for colonic bacteria, particularly with regard to potential fibre and SCFA sources. Interestingly, 6/7 patients given the elimination diet without supplementary formula also entered remission, suggesting a "food-only" approach might achieve high efficacy rates. Other approaches and hypotheses for food-based CD therapy are discussed in detail in Lee et al.[177] Dietary emulsifiers are one area of significant interest that sit outside of the microbial substrate hypothesis, potentially opening avenues for increased pathogenic potential within the host microbiota.[178] The exact mechanisms of CD dietary pathogenesis may of course be multifactorial and complex.

The potential efficacy of solid food elimination diets is exciting in proposing a coeliac-type approach to CD management in the future, potentially more acceptable to adults than traditional exclusive enteral nutrition. Hopefully further study will help stratify the underpinning mechanisms to help refinement of dietary approaches. While it is unlikely that a single fundamental agent as simple as gluten is the key to CD dietary response, further dietary study and control trials of interventions might unlock a greater understanding of the disease pathogenesis and open other avenues for targeted microbial therapy as a byproduct. Further study of diet and CD should be an area of high research priority, underpinned with detailed microbial interrogation of the mechanisms at play.