Kikuchi, Yoshitomo, Hosokawa, Takahiro, Nikoh, Naruo, Meng, Xian-Ying, Kamagata, Yoichi, Fukatsu, Takema
Abstract Background Host-symbiont co-speciation and reductive genome evolution have been commonly observed among obligate endocellular insect symbionts, while such examples have rarely been...
Dinoto, Achmad, Suksomcheep, Akarat, Ishizuka, Satoshi, Kimura, Hanae, Hanada, Satoshi, Kamagata, Yoichi, ...
To investigate the effects of administration of raffinose and encapsulated Bifidobacterium breve JCM 1192T cells on the rat cecal microbiota, in a preclinical synbiotic study groups of male WKAH/Hkm...
Dinoto, Achmad, Suksomcheep, Akarat, Ishizuka, Satoshi, Kimura, Hanae, Hanada, Satoshi, Kamagata, Yoichi, ...
To investigate the effects of administration of raffinose and encapsulated Bifidobacterium breve JCM 1192T cells on the rat cecal microbiota, in a preclinical synbiotic study groups of male WKAH/Hkm...
Dinoto, Achmad, Suksomcheep, Akarat, Ishizuka, Satoshi, Kimura, Hanae, Hanada, Satoshi, Kamagata, Yoichi, ...
To investigate the effects of administration of raffinose and encapsulated Bifidobacterium breve JCM 1192T cells on the rat cecal microbiota, in a preclinical synbiotic study groups of male WKAH/Hkm...
Hattori, Satoshi, Galushko, Alexander S., Kamagata, Yoichi, Schink, Bernhard
Thermacetogenium phaeum is a homoacetogenic bacterium that can grow on various substrates, such aspyruvate, methanol, or H2/CO2. It can also grow on acetate if cocultured with the...
Hattori, Satoshi, Galushko, Alexander S., Kamagata, Yoichi, Schink, Bernhard
Thermacetogenium phaeum is a homoacetogenic bacterium that can grow on various substrates, such as pyruvate, methanol, or H2/CO2. It can also grow on acetate if cocultured with the hydrogen-consuming...
Niamsup, Piyanuch, Sujaya, I Nengah, Tanaka, Michiko, Sone, Teruo, Hanada, Satoshi, Kamagata, Yoichi, ...
Five strains of thermotolerant lactic acid bacteria (G 12,G22,G35T,G43 andG44) isolated from chicken faeces were characterized taxonomically. The strains were facultatively anaerobic, Grampositive,...
Niamsup, Piyanuch, Sujaya, I Nengah, Tanaka, Michiko, Sone, Teruo, Hanada, Satoshi, Kamagata, Yoichi, ...
Five strains of thermotolerant lactic acid bacteria (G 12,G22,G35T,G43 andG44) isolated from
Niamsup, Piyanuch, Sujaya, I Nengah, Tanaka, Michiko, Sone, Teruo, Hanada, Satoshi, Kamagata, Yoichi, ...
Five strains of thermotolerant lactic acid bacteria (G 12,G22,G35T,G43 andG44) isolated from
Of Microorganisms, Yutaka Uyeno, Yuji Sekiguchi, Akiko Sunaga, Hiroki Yoshida, Yoichi Kamagata
A rapid and simple approach to the small-subunit (SSU) rRNA-based quantitative detection of a specific group of microorganisms in complex ecosystems has been developed. The method employs...
Mackie, Roderick I., Aminov, Rustam I., Hu, Wenping, Klieve, Athol V., Ouwerkerk, Diane, Sundset, Monica A., ...
The ecology of the uncultured, but large and morphologically conspicuous, rumen bacterium Oscillospira spp. was studied. Oscillospira-specific 16S rRNA gene sequences were detected in North American...
Kurata, Shinya, Kanagawa, Takahiro, Yamada, Kazutaka, Torimura, Masaki, Yokomaku, Toyokazu, Kamagata, Yoichi, ...
We have developed a simple method for the quantitative detection of specific DNA or RNA molecules based on the finding that BODIPY® FL fluorescence was quenched by its interaction with a uniquely...
Kurata, Shinya, Kanagawa, Takahiro, Yamada, Kazutaka, Torimura, Masaki, Yokomaku, Toyokazu, Kamagata, Yoichi, ...
We have developed a simple method for the quantitative detection of specific DNA or RNA molecules based on the finding that BODIPY® FL fluorescence was quenched by its interaction with a uniquely...
Suyama, Tetsushi, Tokiwa, Yutaka, Ouichanpagdee, Pornpimol, Kanagawa, Takahiro, Kamagata, Yoichi
Thirty-nine morphologically different soil bacteria capable of degrading poly(β-hydroxyalkanoate), poly(ɛ-caprolactone), poly(hexamethylene carbonate), or poly(tetramethylene succinate) were...
Sekiguchi, Yuji, Kamagata, Yoichi, Nakamura, Kazunori, Ohashi, Akiyoshi, Harada, Hideki
16S rRNA-targeted in situ hybridization combined with confocal laser scanning microscopy was used to elucidate the spatial distribution of microbes within two types of methanogenic granular sludge,...
Shigematsu, Toru, Hanada, Satoshi, Eguchi, Masahiro, Kamagata, Yoichi, Kanagawa, Takahiro, Kurane, Ryuichiro
The soluble MMO (sMMO) gene clusters from group I methanotrophs were characterized. An 8.1-kb KpnI fragment from Methylomonas sp. strain KSWIII and a 7.5-kb SalI fragment from Methylomonas sp. strain...
Imachi, Hiroyuki, Sekiguchi, Yuji, Kamagata, Yoichi, Ohashi, Akiyoshi, Harada, Hideki
The thermophilic, anaerobic, propionate-oxidizing bacterial populations present in the methanogenic granular sludge in a thermophilic (55°C) upflow anaerobic sludge blanket reactor were studied by...
Kanagawa, Takahiro, Kamagata, Yoichi, Aruga, Shinobu, Kohno, Tetsuro, Horn, Matthias, Wagner, Michael
Fifteen filamentous strains, morphologically classified as Eikelboom type 021N bacteria, were isolated from bulking activated sludges. Based on comparative 16S ribosomal DNA (rDNA) sequence analysis,...
Bacteria Mediate Methylation of Iodine in Marine and Terrestrial Environments
Amachi, Seigo, Kamagata, Yoichi, Kanagawa, Takahiro, Muramatsu, Yasuyuki
Methyl iodide (CH3I) plays an important role in the natural iodine cycle and participates in atmospheric ozone destruction. However, the main source of this compound in nature is still unclear. Here...
Sekiguchi, Yuji, Takahashi, Hiroki, Kamagata, Yoichi, Ohashi, Akiyoshi, Harada, Hideki
We previously showed that very thin filamentous bacteria affiliated with the division green non-sulfur bacteria were abundant in the outermost layer of thermophilic methanogenic sludge granules fed...
Luo, Hong-Wei, Zhang, Hui, Suzuki, Toshihiko, Hattori, Satoshi, Kamagata, Yoichi
The expression of genes involved in methanogenesis in a thermophilic hydrogen-utilizing methanogen, Methanothermobacter thermoautotrophicus strain TM, was investigated both in a pure culture...
Suzuki, Toshihiko, Kanagawa, Takahiro, Kamagata, Yoichi
Sphaerotilus natans, a filamentous bacterium that causes bulking in activated sludge processes, can assume two distinct morphologies, depending on the substrate concentration for growth; in...
Itoh, Kazuhito, Kanda, Rie, Sumita, Yoko, Kim, Hongik, Kamagata, Yoichi, Suyama, Kousuke, ...
The 2,4-dichlorophenoxyacetate (2,4-D)/α-ketoglutarate dioxygenase gene (tfdA) homolog designated tfdAα was cloned and characterized from 2,4-D-degrading bacterial strain RD5-C2. This Japanese...
Kitagawa, Wataru, Takami, Sachiko, Miyauchi, Keisuke, Masai, Eiji, Kamagata, Yoichi, Tiedje, James M., ...
The tfd genes of Ralstonia eutropha JMP134 are the only well-characterized set of genes responsible for 2,4-dichlorophenoxyacetic acid (2,4-D) degradation among 2,4-D-degrading bacteria. A new family...
Induction of Cellulase by Gentiobiose and Its Sulfur-Containing Analog in Penicillium purpurogenum
Kurasawa, Takashi, Yachi, Makoto, Suto, Manabu, Kamagata, Yoichi, Takao, Shoichi, Tomita, Fusao
Cellulase induction by β-glucodisaccharides was investigated by using non-cellulase-induced mycelia of Penicillium purpurogenum P-26, a highly-cellulase-producing fungus. Gentiobiose induced...
Mackie, Roderick I., Aminov, Rustam I., Hu, Wenping, Klieve, Athol V., Ouwerkerk, Diane, Sundset, Monica A., ...
The ecology of the uncultured, but large and morphologically conspicuous, rumen bacterium Oscillospira spp. was studied. Oscillospira-specific 16S rRNA gene sequences were detected in North American...
Qiu, Yan-Ling, Sekiguchi, Yuji, Imachi, Hiroyuki, Kamagata, Yoichi, Tseng, I-Cheng, Cheng, Sheng-Shung, ...
The microbial populations responsible for anaerobic degradation of phthalate isomers were investigated by enrichment and isolation of those microbes from anaerobic sludge treating wastewater from the...
Itoh, Kazuhito, Tashiro, Yoshiko, Uobe, Kazuko, Kamagata, Yoichi, Suyama, Kousuke, Yamamoto, Hiroki
The distribution of tfdAα and cadA, genes encoding 2,4-dichlorophenoxyacetate (2,4-D)-degrading proteins which are characteristic of the 2,4-D-degrading Bradyrhizobium sp. isolated from pristine...
Uyeno, Yutaka, Sekiguchi, Yuji, Sunaga, Akiko, Yoshida, Hiroki, Kamagata, Yoichi
A rapid and simple approach to the small-subunit (SSU) rRNA-based quantitative detection of a specific group of microorganisms in complex ecosystems has been developed. The method employs...
Kitagawa, Wataru, Kimura, Nobutada, Kamagata, Yoichi
p-Nitrophenol (4-NP) is recognized as an environmental contaminant; it is used primarily for manufacturing medicines and pesticides. To date, several 4-NP-degrading bacteria have been isolated;...
Reevaluation and Reduction of a PCR Bias Caused by Reannealing of Templates
Kurata, Shinya, Kanagawa, Takahiro, Magariyama, Yukio, Takatsu, Kyoko, Yamada, Kazutaka, Yokomaku, Toyokazu, ...
We reevaluated the bias toward a 1:1 ratio of products in multitemplate PCR used in ecological studies and showed that the template reannealing at the annealing step would not cause the bias;...
Mitani, Yasuo, Meng, XianYing, Kamagata, Yoichi, Tamura, Tomohiro
The nocardioform actinomycete Rhodococcus erythropolis has a characteristic cell wall structure. The cell wall is composed of arabinogalactan and mycolic acid and is highly resistant to the cell...
Tamaki, Hideyuki, Sekiguchi, Yuji, Hanada, Satoshi, Nakamura, Kazunori, Nomura, Nakao, Matsumura, Masatoshi, ...
Comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16S rRNA gene clone library and improved cultivation-based...
Hattori, Satoshi, Galushko, Alexander S., Kamagata, Yoichi, Schink, Bernhard
Thermacetogenium phaeum is a homoacetogenic bacterium that can grow on various substrates, such as pyruvate, methanol, or H2/CO2. It can also grow on acetate if cocultured with the hydrogen-consuming...
Yamada, Takeshi, Sekiguchi, Yuji, Imachi, Hiroyuki, Kamagata, Yoichi, Ohashi, Akiyoshi, Harada, Hideki
We previously reported that the thermophilic filamentous anaerobe Anaerolinea thermophila, which is the first cultured representative of subphylum I of the bacterial phylum Chloroflexi, not only was...
Kosaka, Tomoyuki, Uchiyama, Taku, Ishii, Shun-ichi, Enoki, Miho, Imachi, Hiroyuki, Kamagata, Yoichi, ...
Obligate anaerobic bacteria fermenting volatile fatty acids in syntrophic association with methanogenic archaea share the intermediate bottleneck step in organic-matter decomposition. These organisms...
Dinoto, Achmad, Suksomcheep, Akarat, Ishizuka, Satoshi, Kimura, Hanae, Hanada, Satoshi, Kamagata, Yoichi, ...
To investigate the effects of administration of raffinose and encapsulated Bifidobacterium breve JCM 1192T cells on the rat cecal microbiota, in a preclinical synbiotic study groups of male WKAH/Hkm...
Imachi, Hiroyuki, Sekiguchi, Yuji, Kamagata, Yoichi, Loy, Alexander, Qiu, Yan-Ling, Hugenholtz, Philip, ...
The classical perception of members of the gram-positive Desulfotomaculum cluster I as sulfate-reducing bacteria was recently challenged by the isolation of new representatives lacking the ability...
Kurata, Shinya, Kanagawa, Takahiro, Yamada, Kazutaka, Torimura, Masaki, Yokomaku, Toyokazu, Kamagata, Yoichi, ...
We have developed a simple method for the quantitative detection of specific DNA or RNA molecules based on the finding that BODIPY® FL fluorescence was quenched by its interaction with a uniquely...
Suyama, Tetsushi, Tokiwa, Yutaka, Ouichanpagdee, Pornpimol, Kanagawa, Takahiro, Kamagata, Yoichi
Thirty-nine morphologically different soil bacteria capable of degrading poly(β-hydroxyalkanoate), poly(ɛ-caprolactone), poly(hexamethylene carbonate), or poly(tetramethylene succinate) were...
Sekiguchi, Yuji, Kamagata, Yoichi, Nakamura, Kazunori, Ohashi, Akiyoshi, Harada, Hideki
16S rRNA-targeted in situ hybridization combined with confocal laser scanning microscopy was used to elucidate the spatial distribution of microbes within two types of methanogenic granular sludge,...
Shigematsu, Toru, Hanada, Satoshi, Eguchi, Masahiro, Kamagata, Yoichi, Kanagawa, Takahiro, Kurane, Ryuichiro
The soluble MMO (sMMO) gene clusters from group I methanotrophs were characterized. An 8.1-kb KpnI fragment from Methylomonas sp. strain KSWIII and a 7.5-kb SalI fragment from Methylomonas sp. strain...
Imachi, Hiroyuki, Sekiguchi, Yuji, Kamagata, Yoichi, Ohashi, Akiyoshi, Harada, Hideki
The thermophilic, anaerobic, propionate-oxidizing bacterial populations present in the methanogenic granular sludge in a thermophilic (55°C) upflow anaerobic sludge blanket reactor were studied by...
Kanagawa, Takahiro, Kamagata, Yoichi, Aruga, Shinobu, Kohno, Tetsuro, Horn, Matthias, Wagner, Michael
Fifteen filamentous strains, morphologically classified as Eikelboom type 021N bacteria, were isolated from bulking activated sludges. Based on comparative 16S ribosomal DNA (rDNA) sequence analysis,...
Bacteria Mediate Methylation of Iodine in Marine and Terrestrial Environments
Amachi, Seigo, Kamagata, Yoichi, Kanagawa, Takahiro, Muramatsu, Yasuyuki
Methyl iodide (CH3I) plays an important role in the natural iodine cycle and participates in atmospheric ozone destruction. However, the main source of this compound in nature is still unclear. Here...
Sekiguchi, Yuji, Takahashi, Hiroki, Kamagata, Yoichi, Ohashi, Akiyoshi, Harada, Hideki
We previously showed that very thin filamentous bacteria affiliated with the division green non-sulfur bacteria were abundant in the outermost layer of thermophilic methanogenic sludge granules fed...
Luo, Hong-Wei, Zhang, Hui, Suzuki, Toshihiko, Hattori, Satoshi, Kamagata, Yoichi
The expression of genes involved in methanogenesis in a thermophilic hydrogen-utilizing methanogen, Methanothermobacter thermoautotrophicus strain TM, was investigated both in a pure culture...
Suzuki, Toshihiko, Kanagawa, Takahiro, Kamagata, Yoichi
Sphaerotilus natans, a filamentous bacterium that causes bulking in activated sludge processes, can assume two distinct morphologies, depending on the substrate concentration for growth; in...
Itoh, Kazuhito, Kanda, Rie, Sumita, Yoko, Kim, Hongik, Kamagata, Yoichi, Suyama, Kousuke, ...
The 2,4-dichlorophenoxyacetate (2,4-D)/α-ketoglutarate dioxygenase gene (tfdA) homolog designated tfdAα was cloned and characterized from 2,4-D-degrading bacterial strain RD5-C2. This Japanese...
Kitagawa, Wataru, Takami, Sachiko, Miyauchi, Keisuke, Masai, Eiji, Kamagata, Yoichi, Tiedje, James M., ...
The tfd genes of Ralstonia eutropha JMP134 are the only well-characterized set of genes responsible for 2,4-dichlorophenoxyacetic acid (2,4-D) degradation among 2,4-D-degrading bacteria. A new family...
Induction of Cellulase by Gentiobiose and Its Sulfur-Containing Analog in Penicillium purpurogenum
Kurasawa, Takashi, Yachi, Makoto, Suto, Manabu, Kamagata, Yoichi, Takao, Shoichi, Tomita, Fusao
Cellulase induction by β-glucodisaccharides was investigated by using non-cellulase-induced mycelia of Penicillium purpurogenum P-26, a highly-cellulase-producing fungus. Gentiobiose induced...
Mackie, Roderick I., Aminov, Rustam I., Hu, Wenping, Klieve, Athol V., Ouwerkerk, Diane, Sundset, Monica A., ...
The ecology of the uncultured, but large and morphologically conspicuous, rumen bacterium Oscillospira spp. was studied. Oscillospira-specific 16S rRNA gene sequences were detected in North American...
Qiu, Yan-Ling, Sekiguchi, Yuji, Imachi, Hiroyuki, Kamagata, Yoichi, Tseng, I-Cheng, Cheng, Sheng-Shung, ...
The microbial populations responsible for anaerobic degradation of phthalate isomers were investigated by enrichment and isolation of those microbes from anaerobic sludge treating wastewater from the...
Itoh, Kazuhito, Tashiro, Yoshiko, Uobe, Kazuko, Kamagata, Yoichi, Suyama, Kousuke, Yamamoto, Hiroki
The distribution of tfdAα and cadA, genes encoding 2,4-dichlorophenoxyacetate (2,4-D)-degrading proteins which are characteristic of the 2,4-D-degrading Bradyrhizobium sp. isolated from pristine...
Uyeno, Yutaka, Sekiguchi, Yuji, Sunaga, Akiko, Yoshida, Hiroki, Kamagata, Yoichi
A rapid and simple approach to the small-subunit (SSU) rRNA-based quantitative detection of a specific group of microorganisms in complex ecosystems has been developed. The method employs...
Kitagawa, Wataru, Kimura, Nobutada, Kamagata, Yoichi
p-Nitrophenol (4-NP) is recognized as an environmental contaminant; it is used primarily for manufacturing medicines and pesticides. To date, several 4-NP-degrading bacteria have been isolated;...
Reevaluation and Reduction of a PCR Bias Caused by Reannealing of Templates
Kurata, Shinya, Kanagawa, Takahiro, Magariyama, Yukio, Takatsu, Kyoko, Yamada, Kazutaka, Yokomaku, Toyokazu, ...
We reevaluated the bias toward a 1:1 ratio of products in multitemplate PCR used in ecological studies and showed that the template reannealing at the annealing step would not cause the bias;...
Mitani, Yasuo, Meng, XianYing, Kamagata, Yoichi, Tamura, Tomohiro
The nocardioform actinomycete Rhodococcus erythropolis has a characteristic cell wall structure. The cell wall is composed of arabinogalactan and mycolic acid and is highly resistant to the cell...
Tamaki, Hideyuki, Sekiguchi, Yuji, Hanada, Satoshi, Nakamura, Kazunori, Nomura, Nakao, Matsumura, Masatoshi, ...
Comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16S rRNA gene clone library and improved cultivation-based...
Hattori, Satoshi, Galushko, Alexander S., Kamagata, Yoichi, Schink, Bernhard
Thermacetogenium phaeum is a homoacetogenic bacterium that can grow on various substrates, such as pyruvate, methanol, or H2/CO2. It can also grow on acetate if cocultured with the hydrogen-consuming...
Yamada, Takeshi, Sekiguchi, Yuji, Imachi, Hiroyuki, Kamagata, Yoichi, Ohashi, Akiyoshi, Harada, Hideki
We previously reported that the thermophilic filamentous anaerobe Anaerolinea thermophila, which is the first cultured representative of subphylum I of the bacterial phylum Chloroflexi, not only was...
Kosaka, Tomoyuki, Uchiyama, Taku, Ishii, Shun-ichi, Enoki, Miho, Imachi, Hiroyuki, Kamagata, Yoichi, ...
Obligate anaerobic bacteria fermenting volatile fatty acids in syntrophic association with methanogenic archaea share the intermediate bottleneck step in organic-matter decomposition. These organisms...
Dinoto, Achmad, Suksomcheep, Akarat, Ishizuka, Satoshi, Kimura, Hanae, Hanada, Satoshi, Kamagata, Yoichi, ...
To investigate the effects of administration of raffinose and encapsulated Bifidobacterium breve JCM 1192T cells on the rat cecal microbiota, in a preclinical synbiotic study groups of male WKAH/Hkm...
Imachi, Hiroyuki, Sekiguchi, Yuji, Kamagata, Yoichi, Loy, Alexander, Qiu, Yan-Ling, Hugenholtz, Philip, ...
The classical perception of members of the gram-positive Desulfotomaculum cluster I as sulfate-reducing bacteria was recently challenged by the isolation of new representatives lacking the ability...
Nakamura, Kohei , Terada, Takeshi, Sekiguchi, Yuji, Shinzato, Naoya, Meng, Xian-Ying, Enoki, Miho, ...
In situ detection of methanogens within the family Methanobacteriaceae is sometimes known to be unsuccessful due to the difficulty in permeability of oligonucleotide probes. Pseudomurein...
Sakai, Sanae, Imachi, Hiroyuki, Sekiguchi, Yuji, Ohashi, Akiyoshi, Harada, Hideki, Kamagata, Yoichi
Despite the fact that rice paddy fields (RPFs) are contributing 10 to 25% of global methane emissions, the organisms responsible for methane production in RPFs have remained uncultivated and thus...
Morono, Yuki, Kitagawa, Wataru, Kimura, Nobutada, Noda, Naohiro, Nakamura, Kazunori, Kamagata, Yoichi
A specific marking and detection technique is a fundamental requirement for the safer use of genetically modified (GM) organisms. Here we propose a simple and effective method for directly marking...
Qiu, Yan-Ling, Hanada, Satoshi, Ohashi, Akiyoshi, Harada, Hideki, Kamagata, Yoichi, Sekiguchi, Yuji
Phenol degradation under methanogenic conditions has long been studied, but the anaerobes responsible for the degradation reaction are still largely unknown. An anaerobe, designated strain UIT, was...
Kikuchi, Yoshitomo, Hosokawa, Takahiro, Nikoh, Naruo, Meng, Xian-Ying, Kamagata, Yoichi, Fukatsu, Takema
Shinzato, Naoya, Enoki, Miho, Sato, Hiroaki, Nakamura, Kohei, Matsui, Toru, Kamagata, Yoichi
Two methyl coenzyme M reductases (MCRs) encoded by the mcr and mrt operons of the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus ΔH are expressed in response to H2 availability....