REVIEW
10.1111/1469-0691.12799
The potential beneficial role of faecal microbiota transplantation in diseases other than Clostridium difficile infection R. Singh1, M. Nieuwdorp2, I. J. M. ten Berge1, F. J. Bemelman1 and S. E. Geerlings3 1) Renal Transplant Unit, Division of Nephrology, 2) Division of Vascular Medicine and 3) Division of Infectious Diseases, Department of Internal Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
Abstract This review gives an outline of the indications for faecal microbiota transplantation (FMT) for diseases other than Clostridium difficile (C. difficile) infection. The remarkable efficacy of FMT against C. difficile infection has already been demonstrated. The use of FMT for other diseases, such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), and metabolic syndrome, is now being evaluated. The currently available data suggest that FMT might be beneficial for IBD (including ulcerative colitis and, to some extent, Crohn’s disease), IBS, and insulin resistance. Several randomized clinical trials are currently being performed, and data are eagerly awaited. A new field of research for the implementation of FMT is the eradication of pathogenic and multiresistant enteric microorganisms. A few animal studies have been performed within this field, but hardly any research data from human studies are available at present. Keywords: Faecal microbiota transplantation, inflammatory bowel disease, irritable bowel syndrome, multiresistant microorganisms, obesity, type 2 diabetes Article published online: 1 October 2014 Clin Microbiol Infect 2014; 20: 1119–1125
Corresponding author: R. Singh, Academic Medical Center, University of Amsterdam, Room number A3-273, PO Box 22660, 1100 DD Amsterdam, The Netherlands E-mail: [email protected]
multiresistant microorganisms. Also, the association between these diseases and the gut microbiota alterations will be described.
Introduction During the last few years, faecal microbiota transplantation (FMT) also known as donor faeces transplantation or faecal bacteriotherapy, has attracted increased attention. The majority of clinical experience with FMT has been gathered from the treatment of Clostridium difficile (C. difficile) infection. Many case reports, case series and meta-analyses [1,2] on this topic have been published. Furthermore, in a recently published randomized controlled trial, FMT against C. difficile infection was shown to give a cure rate of 90% [3]. Other indications for FMT as a treatment option have also been evaluated, but to different extents. In this review, we discuss and summarize indications for FMT apart from C. difficile infection, such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), obesity, type 2 diabetes, and colonization of the gastrointestinal tract by pathogenic and
The Human Gut Microbiota The human gut microbiota is the term used to describe the composition of the vast amount of microorganisms residing in the human gastrointestinal tract [4,5]. It has been estimated that there are ten times more bacterial cells than somatic cells in each human being, and that approximately 1.5–3 kg of the human body weight consists of bacteria, the majority of which reside in the gastrointestinal tract. The concentration of bacteria within the gastrointestinal tract is lowest in the stomach and increases rapidly throughout the course of the distal parts of the gastrointestinal tract, with the highest concentration being in the large intestine. The
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concentration of microorganisms in the faecal mass within the large intestine is estimated to be 1011–1012 CFU/g of faeces [6]; furthermore, it is estimated that approximately 55% of the solid faecal mass is actually bacterial mass [7]. The microbiota of a healthy individual shows a large diversity in its composition. There are seven main taxonomic divisions of the resident bacteria [4] (i.e. Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Verrucomicrobia, Cyanobacteria, and Actinobacteria). The majority of the microbiota consists of members of the Firmicutes and Bacteroidetes [4,8]. The composition of the gut microbiota is mainly dependent on the diet of the host [9–11]; however, there is evidence that age [12] is also a determinant. Many conditions, of which the use of antibiotics is the best-known example, are able to disrupt and alter the composition of the gut microbiota. The majority of the gut microbiota is located within the large intestine, and has various functions that are thought to be beneficial for the host. The most well-known function is the degradation of non-digestible food remnants (resistant starch) and the consequent production of certain vitamins such as vitamin K. As result of recent advances in molecular techniques, such as 16S ribosomal RNA sequencing-based methods and shotgun metagenome sequencing, it has become clear that the gut microbiota also has a variety of other functions in the field of host defence, energy metabolism, and immune system development [4]. From this, it follows that disruption or alteration in the composition of the gut microbiota may underlie various diseases, such as gastrointestinal infections, metabolic disorders, and IBDs.
IBD IBD consists primarily of Crohn’s disease (CD) and ulcerative colitis, and is characterized by chronic inflammation. Increasing evidence supports the association between the composition of the gut microbiota and IBD [4,13]. It has been shown that the gut microbiota of IBD patients is less diverse and has reduced amounts of members of the Firmicutes and Bacteroidetes as compared with the microbiota of healthy individuals [14]. More importantly, the differences observed in the gut microbiota of IBD patients, in comparison with the microbiota of healthy individuals, seems to be related to its immunomodulatory and nourishing functions. In comparison with healthy controls, IBD patients have decreased amounts of the short-chain fatty acid (SCFA) producers. Butyrate, propionate and acetate are SCFAs that are produced by bacteria as result of resistant starch fermentation. These three SCFAs are known to have anti-inflammatory properties [15,16]. The most
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mentioned bacterium associated with IBD is the butyrate producer Faecalibacterium prausnitzii (F. prausnitzii). Many studies have found that IBD patients have a reduced amount of this bacterium in their gut microbiota [17–20]. It has been shown in patients with CD that F. prausnitzii also has a direct anti-inflammatory effect by secreting metabolites that block nuclear factor-jB activation and prevent the production of interleukin-8 [20,21] (Fig. 1). Butyrate produced by F. prausnitzii not only has direct anti-inflammatory effects but also serves as a nutrient for the colonocytes [13,22], and thereby prevents gut mucosa atrophy [23] and colonocyte autophagy [24]. Indeed, a pilot non-randomized trial providing daily oral butyrate for 8 weeks to IBD (CD) patients showed beneficial effects on (endoscopic and clinical) remission rates as well as on markers of systemic inflammation [25]. The assumed relationship between the gut microbiota composition and IBD is that the altered gut microbiota in IBD patients has reduced anti-inflammatory properties and produces lower amounts of butyrate and other SCFAs. This may lead to increased concentrations of proinflammatory mediators in the gut and impaired intestinal barrier function, resulting in inflammation and increased gut permeability. Altogether, these data indicate that the loss of certain bacterial strains with specific immunomodulatory and mucosa-maintaining functions results in gut dysbiosis, which may, besides genetic factors of the host, contribute to the pathogenesis of IBD. This dysbiosis in the gut could be restored by introducing normal gut microbiota obtained from a healthy individual without IBD. FMT in humans, although in limited numbers, has also been evaluated as a treatment for IBD. No randomized controlled trials on this topic have been published yet, and outcomes of case series show conflicting results. In addition, two systematic reviews have addressed this subject [26,27]. The pooled data of one systematic review [26] showed that, after FMT, the majority of the patients had either reduction in the IBD symptoms (19/25, 76.0%), were able to cease their medication (13/17, 76.5%) within 6 weeks after FMT, or achieved complete remission (15/24, 62.5%). Reported side effects were not only abdominal tenderness, cramping, fever, and diarrhoea, but also an activation of CD requiring medication. Current evidence for the routine use of FMT against IBD is too weak to justify its use in clinical practice, because of the lack of data from properly designed randomized trials. However, at present, there are several clinical trials underway (www. clinicaltrials.gov), of which eight are randomized controlled trials [28–35]. In two of these trials [32,35], candidates of minor age are also eligible to participate, and one trial [34] is focusing solely on the paediatric IBD population.
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Luminal side F. prausnitzii Healthy gut microbiota Gut microbiota of a healthy individual with normal amount of F. prausnitzii and its an inflammatory metabolites. Sufficient butyrate is available to nourish the colonocytes and to prevent an inflammatory reac on.
Butyrate F. prausnitzii metabolite
Colonocyte
Butyrate and metabolites from F. prausnitzii prevent gut inflamma on by blocking NF κ-B and IL-8 secre on.
Luminal side IBD gut microbiota Reduced number of F. prausnitzii results in shortage of butyrate and other an inflammatory metabolites. This provokes gut inflamma on (mediated by NF κ-B and IL-8). In addi on, butyrate shortage causes mucosal atrophy.
Mucosa atrophy NF-κB
NF-κB
NF-κB
IL-8
Gut inflammaƟon FIG. 1. Alterations within the gut microbiota under healthy conditions and in inflammatory bowel disease (IBD). IL-8, interleukin-8; NF-jB, nuclear factor-jB.
IBS IBS is a non-inflammatory gastrointestinal disorder characterized by abdominal pain and altered bowel movements in which diarrhoea or constipation may dominate. Many studies have evaluated the gut microbiota composition of IBS patients. Patients with IBS have, in general, reduced variability of the gut microbiota in comparison with the healthy control group [36]. Moreover, one study [37] found that IBS patients had lower amounts of lactobacilli and lactate-utilizing bacteria, whereas the number of sulphate-reducing bacteria was increased. Additionally, in vitro starch fermentation analysis showed that the microbiota of IBS patients produced a lower amount of butyrate, but greater amounts of sulphides and hydrogen. It is likely that increased production of these gases could promote IBS symptoms, as H2S has a major role in visceral nociception [38]. In contrast to this, two other research groups found increased amounts of lactobacilli among the gut microbiota of IBS patients [39,40]. These differences in the amounts of lactobacilli might be the result of small numbers of participants in the studies, differences in geographical location, and the large symptom heterogeneity of IBS itself. However, a more consistent finding is the reduced amount of bifidobacteria in both the
duodenal microbiota [41] and faecal microbiota [37,39,41] of IBS patients in comparison with healthy controls. In addition to the changed microbiota, IBS patients not only have altered protein and carbohydrate energy metabolism within the gut [39], but also increased amounts of acetic and propionic acids, which are associated with both the severity of abdominal pain and bloating symptoms [40]. These data indicate that both the composition of the gut microbiota and its metabolic functions are altered in IBS patients. The authors of a recently published systematic review with a meta-analysis [42] reported that probiotics are effective treatments for IBS; however, which strain is the most beneficial remains unclear. As the faecal microbiota obtained from a healthy individual represents the most natural composition of the human gut microbiota, FMT might be more beneficial than administering one specific bacterial strain. Research in humans on the use of FMT against IBS has been performed in case series only. One case series on FMT within this patient group showed that 45 IBS patients with chronic constipation underwent FMT. A total of 60% obtained normalized defecation during a follow-up of 9–19 months [43]. At present, one randomized clinical trial [44] is registered (www.clinicaltrials.gov) that is evaluating FMT as a treatment option for IBS.
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Obesity and Type 2 Diabetes Obesity is a well-recognized public health problem in Western society, but is also becoming a growing problem in developing economies [45]. It is associated with many other morbidities, such as type 2 diabetes and cardiovascular diseases. The interaction between the gut microbiota and metabolism is quite complex, and an important question here is whether the microbiota composition associated with the obese phenotype is the result or the cause of obesity. Interesting animal studies have been performed to unravel this causality. For example, germ-free mice do not become obese and nor do they develop insulin resistance after exposure to a high-fat diet [46–48]. Furthermore, the transfer of gut microbiota from a conventionally raised mouse into a germ-free mouse results in an increase in body fat content and insulin resistance, despite reduced food intake [49]. Other animal studies have shown that the consumption of a Western diet, containing high amounts of fat and sugars, leads to a vast increase in members of the Firmicutes and a decrease in members of the Bacteroidetes [50]. These results were in concordance with the data from a mouse study, demonstrating that a high-fat diet determines the composition of the gut microbiota [51]. These animal studies show that obesity has been associated with a decrease in members of the Bacteroidetes and an increase in members of the Firmicutes. However, human studies have shown contradictory results concerning the ratio between members of the Bacteroidetes and Firmicutes between obese individuals in comparison with their lean controls [52–54]. However, a meta-analysis showed that decreases in members of both the Firmicutes and Bifidobacteria are consistently associated with the human obese phenotype, but an altered Bacteroidetes concentration is not [12]. Interestingly, within the genus Lactobacillus, the increase in Lactobacillus reuteri has been found to be linearly associated with an increase in body mass index [55], whereas other species within the same genus, such as Lactobacillus gasseri and Lactobacillus plantarum, have been associated with a lean phenotype [56]. Nevertheless, it has been hypothesized that the gut microbiota associated with an obese phenotype of the host is able to harvest more energy-rich molecules, especially SCFAs, derived from resistant starch than the microbiota of lean individuals [54]. These molecules provide the host with an additional amount of energy, because some SCFAs can enter the citric acid cycle after few modifications, or they can be used for gluconeogenesis, liponeogenesis, and proteogenesis [54,57–59]. One human study focusing solely on type 2 diabetes found that affected individuals have a reduction in members of the Firmicutes and an increase in members of the Bacteroidetes in
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their gut microbiota in comparison with healthy controls. Furthermore, the Bacteroidetes to Firmicutes ratio was positively correlated with reduced glucose tolerance [60]. The observation that obese individuals, whether or not they have type 2 diabetes, have an altered gut microbiota in comparison with control individuals resulted in the hypothesis that FMT could be used as a treatment against metabolic disorders. The most viable route for administering human gut microbiota against metabolic disorders such as type 2 diabetes would be the nasoduodenal route, because carbohydrate and fatty acid uptake, which is crucial for the development of obesity and insulin resistance, occurs primarily within the small intestine. We were the first group to perform a randomized study in humans to evaluate the effect on insulin sensitivity of nasoduodenal FMT with microbiota derived from lean donors in patients with metabolic syndrome [61]. Patients who received microbiota from lean donors had an increase in peripheral insulin sensitivity 6 weeks after FMT in comparison with peripheral insulin sensitivity prior to FMT. Also, an increase in gut microbiota diversity was observed after FMT. Additionally, the total bacterial abundance in small-intestine biopsy samples showed no differences following FMT; however, there was an increase in the amount of the butyrate producer Eubacterium hallii. This increase may have contributed to the increased insulin sensitivity, as butyrate stimulates energy metabolism and prevents insulin resistance [62]. Within this field, another comparable randomized clinical study from a different research group is registered at present (www.clinicaltrials.gov) [63]. Interestingly, in another study [64], treatment with vancomycin was demonstrated to result in impaired peripheral insulin sensitivity in obese subjects with metabolic syndrome, and decreased diversity of the gut microbiota. Members of the phylum Firmicutes were the most affected; some Firmicutes taxa increased and others decreased in abundance after FMT. However, no changes in peripheral insulin sensitivity or in gut microbiota composition were observed after exposure to amoxycillin.
Multiresistant and Pathogenic Microorganisms in the Gastrointestinal Tract The increase in antimicrobial resistance is a major public health problem [65]. The greatest driving force behind antimicrobial resistance is long-term exposure to antibiotics. Therefore, it is not surprising that patients with the greatest risk for acquisition of multiresistant microorganisms, such as extended-spectrum b-lactamase (ESBL) producers and vancomycin-resistant Enterococcus (VRE), are those with high levels
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of comorbidity, including malignancy, the use of immunosuppression, and intensive-care unit admission [66–68]. Systemic antimicrobial therapy, which is mostly given to treat infection outside the gastrointestinal tract, also has its impact on the gut microbiota. It is hypothesized that a healthy heterogeneous gut microbiota is able to prevent the colonization of the host gastrointestinal tract by gut pathogens that may cause enteric diseases. This phenomenon is described as colonization resistance [69]. Exposure to antibiotics leads to the destruction of the healthy gut microbiota, and thereby selection of resistant strains that remain behind and proliferate. Not much research has been performed within this field of antimicrobial resistance and FMT in humans. However, a few interesting animal studies have been published that have evaluated the interaction between the gut microbiota and gut pathogenic microorganisms. One study [70] has illustrated the association between the genetic profile and the gut microbiota between two strains of mice that have different gut microbiota. In this study, the transfer of Citrobacter rodentium (C. rodentium), which is used as a rodent model for human enteropathogenic and enterohaemorrhagic Escherichia coli (E. coli), was evaluated. In NIH Swiss mice, C. rodentium infection is mild and self-limiting, whereas in C3H/HeJ mice, C. rodentium infection was often lethal [71]. Transplantation of the microbiota of NIH Swiss mice to C3H/HeJ mice prior to C. rodentium infection resulted in delayed pathogen colonization and delayed mortality of C3H/HeJ mice [70]. Another research group demonstrated in mice that FMT with microbiota containing Barnesiella species belonging the phylum Bacteroidetes was able to decolonize the recipient from VRE [72]. This study was conducted with mice bearing VRE in their gastrointestinal tract that orally received gut microbiota derived from VRE-negative mice. Within 7 days after FMT, there was a reduction in faeces VRE density, and after 15 days VRE was undetectable. The VRE clearance was enhanced in mice who were recolonized by Barnesiella species after FMT. Additionally, this group performed a study in humans, and prospectively collected and compared faeces samples of patients undergoing haemopoetic stem cell transplantation; they found that patients who did not acquire VRE had higher levels of Barnesiella species in their faeces samples than those who did. These data support the postulate that, besides microbiota diversity, the composition of the microbiota is also important in maintaining colonization resistance. In the future, it would be interesting to investigate whether human FMT with faeces derived from a healthy individual could be used against large-intestine colonization by VRE and other multiresistant microorganisms. Within our department, we are currently performing studies on the feasibility of using FMT against gastrointestinal
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colonization by resistant microorganisms such as ESBL producers. As result of this, we recently published the first case report [73] of a patient in whom we decolonized the large intestine from ESBL-producing E. coli with FMT. Despite this being only a single case, it indicates that FMT might be effective against multiresistant microorganisms residing in the large intestine, and therefore opens a new research field for the implementation of FMT. However, to justify the standard use of FMT against large-intestine colonization by multiresistant microorganisms, further larger controlled studies are needed to demonstrate the efficacy of FMT. Despite the limited available data, we are convinced that FMT could be effective for decolonization of the large intestine from enteropathogenic or multiresistant microorganisms, because various species within the phyla Bacteroidetes, Firmicutes and Actinobacteria confer direct and indirect colonization resistance, not only against C. difficile, but also against VRE, E. coli, Salmonella species and Shigella species, by producing antimicrobial substances and through modulation of the host immune response [74]. Therefore, introducing a diverse gut microbiota into a perturbed microbial environment could restore gut microbiota diversity and subsequently result in increased colonization resistance.
Conclusion Advances in molecular techniques have given additional insights in the many functions of the gut microbiota and its interaction with the host, and have also revealed that many diseases seem to have a certain association with the gut microbiota to a greater or lesser extent (Table 1). Altering the TABLE 1. Summary of the gut microbiota alterations associated with inflammatory bowel disease, irritable bowel syndrome, and metabolic disorders (obesity and type 2 diabetes) Disorder Inflammatory bowel disease
Irritable bowel disease
Obesity
Type 2 diabetes
Alterations within the gut microbiota Diversity ↓ Firmicutes and Bacteroidetes ↓ Faecalibacterium prausnitzii ↓ SCFAs ↓ Diversity ↓ Bifidobacteria ↓ Altered amounts of lactobacilli Altered carbohydrate and protein metabolism within the gut Production of acids and visceral nociceptive gases ↑ Bifidobacteria ↓ Firmicutes ↓ Lactobacillus reuteri ↑ Harvesting of SCFAs by the host ↑ Firmicutes ↓ Bacteroidetes ↑
SCFA, short-chain fatty acid.
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gut microbiota composition by FMT performed with the gut microbiota derived from a healthy individual can be a novel intervention for some diseases. At present, FMT has only been shown to be effective against C. difficile infection. Research is still ongoing in the field of IBD, IBS and type 2 diabetes in humans. Even less is known about the possible therapeutic role of FMT in the eradication of pathogenic and multiresistant enteric microorganisms in the large intestine of humans. Within this field, further research has still to be performed.
Transparency Declaration The authors declare no conflicts of interest.
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57. Wolever TM, Spadafora P, Eshuis H. Interaction between colonic acetate and propionate in humans. Am J Clin Nutr 1991; 53: 681–687. 58. Vernay M. Origin and utilization of volatile fatty acids and lactate in the rabbit: influence of the faecal excretion pattern. Br J Nutr 1987; 57: 371–381. 59. Masoro EJ, Porter E. Propionic acid as a precursor in the biosynthesis of animal fatty acids. J Lipid Res 1961; 2: 177–181. 60. Larsen N, Vogensen FK, van den Berg FW et al. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 2010; 5: e9085. 61. Vrieze A, Van Nood E, Holleman F et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 2012; 143: 913–916. 62. Gao Z, Yin J, Zhang J et al. Butyrate improves insulin sensitivity and increases energy expenditure in mice. Diabetes 2009; 58: 1509–1517. 63. NCT02050607. Fecal microbiota transplantation for the treatment of metabolic syndrome. www.clinicaltrials.gov 2013. 64. Vrieze A, Out C, Fuentes S et al. Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity. J Hepatol 2014; 60: 824–831. 65. Goossens H, Ferech M, Vander Stichele R, Elseviers M. Outpatient antibiotic use in Europe and association with resistance: a cross-national database study. Lancet 2005; 365: 579–587. 66. Calfee DP. Methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci, and other Gram-positives in healthcare. Curr Opin Infect Dis 2012; 25: 385–394. 67. Graffunder EM, Preston KE, Evans AM, Venezia RA. Risk factors associated with extended-spectrum beta-lactamase-producing organisms at a tertiary care hospital. J Antimicrob Chemother 2005; 56: 139–145. 68. Reddy P, Malczynski M, Obias A et al. Screening for extended-spectrum beta-lactamase-producing Enterobacteriaceae among high-risk patients and rates of subsequent bacteremia. Clin Infect Dis 2007; 45: 846–852. 69. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature 2012; 489: 220–230. 70. Willing BP, Vacharaksa A, Croxen M, Thanachayanont T, Finlay BB. Altering host resistance to infections through microbial transplantation. PLoS One 2011; 6: e26988. 71. Vallance BA, Deng W, Jacobson K, Finlay BB. Host susceptibility to the attaching and effacing bacterial pathogen Citrobacter rodentium. Infect Immun 2003; 71: 3443–3453. 72. Ubeda C, Bucci V, Caballero S et al. Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization. Infect Immun 2013; 81: 965–973. 73. Singh R, van Nood E, Nieuwdorp M et al. Donor faeces infusion for eradication of extended-spectrum b-lactamase-producing Escherichia coli in a patient with end-stage renal disease. Clin Microbiol Infect 2014; [Epub ahead of print]. 74. Buffie CG, Pamer EG. Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol 2013; 13: 790–801.
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10.1111/1469-0691.12799
The potential beneficial role of faecal microbiota transplantation in diseases other than Clostridium difficile infection R. Singh1, M. Nieuwdorp2, I. J. M. ten Berge1, F. J. Bemelman1 and S. E. Geerlings3 1) Renal Transplant Unit, Division of Nephrology, 2) Division of Vascular Medicine and 3) Division of Infectious Diseases, Department of Internal Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
Abstract This review gives an outline of the indications for faecal microbiota transplantation (FMT) for diseases other than Clostridium difficile (C. difficile) infection. The remarkable efficacy of FMT against C. difficile infection has already been demonstrated. The use of FMT for other diseases, such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), and metabolic syndrome, is now being evaluated. The currently available data suggest that FMT might be beneficial for IBD (including ulcerative colitis and, to some extent, Crohn’s disease), IBS, and insulin resistance. Several randomized clinical trials are currently being performed, and data are eagerly awaited. A new field of research for the implementation of FMT is the eradication of pathogenic and multiresistant enteric microorganisms. A few animal studies have been performed within this field, but hardly any research data from human studies are available at present. Keywords: Faecal microbiota transplantation, inflammatory bowel disease, irritable bowel syndrome, multiresistant microorganisms, obesity, type 2 diabetes Article published online: 1 October 2014 Clin Microbiol Infect 2014; 20: 1119–1125
Corresponding author: R. Singh, Academic Medical Center, University of Amsterdam, Room number A3-273, PO Box 22660, 1100 DD Amsterdam, The Netherlands E-mail: [email protected]
multiresistant microorganisms. Also, the association between these diseases and the gut microbiota alterations will be described.
Introduction During the last few years, faecal microbiota transplantation (FMT) also known as donor faeces transplantation or faecal bacteriotherapy, has attracted increased attention. The majority of clinical experience with FMT has been gathered from the treatment of Clostridium difficile (C. difficile) infection. Many case reports, case series and meta-analyses [1,2] on this topic have been published. Furthermore, in a recently published randomized controlled trial, FMT against C. difficile infection was shown to give a cure rate of 90% [3]. Other indications for FMT as a treatment option have also been evaluated, but to different extents. In this review, we discuss and summarize indications for FMT apart from C. difficile infection, such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), obesity, type 2 diabetes, and colonization of the gastrointestinal tract by pathogenic and
The Human Gut Microbiota The human gut microbiota is the term used to describe the composition of the vast amount of microorganisms residing in the human gastrointestinal tract [4,5]. It has been estimated that there are ten times more bacterial cells than somatic cells in each human being, and that approximately 1.5–3 kg of the human body weight consists of bacteria, the majority of which reside in the gastrointestinal tract. The concentration of bacteria within the gastrointestinal tract is lowest in the stomach and increases rapidly throughout the course of the distal parts of the gastrointestinal tract, with the highest concentration being in the large intestine. The
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concentration of microorganisms in the faecal mass within the large intestine is estimated to be 1011–1012 CFU/g of faeces [6]; furthermore, it is estimated that approximately 55% of the solid faecal mass is actually bacterial mass [7]. The microbiota of a healthy individual shows a large diversity in its composition. There are seven main taxonomic divisions of the resident bacteria [4] (i.e. Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Verrucomicrobia, Cyanobacteria, and Actinobacteria). The majority of the microbiota consists of members of the Firmicutes and Bacteroidetes [4,8]. The composition of the gut microbiota is mainly dependent on the diet of the host [9–11]; however, there is evidence that age [12] is also a determinant. Many conditions, of which the use of antibiotics is the best-known example, are able to disrupt and alter the composition of the gut microbiota. The majority of the gut microbiota is located within the large intestine, and has various functions that are thought to be beneficial for the host. The most well-known function is the degradation of non-digestible food remnants (resistant starch) and the consequent production of certain vitamins such as vitamin K. As result of recent advances in molecular techniques, such as 16S ribosomal RNA sequencing-based methods and shotgun metagenome sequencing, it has become clear that the gut microbiota also has a variety of other functions in the field of host defence, energy metabolism, and immune system development [4]. From this, it follows that disruption or alteration in the composition of the gut microbiota may underlie various diseases, such as gastrointestinal infections, metabolic disorders, and IBDs.
IBD IBD consists primarily of Crohn’s disease (CD) and ulcerative colitis, and is characterized by chronic inflammation. Increasing evidence supports the association between the composition of the gut microbiota and IBD [4,13]. It has been shown that the gut microbiota of IBD patients is less diverse and has reduced amounts of members of the Firmicutes and Bacteroidetes as compared with the microbiota of healthy individuals [14]. More importantly, the differences observed in the gut microbiota of IBD patients, in comparison with the microbiota of healthy individuals, seems to be related to its immunomodulatory and nourishing functions. In comparison with healthy controls, IBD patients have decreased amounts of the short-chain fatty acid (SCFA) producers. Butyrate, propionate and acetate are SCFAs that are produced by bacteria as result of resistant starch fermentation. These three SCFAs are known to have anti-inflammatory properties [15,16]. The most
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mentioned bacterium associated with IBD is the butyrate producer Faecalibacterium prausnitzii (F. prausnitzii). Many studies have found that IBD patients have a reduced amount of this bacterium in their gut microbiota [17–20]. It has been shown in patients with CD that F. prausnitzii also has a direct anti-inflammatory effect by secreting metabolites that block nuclear factor-jB activation and prevent the production of interleukin-8 [20,21] (Fig. 1). Butyrate produced by F. prausnitzii not only has direct anti-inflammatory effects but also serves as a nutrient for the colonocytes [13,22], and thereby prevents gut mucosa atrophy [23] and colonocyte autophagy [24]. Indeed, a pilot non-randomized trial providing daily oral butyrate for 8 weeks to IBD (CD) patients showed beneficial effects on (endoscopic and clinical) remission rates as well as on markers of systemic inflammation [25]. The assumed relationship between the gut microbiota composition and IBD is that the altered gut microbiota in IBD patients has reduced anti-inflammatory properties and produces lower amounts of butyrate and other SCFAs. This may lead to increased concentrations of proinflammatory mediators in the gut and impaired intestinal barrier function, resulting in inflammation and increased gut permeability. Altogether, these data indicate that the loss of certain bacterial strains with specific immunomodulatory and mucosa-maintaining functions results in gut dysbiosis, which may, besides genetic factors of the host, contribute to the pathogenesis of IBD. This dysbiosis in the gut could be restored by introducing normal gut microbiota obtained from a healthy individual without IBD. FMT in humans, although in limited numbers, has also been evaluated as a treatment for IBD. No randomized controlled trials on this topic have been published yet, and outcomes of case series show conflicting results. In addition, two systematic reviews have addressed this subject [26,27]. The pooled data of one systematic review [26] showed that, after FMT, the majority of the patients had either reduction in the IBD symptoms (19/25, 76.0%), were able to cease their medication (13/17, 76.5%) within 6 weeks after FMT, or achieved complete remission (15/24, 62.5%). Reported side effects were not only abdominal tenderness, cramping, fever, and diarrhoea, but also an activation of CD requiring medication. Current evidence for the routine use of FMT against IBD is too weak to justify its use in clinical practice, because of the lack of data from properly designed randomized trials. However, at present, there are several clinical trials underway (www. clinicaltrials.gov), of which eight are randomized controlled trials [28–35]. In two of these trials [32,35], candidates of minor age are also eligible to participate, and one trial [34] is focusing solely on the paediatric IBD population.
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Luminal side F. prausnitzii Healthy gut microbiota Gut microbiota of a healthy individual with normal amount of F. prausnitzii and its an inflammatory metabolites. Sufficient butyrate is available to nourish the colonocytes and to prevent an inflammatory reac on.
Butyrate F. prausnitzii metabolite
Colonocyte
Butyrate and metabolites from F. prausnitzii prevent gut inflamma on by blocking NF κ-B and IL-8 secre on.
Luminal side IBD gut microbiota Reduced number of F. prausnitzii results in shortage of butyrate and other an inflammatory metabolites. This provokes gut inflamma on (mediated by NF κ-B and IL-8). In addi on, butyrate shortage causes mucosal atrophy.
Mucosa atrophy NF-κB
NF-κB
NF-κB
IL-8
Gut inflammaƟon FIG. 1. Alterations within the gut microbiota under healthy conditions and in inflammatory bowel disease (IBD). IL-8, interleukin-8; NF-jB, nuclear factor-jB.
IBS IBS is a non-inflammatory gastrointestinal disorder characterized by abdominal pain and altered bowel movements in which diarrhoea or constipation may dominate. Many studies have evaluated the gut microbiota composition of IBS patients. Patients with IBS have, in general, reduced variability of the gut microbiota in comparison with the healthy control group [36]. Moreover, one study [37] found that IBS patients had lower amounts of lactobacilli and lactate-utilizing bacteria, whereas the number of sulphate-reducing bacteria was increased. Additionally, in vitro starch fermentation analysis showed that the microbiota of IBS patients produced a lower amount of butyrate, but greater amounts of sulphides and hydrogen. It is likely that increased production of these gases could promote IBS symptoms, as H2S has a major role in visceral nociception [38]. In contrast to this, two other research groups found increased amounts of lactobacilli among the gut microbiota of IBS patients [39,40]. These differences in the amounts of lactobacilli might be the result of small numbers of participants in the studies, differences in geographical location, and the large symptom heterogeneity of IBS itself. However, a more consistent finding is the reduced amount of bifidobacteria in both the
duodenal microbiota [41] and faecal microbiota [37,39,41] of IBS patients in comparison with healthy controls. In addition to the changed microbiota, IBS patients not only have altered protein and carbohydrate energy metabolism within the gut [39], but also increased amounts of acetic and propionic acids, which are associated with both the severity of abdominal pain and bloating symptoms [40]. These data indicate that both the composition of the gut microbiota and its metabolic functions are altered in IBS patients. The authors of a recently published systematic review with a meta-analysis [42] reported that probiotics are effective treatments for IBS; however, which strain is the most beneficial remains unclear. As the faecal microbiota obtained from a healthy individual represents the most natural composition of the human gut microbiota, FMT might be more beneficial than administering one specific bacterial strain. Research in humans on the use of FMT against IBS has been performed in case series only. One case series on FMT within this patient group showed that 45 IBS patients with chronic constipation underwent FMT. A total of 60% obtained normalized defecation during a follow-up of 9–19 months [43]. At present, one randomized clinical trial [44] is registered (www.clinicaltrials.gov) that is evaluating FMT as a treatment option for IBS.
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Obesity and Type 2 Diabetes Obesity is a well-recognized public health problem in Western society, but is also becoming a growing problem in developing economies [45]. It is associated with many other morbidities, such as type 2 diabetes and cardiovascular diseases. The interaction between the gut microbiota and metabolism is quite complex, and an important question here is whether the microbiota composition associated with the obese phenotype is the result or the cause of obesity. Interesting animal studies have been performed to unravel this causality. For example, germ-free mice do not become obese and nor do they develop insulin resistance after exposure to a high-fat diet [46–48]. Furthermore, the transfer of gut microbiota from a conventionally raised mouse into a germ-free mouse results in an increase in body fat content and insulin resistance, despite reduced food intake [49]. Other animal studies have shown that the consumption of a Western diet, containing high amounts of fat and sugars, leads to a vast increase in members of the Firmicutes and a decrease in members of the Bacteroidetes [50]. These results were in concordance with the data from a mouse study, demonstrating that a high-fat diet determines the composition of the gut microbiota [51]. These animal studies show that obesity has been associated with a decrease in members of the Bacteroidetes and an increase in members of the Firmicutes. However, human studies have shown contradictory results concerning the ratio between members of the Bacteroidetes and Firmicutes between obese individuals in comparison with their lean controls [52–54]. However, a meta-analysis showed that decreases in members of both the Firmicutes and Bifidobacteria are consistently associated with the human obese phenotype, but an altered Bacteroidetes concentration is not [12]. Interestingly, within the genus Lactobacillus, the increase in Lactobacillus reuteri has been found to be linearly associated with an increase in body mass index [55], whereas other species within the same genus, such as Lactobacillus gasseri and Lactobacillus plantarum, have been associated with a lean phenotype [56]. Nevertheless, it has been hypothesized that the gut microbiota associated with an obese phenotype of the host is able to harvest more energy-rich molecules, especially SCFAs, derived from resistant starch than the microbiota of lean individuals [54]. These molecules provide the host with an additional amount of energy, because some SCFAs can enter the citric acid cycle after few modifications, or they can be used for gluconeogenesis, liponeogenesis, and proteogenesis [54,57–59]. One human study focusing solely on type 2 diabetes found that affected individuals have a reduction in members of the Firmicutes and an increase in members of the Bacteroidetes in
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their gut microbiota in comparison with healthy controls. Furthermore, the Bacteroidetes to Firmicutes ratio was positively correlated with reduced glucose tolerance [60]. The observation that obese individuals, whether or not they have type 2 diabetes, have an altered gut microbiota in comparison with control individuals resulted in the hypothesis that FMT could be used as a treatment against metabolic disorders. The most viable route for administering human gut microbiota against metabolic disorders such as type 2 diabetes would be the nasoduodenal route, because carbohydrate and fatty acid uptake, which is crucial for the development of obesity and insulin resistance, occurs primarily within the small intestine. We were the first group to perform a randomized study in humans to evaluate the effect on insulin sensitivity of nasoduodenal FMT with microbiota derived from lean donors in patients with metabolic syndrome [61]. Patients who received microbiota from lean donors had an increase in peripheral insulin sensitivity 6 weeks after FMT in comparison with peripheral insulin sensitivity prior to FMT. Also, an increase in gut microbiota diversity was observed after FMT. Additionally, the total bacterial abundance in small-intestine biopsy samples showed no differences following FMT; however, there was an increase in the amount of the butyrate producer Eubacterium hallii. This increase may have contributed to the increased insulin sensitivity, as butyrate stimulates energy metabolism and prevents insulin resistance [62]. Within this field, another comparable randomized clinical study from a different research group is registered at present (www.clinicaltrials.gov) [63]. Interestingly, in another study [64], treatment with vancomycin was demonstrated to result in impaired peripheral insulin sensitivity in obese subjects with metabolic syndrome, and decreased diversity of the gut microbiota. Members of the phylum Firmicutes were the most affected; some Firmicutes taxa increased and others decreased in abundance after FMT. However, no changes in peripheral insulin sensitivity or in gut microbiota composition were observed after exposure to amoxycillin.
Multiresistant and Pathogenic Microorganisms in the Gastrointestinal Tract The increase in antimicrobial resistance is a major public health problem [65]. The greatest driving force behind antimicrobial resistance is long-term exposure to antibiotics. Therefore, it is not surprising that patients with the greatest risk for acquisition of multiresistant microorganisms, such as extended-spectrum b-lactamase (ESBL) producers and vancomycin-resistant Enterococcus (VRE), are those with high levels
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of comorbidity, including malignancy, the use of immunosuppression, and intensive-care unit admission [66–68]. Systemic antimicrobial therapy, which is mostly given to treat infection outside the gastrointestinal tract, also has its impact on the gut microbiota. It is hypothesized that a healthy heterogeneous gut microbiota is able to prevent the colonization of the host gastrointestinal tract by gut pathogens that may cause enteric diseases. This phenomenon is described as colonization resistance [69]. Exposure to antibiotics leads to the destruction of the healthy gut microbiota, and thereby selection of resistant strains that remain behind and proliferate. Not much research has been performed within this field of antimicrobial resistance and FMT in humans. However, a few interesting animal studies have been published that have evaluated the interaction between the gut microbiota and gut pathogenic microorganisms. One study [70] has illustrated the association between the genetic profile and the gut microbiota between two strains of mice that have different gut microbiota. In this study, the transfer of Citrobacter rodentium (C. rodentium), which is used as a rodent model for human enteropathogenic and enterohaemorrhagic Escherichia coli (E. coli), was evaluated. In NIH Swiss mice, C. rodentium infection is mild and self-limiting, whereas in C3H/HeJ mice, C. rodentium infection was often lethal [71]. Transplantation of the microbiota of NIH Swiss mice to C3H/HeJ mice prior to C. rodentium infection resulted in delayed pathogen colonization and delayed mortality of C3H/HeJ mice [70]. Another research group demonstrated in mice that FMT with microbiota containing Barnesiella species belonging the phylum Bacteroidetes was able to decolonize the recipient from VRE [72]. This study was conducted with mice bearing VRE in their gastrointestinal tract that orally received gut microbiota derived from VRE-negative mice. Within 7 days after FMT, there was a reduction in faeces VRE density, and after 15 days VRE was undetectable. The VRE clearance was enhanced in mice who were recolonized by Barnesiella species after FMT. Additionally, this group performed a study in humans, and prospectively collected and compared faeces samples of patients undergoing haemopoetic stem cell transplantation; they found that patients who did not acquire VRE had higher levels of Barnesiella species in their faeces samples than those who did. These data support the postulate that, besides microbiota diversity, the composition of the microbiota is also important in maintaining colonization resistance. In the future, it would be interesting to investigate whether human FMT with faeces derived from a healthy individual could be used against large-intestine colonization by VRE and other multiresistant microorganisms. Within our department, we are currently performing studies on the feasibility of using FMT against gastrointestinal
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colonization by resistant microorganisms such as ESBL producers. As result of this, we recently published the first case report [73] of a patient in whom we decolonized the large intestine from ESBL-producing E. coli with FMT. Despite this being only a single case, it indicates that FMT might be effective against multiresistant microorganisms residing in the large intestine, and therefore opens a new research field for the implementation of FMT. However, to justify the standard use of FMT against large-intestine colonization by multiresistant microorganisms, further larger controlled studies are needed to demonstrate the efficacy of FMT. Despite the limited available data, we are convinced that FMT could be effective for decolonization of the large intestine from enteropathogenic or multiresistant microorganisms, because various species within the phyla Bacteroidetes, Firmicutes and Actinobacteria confer direct and indirect colonization resistance, not only against C. difficile, but also against VRE, E. coli, Salmonella species and Shigella species, by producing antimicrobial substances and through modulation of the host immune response [74]. Therefore, introducing a diverse gut microbiota into a perturbed microbial environment could restore gut microbiota diversity and subsequently result in increased colonization resistance.
Conclusion Advances in molecular techniques have given additional insights in the many functions of the gut microbiota and its interaction with the host, and have also revealed that many diseases seem to have a certain association with the gut microbiota to a greater or lesser extent (Table 1). Altering the TABLE 1. Summary of the gut microbiota alterations associated with inflammatory bowel disease, irritable bowel syndrome, and metabolic disorders (obesity and type 2 diabetes) Disorder Inflammatory bowel disease
Irritable bowel disease
Obesity
Type 2 diabetes
Alterations within the gut microbiota Diversity ↓ Firmicutes and Bacteroidetes ↓ Faecalibacterium prausnitzii ↓ SCFAs ↓ Diversity ↓ Bifidobacteria ↓ Altered amounts of lactobacilli Altered carbohydrate and protein metabolism within the gut Production of acids and visceral nociceptive gases ↑ Bifidobacteria ↓ Firmicutes ↓ Lactobacillus reuteri ↑ Harvesting of SCFAs by the host ↑ Firmicutes ↓ Bacteroidetes ↑
SCFA, short-chain fatty acid.
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gut microbiota composition by FMT performed with the gut microbiota derived from a healthy individual can be a novel intervention for some diseases. At present, FMT has only been shown to be effective against C. difficile infection. Research is still ongoing in the field of IBD, IBS and type 2 diabetes in humans. Even less is known about the possible therapeutic role of FMT in the eradication of pathogenic and multiresistant enteric microorganisms in the large intestine of humans. Within this field, further research has still to be performed.
Transparency Declaration The authors declare no conflicts of interest.
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