Ontology highlight
ABSTRACT:
PROVIDER: PRJNA755820 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15565900_1.fastq.gz | Fastqsanger.gz | |||
| SRR15565900_2.fastq.gz | Fastqsanger.gz | |||
| SRR15566000_1.fastq.gz | Fastqsanger.gz | |||
| SRR15566000_2.fastq.gz | Fastqsanger.gz | |||
| SRR15565901_1.fastq.gz | Fastqsanger.gz |
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Project description:Mostly, lactic acid bacteria (LAB), including food-spoilage-associated, grow in communities consisting of several microbial species. The interspecies interactions eventually shape the structure and global activity of a given microbial community. Generally, the knowledge on system level responses of LAB (especially food-spoilage-associated) during such interactions is very limited. To study transcriptome responses during interactions between three MAP meat-spoilage-associated LAB (Leuconostoc gelidum subsp. gasicomitatum LMG 18811T, Lactococcus piscium MKFS47 and Lactobacillus oligofermentans LMG 22743T) we grew them separately in individual cultures and in mixed cultures pairwise (three combinations) and all together (triple culture) in three replicates on a glucose-containing growth medium (MRS) under microaerobic conditions at 25 C, samples were taken at three time points (3, 5 and 11 h) and extracted RNA were sequenced. The experiments were performed in two batches. At first (batch 1), co-cultivation of Le. gelidum and Lc. piscium accompanied with their individual cultures was performed and processed. The raw RNA-seq data for the individual culture of Lc. piscium from the batch 1 were uploaded earlier and are available in the ArrayExpress database under accession number E-MTAB-3245. Later (batch 2), two other pairwise cultures (Le. gelidum + Lb. oligofermentans and Lc. piscium + Lb. oligofermentans) and the triple culture were grown together with the individual cultures of all three LAB. Designations used for the sample names: G: Le. gelidum; P: Lc. piscium; O: Lb. oligofermentans; GO, PO, PG: pairwise cultures of the corresponding species; OPG: triple culture; b1: batch 1; b2: batch 2. Example: 3G2_b1: 3 h, Le. gelidum, 2nd replicate, batch 1; 11PO3_b2: 11 h, pairwise culture of Lc. piscium and Lb. oligofermentans, 3d replicate, batch 2. One sample (5PO3_b2) had very low number of reads ~ 9000, and, therefore, was not uploaded under this project. RNA extraction and library construction were done analogously as in the study (Andreevskaya M et al., 2015. Appl. Environ. Microbiol. 81:38003811, doi: 10.1128/AEM.00320-15). Ribosomal RNA was omitted. Libraries were sequenced in five lanes using SOLiD 5500XL (Life technologies, Foster City, Ca, USA) to produce 75 bp single-end reads. For the data submission, xsq files obtained from SOLiD 5500XL machine, were converted into fastq files. Adapter sequences were removed using cutadapt 1.4.1.
2018-04-27 | E-MTAB-5499 | biostudies-arrayexpress
Project description:Aiming to reduce food spoilage, the present study developed novel highly active food-grade preservatives affecting a wide range of bacteria. For this purpose, storage proteins were extracted from food plants. After enzymatic hydrolysis by the digestive protease chymotrypsin, the peptide profiles were analyzed by ultrahigh-performance micro-liquid chromatography–triple quadrupole time-of-flight tandem mass spectrometry. Virtual screening identified 21 potential antimicrobial peptides in chickpea legumin. Among those, the peptides Leg1 (RIKTVTSFDLPALRFLKL) and Leg2 (RIKTVTSFDLPALRWLKL) exhibited antimicrobial activity against 16 different bacteria, including pathogens, spoilage-causing bacteria and two antibiotic-resistant strains. Minimum inhibitory concentrations (MIC) down to 15.6 µM indicated 10–1,000-fold higher activity of the novel antimicrobial peptides compared to conventional food preservatives. Moreover, Leg1 and Leg2 showed bactericidal activity in bacterial suspension and during the storage of raw pork meat.
2021-01-11 | PXD019257 | Pride
Project description:A prototype oligonucleotide microarray was designed to detect and identify viable bacterial species with the potential to grow of common beer spoilage microorganisms from the genera Lactobacillus, Megasphaera, Pediococcus and Pectinatus. Probes targeted the intergenic spacer regions (ISR) between 16S and 23S rRNA, which were amplified in a combination of reverse transcriptase (RT) and polymerase chain reaction (PCR) prior to hybridization. This method allows the detection and discrimination of single bacterial species in a complex sample. Furthermore, microarrays using oligonucleotide probes targeting the ISR allow the distinction between viable bacteria with the potential to grow and non-growing bacteria. The results demonstrate the feasibility of oligonucleotide microarrays as a contamination control in food industry for the detection and identification of spoilage microorganisms within mixed population. Keywords: microarray, oligonucleotide, species-specific, detection, beer spoilage bacteria
2007-05-23 | GSE7840 | GEO
Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
2019-11-12 | PXD010845 | Pride