title: Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola.
abstract: Gut microbes play a critical role in human health and disease, and researchers have begun to characterize their genomes, the so-called gut metagenome. Thus far, metagenomics studies have focused on genus- or species-level composition and microbial gene sets, while strain-level composition and single-nucleotide polymorphism (SNP) have been overlooked. The gut metagenomes of type 2 diabetes (T2D) patients have been found to be enriched with butyrate-producing bacteria and sulfate reduction functions. However, it is not known whether the gut metagenomes of T2D patients have characteristic strain patterns or SNP distributions.
  
  
  
  We downloaded public gut metagenome datasets from 170 T2D patients and 174 healthy controls and performed a systematic comparative analysis of their metagenome SNPs. We found that Bacteroides coprocola, whose relative abundance did not differ between the groups, had a characteristic distribution of SNPs in the T2D patient group. We identified 65 genes, all in B. coprocola, that had remarkably different enrichment of SNPs. The first and sixth ranked genes encode glycosyl hydrolases (GenBank accession EDU99824.1 and EDV02301.1). Interestingly, alpha-glucosidase, which is also a glycosyl hydrolase located in the intestine, is an important drug target of T2D. These results suggest that different strains of B. coprocola may have different roles in human gut and a specific set of B. coprocola strains are correlated with T2D.
authors.affiliation: Beijing Institute of Basic Medical Sciences, Beijing, 100850, People's Republic of China.
authors.forename: Yaowen
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Beijing Institute of Basic Medical Sciences, Beijing, 100850, People's Republic of China.
authors.forename: Zongcheng
authors.initials: Z
authors.lastname: Li
authors.affiliation: Beijing Institute of Basic Medical Sciences, Beijing, 100850, People's Republic of China.
authors.forename: Shuofeng
authors.initials: S
authors.lastname: Hu
authors.affiliation: Beijing Institute of Basic Medical Sciences, Beijing, 100850, People's Republic of China.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Beijing Institute of Basic Medical Sciences, Beijing, 100850, People's Republic of China.
authors.forename: Jiaqi
authors.initials: J
authors.lastname: Wu
authors.affiliation: Beijing Institute of Basic Medical Sciences, Beijing, 100850, People's Republic of China.
authors.forename: Ningsheng
authors.initials: N
authors.lastname: Shao
authors.affiliation: Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China.
authors.forename: Xiaochen
authors.initials: X
authors.lastname: Bo
authors.affiliation: Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China. ni.ming@163.com.
authors.forename: Ming
authors.initials: M
authors.lastname: Ni
authors.affiliation: Beijing Institute of Basic Medical Sciences, Beijing, 100850, People's Republic of China. yingxmbio@gmail.com.
authors.forename: Xiaomin
authors.identifier: 0000-0001-6126-7372
authors.initials: X
authors.lastname: Ying
mesh_terms: D001439:Bacteroides / Q000235:genetics*; D003924:Diabetes Mellitus, Type 2; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D006867:Hydrolases / Q000235:genetics; D056186:Metagenomics / Q000379:methods; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D000520:alpha-Glucosidases / Q000235:genetics
chemical_list: D006867:Hydrolases; D000520:alpha-Glucosidases
keywords: Bacteria; Metagenome; Phylogenetic analysis; SNP enrichment; Type 2 diabetes