Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems.


BACKGROUND:Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents exploration of their genomic functions, including those that convey (human) health benefits. METHODS:PacBio SMRT sequencing was used to determine the whole genome seqeunces of two B. longum subsp. longum strains. The B. longum pan-genome was computed using PGAP v1.2 and the core B. longum phylogenetic tree was constructed using a maximum-likelihood based approach in PhyML v3.0. M.blmNCII was cloned in E. coli and an internal fragment if arfBarfB was cloned into pORI19 for insertion mutagenesis. RESULTS:In this study we present the complete genome sequences of two Bifidobacterium longum subsp. longum strains. Comparative analysis with thirty one publicly available B. longum genomes allowed the definition of the B. longum core and dispensable genomes. This analysis also highlighted differences in particular metabolic abilities between members of the B. longum subspecies infantis, longum and suis. Furthermore, phylogenetic analysis of the B. longum core genome indicated the existence of a novel subspecies. Methylome data, coupled to the analysis of restriction-modification systems, allowed us to substantially increase the genetic accessibility of B. longum subsp. longum NCIMB 8809 to a level that was shown to permit site-directed mutagenesis. CONCLUSIONS:Comparative genomic analysis of thirty three B. longum representatives revealed a closed pan-genome for this bifidobacterial species. Phylogenetic analysis of the B. longum core genome also provides evidence for a novel fifth B. longum subspecies. Finally, we improved genetic accessibility for the strain B. longum subsp. longum NCIMB 8809, which allowed the generation of a mutant of this strain.


BMC Genomics


BMC genomics


O'Callaghan A,Bottacini F,O'Connell Motherway M,van Sinderen D




Has Abstract


2015-10-21 00:00:00










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    更新日期:2017-06-20 00:00:00

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    abstract:BACKGROUND:Bombyx mori was domesticated from the Chinese wild silkworm, Bombyx mandarina. Wild and domestic silkworms are good models in which to investigate genes related to silk protein synthesis that may be differentially expressed in silk glands, because their silk productions are very different. Here we used the m...

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    authors: Baton LA,Robertson A,Warr E,Strand MR,Dimopoulos G

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    pub_type: 杂志文章


    authors: Li MW,Lin RQ,Song HQ,Wu XY,Zhu XQ

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    pub_type: 杂志文章


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    pub_type: 杂志文章


    authors: Zhang J,Sharma A,Yu Q,Wang J,Li L,Zhu L,Zhang X,Chen Y,Ming R

    更新日期:2016-06-10 00:00:00

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    pub_type: 杂志文章


    authors: Fu S,Shao J,Roy A,Brlansky RH,Zhou C,Hartung JS

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    pub_type: 杂志文章


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