1. Strong effect of climate on ectomycorrhizal fungal composition: evidence from range overlap between two mountains.

    ISME Journal 9(8):1870 (2015) PMID 25647348 PMCID PMC4511943

    Separating the effects of environmental factors and spatial distance on microbial composition is difficult when these factors covary. We examined the composition of ectomycorrhizal (EM) fungi along elevation gradients on geographically distant mountains to clarify the effect of climate at the re...
  2. Loss of Cytochrome cM Stimulates Cyanobacterial Heterotrophic Growth in the Dark.

    Plant and Cell Physiology 56(2):334 (2015) PMID 25416288

    Although cyanobacteria are photoautotrophs, they have the capability for heterotrophic metabolism that enables them to survive in their natural habitat. However, cyanobacterial species that grow heterotrophically in the dark are rare. It remains largely unknown how cyanobacteria regulate heterot...
  3. Loss of cytochrome cM stimulates cyanobacterial heterotrophic growth in the dark.

    Plant and Cell Physiology 56(2):334 (2015) PMID 25416288

    Although cyanobacteria are photoautotrophs, they have the capability for heterotrophic metabolism that enables them to survive in their natural habitat. However, cyanobacterial species that grow heterotrophically in the dark are rare. It remains largely unknown how cyanobacteria regulate heterot...
  4. Complete nucleotide sequence of the IncN plasmid encoding IMP-6 and CTX-M-2 from emerging carbapenem-resistant Enterobacteriaceae in Japan.

    Antimicrobial Agents and Chemotherapy 59(2):1356 (2015) PMID 25487806 PMCID PMC4335907

    We have determined the DNA sequence of Klebsiella pneumoniae multidrug resistance plasmid pKPI-6, which is a self-transmissible IncN-type plasmid. pKPI-6 harboring blaIMP-6 and blaCTX-M-2 confers a stealth-type carbapenem resistance phenotype on members of the family Enterobacteriaceae that is n...
  5. Complete Nucleotide Sequence of the IncN Plasmid Encoding IMP-6 and CTX-M-2 from Emerging Carbapenem-Resistant Enterobacteriaceae in Japan.

    Antimicrobial Agents and Chemotherapy 59(2):1356 (2015) PMID 25487806

    We have determined the DNA sequence of Klebsiella pneumoniae multidrug resistance plasmid pKPI-6, which is a self-transmissible IncN-type plasmid. pKPI-6 harboring blaIMP-6 and blaCTX-M-2 confers a stealth-type carbapenem resistance phenotype on members of the family Enterobacteriaceae that is n...
  6. Genome Analysis of a Novel Bradyrhizobium sp. DOA9 Carrying a Symbiotic Plasmid.

    PLoS ONE 10(2):e0117392 (2015) PMID 25710540 PMCID PMC4339197

    Bradyrhizobium sp. DOA9 isolated from the legume Aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the Bradyrhizobiaceae. Genome analysis of DOA9 revealed that its genome comprised a single chromosome of 7.1 Mbp and a plasmid ...
  7. Complete Genome Sequence of Bifidobacterium kashiwanohense JCM 15439T, Isolated from Feces from a Healthy Japanese Infant.

    Genome Announcements 3(2) (2015) PMID 25883283 PMCID PMC4400426

    We isolated Bifidobacterium kashiwanohense JCM 15439 from the feces of a healthy Japanese infant and proposed it as the type strain of a novel species within the genus Bifidobacterium. Here, we report the complete genome sequence of this organism. Copyright © 2015 Morita et al.
  8. Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes.

    Microbes and Environments 30(1):44 (2015) PMID 25736980 PMCID PMC4356463

    Diazotrophs had not previously been identified among bacterial species in the phylum Bacteroidetes until the rapid expansion of bacterial genome sequences, which revealed the presence of nitrogen fixation (nif) genes in this phylum. We herein determined the draft genome sequences of Bacteroides ...
  9. Mutual reinforcement of inflammation and carcinogenesis by the Helicobacter pylori CagA oncoprotein.

    Scientific reports 5:10024 (2015) PMID 25944120 PMCID PMC4421872

    Helicobacter pylori cagA-positive strain delivers the CagA oncoprotein into gastric epithelial cells and at the same time elicits stomach inflammation. To experimentally investigate the pathophysiological interplay between CagA and inflammation, transgenic mice systemically expressing the bacter...
  10. Complete Genome Sequence of a Phenanthrene Degrader, Mycobacterium sp. Strain EPa45 (NBRC 110737), Isolated from a Phenanthrene-Degrading Consortium.

    Genome Announcements 3(4) (2015) PMID 26184940 PMCID PMC4505128

    A phenanthrene degrader, Mycobacterium sp. EPa45, was isolated from a phenanthrene-degrading consortium. Here, we report the complete genome sequence of EPa45, which has a 6.2-Mb single circular chromosome. We propose a phenanthrene degradation pathway in EPa45 based on the complete genome seque...
  11. Complete Genome Sequence of Scardovia inopinata JCM 12537T, Isolated from Human Dental Caries.

    Genome Announcements 3(3) (2015) PMID 25977411 PMCID PMC4432351

    Scardovia inopinata JCM 12537(T) was isolated from human dental caries. Here, we report the complete genome sequence of this organism. This paper is the first report to demonstrate the fully sequenced and completely annotated genome of an S. inopinata strain. Copyright © 2015 Oshima et al.
  12. Influence of Proton-Pump Inhibitors on the Luminal Microbiota in the Gastrointestinal Tract.

    Clinical and Translational Gastroenterology 6:e89 (2015) PMID 26065717

    The objective of this study was to investigate comparatively the influence of proton-pump inhibitors (PPI) administration on three bacterial communities in the oral cavity, stomach, and colon along the alimentary tract. Forty-five subjects including 18 patients taking PPI were enrolled. Stimulat...
  13. Draft Genome Sequence of Streptomyces incarnatus NRRL8089, which Produces the Nucleoside Antibiotic Sinefungin.

    Genome Announcements 3(4) (2015) PMID 26159526 PMCID PMC4498112

    A draft genome sequence of Streptomyces incarnatus NRRL8089, which produces the nucleoside antibiotic sinefungin, is described here. The genome contains 8,897,465 bp in 76 contigs and 8,266 predicted genes. Interestingly, the genome encodes an open reading frame for selenocysteine-containing for...
  14. Genome Analysis of a Novel Bradyrhizobium sp. DOA9 Carrying a Symbiotic Plasmid.

    PLoS ONE 10(2):e0117392 (2015) PMID 25710540 PMCID PMC4339197

    Bradyrhizobium sp. DOA9 isolated from the legume Aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the Bradyrhizobiaceae. Genome analysis of DOA9 revealed that its genome comprised a single chromosome of 7.1 Mbp and a plasmid ...
  15. Complete Genome Sequence of Cyanobacterium Geminocystis sp. Strain NIES-3708, Which Performs Type II Complementary Chromatic Acclimation.

    Genome Announcements 3(3) (2015) PMID 25953174 PMCID PMC4424290

    To explore the variation of the light-regulated genes during complementary chromatic acclimation (CCA), we determined the complete genome sequence of the cyanobacterium Geminocystis sp. strain NIES-3708. Within the light-regulated operon for CCA, we found genes for phycoerythrin but not phycocya...
  16. Complete Genome Sequence of Parascardovia denticolens JCM 12538T, Isolated from Human Dental Caries.

    Genome Announcements 3(3) (2015) PMID 25977413 PMCID PMC4432353

    Parascardovia denticolens JCM 12538(T) was isolated from human dental caries. Here, we report the complete genome sequence of this organism. This paper is the first report demonstrating the completely sequenced and assembled genome of P. denticolens. Copyright © 2015 Oshima et al.
  17. Multiple omics uncovers host-gut microbial mutualism during prebiotic fructooligosaccharide supplementation.

    DNA Research 21(5):469 (2014) PMID 24848698 PMCID PMC4195493

    Fructooligosaccharide (FOS), a prebiotic well known for its health-promoting properties, can improve the human gut ecosystem most likely through changes in its microbial composition. However, the detailed mechanism(s) of action of FOS in the modulation of the gut ecosystem remain(s) obscure. Tra...
  18. Multiple omics uncovers host-gut microbial mutualism during prebiotic fructooligosaccharide supplementation.

    DNA Research 21(5):469 (2014) PMID 24848698 PMCID PMC4195493

    Fructooligosaccharide (FOS), a prebiotic well known for its health-promoting properties, can improve the human gut ecosystem most likely through changes in its microbial composition. However, the detailed mechanism(s) of action of FOS in the modulation of the gut ecosystem remain(s) obscure. Tra...
  19. Phylogeny and functions of bacterial communities associated with field-grown rice shoots.

    Microbes and Environments 29(3):329 (2014) PMID 25130883 PMCID PMC4159046

    Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath. In both cultivars, shoot microbiomes were dominated by Alphaproteobacteria (51-52%), Actinobacteria (11-15%), Gammaproteobacteria (9-10%), and Betaprot...
  20. Phylogeny and functions of bacterial communities associated with field-grown rice shoots.

    Microbes and Environments 29(3):329 (2014) PMID 25130883 PMCID PMC4159046

    Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath. In both cultivars, shoot microbiomes were dominated by Alphaproteobacteria (51-52%), Actinobacteria (11-15%), Gammaproteobacteria (9-10%), and Betaprot...