Urban Diets Linked to Gut Microbiome and Metabolome Alterations in Children: A Comparative Cross-Sectional Study in Thailand

Abstract

Loss of traditional diets by food globalization may have adverse impact on the health of human being through the alteration of gut microbial ecosystem. To address this notion, we compared the gut microbiota of urban (n = 17) and rural (n = 28) school-aged children in Thailand in association with their dietary habits. Dietary records indicated that children living in urban Bangkok tended to consume modern high-fat diets, whereas children in rural Buriram tended to consume traditional vegetable-based diets. Sequencing of 16S rRNA genes amplified from stool samples showed that children in Bangkok have less Clostridiales and more Bacteroidales and Selenomonadales compared to children in Buriram and bacterial diversity is significantly less in Bangkok children than in Buriram children. In addition, fecal butyrate and propionate levels decreased in Bangkok children in association with changes in their gut microbial communities. Stool samples of these Thai children were classified into five metabolotypes (MTs) based on their metabolome profiles, each characterized by high concentrations of short and middle chain fatty acids (MT1, n = 17), amino acids (MT2, n = 7), arginine (MT3, n = 6), amino acids, and amines (MT5, n = 8), or an overall low level of metabolites (MT4, n = 4). MT1 and MT4 mainly consisted of samples from Buriram, and MT2 and MT3 mainly consisted of samples from Bangkok, whereas MT5 contained three samples from Bangkok and five from Buriram samples. According to the profiles of microbiota and diets, MT1 and MT2 are characteristic of children in Buriram and Bangkok, respectively. Predicted metagenomics indicated the underrepresentation in MT2 of eight genes involved in pathways of butyrate biosynthesis, notably including paths from glutamate as well as pyruvate. Taken together, this study shows the benefit of high-vegetable Thai traditional diets on gut microbiota and suggests that high-fat and less-vegetable urban dietary habits alter gut microbial communities in Thai children, which resulted in the reduction of colonic short chain fatty acid fermentation.

Evidence for a multi-level trophic organization of the human gut microbiome

“…Around 19 of our predicted metabolites (variable 145 across individuals) were actually among the ones experimentally measured in Ref. [22]. We 146 quantified the quality of our predictions using the Pearson correlation coefficient between the 147 predicted and experimentally measured metabolomes, and it's associated P -value.…”

“…Obtaining metagenomic and metabolomic data 367 To calibrate the key parameters of our model, we used a previously published dataset, namely a 368 16S rRNA sequencing study of 41 human individuals from rural and urban areas in Thailand 369 [22]. From these data, we collected the reported 16S rRNA OTU abundances as well as their 370 corresponding taxonomy.…”

“…139 We carried out these fits of microbial abundances for each of the 41 individuals studied in 140 Ref. [22] for a broad range of two parameters of our model -the byproduct fraction f ranging 141 between 0.1 and 0.99 and the number of trophic levels N between 2 and 10. For each individual 142 and each pair of parameters f and N we used our model to predict the fecal metabolome 143 profile.…”

“…This predicted metabolome was subsequently compared to the experimental data of 144 Ref. [22] measured in the same individual. Around 19 of our predicted metabolites (variable 145 across individuals) were actually among the ones experimentally measured in Ref.…”

“…(A) Heatmap of the Pearson correlation between experimentally measured and predicted metabolomes for different combinations of parameters f and N . The plotted value is the correlation coefficient averaged over 41 individuals in Ref [22]…”