Microarrays for microbiologists

An Optimized Method for Extracting Bacterial RNA from Mouse Skin Tissue Colonized by Mycobacterium ulcerans

Bacterial transcriptome analyses during host colonization are essential to decipher the complexity of the relationship between the bacterium and its host. RNA sequencing (RNA-seq) is a promising approach providing valuable information about bacterial adaptation, the host response and, in some cases, mutual tolerance underlying crosstalk, as recently observed in the context of Mycobacterium ulcerans infection. Buruli ulcer is caused by M. ulcerans. This neglected disease is the third most common mycobacterial disease worldwide. Without treatment, M. ulcerans provokes massive skin ulcers. A healing process may be observed in 5% of Buruli ulcer patients several months after the initiation of disease. This spontaneous healing process suggests that some hosts can counteract the development of the lesions caused by M. ulcerans. Deciphering the mechanisms involved in this process should open up new treatment possibilities. To this end, we recently developed the first mouse model for studies of the spontaneous healing process. We have shown that the healing process is based on mutual tolerance between the bacterium and its host. In this context, RNA-seq seems to be the most appropriate method for deciphering bacterial adaptation. However, due to the low bacterial load in host tissues, the isolation of mycobacterial RNA from skin tissue for RNA-seq analysis remains challenging. We developed a method for extracting and purifying mycobacterial RNA whilst minimizing the amount of host RNA in the sample. This approach was based on the extraction of bacterial RNA by a differential lysis method. The challenge in the development of this method was the choice of a lysis system favoring the removal of host RNA without damage to the bacterial cells. We made use of the thick, resistant cell wall of M. ulcerans to achieve this end.

Profiling of jejunum inflammatory gene expression during murine eimeriosis

To understand the host-parasite relationship during coccidiosis it is necessary to identify the transcriptional profile of the local host. In this study, gene profiling in the mouse jejunum due to infection with Eimeria papillata was investigated using Agilent microarray technology. On day 5 post-infection, the characterization of infected and non-infected mice jejunum transcriptional response was compared. There was an increase in the level of tumour necrosis factor-α, nitrite/nitrate and nitric oxide synthase activity was observed following infection. Also, the activity of glutathione peroxidase was reduced from 86.5 to 38.2 mU/g. In addition, E. papillata infection was associated with an increase in the activities of both the mice alkaline phosphatase and lactate dehydrogenase. Moreover, experimental E. papillata infection in mice induced a significant elevation in protein carbonyl content, by about 70%. Agilent genome microarray detected 11 genes whose expression was up-regulated by more than 10-fold, and 30 genes whose expression was down-regulated by a similar amount five days after infection with E. papillata. The expression profiles of the Fas apoptotic inhibitory molecule 3(FAIM3), chemokine (C-X-C motif) receptor 5 (Cxcr5), succinate receptor 1 (SUCNR1), hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 3 (Hsd3b3) and cytochrome P450, family 2, subfamily b, polypeptide 9 (Cyp2b9) genes, arbitrarily selected from the microarray analysis, closely resemble the expressions determined by quantitative PCR. The data indicate that, E. papillata is associated with the induction of inflammatory response and with gene regulation in mice jejunum.

Nucleic Acid-based approaches for detection of viral hepatitis

CONTEXT

To determining suitable nucleic acid diagnostics for individual viral hepatitis agent, an extensive search using related keywords was done in major medical library and data were collected, categorized, and summarized in different sections.

RESULTS

Various types of molecular biology tools can be used to detect and quantify viral genomic elements and analyze the sequences. These molecular assays are proper technologies for rapidly detecting viral agents with high accuracy, high sensitivity, and high specificity. Nonetheless, the application of each diagnostic method is completely dependent on viral agent.

CONCLUSIONS

Despite rapidity, automation, accuracy, cost-effectiveness, high sensitivity, and high specificity of molecular techniques, each type of molecular technology has its own advantages and disadvantages.

Unraveling microbial biofilms of importance for food microbiology

The presence of biofilms is a relevant risk factors in the food industry due to the potential contamination of food products with pathogenic and spoilage microorganisms. The majority of bacteria are able to adhere and to form biofilms, where they can persist and survive for days to weeks or even longer, depending on the microorganism and the environmental conditions. The biological cycle of biofilms includes several developmental phases such as: initial attachment, maturation, maintenance, and dispersal. Bacteria in biofilms are generally well protected against environmental stress, consequently, extremely difficult to eradicate and detect in food industry. In the present manuscript, some techniques and compounds used to control and to prevent the biofilm formation are presented and discussed. Moreover, a number of novel techniques have been recently employed to detect and evaluate bacteria attached to surfaces, including real-time polymerase chain reaction (PCR), DNA microarray and confocal laser scanning microscopy. Better knowledge on the architecture, physiology and molecular signaling in biofilms can contribute for preventing and controlling food-related spoilage and pathogenic bacteria. The present study highlights basic and applied concepts important for understanding the role of biofilms in bacterial survival, persistence and dissemination in food processing environments.

Current methods for molecular typing of Campylobacter species

Campylobacter remains one of the most common bacterial causes of gastroenteritis worldwide. Tracking sources of this organism is challenging due to the large numbers of human cases, and the prevalence of this organism throughout the environment due to growth in a wide range of animal species. Many molecular subtyping methods have been developed to characterize Campylobacter species, but only a few are commonly used in molecular epidemiology studies. This review examines the applicability of these methods, as well as the role that emerging whole genome sequencing technologies will play in tracking sources of Campylobacter spp. infection.

Pathogenesis in tuberculosis: transcriptomic approaches to unraveling virulence mechanisms and finding new drug targets

Tuberculosis (TB) remains a major health problem worldwide. Attempts to control this disease have proved difficult owing to our poor understanding of the pathobiology of Mycobacterium tuberculosis and the emergence of strains that are resistant to multiple drugs currently available for treatment. Genome-wide expression profiling has provided new insight into the transcriptome signatures of the bacterium during infection, notably of macrophages and dendritic cells. These data indicate that M. tuberculosis expresses numerous genes to evade the host immune responses, to suit its intracellular life style, and to respond to various antibiotic drugs. Among the intracellularly induced genes, several have functions in lipid metabolism, cell wall synthesis, iron uptake, oxidative stress resistance, protein secretion, or inhibition of apoptosis. Herein we review these findings and discuss possible ways to exploit the data to understand the complex etiology of TB and to find new effective drug targets.

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

Background

There has been increased interest in the study of molecular survival mechanisms expressed by foodborne pathogens present on food surfaces. Determining genomic responses of these pathogens to antimicrobials is of particular interest since this helps to understand antimicrobial effects at the molecular level. Assessment of bacterial gene expression by transcriptomic analysis in response to these antimicrobials would aid prediction of the phenotypic behavior of the bacteria in the presence of antimicrobials. However, before transcriptional profiling approaches can be implemented routinely, it is important to develop an optimal method to consistently recover pathogens from the food surface and ensure optimal quality RNA so that the corresponding gene expression analysis represents the current response of the organism. Another consideration is to confirm that there is no interference from the "background" food or meat matrix that could mask the bacterial response.

Findings

Our study involved developing a food model system using chicken breast meat inoculated with mid-log Salmonella cells. First, we tested the optimum number of Salmonella cells required on the poultry meat in order to extract high quality RNA. This was analyzed by inoculating 10-fold dilutions of Salmonella on the chicken samples followed by RNA extraction. Secondly, we tested the effect of two different bacterial cell recovery solutions namely 0.1% peptone water and RNAprotect (Qiagen Inc.) on the RNA yield and purity. In addition, we compared the efficiency of sonication and bead beater methods to break the cells for RNA extraction. To check chicken nucleic acid interference on downstream Salmonella microarray experiments both chicken and Salmonella cDNA labeled with different fluorescent dyes were mixed together and hybridized on a single Salmonella array. Results of this experiment did not show any cross-hybridization signal from the chicken nucleic acids. In addition, we demonstrated the application of this method in a meat model transcriptional profiling experiment by studying the transcriptomic response of Salmonella inoculated on chicken meat and exposed to d-limonene. We successfully applied our method in this experiment to recover the bacterial cells from the meat matrix and to extract the RNA. We obtained high yield and pure RNA. Subsequently, the RNA was used for downstream transcriptional profiling studies using microarrays and over 600 differentially regulated genes were identified.

Conclusions

Our result showed that 8 log cfu/g of Salmonella is ideal to obtain optimal RNA amount and purity. Our results demonstrated that RNAprotect yielded higher RNA amounts (approximately 10 to 30 fold) when compared to 0.1% peptone water. The differences between the RNAprotect and 0.1% peptone samples were significant at a p-value of 0.03 for the bead beater method and 0.0005 for the sonication method, respectively. The microarray experiment demonstrated that the chicken samples do not interfere with the hybridization of Salmonella cDNA on the array slide. Hence, the background chicken RNA will not interfere with the microarray analysis when poultry meat models are used. Finally, we successfully demonstrated the application of the poultry meat model proposed in this study by conducting transcriptional profiling analysis of Salmonella inoculated on the poultry. Results of this study proved that this method has the potential to be employed in other meat model studies.

Microbial cell arrays

The coming of age of whole-cell biosensors, combined with the continuing advances in array technologies, has prepared the ground for the next step in the evolution of both disciplines - the whole cell array. In the present chapter, we highlight the state-of-the-art in the different disciplines essential for a functional bacterial array. These include the genetic engineering of the biological components, their immobilization in different polymers, technologies for live cell deposition and patterning on different types of solid surfaces, and cellular viability maintenance. Also reviewed are the types of signals emitted by the reporter cell arrays, some of the transduction methodologies for reading these signals, and the mathematical approaches proposed for their analysis. Finally, we review some of the potential applications for bacterial cell arrays, and list the future needs for their maturation: a richer arsenal of high-performance reporter strains, better methodologies for their incorporation into hardware platforms, design of appropriate detection circuits, the continuing development of dedicated algorithms for multiplex signal analysis, and - most importantly - enhanced long term maintenance of viability and activity on the fabricated biochips.

New approaches for functional genomic studies in staphylococci

Functional transcriptomics studies have resulted in interesting insights into Staphylococcus aureus diversity and pathogenicity. Here we review the principles, advantages and disadvantages of recent technical developments in the field of transcriptomics and their potential impact on S. aureus research.

Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity

BACKGROUND

The ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evolution and response to intra- and extra-cellular stimuli. Chickpea is the world's third most important food legume grown in over 40 countries representing all the continents. Despite its importance in plant evolution, role in human nutrition and stress adaptation, very little ESTs and differential transcriptome data is available, let alone genotype-specific gene signatures. Present study focuses on Fusarium wilt responsive gene expression in chickpea.

RESULTS

We report 6272 gene sequences of immune-response pathway that would provide genotype-dependent spatial information on the presence and relative abundance of each gene. The sequence assembly led to the identification of a CaUnigene set of 2013 transcripts comprising of 973 contigs and 1040 singletons, two-third of which represent new chickpea genes hitherto undiscovered. We identified 209 gene families and 262 genotype-specific SNPs. Further, several novel transcription regulators were identified indicating their possible role in immune response. The transcriptomic analysis revealed 649 non-cannonical genes besides many unexpected candidates with known biochemical functions, which have never been associated with pathostress-responsive transcriptome.

CONCLUSION

Our study establishes a comprehensive catalogue of the immune-responsive root transcriptome with insight into their identity and function. The development, detailed analysis of CaEST datasets and global gene expression by microarray provide new insight into the commonality and diversity of organ-specific immune-responsive transcript signatures and their regulated expression shaping the species specificity at genotype level. This is the first report on differential transcriptome of an unsequenced genome during vascular wilt.

Insect symbioses: a case study of past, present, and future fungus-growing ant research

Fungus-growing ants (Attini: Formicidae) engage in an obligate mutualism with fungi they cultivate for food. Although biologists have been fascinated with fungus-growing ants since the resurgence of natural history in the modern era, the early stages of research focused mainly on the foraging behavior of the leaf-cutters (the most derived attine lineage). Indeed, the discovery that the ants actually use leaf fragments to manure a fungus did not come until the 1800s. More recently, three additional microbial symbionts have been described, including specialized microfungal parasites of the ant's fungus garden, antibiotic-producing actinobacteria that help protect the fungus garden from the parasite, and a black yeast that parasitizes the ant-actinobacteria mutualism. The fungus-growing ant symbiosis serves as a particularly useful model system for studying insect-microbe symbioses, because, to date, it contains four well-characterized microbial symbionts, including mutualists and parasites that encompass micro-fungi, macro-fungi, yeasts, and bacteria. Here, we discuss approaches for studying insect-microbe symbioses, using the attine ant-microbial symbiosis as our framework. We draw attention to particular challenges in the field of symbiosis, including the establishment of symbiotic associations and symbiont function. Finally, we discuss future directions in insect-microbe research, with particular focus on applying recent advances in DNA sequencing technologies.

Novel developments for improved detection of specific mRNAs by DNA chips

Microarrays have revolutionized gene expression analysis as they allow for highly parallel monitoring of mRNA levels of thousands of genes in a single experiment. Since their introduction some 15 years ago, substantial progress has been achieved with regard to, e.g., faster or more sensitive analyses. In this review, interesting new approaches for a more sensitive detection of specific mRNAs will be highlighted. Particularly, the potential of electrical DNA chip formats that allow for faster mRNA analyses will be discussed.

Evidence of horizontal gene transfer between human and animal commensal Escherichia coli strains identified by microarray

Bacteria exchange genetic material by horizontal gene transfer (HGT). To evaluate the impact of HGT on Escherichia coli genome plasticity, 19 commensal strains collected from the intestinal floras of humans and animals were analyzed by microarrays. Strains were hybridized against an oligoarray containing 2700 E. coli K12 chromosomal genes. A core (genes shared among compared genomes) and a flexible gene pool (genes unique for each genome) have been identified. Analysis of hybridization signals evidenced 1015 divergent genes among the 19 strains and each strain showed a specific genomic variability pattern. Four hundred and fifty-eight genes were characterized by higher rates of interstrain variation and were considered hyperdivergent. These genes are not randomly distributed onto the chromosome but are clustered in precise regions. Hyperdivergent genes belong to the flexible gene pool and show a specific GC content, differing from that of the chromosome, indicating acquisition by HGT. Among these genes, those involved in defense mechanisms and cell motility as well as intracellular trafficking and secretion were far more represented than others. The observed genome plasticity contributes to the maintenance of genetic diversity and may therefore be a source of evolutionary adaptation and survival.

Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris

Construction of a microarray based on the genome of Xanthomonas campestris pv.campestris (Xcc), and its use to analyse 18 other virulent Xcc strains, revealed insights into the genetic diversity and determinants of host specificity of Xcc strains.

Background

Xanthomonas campestris pathovar campestris (Xcc) is the causal agent of black rot disease of crucifers worldwide. The molecular genetic diversity and host specificity of Xcc are poorly understood.

Results

We constructed a microarray based on the complete genome sequence of Xcc strain 8004 and investigated the genetic diversity and host specificity of Xcc by array-based comparative genome hybridization analyses of 18 virulent strains. The results demonstrate that a genetic core comprising 3,405 of the 4,186 coding sequences (CDSs) spotted on the array are conserved and a flexible gene pool with 730 CDSs is absent/highly divergent (AHD). The results also revealed that 258 of the 304 proved/presumed pathogenicity genes are conserved and 46 are AHD. The conserved pathogenicity genes include mainly the genes involved in type I, II and III secretion systems, the quorum sensing system, extracellular enzymes and polysaccharide production, as well as many other proved pathogenicity genes, while the AHD CDSs contain the genes encoding type IV secretion system (T4SS) and type III-effectors. A Xcc T4SS-deletion mutant displayed the same virulence as wild type. Furthermore, three avirulence genes (avrXccC, avrXccE1 and avrBs1) were identified. avrXccC and avrXccE1 conferred avirulence on the hosts mustard cultivar Guangtou and Chinese cabbage cultivar Zhongbai-83, respectively, and avrBs1 conferred hypersensitive response on the nonhost pepper ECW10R.

Conclusion

About 80% of the Xcc CDSs, including 258 proved/presumed pathogenicity genes, is conserved in different strains. Xcc T4SS is not involved in pathogenicity. An efficient strategy to identify avr genes determining host specificity from the AHD genes was developed.

Regulation of whole bacterial pathogen transcription within infected hosts

DNA microarrays are a powerful and promising approach to gain a detailed understanding of the bacterial response and the molecular cross-talk that can occur as a consequence of host-pathogen interactions. However, published studies mainly describe the host response to infection. Analysis of bacterial gene regulation in the course of infection has confronted many challenges. This review summarizes the different strategies used over the last few years to investigate, at the genomic scale, and using microarrays, the alterations in the bacterial transcriptome in response to interactions with host cells. Thirty-seven studies involving 19 different bacterial pathogens were compiled and analyzed. Our in silico comparison of the transcription profiles of bacteria grown in broth or in contact with eukaryotic cells revealed some features commonly observed when bacteria interact with host cells, including stringent response and cell surface remodeling.

The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum

The complete nucleotide sequence of the Corynebacterium glutamicum ATCC 13032 genome was previously determined and allowed the reliable prediction of 3002 protein-coding genes within this genome. Using computational methods, we have defined 158 genes, which form the minimal repertoire for proteins that presumably act as transcriptional regulators of gene expression. Most of these regulatory proteins have a direct role as DNA-binding transcriptional regulator, while others either have less well-defined functions in transcriptional regulation or even more general functions, such as the sigma factors. Recent advances in genome-wide transcriptional profiling of C. glutamicum generated a huge amount of data on regulation of gene expression. To understand transcriptional regulation of gene expression from the perspective of systems biology, rather than from the analysis of an individual regulatory protein, we compiled the current knowledge on the defined DNA-binding transcriptional regulators and their physiological role in modulating transcription in response to environmental signals. This comprehensive data collection provides a solid basis for database-guided reconstructions of the gene regulatory network of C. glutamicum, currently comprising 56 transcriptional regulators that exert 411 regulatory interactions to control gene expression. A graphical reconstruction revealed first insights into the functional modularity, the hierarchical architecture and the topological design principles of the transcriptional regulatory network of C. glutamicum.

Detection of bacteria associated with harmful algal blooms from coastal and microcosm environments using electronic microarrays

With the global expansion of harmful algal blooms (HABs), several measures, including molecular approaches, have been undertaken to monitor its occurrence. Many reports have indicated the significant roles of bacteria in controlling algal bloom dynamics. Attempts have been made to utilize the bacteria/harmful algae relationship in HAB monitoring. In this study, bacterial assemblages monitored during coastal HABs and bacterial communities in induced microcosm blooms were investigated. Samples were analysed using denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene. DGGE bands with peculiar patterns before, during, and after algal blooms were isolated and identified. Probes for six ribotypes representing organisms associated with Chatonella spp., Heterocapsa circularisquama, or Heterosigma akashiwo were used for analysis on NanoChip electronic microarray. In addition, a new approach using cultured bacteria species was developed to detect longer (533 bp) polymerase chain reaction-amplified products on the electronic microarray. The use of fluorescently labelled primers allowed the detection of individual species in single or mixed DNA conditions. The developed approach enabled the detection of the presence or absence and relative abundance of the HAB-related ribotypes in coastal and microcosm blooms. This study indicates the ability of electronic microarray platform to detect or monitor bacteria in natural and induced environments.

Expression profiling of Yersinia pestis during mouse pulmonary infection

Yersinia pestis, the causative agent of plague, can be transmitted by infected flea bite or inhaled aerosol. Both routes of infection have a high mortality rate, and pneumonic infections of Y. pestis represent a significant concern as a tool of bioterrorism. Understanding the transcriptional program of this pathogen during pulmonary infection should be valuable in understanding plague pathogenesis, as well as potentially offering insights into new vaccines and therapeutics. Toward this goal we developed a long oligonucleotide microarray to the plague bacillus and evaluated the expression profiles of Y. pestis in vitro and in the mouse pulmonary infection model in vivo. The in vitro analysis compared expression patterns at 27 versus 37 degrees C, as a surrogate of the transition from the flea to the mammalian host. The in vivo analysis used intranasal challenge to the mouse lung. By amplifying the Y. pestis RNA from individual mouse lungs we were able to map the transcriptional profile of plague at postinfection days 1 to 3. Our data present a very different transcriptional profile between in vivo and in vitro expression, suggesting Y. pestis responds to a variety of host signals during infection. Of note was the number of genes found in genomic regions with altered %GC content that are upregulated within the mouse lung environment. These data suggest these regions may provide particularly promising targets for both vaccines and therapeutics.

The impact of functional genomics on microbiological food quality and safety

In the food processing industry, unwanted occurrence and growth of spoilage and pathogenic microorganisms is a key concern. A prime example is the extremely heat resistant bacterial endospores, microbial survival structures, that create problems due to their ability to survive classical thermal treatments and their ability to subsequently germinate and form actively growing vegetative cells. Research on food spoilage Bacillus subtilis isolates using the Amplified Fragment Length Polymorphism (AFLP) technology and micro-array technology has identified a number of genomic factors correlated to the level of spore heat resistance. Strains could be classified according to these genomic markers. In addition, it was shown with the sequenced B. subtilis laboratory strain that sporulation in the presence of in particular calcium ions in a cocktail of calcium, magnesium, iron, manganese and potassium promotes thermal resistance of developing spores. This physiological observation correlated with an increased expression during sporulation of genes encoding small acid soluble spore proteins. Screening of ingredients using DNA-chip based techniques identifying the above indicated molecular markers, should allow in the future the identification of the occurrence of spoilage and pathogenic bacteria and prediction of their thermal preservation stress resistance. Currently various projects aiming at the integration of genomics data and micro(nano)-technology, a prerequisite if the alluded to ingredient Quality Control is going to succeed, are running or are being set-up. Information from these projects will be used together with the requirements of product organoleptic quality to derive robust integrated food safety and food quality processing parameters. Such parameters should form the basis of future food Quality Assurance systems.

Exploration of soil bacterial communities for their potential as bioresource

Soil is a repository of diverse microorganisms, which has frequently been used to isolate and exploit microbes for industrial, environmental and agricultural applications. Knowledge about the structure and dynamics of bacterial communities in soil has been limited as only a small fraction of bacterial diversity is accessible to culture methods. Traditional enrichment techniques and the pure culture approach for microbiological studies have offered only a narrow portal for examining the soil microbial flora due to their limited selectivity. Therefore, the morphological and nutritional criteria used to describe bacterial community failed to provide a natural taxonomic order according to evolutionary relationship. Molecular methods under an emerging discipline of biology "molecular microbial ecology" are now helping in getting these constraints removed to some extent. Nucleic acid extraction from soil is the first crucial step in the application of most of the molecular techniques, which have largely been dominated by diverse variations of PCR. Due to its rapidity, sensitivity and specificity, PCR-based finger printing techniques have proved extremely useful in assessing the changes in microbial community structure. Such techniques can yield complex community profiles and can also provide useful phylogenetic information. Fluorescent in situ hybridization (FISH) can be used to evaluate the distribution and function of bacterial population in situ. DNA microarray techniques have also been developed and being frequently used for the evaluation of ecological role and phylogenetic affiliations of bacterial populations in the soil.

Rapid bacterial identification using evanescent-waveguide oligonucleotide microarray classification

Bacterial identification relies primarily on culture-based methodologies and requires 48-72 h to deliver results. We developed and used i) a bioinformatics strategy to select oligonucleotide signature probes, ii) a rapid procedure for RNA labelling and hybridization, iii) an evanescent-waveguide oligoarray with exquisite signal/noise performance, and iv) informatics methods for microarray data analysis. Unique 19-mer signature oligonucleotides were selected in the 5'-end of 16s rDNA genes of human pathogenic bacteria. Oligonucleotides spotted onto a Ta(2)O(5)-coated microarray surface were incubated with chemically labelled total bacterial RNA. Rapid hybridization and stringent washings were performed before scanning and analyzing the slide. In the present paper, the eight most abundant bacterial pathogens representing >54% of positive blood cultures were selected. Hierarchical clustering analysis of hybridization data revealed characteristic patterns, even for closely related species. We then evaluated artificial intelligence-based approaches that outperformed conventional threshold-based identification schemes on cognate probes. At this stage, the complete procedure applied to spiked blood cultures was completed in less than 6 h. In conclusion, when coupled to optimal signal detection strategy, microarrays provide bacterial identification within a few hours post-sampling, allowing targeted antimicrobial prescription.

Development and applications of microbial ecogenomic indicators for monitoring water quality: report of a workshop assessing the state of the science, research needs and future directions

This article brings forth recommendations from a workshop sponsored by the U.S. Environmental Protection Agency's Science to Achieve Results (STAR) and Environmental Monitoring and Assessment (EMAP) Programs and by the Council of State Governments, held during May 2002 in Kansas City, Kansas. The workshop assembled microbial ecologists and environmental scientists to determine what research and science is needed to bring existing molecular biological approaches and newer technologies arising from microbial genomic research into environmental monitoring and water quality assessments. Development of genomics and proteomics technologies for environmental science is a very new area having potential to improve environmental water quality assessments. The workshop participants noted that microbial ecologists are already using molecular biological methods well suited for monitoring and water quality assessments and anticipate that genomics-enabled technologies could be made available for monitoring within a decade. Recommendations arising from the workshop include needs for (i) identification of informative microbial gene sequences, (ii) improved understandings of linkages between indicator taxa, gene expression and environmental condition, (iii) technological advancements towards field application, and (iv) development of the appropriate databases.

Molecular techniques in wastewater: Understanding microbial communities, detecting pathogens, and real-time process control

Traditionally, the detection of pathogens in water, wastewater, and other environmental samples is restricted by the ability to culture such organisms from complex environmental samples. During the last decade the use of molecular methods have supplied the means for examining microbial diversity and detecting specific organisms without the need for cultivation. The application of molecular techniques to the study of natural and engineered environmental systems has increased our insight into the vast diversity and interaction of microorganisms present in complex environments. In this paper, we will review the current and emerging molecular approaches for characterizing microbial community composition and structure in wastewater processes. Recent studies show that advances in microarray assays are increasing our capability of detecting hundreds and even thousands of DNA sequences simultaneously and rapidly. With the current progress in microfluidics and optoelectronics, the ability to automate a detection/identification system is now being realized. The status of such a system for wastewater monitoring is discussed.

A novel system for large-scale gene expression analysis: bacterial colonies array

In the present work, we report the use of bacterial colonies to optimize macroarray technique. The devised system is significantly cheaper than other methods available to detect large-scale differential gene expression. Recombinant Escherichia coli clones containing plasmid-encoded copies of 4,608 individual expressed sequence tag (ESTs) were robotically spotted onto nylon membranes that were incubated for 6 and 12 h to allow the bacteria to grow and, consequently, amplify the cloned ESTs. The membranes were then hybridized with a beta-lactamase gene specific probe from the recombinant plasmid and, subsequently, phosphorimaged to quantify the microbial cells. Variance analysis demonstrated that the spot hybridization signal intensity was similar for 3,954 ESTs (85.8%) after 6 h of bacterial growth. Membranes spotted with bacteria colonies grown for 12 h had 4,017 ESTs (87.2%) with comparable signal intensity but the signal to noise ratio was fivefold higher. Taken together, the results of this study indicate that it is possible to investigate large-scale gene expression using macroarrays based on bacterial colonies grown for 6 h onto membranes.

Optimized DNA microarray assay allows detection and genotyping of single PCR-amplifiable target copies

This study was conducted to determine the detection limit of an optimized DNA microarray assay for detection and species identification of chlamydiae. Examination of dilution series of a plasmid standard carrying the target sequence from Chlamydia trachomatis and genomic DNA of this organism revealed that a single PCR-amplifiable target copy was sufficient to obtain a specific hybridization pattern. This performance renders the test suitable for routine testing of clinical samples.

A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus

BACKGROUND

DNA microarray technology is widely used to determine the expression levels of thousands of genes in a single experiment, for a broad range of organisms. Optimal design of immobilized nucleic acids has a direct impact on the reliability of microarray results. However, despite small genome size and complexity, prokaryotic organisms are not frequently studied to validate selected bioinformatics approaches. Relying on parameters shown to affect the hybridization of nucleic acids, we designed freely available software and validated experimentally its performance on the bacterial pathogen Staphylococcus aureus.

RESULTS

We describe an efficient procedure for selecting 40-60 mer oligonucleotide probes combining optimal thermodynamic properties with high target specificity, suitable for genomic studies of microbial species. The algorithm for filtering probes from extensive oligonucleotides libraries fitting standard thermodynamic criteria includes positional information of predicted target-probe binding regions. This algorithm efficiently selected probes recognizing homologous gene targets across three different sequenced genomes of Staphylococcus aureus. BLAST analysis of the final selection of 5,427 probes yielded >97%, 93%, and 81% of Staphylococcus aureus genome coverage in strains N315, Mu50, and COL, respectively. A manufactured oligoarray including a subset of control Escherichia coli probes was validated for applications in the fields of comparative genomics and molecular epidemiology, mapping of deletion mutations and transcription profiling.

CONCLUSION

This generic chip-design process merging sequence information from several related genomes improves genome coverage even in conserved regions.

Exploiting Molecular Methods to Explore Endodontic Infections: Part 1—Current Molecular Technologies for Microbiological Diagnosis

Endodontic infections have been traditionally studied by culture-dependent methods. However, as with other areas of clinical microbiology, culture-based investigations are plagued by significant problems, including the probable involvement of viable but uncultivable micro-organisms with disease causation and inaccurate microbial identification. Innumerous molecular technologies have been used for microbiological diagnosis in clinical microbiology, but only recently some of these techniques have been applied in endodontic microbiology research. This paper intended to review the main molecular methods that have been used or have the potential to be used in the study of endodontic infections. Moreover, advantages and limitations of current molecular techniques when compared to conventional methods for microbial identification are also discussed.

Real-time Fluorescent PCR Techniques to Study Microbial-Host Interactions

This chapter describes how real-time polymerase chain reaction (PCR) performs and how it may be used to detect microbial pathogens and the relationship they form with their host. Research and diagnostic microbiology laboratories contain a mix of traditional and leading-edge, in-house and commercial assays for the detection of microbes and the effects they impart upon target tissues, organs, and systems. The PCR has undergone significant change over the last decade, to the extent that only a small proportion of scientists have been able or willing to keep abreast of the latest offerings. The chapter reviews these changes. It discusses the second-generation of PCR technology-kinetic or real-time PCR, a tool gaining widespread acceptance in many scientific disciplines but especially in the microbiology laboratory.

DNA microarrays — techniques and applications in microbial systems

Genome projects produce a huge amount of sequence information. As a result, the focus of genomics research is turning toward deduction of functional information about newly discovered genes. Thus structural genomics paves the way for a new discipline called functional genomics by providing the information required for microarray manufacture. Microarray technology is the result of automation and miniaturization in the detection of differential gene expression. By using this technology one can make a parallel analysis of RNA abundance and DNA homology for thousands of genes in a single experiment. Over the past several years, this unique technology has been used to explore hundreds transcriptional patterns and genome differences for a variety of microbial species. Applications of microarrays extend beyond the boundaries of basic biology into diagnostics, environmental monitoring, pharmacology, toxicology and biotechnology. We describe comprehensive nature of DNA microarray technology with emphasis on fabrication of DNA microarrays and application of this technology in biological environment with primary accent on microbial systems.

Microarrays and gene expression profiling in microbiology and infectious diseases: a clinician's perspective

Advances in molecular biology, bioinformatics, and robotics have allowed microarray technology to be used for in-depth, basic science studies in all fields of microbiology. Recently, translation of these basic science applications to clinical microbiology and infectious diseases has also progressed. From a clinical infectious disease perspective, genome-based organism identification, pathogen discovery, and antimicrobial susceptibility testing of problematic organisms offer the potential to yield diagnostic information that may not otherwise become available. Moreover, microarray-based studies have the ability to provide “signatures” of host cell transcriptional responses for individual pathogens and/or groups of pathogens. This type of information has the potential to confirm difficult diagnoses, to monitor responses to therapeutic intervention, or even to predict prognosis and sequelae following an infectious disease. Examples are presented to illustrate ways in which microarray technology has already impacted these areas of clinical microbiology.

A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium

Fis is a key DNA-binding protein involved in nucleoid organization and modulation of many DNA transactions, including transcription in enteric bacteria. The regulon of genes whose expression is influenced by Fis inSalmonella entericaserovar Typhimurium (S. typhimurium) has been defined by DNA microarray analysis. These data suggest that Fis plays a central role in coordinating the expression of both metabolic and type III secretion factors. The genes that were most strongly up-regulated by Fis were those involved in virulence and located in the pathogenicity islands SPI-1, SPI-2, SPI-3 and SPI-5. Similarly, motility and flagellar genes required Fis for full expression. This was shown to be a direct effect as purified Fis protein bound to the promoter regions of representative flagella and SPI-2 genes. Genes contributing to aspects of metabolism known to assist the bacterium during survival in the mammalian gut were also Fis-regulated, usually negatively. This category included components of metabolic pathways for propanediol utilization, biotin synthesis, vitamin B12transport, fatty acids and acetate metabolism, as well as genes for the glyoxylate bypass of the tricarboxylic acid cycle. Genes found to be positively regulated by Fis included those for ethanolamine utilization. The data reported reveal the central role played by Fis in coordinating the expression of both housekeeping and virulence factors required byS. typhimuriumduring life in the gut lumen or during systemic infection of host cells.

Biosensors for the detection of bacteria

This review will consider the role of biosensors towards the detection of infectious bacteria, although non-infectious ones will be considered where necessary. Recently, there has been a heightened interest in developing rapid and reliable methods of detection. This is especially true for detection of organisms involved in bioterrorism, food poisoning, and clinical problems such as antibiotic resistance. Biosensors can assist in achieving these goals, and sensors using several of the different types of transduction modes are discussed: electrochemical, high frequency (surface acoustic wave), and optical. The paper concludes with a discussion of three areas that may make a great impact in the next few years: integrated (lab-on-a-chip) systems, molecular beacons, and aptamers.

Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data

Genome2D is a software tool that enables bacterial transcriptome data to be visualized on chromosome maps.

Genome2D is a Windows-based software tool for visualization of bacterial transcriptome and customized datasets on linear chromosome maps constructed from annotated genome sequences. Genome2D facilitates the analysis of transcriptome data by using different color ranges to depict differences in gene-expression levels on a genome map. Such output format enables visual inspection of the transcriptome data, and will quickly reveal transcriptional units, without prior knowledge of expression level cutoff values. The compiled version of Genome2D is freely available for academic or non-profit use from .

Infectious diseases in the 21st century: old challenges and new opportunities

Infectious diseases are the confrontation of two worlds, the microbial world and the world of human physiology. Although these two worlds are as a whole governed by the same laws of nature, they show substantial differences: the microbiological world is 1000 times older, and was initiated by the development of the archaea, the 'living organisms of the extreme': its biomass and its diversity are immense - two to three billion species or 60% of the total biomass of the planet. The number of pathogens that adapted to man, however, is extremely limited - barely 1000. Thus, over billions of years, an evolution of the microbial world took place from 'early life', characterized by chemosynthesis, to the 'modern pathogens', and entailed a dramatic 'concentration' of life conditions and an adaptation towards a narrow range of requirements - those allowing survival in the human body. Within the last two centuries, these two slowly evolving systems, microbial life and human life, were profoundly modified in an unprecedented manner by a third player, human civilization, with its global impact on the environment through physical, chemical, societal, and climatic determinants. An appreciation of the evolution of infectious diseases in the 21st century and of the development of new diagnostic and therapeutic strategies therefore requires a full understanding of these three domains: human physiology, microbiology, and the environment. This review will put major emphasis on the environmental role of civilization on infectious diseases before considering new opportunities to combat them through novel and creative solutions.

The temporal expression profile of Mycobacterium tuberculosis infection in mice

Infection with Mycobacterium tuberculosis causes the illness tuberculosis with an annual mortality of approximately 2 million. Understanding the nature of the host-pathogen interactions at different stages of tuberculosis is central to new strategies for developing chemotherapies and vaccines. Toward this end, we adapted microarray technology to analyze the change in gene expression profiles of M. tuberculosis during infection in mice. This protocol provides the transcription profile of genes expressed during the course of early tuberculosis in immune-competent (BALB/c) and severe combined immune-deficient (SCID) hosts in comparison with growth in medium. The microarray analysis revealed clusters of genes that changed their transcription levels exclusively in the lungs of BALB/c, SCID mice, or medium over time. We identified a set of genes (n = 67) activated only in BALB/c and not in SCID mice at 21 days after infection, a key point in the progression of tuberculosis. A subset of the lung-activated genes was previously identified as induced during mycobacterial survival in a macrophage cell line. Another group of in vivo-expressed genes may also define a previously unreported genomic island. In addition, our analysis suggests the similarity between mycobacterial transcriptional machinery during growth in SCID and in broth, which questions the validity of using the SCID model for assessing mycobacterial virulence. The in vivo expression-profiling technology presented should be applicable to any microbial model of infection.

Computational methods and evaluation of RNA stabilization reagents for genome-wide expression studies

Gene expression studies require high quality messenger RNA (mRNA) in addition to other factors such as efficient primers and labeling reagents. To prevent RNA degradation and to improve the quality of gene array expression data, several commercial reagents have become available. We examined a conventional hot-phenol lysis method and RNA stabilization reagents, and generated comparative gene expression profiles from Escherichia coli cells grown on minimal medium. Our data indicate that certain RNA stabilization reagents induce stress responses and proper caution must be exercised during their use. We observed that the laboratory reagent (phenol/EtOH, 5:95, v/v) worked efficiently in isolating high quality mRNA and reproducibility was such that reliable gene expression profiles were generated. To assist in the analysis of gene expression data, we wrote a number of macros that use the most recent gene annotation and process data in accordance with gene function. Scripts were also written to examine the occurrence of artifacts, based on GC content, length of the individual open reading frame (ORF), its distribution on plus and minus DNA strands, and the distance from the replication origin.

DNA array analysis of gene expression in response to UV irradiation in Escherichia coli

The capacity of DNA macroarrays that contain all 4290 predicted open reading frames of the E. coli K12 genome was evaluated by measuring changes in gene expression in response to irradiation by ultraviolet light (UV). UV and other DNA damaging agents are known to trigger the induction of the SOS response. This is a coordinated increase in the level of expression of a set of approximately 30 unlinked genes, the SOS genes, negatively regulated by the LexA repressor. The analysis was performed on a set of isogenic strains with mutations that affect expression of genes of the SOS system: (i) the lexA+ strain, in which the SOS system can be induced after DNA damage, (ii) lexAind- mutants in which the SOS system cannot be induced, and (iii) lexAdef mutants in which the SOS system is induced constitutively. We found that a large set of genes appeared to be either upregulated or downregulated following UV irradiation. Among the genes which appeared to be upregulated in a LexA-dependent manner, we correctly identified 9 out of 27 SOS genes printed on the arrays and one gene containing a LexA binding site. One gene, dnaN, encoding the beta subunit of DNA polymerase III holoenzyme, was identified as an upregulated gene in a LexA-independent manner. Our results were compared to those of similar studies previously published. Although the SOS response as a whole could not be illustrated by using DNA arrays, the data suggest that regulation of some SOS genes might be more complex than previously thought.

Comparison of fluorescence and resonance light scattering for highly sensitive microarray detection of bacterial pathogens

Microarrays have emerged as potential tools for bacterial detection and identification. Given their high parallelism, they might represent a breakthrough in current diagnostic methods, provided they can be coupled to simplified labeling protocols and detected with adequate sensitivities. We describe here a technique to directly label total bacterial RNA, thus avoiding the multiple steps and possible biases associated with enzymatic amplification (e.g. PCR). We have then compared the performances of one white-light source and two laser-based fluorescence scanners for detection reliability and sensitivity. Our study reveals that nanoparticle-labeled bacterial RNA generates reproducible resonance light scattering signals that are at least 50 times more intense than state-of-the-art confocal-based fluorescence signals.

Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source

A DNA microarray was developed to analyse global gene expression of the amino acid-producing bacterium Corynebacterium glutamicum. PCR products representing 93.4% of the predicted C. glutamicum genes were prepared and spotted in quadruplicate onto 3-aminopropyltrimethoxysilane-coated glass slides. The applicability of the C. glutamicum DNA microarray was demonstrated by co-hybridisation with fluorescently labelled cDNA probes. Analysis of the technical variance revealed that C. glutamicum genes detected with different intensities resulting in ratios greater than 1.52 or smaller than -1.52 can be regarded as differentially expressed with a confidence level of greater than 95%. In a validation example, we measured changes of the mRNA levels during growth of C. glutamicum with acetate and propionate as carbon sources. Acetate-grown C. glutamicum cultures were used as reference. At the 95% confidence interval, 117 genes revealed increased transcript levels in the presence of propionate, while 43 genes showed a decreased expression compared with the acetate-grown culture. Global expression profiling confirmed the induction of the prpD2B2C2 gene cluster already known to be essential for propionate degradation via the 2-methylcitrate cycle. Besides many genes of unknown function, the paralogous prpD1B1C1 gene cluster as well as fasI-B (encoding fatty-acid synthase IB), dtsR1 and dtsR2 (components of acyl-CoA carboxylases), gluABCD (glutamate transport system), putP (proline transport system), and pyc (pyruvate carboxylase) showed significantly increased expression levels. Differential expression of these genes was confirmed by real-time reverse transcription (RT) PCR assays.

Customized cDNA microarray for expression profiling of environmentally important genes of Pseudomonas stutzeri strain KC

DNA microarray is a powerful tool for parallel detection of multiple target genes in biological systems. In this study, a low-density DNA microarray has been custom designed by using Pseudomonas stutzeri strain KC ORFs that are implicated in carbon tetrachloride degradation. PCR amplified strain KC probes of varying lengths were obtained using ORF-specific primers. Purified short probes (80-120 bp) and full-length amplicons were directly immobilized on gamma-aminosilane coated and superaldehyde trade mark glass substrates without any chemical modification. The full-length amplicons exhibited a much higher signal compared to the shorter probes upon hybridization with the Cy5/Cy3-labeled unfragmented cDNA targets. The meager signal with the shorter probes limits the advantage of using the multiple probes of the same genes for enhancing the specificity of hybridization with environmental samples. Nevertheless, expression analysis of strain KC genome, under controlled laboratory conditions, revealed the constitutive expression of at least 11 putative ORFs of the pdt operon. Comparatively weaker hybridization signals with the cDNA from mutant cells suggested a low abundance of mRNA transcripts in the KC 1896 mutant. Similar expression levels of the pdt ORFs I, J, K, M, N, O, P, and fur gene both under iron-limiting conditions and in presence of iron (20 micro M Fe(3+)) suggested metal ion-independent regulation of the pdt operon. The tailor-made array with strain KC gene-specific probes served as a model for demonstrating the utility of cDNA microarray technology in monitoring the expression of environmentally important genes in bacteria.

Acetate metabolism and its regulation in Corynebacterium glutamicum

The amino acid producing Corynebacterium glutamicum grows aerobically on a variety of carbohydrates and organic acids as single or combined sources of carbon and energy. Among the substrates metabolized are glucose and acetate which both can also serve as substrates for amino acid production. Based on biochemical, genetic and regulatory studies and on quantitative determination of metabolic fluxes during utilization of acetate and/or glucose, this review summarizes the present knowledge on the different steps of the fundamental pathways of acetate utilization in C. glutamicum, namely, on acetate transport, acetate activation, tricarboxylic acid (TCA) cycle, glyoxylate cycle and gluconeogenesis. It becomes evident that, although the pathways of acetate utilization follow the same theme in many bacteria, important biochemical, genetic and regulatory peculiarities exist in C. glutamicum. Recent genome wide and comparative expression analyses in C. glutamicum cells grown on glucose and on acetate substantiated previously identified transcriptional regulation of acetate activating enzymes and of glyoxylate cycle enzymes. Additionally, a variety of genes obviously also under transcriptional control in response to the presence or absence of acetate in the growth medium were uncovered. These genes, thus also belonging to the acetate stimulon of C. glutamicum, include genes coding for TCA cycle enzymes (e.g. aconitase and succinate dehydrogenase), for gluconeogenesis (phosphoenolpyruvate carboxykinase), for glycolysis (pyruvate dehydrogenase E1) and genes coding for proteins with hitherto unknown function. Although the basic mechanism of transcriptional regulation of the enzymes involved in acetate metabolism is not yet understood, some recent findings led to a better understanding of the adaptation of C. glutamicum to acetate at the molecular level.

Global analyses of transcriptomes and proteomes of a parent strain and an L-threonine-overproducing mutant strain

We compared the transcriptome, proteome, and nucleotide sequences between the parent strain Escherichia coli W3110 and the L-threonine-overproducing mutant E. coli TF5015. DNA macroarrays were used to measure mRNA levels for all of the genes of E. coli, and two-dimensional gel electrophoresis was used to compare protein levels. It was observed that only 54 of 4,290 genes (1.3%) exhibited differential expression profiles. Typically, genes such as aceA, aceB, icdA, gltA, glnA, leu operon, proA, thrA, thrC, and yigJ, which are involved in the glyoxylate shunt, the tricarboxylic acid cycle, and amino acid biosynthesis (L-glutamine, L-leucine, proline, and L-threonine), were significantly upregulated, whereas the genes dadAX, hdeA, hdeB, ompF, oppA, oppB, oppF, yfiD, and many ribosomal protein genes were downregulated in TF5015 compared to W3110. The differential expression such as upregulation of thr operon and expression of yigJ would result in an accumulation of L-threonine in TF5015. Furthermore, two significant mutations, thrA345 and ilvA97, which are essential for overproduction of L-threonine, were identified in TF5015 by the sequence analysis. In particular, expression of the mutated thrABC (pATF92) in W3110 resulted in a significant incremental effect on L-threonine production. Upregulation of aceBA and downregulation of b1795, hdeAB, oppA, and yfiD seem to be linked to a low accumulation of acetate in TF5015. Such comprehensive analyses provide information regarding the regulatory mechanism of L-threonine production and the physiological consequences in the mutant stain.