Diet-microbiota associations in gastrointestinal research: a systematic review

ABSTRACT

Interactions between diet and gastrointestinal microbiota influence health status and outcomes. Evaluating these relationships requires accurate quantification of dietary variables relevant to microbial metabolism, however current dietary assessment methods focus on dietary components relevant to human digestion only. The aim of this study was to synthesize research on foods and nutrients that influence human gut microbiota and thereby identify knowledge gaps to inform dietary assessment advancements toward better understanding of diet–microbiota interactions. Thirty-eight systematic reviews and 106 primary studies reported on human diet-microbiota associations. Dietary factors altering colonic microbiota included dietary patterns, macronutrients, micronutrients, bioactive compounds, and food additives. Reported diet-microbiota associations were dominated by routinely analyzed nutrients, which are absorbed from the small intestine but analyzed for correlation to stool microbiota. Dietary derived microbiota-relevant nutrients are more challenging to quantify and underrepresented in included studies. This evidence synthesis highlights advancements needed, including opportunities for expansion of food composition databases to include microbiota-relevant data, particularly for human intervention studies. These advances in dietary assessment methodology will facilitate translation of microbiota-specific nutrition therapy to practice.

KEYWORDS:

• Microbiota
• microbiome
• diet
• dietary assessment
• diet-microbiota correlation

Acknowledgments

The authors gratefully acknowledge JH for contributions to the literature search and data extraction for this review.

Disclosure statement

KD, GW, ECH, CEC, SK report no disclosures in relation to this work. NJT reports non-financial support from: Norgine (2021)(IBS interest group), personal fees from Allakos (gastroduodenal eosinophilic disease) (2021), Bayer (IBS) (2020), Planet Innovation (Gas capsule IBS) (2020), twoXAR Viscera Labs, (USA 2021) (IBS-diarrhoea), Dr Falk Pharma (2020) (EoE), Sanofi-aventis, Glutagen (2020) (celiac disease), IsoThrive (2021) (esophageal microbiome), BluMaiden (microbiome advisory board) (2021), Rose Pharma (IBS) (2021), Intrinsic Medicine (2022) (human milk oligosaccharide), Comvita Mānuka Honey (2021) (digestive health), Astra Zeneca (2022), outside the submitted work. In addition, Dr. Talley has a patent Nepean Dyspepsia Index (NDI) 1998, Biomarkers of IBS licensed, a patent Licensing Questionnaires Talley Bowel Disease Questionnaire licensed to Mayo/Talley, a patent Nestec European Patent licensed, and a patent Singapore Provisional Patent “Microbiota Modulation of BDNF Tissue Repair Pathway” issued, “Diagnostic marker for functional gastrointestinal disorders” Australian Provisional Patent Application 2021901692. Committees: OzSage; NHMRC Principal Committee (Research Committee) Asia Pacific Association of Medical Journal Editors, Rome V Working Team Member (Gastroduodenal Committee), International Plausibility Project Co-Chair (Rome Foundation funded), COVID-19 vaccine forum member (by invitation only). Community group: Advisory Board, IFFGD (International Foundation for Functional GI Disorders), AusEE. Editorial: Medical Journal of Australia (Editor in Chief), Mayo Clinic Proceedings (Assoc Ed), Up to Date (Section Editor), Precision and Future Medicine, Sungkyunkwan University School of Medicine, South Korea, Med (Journal of Cell Press). Dr. Talley is supported by funding from the National Health and Medical Research Council (NHMRC) to the Centre for Research Excellence in Digestive Health and he holds an NHMRC Investigator grant.

Data availability statement

The data that support the findings will be available in Open Science Foundation at https://osf.io/mw2ek/following a 12-month embargo from the date of publication to allow for commercialization of research findings.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2024.2350785

Additional information

Funding

This work was supported by NHMRC Centre of Research Excellence in Digestive Health pilot grant funding under University of Newcastle grant GS210011.NJT reports non-financial support from: Norgine (2021)(IBS interest group), personal fees from Allakos (gastroduodenal eosinophilic disease) (2021), Bayer (IBS) (2020), Planet Innovation (Gas capsule IBS) (2020), twoXAR Viscera Labs (USA 2021) (IBS-diarrhea), Dr Falk Pharma (2020) (EoE), Sanofi-aventis, Glutagen (2020) (celiac disease), IsoThrive (2021) (esophageal microbiome), BluMaiden (microbiome advisory board) (2021), Rose Pharma (IBS) (2021), Intrinsic Medicine (2022) (human milk oligosaccharide), Comvita Mānuka Honey (2021) (digestive health), Astra Zeneca (2022), outside the submitted work. In addition, Dr Talley has a patent Nepean Dyspepsia Index (NDI) 1998, Biomarkers of IBS licensed, a patent Licensing Questionnaires Talley Bowel Disease Questionnaire licensed to Mayo/Talley, a patent Nestec European Patent licensed, and a patent Singapore Provisional Patent “Microbiota Modulation of BDNF Tissue Repair Pathway” issued, “Diagnostic marker for functional gastrointestinal disorders” Australian Provisional Patent Application 2,021,901,692. Committees: OzSage; NHMRC Principal Committee (Research Committee) Asia Pacific Association of Medical Journal Editors, Rome V Working Team Member (Gastroduodenal Committee), International Plausibility Project Co-Chair (Rome Foundation funded), COVID-19 vaccine forum member (by invitation only). Community group: Advisory Board, IFFGD (International Foundation for Functional GI Disorders), AusEE. Editorial: Medical Journal of Australia (Editor in Chief), Mayo Clinic Proceedings (Assoc Ed), Up to Date (Section Editor), Precision and Future Medicine, Sungkyunkwan University School of Medicine, South Korea, Med (Journal of Cell Press). Dr Talley is supported by funding from the National Health and Medical Research Council (NHMRC) to the Centre for Research Excellence in Digestive Health and he holds an NHMRC Investigator grant.