Publications by authors named "Hiroko Kawasaki"

80 Publications

Immunoglobulin A-specific deficiency induces spontaneous inflammation specifically in the ileum.

Gut 2021 May 7. Epub 2021 May 7.

Department of Immunology, Medical Research Institute, TMDU, Bunkyo-ku, Tokyo, Japan

Objective: Although immunoglobulin A (IgA) is abundantly expressed in the gut and known to be an important component of mucosal barriers against luminal pathogens, its precise function remains unclear. Therefore, we tried to elucidate the effect of IgA on gut homeostasis maintenance and its mechanism.

Design: We generated various IgA mutant mouse lines using the CRISPR/Cas9 genome editing system. Then, we evaluated the effect on the small intestinal homeostasis, pathology, intestinal microbiota, cytokine production, and immune cell activation using intravital imaging.

Results: We obtained two lines, with one that contained a <50 base pair deletion in the cytoplasmic region of the IgA allele (IgA tail-mutant; IgA) and the other that lacked the most constant region of the IgH α chain, which resulted in the deficiency of IgA production (IgA). IgA exhibited spontaneous inflammation in the ileum but not the other parts of the gastrointestinal tract. Associated with this, there were significantly increased lamina propria CD4 T cells, elevated productions of IFN-γ and IL-17, increased ileal segmented filamentous bacteria and skewed intestinal microflora composition. Intravital imaging using Ca biosensor showed that IgA had elevated Ca signalling in Peyer's patch B cells. On the other hand, IgA seemed to be normal, suggesting that the IgA cytoplasmic tail is dispensable for the prevention of the intestinal disorder.

Conclusion: IgA plays an important role in the mucosal homeostasis associated with the regulation of intestinal microbiota and protection against mucosal inflammation especially in the ileum.
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http://dx.doi.org/10.1136/gutjnl-2020-322873DOI Listing
May 2021

Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements.

Microbiome 2021 04 29;9(1):95. Epub 2021 Apr 29.

Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan.

Background: Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples.

Results: In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories.

Conclusions: The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products. Video Abstract.
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http://dx.doi.org/10.1186/s40168-021-01048-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082873PMC
April 2021

Progress toward improving outcomes in patients with cholangiocarcinoma.

Curr Treat Options Gastroenterol 2021 Mar 30;19(1):153-168. Epub 2021 Jan 30.

Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.

Purpose Of Review: To provide an update on latest advances in treatment of cholangiocarcinoma.

Recent Findings: Incidence of cholangiocarcinoma has been increasing over the past decade. A better understanding of the genetic landscape of cholangiocarcinoma and its risk factors resulted in earlier diagnosis and treatment option expansion to targeted therapy with FGFR inhibitors, and liver transplantation for early perihilar cholangiocarcinoma and early intrahepatic cholangiocarcinoma. IDH1/2 inhibition for intrahepatic cholangiocarcinoma is an emerging targeted therapy approach. Data supports benefits of adjuvant therapy for a subset of patients undergoing surgical resection. Approaches combining different treatment modalities such as chemotherapy, surgery, radiation therapy appear promising.

Summary: Earlier diagnosis and genetic characterization provided additional treatment options for patients with previously incurable cholangiocarcinoma. A precision medicine approach with a focus on actionable genetic alterations and combination of treatment modalities are actively being explored and will further improve outcomes in our patients with cholangiocarcinoma.
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http://dx.doi.org/10.1007/s11938-021-00333-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8054970PMC
March 2021

gcType: a high-quality type strain genome database for microbial phylogenetic and functional research.

Nucleic Acids Res 2021 01;49(D1):D694-D705

Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.
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http://dx.doi.org/10.1093/nar/gkaa957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778895PMC
January 2021

Complete Genome Sequence of Blautia producta JCM 1471.

Microbiol Resour Announc 2020 Apr 23;9(17). Epub 2020 Apr 23.

Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan

We report a complete genome sequence of JCM 1471 The genome consists of a single circular chromosome of 6,197,116 bp with a G+C content of 45.7%. The genome was annotated as containing 5 complete sets of rRNA genes, 70 tRNA genes, and 5,516 protein-coding sequences.
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http://dx.doi.org/10.1128/MRA.00141-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7180277PMC
April 2020

Complete Genome Sequence of Flavonifractor plautii JCM 32125.

Microbiol Resour Announc 2020 Apr 23;9(17). Epub 2020 Apr 23.

Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan

We report the complete genome sequence of JCM 32125 (=VPI 0310). The genome consists of a single circular chromosome of 3,985,392 bp (G+C content, 60.9%) and was predicted to contain 3 complete sets of rRNA genes, 63 tRNA genes, and 3,764 protein-coding sequences.
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http://dx.doi.org/10.1128/MRA.00135-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7180276PMC
April 2020

Complete Genome Sequence of Megamonas funiformis JCM 14723.

Microbiol Resour Announc 2020 Apr 16;9(16). Epub 2020 Apr 16.

Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan

We announce the complete genome sequence of JCM 14723 (YIT 11815). The genome consists of a circular chromosome (2,522,577 bp, 31.5% G+C content) and a plasmid of 46,189 bp (29.4% G+C content). The genome was predicted to contain 6 rRNA operons, 53 tRNA genes, and 2,440 protein-coding sequences.
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http://dx.doi.org/10.1128/MRA.00142-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163012PMC
April 2020

Complete Genome Sequence of Collinsella aerofaciens JCM 10188.

Microbiol Resour Announc 2020 Apr 16;9(16). Epub 2020 Apr 16.

Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan

We report a complete genome sequence of JCM 10188 (=VPI 1003). The genome consists of a circular chromosome (2,428,218 bp with 60.6% G+C content) and two extrachromosomal elements. The genome was predicted to contain 5 sets of rRNA genes, 58 tRNA genes, and 2,079 protein-encoding sequences.
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http://dx.doi.org/10.1128/MRA.00134-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163011PMC
April 2020

Fourteen novel lipomycetaceous yeast species isolated from soil in Japan and transfer of to the genus based on ascospore production phenotype.

Int J Syst Evol Microbiol 2020 Feb;70(2):1372-1397

Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.

Fourteen novel lipomycetaceous yeasts species were isolated from soil samples collected from the Hokkaido, Chiba and Okinawa prefectures of Japan. Phylogenetic analyses of the D1/D2 domains of the large subunit rRNAs and translation elongation factor 1 alpha genes () revealed that five strains of two species from the soil in Furano-shi, Hokkaido were related to and 29 strains representing 12 species from soils in Kamogawa-shi, Chiba and Iriomote Island, Okinawa were in the clade. The two species of form globose or ellipsoid ascospores in their sac-like ascus and pseudohyphae. Furthermore, these species produce ascospores in their pseudohyphae and do not produce an acicular ascus, which is common among the three species including . Therefore, we propose transferring to the genus and amending . Two novel species were described and included in the genus : sp. nov. (holotype NBRC 111233; MycoBank no. MB 829051) and sp. nov. (holotype NBRC 112965; MycoBank no. MB 829053). The 12 species in the clade produce neither ascospores nor pseudohyphae and have different characteristics in assimilating several carbon sources from each other. Thus, we propose that the novel species of be classified as forma asexualis (f.a.). From Kamogawa-shi, Chiba (19 strains representing five species): f.a., sp. nov. (holotype NBRC 111411; MycoBank no. MB 829034), f.a., sp. nov. (holotype NBRC 111424; MycoBank no. MB 829035), f.a., sp. nov. (holotype NBRC 111413; MycoBank no. MB 829036), f.a., sp. nov. (holotype NBRC 112967; MycoBank no. MB 829037), f.a., sp. nov. (holotype NBRC 111420; MycoBank no. MB 829041). From Iriomote island, Okinawa (10 strains representing seven species): f.a., sp. nov. (holotype NBRC 112966; MycoBank no. MB 829042), f.a., sp. nov. (holotype NBRC 110433; MycoBank no. MB 829050), f.a., sp. nov. (holotype NBRC 110436; MycoBank no. MB 829045), f.a., sp. nov. (holotype NBRC 110435; MycoBank no. MB 829046), f.a., sp. nov. (holotype NBRC 110440; MycoBank no. MB 829047), f.a., sp. nov. (holotype NBRC 110434; MycoBank no. MB 829048), f.a., sp. nov. (holotype NBRC 110439; MycoBank no. MB 829049).
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http://dx.doi.org/10.1099/ijsem.0.003924DOI Listing
February 2020

Gene Mutations in During Long-Term Preservation by Repeated Subculturing.

Biopreserv Biobank 2019 Oct 2;17(5):395-400. Epub 2019 Apr 2.

NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan.

Subculturing is frequently used for the preservation of basidiomycetes. In this study, to assess and verify the risks of repeated subculturing on the long-term preservation of strains of culture collections, we performed single nucleotide polymorphism (SNP) analysis in genes encoding enzymes of the mevalonate pathway, 1,3-β-glucan synthesis, lignin degradation, and the tricarboxylic acid (TCA) cycle of mycelia before and after preserving for a 4-year period by the subculturing 30 times every 45 days of NBRC 8346. As a result of analyzing 60 genes of the strain, SNPs were found in 18 genes, and 14 of them were found in the exon region. Nonsynonymous coding SNPs were found in two genes (, ) encoding enzymes of mevalonate pathway and five genes (, , , , ) encoding enzymes of lignin degradation after subculturing of NBRC 8346.
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http://dx.doi.org/10.1089/bio.2018.0149DOI Listing
October 2019

Detection of DNA damage response in nonalcoholic fatty liver disease via p53-binding protein 1 nuclear expression.

Mod Pathol 2019 07 26;32(7):997-1007. Epub 2019 Feb 26.

Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan.

Nonalcoholic fatty liver disease is a major liver disease that leads to cirrhosis and/or hepatocellular carcinoma in a subset of patients. The mechanism underlying disease progression is largely unknown. p53-binding protein 1 (53BP1) is a DNA damage response protein that rapidly localizes at the site of DNA double-strand breaks. In this study, we investigated nuclear 53BP1-positive foci formation as an indicator of DNA double-strand breaks in human nonalcoholic fatty liver disease liver tissues by immunofluorescence microscopy. A total of 52 liver tissue samples, including 43 nonalcoholic fatty liver disease samples and 9 controls, were studied. Our results show that the number of abnormal 53BP1-positive foci in hepatocytes (defined as three or more discrete nuclear foci and/or large foci greater than 1 μM) was significantly increased in nonalcoholic fatty liver disease patients compared to that in controls, both in nonalcoholic fatty liver (p < 0.01) and nonalcoholic steatohepatitis patients (p < 0.01). The number of large foci was significantly increased in the nonalcoholic steatohepatitis cases compared to that in the nonalcoholic fatty liver cases (p < 0.05) and correlated with increased stage of fibrosis. The number of large-foci-expressing hepatocytes was positively correlated with increased age (p < 0.01) and negatively correlated with serum platelet count (p < 0.05). In addition, we performed an in vitro assay using rat hepatocytes treated with the saturated free fatty acid palmitate. Treatment appeared to augment the number of abnormal foci, indicating an induction of double-strand breaks in the hepatocytes through free fatty acid treatment in a caspase-dependent manner. This study demonstrates that 53BP1-positive nuclear foci formation is associated with disease progression in nonalcoholic fatty liver disease patients. Analysis of 53BP1 expression might be a feasible technique to estimate genomic instability in nonalcoholic fatty liver disease.
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http://dx.doi.org/10.1038/s41379-019-0218-8DOI Listing
July 2019

The neutral N-linked glycans of the Basidiomycetous yeasts Pseudozyma antarctica and Malassezia furfur (Subphylum Ustilaginomycotina).

J Gen Appl Microbiol 2019 May 10;65(2):53-63. Epub 2018 Oct 10.

International Center for Biotechnology, Osaka University.

Pseudozyma antarctica and Malassezia furfur are basidiomycetous yeasts under the subphylum Ustilaginomycotina. P. antarctica is a commensal organism found in certain plant species, while M. furfur is associated with several skin diseases of animals including humans. N-linked glycans of P. antarctica and M. furfur were prepared, digested with glycosidases, and structurally analyzed using high performance liquid chromatography (HPLC) and mass spectrometry (MS). Analyses revealed the presence of neutral N-linked glycans ranging in length from ManGlcNAc-PA to ManGlcNAc-PA. The two species shared the most abundant neutral N-linked glycan: Manα1-2Manα1-6(Manα1-3)Manα1-6(Manα1-2Manα1-2Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc (M8A). The second and third most abundant neutral N-linked glycans for P. antarctica were Manα1-2Manα1-6(Manα1-2Manα1-3)Manα1-6(Manα1-2Manα1-2Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc (M9A) and Manα1-6(Manα1-3)Manα1-6(Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc (M5A), respectively. In the case of M. furfur, Manα1-2Manα1-6(Manα1-3)Manα1-6(Manα1-2Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc (M7A) was the second most abundant, while both M8A and M9A were tied for the third most abundant. The presence of putative galactose residues in the hypermannosylated neutral N-linked glycans is also discussed. This report is the first to analyze the neutral N-linked glycans of P. antarctica and M. furfur.
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http://dx.doi.org/10.2323/jgam.2018.05.003DOI Listing
May 2019

Rectal Paraganglioma.

Intern Med 2019 Jan 24;58(2):195-199. Epub 2018 Aug 24.

Department of Gastroenterology and Hepatology, Japanese Red Cross Nagasaki Genbaku Hospital, Japan.

A 57-year-old woman was admitted with lower abdominal pain and bloody bowel discharge. She was diagnosed with rectal tumor by colonoscopy, and a biopsy was performed. Surgery was performed, resulting in a diagnosis of rectal paraganglioma. Since recurrence was confirmed three years later, reoperation was done, and chemotherapy with cyclophosphamide, vincristine and dacarbazine (CVD) was subsequently carried out for further recurrence. After the administration of up to 15 courses of CVD, we delivered best supportive care due to disease progression. She died a year and a half after starting chemotherapy. We herein report this rare disease with a review of the relevant literature.
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http://dx.doi.org/10.2169/internalmedicine.1218-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6378155PMC
January 2019

The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species.

Gigascience 2018 05;7(5)

Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Genomic information is essential for taxonomic, phylogenetic, and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microorganisms. Hence, the GCM aims to promote research by deep-mining genomic data.
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http://dx.doi.org/10.1093/gigascience/giy026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5941136PMC
May 2018

Genetic variation during long-term preservation of bacteria in public culture collections.

Int J Syst Evol Microbiol 2018 May 20;68(5):1815-1821. Epub 2018 Mar 20.

NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shibuyaku, Tokyo 151-0066, Japan.

Phenotypic and genetic changes during long-term preservation have been observed in microbial strains at culture collections (CCs). It is imperative to verify the effects of these changes on quality of the strains preserved at CCs. In this study, we performed genome-wide single-nucleotide polymorphism (SNP) analysis of different production lots, which had been derived from the same origin and preserved at the NITE Biological Resource Center (NBRC) for a 4-38-year period by the vacuum liquid drying method at 4 °C. The analysis was conducted for three sets of lots derived from Cellulomonas fimi NBRC 15513, Corynebacterium glutamicum NBRC 12168, and Saccharomonospora viridis NBRC 12207. SNPs were found in all sets studied for comparison purposes. In sets of two or three lots, genomic SNPs were found in both non-coding sequences (non-CDSs) and in coding sequences (CDSs), and the SNPs in the CDSs resulted in non-synonymous mutations. These data indicated that genomic variation occurred during long-term preservation.
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http://dx.doi.org/10.1099/ijsem.0.002717DOI Listing
May 2018

A case of combined Morgagni and esophageal hiatal hernias successfully repaired by endoscopy and laparoscopy.

Nihon Shokakibyo Gakkai Zasshi 2017;114(10):1836-1844

Department of Gastroenterology and Hepatology, Nagasaki University Graduate School of Biomedical Sciences.

An 87-year-old woman with a 4-month history of postprandial gastrointestinal obstruction was admitted to our facility after suddenly vomiting black matter. Computed tomography and esophagogastroduodenoscopy revealed gastric prolapse and prolapse of the duodenum and transverse colon. Morgagni hernia combined with esophageal hiatal hernia was diagnosed. Gastric and duodenal obstructions were successfully repaired by endoscopy, followed by laparoscopic repair. Endoscopic repair helped the patient avoid fasting before surgery. The patient had a history of several chest bruises, which were detected by chest X-rays and suspected to be the cause of the hernias over time.
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http://dx.doi.org/10.11405/nisshoshi.114.1836DOI Listing
March 2018

Three novel species of d-xylose-assimilating yeasts, Barnettozyma xylosiphila sp. nov., Barnettozyma xylosica sp. nov. and Wickerhamomyces xylosivorus f.a., sp. nov.

Int J Syst Evol Microbiol 2017 Oct 12;67(10):3971-3976. Epub 2017 Sep 12.

Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba, Japan.

This study describes three novel xylose-assimilating yeasts, which were isolated from decayed wood collected from Bung Hatta Botanical Garden in West Sumatra and Cibodas Botanic Garden in West Java, or from litter from Eka Karya Bali Botanic Garden in Bali, Indonesia. Phylogenetic analysis was performed based on the sequences of the D1/D2 domains of the large ribosomal subunit (LSU), the small ribosomal subunit (SSU), the internal transcribed spacer (ITS) and elongation factor-1α (EF-1α), and the three strains were found to represent three novel species belonging to genera Barnettozyma or Wickerhamomyces. The morphological, biochemical and physiological characteristics indicated that the strains were distinct from other closely related species. Strains 13Y206 and 14Y196 belonging to the Barnettozyma clade are described as the type strains of Barnettozyma xylosiphila sp. nov. (type strain 13Y206=NBRC 110202=InaCC Y726; MycoBank MB808598) and Barnettozyma xylosica sp. nov. (type strain 14Y196=NBRC 111558=InaCC Y1030; MycoBank MB819485). Strain 14Y125 belonging to the Wickerhamomyces clade is described as the type strain of Wickerhamomyces xylosivorus f.a., sp. nov. (type strain 14Y125=NBRC 111553=InaCC Y1026; MycoBank MB819484).
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http://dx.doi.org/10.1099/ijsem.0.002233DOI Listing
October 2017

The neutral N-linked glycans of the ustilaginomycete yeast Sympodiomycopsis paphiopedili.

Yeast 2017 07 29;34(7):305-317. Epub 2017 May 29.

International Center for Biotechnology, Osaka University, Japan.

Sympodiomycopsis paphiopedili is a basidiomycetous yeast under the subphylum Ustilaginomycotina and is a commensal organism originally isolated from the nectar of a plant species in Japan. In this study, the neutral N-linked glycans of S. paphiopedili were prepared and structurally analysed using high-performance liquid chromatography (HPLC) and mass spectrometry (MS). Glycosidase digestion analyses were also performed to verify certain glycan linkages. HPLC and MS analyses revealed the presence of neutral N-linked glycans ranging from Man GlcNAc -PA to Man GlcNAc -PA in length. The most abundant neutral N-linked glycan structure in this species was found to be the Manα1-2Manα1-6(Manα1-3)Manα1-6(Manα1-2Manα1-2Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc (M8A). Moreover, the second and third most abundant neutral N-linked glycan in S. paphiopedili were the Manα1-2Manα1-6(Manα1-2Manα1-3)Manα1-6(Manα1-2Manα1-2Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc (M9A) and the Manα1-6(Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc (M3B). On the other hand, the effect of the combination of glycoprotein extraction methods (citrate buffer extraction or bead extraction) and the subsequent glycan release methods (hydrazinolysis or PNGase F digestion) on the detection of N-linked glycan peaks was also examined for S. paphiopedili and Saccharomyces cerevisiae in order to avoid under-representation of N-linked glycan structures. High mannose and possible hypermannosylated glycan peaks were detected in all method combinations in S. cerevisiae with the citrate buffer extraction-hydrazinolysis method giving the highest peak yields as compared with the other methods. Here we report the first account of the structural analysis of the neutral N-linked glycan of S. paphiopedili and the comparison of the effect of combinations of glycoprotein extraction methods and glycan release methods with that of the glycan analysis in S. paphiopedili and S. cerevisiae. Copyright © 2017 John Wiley & Sons, Ltd.
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http://dx.doi.org/10.1002/yea.3233DOI Listing
July 2017

Pichia chibodasensis sp. nov., isolated in Indonesia.

Int J Syst Evol Microbiol 2017 Apr 5;67(4):1024-1027. Epub 2017 May 5.

Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba, Japan.

Three strains (14Y260T, 14Y268 and 14Y276) of xylose-assimilating yeasts were isolated from decayed wood and soil collected in West Java in Indonesia. A phylogenetic analysis was performed based on the sequences of the D1/D2 domains of LSU, SSU and EF-1α, and the three strains were found to belong to the genus Pichia. The morphological, biochemical, physiological and chemotaxonomic characteristics indicated that these strains were distinct from other closely related species. Strains 14Y260T, 14Y268 and 14Y276 belonged to the Pichia clade and represent a novel species, named Pichia chibodasensis sp. nov. ; The type strain is 14Y260T (=NBRC 111569T=InaCC Y1042T).
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http://dx.doi.org/10.1099/ijsem.0.001735DOI Listing
April 2017

Analysis on transglutaminase 1 and its substrates using specific substrate peptide in cultured keratinocytes.

Biochem Biophys Res Commun 2016 09 11;478(1):343-348. Epub 2016 Jul 11.

Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa, Furoh-cho, Nagoya, 464-8601, Japan. Electronic address:

Transglutaminase (TGase) catalyzes protein cross-linking reactions essential for several biological processes. In differentiating keratinocytes, TG1 (keratinocyte-type) is crucial for the cross-linking of substrate proteins required for the complete formation of the cornified envelop, a proteinaceous supermolecule located in the outermost layer of the epidermis. TG1 expressions and its substrate were induced in cultured keratinocytes at differentiation-stage specific manner. In the cultured keratinocytes, we used the TG1-specific substrate peptide, which enables the specific detection of enzymatic activity to investigate its induction patterns. As a further application of the substrate peptide, several substrate candidates of TG1 that may be essential for cornified envelope formation were identified and characterized.
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http://dx.doi.org/10.1016/j.bbrc.2016.07.051DOI Listing
September 2016

Halobium palmae gen. nov., sp. nov., an extremely halophilic archaeon isolated from a solar saltern.

Int J Syst Evol Microbiol 2016 Oct 3;66(10):3799-3804. Epub 2016 Jul 3.

NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan.

A novel and extremely halophilic archaeon, designated strain 2a_47_2T, was isolated from a solar saltern sample collected in Indonesia. Cells of the strain were Gram-stain-negative, non-motile and pleomorphic and formed orange-red pigmented colonies. Strain 2a_47_2T grew at 20-48 °C (optimum 38-41 °C), pH 6.0-8.5 (optimum pH 7.5), >1.7 M NaCl (optimum 2.6 M) and <0.5 M MgCl2 (optimum 0.3 M). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two phospholipids and sulfated diglycosyl diether. The cells mainly contained menaquinone-8. The G+C content in the genomic DNA of the strain was 67.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 2a_47_2T represents a member of the family Halorubraceae and is different from any other known halophilic archaea. This finding was also demonstrated by phylogenetic analyses based on deduced RpoB' amino acid sequences. Collectively, these results show that strain 2a_47_2T represents a novel genus and species in the family Halorubraceae, and the name Halobium palmae gen. nov., sp. nov. is proposed. The type strain is 2a_47_2T (=NBRC 111368T=InaCC Ar34T).
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http://dx.doi.org/10.1099/ijsem.0.001267DOI Listing
October 2016

Haloarchaeobius baliensis sp. nov., isolated from a solar saltern.

Int J Syst Evol Microbiol 2016 Jan 8;66(1):38-43. Epub 2015 Oct 8.

NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan.

A novel halophilic archaeon, designated strain 2b_61_3T, was isolated from a solar saltern in Indonesia. Cells of the strain were Gram-stain-negative, motile, pleomorphic rods that formed orange-red-pigmented colonies on solid medium. The isolate grew optimally at 42-44 °C, pH 6.5-7.0, and with 2.6 M NaCl, and MgCl2 was required for growth. Strain 2b_61_3T had two differential 16S rRNA genes (rrnA and rrnB), and phylogenetic analysis revealed that the strain belonged to the genus Haloarchaeobius. The rrnA and rrnB sequence similarities between strain 2b_61_3T and species of the genus Haloarchaeobius were 98.4-99.2 % and 98.5-98.8 %, respectively. The findings from the 16S rRNA gene analysis were supported by sequence analysis of rpoB', the B' subunit of RNA polymerase. On the basis of the phenotypic characteristics and phylogenetic analyses, as well as DNA-DNA hybridization experiments with Haloarchaeobius iranensis NBRC 110930T, strain 2b_61_3T represents a novel species of the genus Haloarchaeobius, for which the name Haloarchaeobius baliensis sp. nov. is proposed. The type strain is 2b_61_3T ( = NBRC 110517T = InaCC Ar2T).
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http://dx.doi.org/10.1099/ijsem.0.000672DOI Listing
January 2016

Lipomyces chichibuensis sp. nov., isolated in Japan, and reidentification of the type strains of Lipomyces kononenkoae and Lipomyces spencermartinsiae.

Int J Syst Evol Microbiol 2014 Aug 8;64(Pt 8):2566-2572. Epub 2014 May 8.

NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan.

We isolated two strains of a novel Lipomyces species from soil collected in Chichibu forest, Saitama prefecture, Japan. Based on their morphological and biochemical characteristics, along with multilocus sequence typing using the D1/D2 domain of the large-subunit (LSU) rRNA gene, the internal transcribed spacer (ITS) region and the translation elongation factor 1 alpha gene (EF-1α), the two strains were shown to represent a novel species of the genus Lipomyces, described as Lipomyces chichibuensis sp. nov. (type strain CB08-2(T) = NBRC 109582(T) = CBS 12929(T); Mycobank no. MB808164). In addition, we reidentified the type strains of Lipomyces kononenkoae and Lipomyces spencermartinsiae maintained in culture collections based on phenotypic characters and/or DNA-DNA hybridization to ensure correct future identification of species of the genus Lipomyces. The correct type strains of L. kononenkoae and L. spencermartinsiae are NBRC 107661(T) ( = CBS 2514(T)) and NBRC 10376(T) ( = CBS 5608(T)), respectively.
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http://dx.doi.org/10.1099/ijs.0.059972-0DOI Listing
August 2014

[Handling and culture collection of clinical isolate: focus on preservation and distribution of microbial strains for industrial use].

Authors:
Hiroko Kawasaki

Med Mycol J 2014 ;55(1):J3-J12

Biological Resource Center, National Institute of Technology and Evaluation.

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http://dx.doi.org/10.3314/mmj.55.j3DOI Listing
April 2015

Diversity of culturable yeasts in phylloplane of sugarcane in Thailand and their capability to produce indole-3-acetic acid.

World J Microbiol Biotechnol 2014 Jun 19;30(6):1785-96. Epub 2014 Jan 19.

Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand,

Yeasts were isolated by the enrichment technique from the phylloplane of 94 samples of sugarcane leaf collected from seven provinces in Thailand. All sugarcane leaf samples contained yeasts and 158 yeast strains were obtained. On the basis of the D1/D2 domain of the large subunit rRNA gene sequence analysis, 144 strains were identified to 24 known species in 14 genera belonging to the Ascomycota viz. Candida akabanensis, Candida dendronema, Candida mesorugosa, Candida michaelii, Candida nivariensis, Candida rugosa, Candida orthopsilosis, Candida quercitrusa, Candida tropicalis, Candida xylopsoci, Cyberlindnera fabianii, Cyberlindnera rhodanensis, Debaryomyces nepalensis, Hannaella aff. coprosmaensis, Hanseniaspora guilliermondii, Kluyveromyces marxianus, Lachancea thermotolerans, Lodderomyces elongisporus, Metschnikowia koreensis, Meyerozyma caribbica, Millerozyma koratensis, Pichia kudriavzevii, Torulaspora delbrueckii and Wickerhamomyces edaphicus, and 12 species in six genera of the Basidiomycota viz . Cryptococcus flavescens, Cryptococcus laurentii, Cryptococcus rajasthanensis, Kwoniella heveanensis, Rhodosporidium fluviale, Rhodosporidium paludigenum, Rhodotorula mucilaginosa, Rhodotorula sesimbrana, Rhodotorula taiwanensis, Sporidiobolus ruineniae, Sporobolomyces carnicolor and Sporobolomyces nylandii. Seven strains were identical or similar to four undescribed species. Another seven strains represented four novels species in the genus Metschnikowia, Nakazawaea, Wickerhamomyces and Yamadazyma. The results revealed 69 % of the isolated strains were ascomycete yeasts and 31 % were basidiomycete yeast. The most prevalent species was M. caribbica with a 23 % frequency of occurrence followed by Rh. taiwanensis (11 %) and C. tropicalis (10 %). All strains were assessed for indole-3-acetic acid (IAA) producing capability showing that 69 strains had the capability of producing IAA when cultivated in yeast extract peptone dextrose broth supplemented with 1 g/L L-tryptophan. The highest IAA concentration of 565.1 mg/L was produced by R. fluviale DMKU-RK253.
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http://dx.doi.org/10.1007/s11274-014-1602-7DOI Listing
June 2014

Simple and rapid characterization of mycolic acids from Dietzia strains by using MALDI spiral-TOFMS with ultra high mass-resolving power.

J Antibiot (Tokyo) 2013 Dec 28;66(12):713-7. Epub 2013 Aug 28.

Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.

Mycolic acids have been used as important chemotaxonomic markers. In this study, a newly developed matrix-assisted laser desorption/ionization time-of-flight mass spectrometer with a spiral ion trajectory (MALDI spiral-TOFMS) was applied to the characterization of mycolic acids of three type strains of validated species belonging to the genus Dietzia (D. papillomatosis 105045(T), D. kunjamensis NBRC 105042(T) and D. timorensis NBRC 104184(T)), by analysis of total fatty acid methyl ester fractions. In addition, owing to the high mass-resolving power of MALDI spiral-TOFMS, adjacent peaks (0.036 Da mass differences) were successfully separated, and weak peaks corresponding to oxygenated mycolic acids were detected. For all samples, the distributions of carbon-chain lengths were mainly in the range of C30-C42 and the average number of carbon-chain lengths was about 37, which agreed reasonably well with reported results for the genus Dietzia. The number of double bonds and/or cyclopropane rings was 0-2. Relative peak intensities of each mycolic acid methyl ester were used to compare the mycolic acids of the three strains. The mycolic acids of D. papillomatosis and D. kunjamensis were characterized by a high content of mycolic acids with 0-1 double bond or cyclopropane ring and an almost equal content of mycolic acids with odd- and even-numbered carbon-chain lengths. In contrast, mycolic acids of D. timorensis were characterized by a high content of mycolic acids with 1-2 double bonds and/or cyclopropane rings with an even-numbered carbon-chain length. By using MALDI spiral-TOFMS, mycolic acids from three type strains of the genus Dietzia were characterized easily and rapidly.
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http://dx.doi.org/10.1038/ja.2013.79DOI Listing
December 2013

Two novel ascomycetous yeast species, Wickerhamomyces scolytoplatypi sp. nov. and Cyberlindnera xylebori sp. nov., isolated from ambrosia beetle galleries.

Int J Syst Evol Microbiol 2013 Jul 10;63(Pt 7):2706-2711. Epub 2013 May 10.

Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan.

Thirteen strains of yeasts were isolated from ambrosia beetle galleries at several sites in Japan. Based on the morphological and biochemical characteristics and phylogenetic analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene of the yeasts, 10 strains were shown to represent a novel species of the genus Wickerhamomyces, described as Wickerhamomyces scolytoplatypi sp. nov. (type strain NBRC 11029(T) = CBS 12186(T)), and were closely related to Wickerhamomyces hampshirensis. The three other strains represented a novel species of the genus Cyberlindnera, described as Cyberlindnera xylebori sp. nov. (type strain NBRC 11048(T) = CBS 12187(T)), and were closely related to Cyberlindnera euphorbiiphila. It is suggested that these species are associated with ambrosia beetles and we consider ambrosia beetle galleries as good sources of novel yeasts.
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http://dx.doi.org/10.1099/ijs.0.050195-0DOI Listing
July 2013

Wickerhamomyces siamensis sp. nov., a novel yeast species isolated from the phylloplane in Thailand.

Int J Syst Evol Microbiol 2013 Apr 8;63(Pt 4):1568-1573. Epub 2013 Feb 8.

Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.

Strain DMKU-RK359(T), representing a novel yeast species, was isolated from the external surface of a sugar-cane leaf collected in Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, sequence analysis of the D1/D2 region of the large-subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, strain DMKU-RK359(T) was assigned to a novel Wickerhamomyces species. The novel species was closest to Wickerhamomyces ciferrii, but differed from it by 0.7 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene and 6 % nucleotide substitutions in the ITS region. The name Wickerhamomyces siamensis sp. nov. is proposed (type strain DMKU-RK359(T)  = BCC 50732(T)  = NBRC 108900(T)  = CBS 12570(T)).
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http://dx.doi.org/10.1099/ijs.0.050013-0DOI Listing
April 2013

Yamadazyma siamensis sp. nov., Yamadazyma phyllophila sp. nov. and Yamadazyma paraphyllophila sp. nov., three novel yeast species isolated from phylloplane in Thailand and Taiwan.

Antonie Van Leeuwenhoek 2013 Apr 4;103(4):777-88. Epub 2012 Dec 4.

Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.

Four strains representing three novel anamorphic yeast species were isolated from the external surface of sugarcane leaves (DMKU-RK254(T)), corn leaves (DMKU-RK548(T)), bean leaves (K129) in Thailand and hengchun pencilwood leaves (TrB1-1(T)) in Taiwan. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, the sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene, the internal transcribed spacer (ITS) region, the actin gene (ACT1) and the elongation factor 2 gene (EF2), the four strains were determined to represent novel Yamadazyma species although formation of ascospores was not observed. Strain DMKU-RK254(T) was determined to be related to Candida diddensiae, Candida naeodendra and Candida kanchanaburiensis but with 1.8, 1.8 and 2.0 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene, respectively. It was assigned to Yamadazyma siamensis sp. nov. (type strain DMKU-RK254(T) = BCC 50730(T) = NBRC 108901(T) = CBS 12573(T)). The sequences of the D1/D2 region of the LSU rRNA gene, the ITS region, ACT1 gene and EF2 gene of two strains (DMKU-RK548(T) and K129) were identical but differed from that of strain TrB1-1(T) by 0.6, 1.0, 3.3 and 5.9 % nucleotide substitutions, respectively. Therefore, the two strains (DMKU-RK548(T) and K129) and strain TrB1-1(T) were assigned to be two separate species. The closest species in terms of pairwise sequences similarity of the D1/D2 region to the two novel species was Yamadazyma philogaea but with 1.1-1.7 % nucleotide substitutions. The two strains (DMKU-RK548(T) and K129) were assigned to Yamadazyma phyllophila sp. nov. (type strain DMKU-RK548(T) = BCC 50736(T) = NBRC 108906(T) = CBS 12572(T)) and the strain TrB1-1(T) was named Yamadazyma paraphyllophila sp. nov. (type strain TrB1-1(T) = BCRC 23030(T) = CCTCC AY 204005(T) = CBS 9928(T)).
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http://dx.doi.org/10.1007/s10482-012-9860-6DOI Listing
April 2013

Metschnikowia saccharicola sp. nov. and Metschnikowia lopburiensis sp. nov., two novel yeast species isolated from phylloplane in Thailand.

Antonie Van Leeuwenhoek 2012 Nov 12;102(4):743-51. Epub 2012 Jul 12.

Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.

Five strains representing two novel anamorphic yeast species were isolated from the external surface of sugarcane leaves (DMKU-RK16, DMKU-RK24, DMKU-RK198 and DMKU-RK500(T)) and rice leaf (DMKU-RK277(T)) by an enrichment technique. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, the sequence analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer region, the five strains were assigned to be two novel species of the Metschnikowia, although the formation of ascospores was not observed. Four strains (DMKU-RK16, DMKU-RK24, DMKU-RK198 and DMKU-RK500(T)) where the sequences of the D1/D2 domain of the LSU rRNA gene were identical and differed by 4.1 % nucleotide substitutions (20 nucleotide substitutions and four gaps out of 490 nt) from the type strain of Candida succicola, their closest known species in terms of pairwise sequence similarity, represent a single novel species, for which the name Metschnikowia saccharicola sp. nov. is proposed. The type strain is DMKU-RK500(T) (= BCC 50735(T) = NBRC 108904(T) = CBS 12575(T)). Strain DMKU-RK277(T) was closest to Candida hainanensis but with 4.0 % nucleotide substitutions (18 nucleotide substitutions and three gaps out of 449 nt) in the D1/D2 domain of the LSU rRNA gene was assigned to be Metschnikowia lopburiensis sp. nov. (type strain DMKU-RK277(T) = BCC 50731(T) = NBRC 108902(T) = CBS 12574(T)).
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http://dx.doi.org/10.1007/s10482-012-9774-3DOI Listing
November 2012
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