Functional metagenomics of Escherichia coli O157:H7 interactions with spinach indigenous microorganisms during biofilm formation

Understanding of food biofilms by the application of omics techniques

Biofilms constitute a protective barrier for foodborne pathogens to survive under stressful food processing conditions. Therefore, studies into the development and control of biofilms by novel techniques are vital for the food industry. In recent years, foodomics techniques have been developed for biofilm studies, which contributed to a better understanding of biofilm behavior, physiology, composition, as well as their response to antibiofilm methods at different molecular levels including genes, RNA, proteins and metabolic metabolites. Throughout this review, the main studies where foodomics tools used to explore the mechanisms for biofilm formation, dispersal and elimination were reviewed. The data summarized from relevant studies are important to design novel and appropriate biofilm elimination methods for enhancing food safety at any point of food processing lines.

Modeling the evolution of interconnected processes: It is the song and the singers: Tracking units of selection with interaction networks

Recently, Doolittle and Inkpen formulated a thought provoking theory, asserting that evolution by natural selection was responsible for the sideways evolution of two radically different kinds of selective units (also called Domains). The former entities, termed singers, correspond to the usual objects studied by evolutionary biologists (gene, genomes, individuals, species, etc.), whereas the later, termed songs, correspond to re-produced biological and ecosystemic functions, processes, information, and memes. Singers perform songs through selected patterns of interactions, meaning that a wealth of critical phenomena might receive novel evolutionary explanations. However, this theory did not provide an empirical approach to study evolution in such a broadened context. Here, we show that analyzing songs and singers, using patterns of interaction networks as a common ontology for both, offers a novel, actionable, inclusive and mathematical way to analyze not only the re-production but also the evolution and fitness of biological and ecosystemic interconnected processes.

Biotic factors drive distinct DNRA potential rates and contributions in typical Chinese shallow lake sediments

Dissimilatory nitrate reduction to ammonia (DNRA) is an important nitrate reduction pathway in lake sediments; however, little is known about the biotic factors driving the DNRA potential rates and contributions to the fate of nitrate. This study reports the first investigation of DNRA potential rates and contributions in lake sediments linked to DNRA community structures. The results of ¹⁵N isotope-tracing incubation experiments showed that 12 lakes had distinct DNRA potentials, which could be clustered into 2 groups, one with higher DNRA potentials (rates varied from 2.7 to 5.0 nmol N g^-1 h^-1 and contributions varied from 27.5% to 35.4%) and another with lower potentials (rates varied from 0.6 to 2.3 nmol N g^-1 h^-1 and contributions varied from 8.1% to 22.8%). Sediment C/N and the abundance of the nrfA gene were the key abiotic and biotic factors accounting for the distinct DNRA potential rates, respectively. A high-throughput sequencing analysis of the nrfA gene revealed that the sediment C/N could also affect the DNRA potential rates by altering the ecological patterns of the DNRA community composition. In addition, the interactions between the DNRA community and the denitrifying community were found to be obviously different in the two groups. In the higher DNRA potential group, the DNRA community mainly interacted with heterotrophic denitrifiers, while in the lower DNRA potential group, both heterotrophic and sulfur-driven autotrophic denitrifiers might cooperate with the DNRA community. The present study highlighted the role of the sulfur-driven nitrate reduction pathway in C-limited sediments, which has always been overlooked in freshwater environments, and gave new insights into the molecular mechanism influencing the fate of nitrate.

Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains

Cronobacter sakazakii is a Gram-negative opportunistic pathogen that causes life- threatening infantile infections, such as meningitis, septicemia, and necrotizing enterocolitis, as well as pneumonia, septicemia, and urinary tract and wound infections in adults. Here, we report 26 draft genome sequences of C. sakazakii, which were obtained from dried spices from the USA, the Middle East, China, and the Republic of Korea. The average genome size of the C. sakazakii genomes was 4393 kb, with an average of 4055 protein coding genes, and an average genome G + C content of 56.9%. The genomes contained genes related to carbohydrate transport and metabolism, amino acid transport and metabolism, and cell wall/membrane biogenesis. In addition, we identified genes encoding proteins involved in osmotic responses such as DnaJ, Aquaproin Z, ProQ, and TreF, as well as virulence-related and heat shock-related proteins. Interestingly, a metabolic island comprised of a variably-sized xylose utilization operon was found within the spice-associated C. sakazakii genomes, which supports the hypothesis that plants may serve as transmission vectors or alternative hosts for Cronobacter species. The presence of the genes identified in this study can support the remarkable phenotypic traits of C. sakazakii such as the organism's capabilities of adaptation and survival in response to adverse growth environmental conditions (e.g. osmotic and desiccative stresses). Accordingly, the genome analyses provided insights into many aspects of physiology and evolutionary history of this important foodborne pathogen.

Viable-but-Nonculturable Listeria monocytogenes and Salmonella enterica Serovar Thompson Induced by Chlorine Stress Remain Infectious

The microbiological safety of fresh produce is monitored almost exclusively by culture-based detection methods. However, bacterial food-borne pathogens are known to enter a viable-but-nonculturable (VBNC) state in response to environmental stresses such as chlorine, which is commonly used for fresh produce decontamination. Here, complete VBNC induction of green fluorescent protein-tagged Listeria monocytogenes and Salmonella enterica serovar Thompson was achieved by exposure to 12 and 3 ppm chlorine, respectively. The pathogens were subjected to chlorine washing following incubation on spinach leaves. Culture data revealed that total viable L. monocytogenes and Salmonella Thompson populations became VBNC by 50 and 100 ppm chlorine, respectively, while enumeration by direct viable counting found that chlorine caused a <1-log reduction in viability. The pathogenicity of chlorine-induced VBNC L. monocytogenes and Salmonella Thompson was assessed by using Caenorhabditis elegans Ingestion of VBNC pathogens by C. elegans resulted in a significant life span reduction (P = 0.0064 and P < 0.0001), and no significant difference between the life span reductions caused by the VBNC and culturable L. monocytogenes treatments was observed. L. monocytogenes was visualized beyond the nematode intestinal lumen, indicating resuscitation and cell invasion. These data emphasize the risk that VBNC food-borne pathogens could pose to public health should they continue to go undetected.IMPORTANCE Many bacteria are known to enter a viable-but-nonculturable (VBNC) state in response to environmental stresses. VBNC cells cannot be detected by standard laboratory culture techniques, presenting a problem for the food industry, which uses these techniques to detect pathogen contaminants. This study found that chlorine, a sanitizer commonly used for fresh produce, induces a VBNC state in the food-borne pathogens Listeria monocytogenes and Salmonella enterica It was also found that chlorine is ineffective at killing total populations of the pathogens. A life span reduction was observed in Caenorhabditis elegans that ingested these VBNC pathogens, with VBNC L. monocytogenes as infectious as its culturable counterpart. These data show that VBNC food-borne pathogens can both be generated and avoid detection by industrial practices while potentially retaining the ability to cause disease.

Conditional Function of Autoaggregative Protein Cah and Common cah Mutations in Shiga Toxin-Producing Escherichia coli

Cah is a calcium-binding autotransporter protein involved in autoaggregation and biofilm formation. Although cah is widespread in Shiga toxin-producing Escherichia coli (STEC), we detected mutations in cah at a frequency of 31.3% in this pathogen. In STEC O157:H7 supershedder strain SS17, a large deletion results in a smaller coding sequence, encoding a protein lacking the C-terminal 71 amino acids compared with Cah in STEC O157:H7 strain EDL933. We examined the function of Cah in biofilm formation and host colonization to better understand the selective pressures for cah mutations. EDL933-Cah played a conditional role in biofilm formation in vitro: it enhanced E. coli DH5α biofilm formation on glass surfaces under agitated culture conditions that prevented autoaggregation but inhibited biofilm formation under hydrostatic conditions that facilitated autoaggregation. This function appeared to be strain dependent since Cah-mediated biofilm formation was diminished when an EDL933 cah gene was expressed in SS17. Deletion of cah in EDL933 enhanced bacterial attachment to spinach leaves and altered the adherence pattern of EDL933 to bovine recto-anal junction squamous epithelial (RSE) cells. In contrast, in trans expression of EDL933 cah in SS17 increased its attachment to leaf surfaces, and in DH5α, it enhanced its adherence to RSE cells. Hence, the ecological function of Cah appears to be modulated by environmental conditions and other bacterial strain-specific properties. Considering the prevalence of cah in STEC and its role in attachment and biofilm formation, cah mutations might be selected in ecological niches in which inactivation of Cah would result in an increased fitness in STEC during colonization of plants or animal hosts.IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) harbors genes encoding diverse adhesins, and many of these are known to play an important role in bacterial attachment and host colonization. We demonstrated here that the autotransporter protein Cah confers on E. coli DH5α cells a strong autoaggregative phenotype that is inversely correlated with its ability to form biofilms and plays a strain-specific role in plant and animal colonization by STEC. Although cah is widespread in the STEC population, we detected a mutation rate of 31.3% in cah, which is similar to that reported for rpoS and fimH The formation of cell aggregates due to increased bacterium-to-bacterium interactions may be disadvantageous to bacterial populations under conditions that favor a planktonic state in STEC. Therefore, a loss-of-function mutation in cah is likely a selective trait in STEC when autoaggregative properties become detrimental to bacterial cells and may contribute to the adaptability of STEC to fluctuating environments.

Candida krusei isolated from fruit juices ultrafiltration membranes promotes colonization of Escherichia coli O157:H7 and Salmonella enterica on stainless steel surfaces

To clarify the interactions between a common food spoilage yeast and two pathogenic bacteria involved in outbreaks associated with fruit juices, the present paper studies the effect of the interplay of Candida krusei, collected from UF membranes, with Escherichia coli O157:H7 and Salmonella enterica in the overall process of adhesion and colonization of abiotic surfaces. Two different cases were tested: a) co-adhesion by pathogenic bacteria and yeasts, and b) incorporation of bacteria to pre-adhered C. krusei cells. Cultures were made on stainless steel at 25°C using apple juice as culture medium. After 24 h of co-adhesion with C. krusei, both E. coli O157:H7 and S. enterica increased their counts 1.05 and 1.11 log CFU cm², respectively. Similar increases were obtained when incorporating bacteria to pre-adhered cells of Candida. Nevertheless C. krusei counts decreased in both experimental conditions, in a) 0.40 log CFU cm² and 0.55 log CFU cm² when exposed to E. coli O157:H7 and S. enterica and in b) 0.18 and 0.68 log CFU cm², respectively. This suggests that C. krusei, E. coli O157:H7, and S. enterica have a complex relationship involving physical and chemical interactions on food contact surfaces. This study supports the possibility that pathogen interactions with members of spoilage microbiota, such as C. krusei, might play an important role for the survival and dissemination of E. coli O157:H7 and Salmonella enterica in food-processing environments. Based on the data obtained from the present study, much more attention should be given to prevent the contamination of these pathogens in acidic drinks.

Phenological asynchrony between host plant and gypsy moth reduces insect gut microbiota and susceptibility to Bacillus thuringiensis

The phenological synchrony between the emergence of overwintering herbivorous insects and the budding of host plants is considered a crucial factor in the population dynamics of herbivores. However, the mechanisms driving the interactions between the host plant, herbivores, and their pathogens are often obscure. In the current study, an artificially induced phenological asynchrony was used to investigate how the asynchrony between silver birch Betula pendula and gypsy moth Lymantria dispar affects the immunity of the insect to bacteria, its susceptibility to the entomopathogenic bacteria Bacillus thuringiensis, and the diversity in its midgut microbiota. The lysozyme-like activity in both the midgut and hemolymph plasma and the nonspecific esterase activity and antimicrobial peptide gene expression in the midgut were studied in both noninfected and B. thuringiensis-infected larvae. Our results provide the first evidence that phenologically asynchronous larvae are less susceptible to B. thuringiensis infection than phenologically synchronous larvae, and our results show that these effects are related to the high basic levels and B. thuringiensis-induced levels of lysozyme-like activities. Moreover, a 16S rRNA analysis revealed that dramatic decreases in the diversity of the larval gut bacterial consortia occurred under the effect of asynchrony. Larvae infected with B. thuringiensis presented decreased microbiota diversity if the larvae were reared synchronously with the host plant but not if they were reared asynchronously. Our study demonstrates the significant effect of phenological asynchrony on innate immunity-mediated interactions between herbivores and entomopathogenic bacteria and highlights the role of nonpathogenic gut bacteria in these interactions.

Contribution of the Salmonella enterica KdgR Regulon to Persistence of the Pathogen in Vegetable Soft Rots

During their colonization of plants, human enteric pathogens, such as Salmonella enterica, are known to benefit from interactions with phytopathogens. At least in part, benefits derived by Salmonella from the association with a soft rot caused by Pectobacterium carotovorum were shown to be dependent on Salmonella KdgR, a regulator of genes involved in the uptake and utilization of carbon sources derived from the degradation of plant polymers. A Salmonella kdgR mutant was more fit in soft rots but not in the lesions caused by Xanthomonas spp. and Pseudomonas spp. Bioinformatic, phenotypic, and gene expression analyses demonstrated that the KdgR regulon included genes involved in uptake and metabolism of molecules resulting from pectin degradation as well as those central to the utilization of a number of other carbon sources. Mutant analyses indicated that the Entner-Doudoroff pathway, in part controlled by KdgR, was critical for the persistence within soft rots and likely was responsible for the kdgR phenotype.

Biofilm-Forming Abilities of Shiga Toxin-Producing Escherichia coli Isolates Associated with Human Infections

Forming biofilms may be a survival strategy of Shiga toxin-producing Escherichia coli to enable it to persist in the environment and the food industry. Here, we evaluate and characterize the biofilm-forming ability of 39 isolates of Shiga toxin-producing Escherichia coli isolates recovered from human infection and belonging to seropathotypes A, B, or C. The presence and/or production of biofilm factors such as curli, cellulose, autotransporter, and fimbriae were investigated. The polymeric matrix of these biofilms was analyzed by confocal microscopy and by enzymatic digestion. Cell viability and matrix integrity were examined after sanitizer treatments. Isolates of the seropathotype A (O157:H7 and O157:NM), which have the highest relative incidence of human infection, had a greater ability to form biofilms than isolates of seropathotype B or C. Seropathotype A isolates were unique in their ability to produce cellulose and poly-N-acetylglucosamine. The integrity of the biofilms was dependent on proteins. Two autotransporter genes, ehaB and espP, and two fimbrial genes, z1538 and lpf2, were identified as potential genetic determinants for biofilm formation. Interestingly, the ability of several isolates from seropathotype A to form biofilms was associated with their ability to agglutinate yeast in a mannose-independent manner. We consider this an unidentified biofilm-associated factor produced by those isolates. Treatment with sanitizers reduced the viability of Shiga toxin-producing Escherichia coli but did not completely remove the biofilm matrix. Overall, our data indicate that biofilm formation could contribute to the persistence of Shiga toxin-producing Escherichia coli and specifically seropathotype A isolates in the environment.

Intra- and inter-species interactions within biofilms of important foodborne bacterial pathogens

A community-based sessile life style is the normal mode of growth and survival for many bacterial species. Under such conditions, cell-to-cell interactions are inevitable and ultimately lead to the establishment of dense, complex and highly structured biofilm populations encapsulated in a self-produced extracellular matrix and capable of coordinated and collective behavior. Remarkably, in food processing environments, a variety of different bacteria may attach to surfaces, survive, grow, and form biofilms. Salmonella enterica, Listeria monocytogenes, Escherichia coli, and Staphylococcus aureus are important bacterial pathogens commonly implicated in outbreaks of foodborne diseases, while all are known to be able to create biofilms on both abiotic and biotic surfaces. Particularly challenging is the attempt to understand the complexity of inter-bacterial interactions that can be encountered in such unwanted consortia, such as competitive and cooperative ones, together with their impact on the final outcome of these communities (e.g., maturation, physiology, antimicrobial resistance, virulence, dispersal). In this review, up-to-date data on both the intra- and inter-species interactions encountered in biofilms of these pathogens are presented. A better understanding of these interactions, both at molecular and biophysical levels, could lead to novel intervention strategies for controlling pathogenic biofilm formation in food processing environments and thus improve food safety.

Artificial Surfaces in Phyllosphere Microbiology

The study of microorganisms that reside on plant leaf surfaces, or phyllosphere microbiology, greatly benefits from the availability of artificial surfaces that mimic in one or more ways the complexity of foliage as a microbial habitat. These leaf surface proxies range from very simple, such as nutrient agars that can reveal the metabolic versatility or antagonistic properties of leaf-associated microorganisms, to the very complex, such as silicon-based casts that replicate leaf surface topography down to nanometer resolution. In this review, we summarize the various uses of artificial surfaces in experimental phyllosphere microbiology and discuss how these have advanced our understanding of the biology of leaf-associated microorganisms and the habitat they live in. We also provide an outlook into future uses of artificial leaf surfaces, foretelling a greater role for microfluidics to introduce biological and chemical gradients into artificial leaf environments, stressing the importance of artificial surfaces to generate quantitative data that support computational models of microbial life on real leaves, and rethinking the leaf surface ('phyllosphere') as a habitat that features two intimately connected but very different compartments, i.e., the leaf surface landscape ('phylloplane') and the leaf surface waterscape ('phyllotelma').

Mixed culture biofilms of Salmonella Typhimurium and cultivable indigenous microorganisms on lettuce show enhanced resistance of their sessile cells to cold oxygen plasma

Control of foodborne pathogens in fresh produce is crucial for food safety, and numerous Salmonella Typhimurium (ST) outbreaks have been reported already. The present study was done to assess effectiveness of cold oxygen plasma (COP) against biofilms of ST mixed with cultivable indigenous microorganisms (CIM). ST and CIM were grown at 15 °C as monocultures and mixed cultures for planktonic state, biofilm on stainless steel, and lettuce leaves. Thereafter, the samples were treated with COP and surviving populations were counted using plate counting methods. Biofilms and stomatal colonization were examined using field emission scanning electron microscopy (FESEM) and food quality was assessed after treatment. Mixed cultures of ST and CIM showed an antagonistic interaction on lettuce but not on SS or in planktonic state. Mixed cultures showed significantly (p < 0.05) greater resistance to COP compared to monoculture biofilms on lettuce but not on SS or planktonic state. Shift from smooth to rugose colony type was found for planktonic and for biofilms on SS but not on lettuce for ST. Mixed culture biofilms colonized stomata on the inside as demonstrated by FESEM. Although, lettuce quality was not affected by COP, this technology has to be optimized for further development of the successful inactivation of complex multispecies biofilm structures presented by real food environment.

Life on the outside: role of biofilms in environmental persistence of Shiga-toxin producing Escherichia coli

Escherichia coli is a heterogeneous species that can be part of the normal flora of humans but also include strains of medical importance. Among pathogenic members, Shiga-toxin producing E. coli (STEC) are some of the more prominent pathogenic E. coli within the public sphere. STEC disease outbreaks are typically associated with contaminated beef, contaminated drinking water, and contaminated fresh produce. These water- and food-borne pathogens usually colonize cattle asymptomatically; cows will shed STEC in their feces and the subsequent fecal contamination of the environment and processing plants is a major concern for food and public safety. This is especially important because STEC can survive for prolonged periods of time outside its host in environments such as water, produce, and farm soil. Biofilms are hypothesized to be important for survival in the environment especially on produce, in rivers, and in processing plants. Several factors involved in biofilm formation such as curli, cellulose, poly-N-acetyl glucosamine, and colanic acid are involved in plant colonization and adherence to different surfaces often found in meat processing plants. In food processing plants, contamination of beef carcasses occurs at different stages of processing and this is often caused by the formation of STEC biofilms on the surface of several pieces of equipment associated with slaughtering and processing. Biofilms protect bacteria against several challenges, including biocides used in industrial processes. STEC biofilms are less sensitive than planktonic cells to several chemical sanitizers such as quaternary ammonium compounds, peroxyacetic acid, and chlorine compounds. Increased resistance to sanitizers by STEC growing in a biofilm is likely to be a source of contamination in the processing plant. This review focuses on the role of biofilm formation by STEC as a means of persistence outside their animal host and factors associated with biofilm formation.

Enteric pathogen-plant interactions: molecular connections leading to colonization and growth and implications for food safety

Leafy green vegetables have been identified as a source of foodborne illnesses worldwide over the past decade. Human enteric pathogens, such as Escherichia coli O157:H7 and Salmonella, have been implicated in numerous food poisoning outbreaks associated with the consumption of fresh produce. An understanding of the mechanisms responsible for the establishment of pathogenic bacteria in or on vegetable plants is critical for understanding and ameliorating this problem as well as ensuring the safety of our food supply. While previous studies have described the growth and survival of enteric pathogens in the environment and also the risk factors associated with the contamination of vegetables, the molecular events involved in the colonization of fresh produce by enteric pathogens are just beginning to be elucidated. This review summarizes recent findings on the interactions of several bacterial pathogens with leafy green vegetables. Changes in gene expression linked to the bacterial attachment and colonization of plant structures are discussed in light of their relevance to plant-microbe interactions. We propose a mechanism for the establishment and association of enteric pathogens with plants and discuss potential strategies to address the problem of foodborne illness linked to the consumption of leafy green vegetables.

Interactions of O157 and non-O157 Shiga toxin-producing Escherichia coli (STEC) recovered from bovine hide and carcass with human cells and abiotic surfaces

Different structures related to biofilm formation by Shiga toxin-producing Escherichia coli (STEC), particularly O157 strains, have been described, but there are few data regarding their involvement in non-O157 strains. The aim of this study was to determine the ability of 14 O157 and 8 non-O157 strains isolated from bovine hide and carcass to interact with biotic and abiotic surfaces and also to evaluate the role of different adhesins. Biofilm formation assays showed that four O157 and two non-O157 strains were able to adhere to glass, and that only one O157 strain adhered to polystyrene. Reverse transcriptase-polymerase chain reaction was carried out using biofilm-forming strains to determine the expression of antigen 43 (Ag43), curli, type 1 fimbriae, STEC autotransporter contributing to biofilm formation (Sab), calcium-binding antigen 43 homologue (Cah), and autotransporter protein of enterohemorrhagic E. coli (EhaA). Most of these structures were expressed under biofilm conditions. However, the lack of Ag43 in one non-O157 strain, as well as Cah and EhaA in two O157 strains, suggests that other adhesins are involved in biofilm formation in these strains. Despite the fact that adherence to HeLa cells was detected in 20 strains (91%), it was not possible to correlate biofilm formation with adherence patterns. Invasiveness in T84 and Caco-2 cells was observed in four and three O157 strains, respectively. Altogether, we showed that there are different sets of genes involved in the interactions of STEC with biotic and abiotic surfaces. Interestingly, one O157 strain that was able to form biofilm on both glass and polystyrene also adhered to and invaded human cells, indicating an important route for its persistence in the environment and interaction with the host. Additionally, the ability of non-O157 strains not carrying the LEE pathogenicity island to form biofilm highlights an industrial and health problem that cannot be neglected.

Factors that affect proliferation of Salmonella in tomatoes post-harvest: the roles of seasonal effects, irrigation regime, crop and pathogen genotype

Main Objectives

Fresh fruits and vegetables become increasingly recognized as vehicles of human salmonellosis. Physiological, ecological, and environmental factors are all thought to contribute to the ability of Salmonella to colonize fruits and vegetables pre- and post-harvest. The goal of this study was to test how irrigation levels, fruit water congestion, crop and pathogen genotypes affect the ability of Salmonella to multiply in tomatoes post-harvest.

Experimental Design

Fruits from three tomato varieties, grown over three production seasons in two Florida locations, were infected with seven strains of Salmonella and their ability to multiply post-harvest in field-grown tomatoes was tested. The field experiments were set up as a two-factor factorial split plot experiment, with the whole-plot treatments arranged in a randomized complete-block design. The irrigation treatment (at three levels) was the whole-plot factor, and the split-plot factor was tomato variety, with three levels. The significance of the main, two-way, and three-way interaction effects was tested using the (type III) F-tests for fixed effects. Mean separation for each significant fixed effect in the model was performed using Tukey’s multiple comparison testing procedure.

Most Important Discoveries and Significance

The irrigation regime per se did not affect susceptibility of the crop to post-harvest proliferation of Salmonella. However, Salmonella grew significantly better in water-congested tissues of green tomatoes. Tomato maturity and genotype, Salmonella genotype, and inter-seasonal differences were the strongest factors affecting proliferation. Red ripe tomatoes were significantly and consistently more conducive to proliferation of Salmonella. Tomatoes harvested in the driest, sunniest season were the most conducive to post-harvest proliferation of the pathogen. Statistically significant interactions between production conditions affected post-harvest susceptibility of the crop to the pathogen. UV irradiation of tomatoes post-harvest promoted Salmonella growth.

Progress in cultivation-independent phyllosphere microbiology

Most microorganisms of the phyllosphere are nonculturable in commonly used media and culture conditions, as are those in other natural environments. This review queries the reasons for their ‘noncultivability’ and assesses developments in phyllospere microbiology that have been achieved cultivation independently over the last 4 years. Analyses of total microbial communities have revealed a comprehensive microbial diversity. 16S rRNA gene amplicon sequencing and metagenomic sequencing were applied to investigate plant species, location and season as variables affecting the composition of these communities. In continuation to culture-based enzymatic and metabolic studies with individual isolates, metaproteogenomic approaches reveal a great potential to study the physiology of microbial communities in situ. Culture-independent microbiological technologies as well advances in plant genetics and biochemistry provide methodological preconditions for exploring the interactions between plants and their microbiome in the phyllosphere. Improving and combining cultivation and culture-independent techniques can contribute to a better understanding of the phyllosphere ecology. This is essential, for example, to avoid human–pathogenic bacteria in plant food.

Salmonella interactions with plants and their associated microbiota

The increase in the incidence of gastroenteritis outbreaks linked to the consumption of foods of plant origin has ignited public concern and scientific interest in understanding interactions of human enteric pathogens with plants. Enteric disease caused by nontyphoidal Salmonella is a major public health burden, with the number of cases of illness linked to fresh produce, spices, and nuts surpassing those linked to foods of animal origin. Mounting evidence supports the hypothesis that colonization of plants is an important part of the life cycle of this human pathogen. Although plant responses to human pathogens are distinct from the more specific responses to phytopathogens, plants appear to recognize Salmonella, likely by detecting conserved microbial patterns, which subsequently activates basal defenses. Numerous Salmonella genes have been identified as playing a role in its colonization of plant surfaces and tissues, and in its various interactions with other members of the phyto-microbial community. Importantly, Salmonella utilizes diverse and overlapping strategies to interact with plants and their microflora, and to successfully colonize its vertebrate hosts. This review provides insight into the complex behavior of Salmonella on plants and the apparent remarkable adaptation of this human pathogen to a potentially secondary host.

Neonatal testosterone exposure protects adult male rats from stroke

BACKGROUND

Men have a higher stroke incidence compared to women until advanced age. The contribution of hormones to these sex differences has been extensively debated. In experimental stroke, estradiol is neuroprotective, whereas androgens are detrimental. However, prior studies have only examined the effects of acute treatment paradigms; therefore, the timing and mechanism by which ischemic sexual dimorphism arises are unknown.

METHODS

The effects of exogenous neonatal androgen exposure on subsequent injury induced by middle cerebral artery occlusion in adulthood in male rats were examined. Rats were administered vehicle (oil), testosterone propionate (TP) or the non-aromatizable androgen dihydrotestosterone (DHT) for 5 days after birth. At 3 months of age, a focal stroke was induced.

RESULTS

Testosterone-treated rats (but not DHT-treated animals) had decreased infarct volumes (20 vs. 33%, p < 0.05) as well as increased estradiol levels (39.4 vs. 18.6 pg/ml, p < 0.0001) compared to oil-treated animals. TP-injected males had increased testicular aromatase (P450arom) levels (3.6 vs. 0.2 ng/ml, p < 0.0001) compared to oil-treated males. The level of X-linked inhibitor of apoptosis, the primary endogenous inhibitor of caspase-induced apoptosis, was increased in TP-treated rats compared with the oil-treated males.

CONCLUSIONS

Neonatal exposure to exogenous testosterone upregulates testicular aromatase expression in male rats and leads to adult neuroprotection secondary to changes in serum estradiol levels and cell death proteins. This study suggests that early exposure to gonadal hormones can have dramatic effects on the response to adult cerebrovascular injury.

Advances in monitoring environmental microbes

Culture-independent approaches, such as next-generation sequencing and microarray-based tools, provide insight into the identity and functional diversity of microbial communities. Although these approaches are potentially powerful tools in understanding microbial structure and function, there are a number of limitations that may bias conclusions. In order to mitigate these biases, an understanding of potential biases within each stage of the experimental process is necessary. This review focuses on the biases associated with sample collection, nucleic acid extraction, processing, sequencing analyses, and Chip technologies used in microbial ecology studies.