Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome
Open accessAbstract
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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Isolating associations of specific dietary components from other factors affecting the gut microbiota in observational human cohorts is challenging.
“however, this is not unexpected given the known challenges of isolating associations of specific dietary components from other factors known to affect the gut microbiota in observational human cohorts (33, 34).”
From Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response (2021) · cites this paper as [33]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Diet rapidly and reproducibly alters the human gut microbiome
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100 · see citing works
Linking long-term dietary patterns with gut microbial enterotypes
Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513 · see citing works
Self-citationGibson, G. R., Hutkins, R., Sanders, M. E., Prescott, S. L., Reimer, R. A., Salminen, S. J., Scott, K., Stanton, C., Swanson, K. S., Cani, P. D., et al. (2017) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.75 · Cited by 5,634 · see citing works
Self-citationDesai, M. S., Seekatz, A. M., Koropatkin, N. M., Kamada, N., Hickey, C. A., Wolter, M., Pudlo, N. A., Kitamoto, S., Terrapon, N., Muller, A., et al. (2016) · Cell · doi:10.1016/j.cell.2016.10.043 · Cited by 2,805 · see citing works
Self-citationDietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome
Chassaing, B., Koren, O., Goodrich, J. K., Poole, A. C., Srinivasan, S., Ley, R. E., & Gewirtz, A. T. (2015) · Nature · doi:10.1038/nature14232 · Cited by 2,055 · see citing works
Self-citationDiet-induced extinctions in the gut microbiota compound over generations
Sonnenburg, E. D., Smits, S. A., Tikhonov, M., Higginbottom, S. K., Wingreen, N. S., & Sonnenburg, J. L. (2016) · Nature · doi:10.1038/nature16504 · Cited by 1,730 · see citing works
Self-citationHow glycan metabolism shapes the human gut microbiota
Koropatkin, N. M., Cameron, E. A., & Martens, E. C. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2746 · Cited by 1,419 · see citing works
Self-citationAnhê, F. F., Roy, D., Pilon, G., Dudonné, S., Matamoros, S., Varin, T. V., Garofalo, C., Moine, Q., Desjardins, Y., Levy, E., et al. (2015) · Gut · doi:10.1136/gutjnl-2014-307142 · Cited by 1,137 · see citing works
Self-citationTransfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota
Hehemann, J.-H., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., & Michel, G. (2010) · Nature · doi:10.1038/nature08937 · Cited by 1,117 · see citing works
Fat, fibre and cancer risk in African Americans and rural Africans
O’Keefe, S. J. D., Li, J. V., Lahti, L., Ou, J., Carbonero, F., Mohammed, K., Posma, J. M., Kinross, J., Wahl, E., Ruder, E., et al. (2015) · Nature Communications · doi:10.1038/ncomms7342 · Cited by 982 · see citing works
Self-citationLack of Effect of a Low-Fat, High-Fiber Diet on the Recurrence of Colorectal Adenomas
Schatzkin, A. G., Lanza, E., Corle, D. K., Lance, P., Iber, F. L., Caan, B. J., Shike, M., Weissfeld, J. L., Burt, R. W., Cooper, M. R., et al. (2000) · New England Journal of Medicine · doi:10.1056/nejm200004203421601 · Cited by 928 · see citing works
Leone, V., Gibbons, S. M., Martinez, K., Hutchison, A. L., Huang, E. Y., Cham, C. M., Pierre, J. F., Heneghan, A. F., Nadimpalli, A., Hubert, N., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.03.006 · Cited by 908 · see citing works
Self-citationSeasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania
Smits, S. A., Leach, J., Sonnenburg, E. D., Gonzalez, C. G., Lichtman, J. S., Reid, G., Knight, R., Manjurano, A., Changalucha, J., Elias, J. E., et al. (2017) · Science · doi:10.1126/science.aan4834 · Cited by 886 · see citing works
Self-citationSonnenburg, E. D., & Sonnenburg, J. L. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.07.003 · Cited by 871 · see citing works
Self-citationRecognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts
Martens, E. C., Lowe, E. C., Chiang, H. C., Pudlo, N. A., Wu, M., McNulty, N. P., Abbott, D. W., Henrissat, B., Gilbert, H. J., Bolam, D. N., et al. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001221 · Cited by 847 · see citing works
Self-citationLewis, J. D., Chen, E. Z., Baldassano, R. N., Otley, A. R., Griffiths, A. M., Lee, D., Bittinger, K., Bailey, A., Friedman, E. S., Hoffmann, C., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.09.008 · Cited by 823 · see citing works
Self-citationOu, J., Carbonero, F., Zoetendal, E. G., DeLany, J. P., Wang, M., Newton, K., Gaskins, H. R., & O’Keefe, S. J. (2013) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.112.056689 · Cited by 646 · see citing works
Self-citationFiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota
Chen, T., Long, W., Zhang, C., Liu, S., Zhao, L., & Hamaker, B. R. (2017) · Scientific Reports · doi:10.1038/s41598-017-02995-4 · Cited by 608 · see citing works
Self-citationChassaing, B., Van de Wiele, T., De Bodt, J., Marzorati, M., & Gewirtz, A. T. (2017) · Gut · doi:10.1136/gutjnl-2016-313099 · Cited by 590 · see citing works
Self-citationWu, G. D., Compher, C., Chen, E. Z., Smith, S. A., Shah, R. D., Bittinger, K., Chehoud, C., Albenberg, L. G., Nessel, L., Gilroy, E., et al. (2016) · Gut · doi:10.1136/gutjnl-2014-308209 · Cited by 512 · see citing works
Self-citationColonic transit time is related to bacterial metabolism and mucosal turnover in the gut
Roager, H. M., Hansen, L. B. S., Bahl, M. I., Frandsen, H. L., Carvalho, V., Gøbel, R. J., Dalgaard, M. D., Plichta, D. R., Sparholt, M. H., Vestergaard, H., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.93 · Cited by 449 · see citing works
Swanson, K. S., Dowd, S. E., Suchodolski, J. S., Middelbos, I. S., Vester, B. M., Barry, K. A., Nelson, K. E., Torralba, M., Henrissat, B., Coutinho, P. M., et al. (2010) · The ISME Journal · doi:10.1038/ismej.2010.162 · Cited by 422 · see citing works
Self-citationYang, J., Martínez, I., Walter, J., Keshavarzian, A., & Rose, D. J. (2013) · Anaerobe · doi:10.1016/j.anaerobe.2013.06.012 · Cited by 290 · see citing works
Self-citationGastrointestinal Effects of Low-Digestible Carbohydrates
Grabitske, H. A., & Slavin, J. L. (2009) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408390802067126 · Cited by 267 · see citing works
Self-citationDog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks
Vázquez‐Baeza, Y., Hyde, E. R., Suchodolski, J. S., & Knight, R. D. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.177 · Cited by 262 · see citing works
Prebiotics and the Health Benefits of Fiber: Current Regulatory Status, Future Research, and Goals,
Brownawell, A. M., Caers, W., Gibson, G. R., Kendall, C. W. C., Lewis, K. D., Ringel, Y., & Slavin, J. L. (2012) · Journal of Nutrition · doi:10.3945/jn.112.158147 · Cited by 248 · see citing works
Self-citationTunable Expression Tools Enable Single-Cell Strain Distinction in the Gut Microbiome
Whitaker, W. R., Shepherd, E. S., & Sonnenburg, J. L. (2017) · Cell · doi:10.1016/j.cell.2017.03.041 · Cited by 239 · see citing works
Self-citationSchumann, D., Klose, P., Lauche, R., Dobos, G., Langhorst, J., & Cramer, H. (2017) · Nutrition · doi:10.1016/j.nut.2017.07.004 · Cited by 224 · see citing works
Gut microbiota, diet, and obesity-related disorders: the good, the bad, and the future challenges
Portune, K. J., Benítez‐Páez, A., Del Pulgar, E. M. G., Cerrudo, V., & Sanz, Y. (2017) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201600252 · Cited by 201 · see citing works
Role of colonic microbiota in colorectal carcinogenesis: A systematic review
Borges‐Canha, M. (2015) · Revista Española de Enfermedades Digestivas · doi:10.17235/reed.2015.3830/2015 · Cited by 192 · see citing works
Lack of soluble fiber drives diet-induced adiposity in mice
Chassaing, B., Miles, J. P., Pellizzon, M., Ulman, E. A., Ricci, M. R., Zhang, L., Patterson, A. D., Vijay–Kumar, M., & Gewirtz, A. T. (2015) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00172.2015 · Cited by 185 · see citing works
Self-citationFei, L., Meredith A. J., H., Yvonne, S., & Johanna W., L. (2009) · The Journal of Nutrition · doi:10.3945/jn.109.108191 · Cited by 181 · see citing works
McDonald, J. A. K., Schroeter, K., Fuentes, S., Jong, I. H., Khursigara, C. M., de Vos, W. M., & Allen‐Vercoe, E. (2013) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2013.08.008 · Cited by 178 · see citing works
Self-citationHabitual Dietary Intake Is Associated with Stool Microbiota Composition in Monozygotic Twins
Simões, C., Maukonen, J., Kaprio, J. A., Rissanen, A., Pietiläinen, K. H., & Saarela, M. (2013) · Journal of Nutrition · doi:10.3945/jn.112.166322 · Cited by 152 · see citing works
Self-citationSoy and Gut Microbiota: Interaction and Implication for Human Health
Huang, H., Krishnan, H. B., Pham, Q., Yu, L. L., & Wang, T. T. Y. (2016) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.6b03725 · Cited by 138 · see citing works
Colonic Microbiota Encroachment Correlates With Dysglycemia in Humans
Chassaing, B., Raja, S. M., Lewis, J. D., Srinivasan, S., & Gewirtz, A. T. (2017) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2017.04.001 · Cited by 125 · see citing works
Self-citationComparative Analysis of Intestinal Tract Models
Williams, C. F., Walton, G., Jiang, L., Plummer, S. F., Garaiová, I., & Gibson, G. R. (2015) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-022814-015429 · Cited by 116 · see citing works
Miles, J. P., Zou, J., Kumar, M.-V., Pellizzon, M., Ulman, E. A., Ricci, M. R., Gewirtz, A. T., & Chassaing, B. (2017) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000001155 · Cited by 110 · see citing works
Self-citationConsumption of Acidic Water Alters the Gut Microbiome and Decreases the Risk of Diabetes in NOD Mice
Wolf, K. J., Daft, J. G., Tanner, S. M., Hartmann, R., Khafipour, E., & Lorenz, R. G. (2014) · Journal of Histochemistry & Cytochemistry · doi:10.1369/0022155413519650 · Cited by 85 · see citing works
Chevrier, G., Mitchell, P. L., Rioux, L., Hasan, F. M., Jin, T., Roblet, C., Doyen, A., Pilon, G., St‐Pierre, P., Lavigne, C., et al. (2015) · Journal of Nutrition · doi:10.3945/jn.114.208215 · Cited by 60 · see citing works
Self-citationMcDonald, J. A. K., Fuentes, S., Schroeter, K., Jong, I. H., Khursigara, C. M., de Vos, W. M., & Allen‐Vercoe, E. (2014) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2014.11.007 · Cited by 59 · see citing works
Self-citationTen Times More Microbial Cells than Body Cells in Humans?
Rosner, J. L. (2014) · Microbe Magazine · doi:10.1128/microbe.9.47.2 · Cited by 47 · see citing works
Confusion about the species richness of human gut microbiota
Avershina, E., & Rudi, K. (2015) · Beneficial Microbes · doi:10.3920/bm2015.0007 · Cited by 23 · see citing works
Yang, J., & Rose, D. J. (2015) · Food & Function · doi:10.1039/c5fo00987a · Cited by 21 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Swanson, K. S., Gibson, G. R., Hutkins, R., Reimer, R. A., Reid, G., Verbeke, K., Scott, K. P., Holscher, H. D., Azad, M. B., Delzenne, N. M., et al. (2020) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-0344-2 · Cited by 2,196 · see citing works
Self-citationDietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response
Spencer, C. N., McQuade, J. L., Gopalakrishnan, V., McCulloch, J. A., Vetizou, M., Cogdill, A. P., Khan, M. A. W., Zhang, X., White, M. G., Peterson, C. B., et al. (2021) · Science · doi:10.1126/science.aaz7015 · Cited by 966 · see citing works
Microbial regulation of organismal energy homeostasis
Cani, P. D., Van Hul, M., Lefort, C., Depommier, C., Rastelli, M., & Everard, A. (2019) · Nature Metabolism · doi:10.1038/s42255-018-0017-4 · Cited by 569 · see citing works
Rethinking healthy eating in light of the gut microbiome
Armet, A. M., Deehan, E. C., O’Sullivan, A. F., Mota, J. F., Field, C. J., Prado, C. M., Lucey, A. J., & Walter, J. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.04.016 · Cited by 252 · see citing works
Fülling, C., Lach, G., Bastiaanssen, T. F. S., Fouhy, F., O'Donovan, A. N., Ventura-Silva, A.-P., Stanton, C., Dinan, T. G., & Cryan, J. F. (2020) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2020.02.013 · Cited by 36 · see citing works
Mohr, A. E., Pugh, J., O'Sullivan, O., Black, K., Townsend, J. R., Pyne, D. B., Wardenaar, F. C., West, N. P., Whisner, C. M., & McFarland, L. V. (2022) · Frontiers in Nutrition · doi:10.3389/fnut.2022.809983 · Cited by 27 · see citing works
- Authors
- Klurfeld, D. M., Davis, C. D., Karp, R. W., Allen-Vercoe, E., Chang, E. B., Chassaing, B., Fahey, G. C., Hamaker, B. R., Holscher, H. D., Lampe, J. W., Marette, A., Martens, E., O’Keefe, S. J., Rose, D. J., Saarela, M., Schneeman, B. O., Slavin, J. L., Sonnenburg, J. L., Swanson, K. S., Wu, G. D., & Lynch, C. J.
- Affiliations
- Agricultural Research Service (US)
- National Institutes of Health (US)
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
- University of Chicago (US)
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Purdue University West Lafayette (US)
- University of Illinois Urbana-Champaign (US)
- Fred Hutch Cancer Center (US)
- Heart and Lung Institute, Laval University, Québec City, Québec, Canada
- University of Michigan (US)
- University of Pittsburgh (US)
- University of Nebraska–Lincoln (US)
- VTT Technical Research Centre of Finland (FI)
- University of California, Davis (US)
- University of Minnesota (US)
- Stanford University (US)
- University of Pennsylvania (US)
- Corresponding author
- Klurfeld, David M.
- ORCID
- Venue
- American Journal of Physiology-Endocrinology and Metabolism
- Publisher
- American Physiological Society
- Published
- 2018-12-01
- Volume
- 315
- Issue
- 6
- Pages
- E1087-E1097
- ISSN
- 0193-1849 (ISSN-L)
- 1522-1555
- PMC
- PMC6415710
- OpenAlex
- W2888147176
- Cited by
- 61
- References
- 44
- Citations by year
- 2026: 3 · 2025: 6 · 2024: 2 · 2023: 9 · 2022: 11 · 2021: 10 · 2020: 7 · 2019: 11 · 2018: 2
- FWCI
- 2.67
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- American Journal of Physiology-Endocrinology and Metabolism (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Lincoln (University of Nebraska) (submittedVersion)
- Funders
- National Cancer Institute (R01CA204403)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK101674, R01DK085025)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Food composition and properties
- Health Sciences › Nursing › Nutrition and Dietetics › Microbial Metabolites in Food Biotechnology
- Keywords
- dietary fiber, gut microbiota, colonic microbiota, food components, research design, reproducibility, controlled feeding, observational studies, in vitro model, animal models, fermentable carbohydrates, best practices
- MeSH terms
- Gastrointestinal Microbiome, Animals, Diet, Dietary Fiber, Humans, Nutritional Status, Research Design, Models, Animal
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
