Optimization of the RNA extraction method for transcriptome studies of Salmonella inoculated on commercial raw chicken breast samples

RNA-seq-based quanitative transcriptome analysis of meat color and taste from chickens administered by eucalyptus leaf polyphenols extract

To evaluate how eucalyptus leaf polyphenol extract (EPE) affects chicken meat color and taste, we added different levels of EPE (0%, 0.06%, 0.09%, and 0.12%) to chicken feed. The redness (a^* value) and the myoglobin content of breast muscle in EPE group were remarkably higher. Furthermore, the guanosine monophosphate, histidine, and glycine muscle contents were also enhanced. Transcriptome analysis showed that 10 candidate genes related to meat quality were affected by EPE treatment. The identified genes, with functions critical to chicken meat color and taste, will help to determine the molecular mechanisms of EPE.

Effect of sub-lethal chemical disinfection on the biofilm forming ability, resistance to antibiotics and expression of virulence genes of Salmonella Enteritidis biofilm-surviving cells

Although disinfection procedures are widely implemented in food environments, bacteria can survive and present increased virulence/resistance. Since little is known about these phenomena regarding biofilms, this study aimed to investigate the effect of chemical disinfection on biofilm-derived cells of Salmonella Enteritidis. Using a reference strain (NCTC 13349) and a food isolate (350), biofilm susceptibility to benzalkonium chloride (BAC), sodium hypochlorite (SH) and hydrogen peroxide (HP) was evaluated and biofilms were exposed to sub-lethal concentrations of each disinfectant. Biofilm-derived cells were characterized for their biofilm forming ability, antibiotic resistance and expression of virulence-associated genes. Except for a few instances, disinfectant exposure did not alter antibiotic susceptibility. However, SH and HP exposure enhanced the biofilm forming ability of Salmonella Enteritidis NCTC 13349. After BAC and HP exposure, biofilm-derived cells presented a down-regulation of rpoS. Exposure to BAC also revealed an up-regulation of invA, avrA and csgD on Salmonella Enteritidis NCTC 13349. The results obtained suggest that biofilm-derived cells that survive disinfection may represent an increased health risk.

Application of Molecular Approaches for Understanding Foodborne Salmonella Establishment in Poultry Production

Salmonellosis in the United States is one of the most costly foodborne diseases. Given that Salmonella can originate from a wide variety of environments, reduction of this organism at all stages of poultry production is critical. Salmonella species can encounter various environmental stress conditions which can dramatically influence their survival and colonization. Current knowledge of Salmonella species metabolism and physiology in relation to colonization is traditionally based on studies conducted primarily with tissue culture and animal infection models. Consequently, while there is some information about environmental signals that control Salmonella growth and colonization, much still remains unknown. Genetic tools for comprehensive functional genomic analysis of Salmonella offer new opportunities for not only achieving a better understanding of Salmonella pathogens but also designing more effective intervention strategies. Now the function(s) of each single gene in the Salmonella genome can be directly assessed and previously unknown genetic factors that are required for Salmonella growth and survival in the poultry production cycle can be elucidated. In particular, delineating the host-pathogen relationships involving Salmonella is becoming very helpful for identifying optimal targeted gene mutagenesis strategies to generate improved vaccine strains. This represents an opportunity for development of novel vaccine approaches for limiting Salmonella establishment in early phases of poultry production. In this review, an overview of Salmonella issues in poultry, a general description of functional genomic technologies, and their specific application to poultry vaccine developments are discussed.

A universal fixation method based on quaternary ammonium salts (RNAlater) for omics-technologies: Saccharomyces cerevisiae as a case study

Genomics, transcriptomics, proteomics and fluxomics are powerful omics-technologies that play a major role in today's research. For each of these techniques good sample quality is crucial. Major factors contributing to the quality of a sample is the actual sampling procedure itself and the way the sample is stored directly after sampling. It has already been described that RNAlater can be used to store tissues and cells in a way that the RNA quality and quantity are preserved. In this paper, we demonstrate that quaternary ammonium salts (RNAlater) are also suitable to preserve and store samples from Saccharomyces cerevisiae for later use with the four major omics-technologies. Moreover, it is shown that RNAlater also preserves the cell morphology and the potential to recover growth, permitting microscopic analysis and yeast cell culturing at a later stage.

A third mode of surface-associated growth: immobilization of Salmonella enterica serovar Typhimurium modulates the RpoS-directed transcriptional programme

Although the growth of bacteria has been studied for more than a century, it is only in recent decades that surface-associated growth has received attention. In addition to the well-characterized biofilm and swarming lifestyles, bacteria can also develop as micro-colonies supported by structured environments in both food products and the GI tract. This immobilized mode of growth has not been widely studied. To develop our understanding of the effects of immobilization upon a food-borne bacterial pathogen, we used the IFR Gel Cassette model. The transcriptional programme and metabolomic profile of Salmonella enterica serovar Typhimurium ST4/74 were compared during planktonic and immobilized growth, and a number of immobilization-specific characteristics were identified. Immobilized S.Typhimurium did not express motility and chemotaxis genes, and electron microscopy revealed the absence of flagella. The expression of RpoS-dependent genes and the level of RpoS protein were increased in immobilized bacteria, compared with planktonic growth. Immobilized growth prevented the induction of SPI1, SPI4 and SPI5 gene expression, likely mediated by the FliZ transcriptional regulator. Using an epithelial cell-based assay, we showed that immobilized S.Typhimurium was significantly less invasive than planktonic bacteria, and we suggest that S.Typhimurium grown in immobilized environments are less virulent than planktonic bacteria. Our findings identify immobilization as a third type of surface-associated growth that is distinct from the biofilm and swarming lifestyles of Salmonella.

Transcriptome sequencing of Salmonella enterica serovar Enteritidis under desiccation and starvation stress in peanut oil

It is well recognized that Salmonella can survive long-term starvation and desiccation stresses and contaminate foods that have intermediate to low water activities; however, little is known about the specific molecular mechanisms underlying its survival and persistence in low water activity foods. In this study, we used the RNA-seq approach to compare the transcriptomes (27-33 million 36-bp reads per sample) of a Salmonella enterica subsp. enteric serovar Enteritidis strain ATCC BAA-1045 after inoculation in peanut oil (water activity 0.30) for 72 h, 216 h and 528 h to those grown in Luria-Bertani (LB) broth for 12 h and 312 h. Our results showed that desiccated Salmonella cells in peanut oil were in a physiologically dormant state with <5% of its genome being transcribed compared to 78% in LB broth. Among the few detected transcripts in peanut oil, genes involved in heat and cold shock response, DNA protection and regulatory functions likely play roles in cross protecting Salmonella from desiccation and starvation stresses. In addition, non-coding RNAs may also play roles in Salmonella desiccation stress response. This is the first report of using RNA-seq technology in characterizing bacterial transcriptomes in a food matrix.