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1.  Draft Genome Sequences of Psychrobacter Strains JCM 18900, JCM 18901, JCM 18902, and JCM 18903, Isolated Preferentially from Frozen Aquatic Organisms 
Genome Announcements  2014;2(2):e00280-14.
Four Psychrobacter strains, JCM 18900, JCM 18901, JCM 18902, and JCM 18903, related to either Psychrobacter nivimaris or Psychrobacter cibarius, were isolated from frozen marine animals. The genome information of these four strains will be useful for studies of their physiology and adaptation properties to frozen conditions.
doi:10.1128/genomeA.00280-14
PMCID: PMC3974947  PMID: 24699965
2.  Draft Genome Sequence of Cytophaga fermentans JCM 21142T, a Facultative Anaerobe Isolated from Marine Mud 
Genome Announcements  2014;2(2):e00206-14.
Cytophaga fermentans strain JCM 21142T is a marine-dwelling facultative anaerobe. The draft genome sequence of this strain revealed its diverse chemoorganotrophic potential, which makes it capable of metabolizing various polysaccharide substrates. The genome data will facilitate further studies on its taxonomic reclassification, its metabolism, and the mechanisms pertaining to bacterial gliding.
doi:10.1128/genomeA.00206-14
PMCID: PMC3968337  PMID: 24675859
3.  Draft Genome Sequences of Two Lactobacillus Strains, L. farraginis JCM 14108T and L. composti JCM 14202T, Isolated from Compost of Distilled Shōchū Residue 
Genome Announcements  2014;2(2):e00257-14.
Here, we report the draft genome sequences of two type strains of Lactobacillus, Lactobacillus farraginis JCM 14108T and Lactobacillus composti JCM 14202T, isolated from the compost of distilled shōchū residue. Their genome information will be useful for studies of ecological and physiological functions of these Lactobacillus species.
doi:10.1128/genomeA.00257-14
PMCID: PMC3968344  PMID: 24675866
4.  Draft Genome Sequence of Paenibacillus pini JCM 16418T, Isolated from the Rhizosphere of Pine Tree 
Genome Announcements  2014;2(2):e00210-14.
Paenibacillus pini strain JCM 16418T is a cellulolytic bacterium isolated from the rhizosphere of pine trees. Here, we report the draft genome sequence of this strain. This genome information will be useful for studies of rhizosphere bacteria.
doi:10.1128/genomeA.00210-14
PMCID: PMC3961731  PMID: 24652984
5.  Draft Genome Sequences of Cyclodextrin-Producing Alkaliphilic Bacillus Strains JCM 19045, JCM 19046, and JCM 19047 
Genome Announcements  2014;2(2):e00211-14.
Bacillus strains JCM 19045, JCM 19046, and JCM 19047 are alkaliphiles that produce β-cyclodextrin from starch. They are related to Bacillus xiaoxiensis and Bacillus lehensis. The genome information for these three strains will be useful for studies of the physiological role of cyclodextrin and cyclodextrin production.
doi:10.1128/genomeA.00211-14
PMCID: PMC3961732  PMID: 24652985
6.  Draft Genome Sequence of the Boron-Tolerant and Moderately Halotolerant Bacterium Gracilibacillus boraciitolerans JCM 21714T 
Genome Announcements  2014;2(1):e00097-14.
Gracilibacillus boraciitolerans JCM 21714T has been characterized as a highly boron-tolerant and moderately halotolerant bacterium. Here, we report the draft genome sequence of this strain. The genome sequence facilitates an understanding of the biochemical functions of boron and provides a base to identify the gene(s) involved in the boron tolerance mechanism of the strain.
doi:10.1128/genomeA.00097-14
PMCID: PMC3931363  PMID: 24558242
7.  Draft Genome Sequence of Clostridium straminisolvens Strain JCM 21531T, Isolated from a Cellulose-Degrading Bacterial Community 
Genome Announcements  2014;2(1):e00110-14.
Here, we report the draft genome sequence of a fibrolytic bacterium, Clostridium straminisolvens JCM 21531T, isolated from a cellulose-degrading bacterial community. The genome information of this strain will be useful for studies on the degradation enzymes and functional interactions with other members in the community.
doi:10.1128/genomeA.00110-14
PMCID: PMC3931369  PMID: 24558248
8.  Draft Genome Sequence of Bacteroides reticulotermitis Strain JCM 10512T, Isolated from the Gut of a Termite 
Genome Announcements  2014;2(1):e00072-14.
Here we report the draft genome sequence of Bacteroides reticulotermitis strain JCM 10512T, a xylanolytic and cellulolytic bacterium isolated from the gut of a wood-feeding termite. The genome information will facilitate the study of this strain for biomass degradation and adaptation to the gut environment.
doi:10.1128/genomeA.00072-14
PMCID: PMC3924377  PMID: 24526645
9.  Draft Genome Sequences of Three Strains of Bacteroides pyogenes Isolated from a Cat and Swine 
Genome Announcements  2014;2(1):e01242-13.
Here, we report the draft genome sequences of Bacteroides pyogenes JCM 6294T, JCM 6292, and JCM 10003, which were isolated from a cat and swine and were recently classified into a single species, B. pyogenes. Comparative analyses of these genomes revealed the diversification of B. pyogenes strains isolated from different animals.
doi:10.1128/genomeA.01242-13
PMCID: PMC3907732  PMID: 24482517
10.  Draft Genome Sequences of Three Alkaliphilic Bacillus Strains, Bacillus wakoensis JCM 9140T, Bacillus akibai JCM 9157T, and Bacillus hemicellulosilyticus JCM 9152T 
Genome Announcements  2014;2(1):e01258-13.
Here, we report the draft genome sequences of the type strains of three cellulolytic or hemicellulolytic alkaliphilic Bacillus species: Bacillus wakoensis, Bacillus akibai, and Bacillus hemicellulosilyticus. The genome information for these three strains will be useful for studies of alkaliphilic Bacillus species, their evolution, and biotechnological applications for their enzymes.
doi:10.1128/genomeA.01258-13
PMCID: PMC3907737  PMID: 24482522
11.  Draft Genome Sequence of the Alkaliphilic and Xylanolytic Paenibacillus sp. Strain JCM 10914, Isolated from the Gut of a Soil-Feeding Termite 
Genome Announcements  2014;2(1):e01144-13.
Panibacillus sp. strain JCM 10914 is a xylanolytic alkaliphile isolated from the gut of a soil-feeding termite. Its draft genome sequence revealed various genes for hydrolytic enzymes and will facilitate studies on adaptation to the highly alkaline gut environment and its role in digesting soil organic matter in the gut.
doi:10.1128/genomeA.01144-13
PMCID: PMC3900890  PMID: 24459258
12.  Horizontal Gene Acquisition of Liberibacter Plant Pathogens from a Bacteriome-Confined Endosymbiont of Their Psyllid Vector 
PLoS ONE  2013;8(12):e82612.
he Asian citrus psyllid Diaphorina citri is a notorious agricultural pest that transmits the phloem-inhabiting alphaproteobacterial ‘Candidatus Liberibacter asiaticus’ and allied plant pathogens, which cause the devastating citrus disease called Huanglongbing or greening disease. D. citri harbors two distinct bacterial mutualists in the symbiotic organ called bacteriome: the betaproteobacterium ‘Candidatus Profftella armatura’ in the syncytial cytoplasm at the center of the bacteriome, and the gammaproteobacterium ‘Candidatus Carsonella ruddii’ in uninucleate bacteriocytes. Here we report that a putative amino acid transporter LysE of Profftella forms a highly supported clade with proteins of L. asiaticus, L. americanus, and L. solanacearum. L. crescens, the most basal Liberibacter lineage currently known, lacked the corresponding gene. The Profftella-Liberibacter subclade of LysE formed a clade with proteins from betaproteobacteria of the order Burkholderiales, to which Profftella belongs. This phylogenetic pattern favors the hypothesis that the Liberibacter lineage acquired the gene from the Profftella lineage via horizontal gene transfer (HGT) after L. crescens diverged from other Liberibacter lineages. KA/KS analyses further supported the hypothesis that the genes encoded in the Liberibacter genomes are functional. These findings highlight the possible evolutionary importance of HGT between plant pathogens and their insect vector’s symbionts that are confined in the symbiotic organ and seemingly sequestered from external microbial populations.
doi:10.1371/journal.pone.0082612
PMCID: PMC3857777  PMID: 24349319
13.  Genomic Adaptation of the Lactobacillus casei Group 
PLoS ONE  2013;8(10):e75073.
Lactobacillus casei, L. paracasei, and L. rhamnosus form a closely related taxonomic group (Lactobacillus casei group) within the facultatively heterofermentative lactobacilli. Here, we report the complete genome sequences of L. paracasei JCM 8130 and L. casei ATCC 393, and the draft genome sequence of L. paracasei COM0101, all of which were isolated from daily products. Furthermore, we re-annotated the genome of L. rhamnosus ATCC 53103 (also known as L. rhamnosus GG), which we have previously reported. We confirmed that ATCC 393 is distinct from other strains previously described as L. paracasei. The core genome of 10 completely sequenced strains of the L. casei group comprised 1,682 protein-coding genes. Although extensive genome-wide synteny was found among the L. casei group, the genomes of ATCC 53103, JCM 8130, and ATCC 393 contained genomic islands compared with L. paracasei ATCC 334. Several genomic islands, including carbohydrate utilization gene clusters, were found at the same loci in the chromosomes of the L. casei group. The spaCBA pilus gene cluster, which was first identified in GG, was also found in other strains of the L. casei group, but several L. paracasei strains including COM0101 contained truncated spaC gene. ATCC 53103 encoded a higher number of proteins involved in carbohydrate utilization compared with intestinal lactobacilli, and extracellular adhesion proteins, several of which are absent in other strains of the L. casei group. In addition to previously fully sequenced L. rhamnosus and L. paracasei strains, the complete genome sequences of L. casei will provide valuable insights into the evolution of the L. casei group.
doi:10.1371/journal.pone.0075073
PMCID: PMC3792948  PMID: 24116025
14.  Genome Analysis Suggests that the Soil Oligotrophic Bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) Is a Nitrogen-Fixing Symbiont of Aeschynomene indica 
Agromonas oligotrophica (Bradyrhizobium oligotrophicum) S58T is a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. Here, the complete genome sequence of S58 was determined. The S58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1% lacking nodABC genes and the typical symbiosis island. The genome showed a high level of similarity to the genomes of Bradyrhizobium sp. ORS278 and Bradyrhizobium sp. BTAi1, including nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant, Aeschynomene indica, in a Nod factor-independent manner. Although nonsymbiotic (brady)rhizobia are significant components of rhizobial populations in soil, we found that most genes important for nodule development (ndv) and symbiotic nitrogen fixation (nif and fix) with A. indica were well conserved between the ORS278 and S58 genomes. Therefore, we performed inoculation experiments with five A. oligotrophica strains (S58, S42, S55, S72, and S80). Surprisingly, all five strains of A. oligotrophica formed effective nitrogen-fixing nodules on the roots and/or stems of A. indica, with differentiated bacteroids. Nonsymbiotic (brady)rhizobia are known to be significant components of rhizobial populations without a symbiosis island or symbiotic plasmids in soil, but the present results indicate that soil-dwelling A. oligotrophica generally possesses the ability to establish symbiosis with A. indica. Phylogenetic analyses suggest that Nod factor-independent symbiosis with A. indica is a common trait of nodABC- and symbiosis island-lacking strains within the members of the photosynthetic Bradyrhizobium clade, including A. oligotrophica.
doi:10.1128/AEM.00009-13
PMCID: PMC3623176  PMID: 23396330
15.  Complete Genome Sequence of the Equol-Producing Bacterium Adlercreutzia equolifaciens DSM 19450T 
Genome Announcements  2013;1(5):e00742-13.
Adlercreutzia equolifaciens DSM 19450T was isolated from human feces and is able to metabolize daidzeins (soybean isoflavonoids) to equol. Here, we report the finished and annotated genome sequence of this organism.
doi:10.1128/genomeA.00742-13
PMCID: PMC3778203  PMID: 24051320
16.  Complete Genomic DNA Sequence of the East Asian Spotted Fever Disease Agent Rickettsia japonica 
PLoS ONE  2013;8(9):e71861.
Rickettsia japonica is an obligate intracellular alphaproteobacteria that causes tick-borne Japanese spotted fever, which has spread throughout East Asia. We determined the complete genomic DNA sequence of R. japonica type strain YH (VR-1363), which consists of 1,283,087 base pairs (bp) and 971 protein-coding genes. Comparison of the genomic DNA sequence of R. japonica with other rickettsiae in the public databases showed that 2 regions (4,323 and 216 bp) were conserved in a very narrow range of Rickettsia species, and the shorter one was inserted in, and disrupted, a preexisting open reading frame (ORF). While it is unknown how the DNA sequences were acquired in R. japonica genomes, it may be a useful signature for the diagnosis of Rickettsia species. Instead of the species-specific inserted DNA sequences, rickettsial genomes contain Rickettsia-specific palindromic elements (RPEs), which are also capable of locating in preexisting ORFs. Precise alignments of protein and DNA sequences involving RPEs showed that when a gene contains an inserted DNA sequence, each rickettsial ortholog carried an inserted DNA sequence at the same locus. The sequence, ATGAC, was shown to be highly frequent and thus characteristic in certain RPEs (RPE-4, RPE-6, and RPE-7). This finding implies that RPE-4, RPE-6, and RPE-7 were derived from a common inserted DNA sequence.
doi:10.1371/journal.pone.0071861
PMCID: PMC3767692  PMID: 24039725
17.  A Unique Dermal Dendritic Cell Subset That Skews the Immune Response toward Th2 
PLoS ONE  2013;8(9):e73270.
Dendritic cell (DC) subsets in the skin and draining lymph nodes (LNs) are likely to elicit distinct immune response types. In skin and skin-draining LNs, a dermal DC subset expressing macrophage galactose-type C-type lectin 2 (MGL2/CD301b) was found distinct from migratory Langerhans cells (LCs) or CD103+ dermal DCs (dDCs). Lower expression levels of Th1-promoting and/or cross-presentation-related molecules were suggested by the transcriptome analysis and verified by the quantitative real-time PCR analysis in MGL2+ dDCs than in CD103+ dDCs. Transfer of MGL2+ dDCs but not CD103+ dDCs from FITC-sensitized mice induced a Th2-type immune response in vivo in a model of contact hypersensitivity. Targeting MGL2+ dDCs with a rat monoclonal antibody against MGL2 efficiently induced a humoral immune response with Th2-type properties, as determined by the antibody subclass. We propose that the properties of MGL2+ dDCs, are complementary to those of CD103+ dDCs and skew the immune response toward a Th2-type response.
doi:10.1371/journal.pone.0073270
PMCID: PMC3767795  PMID: 24039898
18.  Dysbiosis of Salivary Microbiota in Inflammatory Bowel Disease and Its Association With Oral Immunological Biomarkers 
Analysis of microbiota in various biological and environmental samples under a variety of conditions has recently become more practical due to remarkable advances in next-generation sequencing. Changes leading to specific biological states including some of the more complex diseases can now be characterized with relative ease. It is known that gut microbiota is involved in the pathogenesis of inflammatory bowel disease (IBD), mainly Crohn's disease and ulcerative colitis, exhibiting symptoms in the gastrointestinal tract. Recent studies also showed increased frequency of oral manifestations among IBD patients, indicating aberrations in the oral microbiota. Based on these observations, we analyzed the composition of salivary microbiota of 35 IBD patients by 454 pyrosequencing of the bacterial 16S rRNA gene and compared it with that of 24 healthy controls (HCs). The results showed that Bacteroidetes was significantly increased with a concurrent decrease in Proteobacteria in the salivary microbiota of IBD patients. The dominant genera, Streptococcus, Prevotella, Neisseria, Haemophilus, Veillonella, and Gemella, were found to largely contribute to dysbiosis (dysbacteriosis) observed in the salivary microbiota of IBD patients. Analysis of immunological biomarkers in the saliva of IBD patients showed elevated levels of many inflammatory cytokines and immunoglobulin A, and a lower lysozyme level. A strong correlation was shown between lysozyme and IL-1β levels and the relative abundance of Streptococcus, Prevotella, Haemophilus and Veillonella. Our data demonstrate that dysbiosis of salivary microbiota is associated with inflammatory responses in IBD patients, suggesting that it is possibly linked to dysbiosis of their gut microbiota.
doi:10.1093/dnares/dst037
PMCID: PMC3925391  PMID: 24013298
Crohn's disease; ulcerative colitis; salivary microbiota; 16S rRNA; pyrosequencing
19.  Enterotypes of the human gut microbiome 
Nature  2011;473(7346):174-180.
Our knowledge on species and function composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about their variation across the world. Combining 22 newly sequenced fecal metagenomes of individuals from 4 countries with previously published datasets, we identified three robust clusters (enterotypes hereafter) that are not nation or continent-specific. We confirmed the enterotypes also in two published, larger cohorts suggesting that intestinal microbiota variation is generally stratified, not continuous. This further indicates the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis for a community understanding. While individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.
doi:10.1038/nature09944
PMCID: PMC3728647  PMID: 21508958
20.  Complete Genome Sequence of Burkholderia sp. Strain RPE64, Bacterial Symbiont of the Bean Bug Riptortus pedestris 
Genome Announcements  2013;1(4):e00441-13.
We isolated Burkholderia symbiont strain RPE64 from the bean bug Riptortus pedestris. Analysis of the complete 6.96-Mb genome, which consists of three chromosomes and two plasmids, will facilitate further understanding of insect–microbe symbiosis and the development of pest-control technologies.
doi:10.1128/genomeA.00441-13
PMCID: PMC3703598  PMID: 23833137
21.  Robustness of Gut Microbiota of Healthy Adults in Response to Probiotic Intervention Revealed by High-Throughput Pyrosequencing 
Probiotics are live microorganisms that potentially confer beneficial outcomes to host by modulating gut microbiota in the intestine. The aim of this study was to comprehensively investigate effects of probiotics on human intestinal microbiota using 454 pyrosequencing of bacterial 16S ribosomal RNA genes with an improved quantitative accuracy for evaluation of the bacterial composition. We obtained 158 faecal samples from 18 healthy adult Japanese who were subjected to intervention with 6 commercially available probiotics containing either Bifidobacterium or Lactobacillus strains. We then analysed and compared bacterial composition of the faecal samples collected before, during, and after probiotic intervention by Operational taxonomic units (OTUs) and UniFrac distances. The results showed no significant changes in the overall structure of gut microbiota in the samples with and without probiotic administration regardless of groups and types of the probiotics used. We noticed that 32 OTUs (2.7% of all analysed OTUs) assigned to the indigenous species showed a significant increase or decrease of ≥10-fold or a quantity difference in >150 reads on probiotic administration. Such OTUs were found to be individual specific and tend to be unevenly distributed in the subjects. These data, thus, suggest robustness of the gut microbiota composition in healthy adults on probiotic administration.
doi:10.1093/dnares/dst006
PMCID: PMC3686430  PMID: 23571675
probiotics; gut microbiota; 16S ribosomal RNA gene; pyrosequencing
22.  Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability 
PLoS ONE  2013;8(3):e60521.
We determined the complete genome sequence of Lactobacillus brevis KB290, a probiotic lactic acid bacterium isolated from a traditional Japanese fermented vegetable. The genome contained a 2,395,134-bp chromosome that housed 2,391 protein-coding genes and nine plasmids that together accounted for 191 protein-coding genes. KB290 contained no virulence factor genes, and several genes related to presumptive cell wall-associated polysaccharide biosynthesis and the stress response were present in L. brevis KB290 but not in the closely related L. brevis ATCC 367. Plasmid-curing experiments revealed that the presence of plasmid pKB290-1 was essential for the strain's gastrointestinal tract tolerance and tendency to aggregate. Using next-generation deep sequencing of current and 18-year-old stock strains to detect low frequency variants, we evaluated genome stability. Deep sequencing of four periodic KB290 culture stocks with more than 1,000-fold coverage revealed 3 mutation sites and 37 minority variation sites, indicating long-term stability and providing a useful method for assessing the stability of industrial bacteria at the nucleotide level.
doi:10.1371/journal.pone.0060521
PMCID: PMC3609814  PMID: 23544154
23.  Coordinated Changes in DNA Methylation in Antigen-Specific Memory CD4 T Cells 
Memory CD4+ T cells are central regulators of both humoral and cellular immune responses. T cell differentiation results in specific changes in chromatin structure and DNA methylation of cytokine genes. Although the methylation status of a limited number of gene loci in T cells has been examined, the genome-wide DNA methylation status of memory CD4+ T cells remains unexplored. To further elucidate the molecular signature of memory T cells, we conducted methylome and transcriptome analyses of memory CD4+ T cells generated using T cells from TCR-transgenic mice. The resulting genome-wide DNA methylation profile revealed 1144 differentially methylated regions (DMRs) across the murine genome during the process of T cell differentiation, 552 of which were associated with gene loci. Interestingly, the majority of these DMRs were located in introns. These DMRs included genes such as CXCR6, Tbox21, Chsy1, and Cish, which are associated with cytokine production, homing to bone marrow, and immune responses. Methylation changes in memory T cells exposed to specific Ag appeared to regulate enhancer activity rather than promoter activity of immunologically relevant genes. In addition, methylation profiles differed between memory T cell subsets, demonstrating a link between T cell methylation status and T cell differentiation. By comparing DMRs between naive and Ag-specific memory T cells, this study provides new insights into the functional status of memory T cells.
doi:10.4049/jimmunol.1202267
PMCID: PMC3619526  PMID: 23509353
24.  Chromosome Painting In Silico in a Bacterial Species Reveals Fine Population Structure 
Molecular Biology and Evolution  2013;30(6):1454-1464.
Identifying population structure forms an important basis for genetic and evolutionary studies. Most current methods to identify population structure have limitations in analyzing haplotypes and recombination across the genome. Recently, a method of chromosome painting in silico has been developed to overcome these shortcomings and has been applied to multiple human genome sequences. This method detects the genome-wide transfer of DNA sequence chunks through homologous recombination. Here, we apply it to the frequently recombining bacterial species Helicobacter pylori that has infected Homo sapiens since their birth in Africa and shows wide phylogeographic divergence. Multiple complete genome sequences were analyzed including sequences from Okinawa, Japan, that we recently sequenced. The newer method revealed a finer population structure than revealed by a previous method that examines only MLST housekeeping genes or a phylogenetic network analysis of the core genome. Novel subgroups were found in Europe, Amerind, and East Asia groups. Examination of genetic flux showed some singleton strains to be hybrids of subgroups and revealed evident signs of population admixture in Africa, Europe, and parts of Asia. We expect this approach to further our understanding of intraspecific bacterial evolution by revealing population structure at a finer scale.
doi:10.1093/molbev/mst055
PMCID: PMC3649679  PMID: 23505045
fineSTRUCTURE; homologous recombination; phylogenetic network; human evolution; Helicobacter pylori
25.  Complete Genome Sequence of Bacillus cereus NC7401, Which Produces High Levels of the Emetic Toxin Cereulide 
Journal of Bacteriology  2012;194(17):4767-4768.
We report the complete and annotated genome sequence of Bacillus cereus NC7401, a representative of the strain group that causes emetic-type food poisoning. The emetic toxin, cereulide, is produced by a nonribosomal protein synthesis (NRPS) system that is encoded by a gene cluster on a large resident plasmid, pNCcld.
doi:10.1128/JB.01015-12
PMCID: PMC3415479  PMID: 22887669

Results 1-25 (70)