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Journal ArticleDOI

Gut microbiome composition is linked to whole grain-induced immunological improvements

TL;DR: It is revealed that a short-term intake of whole grains induced compositional alterations of the gut microbiota that coincided with improvements in host physiological measures related to metabolic dysfunctions in humans.
Abstract: The involvement of the gut microbiota in metabolic disorders, and the ability of whole grains to affect both host metabolism and gut microbial ecology, suggest that some benefits of whole grains are mediated through their effects on the gut microbiome. Nutritional studies that assess the effect of whole grains on both the gut microbiome and human physiology are needed. We conducted a randomized cross-over trial with four-week treatments in which 28 healthy humans consumed a daily dose of 60 g of whole-grain barley (WGB), brown rice (BR), or an equal mixture of the two (BR+WGB), and characterized their impact on fecal microbial ecology and blood markers of inflammation, glucose and lipid metabolism. All treatments increased microbial diversity, the Firmicutes/Bacteroidetes ratio, and the abundance of the genus Blautia in fecal samples. The inclusion of WGB enriched the genera Roseburia, Bifidobacterium and Dialister, and the species Eubacterium rectale, Roseburia faecis and Roseburia intestinalis. Whole grains, and especially the BR+WGB treatment, reduced plasma interleukin-6 (IL-6) and peak postprandial glucose. Shifts in the abundance of Eubacterium rectale were associated with changes in the glucose and insulin postprandial response. Interestingly, subjects with greater improvements in IL-6 levels harbored significantly higher proportions of Dialister and lower abundance of Coriobacteriaceae. In conclusion, this study revealed that a short-term intake of whole grains induced compositional alterations of the gut microbiota that coincided with improvements in host physiological measures related to metabolic dysfunctions in humans.

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Citations
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Journal ArticleDOI
19 Nov 2015-Cell
TL;DR: A machine-learning algorithm is devised that integrates blood parameters, dietary habits, anthropometrics, physical activity, and gut microbiota measured in an 800-person cohort and shows that it accurately predicts personalized postprandial glycemic response to real-life meals, and a blinded randomized controlled dietary intervention based on this algorithm resulted in significantly lower postpr andial responses and consistent alterations to gut microbiota configuration.

1,748 citations


Cites background from "Gut microbiome composition is linke..."

  • ..., 2007), and was associated with improved postprandial glycemic and insulinemic responses (Martı́nez et al., 2013), as well as negatively associated with TIIDM (Qin et al....

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Journal ArticleDOI
TL;DR: It is shown that consumption of particular types of food produces predictable shifts in existing host bacterial genera, which affects host immune and metabolic parameters, with broad implications for human health.
Abstract: Recent studies have suggested that the intestinal microbiome plays an important role in modulating risk of several chronic diseases, including inflammatory bowel disease, obesity, type 2 diabetes, cardiovascular disease, and cancer. At the same time, it is now understood that diet plays a significant role in shaping the microbiome, with experiments showing that dietary alterations can induce large, temporary microbial shifts within 24 h. Given this association, there may be significant therapeutic utility in altering microbial composition through diet. This review systematically evaluates current data regarding the effects of several common dietary components on intestinal microbiota. We show that consumption of particular types of food produces predictable shifts in existing host bacterial genera. Furthermore, the identity of these bacteria affects host immune and metabolic parameters, with broad implications for human health. Familiarity with these associations will be of tremendous use to the practitioner as well as the patient.

1,503 citations

Journal ArticleDOI
TL;DR: In this paper, the authors review features of microbiome-immunity crosstalk and their roles in health and disease, while providing examples of molecular mechanisms orchestrating these interactions in the intestine and extra-intestinal organs.
Abstract: The interplay between the commensal microbiota and the mammalian immune system development and function includes multifold interactions in homeostasis and disease. The microbiome plays critical roles in the training and development of major components of the host’s innate and adaptive immune system, while the immune system orchestrates the maintenance of key features of host-microbe symbiosis. In a genetically susceptible host, imbalances in microbiota-immunity interactions under defined environmental contexts are believed to contribute to the pathogenesis of a multitude of immune-mediated disorders. Here, we review features of microbiome-immunity crosstalk and their roles in health and disease, while providing examples of molecular mechanisms orchestrating these interactions in the intestine and extra-intestinal organs. We highlight aspects of the current knowledge, challenges and limitations in achieving causal understanding of host immune-microbiome interactions, as well as their impact on immune-mediated diseases, and discuss how these insights may translate towards future development of microbiome-targeted therapeutic interventions.

1,328 citations


Cites background from "Gut microbiome composition is linke..."

  • ...In humans, individuals with higher fecal abundance of the bacterial genus Dialister and lower levels of Coriobacteriaceae family members show reduced serum levels of the pro-inflammatory cytokine IL-6 after short-term consumption of whole grains.(143) In addition to dietary quantity and content, the timing of dietary intake has been recently shown to affect microbiome composition and in turn immunity....

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Journal ArticleDOI
TL;DR: The current knowledge of the impact of fiber and prebiotic consumption on the composition and metabolic function of the human gastrointestinal microbiota is reviewed, including the effects of physiochemical properties of complex carbohydrates, adequate intake and treatment dosages, and the phenotypic responses related to the composition of thehuman microbiota.
Abstract: The gastrointestinal microbiota has an important role in human health, and there is increasing interest in utilizing dietary approaches to modulate the composition and metabolic function of the mic...

903 citations


Cites background from "Gut microbiome composition is linke..."

  • ...In addition, intervention studies in humans have demonstrated that dietary fiber and whole grain intake increase gut bacterial diversity.(21,22) Low-fiber intake in Western societies is purported to be a driver in the depletion of the human gastrointestinal microbiota and subsequent increases in chronic non-communicable diseases, such as obesity, cardiovascular disease, type 2 diabetes, and colon cancer....

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Journal ArticleDOI
TL;DR: The major principles underlying effects of dietary constituents on the gut microbiota are reviewed, resolving aspects of the diet–microbiota–host crosstalk, and the promises and challenges of incorporating microbiome data into dietary planning are presented.
Abstract: Since the renaissance of microbiome research in the past decade, much insight has accumulated in comprehending forces shaping the architecture and functionality of resident microorganisms in the human gut. Of the multiple host-endogenous and host-exogenous factors involved, diet emerges as a pivotal determinant of gut microbiota community structure and function. By introducing dietary signals into the nexus between the host and its microbiota, nutrition sustains homeostasis or contributes to disease susceptibility. Herein, we summarize major concepts related to the effect of dietary constituents on the gut microbiota, highlighting chief principles in the diet-microbiota crosstalk. We then discuss the health benefits and detrimental consequences that the interactions between dietary and microbial factors elicit in the host. Finally, we present the promises and challenges that arise when seeking to incorporate microbiome data in dietary planning and portray the anticipated revolution that the field of nutrition is facing upon adopting these novel concepts.

806 citations

References
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Journal ArticleDOI
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Abstract: Supplementary Figure 1 Overview of the analysis pipeline. Supplementary Table 1 Details of conventionally raised and conventionalized mouse samples. Supplementary Discussion Expanded discussion of QIIME analyses presented in the main text; Sequencing of 16S rRNA gene amplicons; QIIME analysis notes; Expanded Figure 1 legend; Links to raw data and processed output from the runs with and without denoising.

28,911 citations


"Gut microbiome composition is linke..." refers methods in this paper

  • ...Sequence processing was performed combining features of QIIME (Caporaso et al., 2010) and the Ribosomal Database Project pipeline (Cole et al., 2009)....

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  • ...Chao1 species richness estimator, and Shannon’s and Simpson’s (defined as 1-Dominance) diversity indices were computed with QIIME....

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  • ...Sequence processing was performed combining features of QIIME (Caporaso et al., 2010) and the Ribosomal Database Project pipeline (Cole et al....

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Journal ArticleDOI
TL;DR: The RDP Classifier can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes, and the majority of the classification errors appear to be due to anomalies in the current taxonomies.
Abstract: The Ribosomal Database Project (RDP) Classifier, a naive Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (≥95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.

16,048 citations


"Gut microbiome composition is linke..." refers methods in this paper

  • ...Sequence processing was performed combining features of QIIME (Caporaso et al., 2010) and the Ribosomal Database Project pipeline (Cole et al., 2009)....

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  • ...Sequences were assigned to a bacterial phylum, family and genus using the Classifier tool of the Ribosomal Database Project (Wang et al., 2007)....

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Journal ArticleDOI
21 Dec 2006-Nature
TL;DR: It is demonstrated through metagenomic and biochemical analyses that changes in the relative abundance of the Bacteroidetes and Firmicutes affect the metabolic potential of the mouse gut microbiota and indicates that the obese microbiome has an increased capacity to harvest energy from the diet.
Abstract: The worldwide obesity epidemic is stimulating efforts to identify host and environmental factors that affect energy balance. Comparisons of the distal gut microbiota of genetically obese mice and their lean littermates, as well as those of obese and lean human volunteers have revealed that obesity is associated with changes in the relative abundance of the two dominant bacterial divisions, the Bacteroidetes and the Firmicutes. Here we demonstrate through metagenomic and biochemical analyses that these changes affect the metabolic potential of the mouse gut microbiota. Our results indicate that the obese microbiome has an increased capacity to harvest energy from the diet. Furthermore, this trait is transmissible: colonization of germ-free mice with an 'obese microbiota' results in a significantly greater increase in total body fat than colonization with a 'lean microbiota'. These results identify the gut microbiota as an additional contributing factor to the pathophysiology of obesity.

10,126 citations


"Gut microbiome composition is linke..." refers background in this paper

  • ...Obesity and type 2 diabetes have been linked to alterations in the intestinal microbiota in both the humans and animal models (Ley et al., 2006; Turnbaugh et al., 2006; Cani et al., 2007; Larsen et al., 2010; Vijay-Kumar et al., 2010)....

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Journal ArticleDOI
21 Dec 2006-Nature
TL;DR: It is shown that the relative proportion of Bacteroidetes is decreased in obese people by comparison with lean people, and that this proportion increases with weight loss on two types of low-calorie diet.
Abstract: Two groups of beneficial bacteria are dominant in the human gut, the Bacteroidetes and the Firmicutes. Here we show that the relative proportion of Bacteroidetes is decreased in obese people by comparison with lean people, and that this proportion increases with weight loss on two types of low-calorie diet. Our findings indicate that obesity has a microbial component, which might have potential therapeutic implications.

7,550 citations


"Gut microbiome composition is linke..." refers background or result in this paper

  • ...If systemic inflammation and cholesterol metabolism impact levels of Ruminococcaceae and Bacteroidetes, respectively, then these interactions could explain the discrepancies related to an altered microbiome in obese versus normoweight individuals (Ley et al., 2006; Duncan et al., 2008; Schwiertz et al., 2010)....

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  • ...…the baseline fecal microbiota of the participants was dominated by the phyla Firmicutes and Bacteroidetes, with lower proportions of Verrucomicrobia and Actinobacteria, in agreement with previous molecular characterizations of the human fecal microbiota (Ley et al., 2006; Martı́nez et al., 2010)....

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  • ...Pyrosequencing revealed that the baseline fecal microbiota of the participants was dominated by the phyla Firmicutes and Bacteroidetes, with lower proportions of Verrucomicrobia and Actinobacteria, in agreement with previous molecular characterizations of the human fecal microbiota (Ley et al., 2006; Martı́nez et al., 2010)....

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  • ...Obesity and type 2 diabetes have been linked to alterations in the intestinal microbiota in both the humans and animal models (Ley et al., 2006; Turnbaugh et al., 2006; Cani et al., 2007; Larsen et al., 2010; Vijay-Kumar et al., 2010)....

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  • ...…inflammation and cholesterol metabolism impact levels of Ruminococcaceae and Bacteroidetes, respectively, then these interactions could explain the discrepancies related to an altered microbiome in obese versus normoweight individuals (Ley et al., 2006; Duncan et al., 2008; Schwiertz et al., 2010)....

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Journal ArticleDOI
14 Dec 2006-Nature
TL;DR: Dysfunction of the immune response and metabolic regulation interface can be viewed as a central homeostatic mechanism, dysfunction of which can lead to a cluster of chronic metabolic disorders, particularly obesity, type 2 diabetes and cardiovascular disease.
Abstract: Metabolic and immune systems are among the most fundamental requirements for survival. Many metabolic and immune response pathways or nutrient- and pathogen-sensing systems have been evolutionarily conserved throughout species. As a result, immune response and metabolic regulation are highly integrated and the proper function of each is dependent on the other. This interface can be viewed as a central homeostatic mechanism, dysfunction of which can lead to a cluster of chronic metabolic disorders, particularly obesity, type 2 diabetes and cardiovascular disease. Collectively, these diseases constitute the greatest current threat to global human health and welfare.

7,536 citations


"Gut microbiome composition is linke..." refers background in this paper

  • ...Furthermore, the gut microbiome might exacerbate the systemic inflammation associated with obesity and related metabolic disorders (Hotamisligil, 2006; Ding et al., 2010), possibly through the induction of endotoxemia driven by lipopolysaccharide translocation through the intestinal epithelium…...

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  • ...Together, these associations substantiate the link between adiposity, a low-grade systemic inflammation, and glucose metabolism (Hotamisligil, 2006)....

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  • ...Most importantly, inflammation has been identified as a main cause of metabolic disorders (Hotamisligil, 2006), and the anti-inflammatory effect could provide a mechanism by which whole grains improve glucose metabolism....

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