Complete genome sequence of Bifidobacterium pseudocatenulatum JCM 1200T isolated from infant feces

Toh, Y.; Oshima, Koichiro; Nakano, Akiyo; Arakawa, Kiyoshi; Takayama, Yukiko; Kurokawa, Rina; Takanashi, Kageyasu; Honda, Kenya; Hattori, Masahira

doi:10.1016/j.jbiotec.2015.06.416

Cited by 7 publications

(2 citation statements)

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“…Based on our 5 complete B. pseudocatenulatum genomes and the available public data, including 5 draft B. pseudocatenulatum genomes and the complete genome of B. pseudocatenulatum JCM1200 T ( 25 ), a total of 11 B. pseudocatenulatum genomes were included in the pan-genome analysis. The pan-genome curve showed an asymptotic trend with an average growing rate of 100 genes per genome in the first six iterations and then decreased to a much smaller rate ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Genomic Microdiversity ofBifidobacterium pseudocatenulatumUnderlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention

Zhang

et al. 2017

mBio

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The genomic basis of the response to dietary intervention of human gut beneficial bacteria remains elusive, which hinders precise manipulation of the microbiota for human health. After receiving a dietary intervention enriched with nondigestible carbohydrates for 105 days, a genetically obese child with Prader-Willi syndrome lost 18.4% of his body weight and showed significant improvement in his bioclinical parameters. We obtained five isolates (C1, C15, C55, C62, and C95) of one of the most abundantly promoted beneficial species, Bifidobacterium pseudocatenulatum, from a postintervention fecal sample. Intriguingly, these five B. pseudocatenulatum strains showed differential responses during the dietary intervention. Two strains were largely unaffected, while the other three were promoted to different extents by the changes in dietary carbohydrate resources. The differential responses of these strains were consistent with their functional clustering based on the COGs (Clusters of Orthologous Groups), including those involved with the ABC-type sugar transport systems, suggesting that the strain-specific genomic variations may have contributed to the niche adaption. Particularly, B. pseudocatenulatum C15, which had the most diverse types and highest gene copy numbers of carbohydrate-active enzymes targeting plant polysaccharides, had the highest abundance after the dietary intervention. These studies show the importance of understanding genomic diversity of specific members of the gut microbiota if precise nutrition approaches are to be realized.

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Section: Resultsmentioning

confidence: 99%

Genomic Microdiversity ofBifidobacterium pseudocatenulatumUnderlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention

Zhang

et al. 2017

mBio

View full text Add to dashboard Cite

show abstract

“…We searched the typical genomes of 17 bifidobacterial species ( Schell et al., 2002 ; Sela et al., 2008 ; Ventura et al., 2009 ; Yasui et al., 2009 ; Turroni et al., 2010 ; O'Connell et al., 2011 ; Jans et al., 2013 ; Milani et al., 2013 , 2014 ; Chen et al., 2015 ; Morita et al., 2015a , 2015b , 2015c , 2015d ; Toh et al., 2015 ; Vazquez-Gutierrez et al., 2015 ) for orthologs of housekeeping sortase or SDPs, and found that BF1_0427 was conserved among all these species, whereas the SDPs, especially GHs ( Table 2 ), were specific to B. bifidum . GHs identified and biochemically characterized in B. bifidum so far include BF1_0298 ( Ashida et al., 2018 ), BF1_1449 ( Wakinaka et al., 2013 ), BF1_0299 ( Kiyohara et al., 2011 ), BF1_1506 ( Ashida et al., 2009 ), BF1_1579 ( Wada et al., 2008 ), BF1_0510 ( Katayama et al., 2004 , 2005 ), and BF1_0030 ( Shimada et al., 2015 ).…”

Section: Discussionmentioning

confidence: 99%