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Am J Physiol Endocrinol Metab. 2018 Dec 1;315(6):E1087-E1097. doi: 10.1152/ajpendo.00058.2018. Epub 2018 Aug 21.

Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome.

Author information

1
Agricultural Research Service, United States Department of Agriculture , Beltsville, Maryland.
2
Office of Dietary Supplements, National Institutes of Health , Bethesda, Maryland.
3
National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland.
4
Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario , Canada.
5
Department of Medicine, University of Chicago , Chicago, Illinois.
6
Institute for Biomedical Sciences, Georgia State University , Atlanta, Georgia.
7
Department of Animal Sciences, University of Illinois at Urbana-Champaign , Urbana, Illinois.
8
Whistler Center for Carbohydrate Research, Purdue University , West Lafayette, Indiana.
9
Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign , Urbana, Illinois.
10
Fred Hutchinson Cancer Research Center , Seattle, Washington.
11
Heart and Lung Institute, Laval University , Québec City, Québec , Canada.
12
Institute of Nutrition and Functional Foods, Laval University , Québec City, Québec , Canada.
13
Department of Microbiology & Immunology, University of Michigan Medical School , Ann Arbor, Michigan.
14
Department of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania.
15
Food Science and Technology Department, University of Nebraska-Lincoln , Lincoln, Nebraska.
16
VTT Technical Research Centre of Finland Limited , Espoo , Finland.
17
Department of Nutrition, University of California-Davis , Davis, California.
18
Department of Food Science and Nutrition, University of Minnesota , St. Paul, Minnesota.
19
Department of Microbiology & Immunology, Stanford University , Stanford, California.
20
Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania.
21
Office of Nutrition Research, National Institutes of Health , Bethesda, Maryland.

Abstract

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.

KEYWORDS:

dietary fiber; gastrointestinal; in vitro fermentation; microbiota; nutrition

PMID:
30130151
DOI:
10.1152/ajpendo.00058.2018

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