Examination of a whole food diet (Heart Healthy) compared to a hypocaloric, intermittent fasting, meal replacement-based diet on gut microbiome composition and circulating endotoxin in obese/overweight individuals

Project: Research project

Project Details


Examination of a whole food diet (Heart Healthy) compared to a hypocaloric, intermittent fasting, meal replacement-based diet on gut microbiome composition and circulating endotoxin in obese/overweight individuals Examination of a whole food diet (Heart Healthy) compared to a hypocaloric, intermittent fasting, meal replacement-based diet on gut microbiome composition and circulating endotoxin in obese/overweight individuals The microorganisms comprising the human gut microbiota (GM) are linked to a wide variety of biological systems in the host1 and participate in numerous beneficial host functions.210 Therefore establishing and maintaining a beneficial host-GM interaction is increasingly viewed as an important factor in mediating overall health and wellness.11 Increased microbial biodiversity and richness (total number of bacterial species) are widely viewed as hallmarks of a healthy gut microbiota.12 In contrast, human diseases are often positively correlated with reduced bacterial diversity and an environment favoring increased pathogenic bacterial growth,13,14 a state often referred to as gut dysbiosis.15,16 Symptoms of gut dysbiosis include gastrointestinal dysfunction,17 elevations in expression of lipopolysaccharides (LPS) and other inflammatory factors,18,19 and shifts in GM function and metabolic products.20 As such, there has been interest in the role of the GM in the development of obesity and cardiometabolic diseases.21 In relation, the GM has been proposed as a contributing factor to the pathophysiology of obesity and metabolic dysfunction.20,22,23 Diet is one of the main modulators of the gut microbiota,2426 with observational studies reporting a strong dietary effect on the composition and function of GM in globally distinct human populations.2730 In experimental studies, research has generally investigated short-term dietary interventions with smaller sample sizes,24,31 and is often characterized by extreme and unrealistic dietary intakes24 or specific foods items.3235 However, humans eat complex, mixed diets, and display poor adherence with overly restrictive dietary regiments, such as weight loss interventions.36 Relatedly, dietary interventions incorporating caloric restriction remain the cornerstone for treating obesity. Promising strategies such as intermittent fasting, which encompass eating patterns in which individuals go extended time periods (typically 12 days/week) with little or no energy intake, are increasingly being utilized to promote weight loss and improve body composition.37 Other strategies such as increased protein intake38 and consumption of liquid meal-replacements also appear to be effective for weight loss.39 Previous research combining these three strategies has reported increased effectiveness for weight loss, visceral fat reduction and improving coronary heart disease risk over a whole food diet in obese middle age women.40 In addition, an intermittent fasting, meal replacement-based diet (IFMR-D) was found to be more effective over a whole food, heart healthy diet (WFD) for prevention weight regain after an aggressive period of weight loss in obese men and women.41 These subjects also displayed improved body composition, energy expenditure, and cardiometabolic markers over the WFD.41,42 However, the effects of such a diet on the gut microbiota generally remain unexplored. Previous research with hypocaloric, high-protein diets have reported compositional changes and increased microbial richness.28 Furthermore, a short-term study with a small sample size investigated the effects of a liquid meal-replacement on the GM of healthy subjects.43 While this research reported some compositional changes, the studys short duration, lack of a comparator, and methodological rigor and analyses left many unanswered questions. Finally, low-grade chronic inflammation observed in obesity and metabolic dysfunction may be triggered by elevated endotoxin concentrations resulting from impaired gut permeability and dysbiosis,44 yet its measurement is lacking in clinical weight loss studies assessing the GM. Therefore, we propose to the study the effect of a hypocaloric, IFMR-D on gut microbiome composition and predicted function, as well as circulating endotoxin in obese/overweight individuals. Additionally, we will evaluate the comparative effect versus a WFD. Specific Aims: Our aim is to study compositional and predicted functional changes in the GM over a 12-week intervention comparing an IFMR-D to a WFD in an obese population. A secondary aim is to assess circulating LPS concentrations between diet groups. We hypothesize that a 12-week IFMR-D will: 1) significantly affect the composition of the GM, 2) significantly and positively alter the predictive functions of the GM, and 3) significantly decrease circulating LPS concentrations, as compared to WFD in obese adults during weight loss. Findings from this study are expected to support the use of a calorie restricted IFMR-D based system that can easily be incorporated by individuals to improve indices of gut health and systemic inflammation. Given the prevalence and associated health costs of obesity, a dietary mechanism capable of influencing the gut and related health outcomes is of importance and is expected to advance current nutritional knowledge. Methods: Sample Collection. In collaboration with Dr. Paul Arciero, fecal and plasma samples will be collected from a larger weight loss intervention conducted at Skidmore College (Saratoga Springs, NY). Specifically, individual fecal and plasma samples from 40 subjects will collected at baseline, and weeks 4 and 12 (total n=120) and sent to Arizona State University (Tempe, AZ) by overnight shipping on dry ice. Fecal collection, storage, and transport will follow preestablished, validated methodology for ensuring maximal sample integrity.45 All samples will be stored at -80C until processing. Fecal Microbiome Analysis. Microbial genomic DNA will be extracted from fecal samples at each time point (n=120) using a commercially available kit (DNEASY POWERSOIL KIT Isolation Kit, MoBio Laboratories, Inc., Carlsbad, CA) and bacterial 16S rRNA gene sequences from each sample will be identified by high-throughput sequencing at the ASU Biodesign Institute (Tempe, AZ). Illumina MiSeq will be performed on the variable regions of 16S ribosomal RNA, which is used to characterize genus or species in a diverse microbial population. Following Illumina sequencing, the raw sequences will be interpreted with an open source software, Quantitative insights into microbial ecology version 2 (QIIME 2). QIIME 2 provides an analysis of the sequences as well as graphical displays of the data. Differential microbial abundance differences between time and diet groups will be identified using linear discriminant analysis of effect size (LEfSe) analyses via the online Galaxy module. In addition, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) will be implemented in Galaxy to predict Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathway abundance content from the 16S rDNA data using a closed reference OTU table created in QIIME and the Greengenes reference database. Plasma LPS Analysis. Plasma LPS concentrations will be quantified by a commercially-available kit (Pierce Chromogenic Endotoxin Quant Kit, Thermo Scientific, Rockford, IL) per the manufacturers protocol to examine systemic circulation of LPS on samples collected at baseline and week 12 (n=80).
Effective start/end date3/1/2012/31/22


  • INDUSTRY: Domestic Company: $21,901.00


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