The Microbiome, Epigenome, and Diet in Adults with Obesity during Behavioral Weight Loss

Abstract

Obesity has been linked to the gut microbiome, epigenome, and diet, yet these factors have not been studied together during obesity treatment. Our objective was to evaluate associations among gut microbiota (MB), DNA methylation (DNAme), and diet prior to and during a behavioral weight loss intervention. Adults (n = 47, age 40.9 ± 9.7 years, body mass index (BMI) 33.5 ± 4.5 kg/m2, 77% female) with data collected at baseline (BL) and 3 months (3 m) were included. Fecal MB was assessed via 16S sequencing and whole blood DNAme via the Infinium EPIC array. Food group and nutrient intakes and Healthy Eating Index (HEI) scores were calculated from 7-day diet records. Linear models were used to test for the effect of taxa relative abundance on DNAme and diet cross-sectionally at each time point, adjusting for confounders and a false discovery rate of 5%. Mean weight loss was 6.2 ± 3.9% at 3 m. At BL, one MB taxon, Ruminiclostridium, was associated with DNAme of the genes COL20A1 (r = 0.651, p = 0.029), COL18A1 (r = 0.578, p = 0.044), and NT5E (r = 0.365, p = 0.043). At 3 m, there were 14 unique MB:DNAme associations, such as Akkermansia with DNAme of GUSB (r = −0.585, p = 0.003), CRYL1 (r = −0.419, p = 0.007), C9 (r = −0.439, p = 0.019), and GMDS (r = −0.559, p = 0.046). Among taxa associated with DNAme, no significant relationships were seen with dietary intakes of relevant nutrients, food groups, or HEI scores. Our findings indicate that microbes linked to mucin degradation, short-chain fatty acid production, and body weight are associated with DNAme of phenotypically relevant genes. These relationships offer an initial understanding of the possible routes by which alterations in gut MB may influence metabolism during weight loss.

Comparative analysis of gut microbiota in children with obstructive sleep apnea: assessing the efficacy of 16S rRNA gene sequencing in metabolic function prediction based on weight status

“…Differences in gut microbiota composition can impact nutrient absorption, gut barrier function, inflammation, and interactions with other organ systems ( 70 ). Furthermore, the metabolic pathways, whether involved in short-chain fatty acid production, amino acid metabolism, or other processes, might hold the key to understanding how gut microbiota influence weight and overall health ( 71 – 73 ). Using the full-length method, 35 differentiated metabolic pathways were identified, whereas the V3–V4 region method revealed 28 differentiated metabolic pathways.…”

The Beneficial Effects of Dietary Interventions on Gut Microbiota—An Up-to-Date Critical Review and Future Perspectives

“…The relative abundance of Akkermansia muciniphila, another SCFA producer and mucindegrading bacterium, increased during different restriction programmes in five clinical trials [23,92,97,106,116]. As the level of A. muciniphila is inversely correlated with body weight and directly correlated with the weight loss observed in obese patients after CR restrictions and improvements in multiple indicators of cardio-metabolic health [128][129][130][131], it can be proposed as a prognostic tool in the context of predicting CR success. Further studies are needed to confirm this, as the effect was not consistently observed in all trials.…”