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1.
Genome Announc. 2014 Dec 11;2(6). pii: e01272-14. doi: 10.1128/genomeA.01272-14.

Draft Genome Sequence of the Betaproteobacterial Endosymbiont Associated with the Fungus Mortierella elongata FMR23-6.

Author information

1
Ibaraki University College of Agriculture, Ibaraki, Japan rfujimura.micron@gmail.com.
2
Ibaraki University College of Agriculture, Ibaraki, Japan.
3
National Research Institute for Cultural Properties, Tokyo, Japan.
4
Department of Computational Biology, Graduate School of Frontier Science, the University of Tokyo, Chiba, Japan.

Abstract

The fungus Mortierella elongata FMR23-6 harbors an endobacterium inside its mycelium. Attempts to isolate the endobacterium from the fungus were not yet successful, but a highly purified bacterial fraction was prepared. Here, we report the draft genome sequence of the endobacterium.

2.
Genome Announc. 2014 Dec 4;2(6). pii: e01236-14. doi: 10.1128/genomeA.01236-14.

Draft Genome Sequence of Marine Flavobacterium Jejuia pallidilutea Strain 11shimoA1 and Pigmentation Mutants.

Author information

1
Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
2
Laboratory of Microbiology, Institute of Biology and Solid Action on Globalization and Environment, COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
3
Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
4
Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Ibaraki, Japan.
5
Department of Food and Nutrition, Hakodate Junior College, Hakodate, Japan.
6
Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan sawabe@fish.hokudai.ac.jp.

Abstract

Here, we present the draft genome sequence of a novel carotenoid 2'-isopentenylsaproxanthin producer, Jejuia pallidilutea strain 11shimoA1, isolated from the surface of seaweed in Japan, and the ethyl methanesulfonate-induced pigmentation mutants. This genomic information will help to not only elucidate the 2'-isopentenylsaproxanthin biosynthetic pathway but also understand the evolution of flavobacteria.

3.
Genome Announc. 2014 Nov 13;2(6). pii: e01168-14. doi: 10.1128/genomeA.01168-14.

Draft Genome Sequences of Marine Flavobacterium Algibacter lectus Strains SS8 and NR4.

Author information

1
Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
2
Laboratory of Microbiology, Institute of Biology and Solid Action on Globalization and Environment, COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
3
Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
4
Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Ibaraki, Japan.
5
Department of Food and Nutrition, Hakodate Junior College, Hakodate, Japan.
6
Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan sawabe@fish.hokudai.ac.jp.

Abstract

Here, we present the draft genome sequences of a zeaxanthin-producing flavobacterium, Algibacter lectus strains SS8 and NR4, isolated from coastal sediment and rock surfaces in Hakodate, Japan, respectively. This genomic information represents the first Algibacter genome sequences, which will help us to elucidate the biology and evolution of Flavobacteriaceae bacteria.

4.
Genome Announc. 2014 Nov 13;2(6). pii: e01165-14. doi: 10.1128/genomeA.01165-14.

Draft Genome Sequences of Marine Flavobacterium Nonlabens Strains NR17, NR24, NR27, NR32, NR33, and Ara13.

Author information

1
Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
2
Laboratory of Microbiology, Institute of Biology and Solid Action on Globalization and Environment, COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
3
Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
4
Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Ibaraki, Japan.
5
Department of Food and Nutrition, Hakodate Junior College, Hakodate, Japan.
6
Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan sawabe@fish.hokudai.ac.jp.

Abstract

Here, we present the draft genome sequences of six carotenoid producers affiliated with Nonlabens spp. isolated from marine environments in both the northern and southern parts of Japan. The genomic information will help to elucidate the function and evolution of carotenoid synthetic gene clusters not only in the genus Nonlabens but also in the family Flavobacteriaceae.

5.
Genome Announc. 2014 Oct 30;2(5). pii: e01095-14. doi: 10.1128/genomeA.01095-14.

Draft Genome Sequences of Two Vibrionaceae Species, Vibrio ponticus C121 and Photobacterium aphoticum C119, Isolated as Coral Reef Microbiota.

Author information

1
Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
2
Laboratory of Microbiology, Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
3
Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan.
4
Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Ibaraki, Japan.
5
A.C. Unidad Mazatlán, CIAD, Mazatlán, México.
6
Department of Food and Nutrition, Hakodate Junior College, Hakodate, Japan.
7
Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan sawabe@fish.hokudai.ac.jp.

Abstract

Here, the draft genome sequences of two Vibrionaceae, Vibrio ponticus C121 and Photobacterium aphoticum C119, which were isolated from the coral reef vicinity in Okinawa, Japan, are reported. The genome provides further insight into the genomic plasticity, biocomplexity, and ecophysiology, including pathogenicity and evolution, of these genera.

6.
Microbes Environ. 2014 Sep 17;29(3):329-32. Epub 2014 Aug 12.

Phylogeny and functions of bacterial communities associated with field-grown rice shoots.

Author information

1
Graduate School of Life Sciences, Tohoku University.

Abstract

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 Betaproteobacteria (4-10%). Compared with other rice microbiomes (root, rhizosphere, and phyllosphere) in public databases, the shoot microbiomes harbored abundant genes for C1 compound metabolism and 1-aminocyclopropane-1-carboxylate catabolism, but fewer genes for indole-3-acetic acid production and nitrogen fixation. Salicylate hydroxylase was detected in all microbiomes, except the rhizosphere. These genomic features facilitate understanding of plant-microbe interactions and biogeochemical metabolism in rice shoots.

PMID:
25130883
PMCID:
PMC4159046
DOI:
10.1264/jsme2.me14077
[Indexed for MEDLINE]
Free PMC Article
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7.
Genome Biol Evol. 2014 Aug;6(8):2096-110. doi: 10.1093/gbe/evu160.

Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen.

Author information

1
Interdisciplinary Research Organization, University of Miyazaki, JapanPresent address: Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Japan.
2
Department of Microbiology and Infection Control Science, Kyoto Pharmaceutical University, JapanPresent address: Kashima ONC QC, Oncology DCU, Eisai Demand Chain Systems, Eisai Co., Ltd., Ibaraki, Japan.
3
Centre d'Immunologie de Marseille-Luminy, UM2 Aix-Marseille Université, Marseille, FranceINSERM, U1104, Marseille, FranceCNRS, UMR7280, Marseille, FrancePresent address: CIIL-Inserm U1019, Institut Pasteur de Lille, Lille, France.
4
Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Japan.
5
Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, JapanDepartment of Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Japan.
6
Department of Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Japan.
7
Earth-Life Science Institute, Tokyo Institute of Technology, Kanagawa, Japan.
8
Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan.
9
Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom.
10
Division of Molecular Microbiology, College of Life Sciences, University of Dundee, United Kingdom.
11
Department of Microbiology and Infection Control Science, Kyoto Pharmaceutical University, Japan.
12
Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United KingdomDepartment of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom nrt@sanger.ac.uk thayash@med.miyazaki-u.ac.jp.
13
Centre d'Immunologie de Marseille-Luminy, UM2 Aix-Marseille Université, Marseille, FranceINSERM, U1104, Marseille, FranceCNRS, UMR7280, Marseille, France.
14
Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, JapanDepartment of Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Japan nrt@sanger.ac.uk thayash@med.miyazaki-u.ac.jp.

Abstract

Serratia marcescens is an important nosocomial pathogen that can cause an array of infections, most notably of the urinary tract and bloodstream. Naturally, it is found in many environmental niches, and is capable of infecting plants and animals. The emergence and spread of multidrug-resistant strains producing extended-spectrum or metallo beta-lactamases now pose a threat to public health worldwide. Here we report the complete genome sequences of two carefully selected S. marcescens strains, a multidrug-resistant clinical isolate (strain SM39) and an insect isolate (strain Db11). Our comparative analyses reveal the core genome of S. marcescens and define the potential metabolic capacity, virulence, and multidrug resistance of this species. We show a remarkable intraspecies genetic diversity, both at the sequence level and with regards genome flexibility, which may reflect the diversity of niches inhabited by members of this species. A broader analysis with other Serratia species identifies a set of approximately 3,000 genes that characterize the genus. Within this apparent genetic diversity, we identified many genes implicated in the high virulence potential and antibiotic resistance of SM39, including the metallo beta-lactamase and multiple other drug resistance determinants carried on plasmid pSMC1. We further show that pSMC1 is most closely related to plasmids circulating in Pseudomonas species. Our data will provide a valuable basis for future studies on S. marcescens and new insights into the genetic mechanisms that underlie the emergence of pathogens highly resistant to multiple antimicrobial agents.

KEYWORDS:

Serratia marcescens; genome plasticity; multidrug resistance; virulence

PMID:
25070509
PMCID:
PMC4231636
DOI:
10.1093/gbe/evu160
[Indexed for MEDLINE]
Free PMC Article
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8.
Immunity. 2014 Jul 17;41(1):152-65. doi: 10.1016/j.immuni.2014.05.016. Epub 2014 Jul 10.

Foxp3(+) T cells regulate immunoglobulin a selection and facilitate diversification of bacterial species responsible for immune homeostasis.

Author information

1
Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences (IMS-RCAI), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Kanagawa, Japan.
2
Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, 277-8561 Chiba, Japan.
3
Laboratory for Gut Homeostasis, Center for Integrative Medical Sciences (IMS-RCAI), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Kanagawa, Japan.
4
Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences (IMS-RCAI), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Kanagawa, Japan; Department of Medical Genetics and Developmental Biology, 4(th) Military Medical University, Chang-Le Xi Street #17, Xi'an 710032, China.
5
Laboratory for Tissue Dynamics, Center for Integrative Medical Sciences (IMS-RCAI), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Kanagawa, Japan.
6
Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences (IMS-RCAI), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Kanagawa, Japan. Electronic address: sidonia-f@rcai.riken.jp.

Abstract

Foxp3(+) T cells play a critical role for the maintenance of immune tolerance. Here we show that in mice, Foxp3(+) T cells contributed to diversification of gut microbiota, particularly of species belonging to Firmicutes. The control of indigenous bacteria by Foxp3(+) T cells involved regulatory functions both outside and inside germinal centers (GCs), consisting of suppression of inflammation and regulation of immunoglobulin A (IgA) selection in Peyer's patches, respectively. Diversified and selected IgAs contributed to maintenance of diversified and balanced microbiota, which in turn facilitated the expansion of Foxp3(+) T cells, induction of GCs, and IgA responses in the gut through a symbiotic regulatory loop. Thus, the adaptive immune system, through cellular and molecular components that are required for immune tolerance and through the diversification as well as selection of antibody repertoire, mediates host-microbial symbiosis by controlling the richness and balance of bacterial communities required for homeostasis.

PMID:
25017466
DOI:
10.1016/j.immuni.2014.05.016
[Indexed for MEDLINE]
Free full text
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9.
Int J Syst Evol Microbiol. 2014 Sep;64(Pt 9):3240-6. doi: 10.1099/ijs.0.063503-0. Epub 2014 Jun 30.

Methylocaldum marinum sp. nov., a thermotolerant, methane-oxidizing bacterium isolated from marine sediments, and emended description of the genus Methylocaldum.

Author information

1
Institute for Geo-resources and Environments, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan takeuchi-mio@aist.go.jp.
2
Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
3
Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan.
4
Institute of Geology and Geoinformation, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan.
5
The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-8580, Japan.
6
Department of Physics and Astronomy Graduate School of Science and Engineering/Faculty of Science, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-8580, Japan.
7
Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan Genetic Research Section, Atmosphere and Ocean Research Institute, the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8564, Japan.
8
Institute for Geo-resources and Environments, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan.

Abstract

An aerobic, methane-oxidizing bacterium (strain S8(T)) was isolated from marine sediments in Kagoshima Bay, Japan. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain is closely related to members of the genus Methylocaldum (97.6-97.9 % similarity) within the class Gammaproteobacteria. Strain S8(T) was a Gram-staining-negative, non-motile, coccoid or short rod-shaped organism. The temperature range for growth of strain S8(T) was 20-47 °C (optimum growth at 36 °C). It required NaCl (>0.5 %), tolerated up to 5 % NaCl and utilized methane and methanol. The major cellular fatty acid and major respiratory quinone were C16 : 0 and 18-methylene ubiquinone 8, respectively. The DNA G+C content was 59.7 mol%. Strain S8(T) possessed mmoX, which encodes soluble methane monooxygenase, as well as pmoA, which encodes the particulate methane monooxygenase. On the basis of this morphological, physiological, biochemical and genetic information, the first marine species in the genus Methylocaldum is proposed, with the name Methylocaldum marinum sp. nov. The type strain is S8(T) ( = NBRC 109686(T) = DSM 27392(T)). An emended description of the genus Methylocaldum is also provided.

PMID:
24981325
DOI:
10.1099/ijs.0.063503-0
[Indexed for MEDLINE]
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10.
Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10257-62. doi: 10.1073/pnas.1409284111. Epub 2014 Jun 30.

Evolutionary origin of insect-Wolbachia nutritional mutualism.

Author information

1
Department of Liberal Arts, The Open University of Japan, Chiba 261-8586, Japan;
2
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan; and.
3
Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8561, Japan.
4
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan; and t-fukatsu@aist.go.jp.

Abstract

Obligate insect-bacterium nutritional mutualism is among the most sophisticated forms of symbiosis, wherein the host and the symbiont are integrated into a coherent biological entity and unable to survive without the partnership. Originally, however, such obligate symbiotic bacteria must have been derived from free-living bacteria. How highly specialized obligate mutualisms have arisen from less specialized associations is of interest. Here we address this evolutionary issue by focusing on an exceptional insect-Wolbachia nutritional mutualism. Although Wolbachia endosymbionts are ubiquitously found in diverse insects and generally regarded as facultative/parasitic associates for their insect hosts, a Wolbachia strain associated with the bedbug Cimex lectularius, designated as wCle, was shown to be essential for host's growth and reproduction via provisioning of B vitamins. We determined the 1,250,060-bp genome of wCle, which was generally similar to the genomes of insect-associated facultative Wolbachia strains, except for the presence of an operon encoding the complete biotin synthetic pathway that was acquired via lateral gene transfer presumably from a coinfecting endosymbiont Cardinium or Rickettsia. Nutritional and physiological experiments, in which wCle-infected and wCle-cured bedbugs of the same genetic background were fed on B-vitamin-manipulated blood meals via an artificial feeding system, demonstrated that wCle certainly synthesizes biotin, and the wCle-provisioned biotin significantly contributes to the host fitness. These findings strongly suggest that acquisition of a single gene cluster consisting of biotin synthesis genes underlies the bedbug-Wolbachia nutritional mutualism, uncovering an evolutionary transition from facultative symbiosis to obligate mutualism facilitated by lateral gene transfer in an endosymbiont lineage.

PMID:
24982177
PMCID:
PMC4104916
DOI:
10.1073/pnas.1409284111
[Indexed for MEDLINE]
Free PMC Article
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11.
Genome Announc. 2014 Jun 19;2(3). pii: e00623-14. doi: 10.1128/genomeA.00623-14.

Draft Genome Sequences of Vibrio sp. Strains Isolated from Tetrodotoxin-Bearing Scavenging Gastropod.

Author information

1
Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki, Japan kudot09101@gmail.com mohkuma@riken.jp.
2
Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki, Japan.
3
Graduate School of Science and Technology, Nagasaki University, Nagasaki, Japan.
4
Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Japan.
5
Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, Tsukuba, Japan.
6
Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan.
7
Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, Tsukuba, Japan kudot09101@gmail.com mohkuma@riken.jp.

Abstract

Vibrio sp. strains JCM 18905 and JCM 19053 were isolated from a tetrodotoxin (TTX)-bearing scavenging gastropod, and Vibrio sp. strain JCM 18904 was isolated from a sea cucumber. All these are closely related to Vibrio alginolyticus. Their comparative genome information is useful for studies of TTX production in bacteria.

12.
Genome Announc. 2014 Jun 19;2(3). pii: e00622-14. doi: 10.1128/genomeA.00622-14.

Draft Genome Sequences of Geomicrobium sp. Strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, Isolated from Aquatic Samples.

Author information

1
Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki, Japan kudot09101@gmail.com mohkuma@riken.jp.
2
Graduate School of Science and Technology, Nagasaki University, Nagasaki, Japan.
3
Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki, Japan.
4
Nagasaki Prefectural Institute of Fisheries, Nagasaki, Japan.
5
Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Japan.
6
Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, Tsukuba, Japan.
7
Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan.
8
Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, Tsukuba, Japan kudot09101@gmail.com mohkuma@riken.jp.

Abstract

Haloalkaliphilic strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, closely related to Geomicrobium sediminis, were isolated from aquatic samples, and their draft genome sequences were determined. The genome information of these four strains will be useful for studies of their physiology and ecology.

13.
Genome Announc. 2014 May 29;2(3). pii: e00490-14. doi: 10.1128/genomeA.00490-14.

Complete Genome Sequence of Winogradskyella sp. Strain PG-2, a Proteorhodopsin-Containing Marine Flavobacterium.

Author information

1
Atmosphere and Ocean Research Institute, the University of Tokyo, Kashiwa, Chiba, Japan.
2
yoshizawa@aori.u-tokyo.ac.jp.
3
Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan.

Abstract

Winogradskyella sp. strain PG-2 is a marine flavobacterium isolated from surface seawater. This organism contains proteorhodopsin, which can convert light energy into available forms of biochemical energy. Here, we present its complete genome sequence and annotation, which provide further insights into the life strategy of proteorhodopsin-mediated phototrophy in the ocean.

14.
Genome Announc. 2014 May 22;2(3). pii: e00442-14. doi: 10.1128/genomeA.00442-14.

Draft Genome Sequences of Marinobacter similis A3d10T and Marinobacter salarius R9SW1T.

Author information

1
Swinburne University of Technology, Hawthorn, Victoria, Australia eivanova@swin.edu.au.
2
Swinburne University of Technology, Hawthorn, Victoria, Australia.
3
Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan.
4
Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan.
5
Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Ibaraki, Japan.
6
V. I. Il'ichev Pacific Oceanological Institute of the Far-Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russian Federation.
7
GB Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russian Federation.

Abstract

Here, we present the draft genomes of Marinobacter similis A3d10(T), a potential plastic biodegrader, and Marinobacter salarius R9SW1(T), isolated from radioactive waters. This genomic information will contribute information on the genetic basis of the metabolic pathways for the degradation of both plastic and radionuclides.

15.
DNA Res. 2014 Oct;21(5):469-80. doi: 10.1093/dnares/dsu013. Epub 2014 May 19.

Multiple omics uncovers host-gut microbial mutualism during prebiotic fructooligosaccharide supplementation.

Author information

1
Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Graduate School of Nanobioscience, Yokohama City University, Kanagawa 230-0045, Japan.
2
Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Institute for Advanced Biosciences, Keio University, Yamagata 997-0052, Japan.
3
Center for Omics and Bioinformatics, Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8561, Japan.
4
Graduate School of Medical Life Science, Yokohama City University, Kanagawa 230-0045, Japan Environmental Metabolic Analysis Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa 230-0045, Japan.
5
Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Graduate School of Medical Life Science, Yokohama City University, Kanagawa 230-0045, Japan ohno@rcai.riken.jp.

Abstract

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. Traditional methods of profiling microbes and metabolites could barely show any significant features due to the existence of large interindividual differences, but our novel microbe-metabolite correlation approach, combined with faecal immunoglobulin A (IgA) measurements, has revealed that the induction of mucosal IgA by FOS supplementation correlated with the presence of specific bacteria. Furthermore, the metabolic dynamics of butyrate, L-phenylalanine, L-lysine and tyramine were positively correlated with that of these bacteria and IgA production, whereas p-cresol was negatively correlated. Taken together, our focused intraindividual analysis with omics approaches is a powerful strategy for uncovering the gut molecular network and could provide a new vista for understanding the human gut ecosystem.

KEYWORDS:

commensal microbiota; correlation analysis; gut ecosystem; metabolite; prebiotics

PMID:
24848698
PMCID:
PMC4195493
DOI:
10.1093/dnares/dsu013
[Indexed for MEDLINE]
Free PMC Article
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16.
Genome Announc. 2014 May 8;2(3). pii: e00403-14. doi: 10.1128/genomeA.00403-14.

Draft Genome Sequence of Lactobacillus sucicola JCM 15457T, a Motile Lactic Acid Bacterium Isolated from Oak Sap.

Author information

1
Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan.

Abstract

Here, we report the draft genome sequence of a motile lactic acid bacterium, Lactobacillus sucicola JCM 15457(T), isolated from oak sap. Motility-related genes and their organization in the annotated genome were broadly similar to those in the sequenced genomes of related lactobacilli.

17.
Science. 2014 Apr 25;344(6182):380-6. doi: 10.1126/science.1249656.

Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.

Collaborators (179)

Watanabe J, Hattori M, Berriman M, Lehane MJ, Hall N, Solano P, Aksoy S, Hide W, Touré Y, Attardo GM, Darby AC, Toyoda A, Hertz-Fowler C, Larkin DM, Cotton JA, Watanabe J, Sanders MJ, Swain MT, Hattori M, Berriman M, Quail MA, Inoue N, Ravel S, Taylor TD, Srivastava TP, Sharma V, Warren W, Wilson RK, Suzuki Y, Lawson D, Hughes DS, Megy K, Masiga DK, Mireji PO, Attardo GM, Hansen IA, Van Den Abbeele J, Benoit JB, Bourtzis K, Lehane MJ, Aksoy S, Masiga DK, Obiero GF, Robertson HM, Jones JW, Zhou JJ, Field LM, Friedrich M, Mireji PO, Nyanjom SR, Telleria EL, Caljon G, Van Den Abbeele J, Ribeiro JM, Acosta-Serrano A, Benoit JB, Ooi CP, Rose C, Price DP, Haines LR, Lehane MJ, Christoffels A, Sim C, Pham DQ, Denlinger DL, Geiser L, Omedo IA, Benoit JB, Winzerling JJ, Peyton JT, Marucha KK, Jonas M, Meuti ME, Rawlings ND, Mireji PO, Zhang Q, Macharia RW, Michalkova V, Dashti ZJ, Baumann AA, Gäde G, Marco HG, Hansen IA, Caers J, Schoofs L, Riehle MA, Hu W, Tu Z, Tarone AM, Malacrida AR, Kibet CK, Benoit JB, Scolari F, Attardo GM, Koekemoer JJ, Willis J, Gomulski LM, Falchetto M, Scott MJ, Fu S, Sze SH, Luiz T, Weiss B, Walshe DP, Wang J, Benoit JB, Attardo GM, Wamalwa M, Mwangi S, Aksoy S, Ramphul UN, Snyder AK, Brelsfoard CL, Thomas GH, Tsiamis G, Bourtzis K, Arensburger P, Rio RV, Macdonald SJ, Panji S, Kruger A, Christoffels A, Benkahla A, Balyeidhusa AS, Msangi A, Ooi CP, Okoro CK, Masiga DK, Stephens D, Walshe DP, Stanley EJ, Mpondo F, Wamwiri F, Mramba F, Attardo GM, Siwo G, Obiero GF, Githinji G, Harkins G, Murilla G, Lehväslaiho H, Malele I, Koekemoer JJ, Auma JE, Kinyua JK, Ouma J, Watanabe J, Megy K, Okedi L, Manga L, Jonas M, Wamalwa M, Aslett M, Koffi M, Berriman M, Lehane MJ, Gaunt MW, Makgamathe M, Hall N, Mulder N, Manangwa O, Abila PP, Wincker P, Mireji PO, Gregory R, Rio RV, Bateta R, Sakate R, Aksoy S, Ommeh S, Lehane S, Nyanjom SR, Imanishi T, Taylor TD, Osamor VC, Sharma V, Hide W, Kawahara Y, Benoit JB.

Abstract

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.

PMID:
24763584
PMCID:
PMC4077534
DOI:
10.1126/science.1249656
[Indexed for MEDLINE]
Free PMC Article
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18.
Genome Announc. 2014 Apr 3;2(2). pii: e00280-14. doi: 10.1128/genomeA.00280-14.

Draft Genome Sequences of Psychrobacter Strains JCM 18900, JCM 18901, JCM 18902, and JCM 18903, Isolated Preferentially from Frozen Aquatic Organisms.

Author information

1
Graduate School of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki, Japan.

Abstract

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.

19.
Genome Announc. 2014 Mar 27;2(2). pii: e00257-14. doi: 10.1128/genomeA.00257-14.

Draft Genome Sequences of Two Lactobacillus Strains, L. farraginis JCM 14108T and L. composti JCM 14202T, Isolated from Compost of Distilled Shōchū Residue.

Author information

1
Biomass Research Platform Team, RIKEN Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaragi, Japan.

Abstract

Here, we report the draft genome sequences of two type strains of Lactobacillus, Lactobacillus farraginis JCM 14108(T) and Lactobacillus composti JCM 14202(T), 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.

20.
Genome Announc. 2014 Mar 27;2(2). pii: e00206-14. doi: 10.1128/genomeA.00206-14.

Draft Genome Sequence of Cytophaga fermentans JCM 21142T, a Facultative Anaerobe Isolated from Marine Mud.

Author information

1
Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan.

Abstract

Cytophaga fermentans strain JCM 21142(T) 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.

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