TY - JOUR
T1 - Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome
AU - Klurfeld, David M.
AU - Davis, Cindy D.
AU - Karp, Robert W.
AU - Allen-Vercoe, Emma
AU - Chang, Eugene B.
AU - Chassaing, Benoit
AU - Fahey Jr., George C.
AU - Hamaker, Bruce R.
AU - Holscher, Hannah D.
AU - Lampe, Johanna W.
AU - Marette, Andre
AU - Martens, Eric
AU - O'Keefe, Stephen J.
AU - Rose, Devin J.
AU - Saarela, Maria
AU - Schneeman, Barbara O.
AU - Slavin, Joanne L.
AU - Sonnenburg, Justin L.
AU - Swanson, Kelly S.
AU - Wu, Gary D.
AU - Lynch, Christopher J.
PY - 2018
Y1 - 2018
N2 - A 2-day workshop organized by the National Institutes of Health and U.S. Department of Agriculture included 16 presentations focused on the role of diet in alterations of the gastrointestinal microbiome, primarily that of the colon. Although thousands of research projects have been funded by U.S. federal agencies to study the intestinal microbiome of humans and a variety of animal models, only a minority addresses dietary effects, and a small subset is described in sufficient detail to allow reproduction of a study. Whereas there are standards being developed for many aspects of microbiome studies, such as sample collection, nucleic acid extraction, data handling, etc., none has been proposed for the dietary component; thus this workshop focused on the latter specific point. It is important to foster rigor in design and reproducibility of published studies to maintain high quality and enable designs that can be compared in systematic reviews. Speakers addressed the influence of the structure of the fermentable carbohydrate on the microbiota and the variables to consider in design of studies using animals, in vitro models, and human subjects. For all types of studies, strengths and weaknesses of various designs were highlighted, and for human studies, comparisons between controlled feeding and observational designs were discussed. Because of the lack of published, best-diet formulations for specific research questions, the main recommendation is to describe dietary ingredients and treatments in as much detail as possible to allow reproduction by other scientists.
AB - A 2-day workshop organized by the National Institutes of Health and U.S. Department of Agriculture included 16 presentations focused on the role of diet in alterations of the gastrointestinal microbiome, primarily that of the colon. Although thousands of research projects have been funded by U.S. federal agencies to study the intestinal microbiome of humans and a variety of animal models, only a minority addresses dietary effects, and a small subset is described in sufficient detail to allow reproduction of a study. Whereas there are standards being developed for many aspects of microbiome studies, such as sample collection, nucleic acid extraction, data handling, etc., none has been proposed for the dietary component; thus this workshop focused on the latter specific point. It is important to foster rigor in design and reproducibility of published studies to maintain high quality and enable designs that can be compared in systematic reviews. Speakers addressed the influence of the structure of the fermentable carbohydrate on the microbiota and the variables to consider in design of studies using animals, in vitro models, and human subjects. For all types of studies, strengths and weaknesses of various designs were highlighted, and for human studies, comparisons between controlled feeding and observational designs were discussed. Because of the lack of published, best-diet formulations for specific research questions, the main recommendation is to describe dietary ingredients and treatments in as much detail as possible to allow reproduction by other scientists.
KW - dietary fiber
KW - gastrointestinal
KW - in vitro fermentation
KW - microbiota
KW - nutrition
UR - http://www.scopus.com/inward/record.url?scp=85057964419&partnerID=8YFLogxK
U2 - 10.1152/ajpendo.00058.2018
DO - 10.1152/ajpendo.00058.2018
M3 - Article
SN - 0193-1849
VL - 315
SP - E1087-E1097
JO - American Journal of Physiology: Endocrinology and Metabolism
JF - American Journal of Physiology: Endocrinology and Metabolism
IS - 6
ER -