Naoki Tsukuda

Natural transformation drives large-scale genome mosaicism in human gut bifidobacteria

Y. Watanabe, Kento Orihara, Naoki Tsukuda, Taeko Hara et autres

Although horizontal gene transfer drives bacterial diversification, its contribution to chromosome-scale variation in human gut commensals remains unclear. This study demonstrated that human-associated bifidobacteria undergo extensive chromosomal transfer through natural transformation. Comparative genomics of coexisting Bifidobacterium pseudocatenulatum isolates from a single individual …

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Characterization of Bifidobacterium hominis and proposal of Bifidobacterium catenulatum subsp. puerorum subsp. nov. isolated from human faeces

Kento Orihara, Y. Watanabe, Naoki Tsukuda, Kana Yahagi et autres

Bifidobacteria are among the most dominant members of the human gut microbiota throughout life and are associated with host health. Multiple Bifidobacterium species have been isolated from human faeces, with species composition differing according to host age and between individuals. This species- …

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Enteropathway: the metabolic pathway database for the human gut microbiota

Hirotsugu Shiroma, Youssef Darzi, Etsuko Terajima, Zenichi Nakagawa et autres

The human gut microbiota produces diverse, extensive metabolites that have the potential to affect host physiology. Despite significant efforts to identify metabolic pathways for producing these microbial metabolites, a comprehensive metabolic pathway database for the human gut microbiota is still lacking. Here, …

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Enteropathway: the metabolic pathway database for the human gut microbiota

Hirotsugu Shiroma, Youssef Darzi, Etsuko Terajima, Zenichi Nakagawa et autres

Abstract The human gut microbiota produces diverse, extensive metabolites which have the potential to affect host physiology. Despite significant efforts to identify metabolic pathways for producing these microbial metabolites, a comprehensive metabolic pathway database for the human gut microbiota is still lacking. …

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Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides

Kento Orihara, Yuki Saito, Y. Watanabe, Toshio Sasai et autres

Bifidobacteria are prominent members of the human gut microbiota throughout life. The ability to utilize milk- and plant-derived carbohydrates is important for bifidobacterial colonization of the infant and adult gut. The Bifidobacterium catenulatum subspecies kashiwanohense (B. kashiwanohense) was originally isolated from infant …

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Identification of key bacterial taxa and metabolic pathways affecting gut organic acid profiles in early life

Takahiro Matsuki, Naoki Tsukuda

腸内菌叢の形成過程とその異常は、乳幼児期だけでなく成長後の健康や疾病リスクに影響を及ぼす。腸内菌叢は様々な代謝産物を産生しているが、有機酸は、菌叢と宿主の関係を媒介する重要な代謝物として注目されている。本総説では、乳幼児期の腸内菌叢形成と有機酸プロファイルを詳細に調べた我々の研究を紹介し、有機酸産生に中心的な役割を果たす系統群とその代謝経路、およびそれに影響を与える環境因子について述べる。

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Xylan utilisation promotes adaptation of Bifidobacterium pseudocatenulatum to the human gastrointestinal tract

Y. Watanabe, Yuki Saito, Taeko Hara, Naoki Tsukuda et autres

Dietary carbohydrates impact the composition of the human gut microbiota. However, the relationship between carbohydrate availability for individual bacteria and their growth in the intestinal environment remains unclear. Here, we show that the availability of long-chain xylans (LCX), one of the most …

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Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life

Naoki Tsukuda, Taeko Hara, Y. Watanabe, Hoshitaka Matsumoto et autres

Infant gut microbiota development affects the host physiology throughout life, and short-chain fatty acids (SCFAs) are promising key metabolites mediating microbiota-host relationships. Here, we investigated dense longitudinally collected faecal samples from 12 subjects during the first 2 years (n = 1048) to …

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Multiple Transporters and Glycoside Hydrolases Are Involved in Arabinoxylan-Derived Oligosaccharide Utilization in Bifidobacterium pseudocatenulatum

Yuki Saito, Akira Shigehisa, Y. Watanabe, Naoki Tsukuda et autres

Bifidobacteria commonly reside in the human intestine and possess abundant genes involved in carbohydrate utilization. Arabinoxylan hydrolysates (AXH) are hydrolyzed products of arabinoxylan, one of the most abundant dietary fibers, and they include xylooligosaccharides and those decorated with arabinofuranosyl residues. The molecular …

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Gut microbiota development of preterm infants hospitalised in intensive care units

Hisamichi Tauchi, T. Yamauchi, Taeko Hara, Ryouhei Yamaoka et autres

Gut microbiome development affects infant health and postnatal physiology. The gut microbe assemblages of preterm infants have been reported to be different from that of healthy term infants. However, the patterns of ecosystem development and inter-individual differences remain poorly understood. We investigated …

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3S-Dp01 Metabolic pathway database for Human gut microbiome

Takuji Yamada, Naoki Tsukuda, Sayaka Mizutani, Hiroshi Mori et autres

Effects of ultrasonic intensity and reactor scale on kinetics of enzymatic saccharification of various waste papers in continuously irradiated stirred tanks

Chengzhou Li, Makoto Yoshimoto, Haruki Ogata, Naoki Tsukuda et autres

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