IBD Crohn’s: SCD increased microbiome diversity but Low Residual Diet reduced diversity

SUMMARY:   Specific Carbohydrate Diet (SCD) increased microbiome diversity in Crohn’s patients. The pediatric and adult IBD clinics at UC Davis Medical Center (Sacramento, CA) conducted the study,  Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease, and here, found:  

  1. SCD increased microbiome diversity whereas the low residual diet (LRD) decreased microbiome diversity.  Interestingly, the SCD diet included an increased microbiota representation of F. prausnitzii, an anti-inflammatory commensal.
  2. Patient diet COMPLIANCE was about 80%, and
  3. The SCD MICROBIOME DIVERSITY REMAINED despite a 30 day washout between diets.  

Given that it is now understood that IBD is associated with reduced microbiome diversity, perhaps this aspect of SCD (increasing microbiome diversity) explains the success many find using SCD to manage IBD as well as heal other illnesses.  The followup post, NICE, EATING SCD INCREASED F. PRAUSNITZII… HUGH?!? explains the significance of F. prausnitzii in the microbiome.

I have written often about the Specific Carbohydrate Diet (SCD).  It is a healing diet that many use for management of IBD, celiac (when gluten-free is not enough), IBS and other illnesses.  GAPS is based on SCD and is used for autism and other healing protocols.  PALEO is yet another healing diet, and in the end, all these diets morph into one another once food intolerances are tweaked.  UMass showed in,  An anti-inflammatory diet as treatment for inflammatory bowel disease: a case series report, that a “SCD modified dietary protocol can be used as an adjunctive or alternative therapy for the treatment of IBD.  Notably, 9 out of 11 patients were able to be managed without anti-TNF therapy, and 100% of the patients had their symptoms reduced.”  Details are at the bottom of this post. This study and others showing success of SCD are also explained in the post, FOOD MANAGING IBD & AUTISM: THE STUDIES.

Numerous studies have found that microbiome diversity is reduced and shifted in IBD, EVEN ON MEDICATIONS:


  1.  FEBS Letters Nov. 2014 publication Meta-analyses of human gut microbes associated with obesity and IBD:  IBD has clearer reported taxonomic shifts than obesity, including a depletion of Firmicutes and Bacteroides and enrichment in Proteobacteria and Actinobacteria [34].  Epithelial-associated microbes of the small and large intestine are different than fecal microbiota [35] and [36], and are more likely to be key players in the etiology of IBD because of their more direct interaction with the affected tissues and the mucosal immune system.  Despite this, it was felt that fecal testing could still predict IBD severity.  Small intestinal Crohn’s disease samples (ICD in the below slides) clustered the most distinctly from the healthy controls, and there was substantially more overlap between healthy subjects and ulcerative colitis samples, which again reflects previous observations including a recent large cross-cohort analysis [41].
  2. Decreased Firmicutes abundance and increase Proteobacteria abundance in IBD subjects.  –Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
  3. Increased prevalence of Escherichia coli in the ileum of CD patients [36], and a very recent study has shown the ability of E. coli to trigger and potentiate intestinal inflammation in mouse models [46].  -Perturbation of the Human Microbiome as a Contributor to Inflammatory Bowel Disease
  4. Changes specific to patients with ileal CD included the disappearance of core bacteria, such as Faecalibacterium and Roseburia, and increased amounts of Enterobacteriaceae and Ruminococcus gnavus.A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes.
  5. Increased Mycobacterium avium subspecies paratuberculosis (MAP) in the intestinal tissue of CD patients [50,51].MAP has been defined as the etiology of Johne’s disease in cattle, a chronic granulomatous illness that is clinically and pathologically similar to CD in humans [52].  -Perturbation of the Human Microbiome as a Contributor to Inflammatory Bowel Disease.  Only two of the participants (one Crohn’s and the other UC) were found to have detectable MAP in Meta-analyses of human gut microbes associated with obesity and IBD.  These researchers noted: If Mycobacterium species are present in these IBD patients, they are not detectable in the feces of the subjects.
  6. At baseline, before diet implementation, overall microbial diversity was significantly decreased in IBD samples as compared to the healthy negative controls. IBD patients had more Bacteroides fragilis and a decreased abundance in Clostridium lactatifermentans, indicating a shift in the microbiota away from the composition of the microbial communities in the healthy controls.Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease.
  7. 5 newly diagnosed Crohn’s Disease children were looked at using exclusive enteral nutrition (EEN) therapy: We observed a reduced microbial diversity in CD patients as compared with controls, a finding that has been well documented in the literature.37, 38 Furthermore, we observed dysbiosis within the microbiota of CD patients as compared with controls, which is in line with other studies that consistently report dysbiosis to play a pivotal role in the pathogenesis of CD.37 Interestingly, the microbial profiles of the five CD patients were remarkably different as evidenced by the large variation around the mean values. The variability in the microbiota of CD patients supports the overall conclusion that several microbial species may be involved in the pathogenesis of this disease, as is evidenced by the large number of bacteria associated with this disease.37 However, these differences could also relate to the length of time that the child has had symptoms prior to having colonoscopy as well as the severity of inflammation. -Effect of Exclusive Enteral Nutrition on the Microbiota of Children With Newly Diagnosed Crohn’s Disease
How the shifting IBD microbiome may increase pro-inflammatory blooms

Depletion of certain commensal taxa (Akkermansia muciniphila, F.prausnitzii, Bacteroides uniforms) in IBD (trend is different according to disease type [UC or Crohn’s]) could be responsible for causing inappropriate immune responses in the host [47], [48] and [49], as well as opening up niches for occupation by invasive or pro-inflammatory species. Increased Proteobacteria and Fusobacteria (and a related decrease of less oxygen tolerate taxa, such as many of the Firmicutes) could be due to increased available oxygen in the intestinal lumen of subjects with IBD. These increased oxygen-tolerant taxa have the potential to produce pro-inflammatory responses in the host through flagellin or lipopolysaccharides [50] and [51]. Bifidobacterium may be increased in abundance due to oxygen tolerance relative to other taxa [52]. Previous proteomic data suggests that certain opportunistic Bacteroides sp. pathogens are increased in IBD subjects, at the expense of Prevotella species, which could explain the shifts within Bacteroidetes in our observations [53].  Meta-analyses of human gut microbes associated with obesity and IBD

embellishment7SCD increased microbiome diversity in Crohn’s

The finding in Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease, that SCD increased microbiome diversity is something all users of SCD are happy to hear as increased microbiome diversity means increased immune function.embellishment7

Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease, see also here for linked references, evaluated the impact to the IBD-Crohn’s microbiome based on two differing diets: the Specific Carbohydrate Diet (SCD) and Low Residue Diet (LRD).  8 patients were enrolled — 6 with Crohn’s and two healthy controls.  The findings: SCD increased diversity whereas the LRD decreased microbiome diversity, there was about an 80% diet compliance, and the SCD microbiome diversity was maintained through the 30 day washout between diets despite the participants eating whatever they wanted:

“Fecal samples were obtained from patients with Crohn’s disease in a pilot diet crossover trial comparing the effects of a specific carbohydrate diet (SCD) versus a low residue diet (LRD) on the composition and complexity of the gut microbiota and resolution of IBD symptoms.  Patients and IBD care team were blinded to their diet assignments.  Education packets on both SCD and LRD diets were carefully developed; dietary SCD guidelines as described by E. Gottschall and sample menus were developed from her book “Breaking the vicious cycle.” Ms. Gottschall and her estate approved use of the material prior to starting this study.  LRD instructions were crafted to mimic and display no inferiority to the SCD booklet [50,51].  [LRD is a low fiber diet and serves to prolong intestinal transit time.]  This was done to avoid induction of bias into our subject population. Two healthy participants with no gastrointestinal symptoms or other chronic illnesses were also enrolled to provide a baseline control fecal sample [52,53].  Compliance with the diets, based on weekly phone contacts, was approximately 80%.

After their initial 30 day period, patients went on a “washout” phase for 30 days. During this period the participants resumed their normal pre-study diet. After washout period, patients returned to clinic and the second 30-day trial period began.  All subjects submitted fecal samples at four time points, at the beginning and end of each research diet. For the duration of the study period, Crohn’s disease medications and dosages were unchanged.

The pathogenesis of IBD is multifactorial and is a consequence of interplay between genetics, immune dysregulation and environmental factors… Intestinal epithelial permeability has been shown to be a determining factor in the development and progression of IBD and other inflammatory conditions. Disruption of the integrity of the tight junctions in the epithelial barrier, impaired mucin secretion and Paneth cell functions contribute to the increased permeability [75]. Epithelial barrier defects can be attributed to genetic susceptibility and gut inflammation [76,77].The immunemodulators and biologic agents are being utilized to control gut inflammation. Another approach for controlling the intestinal inflammation may include reshaping the gut microbiota through diet interventions [78,79]. A change in the diet with potential inclusion of prebiotics and/or probiotics can alter the gut microbiota that is beneficial for human health. 

At baseline, before diet implementation, overall microbial diversity was significantly decreased in IBD samples as compared to the healthy negative controls. IBD patients had more Bacteroides fragilis and a decreased abundance in Clostridium lactatifermentans, indicating a shift in the microbiota away from the composition of the microbial communities in the healthy controls.

In terms of improving the microbial diversity that IBD patients lacked, the SCD diet proved to be more effective. Patients on the SCD diet had an increased abundance of some C. leptum species, which typically has been known to be a minor bacterial component in IBD patients [66,67,88]. Interestingly, the increase in microbial diversity with the SCD diet included an increased representation of F. prausnitzii, an anti-inflammatory commensal, in the stool samples [66].

On the contrary, the LRD diet caused a drastic decrease in the Microbiome diversity. 

Following the SCD, the microbial diversity increased to include 134 bacteria belonging to 32 different classes (Figure 8). The LRD diet was associated with a decreased diversity of the microbiome with 11 bacteria belonging to 3 families (Figure 9). The bacterial families over represented in the increase in SCD included over 20 species of the non-pathogenic clostridia family. Many of these species were decreased in the participants of the LRD diet. A shift in the representation of several bacteria of Clostridia spp was observed with the diet change. 

More importantly, the gut Microbiome diversity was maintained [following SCD] and did not return to baseline composition during the washout periods.

Due to the limited data, we were unable to show a significant clinical improvement with the increase in microbial diversity in IBD patients receiving the SCD diet.

The role of microbiota in gut inflammation and IBD has been extensively studied [83-87].The effects of Bacteroides fragilis, on the Th1 responses through the action of the bacterial-derived polysaccharide A (PSA) have been demonstrated. Furthermore, altered microbiota also play a role in activation of a Th17 response which is pro inflammatory, especially in IBD [83]. The global analysis of IBD associated dysbiosis has provided information on the complex interplay between microbiota, the innate and acquired immune system. The gap in knowledge is in the area of whether diet modifications can affect the microbiota in a positive manner and if this change is measurable. Our study has provided data to suggest that changes in the microbial diversity associated with IBD can be altered by dietary changes. While this study utilized a small “n”, the longitudinal samples provided critical evidence of the effects of diet modification on the fecal microbiota.

Diet Modulation of the IBD-Crohn’s Microbiome and SIBO

Other dietary protocols have induced remission in Crohn’s.  Crohn’s and Colitis Canada position paper notes:  Studies on children living with Crohn’s disease have shown that exclusive enteral nutrition (EEN) is an effective treatment used to induce mucosal healing while providing adequate nutrients for proper bone development and growth. It also helps to keep the condition in remission and can delay the need to go on other drugs and biologics. In the United Kingdom, Japan and in some European countries, EEN is a first line therapy for children with Crohn’s disease. In fact, both Japan and the UK have established EEN clinical guidelines for the treatment of Crohn’s disease in children. 1,2 In Canada, there are no guidelines, however, it is common practice for paediatric gastroenterologists to prescribe liquid nutrition since it acts as a safe alternative to steroids and biologic drugs used to induce the remission of Crohn’s disease. 

The study, Effect of Exclusive Enteral Nutrition on the Microbiota of Children With Newly Diagnosed Crohn’s Disease, looked at the mcirobiota for EEN and learned that remission was achieved 80%, or 4 out of 5 IBD children;  EEN led to common and patient-specific alterations in the microbiota, some of which correlate with disease activity. Specific species within the Lachnospiraceae, Ruminococcaceae, and Erysipelotrichaceae were among the key taxa identified to potentially be involved in the perpetuation of gut inflammation in CD. Given the decrease in the number of OTUs and microbial diversity secondary to EEN, and the correlation of disease recurrence with the re-colonization of eradicated taxa post-EEN, a sequential EEN-probiotic therapy may prove beneficial in the improvement of the long-term efficacy of EEN therapy in pediatric CD. 

The SCD/GAPS approach is also used to treat Small Intestinal Bacterial Overgrowth, see Treatments Strategy for SIBOSIBO-Dietary TreatmentsNCNM, Continuing education courses, as well as AHS13 Allison Siebecker — Small Intestine Bacterial Overgrowth: 

Perhaps dietary adjunctive therapy is the ticket to sustaining IBD remission; specific dietary guidance is sorely lacking for those on medications.

Why is diet NOT part of Crohn’s treatment?

The Crohn’s Study Results: 29 Treatments Rated by Patients chart shows the top 10 overall treatments reported for Crohn’s Disease.  Asacol, Entocort, Imurran… and many others are rated below these:

1. Low-Dose Naltrexone (LDN)
2. Surgery
3. Steroids
4. Humira
5. Cannabis
6. Specific Carbohydrate Diet
7. Remicade
8. Stress reduction
9. Small meals
10. Gluten-free/low fiber diets

Cure Together for Crohn's
Source, Crohn’s Study Results: 29 Treatments Rated by Patients, http://curetogether.com/blog/2011/09/20/crohns-study-results-29-treatments-rated-by-patients/

Crohnology.com/ also has an IBD treatment comparison page based on patient experience that I will update.  SCD continually ranks highly.  The updated comparisons: SCD outranks the closest medication which is Remicade:

Stanford pediatric gastroenterologist answers your questions on inflammatory bowel disease answered EC Smit’s question: Why isn’t diet part of the treatment plan for Crohn’s disease when people who have excluded known gastrointestinal irritants, such as gluten and carrageenan, have found relief and remission?

Let me first try to address your concerns and questions with a concession. Interventional dietary alternatives in the treatment of IBD are often underemphasized. Knowing this, our Stanford group is longitudinally recording and making some headway in characterizing how specific and modified carbohydrate diets have impacted health for patients with Crohn’s disease. We’re still in the early phases of our prospective study, but we hope to gain more momentum.With that said, I understand your perspective.

Presently, the medical community in the United States can place more focus on pharmacological therapies than nutritional ones. I think this tendency may have to do with two important considerations. First, although Crohn’s disease is a gastrointestinal disease, it is in essence an autoimmune problem. Conventional and experiential wisdom tells us that controlling immune dysregulation requires immune-modulating agents, such as drugs that can help the body stop attacking its own cells or block the biological response that causes inflammation. And historically, we have found success with this established framework – as most Crohn’s patients achieve sustained remission following an evidence-based treatment plan. Despite the potential severity of the initial disease presentation, most patients return to living life without a noticeable difference in their overall quality-of-life.

Second, patient tolerance and continued adherence to the type of diet programs shown to be potentially effective in Crohn’s disease are difficult, to say the least. As you may know, the Specific Carbohydrate Diet (SCD) is one purported dietary intervention for Crohn’s disease. Although substantially more efficacy data are needed, we know that the SCD dietary plan is a very restrictive low carbohydrate diet, which is difficult to maintain strict adherence for patients, especially among children and adolescents. Similarly, elemental or polymeric diets, which have been reported to be helpful in active Crohn’s disease, are also difficult to perpetuate on a day-to-day basis for long-term disease management. For clinicians, we have to do our part in informing patients of all the alternatives while helping patients and their family to optimize daily quality-of-life.

But please note Commenter Carol Frilegh Says: 

The SCD (Specific Carbohydrate Diet) is NOT a low-carb diet. It restricts a category of carbs (polysaccharides) and allows monosaccharides which are more easily digested. The daily amount of permitted carbs is not limited and the diet is designed to be balanced and nutritious. At the beginning, a full range of allowed foods is not given immediately but reached with gradual increases as tolerated. There are hundreds of recipes, some compliant ready made food. It is really so inaccurate that professionals mistakenly say SCD is Low Carb!

CCFA, Diet and Nutrition and The Specific Carbohydrate Diet (SCD) says:

Is there a special diet for people with IBD?  There is no one single diet or eating plan that will do the trick for everyone with IBD. Dietary recommendations must be individualized. They should be tailored just for you — depending on which disease you have and what part of your intestine is affected. Furthermore, these diseases are not static; they change over time, and eating patterns should reflect those changes. The key point is to strive for a well-balanced, healthy diet. Healthy eating habits, of course, are desirable for everyone but they’re especially important for people with IBD.

Often, patients have questions regarding The Specific Carbohydrate Diet ™ (SCD), popularized by Elaine Gottschall, M.S., author of Breaking the Vicious Cycle. At this time, the SCD is supported only by patient testimonials, not by systematic studies. With diseases like ulcerative colitis and Crohn’s disease, the only way to see if any treatment has widespread value is by appropriate, rigorous testing.The diet itself is not particularly unbalanced, but many patients find it particularly onerous to maintain. Decreasing poorly digestible carbohydrates may decrease symptoms of gas, bloat, cramps, and diarrhea in patients with IBD, but that is not the same thing as decreasing the inflammation, or affecting the disease process. Unlike the gluten-free diet for celiac sprue, which has a well-researched basis, and well-demonstrated track record for affecting the underlying mechanisms at work in the disease process, the SCD does not. Bottom line: it may be worth a try (there are plenty of other diets being touted in the marketplace), but do not abandon your conventional treatment, and keep in touch with your doctor.

To date, there have been limited scientific studies on the use of the Specific Carbohydrate Diet in relation to Crohn’s disease and/or ulcerative colitis.  For a sample of some of the current and previous studies involving the SCD Diet, follow the links below.  Please note that this is not an exhaustive list.

Seattle Children’s Hospital and University of Washington

Rush University Medical Center

Stanford University

Journal of Pediatric Gastroenterology and Nutrition

UMass study shows potential for the IBD-AID (modified SCD) as an adjunct dietary therapy for IBD

An anti-inflammatory diet as treatment for inflammatory bowel disease: a case series report.

To provide a dietary therapy approach addressing nutrient adequacy, malabsorption issues, and symptoms, we developed the IBD-Anti-Inflammatory Diet, or IBD-AID [1315].

Methods:  Forty patients with IBD were consecutively offered the IBD-AID to help treat their disease, and were retrospectively reviewed. Medical records of 11 of those patients underwent further review to determine changes in the Harvey Bradshaw Index (HBI) or Modified Truelove and Witts Severity Index (MTLWSI), before and after the diet.

Results:  Of the 40 patients with IBD, 13 patients chose not to attempt the diet (33%). Twenty-four patients had either a good or very good response after reaching compliance (60%), and 3 patients’ results were mixed (7%). Of those 11 adult patients who underwent further medical record review, 8 with CD, and 3 with UC, the age range was 19–70 years, and they followed the diet for 4 or more weeks. After following the IBD-AID, all (100%) patients were able to discontinue at least one of their prior IBD medications, and all patients had symptom reduction including bowel frequency. The mean baseline HBI was 11 (range 1–20), and the mean follow-up score was 1.5 (range 0–3). The mean baseline MTLWSI was 7 (range 6–8), and the mean follow-up score was 0. The average decrease in the HBI was 9.5 and the average decrease in the MTLWSI was 7.

Conclusion:  This case series indicates potential for the IBD-AID as an adjunct dietary therapy for the treatment of IBD. A randomized clinical trial is warranted.

In conclusion,

Try SCD… what do you have to lose?   Related posts:

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In health through awareness,


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