Cited by 141Gut microbiota and healthNutritional Studies and DietNutrition, Genetics, and Disease

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Use of dietary indices to control for diet in human gut microbiota studies

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Bowyer, Ruth C. E., Jackson, Matthew A., Pallister, Tess, Skinner, Jane, Spector, Tim D., Welch, Ailsa A., Steves, Claire J.·2018·Microbiome

DOI 10.1186/s40168-018-0455-yPMC PMC5918560

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Abstract

BACKGROUND: Environmental factors have a large influence on the composition of the human gut microbiota. One of the most influential and well-studied is host diet. To assess and interpret the impact of non-dietary factors on the gut microbiota, we endeavoured to determine the most appropriate method to summarise community variation attributable to dietary effects. Dietary habits are multidimensional with internal correlations. This complexity can be simplified by using dietary indices that quantify dietary variance in a single measure and offer a means of controlling for diet in microbiota studies. However, to date, the applicability of different dietary indices to gut microbiota studies has not been assessed. Here, we use food frequency questionnaire (FFQ) data from members of the TwinsUK cohort to create three different dietary measures applicable in western-diet populations: The Healthy Eating Index (HEI), the Mediterranean Diet Score (MDS) and the Healthy Food Diversity index (HFD-Index). We validate and compare these three indices to determine which best summarises dietary influences on gut microbiota composition. RESULTS: All three indices were independently validated using established measures of health, and all were significantly associated with microbiota measures; the HEI had the highest t values in models of alpha diversity measures, and had the highest number of associations with microbial taxa. Beta diversity analyses showed the HEI explained the greatest variance of microbiota composition. In paired tests between twins discordant for dietary index score, the HEI was associated with the greatest variation of taxa and twin dissimilarity. CONCLUSIONS: We find that the HEI explains the most variance in, and has the strongest association with, gut microbiota composition in a western (UK) population, suggesting that it may be the best summary measure to capture gut microbiota variance attributable to habitual diet in comparable populations.

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Fig. 1 Standardised coefficients indicating correlation magnitude from mixed-effects models of three dietary indices (the Healthy Eating Index (HEI), Mediterranean Diet Score (MDS) and the Healthy Food Diversity index (HFD-index) for four measures of microbial alpha diversity; Chao1, observed OTUs, Shannon index and the Simpson index. Only significant results included, p values are *< 0.05, **< 0.01, ***< 0.001. Full results, including model AIC and t values are in Additional file 1: Table S3. Alpha diversity metrics were rarefied and adjusted for age, sex, gender and technical covariatesCC BY · PubMed Central

Fig. 2 Box plot of OTU residuals (see the “Methods” section) significantly different between twins discordant for the Healthy Eating Index (HEI). Twins were characterised as healthy or less healthy relative to their co-twin if they were in differing HEI quantiles and their score differed by greater than 1 standard deviation (number of discordant twins pairs = 250). Of the 167 FDR-significant associations observed in mixed-effects models with the HEI, the 17 Qiime de novo derived operational taxonomic units (OTUs) presented here differed (FDR q < 0.05) between twin pairs in paired Wilcoxon rank-sum tests. X axis labels indicate the lowest taxonomic level assigned to each de novo OTU used in the analysisCC BY · PubMed Central

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Authors: Bowyer, R. C. E., Jackson, M. A., Pallister, T., Skinner, J., Spector, T. D., Welch, A. A., & Steves, C. J.
Affiliations: St Thomas' Hospital (GB)
University of East Anglia (GB)
Corresponding author: Steves, Claire J.
ORCID: Bowyer, Ruth C. E.
Jackson, Matthew A.
Skinner, Jane
Spector, Tim D.
Welch, Ailsa A.
Steves, Claire J.
Venue: Microbiome
Publisher: Springer Science and Business Media LLC
Published: 2018-04-25
Volume: 6
Issue: 1
Pages: 77-77
ISSN: 2049-2618 (ISSN-L)
DOI: 10.1186/s40168-018-0455-y
PMC: PMC5918560
OpenAlex: W2802332168
Cited by: 140
References: 57
Citations by year: 2026: 19 · 2025: 17 · 2024: 11 · 2023: 4 · 2022: 23 · 2021: 26 · 2020: 22 · 2019: 15 · 2018: 3
FWCI: 5.84
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (tdm)
Locations: Microbiome (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, other-oa)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
UEA Digital Repository (University of East Anglia) (acceptedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Research Portal (King's College London) (submittedVersion, cc-by)
Funders: Wellcome Trust (WT081878MA)
Kings College London
Guy's and St Thomas' NHS Foundation Trust
University of East Anglia
Chronic Disease Research Foundation (CDRF/10/06/2014)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Nutritional Studies and Diet
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Nutrition, Genetics, and Disease
Keywords: dietary indices, gut microbiota, Healthy Eating Index, Mediterranean diet score, food frequency questionnaire, alpha diversity, beta diversity, twin discordance, Western diet, microbiota composition
MeSH terms: Gastrointestinal Microbiome, Diet, Healthy, Diet, Feeding Behavior, Humans, Reproducibility of Results, Biodiversity

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Use of dietary indices to control for diet in human gut microbiota studies

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