Higher alpha diversity and Lactobacillus blooms are associated with better engraftment after Fecal Microbiota Transplant in Inflammatory Bowel Disease.

Background: Fecal Microbiota Transplant (FMT) has proven effective in treating recurrent Clostridioides difficile infection (rCDI) and has shown some success in treating inflammatory bowel diseases (IBD). There is emerging evidence that host engraftment of donor taxa is a tenet of successful FMT. However, there is little known regarding predictors of engraftment. We undertook a double-blind, randomized, placebo-controlled pilot study to characterize the response to FMT in children and young adults with mild to moderate active Crohn's disease (CD) and ulcerative colitis (UC). Results: Subjects with CD or UC were randomized to receive antibiotics and weekly FMT or placebo in addition to baseline medications. The treatment arm received seven days of antibiotics followed by FMT enema and then capsules weekly for seven weeks. We enrolled four subjects with CD and 11 with UC, ages 14-29 years. Due to weekly stool sampling, we were able to create a time series of alpha diversity, beta diversity and engraftment as they related to clinical response. Subjects exhibited a wide range of microbial diversity and donor engraftment as FMT progressed. Specifically, engraftment ranged from 26% to 90% at week 2 and 3% to 92% at two months. Consistent with the current literature, increases over time of both alpha diversity (p< 0.05) and donor engraftment (p< 0.05) correlated with improved clinical response. Additionally, our weekly time series enabled an investigation into the clinical and microbial correlates of engraftment at various time points. We discovered that the post-antibiotic but pre-FMT time point, often overlooked in FMT trials, was rich in microbial correlates of eventual engraftment. Greater residual alpha diversity after antibiotic treatment was positively correlated with engraftment and subsequent clinical response. Interestingly, a transient rise in the relative abundance of Lactobacillus was also positively correlated with engraftment, a finding that we recapitulated with our analysis of another FMT trial with publicly available weekly sequencing data. Conclusions: We found that higher residual alpha diversity and Lactobacillus blooms after antibiotic treatment correlated with improved engraftment and clinical response to FMT. Future studies should closely examine the host microbial communities pre-FMT and the impact of antibiotic preconditioning on engraftment and response.

Loss of response to biologics versus increased risk of lymphoma in children with inflammatory bowel disease: the clinician's conundrum.

Inflammatory bowel disease in children can be marked by aggressive disease both at presentation and over time. Risk stratification of individual patients may help identify when early biologic therapy is justified. Currently, combination biologic and immunomodulator therapy for moderate-to-severe Crohn's disease is the most effective treatment regimen. The clinician's conundrum arises from the recent understanding that rare but serious adverse events do occur with use of these strong immune suppressive drugs and may be more prevalent with combination therapy. An understanding of the natural history of Crohn's disease and ulcerative colitis and the benefits and risks of the current medical armamentarium is essential to provide optimal care for each child with inflammatory bowel disease.

Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease.

BACKGROUND: Pediatric inflammatory bowel disease (IBD) is challenging to diagnose because of the non-specificity of symptoms; an unequivocal diagnosis can only be made using colonoscopy, which clinicians are reluctant to recommend for children. Diagnosis of pediatric IBD is therefore frequently delayed, leading to inappropriate treatment plans and poor outcomes. We investigated the use of 16S rRNA sequencing of fecal samples and new analytical methods to assess differences in the microbiota of children with IBD and other gastrointestinal disorders. METHODOLOGY/PRINCIPAL FINDINGS: We applied synthetic learning in microbial ecology (SLiME) analysis to 16S sequencing data obtained from i) published surveys of microbiota diversity in IBD and ii) fecal samples from 91 children and young adults who were treated in the gastroenterology program of Children's Hospital (Boston, USA). The developed method accurately distinguished control samples from those of patients with IBD; the area under the receiver-operating-characteristic curve (AUC) value was 0.83 (corresponding to 80.3% sensitivity and 69.7% specificity at a set threshold). The accuracy was maintained among data sets collected by different sampling and sequencing methods. The method identified taxa associated with disease states and distinguished patients with Crohn's disease from those with ulcerative colitis with reasonable accuracy. The findings were validated using samples from an additional group of 68 patients; the validation test identified patients with IBD with an AUC value of 0.84 (e.g. 92% sensitivity, 58.5% specificity). CONCLUSIONS/SIGNIFICANCE: Microbiome-based diagnostics can distinguish pediatric patients with IBD from patients with similar symptoms. Although this test can not replace endoscopy and histological examination as diagnostic tools, classification based on microbial diversity is an effective complementary technique for IBD detection in pediatric patients.

Complementary medicine use in children and young adults with inflammatory bowel disease.

OBJECTIVES: We examined the use of complementary alternative medicine (CAM) in children and young adults with inflammatory bowel disease. METHODS: After validation of a questionnaire and completion of a pilot survey, children and young adults with inflammatory bowel disease were enrolled in three centers of pediatric gastroenterology (Boston, Detroit, and London). RESULTS: Two hundred eight questionnaires were completed in total (Boston, 120; Detroit, 37; London, 51). Ages ranged from 3.8 to 23.0 yr, 58% were male, 57% had Crohn's disease, and 35% had ulcerative colitis. The frequency of CAM use was 41%. The most common CAMs were megavitamin therapy (19%), dietary supplements (17%), and herbal medicine (14%). Parental CAM use and the number of adverse effects from conventional medicines were predictors of CAM use (odds ratio = 1.9, 95% CI = 1.2-3.1, p = 0.02; odds ratio = 1.3, 95% CI = 1.2-1.5, p < 0.001, respectively). The most important reasons respondents gave for using CAM were side effects from prescribed medicines, prescribed medicines not working as well as they had hoped, and hoping for a cure. Fifty-nine percent of respondents not taking CAM were interested in learning more about it. CONCLUSIONS: In our survey over 40% of children with chronic inflammatory bowel disease used complementary medicine in addition to conventional therapies. Parental CAM use and number of adverse effects from conventional therapies were the only independent predictors of CAM use. Some complementary therapies have potential for adverse effects and for drug interactions with conventional treatments. Physicians should take a thorough history of CAM use in children with chronic inflammatory bowel disease.