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

David M. Klurfeld (Corresponding Author), Cindy D. Davis, Robert W. Karp, Emma Allen-Vercoe, Eugene B. Chang, Benoit Chassaing, George C. Fahey Jr., Bruce R. Hamaker, Hannah D. Holscher, Johanna W. Lampe, Andre Marette, Eric Martens, Stephen J. O'Keefe, Devin J. Rose, Maria Saarela, Barbara O. Schneeman, Joanne L. Slavin, Justin L. Sonnenburg, Kelly S. Swanson, Gary D. WuChristopher J. Lynch

Research output: Contribution to journalArticleScientificpeer-review

8 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to) E1087-E1097
JournalAmerican Journal of Physiology: Endocrinology and Metabolism
Volume315
Issue number6
DOIs
Publication statusPublished - 2018
MoE publication typeNot Eligible

Fingerprint

Practice Guidelines
Microbiota
Reproduction
Diet
Education
National Institutes of Health (U.S.)
Agriculture
Research
Nucleic Acids
Colon
Animal Models
Carbohydrates
Gastrointestinal Microbiome

Keywords

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

Cite this

Klurfeld, David M. ; Davis, Cindy D. ; Karp, Robert W. ; Allen-Vercoe, Emma ; Chang, Eugene B. ; Chassaing, Benoit ; Fahey Jr., George C. ; Hamaker, Bruce R. ; Holscher, Hannah D. ; Lampe, Johanna W. ; Marette, Andre ; Martens, Eric ; O'Keefe, Stephen J. ; Rose, Devin J. ; Saarela, Maria ; Schneeman, Barbara O. ; Slavin, Joanne L. ; Sonnenburg, Justin L. ; Swanson, Kelly S. ; Wu, Gary D. ; Lynch, Christopher J. / Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome. In: American Journal of Physiology: Endocrinology and Metabolism. 2018 ; Vol. 315, No. 6. pp. E1087-E1097.
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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",
author = "Klurfeld, {David M.} and Davis, {Cindy D.} and Karp, {Robert W.} and Emma Allen-Vercoe and Chang, {Eugene B.} and Benoit Chassaing and {Fahey Jr.}, {George C.} and Hamaker, {Bruce R.} and Holscher, {Hannah D.} and Lampe, {Johanna W.} and Andre Marette and Eric Martens and O'Keefe, {Stephen J.} and Rose, {Devin J.} and Maria Saarela and Schneeman, {Barbara O.} and Slavin, {Joanne L.} and Sonnenburg, {Justin L.} and Swanson, {Kelly S.} and Wu, {Gary D.} and Lynch, {Christopher J.}",
year = "2018",
doi = "10.1152/ajpendo.00058.2018",
language = "English",
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Klurfeld, DM, Davis, CD, Karp, RW, Allen-Vercoe, E, Chang, EB, Chassaing, B, Fahey Jr., GC, Hamaker, BR, Holscher, HD, Lampe, JW, Marette, A, Martens, E, O'Keefe, SJ, Rose, DJ, Saarela, M, Schneeman, BO, Slavin, JL, Sonnenburg, JL, Swanson, KS, Wu, GD & Lynch, CJ 2018, 'Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome', American Journal of Physiology: Endocrinology and Metabolism, vol. 315, no. 6, pp. E1087-E1097. https://doi.org/10.1152/ajpendo.00058.2018

Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome. / Klurfeld, David M. (Corresponding Author); Davis, Cindy D.; Karp, Robert W.; Allen-Vercoe, Emma; Chang, Eugene B.; Chassaing, Benoit; Fahey Jr., George C. ; Hamaker, Bruce R.; Holscher, Hannah D.; Lampe, Johanna W.; Marette, Andre; Martens, Eric; O'Keefe, Stephen J.; Rose, Devin J.; Saarela, Maria; Schneeman, Barbara O.; Slavin, Joanne L.; Sonnenburg, Justin L.; Swanson, Kelly S.; Wu, Gary D.; Lynch, Christopher J.

In: American Journal of Physiology: Endocrinology and Metabolism, Vol. 315, No. 6, 2018, p. E1087-E1097.

Research output: Contribution to journalArticleScientificpeer-review

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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.

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KW - gastrointestinal

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KW - nutrition

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