Microbial composition in patients with CC
A principal coordinate analysis (PCoA) scatter plot indicated that samples seemed to separate according to CC vs healthy controls, and the ANOSIM confirmed the statistical difference between the 2 groups. To explore the impact of potential confounders, PCoA plots and ANOSIM were assessed based on sex, age, and body mass index (BMI) among patients with CC and healthy controls (see Figure 2, Supplementary Digital Content, http://links.lww.com/CTG/A61). No separation was observed with respect to sex and age, but samples separated significantly when assessed based on BMI. However, no difference in BMI was observed between patients with CC and healthy controls (P = 0.88).
Based on the ANOSIM, we explored which taxa caused the observed differences between patients with CC and healthy controls. Patients with CC had a lower abundance of 11 different taxa (see Figures 3, Supplementary Digital Content, http://links.lww.com/CTG/A61) and displayed a consistent lower abundance of several OTUs belonging to the Ruminococcaceae family (Table 3). By contrast, a diverse pattern was observed for several other families, where the mean relative abundance was increased for some OTUs but decreased for other OTUs within the same family (Table 3).
Associations between fecal microbiota and clinical data in patients with CC
We then characterized the microbiome of patients with CC further by stratifying for disease activity and corticosteroid treatment when analyzing the taxa that were identified as associated with CC. Patients were categorized into two categories: patients in remission without corticosteroid therapy and patients with active disease or ongoing corticosteroid therapy.
The relative abundance of several taxa differed between the two groups (Figure 3). An association between active disease/ongoing corticosteroid therapy and a decreased relative abundance of Collinsella, unclassified Ruminococcaceae, unclassified Coriobacteriaceae, and unclassified Clostridiales was observed. Consistently, a decreased abundance of several OTUs corresponding to the Ruminococcaceae family was observed in patients with active disease/ongoing corticosteroid therapy but not in patients with CC in remission when taxa were compared at an OTU level (see Figures 4, Supplementary Digital Content, http://links.lww.com/CTG/A61).
Shared microbial signatures between patients with CD, UC, and CC
To explore the possible common microbial signatures, the microbial composition of patients with CC was compared with that of patients with CD and UC, restricting the analyses to taxa that separated patients with CC in remission from patients with active disease/ongoing corticosteroid treatment. Similar to the observed microbial shift in patients with CC, a decreased abundance of several OTUs corresponding to the Ruminococcaceae family was also found in patients with IBD. Of the 10 OTUs within the Ruminococcaceae family that were decreased in patients with active CC or corticosteroid treatment, 9 were also decreased in patients with CD and 4 in patients with UC (see Figure 5, Supplementary Digital Content, http://links.lww.com/CTG/A61).
By examining fecal samples from a well-characterized cohort of patients, we demonstrate that CC is associated with a specific gut microbiome and that this microbial shift is seen primarily in patients with active disease or ongoing corticosteroid treatment. By contrast, the fecal microbiome of patients with CC in remission resembled the microbiome of healthy controls. To our knowledge, this is the first detailed characterization of the microbiome of patients with CC which also identifies the possible common microbial shifts in patients with CC and IBD. Two descriptive reports on small series have been published previously (14,15). Consistent with our findings, Fischer et al. reported a marked reduction of Verrucomicrobia, Akkermansia spp., in 10 cases with CC. Interestingly, in our study, the patients with CC displayed a shift in some taxa, like the Ruminococcaceae family, which resembles the previously described IBD-associated dysbiosis (21,22). This could indicate that the microbiome plays a similar role in CC and IBD and that the pathogenesis of the diseases might have mechanisms related to the gut microbiome in common. The fact that we observed some of these microbial shifts in our cohort of patients with IBD strengthens this theory further.
Similar to the hypothesis in IBD, it has been proposed that microscopic colitis could result from an aberrant immune response to the commensal gut microbiome (9). This is supported by the observed clinical improvement and histologic restoration in patients with CC after fecal stream diversion due to an ileostomy. Intriguingly, clinic relapse is most often seen at subsequent restoration of intestinal continuity (4,5). An infectious etiology to CC has also been proposed. The epithelial lymphocytosis in microscopic colitis is similar to the histologic findings of “Brainerd diarrhea,” i.e., outbreaks of long-standing acute watery diarrhea (23). Similarly, the reported seasonal variation in the onset of microscopic colitis and possible positive effect of antibiotics might point to the importance of an infectious agent or a microbial component (24,25). In a recent case report on the effect of fecal transplantation, a conversion from UC to CC was observed in a patient who experienced a pronounced change in the gut microbiota due to the treatment (26). In another case report, a beneficial effect of fecal transplantation was reported in a patient with steroid-resistant CC (27). Based on these observations, we aimed to characterize the fecal microbiota of patients with CC comparing with that of healthy controls and to identify possible changes, in common with patients with CD and UC, using 16S rRNA sequencing. We could not show any significant difference in the overall microbial composition, based on the SDI when patients with CC or UC were compared with healthy controls. Consistent with previous studies (11,28,29), patients with CD had a significant lower diversity compared with healthy controls. However, overall diversity might be a too simplified measure of the gut microbiota. In UC, conflicting results with both indifferent and reduced biodiversity have been shown when comparing microbiota in patients with healthy controls (28,30,31). An increasing difference in microbial composition between patients with CC and healthy controls was also observed with the degree of taxonomic resolution, becoming significant when comparing OTUs in our cohort. When specific OTUs were compared between patients with CC and healthy controls, we observed a difference in mean relative abundance of 36 OTUs. For most of these OTUs, a complex pattern was observed when analyzing the data at a family level, with an increased relative abundance for some OTUs but a decreased relative abundance for other OTUs within the same family. However, with respect to the Ruminococcaceae family, a consistent decrease in several OTUs was observed.
The Ruminococcaceae family is a member of the Firmicutes phylum and comprises a broad spectrum of species with different functional properties. An underrepresentation of species belonging to the family has previously been reported in IBD, especially in CD (22,32). Several species within the Ruminococcaceae family, like Ruminococcus species, are of importance for the maintenance of gut homeostasis, because they produce short-chain fatty acids and primarily butyrate. Butyrate is an important energy substrate for the intestinal mucosa and of importance for intestinal health, resistance to pathogenic microbes, and protection against colitis (11,33,34). Both in vitro and in vivo data indicate that F. prausnitzii, another member of the Ruminococcaceae family, also seem to have anti-inflammatory properties (11,34,35).
To explore the role of the microbiome in CC further, we stratified patients with CC based on clinical variables, i.e., disease activity and corticosteroid treatment. Budesonide, a corticosteroid, is the drug of choice for treating CC, because it is effective in both inducing and maintaining remission (36). However, the relapse rate is high at dose reduction and after discontinuation (37). Therefore, many patients are kept at a minimal dose of corticosteroid to maintain remission. The patients with CC were divided into 2 categories; patients in remission without corticosteroid therapy and patients with active disease or ongoing corticosteroid therapy. For several taxa, a difference in relative abundance was observed in patients with active disease or ongoing corticosteroid treatment only, when compared with healthy controls. Thus, some taxa seem to be associated with disease activity, although our study design does not allow us to confirm causality. Several of the taxa that showed an association with disease activity or ongoing corticosteroid treatment belonged to the Ruminococcaceae family. However, a decreased relative abundance of Collinsella, Clostridiales, Coriobacteriaceae, and Erysipelotrichaceae was also observed in this subgroup of patients with CC.
Similar to the findings in patients with CC, a decreased abundance of several OTUs corresponding to the Ruminococcaceae family was also observed in patients with IBD. The shared microbial shift between CC and IBD is of great interest, because a shift from CC to IBD and vice versa has been reported in some patients (6,7). Thus, further characterization of virulence factors and gene expression profiles of taxa within the Ruminococcaceae family might be of importance to clarify the possible common microbial pathways of CC and IBD.
The thorough clinical characterization of the patients with CC is a major strength of our study, although clinical activity at acquisition of fecal samples was not confirmed by histologic assessment. Comparisons with patients with CD and UC and with healthy controls from the general population strengthen the results further. Even though our study included 122 individuals, the number of patients with CC in each subgroup was limited when stratifying for disease activity and corticosteroid medication. The comparisons of patients with CD and UC with healthy controls were hampered by differences in age and sex, because the matching was performed on the basis of age and sex of the patients with CC. A limitation with the present study was that, in common with many previous studies of the gut microbiome in relation to various diagnoses, samples were obtained at a single point in time. Analyses of sequential samples from patients with CC, including those which cover periods of remission, relapse, and changes in treatment, as well as matched samples obtained over time from healthy controls would be a more powerful design to reveal the influence of the microbiome in CC. The use of fecal samples is another possible limitation, because it can be anticipated that it is the mucosal microbiome that is most important in CC. Further research on mucosal biopsies should be undertaken to investigate host-microbiota interactions in patients with CC. Alterations in the gut microbiota secondary to induced diarrhea and functional diarrhea have previously been described. Some of the shifts in the gut microbiota composition that have been associated with bowel cleansing resemble the alterations that have been seen in IBD (22,38,39). By contrast, the gut microbiota in patients with irritable bowel syndrome with diarrhea has shown a different pattern. This indicates that diarrhea per se might have an impact on microbial composition and may represent a limitation for this study, even though the previous literature is inconsistent (40,41). Effects of retarded growth of certain species and overgrowth of other species due to environmental factors could have been minimized using a DNA-stabilizing agent. In general, samples are expected to have been shipped within 24 hours, but the fact that the duration of individual shipments was not specifically recorded limits the study further. Intersample differences in the number of obtained reads represent another potential source of uncertainty because we did not normalize the data by randomly picking a fixed number of reads. However, no correlation between the number of reads and number of OTUs or SDI was observed. The use of 16S amplicon sequencing may have negatively affected our possibilities to identify rare taxa, because the technique has limited the ability to detect low abundant taxa. Thus, the absence of CC-specific taxa must be interpreted with caution. Enrichment of antigens prevalent in different species of bacteria may also be of importance, with respect to the pathogenesis of CC. However, such enrichment cannot be detected by the method used, and further shotgun metagenomic sequencing-based studies of individuals with CC are warranted. Other clinical factors such as diet, blood trait, age, sex, BMI, and host genotype have also been associated with gut microbiota composition (42). Especially age, sex, and BMI have been identified as important potential confounders. To rule out that the results were confounded by any of these variables, the impact of age, sex, and BMI was examined by a principal coordinate analysis and an ANOSIM (see Figures 2, Supplementary Digital Content, http://links.lww.com/CTG/A61). However, no differences were found, except for BMI, where a difference was observed between lean (BMI < 25) and obese (BMI > 30) participants. However, because obese participants were equally distributed in CC group and controls, we do not expect any impact on the observed differences between CC and healthy controls.
To our knowledge, this is the first study to demonstrate that CC is associated with a specific gut microbiome and that the altered microbiota is seen primarily in patients with active disease and/or corticosteroid treatment. Interestingly, the shift in some taxa, like the Ruminococcaceae family, resembles an IBD-associated dysbiosis and was also observed in patients with IBD in our study. This may indicate that CC and IBD are underpinned by similar microbial mechanisms.
CONFLICTS OF INTEREST
Guarantor of the article: Jonas Halfvarson, MD, PhD.
Specific author contributions: A.C.: planned and conducted the study; collected, analyzed, and interpreted the data; drafted the manuscript; and approved the final version submitted. J.D.: planned the study, analyzed and interpreted the data, drafted the manuscript, and approved the final draft submitted. R.N., M.L.: analyzed and interpreted the data and approved the final draft submitted. A.A.: collected data, revised the manuscript, and approved the final draft submitted. J.B.: collected material and data, revised the manuscript, and approved the final draft submitted. C.T.: collected material, interpreted the data, planned, revised the manuscript, and approved the final draft submitted. N.T., L.A.: collected data, revised the manuscript, and approved the final draft submitted. L.E.: planned and conducted the study, collected and interpreted the data, revised the manuscript, and approved the final draft submitted. J.H.: planned and conducted the study, interpreted the data, drafted the manuscript, and approved the final draft submitted.
Financial support: This project was supported by Örebro University, Örebro University Hospital Research Foundation, The Swedish Foundation for Gastrointestinal Research, Swedish Research Council (521-2011-2764 to JH and 521-2012-1930 to LE), and Soderbergs foundation.
Potential competing interests: A.C.: served as a speaker for Tillotts Pharma. J.D., R.N., A.A., J.B.: None to declare. C.T.: served as a speaker for Dr Falk Pharma, Tillotts Pharma, Ferring, MSD, and AstraZeneca. N.T.: None declared. L.A., L.E.: None to declare. J.H.: Has received research grants from the Swedish Research Council (521-2011-2764) and the Örebro University Hospital Research Foundation (grant OLL-507001); has served as a speaker, a consultant, and/or an advisory board member for Abbvie, Celgene, Celltrion, Ferring, Hospira, Janssen, Medivir, MSD, Novartis, Pfizer, Prometheus, Sandoz, Shire, Takeda, Tillotts Pharma, and Vifor Pharma; and also has received research grants from Janssen, MSD, and Takeda.
Ethics approval and consent to participate: The Ethics Committee of Uppsala University (Dnr 2007/291) and the local Ethics Committee at Karolinska Institutet (Forskningskommitté Syd) (Dnr 394/01) approved the study. All participants submitted written consent to participate in the study.
Availability of data and materials: The datasets used and analyzed during the current study are available from the corresponding author on reasonable request.
WHAT IS KNOWN
- ✓ Gut microbiota is of importance for the maintenance of health.
- ✓ Similar to IBD, CC is characterized by an aberrant immune response to luminal factors.
- ✓ Gut microbiota plays an important role in the pathogenesis of IBD, but its potential role in CC is largely unknown.
WHAT IS NEW HERE
- ✓ Analysis of fecal samples revealed an altered microbial composition, with decreased abundance of several members of the Ruminococcaceae family in patients with CC.
- ✓ Alterations in the gut microbiota composition is associated with active CC or ongoing corticosteroid treatment, whereas the microbiome of patients with CC in remission resembled that of healthy controls.
- ✓ Common mechanisms related to the pathogenesis of CC and IBD may exist, because similar alterations were observed in both groups.
- ✓ Future microbiota-directed therapies may be of interest in patients with active CC.
We thank Daniel Lundin for data processing and taxonomic identification. Computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX). We also thank the Science for Life Laboratory, SciLifeLab, for computational aid and pyrosequencing facilities.
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