title: Nucleotide 9-mers characterize the type II diabetic gut metagenome.
abstract: Discoveries of new biomarkers for frequently occurring diseases are of special importance in today's medicine. While fully developed type II diabetes (T2D) can be detected easily, the early identification of high risk individuals is an area of interest in T2D, too. Metagenomic analysis of the human bacterial flora has shown subtle changes in diabetic patients, but no specific microbes are known to cause or promote the disease. Moderate changes were also detected in the microbial gene composition of the metagenomes of diabetic patients, but again, no specific gene was found that is present in disease-related and missing in healthy metagenome. However, these fine differences in microbial taxon- and gene composition are difficult to apply as quantitative biomarkers for diagnosing or predicting type II diabetes. In the present work we report some nucleotide 9-mers with significantly differing frequencies in diabetic and healthy intestinal flora. To our knowledge, it is the first time such short DNA fragments have been associated with T2D. The automated, quantitative analysis of the frequencies of short nucleotide sequences seems to be more feasible than accurate phylogenetic and functional analysis, and thus it might be a promising direction of diagnostic research.
authors.affiliation: PIT Bioinformatics Group, Eötvös University, H-1117 Budapest, Hungary. Electronic address: szalkai@pitgroup.org.
authors.forename: Balázs
authors.initials: B
authors.lastname: Szalkai
authors.affiliation: PIT Bioinformatics Group, Eötvös University, H-1117 Budapest, Hungary; Uratim Ltd., H-1118 Budapest, Hungary. Electronic address: grolmusz@pitgroup.org.
authors.forename: Vince
authors.initials: V
authors.lastname: Grolmusz
mesh_terms: D015415:Biomarkers / Q000737:chemistry; D016022:Case-Control Studies; D003924:Diabetes Mellitus, Type 2 / Q000382:microbiology*; D005260:Female; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D008297:Male; D054892:Metagenome; D009711:Nucleotides / Q000737:chemistry* / Q000302:isolation & purification; D009765:Obesity / Q000382:microbiology; D013851:Thinness / Q000382:microbiology
chemical_list: D015415:Biomarkers; D009711:Nucleotides
keywords: Biomarkers; G-C content; Metagenome; Oligomers; Short nucleotide sequences; Tetranucleotides; Type II diabetes