The evolution of Pyrosequencing® for microbiology: From genes to genomes

Mining the diversity and functional profile of bacterial symbionts from the larvae of Chironomus circumdatus (bloodworms)

Chironomids are the most abundant aquatic insects in freshwater habitats that can survive in extreme conditions. In this study, as the microbiome provides extended genotype to the host to perform various functions, we explored the microbiota of the Chironomus circumdatus larvae to find out the putative role played by the symbiotic bacteria for the host. The metabarcoding analyses of the larvae revealed that the insect harbors 1771 phylotypes. Out of the various microbial communities found, the majority corresponded to the phyla Proteobacteria (52.59%) and Actinobacteria (20.56%), respectively. The midges also harbored Klebsiella (2.57%), Enterobacter (1.32%), Bacillus (2.29%), and Acinetobacter (2.13%) genera that are involved in detoxification of xenobiotics present in the water. The presence of radiation-resistant genera like Deinococcus, including bacterial species like radiodurans, a highly radiation-resistant bacterium, indicates its potential to support the host's ability to sustain in adverse environments. The functional profiling of the bacteria showed the relative abundance of many enzyme groups, such as transferases (40.62%), oxidoreductases (23.49%), and hydrolases (3.77%). The results indicate that the larvae harbor a considerable variety of bacteria that help the host adapt and survive in the polluted waters. The present study provides thorough insights into the microbiome of the C. circumdatus larvae that can be exploited for the bioremediation of certain pollutants through biomimetic strategies. It also gives us a wake-up call to take a good look at the guts of these disease-carrying insects' inabilities to spread deadly human diseases.

An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists

High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the “dos and don’ts” involved in conducting a precise microbial ecology study.

Human microbial ecology and the rising new medicine

The first life forms on earth were Prokaryotic, and the evolution of all Eukaryotic life occurred with the help of bacteria. Animal-associated microbiota also includes members of the archaea, fungi, protists, and viruses. The genomes of this host-associated microbial life are called the microbiome. Across the mammalian tree, microbiomes guarantee the development of immunity, physiology, and resistance to pathogens. In humans, all surfaces and cavities are colonized by a microbiome, maintained by a careful balance between the host response and its colonizers-thus humans are considered now supraorganisms. These microbiomes supply essential ecosystem services that benefit health through homeostasis, and the loss of the indigenous microbiota leads to dysbiosis, which can have significant consequences to disease. This educational review aims to describe the importance of human microbial ecology, explain the ecological terms applied to the study of the human microbiome, developments within the cutting-edge microbiome field, and implications to diagnostic and treatment.

The human microbiome and metabolomics: Current concepts and applications

The mammalian gastrointestinal tract has co-developed with a large number of microbes in a symbiotic relationship over millions of years. Recent studies indicate that indigenous bacteria are intimate with the intestine and play essential roles in health and disease. In the quest to maintain a stable niche, these prokaryotes influence multiple host metabolic pathways, resulting from an interactive host-microbiota metabolic signaling and impacting strongly on the metabolic phenotypes of the host. Since dysbiosis of the gut bacteria result in alteration in the levels of certain microbial and host co-metabolites, identifying these markers could enhance early detection of diseases. Also, identification of these metabolic fingerprints could give us clues as to how to manipulate the microbiome to promote health or treat diseases. This review provides an overview of our current knowledge of the microbiome and metablomics, applications and the future perspectives.

Reef-Building Corals as a Tool for Climate Change Research in the Genomics Era

Coral reef ecosystems are among the most biodiverse habitats in the marine realm. They not only contribute with a plethora of ecosystem services, but they also are beneficial to humankind via nurturing marine fisheries and sustaining recreational activities. We will discuss the biology of coral reefs and their ecophysiology including the complex bacterial microbiota associated with them.

A Pyrosequencing-Based Approach to High-Throughput Identification of Influenza A(H3N2) Virus Clades Harboring Antigenic Drift Variants

The rapid evolution of influenza A(H3N2) viruses necessitates close monitoring of their antigenic properties so the emergence and spread of antigenic drift variants can be rapidly identified. Changes in hemagglutinin (HA) acquired by contemporary A(H3N2) viruses hinder antigenic characterization by traditional methods, thus complicating vaccine strain selection. Sequence-based approaches have been used to infer virus antigenicity; however, they are time consuming and mid-throughput. To facilitate virological surveillance and epidemiological studies, we developed and validated a pyrosequencing approach that enables identification of six HA clades of contemporary A(H3N2) viruses. The identification scheme of viruses of the H3 clades 3C.2, 3C.2a, 3C.2b, 3C.3, 3C.3a, and 3C.3b is based on the interrogation of five single nucleotide polymorphisms (SNPs) within three neighboring HA regions, namely 412 to 431, 465 to 481, and 559 to 571. Two bioinformatics tools, IdentiFire (Qiagen) and FireComb (developed in-house), were utilized to expedite pyrosequencing data analysis. The assay's analytical sensitivity was 10 focus forming units, and respiratory specimens with threshold cycle (C_T) values of <34 typically produced good quality pyrograms. When applied to 120 A(H3N2) virus isolates and 27 respiratory specimens, the assay displayed 100% agreement with clades determined by HA sequencing coupled with phylogenetics. The multi-SNP analysis described here was readily adopted by another laboratory with pyrosequencing capabilities. The implementation of this approach enhanced the findings from virological surveillance and epidemiological studies between 2013 and 2016, which examined more than 3,000 A(H3N2) viruses.

Rapid identification of nine species of diphyllobothriidean tapeworms by pyrosequencing

The identification of diphyllobothriidean tapeworms (Cestoda: Diphyllobothriidea) that infect humans and intermediate/paratenic hosts is extremely difficult due to their morphological similarities, particularly in the case of Diphyllobothrium and Spirometra species. A pyrosequencing method for the molecular identification of pathogenic agents has recently been developed, but as of yet there have been no reports of pyrosequencing approaches that are able to discriminate among diphyllobothriidean species. This study, therefore, set out to establish a pyrosequencing method for differentiating among nine diphyllobothriidean species, Diphyllobothrium dendriticum, Diphyllobothrium ditremum, Diphyllobothrium latum, Diphyllobothrium nihonkaiense, Diphyllobothrium stemmacephalum, Diplogonoporus balaenopterae, Adenocephalus pacificus, Spirometra decipiens and Sparganum proliferum, based on the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene as a molecular marker. A region of 41 nucleotides in the cox1 gene served as a target, and variations in this region were used for identification using PCR plus pyrosequencing. This region contains nucleotide variations at 12 positions, which is enough for the identification of the selected nine species of diphyllobothriidean tapeworms. This method was found to be a reliable tool not only for species identification of diphyllobothriids, but also for epidemiological studies of cestodiasis caused by diphyllobothriidean tapeworms at public health units in endemic areas.

Rapid Identification and Quantification of Aureococcus anophagefferens by qPCR Method (Taqman) in the Qinhuangdao Coastal Area: A Region for Recurrent Brown Tide Breakout in China

Since 2009, Aureococcus anophagefferens has caused brown tide to occur recurrently in Qinhuangdao coastal area, China. Because the algal cells of A. anophagefferens are so tiny (~3 µm) that it is very hard to identify exactly under a microscope for natural water samples, it is very urgent to develop a method for efficient and continuous monitoring. Here specific primers and Taqman probe are designed to develop a real-time quantitative PCR (qPCR) method for identification and quantification continually. The algal community and cell abundance of A. anophagefferens in the study area (E 119°20'-119°50' and N 39°30'-39°50') from April to October in 2013 are detected by pyrosequencing, and are used to validate the specification and precision of qPCR method for natural samples. Both pyrosequencing and qPCR shows that the targeted cells are present only in May, June and July, and the cell abundance are July > June > May. Although there are various algal species including dinoflagellata, diatom, Cryptomonadales, Chrysophyceae and Chlorophyta living in the natural seawater simultaneously, no disturbance happens to qPCR method. This qPCR method could detect as few as 10 targeted cells, indicating it is able to detect the algal cells at pre-bloom levels. Therefore, qPCR with Taqman probe provides a powerful and sensitive method to monitor the brown tide continually in Qinhuangdao coastal area, China. The results provide a necessary technology support for forecasting the brown tide initiation, in China.

Identification of abiotic and biotic reductive dechlorination in a chlorinated ethene plume after thermal source remediation by means of isotopic and molecular biology tools

Thermal tetrachloroethene (PCE) remediation by steam injection in a sandy aquifer led to the release of dissolved organic carbon (DOC) from aquifer sediments resulting in more reduced redox conditions, accelerated PCE biodegradation, and changes in microbial populations. These changes were documented by comparing data collected prior to the remediation event and eight years later. Based on the premise that dual C-Cl isotope slopes reflect ongoing degradation pathways, the slopes associated with PCE and TCE suggest the predominance of biotic reductive dechlorination near the source area. PCE was the predominant chlorinated ethene near the source area prior to thermal treatment. After thermal treatment, cDCE became predominant. The biotic contribution to these changes was supported by the presence of Dehalococcoides sp. DNA (Dhc) and Dhc targeted rRNA close to the source area. In contrast, dual C-Cl isotope analysis together with the almost absent VC (13)C depletion in comparison to cDCE (13)C depletion suggested that cDCE was subject to abiotic degradation due to the presence of pyrite, possible surface-bound iron (II) or reduced iron sulphides in the downgradient part of the plume. This interpretation is supported by the relative lack of Dhc in the downgradient part of the plume. The results of this study show that thermal remediation can enhance the biodegradation of chlorinated ethenes, and that this effect can be traced to the mobilisation of DOC due to steam injection. This, in turn, results in more reduced redox conditions which favor active reductive dechlorination and/or may lead to a series of redox reactions which may consecutively trigger biotically induced abiotic degradation. Finally, this study illustrates the valuable complementary application of compound-specific isotopic analysis combined with molecular biology tools to evaluate which biogeochemical processes are taking place in an aquifer contaminated with chlorinated ethenes.

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

The advent of next generation sequencing (NGS) has enabled investigations of the gut microbiome with unprecedented resolution and throughput. This has stimulated the development of sophisticated bioinformatics tools to analyze the massive amounts of data generated. Researchers therefore need a clear understanding of the key concepts required for the design, execution and interpretation of NGS experiments on microbiomes. We conducted a literature review and used our own data to determine which approaches work best. The two main approaches for analyzing the microbiome, 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics, are illustrated with analyses of libraries designed to highlight their strengths and weaknesses. Several methods for taxonomic classification of bacterial sequences are discussed. We present simulations to assess the number of sequences that are required to perform reliable appraisals of bacterial community structure. To the extent that fluctuations in the diversity of gut bacterial populations correlate with health and disease, we emphasize various techniques for the analysis of bacterial communities within samples (α-diversity) and between samples (β-diversity). Finally, we demonstrate techniques to infer the metabolic capabilities of a bacteria community from these 16S and shotgun data.

Pyrosequencing as a fast and reliable tool to determine clade affiliation for equine Influenza A virus

The objective of our study was to determine the clade affiliation of 116 contemporary equine Influenza A virus (EIV) isolates using pyrosequencing. The EIV isolates originated from horses with clinical signs of equine influenza and laboratory confirmation of EIV by real-time quantitative PCR (qPCR) in nasal secretions. Clade affiliation was performed on the basis of a single nucleotide polymorphism at 2 positions of the hemagglutinin 1 gene. Pyrosequencing was able to clearly classify EIV Florida sublineage prototype A/equine/Ohio/1/2003 and prototype A/equine/Richmond/1/2007 as clade 1 and 2, respectively. Out of the 116 EIV qPCR-positive samples, 113 (97.4%) were classified as belonging to clade 1 Florida sublineage, whereas 3 (2.6%) were classified as clade 2. All clade 1 EIV strains were detected in domestic horses, whereas the 3 clade 2 EIV strains originated from horses recently imported to the United States. Although clade 1 EIV strains are endemic in the United States, international transportation of horses represents a real risk in introducing clade 2 EIV strains into North America.

Optimization of biostimulant for bioremediation of contaminated coastal sediment by response surface methodology (RSM) and evaluation of microbial diversity by pyrosequencing

The present study aims to optimize the slow release biostimulant ball (BSB) for bioremediation of contaminated coastal sediment using response surface methodology (RSM). Different bacterial communities were evaluated using a pyrosequencing-based approach in contaminated coastal sediments. The effects of BSB size (1-5cm), distance (1-10cm) and time (1-4months) on changes in chemical oxygen demand (COD) and volatile solid (VS) reduction were determined. Maximum reductions of COD and VS, 89.7% and 78.8%, respectively, were observed at a 3cm ball size, 5.5cm distance and 4months; these values are the optimum conditions for effective treatment of contaminated coastal sediment. Most of the variance in COD and VS (0.9291 and 0.9369, respectively) was explained in our chosen models. BSB is a promising method for COD and VS reduction and enhancement of SRB diversity.

Pros and cons of ion-torrent next generation sequencing versus terminal restriction fragment length polymorphism T-RFLP for studying the rumen bacterial community

The development of next generation sequencing has challenged the use of other molecular fingerprinting methods used to study microbial diversity. We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP). Although absolute number differed, there was a high correlation between NGS and T-RFLP in terms of richness and diversity with R values of 0.836 and 0.781 for richness and Shannon-Wiener index, respectively. Dendrograms for both datasets were also highly correlated (Mantel test = 0.742). Eighteen OTUs and ten genera were significantly impacted by the addition of rumen protozoa, with an increase in the relative abundance of Prevotella, Bacteroides and Ruminobacter, related to an increase in free ammonia levels in the rumen. Our findings suggest that classic fingerprinting methods are still valuable tools to study microbial diversity and structure in complex environments but that NGS techniques now provide cost effect alternatives that provide a far greater level of information on the individual members of the microbial population.

Analysis of genomic imprinting by quantitative allele-specific expression by Pyrosequencing(®)

Genomic imprinting is a parent-of-origin phenomenon whereby gene expression is restricted to the allele inherited from either the maternal or paternal parent. It has been described from flowering plants and eutherian mammals and may have evolved due to parental conflicts over resource allocation. In mammals, imprinted genes are responsible for ensuring correct rates of embryo development and for preventing parthenogenesis. The molecular basis of imprinting depends upon the presence of differential epigenetic marks on the alleles inherited from each parent, although in plants the exact mechanisms that control imprinting are still unclear in many cases. Recent studies have identified large numbers of candidate imprinted genes from Arabidopsis thaliana and other plants (see Chap. 7 by Köhler and colleagues elsewhere in this volume) providing the tools for more thorough investigation into how imprinted gene networks (IGNs) are regulated. Analysis of genomic imprinting in animals has revealed important information on how IGNs are regulated during development, which often involves intermediate levels of imprinting. In some instances, small but significant changes in the degree of parental bias in gene expression have been linked to developmental traits, livestock phenotypes, and human disease. As some of the imprinted genes recently reported from plants show differential rather than complete (binary) imprinting, there is a clear need for tools that can quantify the degree of allelic expression bias occurring at a transcribed locus. In this chapter, we describe the use of Quantification of Allele-Specific Expression by Pyrosequencing(®) (QUASEP) as a tool suitable for this challenge. We describe in detail the factors which ensure that a Pyrosequencing(®) assay will be suitable for giving robust QUASEP and the problems which may be encountered during the study of imprinted genes by Pyrosequencing(®), with particular reference to our work in A. thaliana and in cattle. We also discuss some considerations with respect to the statistical analysis of the resulting data. Finally, we provide a brief overview of the future possibility of adapting Pyrosequencing(®) for analyzing other aspects of imprinting including the analysis of methylated regions.

Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems

The Brazilian Savanna, also known as "Cerrado", is the richest and most diverse savanna in the world and has been ranked as one of the main hotspots of biodiversity. The Cerrado is a representative biome in Central Brazil and the second largest biome in species diversity of South America. Nevertheless, large areas of native vegetation have been converted to agricultural land including grain production, livestock, and forestry. In this view, understanding how land use affects microbial communities is fundamental for the sustainable management of agricultural ecosystems. The aim of this work was to analyze and compare the soil bacterial communities from the Brazilian Cerrado associated with different land use systems using high throughput pyrosequencing of 16S rRNA genes. Relevant differences were observed in the abundance and structure of bacterial communities in soils under different land use systems. On the other hand, the diversity of bacterial communities was not relevantly changed among the sites studied. Land use systems had also an important impact on specific bacterial groups in soil, which might change the soil function and the ecological processes. Acidobacteria, Proteobacteria, and Actinobacteria were the most abundant groups in the Brazilian Cerrado. These findings suggest that more important than analyzing the general diversity is to analyze the composition of the communities. Since soil type was the same among the sites, we might assume that land use was the main factor defining the abundance and structure of bacterial communities.

Pyrosequencing for microbial identification and characterization

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns.

Analysis of the bacterial community in the two typical intertidal sediments of Bohai Bay, China by pyrosequencing

For full understanding of the bacterial community in the intertidal zones of Bohai Bay, China, we used pyrosequencing-based approach to analyze the 16S rRNA gene of bacteria in the sediments from the two typically intertidal zones - Qikou (Qi) and Gaoshaling (Ga). Results showed that, at a 0.03 distance, the sequences from the Qi sediment were assigned to 3252 operational taxonomic units (OTUs) which belong to 34 phyla, 69 classes and 119 genera, while the 3740 OTUs from the Ga sediment were affiliated with 33 phyla, 66 classes and 146 genera. Comparing the bacterial communities inhabiting in the two intertidal sediments, we observed significant difference in the dominant composition and distribution at phylum, class and genus levels. Canonical correspondence analysis (CCA) showed that the median grain size and DO were the most important factors regulating the bacterial abundance and diversity, while the other environmental factors have effects with different degree.

Pyrosequencing analysis of the bacterial community in drinking water wells

Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the iron-oxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.

Identification of hepatotropic viruses from plasma using deep sequencing: a next generation diagnostic tool

We conducted an unbiased metagenomics survey using plasma from patients with chronic hepatitis B, chronic hepatitis C, autoimmune hepatitis (AIH), non-alcoholic steatohepatitis (NASH), and patients without liver disease (control). RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Hepatitis viruses were readily detected at high coverage in patients with chronic viral hepatitis B and C, but only a limited number of sequences resembling other viruses were found. The exception was a library from a patient diagnosed with hepatitis C virus (HCV) infection that contained multiple sequences matching GB virus C (GBV-C). Abundant GBV-C reads were also found in plasma from patients with AIH, whereas Torque teno virus (TTV) was found at high frequency in samples from patients with AIH and NASH. After taxonomic classification of sequences by BLASTn, a substantial fraction in each library, ranging from 35% to 76%, remained unclassified. These unknown sequences were assembled into scaffolds along with virus, phage and endogenous retrovirus sequences and then analyzed by BLASTx against the non-redundant protein database. Nearly the full genome of a heretofore-unknown circovirus was assembled and many scaffolds that encoded proteins with similarity to plant, insect and mammalian viruses. The presence of this novel circovirus was confirmed by PCR. BLASTx also identified many polypeptides resembling nucleo-cytoplasmic large DNA viruses (NCLDV) proteins. We re-evaluated these alignments with a profile hidden Markov method, HHblits, and observed inconsistencies in the target proteins reported by the different algorithms. This suggests that sequence alignments are insufficient to identify NCLDV proteins, especially when these alignments are only to small portions of the target protein. Nevertheless, we have now established a reliable protocol for the identification of viruses in plasma that can also be adapted to other patient samples such as urine, bile, saliva and other body fluids.

The characteristics of intramucosal bacteria in chronic rhinosinusitis: a prospective cross-sectional analysis

BACKGROUND

We have observed subepithelial bacterial microcolonies within the mucosa of patients with chronic rhinosinusitis (CRS). These were predominantly Staphylococcus aureus and did not appear to elicit a local inflammatory response. We hypothesized that these microcolonies had made adaptations allowing them to exist apparently undetected within the mucosa. We sought to determine whether the tissue colonies had genotypic or phenotypic variations from the surface bacteria.

METHODS

Mucosal swabs and tissue biopsies were taken from 31 patients with CRS undergoing functional endoscopic sinus surgery, and 9 with normal sinuses having transnasal pituitary surgery. Biopsied tissues were assessed histologically, by routine culture, and by culture techniques facilitating growth of small colony variants (SCVs). Genotypic typing compared isolates of S. aureus that were cultured from both swab and tissue samples. The activity of the accessory gene regulator (agr) gene, a global regulator of S. aureus virulence, was evaluated indirectly by determining the hemolytic activity of the colonies on blood agar.

RESULTS

SCVs were grown from 2 samples but these were found not to possess the nuc gene, specific to S. aureus. When S. aureus was recovered from both swab and mucosa, the genetic profiles were indistinguishable in all but 1 patient. All S. aureus cultured from mucosa demonstrated β-hemolysis, implying normal agr activity.

CONCLUSION

Intramucosal S. aureus are genetically closely related and phenotypically similar to surface S. aureus. Further studies are needed to explore the possible mechanisms by which intramucosal colonies become less immunogenic, and the role of the colonies in the pathophysiology of CRS.

A review of methods for detect human Papillomavirus infection

Human Papillomavirus (HPV) is the most common sexually transmitted virus. Worldwide, the most common high-risk (HR)-HPV are -16/18, and approximately 70% of cervical cancers (CC) are due to infection by these genotypes. Persistent infection by HR-HPV is a necessary but not sufficient cause of this cancer, which develops over a long period through precursor lesions, which can be detected by cytological screening. Although this screening has decreased the incidence of CC, HPV-related cervical disease, including premalignant and malignant lesions, continues to be a major burden on health-care systems. Although not completely elucidated, the HPV-driven molecular mechanisms underlying the development of cervical lesions have provided a number of potential biomarkers for both diagnostic and prognostic use in the clinical management of women with HPV-related cervical disease, and these biomarkers can also be used to increase the positive predictive value of current screening methods. In addition, they can provide insights into the biology of HPV-induced cancer and thus lead to the development of nonsurgical therapies. Considering the importance of detecting HPV and related biomarkers, a variety of methods are being developed for these purposes. This review summarizes current knowledge of detection methods for HPV, and related biomarkers that can be used to discriminate lesions with a high risk of progression to CC.

Transcriptome analysis using next-generation sequencing

Up to date research in biology, biotechnology, and medicine requires fast genome and transcriptome analysis technologies for the investigation of cellular state, physiology, and activity. Here, microarray technology and next generation sequencing of transcripts (RNA-Seq) are state of the art. Since microarray technology is limited towards the amount of RNA, the quantification of transcript levels and the sequence information, RNA-Seq provides nearly unlimited possibilities in modern bioanalysis. This chapter presents a detailed description of next-generation sequencing (NGS), describes the impact of this technology on transcriptome analysis and explains its possibilities to explore the modern RNA world.

Principal methods for isolation and identification of soil microbial communities

Soil microbial populations play crucial role in soil properties and influence below-ground ecosystem processes. Microbial composition and functioning changes the soil quality through decomposition of organic matter, recycling of nutrients, and biological control of parasites of plants. Moreover, the discovery that soil microbes may translate into benefits for biotechnology, management of agricultural, forest, and natural ecosystems, biodegradation of pollutants, and waste treatment systems maximized the need of scientists for the isolation and their characterization. Operations such as the production of antibiotics and enzymic activities from microorganisms of soil constitute objectives of industry in her effort to cope with the increase of population of earth and disturbance of environment and may ameliorate the effects of global climate change. In the past decades, new biochemical and molecular techniques have been developed in our effort to identify and classify soil bacteria. The goal of measuring the soil microbial diversity is difficult because of the limited knowledge about bacteria species and classification through families and orders. Molecular techniques extend our knowledge about microbial diversity and help the taxonomy of species. Measuring and monitoring soil microbial communities can lead us to better understanding of their composition and function in many ecosystem processes.

Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes

The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the introduction of amplicon pyrosequencing. The possibility of barcoding gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing, similar to the early days of community fingerprinting. In this study we demonstrate the reproducibility of bacterial 454 pyrotag sequencing over biological and technical replicates of aquifer sediment bacterial communities. Moreover, we explore the potential of recovering specific template ratios via quantitatively defined template spiking to environmental DNA. We sequenced pyrotag libraries of triplicate sediment samples taken in annual sampling campaigns at a tar oil contaminated aquifer in Düsseldorf, Germany. The abundance of dominating lineages was highly reproducible with a maximal standard deviation of ∼4% read abundance across biological, and ∼2% across technical replicates. Our workflow also allows for the linking of read abundances within defined assembled pyrotag contigs to that of specific ‘in vivo’ fingerprinting signatures. Thus we demonstrate that both terminal restriction fragment length polymorphism (T-RFLP) analysis and pyrotag sequencing are capable of recovering highly comparable community structure. Overall diversity was roughly double in amplicon sequencing. Pyrotag libraries were also capable of linearly recovering increasing ratios (up to 20%) of 16S rRNA gene amendments from a pure culture of Aliivibrio fisheri spiked to sediment DNA. Our study demonstrates that 454 pyrotag sequencing is a robust and reproducible method, capable of reliably recovering template abundances and overall community structure within natural microbial communities.