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Background  Constipation is a frequent problem in adults with Prader–Willi syndrome. Certain probiotics have been shown to improve transit and gastrointestinal symptoms of adults with functional constipation. The aim of this study is to determine the effect of daily consumption of  Bifidobacterium animalis  ssp.  lactis  B94 ( B. lactis  B94) on stool frequency, stool form, and gastrointestinal symptoms in adults with Prader–Willi syndrome.    Methods  Adults with Prader–Willi syndrome (18–75 years old,  n  = 36) will be recruited and enrolled in a 20-week, randomized, double-blind, placebo-controlled, crossover study. Study subjects will be randomized to  B. lactis  B94 or placebo each for a 4-week period, preceded by a 4-week baseline and followed by 4-week washouts. Subjects will complete daily records of stool frequency and stool form (a proxy of transit time). Dietary intake data also will be collected. Stools, one in each period, will be collected for exploratory microbiota analyses.    Discussion  To our knowledge, this is the first randomized controlled trial evaluating the effectiveness of  B. lactis  in adults with Prader–Willi syndrome. The results of this study will provide evidence of efficacy for future clinical trials in patient populations with constipation.    Trial registration  ClinicalTrials.gov ( NCT03277157 ). Registered on 08 September 2017.    Electronic supplementary material  The online version of this article (10.1186/s13063-018-2648-x) contains supplementary material, which is available to authorized users.

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The effects of Bifidobacterium animalis ssp. lactis B94 on gastrointestinal wellness in adults with Prader–Willi syndrome: study protocol for a randomized controlled trial