Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog. 2012;8:e1002995. [PMID: 23133377 PMCID: PMC3486913 DOI: 10.1371/journal.ppat.1002995]

Emergence of collective territorial defense in bacterial communities: horizontal gene transfer can stabilize microbiomes

Multispecies bacterial communities such as the microbiota of the gastrointestinal tract can be remarkably stable and resilient even though they consist of cells and species that compete for resources and also produce a large number of antimicrobial agents. Computational modeling suggests that horizontal transfer of resistance genes may greatly contribute to the formation of stable and diverse communities capable of protecting themselves with a battery of antimicrobial agents while preserving a varied metabolic repertoire of the constituent species. In other words horizontal transfer of resistance genes makes a community compatible in terms of exoproducts and capable to maintain a varied and mature metagenome. The same property may allow microbiota to protect a host organism, or if used as a microbial therapy, to purge pathogens and restore a protective environment.

Isolation and gut microbiota modulation of antibiotic-resistant probiotics from human feces

Antibiotic-resistant probiotics may be advantageous for antibiotic-induced gut microbiota imbalance. In this article, we aimed to isolate antibiotic-resistant bacteria as potential probiotics. Feces from 3 healthy adults and 2 infants were used to isolate the antibiotic-resistant bacteria. Then we established gut microbiota imbalance mice model by antibiotics treatment and used it to assess the effect of the probiotics. Finally, we identified 8 isolates, and 6 of them were used as probiotics cocktail. Number of anaerobe, lactobacilli, and Bifidobacterium in feces were higher in the probiotic group (9.47±0.35 log10CFU/g, 8.74±0.18 log10CFU/g, 7.24±0.38 log10CFU/g, respectively) compared with model group (P<0.05). Richness and diversity index of probiotic group (19.79±0.29 and 2.95±0.06, respectively) were larger than model group (P<0.05). Diarrhea and mucosal edema had been alleviated during probiotic treatment. Our results validated that bacteriotherapy was available to treat gut microbiota imbalance.

Commensal bacteria mediated defenses against pathogens

Commensal bacterial communities residing within the intestinal lumen of mammals have evolved to flourish in this microenvironment. To preserve this niche, commensal bacteria act with the host to prevent colonization by invasive pathogens that induce inflammation and disrupt the intestinal niche commensal bacteria occupy. Thus, it is mutually beneficial to the host and commensal bacteria to inhibit a pathogen's ability to establish an infection. Commensal bacteria express factors that support colonization, maximize nutrient uptake, and produce metabolites that confer a survival advantage over pathogens. Further, commensal bacteria stimulate the host's immune defenses and drive tonic expression of anti-microbial factors. In combination, these mechanisms preserve the niche for commensal bacteria and assist the host in preventing infection.

Intestinal microbiota and the efficacy of fecal microbiota transplantation in gastrointestinal disease

Fecal microbiota transplantation (FMT) refers to the infusion of a fecal suspension from a healthy person into the gastrointestinal (GI) tract of another person to cure a specific disease. FMT is by no means a new therapeutic modality, although it was only relatively recently that stool was shown to be a biologically active, complex mixture of living organisms with great therapeutic potential for recurrent Clostridium difficile infection and perhaps other GI and non-GI disorders. The published revelations about the human microbiome are bringing the strength of science to clinical observation and enhancing the understanding of not only disease but also how much of a person's daily function and health depends on the microorganisms living in intimate relationship with each cell in the body.

Finding a sugary foothold: how antibiotics pave the way for enteric pathogens

Antibiotic therapy predisposes the host to infections with human enteropathogens. In a recent study, Ng et al. (2013) demonstrate that antibiotic-mediated disruption of the microbial food web gives rise to free microbiota-liberated monosaccharides in the gut, which can promote growth of enteropathogenic bacteria.

Clostridium difficile: biological therapies

PURPOSE OF REVIEW

Biological therapies for Clostridium difficile infection (CDI) include probiotics and faecal microbiota transplant (FMT). There is significant interest in their use in treating refractory/recurrent CDI. This review summarizes the latest evidence for these approaches.

RECENT FINDINGS

The small number of randomized controlled trials (RCTs) using probiotics in CDI have produced variable results; the most recent showed no benefit in preventing disease. However, several meta-analyses published in the last year have suggested benefit in their use, but these conclusions are limited by the poor quality of many of the primary studies, and lack of standardization of the probiotic administered. In contrast, FMT appears highly effective for the treatment of CDI. In the only published RCT, the cure rate was 81%, which is close to the rate shown by meta-analyses of previous case series. The use of artificially produced bacterial mixtures in place of faecal samples is now under investigation.

SUMMARY

Biological therapies for CDI, especially FMT, will continue to attract attention. Further, large-scale RCTs are required to identify which patients are most likely to benefit from these therapies in the future.

Recent insights into Clostridium difficile pathogenesis

PURPOSE OF REVIEW

Clostridium difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea and pseudomembranous colitis in the healthcare setting. An emerging consensus suggests that CDI is caused by pathogenic toxin production, gut microbial dysbiosis and altered host inflammatory responses. The aim of this review is to summarize and highlight recent advances focused on CDI pathogenic mechanisms.

RECENT FINDINGS

Potential paradigm shifts relating to the mechanisms of toxin action and inhibition have recently been reported, with new insights into spore germination and surface protein function also gaining traction. Multiomic analysis of microbiome dysbiosis has identified important CDI-associated microbial community shifts that may form the basis of future targeted bacteriotherapy, and functional metabolite biomarkers that require further characterization. Classical innate and adaptive immunity against CDI is rapidly being delineated, with novel innate S-nitrosylation signals also being identified.

SUMMARY

Studies in patients and animal disease models are shedding new light on the critical roles of the microbiota, metabolome and host responses in primary and recurrent CDI. An improved understanding of the CDI disease pathogenesis will provide the basis for developing new therapies for treating disease and preventing recurrence.

Vaccination against Clostridium difficile using toxin fragments: Observations and analysis in animal models

Clostridium difficile is a major cause of antibiotic associated diarrhea. Recently, we have shown that effective protection can be mediated in hamsters through the inclusion of specific recombinant fragments from toxin A and B in a systemically delivered vaccine. Interestingly while neutralizing antibodies to the binding domains of both toxin A and B are moderately protective, enhanced survival is observed when fragments from the glucosyltransferase region of toxin B replace those from the binding domain of this toxin. In this addendum, we discuss additional information that has been derived from such vaccination studies. This includes observations on efficacy and cross-protection against different ribotypes mediated by these vaccines and the challenges that remain for a vaccine which prevents clinical symptoms but not colonization. The use and value of vaccination both in the prevention of infection and for treatment of disease relapse will be discussed.

Fecal microbiota transplantation: effectiveness, complexities, and lingering concerns

The mammalian colon is home to a microbial ecosystem that enhances resistance to infection, stimulates mucosal immune defenses, synthesizes essential vitamins, and promotes caloric uptake by hydrolyzing complex carbohydrates. The bacterial populations inhabiting the gut are complex and vary between different individuals. Clinical and experimental studies reveal that the colonic microbiota can enhance or ameliorate intestinal and systemic inflammatory diseases. Because of its potential to enhance resistance to infection and to reduce inflammatory diseases, targeted manipulation of microbial populations is a growing focus of investigation. The most dramatic manipulation of the intestinal microbiota involves fecal microbiota transplantation (FMT) from healthy donors to individuals with specific diseases. Remarkable clinical effectiveness of FMT has been demonstrated for recurrent Clostridium difficile infection and ongoing studies are investigating FMT for other diseases. Transplantation of complex microbial populations to recipients likely triggers mucosal immune responses that, depending on the microbiota composition and the recipient's genotype, could range from pro- to anti-inflammatory. The impact of FMT on the recipient immune system is complex and unpredictable. Ongoing discovery of commensal microbes and investigations of their impact on the host will lead to the development of new probiotic agents and microbial consortia that will eventually replace FMT.

Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection

Recurrent Clostridium difficile infection (CDI) can be effectively treated by infusion of a healthy donor faeces suspension. However, it is unclear what factors determine treatment efficacy. By using a phylogenetic microarray platform, we assessed composition, diversity and dynamics of faecal microbiota before, after and during follow-up of the transplantation from a healthy donor to different patients, to elucidate the mechanism of action of faecal infusion. Global composition and network analysis of the microbiota was performed in faecal samples from nine patients with recurrent CDI. Analyses were performed before and after duodenal donor faeces infusion, and during a follow-up of 10 weeks. The microbiota data were compared with that of the healthy donors. All patients successfully recovered. Their intestinal microbiota changed from a low-diversity diseased state, dominated by Proteobacteria and Bacilli, to a more diverse ecosystem resembling that of healthy donors, dominated by Bacteroidetes and Clostridium groups, including butyrate-producing bacteria. We identified specific multi-species networks and signature microbial groups that were either depleted or restored as a result of the treatment. The changes persisted over time. Comprehensive and deep analyses of the microbiota of patients before and after treatment exposed a therapeutic reset from a diseased state towards a healthy profile. The identification of microbial groups that constitute a niche for C. difficile overgrowth, as well as those driving the reinstallation of a healthy intestinal microbiota, could contribute to the development of biomarkers predicting recurrence and treatment outcome, identifying an optimal microbiota composition that could lead to targeted treatment strategies.

Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism

BACKGROUND

Clostridium difficile is an anaerobic, Gram-positive bacterium that can reside as a commensal within the intestinal microbiota of healthy individuals or cause life-threatening antibiotic-associated diarrhea in immunocompromised hosts. C. difficile can also form highly resistant spores that are excreted facilitating host-to-host transmission. The C. difficile spo0A gene encodes a highly conserved transcriptional regulator of sporulation that is required for relapsing disease and transmission in mice.

RESULTS

Here we describe a genome-wide approach using a combined transcriptomic and proteomic analysis to identify Spo0A regulated genes. Our results validate Spo0A as a positive regulator of putative and novel sporulation genes as well as components of the mature spore proteome. We also show that Spo0A regulates a number of virulence-associated factors such as flagella and metabolic pathways including glucose fermentation leading to butyrate production.

CONCLUSIONS

The C. difficile spo0A gene is a global transcriptional regulator that controls diverse sporulation, virulence and metabolic phenotypes coordinating pathogen adaptation to a wide range of host interactions. Additionally, the rich breadth of functional data allowed us to significantly update the annotation of the C. difficile 630 reference genome which will facilitate basic and applied research on this emerging pathogen.

Spore formation and toxin production in Clostridium difficile biofilms

The ability to grow as a biofilm can facilitate survival of bacteria in the environment and promote infection. To better characterize biofilm formation in the pathogen Clostridium difficile, we established a colony biofilm culture method for this organism on a polycarbonate filter, and analyzed the matrix and the cells in biofilms from a variety of clinical isolates over several days of biofilm culture. We found that biofilms readily formed in all strains analyzed, and that spores were abundant within about 6 days. We also found that extracellular DNA (eDNA), polysaccharide and protein was readily detected in the matrix of all strains, including the major toxins A and/or B, in toxigenic strains. All the strains we analyzed formed spores. Apart from strains 630 and VPI10463, which sporulated in the biofilm at relatively low frequencies, the frequencies of biofilm sporulation varied between 46 and 65%, suggesting that variations in sporulation levels among strains is unlikely to be a major factor in variation in the severity of disease. Spores in biofilms also had reduced germination efficiency compared to spores obtained by a conventional sporulation protocol. Transmission electron microscopy revealed that in 3 day-old biofilms, the outermost structure of the spore is a lightly staining coat. However, after 6 days, material that resembles cell debris in the matrix surrounds the spore, and darkly staining granules are closely associated with the spores surface. In 14 day-old biofilms, relatively few spores are surrounded by the apparent cell debris, and the surface-associated granules are present at higher density at the coat surface. Finally, we showed that biofilm cells possess 100-fold greater resistance to the antibiotic metronidazole then do cells cultured in liquid media. Taken together, our data suggest that C. difficile cells and spores in biofilms have specialized properties that may facilitate infection.

Small animal models for the study of Clostridium difficile disease pathogenesis

Clostridium difficile is the leading cause of bacterial antibiotic-associated diarrhoea in hospitals in the developed world. Despite this notoriety, the complex mechanisms employed by this pathogen to overcome innate host defences and induce fulminant disease are poorly understood. Various animal models have been used extensively for C. difficile research to study disease pathogenesis. Until recently, the most commonly used C. difficile disease model has utilised hamsters; however, mouse and pig models have now been developed that unravel different aspects of C. difficile pathology. This review summarises key aspects of the small animal models currently used in C. difficile studies with a specific focus on major differences between them. Furthermore, this review highlights the advantages and disadvantages of each model and illustrates that careful consideration is required when selecting models for use in C. difficile research.

Fecal microbiota transplantation for Clostridium difficile infection: benefits and barriers

PURPOSE OF REVIEW

The incidence and severity of Clostridium difficile infection (CDI) have increased worldwide in the past two decades. A principal function of the gut microbiota is to protect the intestine against colonization by exogenous pathogens. Increasingly, the gut microbiota have been shown to influence susceptibility to other genetic and environmentally acquired conditions. Transplantation of healthy donor fecal material in patients with CDI may re-establish the normal composition of the gut microbiota and has been shown to be effective in recurrent CDI. We intend to review the most recent data on fecal microbiota transplantation (FMT) and critically discuss potential advantages and handicaps of this new therapeutic approach.

RECENT FINDINGS

Evidence from case series and only one randomized clinical trial suggests that FMT is able to restore the wide diversity of microflora, improve C. difficile-related symptoms and prevent CDI recurrence.

SUMMARY

FMT is a promising treatment option for serious and recurrent CDI, and current evidence (although weak) demonstrates consistent and excellent efficacy in clinical outcomes. However, many questions should be answered before it may be recommended as routine standard treatment. Mechanisms of action need to be better understood. Long-term follow-up studies are needed to determine long-lasting effects (including the association with autoimmune diseases).

Microbial and metabolic interactions between the gastrointestinal tract and Clostridium difficile infection

Antibiotics disturb the gastrointestinal tract microbiota and in turn reduce colonization resistance against Clostridium difficile. The mechanism for this loss of colonization resistance is still unknown but likely reflects structural (microbial) and functional (metabolic) changes to the gastrointestinal tract. Members of the gut microbial community shape intestinal metabolism that provides nutrients and ultimately supports host immunity. This review will discuss how antibiotics alter the structure of the gut microbiota and how this impacts bacterial metabolism in the gut. It will also explore the chemical requirements for C. difficile germination, growth, toxin production and sporulation. Many of the metabolites that influence C. difficile physiology are products of gut microbial metabolism including bile acids, carbohydrates and amino acids. To restore colonization resistance against C. difficile after antibiotics a targeted approach restoring both the structure and function of the gastrointestinal tract is needed.

Structural and functional changes in the gut microbiota associated to Clostridium difficile infection

Antibiotic therapy is a causative agent of severe disturbances in microbial communities. In healthy individuals, the gut microbiota prevents infection by harmful microorganisms through direct inhibition (releasing antimicrobial compounds), competition, or stimulation of the host's immune defenses. However, widespread antibiotic use has resulted in short- and long-term shifts in the gut microbiota structure, leading to a loss in colonization resistance in some cases. Consequently, some patients develop Clostridium difficile infection (CDI) after taking an antibiotic (AB) and, at present, this opportunistic pathogen is one of the main causes of antibiotic-associated diarrhea in hospitalized patients. Here, we analyze the composition and functional differences in the gut microbiota of C. difficile infected (CDI) vs. non-infected patients, both patient groups having been treated with AB therapy. To do so we used 16S rRNA gene and metagenomic 454-based pyrosequencing approaches. Samples were taken before, during and after AB treatment and were checked for the presence of the pathogen. We performed different analyses and comparisons between infected (CD+) vs. non-infected (CD-) samples, allowing proposing putative candidate taxa and functions that might protect against C. difficile colonization. Most of these potentially protective taxa belonged to the Firmicutes phylum, mainly to the order Clostridiales, while some candidate protective functions were related to aromatic amino acid biosynthesis and stress response mechanisms. We also found that CDI patients showed, in general, lower diversity and richness than non-infected, as well as an overrepresentation of members of the families Bacteroidaceae, Enterococcaceae, Lactobacillaceae and Clostridium clusters XI and XIVa. Regarding metabolic functions, we detected higher abundance of genes involved in the transport and binding of carbohydrates, ions, and others compounds as a response to an antibiotic environment.

Therapeutic faecal microbiota transplantation: current status and future developments

PURPOSE OF REVIEW

Faecal microbiota transplantation (FMT) has undergone dramatic progression over the past year and continues to evolve as knowledge of the gastrointestinal microbiota (GiMb) develops. This review summarizes therapeutic advances in FMT, latest FMT therapies and presents the potential of FMT therapeutics in other gastrointestinal and extra-intestinal conditions.

RECENT FINDINGS

The GiMb is now known to have a central role in the pathogenesis of many diseases. The success of FMT in curing Clostridium difficile infection (CDI) is well established and preliminary findings in other gastrointestinal conditions are promising. Published data from over 500 CDI cases suggest that FMT is generally well tolerated with minimal side effects. The commercial potential of FMT is being explored with several products under development, including frozen GiMb extract, which has been shown highly effective in treating relapsing CDI. Such products will likely become more available in coming years and revolutionize the availability and method of delivery of GiMb.

SUMMARY

Recent literature unequivocally supports the use of FMT in treating relapsing CDI. Trials are underway to determine the therapeutic potential of FMT in other conditions, particularly inflammatory bowel disease. Therapeutic FMT is a dynamic field with new and emerging indications along with ongoing developments in optimal mode of administration.

Fecal Microbiota Transplantation for Clostridium difficile Infection: The Ochsner Experience

BACKGROUND

Clostridium difficile infection (CDI) accounts for 20%-30% of cases of antibiotic-associated diarrhea and is the most commonly recognized cause of infectious diarrhea in healthcare settings. The incidence of CDI is rising, while the effectiveness of antibiotics for treatment decreases with recurrent episodes. The use of fecal microbiota transplantation (FMT) for cure of CDI has been reported since 1958, and the worldwide cure rate is reported to be 93%. We report our experience with FMT for the treatment of CDI.

METHODS

We performed a retrospective chart review of patients undergoing FMT for CDI at Ochsner Clinic Foundation from August 2012 to November 2013. FMT was administered via colonoscopy for patients with recurrent or severe CDI. Stool donors were screened for infections in the majority of cases.

RESULTS

FMT was performed in 20 CDI patients. The 16 female and 4 male patients ranged in age from 27 to 89 years (mean 62 years). The average duration of illness from diagnosis to treatment was 49.6 weeks, based on available data. Only 3 donors were unscreened for infectious pathogens. Nine donors were related to the recipients by blood; most of the other donors were spouses. The average length of follow-up after FMT was 3 months. No recurrences of CDI after treatment have been documented. Adverse events reported after treatment included abdominal cramping, bloating, flatulence, and nausea that resolved.

CONCLUSION

Although the US Food and Drug Administration currently considers FMT an experimental therapy, we demonstrate that FMT is safe, well tolerated, and effective for recurrent and severe CDI.

Interactions in the microbiome: communities of organisms and communities of genes

A central challenge in microbial community ecology is the delineation of appropriate units of biodiversity, which can be taxonomic, phylogenetic, or functional in nature. The term 'community' is applied ambiguously; in some cases, the term refers simply to a set of observed entities, while in other cases, it requires that these entities interact with one another. Microorganisms can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings. Trait-based approaches offer a useful alternative, but many traits can be defined based on gene functions, metabolic modules, and genomic properties, and the optimal set of traits to choose is often not obvious. An analysis that considers taxon assignment and traits in concert may be ideal, with the strengths of each approach offsetting the weaknesses of the other. Individual genes also merit consideration as entities in an ecological analysis, with characteristics such as diversity, turnover, and interactions modeled using genes rather than organisms as entities. We identify some promising avenues of research that are likely to yield a deeper understanding of microbial communities that shift from observation-based questions of 'Who is there?' and 'What are they doing?' to the mechanistically driven question of 'How will they respond?'

Emerging insights on intestinal dysbiosis during bacterial infections

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Diverse enteric pathogens often induce significant perturbations to the microbiota or thrive during dysbiosis.

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Infection-associated dysbiosis is commonly characterized by decreased diversity and metabolic function.

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The dysbiotic microbiota may act as a pathogenic community to perpetuate host pathology.

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Pathogens can exploit dysbiosis for host colonization, genome evolution, and transmission.

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Bacteriotherapy represents a potential viable strategy to restore intestinal homeostasis.

Infection of the gastrointestinal tract is commonly linked to pathological imbalances of the resident microbiota, termed dysbiosis. In recent years, advanced high-throughput genomic approaches have allowed us to examine the microbiota in an unprecedented manner, revealing novel biological insights about infection-associated dysbiosis at the community and individual species levels. A dysbiotic microbiota is typically reduced in taxonomic diversity and metabolic function, and can harbour pathobionts that exacerbate intestinal inflammation or manifest systemic disease. Dysbiosis can also promote pathogen genome evolution, while allowing the pathogens to persist at high density and transmit to new hosts. A deeper understanding of bacterial pathogenicity in the context of the intestinal microbiota should unveil new approaches for developing diagnostics and therapies for enteropathogens.

Emerging roles of the microbiome in cancer

Gene-environment interactions underlie cancer susceptibility and progression. Yet, we still have limited knowledge of which environmental factors are important and how they function during tumorigenesis. In this respect, the microbial communities that inhabit our gastrointestinal tract and other body sites have been unappreciated until recently. However, our microbiota are environmental factors that we are exposed to continuously, and human microbiome studies have revealed significant differences in the relative abundance of certain microbes in cancer cases compared with controls. To characterize the function of microbiota in carcinogenesis, mouse models of cancer have been treated with antibiotics. They have also been maintained in a germfree state or have been colonized with specific bacteria in specialized (gnotobiotic) facilities. These studies demonstrate that microbiota can increase or decrease cancer susceptibility and progression by diverse mechanisms such as by modulating inflammation, influencing the genomic stability of host cells and producing metabolites that function as histone deacetylase inhibitors to epigenetically regulate host gene expression. One might consider microbiota as tractable environmental factors because they are highly quantifiable and relatively stable within an individual compared with our exposures to external agents. At the same time, however, diet can modulate the composition of microbial communities within our gut, and this supports the idea that probiotics and prebiotics can be effective chemoprevention strategies. The trajectory of where the current work is headed suggests that microbiota will continue to provide insight into the basic mechanisms of carcinogenesis and that microbiota will also become targets for therapeutic intervention.

The microbiome in inflammatory bowel disease and beyond

The diverse and complex community of microorganisms that has co-evolved with the human gut is vital to intestinal functioning, and disturbances in the microbiota and its relationship with the host immune system have been linked to inflammatory bowel diseases, including Crohn's disease and ulcerative colitis. This has suggested several treatment options, including antibiotics, probiotics and faecal transplantation. The human microbiome project has been established to enable comprehensive characterisation of the human microbiota and in the coming years, knowledge in this area is expected to continue to expand.

Murine models to study Clostridium difficile infection and transmission

Clostridium difficile is the leading cause of antibiotic-associated diarrhea in healthcare facilities worldwide. C. difficile infections are difficult to treat because of the high rate of disease recurrence after antibiotic therapy, leaving few treatment options for patients. C. difficile is also difficult to contain within a healthcare setting due to a highly-transmissible, resistant spore form that challenges standard infection control measures. The recent development of murine infection models to study the interactions between C. difficile, the host and the microbiota are providing novel insight into the mechanisms of pathogenesis and transmission that should guide the development of therapies and intervention measures.

Microbiota dynamics in patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection

Clostridium difficile causes antibiotic-associated diarrhea and pseudomembraneous colitis and is responsible for a large and increasing fraction of hospital-acquired infections. Fecal microbiota transplantation (FMT) is an alternate treatment option for recurrent C. difficile infection (RCDI) refractory to antibiotic therapy. It has recently been discussed favorably in the clinical and scientific communities and is receiving increasing public attention. However, short- and long-term health consequences of FMT remain a concern, as the effects of the transplanted microbiota on the patient remain unknown. To shed light on microbial events associated with RCDI and treatment by FMT, we performed fecal microbiota analysis by 16S rRNA gene amplicon pyrosequencing of 14 pairs of healthy donors and RCDI patients treated successfully by FMT. Post-FMT patient and healthy donor samples collected up to one year after FMT were studied longitudinally, including one post-FMT patient with antibiotic-associated relapse three months after FMT. This analysis allowed us not only to confirm prior reports that RCDI is associated with reduced diversity and compositional changes in the fecal microbiota, but also to characterize previously undocumented post-FMT microbiota dynamics. Members of the Streptococcaceae, Enterococcaceae, or Enterobacteriaceae were significantly increased and putative butyrate producers, such as Lachnospiraceae and Ruminococcaceae were significantly reduced in samples from RCDI patients before FMT as compared to post-FMT patient and healthy donor samples. RCDI patient samples showed more case-specific variations than post-FMT patient and healthy donor samples. However, none of the bacterial groups were invariably associated with RCDI or successful treatment by FMT. Overall microbiota compositions in post-FMT patients, specifically abundances of the above-mentioned Firmicutes, continued to change for at least 16 weeks after FMT, suggesting that full microbiota recovery from RCDI may take much longer than expected based on the disappearance of diarrheal symptoms immediately after FMT.

Prospects and challenges for intestinal microbiome therapy in pediatric gastrointestinal disorders

Fecal microbiome (microbiota) transplantation is an emerging treatment not only for refractory/recurrent Clostridium difficile infections and chronic gastrointestinal diseases, but also for metabolic syndrome, and even possibly for neurological disorders. This non-conventional therapy has been perhaps more appropriately designated as fecal bacteriotherapy (FB) as well. The employment of FB is spreading into pediatric gastroenterology. This focused review highlights the pediatric applications of FB and discusses hypotheses for its mechanism of action. We propose that intestinal microbiome therapy may be a more appropriate term for FB, which integrates its potential future applications.

Bile salt inhibition of host cell damage by Clostridium difficile toxins

Virulent Clostridium difficile strains produce toxin A and/or toxin B that are the etiological agents of diarrhea and pseudomembranous colitis. Treatment of C. difficile infections (CDI) has been hampered by resistance to multiple antibiotics, sporulation, emergence of strains with increased virulence, recurrence of the infection, and the lack of drugs that preserve or restore the colonic bacterial flora. As a result, there is new interest in non-antibiotic CDI treatments. The human conjugated bile salt taurocholate was previously shown in our laboratory to inhibit C. difficile toxin A and B activities in an in vitro assay. Here we demonstrate for the first time in an ex vivo assay that taurocholate can protect Caco-2 colonic epithelial cells from the damaging effects of the C. difficile toxins. Using caspase-3 and lactate dehydrogenase assays, we have demonstrated that taurocholate reduced the extent of toxin B-induced apoptosis and cell membrane damage. Confluent Caco-2 cells cultured with toxin B induced elevated caspase-3 activity. Remarkably, addition of 5 mM taurocholate reduced caspase-3 activity in cells treated with 2, 4, 6, and 12 µg/ml of toxin B by 99%, 78%, 64%, and 60%, respectively. Furthermore, spent culture medium from Caco-2 cells incubated with both toxin B and taurocholate exhibited significantly decreased lactate dehydrogenase activity compared to spent culture medium from cells incubated with toxin B only. Our results suggest that the mechanism of taurocholate-mediated inhibition functions at the level of toxin activity since taurocholate did not affect C. difficile growth and toxin production. These findings open up a new avenue for the development of non-antibiotic therapeutics for CDI treatment.

Microbiota-mediated colonization resistance against intestinal pathogens

Commensal bacteria inhabit mucosal and epidermal surfaces in mice and humans, and have effects on metabolic and immune pathways in their hosts. Recent studies indicate that the commensal microbiota can be manipulated to prevent and even to cure infections that are caused by pathogenic bacteria, particularly pathogens that are broadly resistant to antibiotics, such as vancomycin-resistant Enterococcus faecium, Gram-negative Enterobacteriaceae and Clostridium difficile. In this Review, we discuss how immune- mediated colonization resistance against antibiotic-resistant intestinal pathogens is influenced by the composition of the commensal microbiota. We also review recent advances characterizing the ability of different commensal bacterial families, genera and species to restore colonization resistance to intestinal pathogens in antibiotic-treated hosts.

Faecal microbiota transplantation for the treatment of recurrent Clostridium difficile infection: current promise and future needs

PURPOSE OF REVIEW

The use of faecal microbiota transplantation (FMT) as treatment for recurrent Clostridium difficile infection (CDI) has increased rapidly over the past few years. In this review, we highlight clinical studies of FMT for treatment of recurrent CDI and discuss the safety, standardization and future of this treatment option. The major risk factor for CDI is prior antibiotic use, which results in an altered state of the gut microbiota characterized by decreased microbial diversity. This altered gut microbiota increases the patient's susceptibility to CDI. In patients with recurrent CDI, the microbiota remains in a state with decreased diversity, and FMT from a healthy individual restores the gut microbiota and subsequently colonization resistance against the pathogen.

RECENT FINDINGS

Recent studies have shown the success rate for FMT as treatment for recurrent CDI being greater than 90%. Standardized, frozen preparations of faeces can be used, which increases the availability of faeces for FMT and decreases the cost of screening individual donors. In addition, there have been recent advances in identifying a defined microbial community isolated from faeces that can restore colonization resistance against C. difficile.

SUMMARY

The use of FMT is a successful treatment for recurrent CDI when primary treatment options have failed. However, more work needs to define potential long-term consequences of this treatment and understand how specific members of the gut microbiota can restore colonization resistance against C. difficile.

Understanding and modulating mammalian-microbial communication for improved human health

The fact that the bacteria in the human gastrointestinal (GI) tract play a symbiotic role was noted as early as 1885, well before we began to manage microbial infections using antibiotics. However, even with the first antimicrobial compounds used in humans, the sulfa drugs, microbes were recognized to be critically involved in the biotransformation of these therapeutics. Thus, the roles played by the microbiota in physiology and in the management of human health have long been appreciated. Detailed examinations of GI symbiotic bacteria that started in the early 2000s and the first phases of the Human Microbiome Project that were completed in 2012 have ushered in an exciting period of granularity with respect to the ecology, genetics, and chemistry of the mammalian-microbial axes of communication. Here we review aspects of the biochemical pathways at play between commensal GI bacteria and several mammalian systems, including both local-epithelia and nonlocal responses impacting inflammation, immunology, metabolism, and neurobiology. Finally, we discuss how the microbial biotransformation of therapeutic compounds, such as anticancer or nonsteroidal anti-inflammatory drugs, can be modulated to reduce toxicity and potentially improve therapeutic efficacy.

Understanding and modulating mammalian-microbial communication for improved human health

The molecular basis for the regulation of the intestinal barrier is a very fertile research area. A growing body of knowledge supports the targeting of various components of intestinal barrier function as means to treat a variety of diseases, including the inflammatory bowel diseases. Herein, we will summarize the current state of knowledge of key xenobiotic receptor regulators of barrier function, highlighting recent advances, such that the field and its future are succinctly reviewed. We posit that these receptors confer an additional dimension of host-microbe interaction in the gut, by sensing and responding to metabolites released from the symbiotic microbiota, in innate immunity and also in host drug metabolism. The scientific evidence for involvement of the receptors and its molecular basis for the control of barrier function and innate immunity regulation would serve as a rationale towards development of non-toxic probes and ligands as drugs.

Colonization resistance against genetically modified Escherichia coli K12 (W3110) strains is abrogated following broad-spectrum antibiotic treatment and acute ileitis

Escherichia coli K12 (EcK12) is commonly used for gene technology purposes and regarded as a security strain due to its inability to adhere to epithelial cells. The conventional intestinal microbiota composition is critical for physiological colonization resistance against most bacterial species including pathogens. We were therefore interested whether intestinal colonization by a genetically modified EcK12 (W3110) strain carrying a chloramphenicol resistance cassette was facilitated following broad-spectrum antibiotic treatment eradicating the intestinal microbiota or induction of small intestinal inflammation accompanied by distinct microbiota shifts. Whereas conventional C57BL/6 and BALB/c mice had virtually expelled the EcK12 (W3110) strain within the first 3 days upon peroral infection, EcK12 (W3110) could establish within the small and large intestines of gnotobiotic mice generated by quintuple antibiotic treatment. Gnotobiotic mice perorally infected with EcK12 (W3110) plus fecal transplant from conventional donors harbored lower intestinal EcK12 (W3110) loads compared to animals challenged with EcK12 (W3110) alone. Furthermore, EcK12 (W3110) infection of conventional mice after but not before induction of ileitis resulted in stable colonization of ileum and colon by EcK12 (W3110). Taken together, broad-spectrum antibiotic treatment and intestinal inflammation compromise colonization resistance and thus facilitate colonization of the intestinal tract with genetically modified EcK12 security strains.

Therapy of Clostridium difficile infection: perspectives on a changing paradigm

INTRODUCTION

Clostridium difficile disease (CDI) have increased in frequency and severity over the past decade and are a leading cause of hospital acquired infections, contributing to increased hospital length of stay and costs, as well as associated increased mortality, especially amongst the elderly. Standard therapy has been associated with 20 - 30% relapse rates. Consequently, new CDI therapeutic approaches have emerged.

AREAS COVERED

The role of metronidazole, vancomycin, fidaxomicin, rifaximin, nitizoxanide, tigecycline, fusidic acid, LFF-571, cardazolid, SMT 19969, CamSA and surotomycin were reviewed.

EXPERT OPINION

New IDSA/SHEA guidelines are expected within the next year and may impact selection of primary therapy for CDI. Until then, metronidazole will likely remain as first line therapy because of low cost and despite its inferiority compared to vancomycin. Vancomycin will likely see increasing use, especially as generics become available. Fidaxomicin will emerge as an important therapy for relapse patients and perhaps as initial therapy for patients at greatest risk for relapse, with concomitant antibiotics, multiple comorbidities and renal insufficiency, advanced age and hypoalbuminemia. Biotherapeutics such as fecal microbiota transplantation and non-toxogenic C. difficile prevention will emerge as the preferred therapy in multiple relapse patients and the development of an oral formulation will occur within five years.

Muricholic acids inhibit Clostridium difficile spore germination and growth

Infections caused by Clostridium difficile have increased steadily over the past several years. While studies on C. difficile virulence and physiology have been hindered, in the past, by lack of genetic approaches and suitable animal models, newly developed technologies and animal models allow these processes to be studied in detail. One such advance is the generation of a mouse-model of C. difficile infection. The development of this system is a major step forward in analyzing the genetic requirements for colonization and infection. While important, it is equally as important in understanding what differences exist between mice and humans. One of these differences is the natural bile acid composition. Bile acid-mediated spore germination is an important step in C. difficile colonization. Mice produce several different bile acids that are not found in humans. These muricholic acids have the potential to impact C. difficile spore germination. Here we find that the three muricholic acids (α-muricholic acid, β-muricholic acid and ω-muricholic acid) inhibit C. difficile spore germination and can impact the growth of vegetative cells. These results highlight an important difference between humans and mice and may have an impact on C. difficile virulence in the mouse-model of C. difficile infection.

New concepts in diagnostics for infectious diarrhea

Conventional approaches to the diagnosis of infectious diarrhea must include several modalities to detect an array of potential viruses, bacteria, and parasites. We will provide a general overview of the wide range of diagnostic modalities available for enteropathogens, briefly discuss some of the limitations of conventional methods, and then focus on new molecular methods, including real-time PCR and next-generation sequencing. In particular, we will discuss quantitation of pathogen load with these techniques. We will then describe examples whereby novel diagnostics may help illuminate the etiology of infectious diarrhea, where they may not, and how they may benefit studies of immunity to enteric infections.

Moving fecal microbiota transplantation into the mainstream

In recent years, fecal microbiota transplantation (aka fecal transplantation, fecal bacteriotherapy, FMT) has become increasing utilized to treat recurrent and refractory Clostridium difficile infection (CDI). Almost 600,000 cases of CDI occur each year in the United States. Of these, an estimated 15,000 patients have a recurrence. The management of recurrent disease has been challenging for patients and clinicians. Increasingly, FMT has been recognized as an effective option for these patients. This article explores why FMT has reemerged as a practical therapeutic modality. In the process, the logistics by which the procedure is performed and the factors that may affect quality, safety, and patient outcomes will be described.

Plasmacytoid dendritic cells are crucial in Bifidobacterium adolescentis-mediated inhibition of Yersinia enterocolitica infection

In industrialized countries bacterial intestinal infections are commonly caused by enteropathogenic Enterobacteriaceae. The interaction of the microbiota with the host immune system determines the adequacy of an appropriate response against pathogens. In this study we addressed whether the probiotic Bifidobacterium adolescentis is protective during intestinal Yersinia enterocolitica infection. Female C57BL/6 mice were fed with B. adolescentis, infected with Yersinia enterocolitica, or B. adolescentis fed and subsequently infected with Yersinia enterocolitica. B. adolescentis fed and Yersinia infected mice were protected from Yersinia infection as indicated by a significantly reduced weight loss and splenic Yersinia load when compared to Yersinia infected mice. Moreover, protection from infection was associated with increased intestinal plasmacytoid dendritic cell and regulatory T-cell frequencies. Plasmacytoid dendritic cell function was investigated using depletion experiments by injecting B. adolescentis fed, Yersinia infected C57BL/6 mice with anti-mouse PDCA-1 antibody, to deplete plasmacytoid dendritic cells, or respective isotype control. The B. adolescentis-mediated protection from Yersinia dissemination to the spleen was abrogated after plasmacytoid dendritic cell depletion indicating a crucial function for pDC in control of intestinal Yersinia infection. We suggest that feeding of B. adolescentis modulates the intestinal immune system in terms of increased plasmacytoid dendritic cell and regulatory T-cell frequencies, which might account for the B. adolescentis-mediated protection from Yersinia enterocolitica infection.

Fecal microbiota transplantation: indications, methods, evidence, and future directions

Fecal microbiota transplantation (FMT) has attracted great interest in recent years, largely due to the global Clostridium difficile infection (CDI) epidemic and major advances in metagenomic sequencing of the gastrointestinal (GI) microbiota, with growing understanding of its structure and function. FMT is now recommended as the most effective therapy for relapsing CDI and, with further refinement, may even be used in "first-time" CDI. There is interest also in other conditions related to GI dysbiosis--for example, inflammatory bowel disease, irritable bowel syndrome, obesity, and diabetes mellitus--although quality evidence is at present lacking. A few trials are now underway in FMT for ulcerative colitis. Many unanswered questions remain, including FMT methodology--for example, optimal route of administration, what makes a "good donor," safety issues, and long-term effects of FMT.

The agr locus regulates virulence and colonization genes in Clostridium difficile 027

The transcriptional regulator AgrA, a member of the LytTR family of proteins, plays a key role in controlling gene expression in some Gram-positive pathogens, including Staphylococcus aureus and Enterococcus faecalis. AgrA is encoded by the agrACDB global regulatory locus, and orthologues are found within the genome of most Clostridium difficile isolates, including the epidemic lineage 027/BI/NAP1. Comparative RNA sequencing of the wild type and otherwise isogenic agrA null mutant derivatives of C. difficile R20291 revealed a network of approximately 75 differentially regulated transcripts at late exponential growth phase, including many genes associated with flagellar assembly and function, such as the major structural subunit, FliC. Other differentially regulated genes include several involved in bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) synthesis and toxin A expression. C. difficile 027 R20291 agrA mutant derivatives were poorly flagellated and exhibited reduced levels of colonization and relapses in the murine infection model. Thus, the agr locus likely plays a contributory role in the fitness and virulence potential of C. difficile strains in the 027/BI/NAP1 lineage.

The intestinal microbiota and susceptibility to infection in immunocompromised patients

PURPOSE OF REVIEW

Many infections of immunocompromised patients originate from the gastrointestinal tract. The pathogenesis of these infections often begins with alteration of the intestinal microbiota. Understanding the microbiota and how it can either cause or prevent infection is vital for the development of more effective prevention and treatment of these infections. This article reviews and discusses recent work providing insight into the intestinal microbiota of these at-risk immunocompromised patients.

RECENT FINDINGS

Studies continue to support the premise that commensal bacteria, largely anaerobic, serve to maintain microbial stability and colonization resistance by preventing overgrowth or domination with more pathogenic bacteria, through interactions within the microbial community and with the host. In patients with immune suppression due to high-dose chemotherapy or hematopoietic stem cell transplantation, disruption of the microbiota through antibiotics as well as impairment of host immunity gives rise to perturbations favoring intestinal domination by pathogenic species, leading to increased bacterial translocation and susceptibility to systemic infection.

SUMMARY

An understanding of the intestinal microbiota and the impact of antibiotics will help to guide our treatment of these gut-originating infections.