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










  • A SNP in intron 8 of CD46 causes a novel transcript associated with mastitis in Holsteins.

    abstract:BACKGROUND:The membrane protein CD46, a ubiquitous cell surface pathogen receptor, can bind Streptococcus to trigger cell autophagy, which is a critical step in the control of infection. RESULTS:In this study, we found a new splice variant designated CD46 transcript variant (CD46-TV). The splice variant is characteriz...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wang X,Zhong J,Gao Y,Ju Z,Huang J

    更新日期:2014-07-28 00:00:00

  • Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis.

    abstract:BACKGROUND:Insertion sequences (ISs) are approximately 1 kbp long "jumping" genes found in prokaryotes. ISs encode the protein Transposase, which facilitates the excision and reinsertion of ISs in genomes, making these sequences a type of class I ("cut-and-paste") Mobile Genetic Elements. ISs are proposed to be involve...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Vigil-Stenman T,Larsson J,Nylander JA,Bergman B

    更新日期:2015-03-17 00:00:00

  • Bayesian prediction of bacterial growth temperature range based on genome sequences.

    abstract:BACKGROUND:The preferred habitat of a given bacterium can provide a hint of which types of enzymes of potential industrial interest it might produce. These might include enzymes that are stable and active at very high or very low temperatures. Being able to accurately predict this based on a genomic sequence, would thu...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Jensen DB,Vesth TC,Hallin PF,Pedersen AG,Ussery DW

    更新日期:2012-01-01 00:00:00

  • Identification of a radiosensitivity signature using integrative metaanalysis of published microarray data for NCI-60 cancer cells.

    abstract:BACKGROUND:In the postgenome era, a prediction of response to treatment could lead to better dose selection for patients in radiotherapy. To identify a radiosensitive gene signature and elucidate related signaling pathways, four different microarray experiments were reanalyzed before radiotherapy. RESULTS:Radiosensiti...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kim HS,Kim SC,Kim SJ,Park CH,Jeung HC,Kim YB,Ahn JB,Chung HC,Rha SY

    更新日期:2012-07-30 00:00:00

  • The nuclear and mitochondrial genomes of Frieseomelitta varia - a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste.

    abstract:BACKGROUND:Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: de Paula Freitas FC,Lourenço AP,Nunes FMF,Paschoal AR,Abreu FCP,Barbin FO,Bataglia L,Cardoso-Júnior CAM,Cervoni MS,Silva SR,Dalarmi F,Del Lama MA,Depintor TS,Ferreira KM,Gória PS,Jaskot MC,Lago DC,Luna-Lucena D,Moda L

    更新日期:2020-06-03 00:00:00

  • A simplified transposon mutagenesis method to perform phenotypic forward genetic screens in cultured cells.

    abstract:BACKGROUND:The introduction of genome-wide shRNA and CRISPR libraries has facilitated cell-based screens to identify loss-of-function mutations associated with a phenotype of interest. Approaches to perform analogous gain-of-function screens are less common, although some reports have utilized arrayed viral expression ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Feddersen CR,Wadsworth LS,Zhu EY,Vaughn HR,Voigt AP,Riordan JD,Dupuy AJ

    更新日期:2019-06-17 00:00:00

  • Functional elucidation of the non-coding RNAs of Kluyveromyces marxianus in the exponential growth phase.

    abstract:BACKGROUND:Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of i...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cho YB,Lee EJ,Cho S,Kim TY,Park JH,Cho BK

    更新日期:2016-02-29 00:00:00

  • Deep sequencing of the uterine immune response to bacteria during the equine oestrous cycle.

    abstract:BACKGROUND:The steroid hormone environment in healthy horses seems to have a significant impact on the efficiency of their uterine immune response. The objective of this study was to characterize the changes in gene expression in the equine endometrium in response to the introduction of bacterial pathogens and the infl...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Marth CD,Young ND,Glenton LY,Noden DM,Browning GF,Krekeler N

    更新日期:2015-11-14 00:00:00

  • Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey.

    abstract:BACKGROUND:The development of second generation sequencing methods has enabled large scale DNA variation studies at moderate cost. For the high throughput discovery of single nucleotide polymorphisms (SNPs) in species lacking a sequenced reference genome, we set-up an analysis pipeline based on a short read de novo seq...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kerstens HH,Crooijmans RP,Veenendaal A,Dibbits BW,Chin-A-Woeng TF,den Dunnen JT,Groenen MA

    更新日期:2009-10-16 00:00:00

  • Comparative transcript profiling of the fertile and sterile flower buds of pol CMS in B. napus.

    abstract:BACKGROUND:The Polima (pol) system of cytoplasmic male sterility (CMS) and its fertility restoration gene Rfp have been used in hybrid breeding in Brassica napus, which has greatly improved the yield of rapeseed. However, the mechanism of the male sterility transition in pol CMS remains to be determined. RESULTS:To in...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: An H,Yang Z,Yi B,Wen J,Shen J,Tu J,Ma C,Fu T

    更新日期:2014-04-03 00:00:00

  • Waking the sleeping dragon: gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticeps.

    abstract:BACKGROUND:Hibernation is a physiological state exploited by many animals exposed to prolonged adverse environmental conditions associated with winter. Large changes in metabolism and cellular function occur, with many stress response pathways modulated to tolerate physiological challenges that might otherwise be letha...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Capraro A,O'Meally D,Waters SA,Patel HR,Georges A,Waters PD

    更新日期:2019-06-06 00:00:00

  • Deep sequencing of transcriptomes from the nervous systems of two decapod crustaceans to characterize genes important for neural circuit function and modulation.

    abstract:BACKGROUND:Crustaceans have been studied extensively as model systems for nervous system function from single neuron properties to behavior. However, lack of molecular sequence information and tools have slowed the adoption of these physiological systems as molecular model systems. In this study, we sequenced and perfo...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Northcutt AJ,Lett KM,Garcia VB,Diester CM,Lane BJ,Marder E,Schulz DJ

    更新日期:2016-11-04 00:00:00

  • Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

    abstract:BACKGROUND:Cattle and other ruminants have evolved the ability to derive most of their metabolic energy requirement from otherwise indigestible plant matter through a symbiotic relationship with plant fibre degrading microbes within a specialised fermentation chamber, the rumen. The genetic changes underlying the evolu...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wheeler TT,Hood KA,Maqbool NJ,McEwan JC,Bingle CD,Zhao S

    更新日期:2007-03-15 00:00:00

  • DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content.

    abstract:BACKGROUND:Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lopdell TJ,Tiplady K,Struchalin M,Johnson TJJ,Keehan M,Sherlock R,Couldrey C,Davis SR,Snell RG,Spelman RJ,Littlejohn MD

    更新日期:2017-12-15 00:00:00

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    pub_type: 杂志文章


    authors: Datson NA,Morsink MC,Atanasova S,Armstrong VW,Zischler H,Schlumbohm C,Dutilh BE,Huynen MA,Waegele B,Ruepp A,de Kloet ER,Fuchs E

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ng YK,Wu W,Zhang L

    更新日期:2009-01-22 00:00:00

  • De novo transcriptome characterization and gene expression profiling of the desiccation tolerant moss Bryum argenteum following rehydration.

    abstract:BACKGROUND:The desiccation-tolerant moss Bryum argenteum is an important component of the Biological Soil Crusts (BSCs) found in the Gurbantunggut desert. Desiccation tolerance is defined as the ability to revive from the air dried state. To elucidate the molecular mechanisms related to desiccation tolerance, we employ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Gao B,Zhang D,Li X,Yang H,Zhang Y,Wood AJ

    更新日期:2015-05-28 00:00:00

  • Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Aftab MN,He H,Skogerbø G,Chen R

    更新日期:2008-06-11 00:00:00

  • Markedly different genome arrangements between serotype a strains and serotypes b or c strains of Aggregatibacter actinomycetemcomitans.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kittichotirat W,Bumgarner R,Chen C

    更新日期:2010-09-08 00:00:00

  • Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization.

    abstract:BACKGROUND:The pathogenesis-related (PR) group of proteins are operationally defined as polypeptides that increase in concentration in plant tissues upon contact with a pathogen. To date, 17 classes of highly divergent proteins have been described that act through multiple mechanisms of pathogen resistance. Characteriz...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Fister AS,Mejia LC,Zhang Y,Herre EA,Maximova SN,Guiltinan MJ

    更新日期:2016-05-17 00:00:00

  • Improvement of the clinical applicability of the Genomic Grade Index through a qRT-PCR test performed on frozen and formalin-fixed paraffin-embedded tissues.

    abstract:BACKGROUND:Proliferation and tumor differentiation captured by the genomic grade index (GGI) are important prognostic indicators in breast cancer (BC) especially for the estrogen receptor positive (ER+) disease. The aims of this study were to convert this microarray index to a qRT-PCR assay (PCR-GGI), which could be re...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Toussaint J,Sieuwerts AM,Haibe-Kains B,Desmedt C,Rouas G,Harris AL,Larsimont D,Piccart M,Foekens JA,Durbecq V,Sotiriou C

    更新日期:2009-09-10 00:00:00

  • Mosquito transcriptome changes and filarial worm resistance in Armigeres subalbatus.

    abstract:BACKGROUND:Armigeres subalbatus is a natural vector of the filarial worm Brugia pahangi, but it rapidly and proficiently kills Brugia malayi microfilariae by melanotic encapsulation. Because B. malayi and B. pahangi are morphologically and biologically similar, the Armigeres-Brugia system serves as a valuable model for...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Aliota MT,Fuchs JF,Mayhew GF,Chen CC,Christensen BM

    更新日期:2007-12-18 00:00:00

  • Bos taurus genome assembly.

    abstract:BACKGROUND:We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. RESULTS:The assembly process consisted of multipl...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Liu Y,Qin X,Song XZ,Jiang H,Shen Y,Durbin KJ,Lien S,Kent MP,Sodeland M,Ren Y,Zhang L,Sodergren E,Havlak P,Worley KC,Weinstock GM,Gibbs RA

    更新日期:2009-04-24 00:00:00

  • Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq.

    abstract:BACKGROUND:The MHC and KIR loci are clinically relevant regions of the genome. Typing the sequence of these loci has a wide range of applications including organ transplantation, drug discovery, pharmacogenomics and furthering fundamental research in immune genetics. Rapid advances in biochemical and next-generation se...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Selvaraj S,Schmitt AD,Dixon JR,Ren B

    更新日期:2015-11-05 00:00:00

  • Transcriptional profiling of putative human epithelial stem cells.

    abstract:BACKGROUND:Human interfollicular epidermis is sustained by the proliferation of stem cells and their progeny, transient amplifying cells. Molecular characterization of these two cell populations is essential for better understanding of self renewal, differentiation and mechanisms of skin pathogenesis. The purpose of th...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Koçer SS,Djurić PM,Bugallo MF,Simon SR,Matic M

    更新日期:2008-07-30 00:00:00

  • Transcriptome analysis reveals key roles of AtLBR-2 in LPS-induced defense responses in plants.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Iizasa S,Iizasa E,Watanabe K,Nagano Y

    更新日期:2017-12-29 00:00:00

  • Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum.

    abstract:BACKGROUND:Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koala...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Bachmann NL,Fraser TA,Bertelli C,Jelocnik M,Gillett A,Funnell O,Flanagan C,Myers GS,Timms P,Polkinghorne A

    更新日期:2014-08-08 00:00:00

  • Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Williamson CH,Sahl JW,Smith TJ,Xie G,Foley BT,Smith LA,Fernández RA,Lindström M,Korkeala H,Keim P,Foster J,Hill K

    更新日期:2016-03-03 00:00:00

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Brown CW,Sridhara V,Boutz DR,Person MD,Marcotte EM,Barrick JE,Wilke CO

    更新日期:2017-04-17 00:00:00

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Koyama T,Asakawa S,Katagiri T,Shimizu A,Fagutao FF,Mavichak R,Santos MD,Fuji K,Sakamoto T,Kitakado T,Kondo H,Shimizu N,Aoki T,Hirono I

    更新日期:2010-02-26 00:00:00