Listeria monocytogenes Biofilm Adaptation to Different Temperatures Seen Through Shotgun Proteomics

Differential analysis of transcriptome of psychrophilic bacteria under different culture temperatures

BACKGROUND

Psychrophilic bacteria can survive in a unique living environment.

OBJECTIVE

To explore the mechanism of low temperature adaptation and the physiological function of thermophilic metabolic genes.

METHOD

Serratia marcescens strain F13 stored in microbial laboratory was cultured at 5∘C, 10∘C and 25∘C respectively, and the obtained strains were sequenced by high-throughput transcriptome. Serratia marcescens strain CAV1761 was used as the reference strain. The data produced by transcriptome sequencing were statistically analyzed by biostatistics software such as soapnuke, soap and edger. The differentially expressed genes were found based on the gene expression, and analyzed by Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis.

RESULTS

The results showed that there were 718 differential genes in F13-10 vs F13-5 comparison group, 1614 differential genes in F13-25 vs F13-5 comparison group and 1636 differential genes in F13-25 vs F13-10 comparison group. GO function enrichment analysis showed that the GO term mainly enriched by different genes in the three comparison groups was mostly related to the migration and transport of cellular or subcellular components, cell localization and transmembrane transporter activity, as well as cilia or flagella dependent cell movement. In the enrichment analysis of KEGG pathway, the three comparison groups all enriched the largest number of differential genes in the branch pathway of KEGG metabolism, followed by the branch pathway of environmental information processing.

CONCLUSION

In F13-10 vs F13-5, the differential genes were mainly concentrated in 20 pathways such as ATP-binding cassette transport (ABC) transporters, thiamine metabolism and flagella assembly; In F13-25 vs F13-5, the differential genes are mainly concentrated in 20 pathways, such as (ABC) transporters, arginine and proline metabolism, two-component system and so on; In F13-25 vs F13-10, the differential genes are mainly concentrated in 20 pathways such as various types of glycan synthesis, two-component system and arginine metabolism.

Contrasting genes conferring short- and long-term biofilm adaptation in Listeria

Listeria monocytogenes is an opportunistic food-borne bacterium that is capable of infecting humans with high rates of hospitalization and mortality. Natural populations are genotypically and phenotypically variable, with some lineages being responsible for most human infections. The success of L. monocytogenes is linked to its capacity to persist on food and in the environment. Biofilms are an important feature that allow these bacteria to persist and infect humans, so understanding the genetic basis of biofilm formation is key to understanding transmission. We sought to investigate the biofilm-forming ability of L. monocytogenes by identifying genetic variation that underlies biofilm formation in natural populations using genome-wide association studies (GWAS). Changes in gene expression of specific strains during biofilm formation were then investigated using RNA sequencing (RNA-seq). Genetic variation associated with enhanced biofilm formation was identified in 273 genes by GWAS and differential expression in 220 genes by RNA-seq. Statistical analyses show that the number of overlapping genes flagged by either type of experiment is less than expected by random sampling. This novel finding is consistent with an evolutionary scenario where rapid adaptation is driven by variation in gene expression of pioneer genes, and this is followed by slower adaptation driven by nucleotide changes within the core genome.

Proteomic analysis to unravel the biochemical mechanisms triggered by Bacillus toyonensis SFC 500-1E under chromium(VI) and phenol stress

Bacillus toyonensis SFC 500-1E is a member of the consortium SFC 500-1 able to remove Cr(VI) and simultaneously tolerate high phenol concentrations. In order to elucidate mechanisms utilized by this strain during the bioremediation process, the differential expression pattern of proteins was analyzed when it grew with or without Cr(VI) (10 mg/L) and Cr(VI) + phenol (10 and 300 mg/L), through two complementary proteomic approaches: gel-based (Gel-LC) and gel-free (shotgun) nanoUHPLC-ESI-MS/MS. A total of 400 differentially expressed proteins were identified, out of which 152 proteins were down-regulated under Cr(VI) and 205 up-regulated in the presence of Cr(VI) + phenol, suggesting the extra effort made by the strain to adapt itself and keep growing when phenol was also added. The major metabolic pathways affected include carbohydrate and energetic metabolism, followed by lipid and amino acid metabolism. Particularly interesting were also ABC transporters and the iron-siderophore transporter as well as transcriptional regulators that can bind metals. Stress-associated global response involving the expression of thioredoxins, SOS response, and chaperones appears to be crucial for the survival of this strain under treatment with both contaminants. This research not only provided a deeper understanding of B. toyonensis SFC 500-1E metabolic role in Cr(VI) and phenol bioremediation process but also allowed us to complete an overview of the consortium SFC 500-1 behavior. This may contribute to an improvement in its use as a bioremediation strategy and also provides a baseline for further research.

Influence of temperature on regulation of key virulence and stress response genes in Listeria monocytogenes biofilms

Temperature is a major determinant of Listeria (L.) monocytogenes adherence and biofilm formation on abiotic surfaces. However, its role on gene regulation of L. monocytogenes mature biofilms has not been investigated. In the present study, we aimed to evaluate the impact of temperature up- and down-shift on L. monocytogenes biofilms gene transcription. L. monocytogenes strain EGD-e biofilms were first developed on stainless steel surfaces in Brain Heart Infusion broth at 20 °C for 48 h. Then, nutrient broth was renewed, and mature biofilms were exposed to 10 °C, 20 °C or 37 °C for 24 h. Biofilm cells were harvested and RNA levels of plcA, prfA, hly, mpl, plcB, sigB, bapL, fbpA, fbpB, lmo2178, lmo0880, lmo0160, lmo1115, lmo 2089, lmo2576, lmo0159 and lmo0627 were evaluated by quantitative RT-PCR. The results revealed an over-expression of all genes tested in biofilm cells compared to planktonic cells. When biofilms were further allowed to proliferate at 20 °C for 24 h, the transcription levels of key virulence, stress response and putative binding proteins genes plcA, sigB, fbpA, fbpB, lmo1115, lmo0880 and lmo2089 decreased. A temperature-dependent transcription for sigB, plcA, hly, and lmo2089 genes was observed after biofilm proliferation at 10 °C or 37 °C. Our findings suggest that temperature differentially affects gene regulation of L. monocytogenes mature biofilms, thus modulating attributes such as virulence, stress response and pathogenesis.

Pseudomonas aeruginosa responds to altered membrane phospholipid composition by adjusting the production of two-component systems, proteases and iron uptake proteins

Membrane protein and phospholipid (PL) composition changes in response to environmental cues and during infections. To achieve these, bacteria use adaptation mechanisms involving covalent modification and remodelling of the acyl chain length of PLs. However, little is known about bacterial pathways regulated by PLs. Here, we investigated proteomic changes in the biofilm of P. aeruginosa phospholipase mutant (∆plaF) with altered membrane PL composition. The results revealed profound alterations in the abundance of many biofilm-related two-component systems (TCSs), including accumulation of PprAB, a key regulator of the transition to biofilm. Furthermore, a unique phosphorylation pattern of transcriptional regulators, transporters and metabolic enzymes, as well as differential production of several proteases, in ∆plaF, indicate that PlaF-mediated virulence adaptation involves complex transcriptional and posttranscriptional response. Moreover, proteomics and biochemical assays revealed the depletion of pyoverdine-mediated iron uptake pathway proteins in ∆plaF, while proteins from alternative iron-uptake systems were accumulated. These suggest that PlaF may function as a switch between different iron-acquisition pathways. The observation that PL-acyl chain modifying and PL synthesis enzymes were overproduced in ∆plaF reveals the interconnection of degradation, synthesis and modification of PLs for proper membrane homeostasis. Although the precise mechanism by which PlaF simultaneously affects multiple pathways remains to be elucidated, we suggest that alteration of PL composition in ∆plaF plays a role for the global adaptive response in P. aeruginosa mediated by TCSs and proteases. Our study revealed the global regulation of virulence and biofilm by PlaF and suggests that targeting this enzyme may have therapeutic potential.

Bioprotective cultures and bacteriocins as food preservatives

Food preservation technologies face the challenge of extending product shelf life applying different factors to prevent the microbiological spoilage of food and inhibit/inactivate food borne pathogens maintaining or even enhancing its quality. One such preservation strategy is the application of bacteriocins or bacteriocin-producer cultures as a kind of food biopreservation. Bacteriocins are ribosomally synthesized small polypeptide molecules that exert antagonistic activity against closely related and unrelated bacteria without harming the producing strain by specific immunity proteins. This chapter aims to contribute to current knowledge about innovative natural preservative agents and their application in the food industry. Specifically, its purpose is to analyze the classification of bacteriocins from lactic acid bacteria (LAB), desirable characteristics of bacteriocins that position them in a privileged place in food biopreservation technology, their success story as well as the bacteriocinogenic LAB in various food systems. Finally, challenges and barrier strategies used to enhance the efficiency of the bacteriocins antimicrobial effect are presented in this chapter.

Pseudomonas fragi biofilm on stainless steel (at low temperatures) affects the survival of Campylobacter jejuni and Listeria monocytogenes and their control by a polymer molybdenum oxide nanocomposite coating

Pseudomonas spp. are widely distributed bacteria on surfaces in the food production and processing environment, where they form extracellular polymeric substance rich biofilms that interact with other bacteria. In this study, the influence of biofilm of Pseudomonas fragi ATCC 4973 on Listeria monocytogenes ATCC 19115 and Campylobacter jejuni NCTC 11168 was investigated at 5 °C and 15 °C on stainless steel in broth and food homogenates (fish or chicken meat). Stainless steel was then coated with PVDF-HFP/PVP/MoO₃ nanocomposite and examined for surface changes (scanning electron microscope, static contact angle, Vickers hardness and elastic modulus). The effect of the prepared nanocomposite coating on P. fragi and on L. monocytogenes and C. jejuni was evaluated in mono- and co-culture. P. fragi produced more biofilm at 15 °C than at 5 °C, especially when food homogenates were used as growth media. Co-cultivation with pathogens did not affect biofilm production by P. fragi, but significant changes were observed in L. monocytogenes and C. jejuni, resulting in a decrease and increase, respectively, in the determined number of culturable biofilm cells. The first change was probably due to competition for the surface, and the second to the oxygen gradient. Stainless steel was then coated with a PVDF-HFP/PVP/MoO₃ nanocomposite, which was characterised by lower roughness and higher wettability, but lower hardness compared to uncoated stainless steel. The prepared nanocoating showed bactericidal activity when tested in phosphate buffered saline. When used in food homogenates, a reduction of over 95 % in bacterial counts was observed. An abundant biofilm of P. fragi proved protective to L. monocytogenes and C. jejuni against the functionalised nanocomposite surface when tested in food homogenates. The control of spoilage Pseudomonas spp., which are common in the food production and processing environment, is important for reducing the contamination of food with spoilage bacteria and with pathogens such as L. monocytogenes and C. jejuni, which may be present in the same environment. The PVDF-HFP/PVP/MoO₃ nanocomposite showed good potential for use as a coating for food contact surfaces, but possible migration of nanoparticles from the nanocomposite coating to food should be evaluated before its commercial use.

Antimicrobial Activity of Sertraline on Listeria monocytogenes

We explored the antimicrobial activity of sertraline on Listeria monocytogenes and further investigated the effects of sertraline on biofilm formation and the virulence gene expression of L. monocytogenes. The minimum inhibitory concentration and minimum bactericidal concentration for sertraline against L. monocytogenes were in the range of 16-32 μg/mL and 64 μg/mL, respectively. Sertraline-dependent damage of the cell membrane and a decrease in intracellular ATP and pH_in in L. monocytogenes were observed. In addition, sertraline reduced the biofilm formation efficiency of the L. monocytogenes strains. Importantly, low concentrations (0.1 μg/mL and 1 μg/mL) of sertraline significantly down-regulated the expression levels of various L. monocytogens virulence genes (prfA, actA, degU, flaA, sigB, ltrC and sufS). These results collectively suggest a role of sertraline for the control of L. monocytogenes in the food industry.

Anti-Biofilm Activity of Cell Free Supernatants of Selected Lactic Acid Bacteria against Listeria monocytogenes Isolated from Avocado and Cucumber Fruits, and from an Avocado Processing Plant

Listeria monocytogenes forms biofilms on food contact surfaces, a niche from where it dislodges to contaminate food products including fresh produce. Probiotics and their derivatives are considered promising alternative strategies to curb the presence of L. monocytogenes in varied food applications. Nonetheless, studies on their anti-biofilm effects against L. monocytogenes from avocados and cucumbers are sparse. This study screened the biofilm formation capabilities of L. monocytogenes strains Avo and Cuc isolated from the avocado and cucumber fruits respectively, and strain 243 isolated from an avocado processing plant; and evaluated the anti-biofilm effects of cell free supernatants (CFS) of Lactobacillus acidophilus La14 150B, Lactiplantibacillus plantarum B411 and Lacticaseibacillus rhamnosus ATCC 53103 against their biofilms formed on polyvinyl chloride (PVC) and stainless steel. All the L. monocytogenes strains formed biofilms (classified either as moderate or strong biofilm formers) on these materials. The presence of CFS reduced the biofilm formation capabilities of these strains and disrupted the integrity of their pre-formed biofilms. Quantitative reverse transcriptase polymerase chain reaction revealed significant reduction of positive regulatory factor A (prfA) gene expression by L. monocytogenes biofilm cells in the presence of CFS (p < 0.05). Thus, these CFS have potential as food grade sanitizers for control of L. monocytogenes biofilms in the avocado and cucumber processing facilities.

Transcriptomic analysis reveals Aspergillus oryzae responds to temperature stress by regulating sugar metabolism and lipid metabolism

Aspergillus oryzae is widely used in industrial applications, which always encounter changes within multiple environmental conditions during fermentation, such as temperature stress. However, the molecular mechanisms by which A. oryzae protects against temperature stress have not been elucidated. Therefore, this study aimed to characterize the fermentative behavior, transcriptomic profiles, and metabolic changes of A. oryzae in response to temperature stress. Both low and high temperatures inhibited mycelial growth and conidial formation of A. oryzae. Transcriptomic analysis revealed that most differentially expressed genes (DEGs) were involved in sugar metabolism and lipid metabolism under temperature stress. Specifically, the DEGs in trehalose synthesis and starch metabolism were upregulated under low-temperature stress, while high temperatures inhibited the expression of genes involved in fructose, galactose, and glucose metabolism. Quantitative analysis of intracellular sugar further revealed that low temperature increased trehalose accumulation, while high temperature increased the contents of intracellular trehalose, galactose, and glucose, consistent with transcriptome analysis. In addition, most DEGs involved in lipid metabolism were significantly downregulated under low-temperature stress. Furthermore, the metabolomic analysis revealed that linoleic acid, triacylglycerol, phosphatidylethanolamine, and phosphoribosyl were significantly decreased in response to low-temperature stress. These results increase our understanding of the coping mechanisms of A. oryzae in response to temperature stress, which lays the foundation for future improvements through genetic modification to enhance A. oryzae against extreme temperature stress.

Ability of Two Strains of Lactic Acid Bacteria To Inhibit Listeria monocytogenes by Spot Inoculation and in an Environmental Microbiome Context

We evaluated the ability of two strains of lactic acid bacteria (LAB) to inhibit L. monocytogenes using spot inoculation and environmental microbiome attached-biomass assays. LAB strains (PS01155 and PS01156) were tested for antilisterial activity toward 22 phylogenetically distinct L. monocytogenes strains isolated from three fruit packing environments (F1, F2, and F3). LAB strains were tested by spot inoculation onto L. monocytogenes lawns (10⁸ and 10⁷ CFU/mL) and incubated at 15, 20, 25, or 30°C for 3 days. The same LAB strains were also cocultured at 15°C for 3, 5, and 15 days in polypropylene conical tubes with L. monocytogenes and environmental microbiome suspensions collected from F1, F2, and F3. In the spot inoculation assay, PS01156 was significantly more inhibitory toward less concentrated L. monocytogenes lawns than more concentrated lawns at all the tested temperatures, while PS01155 was significantly more inhibitory toward less concentrated lawns only at 15 and 25°C. Furthermore, inhibition of L. monocytogenes by PS01156 was significantly greater at 15°C than higher temperatures, whereas the temperature did not have an effect on the inhibitory activity of PS01155. In the assay using attached environmental microbiome biomass, L. monocytogenes concentration was significantly reduced by PS01156, but not PS01155, when cocultured with microbiomes from F1 and F3 and incubated for 3 days at 15°C. Attached biomass microbiota composition was significantly affected by incubation time but not by LAB strain. This study demonstrates that LAB strains that may exhibit inhibitory properties toward L. monocytogenes in a spot inoculation assay may not maintain antilisterial activity within a complex microbiome.

IMPORTANCEListeria monocytogenes has previously been associated with outbreaks of foodborne illness linked to consumption of fresh produce. In addition to conventional cleaning and sanitizing, lactic acid bacteria (LAB) have been studied for biocontrol of L. monocytogenes in food processing environments that are challenging to clean and sanitize. We evaluated whether two specific LAB strains, PS01155 and PS01156, can inhibit the growth of L. monocytogenes strains in a spot inoculation and in an attached-biomass assay, in which they were cocultured with environmental microbiomes collected from tree fruit packing facilities. LAB strains PS01155 and PS01156 inhibited L. monocytogenes in a spot inoculation assay, but the antilisterial activity was lower or not detected when they were grown with environmental microbiota. These results highlight the importance of conducting biocontrol challenge tests in the context of the complex environmental microbiomes present in food processing facilities to assess their potential for application in the food industry.

Functional Genomics Identified Novel Genes Involved in Growth at Low Temperatures in Listeria monocytogenes

Listeria monocytogenes (Lm) is a foodborne pathogen that can cause severe human illness. Standard control measures for restricting bacterial growth, such as refrigeration, are often inadequate as Lm grows well at low temperatures. To identify genes involved in growth at low temperatures, a powerful functional genomics method Tn-seq was performed in this study. This genome-wide screening comprehensively identified the known and novel genetic determinants involved in low-temperature growth. A novel gene lmo1366, encoding rRNA methyltransferase, was identified to play an essential role in Lm growth at 16°C. In contrast, the inactivation of lmo2301, a gene encoding the terminase of phage A118, significantly enhanced the growth of Lm at 16°C. The deletion of lmo1366 or lmo2301 resulted in cell morphology alterations and impaired the growth rate in milk and other conditions at low temperatures. Transcriptomic analysis revealed that the Δlmo1366 and Δlmo2301 mutants exhibited altered transcriptional patterns compared to the wild-type strain at 16°C with significant differences in genes involved in ribosome structural stability and function, and membrane biogenesis, respectively. This work uncovered novel genetic determinants involved in Lm growth at 16°C, which could lead to a better understanding of how bacteria survive and multiply at low temperatures. Furthermore, these findings could potentially contribute to developing novel antibacterial strategies under low-temperature conditions.

IMPORTANCEListeria monocytogenes is a Gram-positive pathogen that contributes to foodborne outbreaks due to its ability to survive at low temperatures. However, the genetic determinants of Lm involved in growth at low temperatures have not been fully defined. Here, the genetic determinants involved in the low-temperature growth of Lm were comprehensively identified on a genome-wide scale by Tn-seq. The gene lmo1366, encoding rRNA methyltransferase, was identified essential for growth under low-temperature conditions. On the other hand, the gene lmo2301, encoding terminase of phage A118, plays a negative role in bacterial growth at low temperatures. The transcriptomic analysis revealed the potential mechanisms. These findings lead to a better understanding of how bacteria survive and multiply at low temperatures and could provide unique targets for novel antibacterial strategies under low-temperature conditions.

Listeria monocytogenes - How This Pathogen Survives in Food-Production Environments?

The foodborne pathogen Listeria monocytogenes is the causative agent of human listeriosis, a severe disease, especially dangerous for the elderly, pregnant women, and newborns. Although this infection is comparatively rare, it is often associated with a significant mortality rate of 20-30% worldwide. Therefore, this microorganism has an important impact on food safety. L. monocytogenes can adapt, survive and even grow over a wide range of food production environmental stress conditions such as temperatures, low and high pH, high salt concentration, ultraviolet lights, presence of biocides and heavy metals. Furthermore, this bacterium is also able to form biofilm structures on a variety of surfaces in food production environments which makes it difficult to remove and allows it to persist for a long time. This increases the risk of contamination of food production facilities and finally foods. The present review focuses on the key issues related to the molecular mechanisms of the pathogen survival and adaptation to adverse environmental conditions. Knowledge and understanding of the L. monocytogenes adaptation approaches to environmental stress factors will have a significant influence on the development of new, efficient, and cost-effective methods of the pathogen control in the food industry, which is critical to ensure food production safety.

Plasma proteomics reveals crosstalk between lipid metabolism and immunity in dairy cows receiving essential fatty acids and conjugated linoleic acid

Essential fatty acids (EFA) and conjugated linoleic acids (CLA) are unsaturated fatty acids with immune-modulatory effects, yet their synergistic effect is poorly understood in dairy cows. This study aimed at identifying differentially abundant proteins (DAP) and their associated pathways in dairy cows supplied with a combination of EFA and CLA during the transition from antepartum (AP) to early postpartum (PP). Sixteen Holstein cows were abomasally infused with coconut oil as a control (CTRL) or a mixture of EFA (linseed + safflower oil) and CLA (Lutalin, BASF) (EFA + CLA) from − 63 to + 63 days relative to parturition. Label-free quantitative proteomics was performed on plasma samples collected at days − 21, + 1, + 28, and + 63. During the transition time, DAP, consisting of a cluster of apolipoproteins (APO), including APOE, APOH, and APOB, along with a cluster of immune-related proteins, were related to complement and coagulation cascades, inflammatory response, and cholesterol metabolism. In response to EFA + CLA, specific APO comprising APOC3, APOA1, APOA4, and APOC4 were increased in a time-dependent manner; they were linked to triglyceride-enriched lipoprotein metabolisms and immune function. Altogether, these results provide new insights into metabolic and immune adaptation and crosstalk between them in transition dairy cows divergent in EFA + CLA status.

Evaluation of the Persistence and Characterization of Listeria monocytogenes in Foodservice Operations

Listeria monocytogenes is a major foodborne pathogen that can contaminate food products and colonize food-producing facilities. Foodservice operations (FSOp) are frequently responsible for foodborne outbreaks due to food safety practices failures. We investigated the presence of and characterized L. monocytogenes from two FSOp (cafeterias) distributing ready-to-eat meals and verified FSOp’s compliance with good manufacturing practices (GMP). Two facilities (FSOp-A and FSOp-B) were visited three times each over 5 months. We sampled foods, ingredients, and surfaces for microbiological analysis, and L. monocytogenes isolates were characterized by phylogenetic analyses and phenotypic characteristics. GMP audits were performed in the first and third visits. A ready-to-eat salad (FSOp-A) and a frozen ingredient (FSOp-B) were contaminated with L. monocytogenes, which was also detected on Zone 3 surfaces (floor, drains, and a boot cover). The phylogenetic analysis demonstrated that FSOp-B had persistent L. monocytogenes strains, but environmental isolates were not closely related to food or ingredient isolates. GMP audits showed that both operations worked under “fair” conditions, and “facilities and equipment” was the section with the least compliances. The presence of L. monocytogenes in the environment and GMP failures could promote food contamination with this pathogen, presenting a risk to consumers.

Liver proteome profiling in dairy cows during the transition from gestation to lactation: Effects of supplementation with essential fatty acids and conjugated linoleic acids as explored by PLS-DA

This study aimed at investigating the synergistic effects of essential fatty acids (EFA) and conjugated linoleic acids (CLA) on the liver proteome profile of dairy cows during the transition to lactation. 16 Holstein cows were infused from 9 wk. antepartum to 9 wk. postpartum into the abomasum with either coconut oil (CTRL) or a mixture of EFA (linseed + safflower oil) and CLA (EFA + CLA). Label-free quantitative proteomics was performed in liver tissue biopsied at days -21, +1, +28, and + 63 relative to calving. Differentially abundant proteins (DAP) between treatment groups were identified at the intersection between a multivariate and a univariate analysis. In total, 1680 proteins were identified at each time point, of which between groups DAP were assigned to the metabolism of xenobiotics by cytochrome P450, drug metabolism - cytochrome P450, steroid hormone biosynthesis, glycolysis/gluconeogenesis, and glutathione metabolism. Cytochrome P450, as a central hub, enriched with specific CYP enzymes comprising: CYP51A1 (d - 21), CYP1A1 & CYP4F2 (d + 28), and CYP4V2 (d + 63). Collectively, supplementation of EFA + CLA in transition cows impacted hepatic lipid metabolism and enriched several common biological pathways at all time points that were mainly related to ω-oxidation of fatty acids through the Cytochrome p450 pathway. SIGNIFICANCE: In three aspects this manuscript is notable. First, this is among the first longitudinal proteomics studies in nutrition of dairy cows. The selected time points are critical periods around parturition with profound endocrine and metabolic adaptations. Second, our findings provided novel information on key drivers of biologically relevant pathways suggested according to previously reported performance, zootechnical, and metabolism data (already published elsewhere). Third, our results revealed the role of cytochrome P450 that is hardly investigated, and of ω-oxidation pathways in the metabolism of fatty acids with the involvement of specific enzymes.

Thermogenetics: Applications come of age

Temperature is a ubiquitous physical cue that is non-invasive, penetrative and easy to apply. In the growing field of thermogenetics, through beneficial repurposing of natural thermosensing mechanisms, synthetic biology is bringing new opportunities to design and build robust temperature-sensitive (TS) sensors which forms a thermogenetic toolbox of well characterised biological parts. Recent advancements in technological platforms available have expedited the discovery of novel or de novo thermosensors which are increasingly deployed in many practical temperature-dependent biomedical, industrial and biosafety applications. In all, the review aims to convey both the exhilarating recent technological developments underlying the advancement of thermosensors and the exciting opportunities the nascent thermogenetic field holds for biomedical and biotechnology applications.

Rhizobacteria Impact Colonization of Listeria monocytogenes on Arabidopsis thaliana Roots

In spite of its relevance as a foodborne pathogen, we have limited knowledge about Listeria monocytogenes in the environment. L. monocytogenes outbreaks have been linked to fruits and vegetables; thus, a better understanding of the factors influencing its ability to colonize plants is important. We tested how environmental factors and other soil- and plant-associated bacteria influenced L. monocytogenes' ability to colonize plant roots using Arabidopsis thaliana seedlings in a hydroponic growth system. We determined that the successful root colonization of L. monocytogenes 10403S was modestly but significantly enhanced by the bacterium being pregrown at higher temperatures, and this effect was independent of the biofilm and virulence regulator PrfA. We tested 14 rhizosphere-derived bacteria for their impact on L. monocytogenes 10403S, identifying one that enhanced and 10 that inhibited the association of 10403S with plant roots. We also characterized the outcomes of these interactions under both coinoculation and invasion conditions. We characterized the physical requirements of five of these rhizobacteria to impact the association of L. monocytogenes 10403S with roots, visualizing one of these interactions by microscopy. Furthermore, we determined that two rhizobacteria (one an inhibitor, the other an enhancer of 10403S root association) were able to similarly impact 10 different L. monocytogenes strains, indicating that the effects of these rhizobacteria on L. monocytogenes are not strain specific. Taken together, our results advance our understanding of the parameters that affect L. monocytogenes plant root colonization, knowledge that may enable us to deter its association with and, thus, downstream contamination of, food crops. IMPORTANCE Listeria monocytogenes is ubiquitous in the environment, being found in or on soil, water, plants, and wildlife. However, little is known about the requirements for L. monocytogenes' existence in these settings. Recent L. monocytogenes outbreaks have been associated with contaminated produce; thus, we used a plant colonization model to investigate factors that alter L. monocytogenes' ability to colonize plant roots. We show that L. monocytogenes colonization of roots was enhanced when grown at higher temperatures prior to inoculation but did not require a known regulator of virulence and biofilm formation. Additionally, we identified several rhizobacteria that altered the ability of 11 different strains of L. monocytogenes to colonize plant roots. Understanding the factors that impact L. monocytogenes physiology and growth will be crucial for finding mechanisms (whether chemical or microbial) that enable its removal from plant surfaces to reduce L. monocytogenes contamination of produce and eliminate foodborne illness.

Three faces of biofilms: a microbial lifestyle, a nascent multicellular organism, and an incubator for diversity

Biofilms are organised heterogeneous assemblages of microbial cells that are encased within a self-produced matrix. Current estimates suggest that up to 80% of bacterial and archaeal cells reside in biofilms. Since biofilms are the main mode of microbial life, understanding their biology and functions is critical, especially as controlling biofilm growth is essential in industrial, infrastructure and medical contexts. Here we discuss biofilms both as collections of individual cells, and as multicellular biological individuals, and introduce the concept of biofilms as unique incubators of diversity for the microbial world.

Time-Resolved Proteome Analysis of Listeria monocytogenes during Infection Reveals the Role of the AAA+ Chaperone ClpC for Host Cell Adaptation

The cellular proteome comprises all proteins expressed at a given time and defines an organism's phenotype under specific growth conditions. The proteome is shaped and remodeled by both protein synthesis and protein degradation. Here, we developed a new method which combines metabolic and chemical isobaric peptide labeling to simultaneously determine the time-resolved protein decay and de novo synthesis in an intracellular human pathogen. We showcase this method by investigating the Listeria monocytogenes proteome in the presence and absence of the AAA+ chaperone protein ClpC. ClpC associates with the peptidase ClpP to form an ATP-dependent protease complex and has been shown to play a role in virulence development in L. monocytogenes. However, the mechanism by which ClpC is involved in the survival and proliferation of intracellular L. monocytogenes remains elusive. Employing this new method, we observed extensive proteome remodeling in L. monocytogenes upon interaction with the host, supporting the hypothesis that ClpC-dependent protein degradation is required to initiate bacterial adaptation mechanisms. We identified more than 100 putative ClpC target proteins through their stabilization in a clpC deletion strain. Beyond the identification of direct targets, we also observed indirect effects of the clpC deletion on the protein abundance in diverse cellular and metabolic pathways, such as iron acquisition and flagellar assembly. Overall, our data highlight the crucial role of ClpC for L. monocytogenes adaptation to the host environment through proteome remodeling. IMPORTANCE Survival and proliferation of pathogenic bacteria inside the host depend on their ability to adapt to the changing environment. Profiling the underlying changes on the bacterial proteome level during the infection process is important to gain a better understanding of the pathogenesis and the host-dependent adaptation processes. The cellular protein abundance is governed by the interplay between protein synthesis and decay. The direct readout of these events during infection can be accomplished using pulsed stable-isotope labeling by amino acids in cell culture (SILAC). Combining this approach with tandem-mass-tag (TMT) labeling enabled multiplexed and time-resolved bacterial proteome quantification during infection. Here, we applied this integrated approach to investigate protein turnover during the temporal progression of adaptation of the human pathogen L. monocytogenes to its host on a system-wide scale. Our experimental approach can easily be transferred to probe the proteome remodeling in other bacteria under a variety of perturbations.

Proteomic Characterization of Antibiotic Resistance in Listeria and Production of Antimicrobial and Virulence Factors

Some Listeria species are important human and animal pathogens that can be found in contaminated food and produce a variety of virulence factors involved in their pathogenicity. Listeria strains exhibiting multidrug resistance are known to be progressively increasing and that is why continuous monitoring is needed. Effective therapy against pathogenic Listeria requires identification of the bacterial strain involved, as well as determining its virulence factors, such as antibiotic resistance and sensitivity. The present study describes the use of liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) to do a global shotgun proteomics characterization for pathogenic Listeria species. This method allowed the identification of a total of 2990 non-redundant peptides, representing 2727 proteins. Furthermore, 395 of the peptides correspond to proteins that play a direct role in Listeria pathogenicity; they were identified as virulence factors, toxins and anti-toxins, or associated with either antibiotics (involved in antibiotic-related compounds production or resistance) or resistance to toxic substances. The proteomic repository obtained here can be the base for further research into pathogenic Listeria species and facilitate the development of novel therapeutics for these pathogens.

The role of the Listeria monocytogenes surfactome in biofilm formation

Listeria monocytogenes is a highly pathogenic foodborne bacterium that is ubiquitous in the natural environment and capable of forming persistent biofilms in food processing environments. This species has a rich repertoire of surface structures that enable it to survive, adapt and persist in various environments and promote biofilm formation. We review current understanding and advances on how L. monocytogenes organizes its surface for biofilm formation on surfaces associated with food processing settings, because they may be an important target for development of novel antibiofilm compounds. A synthesis of the current knowledge on the role of Listeria surfactome, comprising peptidoglycan, teichoic acids and cell wall proteins, during biofilm formation on abiotic surfaces is provided. We consider indications gained from genome-wide studies and discuss surfactome structures with established mechanistic aspects in biofilm formation. Additionally, we look at the analogies to the species L. innocua, which is closely related to L. monocytogenes and often used as its model (surrogate) organism.

Proteomic Analysis of Listeria monocytogenes FBUNT During Biofilm Formation at 10°C in Response to Lactocin AL705

Listeria monocytogenes is one of the major food-related pathogens and is able to survive and multiply under different stress conditions. Its persistence in industrial premises and foods is partially due to its ability to form biofilm. Thus, as a natural strategy to overcome L. monocytogenes biofilm formation, the treatment with lactocin AL705 using a sublethal dose (20AU/ml) was explored. The effect of the presence of the bacteriocin on the biofilm formation at 10°C of L. monocytogenes FBUNT was evaluated for its proteome and compared to the proteomes of planktonic and sessile cells grown at 10°C in the absence of lactocin. Compared to planktonic cells, adaptation of sessile cells during cold stress involved protein abundance shifts associated with ribosomes function and biogenesis, cell membrane functionality, carbohydrate and amino acid metabolism, and transport. When sessile cells were treated with lactocin AL705, proteins’ up-regulation were mostly related to carbohydrate metabolism and nutrient transport in an attempt to compensate for impaired energy generation caused by bacteriocin interacting with the cytoplasmic membrane. Notably, transport systems such as β-glucosidase IIABC (lmo0027), cellobiose (lmo2763), and trehalose (lmo1255) specific PTS proteins were highly overexpressed. In addition, mannose (lmo0098), a specific PTS protein indicating the adaptive response of sessile cells to the bacteriocin, was downregulated as this PTS system acts as a class IIa bacteriocin receptor. A sublethal dose of lactocin AL705 was able to reduce the biofilm formation in L. monocytogenes FBUNT and this bacteriocin induced adaptation mechanisms in treated sessile cells. These results constitute valuable data related to specific proteins targeting the control of L. monocytogenes biofilm upon bacteriocin treatment.

Decline of Listeria monocytogenes on fresh apples during long-term, low-temperature simulated international sea-freight transport

Listeria monocytogenes has caused outbreaks of foodborne illness from apples in the USA, and is also a major issue for regulatory compliance worldwide. Due to apple's significance as an important export product from New Zealand, we aimed to determine the effect of long-term, low-temperature sea-freight from New Zealand to the USA (July) and Europe (March-April), two key New Zealand markets, on the survival and/or growth of L. monocytogenes on fresh apples. Temperature and humidity values were recorded during a shipment to each market (USA and Europe), then the observed variations around the 0.5 °C target temperature were simulated in laboratory trials using open ('Scired') and closed ('Royal Gala' for the USA and 'Cripps Pink' for Europe) calyx cultivars of apples inoculated with a cocktail of 10⁷-10⁸ cells of seven strains of L. monocytogenes. Samples were analysed for L. monocytogenes quantification at various intervals during the simulation and on each occasion, an extra set was analysed after a subsequent 8 days at 20 °C. When both the sea-freight simulations concluded, L. monocytogenes showed 5 log reductions on the equatorial surface of skin of apples, but only about 2.5 log reduction for USA and about 3.3 log reduction for Europe in the calyx. Cultivar type had no significant effect on the survival of L. monocytogenes for both sea-freight simulations, either in the calyx or on the skin (P > 0.05). Most of the reduction in the culturable cells on the skin occurred during the initial 2 weeks of the long-term storage simulations. There was also no significant difference in the reduction of L. monocytogenes at 0.5 or 20 °C. No correlation was observed between firmness or total soluble solids and survival of L. monocytogenes. Because the inoculated bacterial log reduction was lower in the calyx than on the skin, it is speculated that the risk of causing illness is higher if contaminated apple cores are eaten. The result suggested that the international sea-freight transportation does not result in the growth of L. monocytogenes irrespective of time and temperature. The results of this study provide useful insights into the survival of L. monocytogenes on different apple cultivars that can be used to develop effective risk mitigation strategies for fresh apples during long-term, low-temperature international sea-freight transportation.

Development of antiviral and bacteriostatic chitosan-based food packaging material with grape seed extract for murine norovirus, Escherichia coli and Listeria innocua control

Edible coatings and films based on chitosan, and containing grape seed extract (GSE), were developed and their activities tested against murine norovirus (MNV-1), Listeria innocua and Escherichia coli K12. Grape seed extract concentrations of 1%, 1.5%, and 2.5% dissolved in deionized water resulted in MNV-1 plaque reductions (p < .05) of 1.75, 2.60, and 3.58 log PFU/ml, respectively after 3 hr. Two percent (w/w) chitosan solutions incorporated with 2.5% and 5% GSE also significantly (p < .05) reduced MNV-1 titers by 2.68 and 4.00 log PFU/ml, respectively after 3 hr. Additionally, incorporation of the GSE into the chitosan films also showed antimicrobial efficacy against MNV-1, L. innocua, and E. coli K12. Chitosan films containing 5%, 10%, and 15% GSE caused MNV-1 reductions of 0.92, 1.89, and 2.27 log PFU/ml, respectively, after 4 hr of incubation. Also, after 24 hr, the 5% and 10% GSE films reduced MNV-1 titers by 1.90 and 3.26 log PFU/ml, respectively, while the 15% GSE film reduced MNV-1 to undetectable levels. For E. coli K12, there were reductions of 2.28, 5.18, and 7.14 log CFU/ml after 24 hr exposure by the 5%, 10%, and 15% GSE films, respectively. Also, L. innocua counts were reduced by 3.06, 6.15, and 6.91 log CFU/ml by the 5%, 10%, and 15% GSE films, respectively. This study demonstrated that GSE in edible films and coatings is effective against the organisms tested, and this shows that they are effective against foodborne microbes of public health concerns.

Biofilm formation and extracellular microvesicles-The way of foodborne pathogens toward resistance

Almost all known foodborne pathogens are able to form biofilms as one of the strategies for survival under harsh living conditions, to ward off the inhibition and the disinfection during food production, transport and storage, as well as during cleaning and sanitation of corresponding facilities. Biofilms are communities where microbial cells live under constant intracellular interaction and communication. Members of the biofilm community are embedded into extracellular matrix that contains polysaccharides, DNA, lipids, proteins, and small molecules that protect microorganisms and enable their intercellular communication under stress conditions. Membrane vesicles (MVs) are produced by both Gram positive and Gram negative bacteria. These lipid membrane-enveloped nanoparticles play an important role in biofilm genesis and in communication between different biofilm members. Furthermore, MVs are involved in other important steps of bacterial life like cell wall modeling, cellular division, and intercellular communication. They also carry toxins and virulence factors, as well as nucleic acids and different metabolites, and play a key role in host infections. After entering host cells, MVs can start many pathologic processes and cause serious harm and cell death. Prevention and inhibition of both biofilm formation and shedding of MVs by foodborne pathogens has a very important role in food production, storage, and food safety in general. Better knowledge of biofilm formation and maintaining, as well as the role of microbial vesicles in this process and in the process of host cells' infection is essential for food safety and prevention of both food spoilage and host infection.

Search of Potential Vaccine Candidates against Trueperella pyogenes Infections through Proteomic and Bioinformatic Analysis

Trueperella pyogenes is an opportunistic pathogen, responsible for important infections in pigs and significant economic losses in swine production. To date, there are no available commercial vaccines to control diseases caused by this bacterium. In this work, we performed a comparative proteomic analysis of 15 T. pyogenes clinical isolates, by “shaving” live cells, followed by LC-MS/MS, aiming at the identification of the whole set of surface proteins (i.e., the “pan-surfome”) as a source of antigens to be tested in further studies as putative vaccine candidates, or used in diagnostic tools. A total of 140 surface proteins were detected, comprising 25 cell wall proteins, 10 secreted proteins, 23 lipoproteins and 82 membrane proteins. After describing the “pan-surfome”, the identified proteins were ranked in three different groups based on the following criteria: to be (i) surface-exposed, (ii) highly conserved and (iii) widely distributed among different isolates. Two cell wall proteins, three lipoproteins, four secreted and seven membrane proteins were identified in more than 70% of the studied strains, were highly expressed and highly conserved. These proteins are potential candidates, alone or in combination, to obtain effective vaccines against T. pyogenes or to be used in the diagnosis of this pathogen.

Ascorbic Acid Changes Growth of Food-Borne Pathogens in the Early Stage of Biofilm Formation

Since bacterial biofilm may contribute to the secondary contamination of food during the manufacturing/processing stage there is a need for new methods allowing its effective eradication. Application of food additives such as vitamin C already used in food industry as antioxidant food industry antioxidants may be a promising solution. The aim of this research was evaluation of the impact of vitamin C (ascorbic acid), in a range of concentrations 2.50 µg mL-1-25.0 mg mL-1, on biofilms of Staphylococcus aureus, Escherichia coli, and Listeria monocytogenes strains isolated from food. The efficacy of ascorbic acid was assessed based on the reduction of optical density (λ = 595 nm). The greatest elimination of the biofilm was achieved at the concentration of vitamin C of 25.0 mg mL-1. The effect of the vitamin C on biofilm, however, was strain dependent. The concentration of 25.0 mg mL-1 reduced 93.4%, 74.9%, and 40.5% of E. coli, L. monocytogenes, and S. aureus number, respectively. For E. coli and S. aureus lower concentrations were ineffective. In turn, for L. monocytogenes the biofilm inhibition was observed even at the concentration of 0.25 mg mL-1. The addition of vitamin C may be helpful in the elimination of bacterial biofilms. Nonetheless, some concentrations can induce growth of the pathogens, posing risk for the consumers' health.

The Uptake and Release of Amino Acids by Staphylococcus aureus at Mid-Exponential and Stationary Phases and Their Corresponding Responses to Changes in Temperature, pH and Osmolality

Staphylococcus aureus is an important pathogen that is associated with nosocomial infections, as well as food poisoning. This bacterium is resistant to antimicrobial agents and can survive in a wide range of environmental conditions. The aim of this study was to measure the uptake and release of amino acids by S. aureus at mid-exponential and stationary phases of growth following exposure to a combination of conditions including variations in temperature, pH and NaCl. Bacterial cells were grown up to mid-exponential and stationary phases in tryptic soy broth (TSB), where the supernatants were collected for analyses of amino acids to determine the uptake and release characteristics. The uptake/release of amino acids was estimated by subtracting the initial levels of the free amino acids in the media from those measured at mid-exponential and stationary phases of growth. When cells were grown at ideal conditions, the analyses revealed that significant uptake of amino acids had occurred by stationary phase compared with the mid-exponential phase. A substantial release of valine and tyrosine into the external media was observed by cells at stationary phase. At both phases, the uptake and release patterns were significantly different between cells grown under ideal control conditions, when compared with those grown under various combinations of sub-optimal environmental conditions. The analyses of the supernatants harvested from controls and treatment groups at exponential phase indicated that the total uptake of amino acids was reduced approximately five times by cells grown with addition of 2.5% NaCl or with pH6 at 35°C, and 2-fold by cells grown at pH8 at 35°C. However, the final quantities of amino acids taken up by cells grown to stationary phase did not significantly alter between control and treated samples. Valine was found to be the most abundant amino acid that was significantly released into the media at stationary phase by both control and treated samples. It was evident that diverse environmental conditions resulted in differential patterns of amino acid uptake and release during adaptation to designated conditions.

Disinfectant Susceptibility of Biofilm Formed by Listeria monocytogenes under Selected Environmental Conditions

Listeria monocytogenes is a one of the most important food-borne pathogens. Its ability to form biofilm contributes to increased resistance to disinfectants and inefficient disinfection, posing a serious threat for the food industry, and in the end the consumer. The aim of this study was the comparison of the biofilm formation ability of L. monocytogenes strains on stainless steel, under different environmental conditions (temperature, pH, NaCl concentration, nutrients availability), and the assessment of biofilm susceptibility to disinfectants. The bactericidal activity of four disinfectants in two concentrations (100% and 50% of working solution) against biofilm was conducted on four clinical strains, four strains isolated from food and one reference strain ATCC 19111. It was found that biofilm susceptibility to disinfectants was influenced by environmental conditions. Biofilm susceptibility correlated with the decrease of temperature, pH, nutrients availability and salinity of the environment. The least sensitive to disinfectants was biofilm produced at pH = 4 (the bacterial number ranged from 0.25 log CFU × cm-2 to 1.72 log CFU × cm-2) whereas the most sensitive was biofilm produced at pH = 9 (5.16 log CFU × cm-2 to 7.84 log CFU × cm-2). Quatosept was the most effective disinfectant, regardless of the conditions. In conclusion, biofilm susceptibility to disinfectants is strain-dependent and is affected by environmental conditions.