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Conventional culture-based techniques are largely inadequate in elucidating the microbiota contained in an environment, due to low recovery within a complex bacterial community. This limitation has been mitigated by the use of next-generation sequencing (NGS)-based approaches thereby facilitating the identification and classification of both culturable and uncultivable microorganisms. Amplicon targeted NGS methods, such as 16S ribosomal RNA (16S rRNA) and shotgun metagenomics, are increasingly being applied in various settings such as in food production environments to decipher the microbial consortium therein. Even though multiple food matrices/food production environments have been studied, the low-moisture environment associated with bakery food production remains to be investigated. To address this knowledge gap, in this study, we investigated the microbiome associated with two bakery production sites (designated as A and B) located in Ireland using 16S rRNA-amplicon-based sequencing. Amplicons corresponding to a hypervariable region contained within the 16S rRNA gene were amplified from DNA samples purified from environmental swabs and ingredients collected at both sites at various stages (preparation, production, postproduction, and storage) across the bakery production chain, over three seasons (winter, spring, and summer). These amplicons were sequenced, and data were analyzed using the mothur pipeline and visualized using MicrobiomeAnalyst and a series of R packages. The top seven bacterial phyla identified at both sites were composed of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Patescibacteria, and Verrucomicrobia. In addition, the phyla Tenericutes (Mycoplasmatota) and Acidobacteria were observed only in samples taken at site B. Different bacterial compositions were identified at each stage of production. These same bacteria were also found to be present in the final processed food suggesting the influence of the environment on the food matrix. This study is the first demonstration of the utility of 16S rRNA amplicon-based sequencing to describe the microbiota associated with bakery processing environments.

Antimicrobial resistance is a serious threat to public health that dramatically undermines our ability to treat bacterial infections. Microorganisms exhibit resistance to different drug classes by acquiring resistance determinants through multiple mechanisms including horizontal gene transfer. The presence of drug resistance genotypes is mostly associated with corresponding phenotypic resistance against the particular antibiotic. However, bacterial communities harbouring silent antimicrobial resistance genes—genes whose presence is not associated with a corresponding resistant phenotype do exist. Under suitable conditions, the expression pattern of such genes often revert and regain resistance and could potentially lead to therapeutic failure. We often miss the presence of silent genes, since the current experimental paradigms are focused on resistant strains. Therefore, the knowledge on the prevalence, importance and mechanism of silent antibiotic resistance genes in bacterial pathogens are very limited. Silent genes, therefore, provide an additional level of complexity in the war against drug-resistant bacteria, reminding us that not only phenotypically resistant strains but also susceptible strains should be carefully investigated. In this review, we discuss the presence of silent antimicrobial resistance genes in bacteria, their relevance and their importance in public health.

Microbial safety is critically important for powdered infant formula (PIF) fed to neonates, with under-developed immune systems. The quality and safety of food products are dictated by those microorganisms found in both raw materials and the built production environment. In this study, a 2-year monitoring program of a production environment was carried out in two PIF factories located in the Republic of Ireland, and the environmental microbiome in different care areas of these sites was studied by using a 16S ribosomal RNA (rRNA)-based sequencing technique. Results highlighted a core microbiome associated with the PIF factory environment containing 24 bacterial genera representing five phyla, with

Cronobacter sakazakii is a typical example of a xerotolerant bacterium. It is epidemiologically linked to low-moisture foods like powdered infant formula (PIF) and is associated with high fatality rates among neonates. We characterized the xerotolerance in a clinically isolated strain, Cronobacter sakazakii ATCC™29544(T), and compared the desiccation tolerance with that of an environmental strain, C. sakazakii SP291, whose desiccation tolerance was previously characterized. We found that, although the clinical strain was desiccation-tolerant, the level of tolerance was compromised when compared with that of the environmental strain. Transcriptome sequencing (RNA-seq)-based deep transcriptomic characterization identified a unique transcriptional profile in the clinical strain compared with what was already known for the environmental strain. As RNA-seq was also carried out under different TSB growth conditions, genes that were expressed specifically under desiccated conditions were identified and denoted as desiccation responsive genes (DRGs). Interestingly, these DRGs included transcriptomic factors like fnr, ramA, and genes associated with inositol metabolism, a phenotype as yet unreported in C. sakazakii. Further, the clinical strain did not express the proP gene, which was previously reported to be very important for desiccation survival and persistence. Interestingly, analysis of the plasmid genes showed that the iron metabolism in desiccated C. sakazakii ATCC™29544(T) cells specifically involved the siderophore cronobactin, encoded by the iucABCD genes. Confirmatory studies using quantitative reverse transcription-PCR (qRT-PCR) determined that, though the secondary desiccation response genes were upregulated in C. sakazakii ATCC™29544(T), the level of upregulation was lower than that in C. sakazakii SP291. All these factors may collectively contribute to the compromised desiccation tolerance in the clinical strain. IMPORTANCE Cronobacter sakazakii has led to outbreaks in the past, particularly associated with foods that are low in moisture content. This species has adapted to survive in low water conditions and can survive in such environments for long periods. These characteristics have enabled the pathogen to contaminate powder infant formula, a food matrix with which the pathogen has been epidemiologically associated. Even though clinically adapted strains can also be isolated, there is no information on how the clinical strains adapt to low moisture environments. Our research assessed the adaptation of a clinically isolated strain to low moisture survival on sterile stainless steel coupons and compared the survival with that of a highly desiccation-tolerant environmental strain. We found that, even though the clinical strain is desiccation-tolerant, the rate of tolerance was compromised compared with that of the environmental strain. A deeper investigation using RNA-seq identified that the clinical strain used pathways different from that of the environmental strain to adapt to low-moisture conditions. This shows that the adaptation to desiccation conditions, at least for C. sakazakii, is strain-specific and that different strains have used different evolutionary strategies for adaptation.

In recent years, the concept of bacteria-mediated cancer therapy has gained significant attention as an alternative to conventional therapy. The focus has been on non-typhoidal Salmonella (NTS), particularly S. Typhimurium, for its anti-cancer properties, however, other NTS serovars such as Salmonella Oslo, which are associated with foodborne illnesses could potentially be effective anti-cancer agents. Here, we report the draft genome sequence of Salmonella Oslo isolated from seafood and its laboratory generated auxotrophic mutant.

Microorganisms express various transmembrane complexes collectively known as efflux pumps that influence their survival under stressful growth conditions. Although efflux pumps are important in resistance to antibiotics, disinfectants, and preservatives, little information about their presence and roles in Cronobacter spp. is available. To better understand the phylogeny, prevalence, and distribution of efflux pumps among strains of Cronobacter spp., whole genome sequencing (WGS) and pan-genomic DNA microarray (MA) analysis were carried out. Targeted MA analysis with 156 probe set alleles representing efflux pump genetic loci showed that all seven Cronobacter species possessed species-specific efflux pump orthologues. Distribution of the efflux pump genes and sequence variations were studied using WGS datasets. Phylogenetic and molecular clock analyses showed that the acquisition of these efflux pump genes possibly occurred at separate evolutionary events, which most likely correlated with the evolution of sequence type (ST) lineages. The acquisition of efflux pump genes either occurred as independent evolutionary events through horizontal gene transfer, or in certain situations, such as that for ST83 and ST4 strains, they could have been acquired through a robust microevolutionary selective process, some of which may have provided functional advantages. Efflux pump activity is very important in osmotic adaptation, survival, and persistence of Cronobacter species and are involved in several important physiological processes including protein, heavy metal, and sugar efflux. Understanding the mechanisms of Cronobacter adaptation in a wide range of environments, could eventually lead to development of methods to control the contamination of foods by these organisms.

Bioactive peptides derived from milk proteins are widely known to possess antibacterial activities. Even though the antibacterial effects of milk-derived peptides are widely characterized, not much focus is given to their antifungal characterization. Therefore, in this study, we investigated the antifungal properties of camel and cow whey and casein hydrolysates against various species of pathogenic Candida. The hydrolysates were produced using 2 enzymes (alcalase and protease) at differing hydrolysis durations (2, 4, and 6 h) and tested for their antifungal properties. The results showed that intact cow whey and casein proteins did not display any anti-Candida albicans properties, whereas the alcalase-derived 2 h camel casein hydrolysate (CA-C-A2) displayed a higher percentage of inhibition against Candida albicans (93.69 ± 0.26%) followed by the cow casein hydrolysate generated by protease-6 h (Co-C-P6; 81.66 ± 0.99%), which were significantly higher than that of fluconazole, a conventional antifungal agent (76.92 ± 4.72%). Interestingly, when tested again Candida krusei, camel casein alcalase 2 and 4 h (CA-C-A2 and CA-C-A4), and cow whey alcalase-6 h (CO-W-A6) hydrolysates showed higher antifungal potency than fluconazole. However, for Candida parapsilosis only camel casein alcalase-4 h (Ca-C-A4) and cow casein protease-6 h (Co-C-P6) hydrolysates were able to inhibit the growth of C. parapsilosis by 19.31 ± 0.84% and 23.82 ± 4.14%, respectively, which was lower than that shown by fluconazole (29.86 ± 1.11%). Overall, hydrolysis of milk proteins from both cow and camel enhanced their antifungal properties. Camel milk protein hydrolysates were more potent in inhibiting pathogenic Candida species as compared with cow milk protein hydrolysates. This is the first study that highlights the antifungal properties of camel milk protein hydrolysates.

In bacteria, the defense system deployd to counter oxidative stress is orchestrated by three transcriptional factors – SoxS, SoxR, and OxyR. Although the regulon that these factors control is known in many bacteria, similar data is not available forKlebsiella pneumoniae. To address this data gap, oxidative stress was artificially induced inK. pneumoniaeMGH 78578 using paraquat and the corresponding oxidative stress regulon recorded using RNA-seq. ThesoxSgene was significantly induced during oxidative stress and a knock-out mutant was constructed, to explore its functionality. The wild-type and mutant were grown in the presence of paraquat and subjected to RNA-seq to elucidate thesoxSregulon inK. pneumoniaeMGH78578. Genes that are commonly regulated both in the oxidative stress regulon andsoxSregulon were identified and denoted as the ‘oxidative SoxS regulon’ – these included a stringent group of genes specifically regulated by SoxS. Efflux pump encoding genes such asacrAB-tolC, acrE, and global regulators such asmarRABwere identified as part of this regulon. Consequently, the isogenicsoxSmutant was found to exhibit a reduction in the minimum bactericidal concentration against tetracycline compared to that of the wild type. Impaired efflux activity, allowing tetracycline to be accumulated in the cytoplasm to bactericidal levels, was further evaluated using a tetraphenylphosphonium (TPP+) accumulation assay. ThesoxSmutant was also susceptible to tetracyclinein vivo, in a zebrafish embryo model. We conclude that thesoxSgene could be considered as a genetic target against which an inhibitor could be developed in the future and used in combinatorial therapy with tetracycline to combat infections associated with multi-drug resistantK. pneumoniae.

Cronobacter spp. are opportunistic, foodborne pathogens capable of causing severe illnesses predominantly in premature and low-birth-weight infants. These organisms have evolved features, which aid them to survive under harsh environmental conditions but may also contribute to pathogenesis during infection. In this review, we highlight efforts to study genetic diversity and evolutionary aspects, osmotic adaptation and pathogenesis of these pathogens. Next-generation genome sequencing-based techniques elucidated a species-level bidirectional divergence driven by niche adaptation in Cronobacter spp. Whole genome comparisons and proteomics revealed genes and pathways contributing to the survival and persistence phenotype in low-moisture environments. In silico genome comparisons and application of suitable in vivo models provided answers to pathogenesis-related questions. Development and application of innovative molecular techniques and in vivo infection models have shed light on how Cronobacter spp. adapt to challenges experienced in natural, food processing and host-related environments.

Cronobacter species are considered an opportunistic group of foodborne pathogenic bacteria capable of causing both intestinal and systemic human disease. This review describes common virulence themes shared among the seven Cronobacter species and describes multiple exoproteins secreted by Cronobacter, many of which are bacterial toxins that may play a role in human disease. The review will particularly concentrate on the virulence factors secreted by C. sakazakii, C. malonaticus, and C. turicensis, which are the primary human pathogens of interest. It has been discovered that various species-specific virulence factors adversely affect a wide range of eukaryotic cell processes including protein synthesis, cell division, and ion secretion. Many of these factors are toxins which have been shown to also modulate the host immune response. These factors are encoded on a variety of mobile genetic elements such as plasmids and transposons; this genomic plasticity implies ongoing re-assortment of virulence factor genes which has complicated our efforts to categorize Cronobacter into sharply defined genomic pathotypes.

In recent years, the concept of bacteria-mediated cancer therapy has gained significant attention as an alternative to conventional therapy. The focus has been on non-typhoidal Salmonella (NTS), particularly S. Typhimurium, for its anti-cancer properties, however, other NTS serovars such as Salmonella Oslo, which are associated with foodborne illnesses could potentially be effective anti-cancer agents. Here, we report the draft genome sequence of Salmonella Oslo isolated from seafood and its laboratory generated auxotrophic mutant.

The aim of this study was to develop appropriate protocols for flow cytometric (FCM) and 16S rDNA sequencing investigation of the microbiome in a powdered infant formula (PIF) production facility. Twenty swabs were collected from each of the three care zones of a PIF production facility and used for preparing composite samples. For FCM studies, the swabs were washed in 200 mL phosphate buffer saline (PBS). The cells were harvested by three-step centrifugation followed by a single stage filtration. Cells were dispersed in fresh PBS and analyzed with a flow cytometer for membrane integrity, metabolic activity, respiratory activity and Gram characteristics of the microbiome using various fluorophores. The samples were also plated on agar plates to determine the number of culturable cells. For 16S rDNA sequencing studies, the cells were harvested by centrifugation only. Genomic DNA was extracted using a chloroform-based method and used for 16S rDNA sequencing studies. Compared to the dry low and high care zones, the wet medium care zone contained a greater number of viable, culturable, and metabolically active cells. Viable but non-culturable cells were also detected in dry-care zones. In total, 243 genera were detected in the facility of which 42 were found in all three care zones. The greatest diversity in the microbiome was observed in low care. The genera present in low, medium and high care were mostly associated with soil, water, and humans, respectively. The most prevalent genera in low, medium and high care were Pseudomonas, Acinetobacter, and Streptococcus, respectively. The integration of FCM and metagenomic data provided further information on the density of different species in the facility.

The combination of genomics and high-throughput cDNA sequencing technologies has facilitated the identification of many small RNAs (sRNAs) that play a central role in the post-transcriptional gene regulation of Salmonella enterica serovar Typhimurium. To date, most of the functionally characterized sRNAs have been involved in the regulation of processes which are not directly linked to virulence. Just five sRNAs have been found to affect the ability of Salmonella to replicate within mammalian cells, but the precise regulatory mechanisms that are used by sRNAs to control Salmonella pathogenicity at the post-transcriptional level remain to be identified. It is anticipated that an improved understanding of sRNA biology will shed new light on the virulence of Salmonella.

Phenotypic variation is widespread among prokaryotes, and its underlying molecular mechanisms include genetic changes such as genomic inversion and strand-slippage mechanisms, epigenetic variations depending on DNA methylation, and feedback-based multistability characterized by at least two distinct phenotypes within an isogenic population (36). Per definition, bistability must arise stochastically at the cellular level (9). A common regulatory arrangement exhibiting bistability includes a positive-feedback loop with a cooperative response to an activator (10). This was first described for lactose utilization by Escherichia coli in which a population is split into cells highly or not at all expressing the lac operon (11, 28). Further prominent examples are the bistable switch between lysogeny and lysis of bacteriophage λ depending on the fragile balance between the regulators Cro and CI (4), and the Bacillus subtilis K-status (competence) system in which 10 to 20% of the cells in stationary phase highly express genes permitting transformation competence (24, 35). The survival of Staphylococcus aureus against antibiotic treatment requires that some cells called persisters enter a condition of reduced growth (5), and population heterogeneity is also observed during B. subtilis sporulation (13). Very recently, it was demonstrated that biofilm formation by Salmonella enterica serovar Typhimurium strain 14028 (S. Typhimurium 14028) involves the bistable expression of CsgD, the major biofilm regulator (14). Even more intriguing, when this pathogen infects hosts, a stochastic switch takes place that results in a self-destructive fraction and another that benefits from the dying one (3). myo-Inositol (MI) is a polyol abundant in soil. The iol genes of S. Typhimurium 14028 responsible for utilization of MI as carbon and energy source are located on a 22.6-kb genomic island (GEI4417/4436) that is absent in all but six Salmonella serovars sequenced thus far (21). All genes on this island necessary for MI degradation are induced during growth with this substrate as the sole carbon source. The catabolic pathway requires IolG and IolE converting MI to 3D-trihydroxycyclohexane-1,2-dione, which is further hydrolyzed by IolD. 5-deoxy-glucuronic acid is isomerized by IolB to 2-deoxy-5-keto-d-gluconic acid that is then phosphorylated by the kinase IolC and degraded to dihydroxyacetone phosphate, acetyl coenzyme A, and CO2. In rich medium, the negative regulator IolR represses all but one promoter of the iol divergon, including its own (21). A protein belonging to the major facilitator superfamily, IolT1, has recently been identified as the predominant MI transporter of S. Typhimurium 14028, and IolR was revealed to also inhibit the transcription of iolT1 (22). The ability to degrade MI is known for the Gram-positive species Bacillus subtilis (26, 39, 41), Corynebacterium glutamicum (20), Clostridium perfringens (17), and Lactobacillus casei BL23 (38), as for several Gram-negative species such as Serratia, Klebsiella, and Pseudomonas (6, 12, 23, 30). Although a comparison of the respective gene clusters revealed a high variability of their chromosomal organization, the negative regulation of the iol genes by the IolR repressor is a common feature of all MI divergons investigated thus far. An intermediate of MI degradation, 2-deoxy-5-keto-d-gluconic acid 6-phosphate (DKP), has been shown to antagonize IolR binding, thus inducing the expression of iol genes (40, 42). A remarkable and unique property of S. Typhimurium 14028 is its long lag phase in the presence of MI. We show here for the first time that phenotypic variation is involved in this growth phenomenon and that the deletion of IolR and the addition of bicarbonate induce growth of the pathogen in MI. A model of the molecular mechanism underlying bistability in the presence of MI is proposed.

Objective Epicardial fat is considered as indicator of cardiovascular risk. Several studies have tested the association between epicardial fat thickness (EFT) and coronary artery disease. The aim of our study is to test the hypothesis that echocardiographic EFT is a marker of coronary artery disease. Methods One hundred and ten patients (70 males and 40 females with mean age of 51.5 ± 10.6 and 52.6 ± 9.6, respectively) admitted for coronary angiogram underwent assessment of epicardial fat thickness by echocardiography. Routine clinical examination, evaluation of risk factor profile, and anthropometric variables were also done. Epicardial fat thickness was measured on the free wall of right ventricle in parasternal long- and short-axis views at end-systole for 3 cardiac cycles. Results Mean epicardial fat thickness in angiographically normal patients and acute coronary syndromes were 4.4 ± 1.2 and 6.9 ± 1.9, respectively. Epicardial fat thickness in males and females were not statistically different. Burden of coronary arterial lesions denoted by Gensini score shows linear association with epicardial fat thickness and the severity of the coronary disease. Conclusion Epicardial fat is independently and linearly associated with CAD and its severity.

The Hha family of proteins is involved in the regulation of gene expression in enterobacteria by forming complexes with H-NS-like proteins. Whereas several amino acid residues of both proteins participate in the interaction, some of them play a key role. Residue D48 of Hha protein is essential for the interaction with H-NS, thus the D48N substitution in Hha protein abrogates H-NS/Hha interaction. Despite being a paralog of H-NS protein, StpA interacts with HhaD48N with higher affinity than with the wild type Hha protein. To analyze whether Hha is capable of acting independently of H-NS and StpA, we conducted transcriptomic analysis on the hha and stpA deletion strains and the hhaD48N substitution strain of Salmonella Typhimurium using a custom microarray. The results obtained allowed the identification of 120 genes regulated by Hha in an H-NS/StpA-independent manner, 38% of which are horizontally acquired genes. A significant number of the identified genes are involved in functions related to cell motility, iron uptake, and pathogenicity. Thus, motility assays, siderophore detection and intra-macrophage replication assays were performed to confirm the transcriptomic data. Our findings point out the importance of Hha protein as an independent regulator in S. Typhimurium, highlighting a regulatory role on virulence.

We constructed two collections of targeted single gene deletion (SGD) mutants and two collections of targeted multi-gene deletion (MGD) mutants in Salmonella enterica sv Typhimurium 14028s. The SGD mutant collections contain (1), 3517 mutants in which a single gene is replaced by a cassette containing a kanamycin resistance (KanR) gene oriented in the sense direction (SGD-K), and (2), 3376 mutants with a chloramphenicol resistance gene (Cam R) oriented in the antisense direction (SGD-C). A combined total of 3773 individual genes were deleted across these SGD collections. The MGD collections contain mutants bearing deletions of contiguous regions of three or more genes and include (3), 198 mutants spanning 2543 genes replaced by a KanR cassette (MGD-K), and (4), 251 mutants spanning 2799 genes replaced by a CamR cassette (MGD-C). Overall, 3476 genes were deleted in at least one MGD collection. The collections with different antibiotic markers permit construction of all viable combinations of mutants in the same background. Together, the libraries allow hierarchical screening of MGDs for different phenotypic followed by screening of SGDs within the target MGD regions. The mutants of these collections are stored at BEI Resources (www.beiresources.org) and publicly available. © 2014 Porwollik et al.

Only three pathogenic bacterial species, Salmonella enterica , Clostridium perfringens , and Listeria monocytogenes , are able to utilize both ethanolamine and 1,2-propanediol as a sole carbon source. Degradation of these substrates, abundant in food and the gut, depends on cobalamin, which is synthesized de novo only under anaerobic conditions. Although the eut , pdu , and cob - cbi gene clusters comprise 40 kb, the conditions under which they confer a selection advantage on these food-borne pathogens remain largely unknown. Here we used the luciferase reporter system to determine the response of the Salmonella enterica serovar Typhimurium promoters P eutS , P pocR , P pduF , and P pduA to a set of carbon sources, to egg yolk, to whole milk, and to milk protein or fat fractions. Depending on the supplements, specific inductions up to 3 orders of magnitude were observed for P eutS and P pduA , which drive the expression of most eut and pdu genes. To correlate these significant expression data with growth properties, nonpolar deletions of pocR , regulating the pdu and cob - cbi genes, and of eutR , involved in eut gene activation, were constructed in S . Typhimurium strain 14028. During exponential growth of the mutants 14028Δ pocR and 14028Δ eutR , 2- to 3-fold-reduced proliferation in milk and egg yolk was observed. Using the Caenorhabditis elegans infection model, we could also demonstrate that the proliferation of S . Typhimurium in the nematode is supported by an active ethanolamine degradation pathway. Taking these findings together, this study quantifies the differential expression of eut and pdu genes under distinct conditions and provides experimental evidence that the ethanolamine utilization pathway allows salmonellae to occupy specific metabolic niches within food environments and within their host organisms.

Biofilm formation by Salmonella is a serious concern in the food-processing industry and the persistence of the organism in biofilms becomes a constant source of contamination. Since there is zero tolerance for Salmonella in foods, it is important to understand the mechanism of biofilm formation and to prevent the formation. Therefore, this study aimed at investigating the biofilm-forming ability of seafood isolates of Salmonella enterica serovar Weltevreden (S. Weltevreden) under two different nutrient conditions (normal strength trypticase soy broth (TSB) and 1:100 diluted TSB). The role of cellulose production in biofilm formation and in the expression of multicellular behavior (rough, dark, red morphotype: rdar) was investigated. Fourteen isolates of seafood associated S. Weltevreden were studied for biofilm production in polystyrene microtitre plates. Only one (SW49) of 14 was a strong biofilm former on polystyrene template and was able to produce biofilm in both undiluted TSB and 1:100 diluted TSB at 24h. All others produced moderate or weak biofilms which was higher in 1:100 diluted TSB compared to undiluted medium. All the isolates except one were positive by PCR for the three genes, gcpA (stm1987), adrA (yaiC) and csgD. Gene expression of gcpA, adrA and csgD was studied by real-time PCR with the one strong (SW49) and one representative weak (SW30) biofilm former. In SW49 at 24h of incubation, the expression of gcpA from biofilm cells was 33 and 36 times higher than from planktonic cells grown in TSB and diluted TSB respectively and at 72h the expression from biofilm cells was 57 and 61 times higher than that from planktonic cells. Quantification of gene expression did not reveal any significant difference in the expression of csgD and adrA gene. Deletion of gcpA in SW49 resulted in its inability to produce cellulose and consequent inability to bind calcoflour, inability to form rdar colony on Congo Red-agar plates and failure to produce biofilm on polystyrene substrate. The data indicated that, in case of S. Weltevreden, gcpA is critical for activating cellulose synthesis and biofilm formation both in undiluted and diluted TSB. The results of this study suggest the existence of an alternative biofilm regulatory pathway in S. Weltevreden. Role of adrA in cellulose production in nutrient rich medium is known but role of gepA in the above phenomenon is proved in this study. An understanding of the genes involved would help in looking at strategies of repression of the gene to control formation of biofilm.

SummaryBacterial transcriptional networks consist of hundreds of transcription factors and thousands of promoters. However, the true complexity of transcription in a bacterial pathogen and the effect of the environments encountered during infection remain to be established. We present a simplified approach for global promoter identification in bacteria using RNA-seq-based transcriptomic analyses of 22 distinct infection-relevant environmental conditions. Individual RNA samples were combined to identify most of the 3,838 Salmonella enterica serovar Typhimurium promoters in just two RNA-seq runs. Individual in vitro conditions stimulated characteristic transcriptional signatures, and the suite of 22 conditions induced transcription of 86% of all S. Typhimurium genes. We highlight the environmental conditions that induce the Salmonella pathogenicity islands and present a small RNA expression landscape of 280 sRNAs. This publicly available compendium of environmentally controlled expression of every transcriptional feature of S. Typhimurium constitutes a useful resource for the bacterial research community.