Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genomes of DPC5364, DPC5365, DPC5352, DPC5367, DPC5360, DPC5394, DPC5607, CNRZ32, DPC5389 vs DPC4571

ABSTRACT: Genomic rearrangement, often driven by insertion sequence (IS) elements, is one of the major processes in the evolution of prokaryotes. Sequence analysis of 16S rRNA of Lactobacillus helveticus, an organism that evolved in a dairy environment and Lactobacillus acidiophilus an organism that evolved associated with the gastrointestinal tract (GIT) demonstrated 98.4% identity suggesting that they divergently evolved from a common ancestor. Moreover, complete genome sequence analysis of both organisms has demonstrated a remarkable degree of gene synteny (75% homologous genes) despite the presence of an exceptionally high number and diversity of IS elements in the Lb. helveticus genome. Array based comparative genomic hybridization (aCGH) performed on nine strains of Lb. helveticus revealed sixteen clusters of open reading frames (ORFs) flanked by IS elements. Four of these ORFs are associated with restriction/modification which may have played a role in accelerated evolution of strains in a commercially intensive ecosystem undoubtedly challenged through successive phage attack. Furthermore, analysis of the IS-flanked clusters demonstrated that the most frequently encountered IS were also those most abundant in the genome (IS1201, ISL2, ISLhe1, ISLhe2, ISLhe65 and ISLhe63). These findings contribute to the overall viewpoint on a versatile character of IS elements and the role they may play in bacterial genome plasticity. 2164 ORFs of Lb. helvetiucs DPC4571 spotted on the array in duplicate. Two arrays per each strain.

ORGANISM(S): Lactobacillus helveticus

SUBMITTER: Gerald Fitzgerald

PROVIDER: E-GEOD-16553 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Crucial role for insertion sequence elements in Lactobacillus helveticus evolution as revealed by interstrain genomic comparison.

Kaleta Pawel P O'Callaghan John J Fitzgerald Gerald F GF Beresford Thomas P TP Ross R Paul RP

Applied and environmental microbiology 20091030 1

Lactobacillus helveticus is a versatile dairy bacterium found to possess heterogeneous genotypes depending on the ecosystem from which it was isolated. The recently published genome sequence showed the remarkable flexibility of its structure, demonstrated by a substantial level of insertion sequence (IS) element expansion in association with massive gene decay. To assess this diversity and examine the level of genome plasticity within the L. helveticus species, an array-based comparative genome ...[more]

PMID: 19880644

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Project description:Background. The bacterial foodborne pathogen Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the postinfectious neuropathies, Guillain-BarrÃ© and Miller Fisher syndromes. This study described the use of multilocus sequence typing and DNA microarrays to examine the genetic content of a collection of South African C. jejuni strains, recovered from patients with enteritis, Guillain-BarrÃ© or Miller Fisher syndromes. Methodology/Principal Findings. The comparative genomic analysis by using multilocus sequence typing and DNA microarrays demonstrated that the South African strains with Penner heat-stable (HS) serotype HS:41 were clearly distinct from the other South African strains. Further analysis of the DNA microarray data demonstrated that the serotype HS:41 strains from South African GBS and enteritis patients are highly similar in gene content. Interestingly, the South African HS:41 strains were distinct in gene content when compared to serotype HS:41 strains from other geographical locations due to the presence of genomic islands, referred to as Campylobacter jejuni integrated elements. Only the genomic integrated element CJIE1, a Campylobacter Mu-like prophage, was present in the South African HS:41 strains whereas absent in the closely-related HS:41 strains from Mexico. A more distantly-related HS:41 strain from Canada possessed both genomic integrated elements CJIE1 and CJIE2. Conclusion/Significance. These findings demonstrated that these C. jejuni integrated elements may contribute to the differentiation of closely-related C. jejuni strains. In addition, the presence of bacteriophage-related genes in CJIE1 may probably contribute to increasing the genomic diversity of these C. jejuni strains. This comparative genomic analysis of the foodborne pathogen C. jejuni provides fundamental information that potentially could lead to improved methods for analyzing the epidemiology of disease outbreaks and their sources. The genomic diversity of 33 South African, 2 Mexican and 1 Canadian Campylobacter jejuni strains from humans were examined by microarray-based comparative genomic indexing (CGI) analysis. The CGI analysis allowed the assessment of CDS content for each C. jejuni strain relative to the C. jejuni DNA microarray, which comprises ORFs from strains NCTC 11168, RM1221. ORFs were spotted in duplicate. Genomic DNA from strains NCTC 11168/RM1221 were used as a reference DNA and competitively hybridized with genomic DNA from each of the other C. jejuni strains. Two or three replicates for each strain were performed. Data normalization was performed as in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135.

Dataset Information

Genomes of DPC5364, DPC5365, DPC5352, DPC5367, DPC5360, DPC5394, DPC5607, CNRZ32, DPC5389 vs DPC4571

Publications

Crucial role for insertion sequence elements in Lactobacillus helveticus evolution as revealed by interstrain genomic comparison.

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