title: Analysis of bacterial xylose isomerase gene diversity using gene-targeted metagenomics.
abstract: Bacterial xylose isomerases (XI) are promising resources for efficient biofuel production from xylose in lignocellulosic biomass. Here, we investigated xylose isomerase gene (xylA) diversity in three soil metagenomes differing in plant vegetation and geographical location, using an amplicon pyrosequencing approach and two newly-designed primer sets. A total of 158,555 reads from three metagenomic DNA replicates for each soil sample were classified into 1127 phylotypes, detected in triplicate and defined by 90% amino acid identity. The phylotype coverage was estimated to be within the range of 84.0-92.7%. The xylA gene phylotypes obtained were phylogenetically distributed across the two known xylA groups. They shared 49-100% identities with their closest-related XI sequences in GenBank. Phylotypes demonstrating <90% identity with known XIs in the database accounted for 89% of the total xylA phylotypes. The differences among xylA members and compositions within each soil sample were significantly smaller than they were between different soils based on a UniFrac distance analysis, suggesting soil-specific xylA genotypes and taxonomic compositions. The differences among xylA members and their compositions in the soil were strongly correlated with 16S rRNA variation between soil samples, also assessed by amplicon pyrosequencing. This is the first report of xylA diversity in environmental samples assessed by amplicon pyrosequencing. Our data provide information regarding xylA diversity in nature, and can be a basis for the screening of novel xylA genotypes for practical applications.
authors: Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
authors: Dini
authors: D
authors: Nurdiani
authors: Institute for Nanoscience and Nanotechnology, Waseda University, 513 Waseda-tsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Core Research for Evolutionary Science and Technology Project (CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
authors: Michihiro
authors: M
authors: Ito
authors: Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Core Research for Evolutionary Science and Technology Project (CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
authors: Toru
authors: T
authors: Maruyama
authors: Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
authors: Takeshi
authors: T
authors: Terahara
authors: Core Research for Evolutionary Science and Technology Project (CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; International Center for Science and Engineering Programs (ICSEP), Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.
authors: Tetsushi
authors: T
authors: Mori
authors: Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan.
authors: Shin
authors: S
authors: Ugawa
authors: Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Institute for Nanoscience and Nanotechnology, Waseda University, 513 Waseda-tsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Core Research for Evolutionary Science and Technology Project (CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan. Electronic address: haruko-takeyama@waseda.jp.
authors: Haruko
authors: H
authors: Takeyama
mesh_terms: D019747:Aldose-Ketose Isomerases / Q000145:classification / Q000235:genetics*; D000595:Amino Acid Sequence; D001483:Base Sequence; D056804:Biofuels / Q000600:supply & distribution; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D030561:Databases, Nucleic Acid; D005798:Genes, Bacterial / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D008031:Lignin / Q000378:metabolism; D054892:Metagenome / Q000235:genetics*; D056186:Metagenomics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D014994:Xylose / Q000378:metabolism
chemical_list: D056804:Biofuels; D017931:DNA Primers; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; C036909:lignocellulose; D008031:Lignin; D014994:Xylose; D019747:Aldose-Ketose Isomerases; C023298:xylose isomerase
keywords: Biodiversity; Bioethanol production; Lignocellulosic biomass; Metagenome; Next generation sequencing; Xylose; Xylose isomerase