Microbial Resources and Systematics
Online ISSN : 2759-2006
Print ISSN : 1342-4041
Volume 32, Issue 1
Displaying 1-4 of 4 articles from this issue
  • Akira Hiraishi
    2016 Volume 32 Issue 1 Pages 1-11
    Published: 2016
    Released on J-STAGE: November 22, 2024
    JOURNAL RESTRICTED ACCESS

    It is common knowledge in microbial ecology that most microorganisms in nature are not recovered on standard culture media. Therefore, although microbiologists are still making efforts to isolate unknown microorganisms, culture-independent molecular approaches to the analysis of microbial diversity are essential in this research area. High-throughput next-generation sequencing (NGS) is accelerating the growth of microbial ecology and phylogenetics strategies based on genomic and metagenomic information. In light of the current status of this research, we need to reconsider the significance of bacteria isolated as colony-forming units from the environment. One of the major foci regarding the culturability of bacteria is their ecological importance as “rare biospheres” of complex microbial communities. Another area of interest in culturable bacteria in the environment is whether their phylotypes can be covered completely by NGS-aided amplicon analyses. This paper focuses on the extent to which NGS and clone library approaches and conventional culture methods share the numbers of operational taxonomic units of environmentally derived bacteria. Biases in cultureindependent molecular approaches are also discussed on the basis of comparative data on 16S rRNA gene amplicons and respiratory quinone as biomarkers.

    Download PDF (1009K)
  • Mika Miyashita, Masako Sugimoto, Yuki Kamakura, Pattaraporn Yukphan, W ...
    2016 Volume 32 Issue 1 Pages 13-24
    Published: 2016
    Released on J-STAGE: November 22, 2024
    JOURNAL RESTRICTED ACCESS

    To evaluate the usefulness of the lactic acid bacteria and staphylococci isolated from Thai fermented foods, we investigated their environmental adaptability and stress tolerance. Most of the strains isolated were tolerant to acidic conditions (pH 3.5 or 4.0). There were also some strains tolerant to high NaCl concentration (10%NaCl), high temperature (45℃), or alkalinity (pH 8.5 or 9.0). Tolerance to stress, acidity, and high temperature was found mainly among lactic acid bacteria strains, whereas tolerance to alkalis and high NaCl concentration occurred mainly in Staphylococcus strains. Comparison of strains isolated from Thai fermented foods and those isolated from Japanese fermented foods showed that the percentage of acid-resistant strains was significantly higher in Thai fermented foods, and that strains with both acid and high-temperature tolerance were isolated only from the Thai foods. Adaptability to a broad pH range was also greater in the strains isolated from Thai fermented foods. Resistance to alkaline conditions or high NaCl concentration was found mainly in Staphylococcus strains, isolated from either Thai or Japanese fermented foods. Our finding that all of the Staphylococcus species isolated showed either alkaline or high-NaCl-concentration tolerance, or both, indicated that Staphylococcus species with these tolerances were widely distributed in these fermented foods. Because the relationship between tolerance and source locality of the isolates was low, and the characteristics of the species isolated differed between Thailand and Japan, there appear to be differences in environmental adaptability and stress tolerance among the different constituent species. Strains that showed tolerance to acid or high temperature and were isolated from Thai fermented foods were assigned to a greater diversity of species than were the Japanese isolates. Furthermore, strains of the same species isolated from Thai fermented foods showed a variety of tolerances to environmental stress. These results reveal the distinctive nature of the strains isolated from Thai fermented foods; these strains are unique bioresources that should be suitable for various applications.

    Download PDF (455K)
  • Takuya Mizuno, Tatsuya Natori, Izumi Kanazawa, Ibrahim Eldesouky, Haji ...
    2016 Volume 32 Issue 1 Pages 25-37
    Published: 2016
    Released on J-STAGE: November 22, 2024
    JOURNAL RESTRICTED ACCESS

    We generated and analyzed draft genomes for 42 Mycobacterium strains representing 30 different species to select core housekeeping proteins (HKPs) that would be useful for differentiating among closely related Mycobacterium species.

    HKPs of Mycobacterium tuberculosis H37Rv were selected as reference proteins, and values (designated diversity values) representing the amino acid differences between these H37Rv HKPs and those of other individual Mycobacterium species were calculated for each HKP. From seven NCBI protein categories, we analyzed the 107 proteins commonly found in all 30 Mycobacterium species. We then selected the 12 most variable HKPs to construct a concatenated protein sequence (designated C12HKP). The average C12HKP diversity value for these 30 Mycobacterium species was 22.50%. Phylogenetic trees constructed with either C12HKP or C50RP (50 concatenated sequences from 50S and 30S ribosomal proteins) had reliable bootstrap values that were higher than those of a 16S rRNA gene tree. Of the three entities (C12HKP, 16S rRNA gene, and C50RP), C12HKP exhibited the greatest diversity. To differentiate among closely related species within the genus Mycobacterium, the C12HKP entity provided the most powerful and discriminating dataset.

    Download PDF (770K)
  • Tamaki Uehara-Ichiki, Shin-ichi Fuji, Ruriko Sugimoto, Miho Ohashi, Ky ...
    2016 Volume 32 Issue 1 Pages 39-47
    Published: 2016
    Released on J-STAGE: November 22, 2024
    JOURNAL RESTRICTED ACCESS

    The Genebank Project at the National Agriculture and Food Research Organization (NARO) is working to conserve and promote agrobiological genetic resources. The Microorganism section of the Genebank collects, characterizes, preserves, and distributes microorganism genetic resources such as fungi, bacteria, and plant viruses. These resources, which are assigned descriptors called MAFF numbers, totaled about 32,500 strains as of 2016. Plant virus strains in the Microorganism section have been classified on the basis of scientific data from depositors and their experimental characterization in comparison with reports of the International Committee on Taxonomy of Viruses. To improve the convenience of use and reliability of virus strains, we are working on determining and providing the base sequences of the capsid/coat protein (CP) genes of virus strains. Here, we demonstrate the successful use of over 60 gene-specific primer pairs for sequence definition of viral CP genes, as well as the experimental conditions used for RT-PCR.

    By using these primer pairs we were able to completely amplify the CP genes of the target virus strains. We also report several virus strains belonging to Necrovirus, Tobamovirus, and Fabavirus that were re-identified on the basis of their CP gene sequences.

    Download PDF (291K)
feedback
Top