Boekhorst J

References (9)

Title : Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment - Caspers_2013_Genome.Announc_1_e00010
Author(s) : Caspers MP , Boekhorst J , Abee T , Siezen RJ , Kort R
Ref : Genome Announc , 1 : , 2013
Abstract : Spores of thermophilic spore-forming bacteria are a common cause of contamination in dairy products. We isolated the thermophilic strain Anoxybacillus flavithermus TNO-09.006 from a milk-processing plant, and we report the complete genome of this isolate consisting of a single chromosome of 2.65 Mb.
ESTHER : Caspers_2013_Genome.Announc_1_e00010
PubMedSearch : Caspers_2013_Genome.Announc_1_e00010
PubMedID: 23469333
Gene_locus related to this paper: anofw-b7glx5

Title : Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman - Anukam_2013_PLoS.One_8_e59239
Author(s) : Anukam KC , Macklaim JM , Gloor GB , Reid G , Boekhorst J , Renckens B , van Hijum SA , Siezen RJ
Ref : PLoS ONE , 8 :e59239 , 2013
Abstract : The vaginal microbiota, in particular Lactobacillus species, play an important role in female health through modulation of immunity, countering pathogens and maintaining a pH below 4.7. We report the isolation and genome sequence of Lactobacillus pentosus strain KCA1 (formally known as L. plantarum) from the vagina of a healthy Nigerian woman. The genome was sequenced using Illumina GA II technology. The resulting 16,920,226 paired-end reads were assembled with the Velvet tool. Contigs were annotated using the RAST server, and manually curated. A comparative analysis with the available genomes of L. pentosus IG1 and L. plantarum WCFS1 showed that over 15% of the predicted functional activities are found only in this strain. The strain has a chromosome sequence of 3,418,159 bp with a G+C content of 46.4%, and is devoid of plasmids. Novel gene clusters or variants of known genes relative to the reference genomes were found. In particular, the strain has loci encoding additional putative mannose phosphotransferase systems. Clusters of genes include those for utilization of hydantoin, isopropylmalate, malonate, rhamnosides, and genes for assimilation of polyglycans, suggesting the metabolic versatility of L. pentosus KCA1. Loci encoding putative phage defense systems were also found including clustered regularly interspaced short palindromic repeats (CRISPRs), abortive infection (Abi) systems and toxin-antitoxin systems (TA). A putative cluster of genes for biosynthesis of a cyclic bacteriocin precursor, here designated as pentocin KCA1 (penA) were identified. These findings add crucial information for understanding the genomic and geographic diversity of vaginal lactobacilli.
ESTHER : Anukam_2013_PLoS.One_8_e59239
PubMedSearch : Anukam_2013_PLoS.One_8_e59239
PubMedID: 23527145
Gene_locus related to this paper: lacpl-LP.0796

Title : Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity - Smokvina_2013_PLoS.One_8_e68731
Author(s) : Smokvina T , Wels M , Polka J , Chervaux C , Brisse S , Boekhorst J , van Hylckama Vlieg JE , Siezen RJ
Ref : PLoS ONE , 8 :e68731 , 2013
Abstract : Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its "pan-genome". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon) are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis, in order to link the distribution pattern of a specific phenotype to the presence/absence of specific sets of genes.
ESTHER : Smokvina_2013_PLoS.One_8_e68731
PubMedSearch : Smokvina_2013_PLoS.One_8_e68731
PubMedID: 23894338
Gene_locus related to this paper: laccb-b3wcx2

Title : Draft Genome Sequence of Enterococcus sp. Strain HSIEG1, Isolated from the Human Small Intestine - van den Bogert_2013_Genome.Announc_1_e01013
Author(s) : van den Bogert B , Boekhorst J , Smid EJ , Zoetendal EG , Kleerebezem M
Ref : Genome Announc , 1 : , 2013
Abstract : Enterococcus sp. strain HSIEG1 was isolated from the human small intestine. Its draft genome predicts a broad carbohydrate fermentation capability, which matches well with the observed physiological characteristics of this strain. This metabolic flexibility is expected to be of importance for survival and growth in the small intestinal habitat.
ESTHER : van den Bogert_2013_Genome.Announc_1_e01013
PubMedSearch : van den Bogert_2013_Genome.Announc_1_e01013
PubMedID: 24336366
Gene_locus related to this paper: 9ente-g5itk7

Title : Genome sequence of the naturally plasmid-free Lactobacillus plantarum strain NC8 (CCUG 61730) - Axelsson_2012_J.Bacteriol_194_2391
Author(s) : Axelsson L , Rud I , Naterstad K , Blom H , Renckens B , Boekhorst J , Kleerebezem M , van Hijum S , Siezen RJ
Ref : Journal of Bacteriology , 194 :2391 , 2012
Abstract : Lactobacillus plantarum is a highly versatile lactic acid bacterium found in various ecological niches, such as fermented vegetable, meat, and dairy products and the gastrointestinal tract. We sequenced the genome of L. plantarum NC8, a naturally plasmid-free strain, which has been used as a model strain in many laboratories worldwide.
ESTHER : Axelsson_2012_J.Bacteriol_194_2391
PubMedSearch : Axelsson_2012_J.Bacteriol_194_2391
PubMedID: 22493200
Gene_locus related to this paper: lacpl-PEPI , lacpl-PEPR1 , lacpl-tanL

Title : Comparative genomics of prevaccination and modern Bordetella pertussis strains - Bart_2010_BMC.Genomics_11_627
Author(s) : Bart MJ , van Gent M , van der Heide HG , Boekhorst J , Hermans P , Parkhill J , Mooi FR
Ref : BMC Genomics , 11 :627 , 2010
Abstract : BACKGROUND: Despite vaccination since the 1950s, pertussis has persisted and resurged. It remains a major cause of infant death worldwide and is the most prevalent vaccine-preventable disease in developed countries. The resurgence of pertussis has been associated with the expansion of Bordetella pertussis strains with a novel allele for the pertussis toxin (Ptx) promoter, ptxP3, which have replaced resident ptxP1 strains. Compared to ptxP1 strains, ptxP3 produce more Ptx resulting in increased virulence and immune suppression. To elucidate how B. pertussis has adapted to vaccination, we compared genome sequences of two ptxP3 strains with four strains isolated before and after the introduction vaccination.
RESULTS: The distribution of SNPs in regions involved in transcription and translation suggested that changes in gene regulation play an important role in adaptation. No evidence was found for acquisition of novel genes. Modern strains differed significantly from prevaccination strains, both phylogenetically and with respect to particular alleles. The ptxP3 strains were found to have diverged recently from modern ptxP1 strains. Differences between ptxP3 and modern ptxP1 strains included SNPs in a number of pathogenicity-associated genes. Further, both gene inactivation and reactivation was observed in ptxP3 strains relative to modern ptxP1 strains.
CONCLUSIONS: Our work suggests that B. pertussis adapted by successive accumulation of SNPs and by gene (in)activation. In particular changes in gene regulation may have played a role in adaptation.
ESTHER : Bart_2010_BMC.Genomics_11_627
PubMedSearch : Bart_2010_BMC.Genomics_11_627
PubMedID: 21070624

Title : Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island - van Schaik_2010_BMC.Genomics_11_239
Author(s) : van Schaik W , Top J , Riley DR , Boekhorst J , Vrijenhoek JE , Schapendonk CM , Hendrickx AP , Nijman IJ , Bonten MJ , Tettelin H , Willems RJ
Ref : BMC Genomics , 11 :239 , 2010
Abstract : BACKGROUND: The Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients.
RESULTS: We present a pyrosequencing-based comparative genome analysis of seven E. faecium strains that were isolated from various sources. In the genomes of clinical isolates several antibiotic resistance genes were identified, including the vanA transposon that confers resistance to vancomycin in two strains. A functional comparison between E. faecium and the related opportunistic pathogen E. faecalis based on differences in the presence of protein families, revealed divergence in plant carbohydrate metabolic pathways and oxidative stress defense mechanisms. The E. faecium pan-genome was estimated to be essentially unlimited in size, indicating that E. faecium can efficiently acquire and incorporate exogenous DNA in its gene pool. One of the most prominent sources of genomic diversity consists of bacteriophages that have integrated in the genome. The CRISPR-Cas system, which contributes to immunity against bacteriophage infection in prokaryotes, is not present in the sequenced strains. Three sequenced isolates carry the esp gene, which is involved in urinary tract infections and biofilm formation. The esp gene is located on a large pathogenicity island (PAI), which is between 64 and 104 kb in size. Conjugation experiments showed that the entire esp PAI can be transferred horizontally and inserts in a site-specific manner.
CONCLUSIONS: Genes involved in environmental persistence, colonization and virulence can easily be aquired by E. faecium. This will make the development of successful treatment strategies targeted against this organism a challenge for years to come.
ESTHER : van Schaik_2010_BMC.Genomics_11_239
PubMedSearch : van Schaik_2010_BMC.Genomics_11_239
PubMedID: 20398277
Gene_locus related to this paper: entfc-c2hcr4 , entfc-q3xwb2 , entfc-q3xwy1 , entfc-q3xzi8 , entfc-q3y367

Title : Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche - Siezen_2008_Appl.Environ.Microbiol_74_424
Author(s) : Siezen RJ , Starrenburg MJ , Boekhorst J , Renckens B , Molenaar D , van Hylckama Vlieg JE
Ref : Applied Environmental Microbiology , 74 :424 , 2008
Abstract : Lactococcus lactis is a primary constituent of many starter cultures used for the manufacturing of fermented dairy products, but the species also occurs in various nondairy niches such as (fermented) plant material. Three genome sequences of L. lactis dairy strains (IL-1403, SK11, and MG1363) are publicly available. An extensive molecular and phenotypic diversity analysis was now performed on two L. lactis plant isolates. Diagnostic sequencing of their genomes resulted in over 2.5 Mb of sequence for each strain. A high synteny was found with the genome of L. lactis IL-1403, which was used as a template for contig mapping and locating deletions and insertions in the plant L. lactis genomes. Numerous genes were identified that do not have homologs in the published genome sequences of dairy L. lactis strains. Adaptation to growth on substrates derived from plant cell walls is evident from the presence of gene sets for the degradation of complex plant polymers such as xylan, arabinan, glucans, and fructans but also for the uptake and conversion of typical plant cell wall degradation products such as alpha-galactosides, beta-glucosides, arabinose, xylose, galacturonate, glucuronate, and gluconate. Further niche-specific differences are found in genes for defense (nisin biosynthesis), stress response (nonribosomal peptide synthesis and various transporters), and exopolysaccharide biosynthesis, as well as the expected differences in various mobile elements such as prophages, plasmids, restriction-modification systems, and insertion sequence elements. Many of these genes were identified for the first time in Lactococcus lactis. In most cases good correspondence was found with the phenotypic characteristics of these two strains.
ESTHER : Siezen_2008_Appl.Environ.Microbiol_74_424
PubMedSearch : Siezen_2008_Appl.Environ.Microbiol_74_424
PubMedID: 18039825
Gene_locus related to this paper: lacla-cpo , lacla-menX , lacla-YQAG , laclk-a9qsc5 , laclk-a9qse8 , laclk-d2bl62

Title : Complete genome sequence of Lactobacillus plantarum WCFS1 - Kleerebezem_2003_Proc.Natl.Acad.Sci.U.S.A_100_1990
Author(s) : Kleerebezem M , Boekhorst J , van Kranenburg R , Molenaar D , Kuipers OP , Leer R , Tarchini R , Peters SA , Sandbrink HM , Fiers MW , Stiekema W , Lankhorst RM , Bron PA , Hoffer SM , Groot MN , Kerkhoven R , De Vries M , Ursing B , de Vos WM , Siezen RJ
Ref : Proc Natl Acad Sci U S A , 100 :1990 , 2003
Abstract : The 3,308,274-bp sequence of the chromosome of Lactobacillus plantarum strain WCFS1, a single colony isolate of strain NCIMB8826 that was originally isolated from human saliva, has been determined, and contains 3,052 predicted protein-encoding genes. Putative biological functions could be assigned to 2,120 (70%) of the predicted proteins. Consistent with the classification of L. plantarum as a facultative heterofermentative lactic acid bacterium, the genome encodes all enzymes required for the glycolysis and phosphoketolase pathways, all of which appear to belong to the class of potentially highly expressed genes in this organism, as was evident from the codon-adaptation index of individual genes. Moreover, L. plantarum encodes a large pyruvate-dissipating potential, leading to various end-products of fermentation. L. plantarum is a species that is encountered in many different environmental niches, and this flexible and adaptive behavior is reflected by the relatively large number of regulatory and transport functions, including 25 complete PTS sugar transport systems. Moreover, the chromosome encodes >200 extracellular proteins, many of which are predicted to be bound to the cell envelope. A large proportion of the genes encoding sugar transport and utilization, as well as genes encoding extracellular functions, appear to be clustered in a 600-kb region near the origin of replication. Many of these genes display deviation of nucleotide composition, consistent with a foreign origin. These findings suggest that these genes, which provide an important part of the interaction of L. plantarum with its environment, form a lifestyle adaptation region in the chromosome.
ESTHER : Kleerebezem_2003_Proc.Natl.Acad.Sci.U.S.A_100_1990
PubMedSearch : Kleerebezem_2003_Proc.Natl.Acad.Sci.U.S.A_100_1990
PubMedID: 12566566
Gene_locus related to this paper: lacpl-EST1 , lacpl-EST2 , lacpl-HPO , lacpl-LP.0461 , lacpl-LP.0618 , lacpl-LP.0796 , lacpl-LP.0973 , lacpl-LP.1002 , lacpl-LP.1124 , lacpl-LP.1156 , lacpl-LP.1165 , lacpl-LP.1760 , lacpl-LP.1774 , lacpl-LP.1935 , lacpl-LP.2519 , lacpl-LP.2586 , lacpl-LP.2620 , lacpl-LP.2631 , lacpl-LP.2737 , lacpl-LP.2923 , lacpl-LP.2953 , lacpl-LP.3205 , lacpl-LP.3265 , lacpl-LP.3341 , lacpl-LP.3393 , lacpl-LP.3561 , lacpl-LP.3562 , lacpl-PEPI , lacpl-PEPR1 , lacpl-PEPR2 , lacpl-pepx , lacpl-tanL