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Pediococcus claussenii ATCC BAA-344

ABSTRACT: Pediococcus claussenii ATCC BAA-344 Transcriptome or Gene expression

PROVIDER: PRJNA185806 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR647760_1.fastq.gz	Fastqsanger.gz
	SRR647760_2.fastq.gz	Fastqsanger.gz
	SRR647762_1.fastq.gz	Fastqsanger.gz
	SRR647762_2.fastq.gz	Fastqsanger.gz
	SRR647804_1.fastq.gz	Fastqsanger.gz

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Pediococcus claussenii ATCC BAA-344

Project description:Pediococcus claussenii ATCC BAA-344 genome sequencing project

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Transcriptome sequence and plasmid copy number analysis of the brewery isolate Pediococcus claussenii ATCC BAA-344 T during growth in beer.

Project description:Growth of specific lactic acid bacteria in beer leads to spoiled product and economic loss for the brewing industry. Microbial growth is typically inhibited by the combined stresses found in beer (e.g., ethanol, hops, low pH, minimal nutrients); however, certain bacteria have adapted to grow in this harsh environment. Considering little is known about the mechanisms used by bacteria to grow in and spoil beer, transcriptome sequencing was performed on a variant of the beer-spoilage organism Pediococcus claussenii ATCC BAA-344(T) (Pc344-358). Illumina sequencing was used to compare the transcript levels in Pc344-358 growing mid-exponentially in beer to those in nutrient-rich MRS broth. Various operons demonstrated high gene expression in beer, several of which are involved in nutrient acquisition and overcoming the inhibitory effects of hop compounds. As well, genes functioning in cell membrane modification and biosynthesis demonstrated significantly higher transcript levels in Pc344-358 growing in beer. Three plasmids had the majority of their genes showing increased transcript levels in beer, whereas the two cryptic plasmids showed slightly decreased gene expression. Follow-up analysis of plasmid copy number in both growth environments revealed similar trends, where more copies of the three non-cryptic plasmids were found in Pc344-358 growing in beer. Transcriptome sequencing also enabled the addition of several genes to the P. claussenii ATCC BAA-344(T) genome annotation, some of which are putatively transcribed as non-coding RNAs. The sequencing results not only provide the first transcriptome description of a beer-spoilage organism while growing in beer, but they also highlight several targets for future exploration, including genes that may have a role in the general stress response of lactic acid bacteria.

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Complete genome sequence of the beer spoilage organism Pediococcus claussenii ATCC BAA-344T.

Project description:Pediococcus claussenii is a common brewery contaminant. We have sequenced the chromosome and plasmids of the type strain P. claussenii ATCC BAA-344. A ropy variant was chosen for sequencing to obtain genetic information related to growth in beer, as well as exopolysaccharide and possibly biofilm formation by this organism.

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Project description:Helicobacter cinaedi is an emerging bacterial pathogen of immunosuppressed individuals. The species is traditionally thought to require an H2-enhanced microaerobic atmosphere for growth, although it can proliferate under aerobic conditions when co-cultured with epithelial monolayers or supplemented with certain metabolites (notably, L-lactate). The goal of this experiment was to assess the global transcription changes that occur in the H. cinaedi type strain (ATCC BAA-847) under various media and atmospheric conditions. These include bacterial monoculture, as well as co-culture with Caco-2 intestinal epithelial cells. In total, Illumina mRNA-seq (stranded, paired-end) was performed on H. cinaedi grown under 9 in vitro culture conditions (4-5 biologic replicates per condition).

2016-09-19 | E-MTAB-5062 | biostudies-arrayexpress

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