Dietary Patterns and Gut Microbiome Composition in a Large Population-Based Cohort

Abstract Objectives Effects of diet on health and disease risk may be mediated by changes in gut microbiome composition. Our aim was to examine associations between intake of food groups and overall diet quality with gut microbiome composition in a large population-based cohort. Methods We analyzed data of 1130 participants (median age 57 years) from the Rotterdam Study, a population-based cohort study in the Netherlands. We measured dietary intake using a 389-item FFQ, and assessed adherence to dietary guidelines for 14 food groups and combined into a diet quality score. We assessed gut microbiome composition using 16S rRNA gene sequencing. Data were available for 11 phyla, 19 classes, 25 orders, 44 families, and 184 genera. Alpha diversity was quantified by Shannon index and Richness, and beta diversity was qualified by Bray-Curtis distance. We used linear models to examine associations with Shannon index and Richness, Adonis function to examine variations of Bray-Curtis distance, and Multivariate Association with Linear Models to examine associations with gut microbial communities. Models were adjusted for technical covariates, energy intake, age, sex, physical activity, education, smoking and BMI. Results After adjustment, higher diet quality was associated with more alpha diversity and explained part of the variation in beta diversity (P < 0.001). Overall diet quality was associated with relative abundance of four families (Erysipelotrichaceae, Ruminococcaceae, Lachnospiraceae, Christensenellaceae), and 15 genera (Torques group, RuminococcaceaeUCG002, RuminococcaceaeUCG003, RuminococcaceaeUCG005, RuminococcaceaeUCG010, Xylanophilum group, Blautia, RuminococcaceaeNK4A214 group, Eligens group, Coprococcus3, Senegalimassilia, Lachnospira, Halliigroup, ChristensenellaceaeR7 group, Ventriosum group) (adjusted p: q < 0.05). Results were not explained by any single food group. Higher intake of fruits, vegetables, whole grains, and tea, and lower intake of red meat and alcohol were all related to microbiome composition. Replication analyses are ongoing. Conclusions Better overall diet quality may improve overall gut microbial diversity. Furthermore, diet quality may influence abundance of certain gut microbial communities, several of which have previously been linked to lower risk of metabolic and inflammatory diseases. Funding Sources N/A.

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Immune Gene Expression Covaries with Gut Microbiome Composition in Stickleback

mBio ◽

10.1128/mbio.00145-21 ◽

2021 ◽

Vol 12 (3) ◽

Author(s):

Lauren E. Fuess ◽

Stijn den Haan ◽

Fei Ling ◽

Jesse N. Weber ◽

Natalie C. Steinel ◽

...

Keyword(s):

Gene Expression ◽

Microbial Communities ◽

Gut Microbiome ◽

Alpha Diversity ◽

Host Immunity ◽

Host Gene ◽

Microbiota Composition ◽

Host Gene Expression ◽

Microbiome Composition ◽

Immune Genes

ABSTRACT Commensal microbial communities have immense effects on their vertebrate hosts, contributing to a number of physiological functions, as well as host fitness. In particular, host immunity is strongly linked to microbiota composition through poorly understood bi-directional links. Gene expression may be a potential mediator of these links between microbial communities and host function. However, few studies have investigated connections between microbiota composition and expression of host immune genes in complex systems. Here, we leverage a large study of laboratory-raised fish from the species Gasterosteus aculeatus (three-spined stickleback) to document correlations between gene expression and microbiome composition. First, we examined correlations between microbiome alpha diversity and gene expression. Our results demonstrate robust positive associations between microbial alpha diversity and expression of host immune genes. Next, we examined correlations between host gene expression and abundance of microbial taxa. We identified 15 microbial families that were highly correlated with host gene expression. These families were all tightly correlated with host expression of immune genes and processes, falling into one of three categories—those positively correlated, negatively correlated, and neutrally related to immune processes. Furthermore, we highlight several important immune processes that are commonly associated with the abundance of these taxa, including both macrophage and B cell functions. Further functional characterization of microbial taxa will help disentangle the mechanisms of the correlations described here. In sum, our study supports prevailing hypotheses of intimate links between host immunity and gut microbiome composition. IMPORTANCE Here, we document associations between host gene expression and gut microbiome composition in a nonmammalian vertebrate species. We highlight associations between expression of immune genes and both microbiome diversity and abundance of specific microbial taxa. These findings support other findings from model systems which have suggested that gut microbiome composition and host immunity are intimately linked. Furthermore, we demonstrate that these correlations are truly systemic; the gene expression detailed here was collected from an important fish immune organ (the head kidney) that is anatomically distant from the gut. This emphasizes the systemic impact of connections between gut microbiota and host immune function. Our work is a significant advancement in the understanding of immune-microbiome links in nonmodel, natural systems.

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Topological Data Analysis Highlights Novel Geographical Signatures of the Human Gut Microbiome

Frontiers in Artificial Intelligence ◽

10.3389/frai.2021.680564 ◽

2021 ◽

Vol 4 ◽

Author(s):

Eva Lymberopoulos ◽

Giorgia Isabella Gentili ◽

Muhannad Alomari ◽

Nikhil Sharma

Keyword(s):

Data Analysis ◽

Gut Microbiome ◽

Large Population ◽

Enrichment Analysis ◽

Population Based ◽

Topological Data Analysis ◽

Microbiome Composition ◽

Demographical Data ◽

Microbiome Data ◽

Topological Data

Background: There is growing interest in the connection between the gut microbiome and human health and disease. Conventional approaches to analyse microbiome data typically entail dimensionality reduction and assume linearity of the observed relationships, however, the microbiome is a highly complex ecosystem marked by non-linear relationships. In this study, we use topological data analysis (TDA) to explore differences and similarities between the gut microbiome across several countries.Methods: We used curated adult microbiome data at the genus level from the GMrepo database. The dataset contains OTU and demographical data of over 4,400 samples from 19 studies, spanning 12 countries. We analysed the data with tmap, an integrative framework for TDA specifically designed for stratification and enrichment analysis of population-based gut microbiome datasets.Results: We find associations between specific microbial genera and groups of countries. Specifically, both the USA and UK were significantly co-enriched with the proinflammatory genera Lachnoclostridium and Ruminiclostridium, while France and New Zealand were co-enriched with other, butyrate-producing, taxa of the order Clostridiales.Conclusion: The TDA approach demonstrates the overlap and distinctions of microbiome composition between and within countries. This yields unique insights into complex associations in the dataset, a finding not possible with conventional approaches. It highlights the potential utility of TDA as a complementary tool in microbiome research, particularly for large population-scale datasets, and suggests further analysis on the effects of diet and other regionally varying factors.

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Consumption of Stilbenes and Flavonoids is Linked to Reduced Risk of Obesity Independently of Fiber Intake

Nutrients ◽

10.3390/nu12061871 ◽

2020 ◽

Vol 12 (6) ◽

pp. 1871

Author(s):

Olatz Mompeo ◽

Tim D. Spector ◽

Marisa Matey Hernandez ◽

Caroline Le Roy ◽

Geoffrey Istas ◽

...

Keyword(s):

Gut Microbiome ◽

Alpha Diversity ◽

Shannon Index ◽

Fiber Intake ◽

Mediation Analyses ◽

Microbiome Composition ◽

Metabolic Outcomes ◽

16S Rna ◽

Flavonoid Intake ◽

Reduced Risk

Background: Polyphenol consumption is implicated in gut microbiome composition and improved metabolic outcomes, but it is unclear whether the effect is independent of dietary fiber. Methods: We investigated the links between (poly)phenol intake, gut microbiome composition (16s RNA) and obesity independently of fiber intake in UK women (n = 1810) and in a small group of UK men (n = 64). Results: (Poly)phenol intakes correlated with microbiome alpha diversity (Shannon Index) after adjusting for confounders and fiber intake. Moreover, flavonoid intake was significantly correlated with the abundance of Veillonella, (a genus known to improve physical performance), and stilbene intake with that of butyrate-producing bacteria (Lachnospira and Faecalibacterium). Stilbene and flavonoid intake also correlated with lower odds of prevalent obesity (Stilbenes: Odds Ratio (95% Confidence Interval) (OR(95%CI)) = 0.80 (0.73, 0.87), p = 4.90 × 10−7; Flavonoids: OR(95%CI) = 0.77 (0.65, 0.91), p = 0.002). Formal mediation analyses revealed that gut microbiome mediates ~11% of the total effect of flavonoid and stilbene intake on prevalent obesity. Conclusions: Our findings highlight the importance of (poly)phenol consumption for optimal human health.

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Immune gene expression covaries with gut microbiome composition in stickleback

10.1101/2020.08.04.236786 ◽

2020 ◽

Author(s):

Lauren Fuess ◽

Stijn den Haan ◽

Fei Ling ◽

Jesse N. Weber ◽

Natalie C. Steinel ◽

...

Keyword(s):

Gene Expression ◽

Microbial Communities ◽

Gut Microbiome ◽

Alpha Diversity ◽

Host Immunity ◽

Host Gene ◽

Microbiota Composition ◽

Host Gene Expression ◽

Microbiome Composition ◽

Immune Genes

ABSTRACTCommensal microbial communities have immense effects on their vertebrate hosts, contributing to a number of physiological functions as well as host fitness. In particular, host immunity is strongly linked to microbiota composition through poorly understood bi-directional links. Gene expression may be a potential mediator of these links between microbial communities and host function. However few studies have investigated connections between microbiota composition and expression of host immune genes in complex systems. Here we leverage a large study of laboratory-raised fish from the species Gasterosteus aculeatus (three-spined stickleback) to document correlations between gene expression and microbiome composition. First, we examined correlations between microbiome alpha diversity and gene expression. Our results demonstrate robust positive associations between microbial alpha diversity and expression of host immunity. Next, we examined correlations between host gene expression and abundance of microbial taxa. We identified 15 microbial families that were highly correlated to host gene expression. These families were all tightly correlated to host expression of immune genes and processes, falling into one of three categories: those positively correlated, negatively correlated, and neutrally related to immune processes. Furthermore, we highlight several important immune processes that are commonly associated with abundance of these taxons, including both macrophage and B cell functions. Further functional characterization of microbial taxa will help disentangle the mechanisms of the correlations described here. In sum, our study supports prevailing hypotheses of intimate links between host immunity and gut microbiome composition.

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Long-term Association between Diet Quality and Characteristics of the Gut Microbiome in the Multiethnic Cohort Study

British Journal Of Nutrition ◽

10.1017/s0007114521002968 ◽

2021 ◽

pp. 1-29

Author(s):

Erica Ma ◽

Gertraud Maskarinec ◽

Unhee Lim ◽

Carol J. Boushey ◽

Lynne R. Wilkens ◽

...

Keyword(s):

Diet Quality ◽

Gut Microbiome ◽

Alpha Diversity ◽

Healthy Eating Index ◽

Shannon Index ◽

Rrna Gene ◽

Microbial Composition ◽

Multiethnic Cohort

Abstract As past usual diet quality may affect gut microbiome (GM) composition, we examined the association of the Healthy Eating Index (HEI)-2015 assessed 21 and 9 years before stool collection with measures of fecal microbial composition in a subset of the Multiethnic Cohort. A total of 5,936 participants completed a validated quantitative food frequency questionnaire (QFFQ) at cohort entry (Q1, 1993-96), 5,280 at follow-up (Q3, 2003-08), and 1,685 also at a second follow-up (Adiposity Phenotype Study (APS), 2013–16). All participants provided a stool sample in 2013-2016. Fecal microbial composition was obtained from 16S rRNA gene sequencing (V1-V3 region). HEI-2015 scores were computed based on each QFFQ. Using linear regression adjusted for relevant covariates, we calculated associations of HEI-2015 scores with gut microbial diversity and 152 individual genera. The mean HEI-2015 scores increased from Q1 (67±10) to Q3 (71±11) and APS (72±10). Alpha diversity assessed by the Shannon Index was significantly higher with increasing tertiles of HEI-2015. Of the 152 bacterial genera tested, seven (Anaerostipes, Coprococcus_2, Eubacterium eligens, Lachnospira, Lachnospiraceae_ND3007, Ruminococcaceae_UCG-013, and Ruminococcus_1) were positively and five (Collinsella, Parabacteroides, Ruminiclostridium_5, Ruminococcus gnavus, and Tyzzerella) were inversely associated with HEI-2015 assessed in Q1, Q3, and APS. The estimates of change per unit of the HEI-2015 score associated with the abundance of these 12 genera were consistent across the three questionnaires. The quality of past diet, assessed as far as ˜20 years before stool collection, is equally predictive of GM composition as concurrently assessed diet, indicative of the long-term consistency of this relation.

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Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

Genome Biology ◽

10.1186/s13059-019-1831-z ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 14

Author(s):

Robert C. Kaplan ◽

Zheng Wang ◽

Mykhaylo Usyk ◽

Daniela Sotres-Alvarez ◽

Martha L. Daviglus ◽

...

Keyword(s):

Community Health ◽

Gut Microbiome ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Shannon Index ◽

Health Study ◽

Rrna Gene ◽

Cross Sectional ◽

Hispanic Community ◽

The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

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Cruciferous Vegetable Intake Results in Differentially Modified Gut Microbiome Composition of Mice Fed a High Fat Diet or a Western Diet

Current Developments in Nutrition ◽

10.1093/cdn/nzaa062_052 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 1595-1595

Author(s):

Sabrina Trudo ◽

Rosa Moreno ◽

Jeong Hoon Pan ◽

Daniel Gallaher ◽

Jae Kyeom Kim ◽

...

Keyword(s):

Gut Microbiome ◽

Vegetable Intake ◽

Body Weight Gain ◽

Alpha Diversity ◽

Western Diet ◽

Index Number ◽

Standard Diet ◽

Jaccard Distance ◽

Microbiome Composition ◽

Distinct Cluster

Abstract Objectives Cruciferous (CRU; rich in glucosinolates) and apiaceous (API; rich in furanocoumarins) vegetable intake decrease colon cancer risk markers, likely through different mechanisms. Previous reports suggest background diets influence efficacy of bioactives. Here, we determined the effects on the composition of the gut microbiome of CRU and API supplementation to different background diets, diet-induced obesity (DIO) and the total western diet (TWD). Methods C57BL/6J male mice were fed standard diet (AIN93G), DIO, DIO with 21% (w/w) CRU (DIO + CRU), DIO with 21% (w/w) API (DIO + API), TWD, TWD with CRU (TWD + CRU), or TWD with API (TWD + API). After 12 weeks, cecal contents were collected for 16S rRNA sequencing and data analyzed by mothur. Results There were no differences in body weight gain except mice fed DIO + CRU gained more than mice fed AIN-93G or TWD. Lachnospiraceae was increased by CRU supplementation to both DIO and TWD and by API supplementation to TWD. CRU increased alpha diversity [Shannon Index, number of observed Operational Taxonomic Unit (OTUs)] compared to DIO and TWD. Regarding beta diversity, DIO + CRU showed distinct cluster compared to DIO (Bray-Curtis, ANOSIM, R = 0.35, P < 0.001; Jaccard distance, R = 0.47, P < 0.001). TWD + CRU showed distinct cluster compared to TWD (Bray-Curtis, R = 0.59, P < 0.001; Jaccard distance, R = 0.62, P < 0.001). API did not change alpha diversity, but did affect beta diversities with distinct clusters between API groups and their basal diet groups (Jaccard distance, R = 0.36 and 0.31 for DIO and TWD, respectively, P < 0.05). Among top 25 discriminating features between DIO and TWD and their supplementation of API and CRU, there were 9 shared OTUs including Lachnospiraceae, Clostridium XlVa, Clostridiales, Eisenbergiella, and Clostridium IV. Akkermansia were decreased in DIO + CRU compared with DIO. In TWD panel, Bifidobacterium and Erysipelotrichaceae decreased in TWD + CRU, while Turicibacter were identified as TWD + CRU signature. Erysipelotrichaceae and Bifidobacterium differentiated AIN-93G, DIO, and TWD. Conclusions CRU supplementation of DIO and TWD altered gut microbiome composition with some differences based on background diet. API also altered composition, albeit to a lesser extent. Funding Sources University of Arkansas, Fulbright Nicaragua Fellow.

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Dietary Protein, Fiber and Coffee Are Associated with Small Intestine Microbiome Composition and Diversity in Patients with Liver Cirrhosis

Nutrients ◽

10.3390/nu12051395 ◽

2020 ◽

Vol 12 (5) ◽

pp. 1395 ◽

Cited By ~ 1

Author(s):

Shehnaz K. Hussain ◽

Tien S. Dong ◽

Vatche Agopian ◽

Joseph R. Pisegna ◽

Francisco A. Durazo ◽

...

Keyword(s):

Liver Cirrhosis ◽

Diet Quality ◽

Alpha Diversity ◽

Healthy Eating Index ◽

Sequencing Data ◽

Microbiome Composition ◽

Coffee Drinking ◽

Microbial Profile ◽

Protein Fiber ◽

Fiber Consumption

The gut microbiome is a key factor in chronic liver disease progression. In prior research, we found that the duodenal microbiome was associated with sex, ethnicity, and cirrhosis complications. Here, we examined the association between diet and the duodenal microbiome in patients with liver cirrhosis. This study included 51 participants who completed a detailed food frequency questionnaire and donated duodenal biopsies for microbiome characterization by 16S ribosomal RNA gene sequencing. Data were analyzed for alpha diversity, beta diversity, and association of taxa abundance with diet quality and components using QIIME 2 pipelines. Diet quality was assessed through calculation of the Healthy Eating Index 2010. Participants with higher adherence to protein recommendations exhibited increased microbial richness and evenness (p = 0.03) and a different microbial profile compared to those with lower adherence (p = 0.03). Prevotella-9 and Agathobacter were increased in association with increased protein adherence. Fiber consumption was also associated with the duodenal microbial profile (p = 0.01), with several taxa exhibiting significantly decreased or increased abundance in association with fiber intake. Coffee drinking was associated with microbial richness and evenness (p = 0.001), and there was a dose–response association between coffee drinking and relative abundance of Veillonella (p = 0.01). We conclude that protein, fiber, and coffee are associated with diversity and composition of the duodenal microbiome in liver cirrhosis.

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Intestinal microbiome composition and its relation to joint pain and inflammation

Nature Communications ◽

10.1038/s41467-019-12873-4 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 28

Author(s):

Cindy G. Boer ◽

Djawad Radjabzadeh ◽

Carolina Medina-Gomez ◽

Sanzhima Garmaeva ◽

Dieuwke Schiphof ◽

...

Keyword(s):

Knee Pain ◽

Joint Pain ◽

Large Population ◽

Absolute Quantification ◽

Population Based ◽

Intestinal Microbiome ◽

Gastrointestinal Microbiome ◽

Microbiome Composition ◽

Show Evidence ◽

The Relationship

Abstract Macrophage-mediated inflammation is thought to have a causal role in osteoarthritis-related pain and severity, and has been suggested to be triggered by endotoxins produced by the gastrointestinal microbiome. Here we investigate the relationship between joint pain and the gastrointestinal microbiome composition, and osteoarthritis-related knee pain in the Rotterdam Study; a large population based cohort study. We show that abundance of Streptococcus species is associated with increased knee pain, which we validate by absolute quantification of Streptococcus species. In addition, we replicate these results in 867 Caucasian adults of the Lifelines-DEEP study. Finally we show evidence that this association is driven by local inflammation in the knee joint. Our results indicate the microbiome is a possible therapeutic target for osteoarthritis-related knee pain.

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Dietary predictors of plasma total homocysteine in the Hordaland Homocysteine Study

British Journal Of Nutrition ◽

10.1017/s0007114507691788 ◽

2007 ◽

Vol 98 (1) ◽

pp. 201-210 ◽

Cited By ~ 31

Author(s):

Svetlana V. Konstantinova ◽

Stein Emil Vollset ◽

Paula Berstad ◽

Per Magne Ueland ◽

Christian A. Drevon ◽

...

Keyword(s):

Large Population ◽

Population Based ◽

B Vitamins ◽

Processed Meat ◽

Food Groups ◽

Thcy Level ◽

Food Items ◽

Total Homocysteine ◽

Dietary Components ◽

Plasma Total Homocysteine

Established dietary predictors of plasma total homocysteine (tHcy) include folate, riboflavin, and vitamins B6and B12, while information is scarce regarding other dietary components. The aim of this study was to examine the relation between a variety of food groups, food items and nutrients, and plasma tHcy in a large population-based study. The study population included 5812 men and women aged 47–49 and 71–74 years who completed a 169-item FFQ. tHcy was examined across quartiles of dietary components by multiple linear regression analyses adjusting for age, sex, energy intake, various risk factors for elevated tHcy, as well as for dietary and plasma B-vitamins. Among 4578 non-users of vitamin supplements, intake of vegetables, fruits, cereals, eggs, fish and milk, as well as chicken and non-processed meats were inversely associated with tHcy level. The estimated mean difference in tHcy per increasing quartile of intake ranged from − 0·11 (95 % CI − 0·21, − 0·01) μmol/l for milk to − 0·32 (95 % CI − 0·42, − 0·22) μmol/l for vegetables. Positive associations were found for sweets and cakes. Whole-grain bread was significantly inversely related to tHcy only after additional adjustment for dietary and plasma B-vitamins. The nutrients folate, vitamin B6, B12, and riboflavin were inversely related to tHcy. Complex carbohydrates were inversely, and fat positively associated with tHcy, also after adjustment for dietary and plasma B-vitamins. In conclusion, food items rich in B-vitamins and with a low content of fat and sugar were related to lower tHcy levels. Eggs, chicken, non-processed meat, fish and milk were inversely associated with tHcy.

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