Guiding longitudinal sampling in IBD cohorts

We read with interest the work by Pascal et al published recently in Gut .1 Here, they report the volatile microbial signatures of patients with Crohn’s disease (CD), a quality that greatly hinders our ability to classify healthy from affected subjects using 16S rRNA profiles from stool. Nonetheless, their work overcame these and other complications,2 producing a decision tree that classifies subjects with CD, UC, irritable bowel syndrome and anorexia. Although the authors note that both subtypes of IBD, particularly CD, have increased microbial community instability, this information is not used as a feature to improve classifier accuracy. Could microbiome instability become actionable by creating a new classifier that benefits from repeated measurements? If so, how many samples per individual are needed to assess instability? We collected daily stool samples for up to 6 weeks from 19 CD subjects and 12 controls (see the analysis notebook for cohort description, methods and data, https://github.com/knightlab-analyses/longitudinal-ibd) over two separate periods of 2 or 4 weeks spread over 2 and 5 months, for a total of 960 samples. We believe that this is the most densely sampled longitudinal study …