Maire A. Conrad

Optimizing methods and dodging pitfalls in microbiome research

Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organized in the typical order in which studies are carried out. We first review best practices in experimental design and introduce common confounders such as age, diet, antibiotic use, pet ownership, longitudinal instability, and microbial sharing during cohousing in animal studies. Typically, samples will need to be stored, so we provide data on best practices for several sample types. We then discuss design and analysis of positive and negative controls, which should always be run with experimental samples. We introduce a convenient set of non-biological DNA sequences that can be useful as positive controls for high-volume analysis. Careful analysis of negative and positive controls is particularly important in studies of samples with low microbial biomass, where contamination can comprise most or all of a sample. Lastly, we summarize approaches to enhancing experimental robustness by careful control of multiple comparisons and to comparing discovery and validation cohorts. We hope the experimental tactics summarized here will help researchers in this exciting field advance their studies efficiently while avoiding errors.

Vedolizumab Therapy in Severe Pediatric Inflammatory Bowel Disease.

Background:Vedolizumab is effective for inducing and maintaining remission in adults with inflammatory bowel disease (IBD); however, there is limited pediatric data. This study aimed to describe the adverse events and clinical response to vedolizumab in refractory pediatric IBD. Methods:Disease activity indices, clinical response, concomitant medication use, and adverse events were measured over 22 weeks in an observational prospective cohort study of children with refractory IBD who had failed anti–tumor necrosis factor therapy and subsequently initiated vedolizumab therapy. Results:Twenty-one subjects, 16 with Crohn disease, received vedolizumab. Clinical response was observed in 6/19 (31.6%) of the evaluable subjects at week 6 and in 11/19 (57.9%) by week 22. Before induction, 15/21 (71.4%) participants were treated with systemic corticosteroids, as compared with 7/21 (33.3%) subjects at 22 weeks. Steroid-free remission was seen in 1/20 (5.0%) subjects at 6 weeks, 3/20 (15.0%) at 14 weeks, and 4/20 (20.0%) at 22 weeks. There was statistically significant improvement in serum albumin and hematocrit; however, C-reactive protein increased by week 22 (P < 0.05). There were no infusion reactions. Vedolizumab was discontinued in 2 patients because of severe colitis, requiring surgical intervention. Conclusions:There is limited experience with vedolizumab therapy in pediatric IBD. There seems to be a marked number of subjects with clinical response in the first 6 weeks that increases further by week 22 despite the severity of disease in this cohort. Adverse events may not be directly related to vedolizumab. This study is limited by small sample size, and larger prospective studies are warranted.

A new Procedure for the Synthesis of (E)-1-iodo-1-alkenes.

(E)-1-iodo-1-alkenes 4 can be prepared stereoselectively from aldehydes 1 via 1H-elimination of 1, 1-Di-iodoalkanes 3 with DBU.

Pediatric Inflammatory Bowel Disease

Inflammatory bowel disease (IBD), including Crohn disease, ulcerative colitis, and IBD-unspecified, is a chronic immune-mediated condition of the gastrointestinal tract in which the goal of treatment is to induce and maintain durable remission. In pediatrics, there is a wide spectrum of presenting symptoms, but esophagogastroduodenoscopy and colonoscopy are imperative to confirming the diagnosis. Treatment goals include achieving mucosal healing of the gastrointestinal tract, reaching growth potential, limiting medication toxicities, and optimizing quality of life for all patients.