Marlene Remely

Effects of short chain fatty acid producing bacteria on epigenetic regulation of FFAR3 in type 2 diabetes and obesity

The human gut microbiota and microbial influences on lipid and glucose metabolism, satiety, and chronic low-grade inflammation are known to be involved in metabolic syndrome. Fermentation end products, especially short chain fatty acids, are believed to engage the epigenetic regulation of inflammatory reactions via FFARs (free fatty acid receptor) and other short chain fatty acid receptors. We studied a potential interaction of the microbiota with epigenetic regulation in obese and type 2 diabetes patients compared to a lean control group over a four month intervention period. Intervention comprised a GLP-1 agonist (glucagon-like peptide 1) for type 2 diabetics and nutritional counseling for both intervention groups. Microbiota was analyzed for abundance, butyryl-CoA:acetate CoA-transferase gene and for diversity by polymerase chain reaction and 454 high-throughput sequencing. Epigenetic methylation of the promoter region of FFAR3 and LINE1 (long interspersed nuclear element 1) was analyzed using bisulfite conversion and pyrosequencing. The diversity of the microbiota as well as the abundance of Faecalibacterium prausnitzii were significantly lower in obese and type 2 diabetic patients compared to lean individuals. Results from Clostridium cluster IV and Clostridium cluster XIVa showed a decreasing trend in type 2 diabetics in comparison to the butyryl-CoA:acetate CoA-transferase gene and according to melt curve analysis. During intervention no significant changes were observed in either intervention group. The analysis of five CpGs in the promoter region of FFAR3 showed a significant lower methylation in obese and type 2 diabetics with an increase in obese patients over the intervention period. These results disclosed a significant correlation between a higher body mass index and lower methylation of FFAR3. LINE-1, a marker of global methylation, indicated no significant differences between the three groups or the time points, although methylation of type 2 diabetics tended to increase over time. Our results provide evidence that a different composition of gut microbiota in obesity and type 2 diabetes affect the epigenetic regulation of genes. Interactions between the microbiota and epigenetic regulation may involve not only short chain fatty acids binding to FFARs. Therefore dietary interventions influencing microbial composition may be considered as an option in the engagement against metabolic syndrome.

Changes in Human Fecal Microbiota Due to Chemotherapy Analyzed by TaqMan-PCR, 454 Sequencing and PCR-DGGE Fingerprinting

Background We investigated whether chemotherapy with the presence or absence of antibiotics against different kinds of cancer changed the gastrointestinal microbiota. Methodology/Principal Findings Feces of 17 ambulant patients receiving chemotherapy with or without concomitant antibiotics were analyzed before and after the chemotherapy cycle at four time points in comparison to 17 gender-, age- and lifestyle-matched healthy controls. We targeted 16S rRNA genes of all bacteria, Bacteroides, bifidobacteria, Clostridium cluster IV and XIVa as well as C. difficile with TaqMan qPCR, denaturing gradient gel electrophoresis (DGGE) fingerprinting and high-throughput sequencing. After a significant drop in the abundance of microbiota (p = 0.037) following a single treatment the microbiota recovered within a few days. The chemotherapeutical treatment marginally affected the Bacteroides while the Clostridium cluster IV and XIVa were significantly more sensitive to chemotherapy and antibiotic treatment. DGGE fingerprinting showed decreased diversity of Clostridium cluster IV and XIVa in response to chemotherapy with cluster IV diversity being particularly affected by antibiotics. The occurrence of C. difficile in three out of seventeen subjects was accompanied by a decrease in the genera Bifidobacterium, Lactobacillus, Veillonella and Faecalibacterium prausnitzii. Enterococcus faecium increased following chemotherapy. Conclusions/Significance Despite high individual variations, these results suggest that the observed changes in the human gut microbiota may favor colonization with C.difficile and Enterococcus faecium. Perturbed microbiota may be a target for specific mitigation with safe pre- and probiotics.

Microbiota and epigenetic regulation of inflammatory mediators in type 2 diabetes and obesity

Metabolic syndrome is associated with alterations in the structure of the gut microbiota leading to low-grade inflammatory responses. An increased penetration of the impaired gut membrane by bacterial components is believed to induce this inflammation, possibly involving epigenetic alteration of inflammatory molecules such as Toll-like receptors (TLRs). We evaluated changes of the gut microbiota and epigenetic DNA methylation of TLR2 and TLR4 in three groups of subjects: type 2 diabetics under glucagon-like peptide-1 agonist therapy, obese individuals without established insulin resistance, and a lean control group. Clostridium cluster IV, Clostridium cluster XIVa, lactic acid bacteria, Faecalibacterium prausnitzii and Bacteroidetes abundances were analysed by PCR and 454 high-throughput sequencing. The epigenetic methylation in the regulatory region of TLR4 and TLR2 was analysed using bisulfite conversion and pyrosequencing. We observed a significantly higher ratio of Firmicutes/ Bacteroidetes in type 2 diabetics compared to lean controls and obese. Major differences were shown in lactic acid bacteria, with the highest abundance in type 2 diabetics, followed by obese and lean participants. In comparison, F. prausnitzii was least abundant in type 2 diabetics, and most abundant in lean controls. Methylation analysis of four CpGs in the first exon of TLR4 showed significantly lower methylation in obese individuals, but no significant difference between type 2 diabetics and lean controls. Methylation of seven CpGs in the promoter region of TLR2 was significantly lower in type 2 diabetics compared to obese subjects and lean controls. The methylation levels of both TLRs were significantly correlated with body mass index. Our data suggest that changes in gut microbiota and thus cell wall components are involved in the epigenetic regulation of inflammatory reactions. An improved diet targeted to induce gut microbial balance and in the following even epigenetic changes of pro-inflammatory genes may be effective in the prevention of metabolic syndrome.

Therapeutic perspectives of epigenetically active nutrients.

Many nutrients are known for a wide range of activities in prevention and alleviation of various diseases. Recently, their potential role in regulating human health through effects on epigenetics has become evident, although specific mechanisms are still unclear. Thus, nutriepigenetics/nutriepigenomics has emerged as a new and promising field in current epigenetics research in the past few years. In particular, polyphenols, as part of the central dynamic interaction between the genome and the environment with specificity at physiological concentrations, are well known to affect mechanisms underlying human health. This review summarizes the effects of dietary compounds on epigenetic mechanisms in the regulation of gene expression including expression of enzymes and other molecules responsible for drug absorption, distribution, metabolism and excretion in cancer, metabolic syndrome, neurodegenerative disorders and hormonal dysfunction.

Increased gut microbiota diversity and abundance of Faecalibacterium prausnitzii and Akkermansia after fasting: a pilot study

SummaryBackgroundAn impaired gut microbiota has been reported as an important factor in the pathogenesis of obesity. Weight reduction has already been mentioned to improve gut microbial subpopulations involved in inflammatory processes, though other subpopulations still need further investigation. Thus, weight reduction in the context of a fasting program together with a probiotic intervention may improve the abundance and diversity of gut microbiota.MethodsIn this pilot study, overweight people underwent a fasting program with laxative treatment for 1 week followed by a 6 week intervention with a probiotic formula. Gut microbiota were analyzed on the basis of 16s rDNA with a quantitative real time polymerase chain reaction. Additionally, a food frequency questionnaire with questions about nutritional behavior, lifestyle, and physical activity was administered before and after the intervention.ResultsWe observed an increase in microbial diversity over the study period. No significant changes in abundance of total bacteria, or of Bacteroidetes, Prevotella, Clostridium cluster XIVa, or Clostridium cluster IV were found, although Faecalibacterium prausnitzii showed an increase over the study period. In addition, Akkermanisa and Bifidobacteria increased in abundance due to intervention. The inflammation-associated gut microbes Enterobacteria and Lactobacilli increased during the first week and then declined by the end of the intervention. Two-thirds of the study participants harbored Archaea. No significant improvements of eating habits were reported, although physical activity improved due to the intervention.ConclusionsOur results show that caloric restriction affects gut microbiota by proliferating mucin-degrading microbial subpopulations. An additional intervention with a probiotic formula increased probiotic-administered gut microbial populations.

Nutriepigenomics: the role of nutrition in epigenetic control of human diseases.

Purpose of reviewNutrients or even diets affect the epigenome by lifelong remodeling. Nutritional imbalances are associated with noncommunicable diseases. Thus, nutriepigenomics is a promising field in the treatment of complex human diseases. Recent findingsThe epigenome is susceptible to changes and can be shaped by nutritional states, especially in prenatal period through transgenerational mechanisms and in early postnatal life when critical developmental processes are taking place. Although more stable, the epigenetic marks in adulthood are also dynamic and modifiable by environmental factors including diet. SummaryThe present review is focused on the most recent knowledge of epigenetically active nutrients/diets including transgenerational inheritance and prenatal predispositions related to increased risk for cancer, metabolic syndrome, and neurodegenerative diseases.

Effects of antibiotic therapy on the gastrointestinal microbiota and the influence of Lactobacillus casei

Aims of methods Effects of intervention with Lactobacillus casei Shirota (LcS) on the incidence of antibiotic-associated diarrhoea (AAD), Clostridium difficile infection (CDI) and changes in faecal microbiota were analysed using C. difficile ELISA (678 patients), qPCR using 16S rRNA group-specific primers, C. difficile-toxin kit and polymerase chain reaction/denaturing gradient gel electrophoresis (56 patients). Results Results As much as 18.5% of antibiotic treated group developed AAD, but only 5% of patients treated with antibiotics and LcS. Following antibiotic therapy, a decrease in the abundance of total Bacteria, Clostridium cluster IV and XI, Bifidobacterium spp. and butyryl-CoA CoA transferase genes was observed, whereas Enterobacteriaceae increased. LcS intervention reduced the antibiotic-associated decrease in the diversity of microbiota, increased the abundance of Lactobacillus spp. and reduced the antibiotic-induced decrease of Bifidobacterium spp. Conclusions Antibiotic treatment affects the diversity and the composition of the microbiota impairing butyrate production. Intervention with certain Lactobacillus strains may antagonise some of these changes, and more potent short-chain fatty acid-stimulating probiotics are desirable for intervention in AAD.

Gut Microbiota of Obese, Type 2 Diabetic Individuals is Enriched in Faecalibacterium prausnitzii, Akkermansia muciniphila and Peptostreptococcus anaerobius after Weight Loss

BACKGROUND Beside the influence of nutritional habits and reduced physical activity, metabolic syndrome is associated with alterations in the structure of gut microbiota influencing the inflammatory immune responses. Gut microbiota and microbial metabolic activities are known to affect the lipid and glucose metabolism, satiety and chronic low-grade inflammation in the metabolic syndrome. The aim of the study was to identify genera or even species affecting host metabolism in obesity and type 2 diabetes beside the common used indicator: Firmicutes/ Bacteroidetes ratio. METHODS Differences in gut microbiota were investigated in three groups of subjects over a four month intervention period: type 2 diabetics under GLP1-Agonist therapy, obese individuals without established insulin resistance, both receiving nutritional counseling concerning weight reduction, and a lean control group. Collection of fecal samples was accomplished at two time points, before treatment, and after four months of treatment. For identification of bacteria at species-level we used 454 high-throughput sequencing and fragment length polymorphism analysis based on IS-pro (Intergenic-Spacer-profiling). Five bacterial species, two bacterial genera, total bacterial abundance, and the Firmicutes/Bacteroidetes ratio were determined. RESULTS Type 2 diabetics showed a higher Firmicutes/Bacteroidetes ratio even with an increase to the second time point (p=0.07). The abundance of B. thetaiotaomicron remained unaffected, whereas B. vulgatus significantly increased in type 2 diabetics (p=0.07) over the study period. Either Alistipes spp. showed an increase in type 2 diabetics between the time points (p=0.06). The abundance of F. prausnitzii (p=0.03) and A. muciniphila (p=0.03) also increased in type 2 diabetics over study period. In addition, the concentration of P. anaerobius (p=0.03) was significantly higher in type 2 diabetics after intervention compared to lean and obese controls. CONCLUSION Our results clearly show a difference in the gut bacterial composition in type 2 diabetics compared to lean controls or obesity. Therefore, the ratio of Fimicutes/Bacteroidetes might only be an indicator, but a detailed view at species level is even more important in regard to distinction of their functions.

Obesity: epigenetic regulation – recent observations

Abstract Genetic and environmental factors, especially nutrition and lifestyle, have been discussed in the literature for their relevance to epidemic obesity. Gene-environment interactions may need to be understood for an improved understanding of the causes of obesity, and epigenetic mechanisms are of special importance. Consequences of epigenetic mechanisms seem to be particularly important during certain periods of life: prenatal, postnatal and intergenerational, transgenerational inheritance are discussed with relevance to obesity. This review focuses on nutrients, diet and habits influencing intergenerational, transgenerational, prenatal and postnatal epigenetics; on evidence of epigenetic modifiers in adulthood; and on animal models for the study of obesity.

EGCG Prevents High Fat Diet-Induced Changes in Gut Microbiota, Decreases of DNA Strand Breaks, and Changes in Expression and DNA Methylation of Dnmt1 and MLH1 in C57BL/6J Male Mice

Obesity as a multifactorial disorder involves low-grade inflammation, increased reactive oxygen species incidence, gut microbiota aberrations, and epigenetic consequences. Thus, prevention and therapies with epigenetic active antioxidants, (−)-Epigallocatechin-3-gallate (EGCG), are of increasing interest. DNA damage, DNA methylation and gene expression of DNA methyltransferase 1, interleukin 6, and MutL homologue 1 were analyzed in C57BL/6J male mice fed a high-fat diet (HFD) or a control diet (CD) with and without EGCG supplementation. Gut microbiota was analyzed with quantitative real-time polymerase chain reaction. An induction of DNA damage was observed, as a consequence of HFD-feeding, whereas EGCG supplementation decreased DNA damage. HFD-feeding induced a higher inflammatory status. Supplementation reversed these effects, resulting in tissue specific gene expression and methylation patterns of DNA methyltransferase 1 and MutL homologue 1. HFD feeding caused a significant lower bacterial abundance. The Firmicutes/Bacteroidetes ratio is significantly lower in HFD + EGCG but higher in CD + EGCG compared to control groups. The results demonstrate the impact of EGCG on the one hand on gut microbiota which together with dietary components affects host health. On the other hand effects may derive from antioxidative activities as well as epigenetic modifications observed on CpG methylation but also likely to include other epigenetic elements.