Analysis of bacterial xylose isomerase gene diversity using gene-targeted metagenomics

Dini Nurdiani, Michihiro Ito, Toru Maruyama, Takeshi Terahara, Tetsushi Mori, Shin Ugawa, Haruko Takeyama

    Research output: Contribution to journalArticle

    5 Citations (Scopus)

    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.

    Original languageEnglish
    Pages (from-to)174-180
    Number of pages7
    JournalJournal of Bioscience and Bioengineering
    Volume120
    Issue number2
    DOIs
    Publication statusPublished - 2015 Aug 1

    Fingerprint

    xylose isomerase
    Metagenomics
    Xylose
    Soil
    Genes
    Soils
    Chemical analysis
    Genotype
    Metagenome
    Biofuels
    Nucleic Acid Databases
    Biomass
    Amino acids
    Screening
    DNA
    Databases

    Keywords

    • Biodiversity
    • Bioethanol production
    • Lignocellulosic biomass
    • Metagenome
    • Next generation sequencing
    • Xylose
    • Xylose isomerase

    ASJC Scopus subject areas

    • Biotechnology
    • Applied Microbiology and Biotechnology
    • Bioengineering

    Cite this

    Analysis of bacterial xylose isomerase gene diversity using gene-targeted metagenomics. / Nurdiani, Dini; Ito, Michihiro; Maruyama, Toru; Terahara, Takeshi; Mori, Tetsushi; Ugawa, Shin; Takeyama, Haruko.

    In: Journal of Bioscience and Bioengineering, Vol. 120, No. 2, 01.08.2015, p. 174-180.

    Research output: Contribution to journalArticle

    Nurdiani, Dini ; Ito, Michihiro ; Maruyama, Toru ; Terahara, Takeshi ; Mori, Tetsushi ; Ugawa, Shin ; Takeyama, Haruko. / Analysis of bacterial xylose isomerase gene diversity using gene-targeted metagenomics. In: Journal of Bioscience and Bioengineering. 2015 ; Vol. 120, No. 2. pp. 174-180.
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