Gut Microbial SNPs Induced by High-Fiber Diet Dominate Nutrition Metabolism and Environmental Adaption of Faecalibacterium prausnitzii in Obese Children.

Hui Li,Menghui Zhang,Liping Zhao

doi:10.3389/fmicb.2021.683714

Abstract

Dietary intervention is effective in human health promotion through modulation of gut microbiota. Diet can cause single-nucleotide polymorphisms (SNPs) to occur in the gut microbiota, and some of these variations may lead to functional changes in human health. In this study, we performed a systematic SNP analysis based on metagenomic data collected from children with Prader–Willi syndrome (PWS, n = 17) and simple obese (SO) children (n = 19), who had better healthy conditions after receiving high-fiber diet intervention. We found that the intervention increased the SNP proportions of Faecalibacterium, Bifidobacterium, and Clostridium and decreased those of Bacteroides in all children. Besides, the PWS children had Collinsella increased and Ruminococcus decreased, whereas the SO had Blautia and Escherichia decreased. There were much more BiasSNPs in PWS than in SO (4,465 vs 303), and only 81 of them appeared in both groups, of which 78 were from Faecalibacterium prausnitzii, and 51 were nonsynonymous mutations. These nonsynonymous variations were mainly related to pathways of environmental adaptation and nutrition metabolism, particularly to carbohydrate and nucleotide metabolism. In addition, dominant strains carrying BiasSNPs in all children shifted from F. prausnitzii AF32-8AC and F. prausnitzii 942/30-2 to F. prausnitzii SSTS Bg7063 and F. prausnitzii JG BgPS064 after the dietary intervention. Furthermore, although the abundance of Bifidobacterium increased significantly by the intervention and became dominant strains responsible for nutrition metabolism, they had less BiasSNPs between the pre- and post-intervention group in comparison with Faecalibacterium. The finding of F. prausnitzii as important functional strains influenced by the intervention highlights the superiority of applying SNP analysis in studies of gut microbiota. This study provided evidence and support for the effect of dietary intervention on gut microbial SNPs, and gave some enlightenments for disease treatment.

Highlights

Single-nucleotide polymorphism (SNP) is the most common genetic variation in DNA sequence in order to better adapt to the external environment in the evolutionary process (Haraksingh and Snyder, 2013)
A total of 218,343 SNPs were detected in the gut microbiota of the 36 obese children
All children had the dominant SNPs at genus level, which were from Faecalibacterium, Ruminococcus, and Bacteroides

Summary

Introduction

Single-nucleotide polymorphism (SNP) is the most common genetic variation in DNA sequence in order to better adapt to the external environment in the evolutionary process (Haraksingh and Snyder, 2013). SNPs in the coding region can be classified as nonsynonymous mutation and synonymous mutation. Nonsynonymous mutation changes the sequence of amino acids and affects the genetic function, while the synonymous mutation does not affect the genetic function (Tennessen, 2008). Environmental pressure caused by the change in the diet alter the structure of the gut microbiota and led to genetic variations in the microbes (Truong et al, 2017). These variations can lead to different functions in strains, which, in turn, affect the health of the host

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