In microbial food safety, molecular methods such as quantitative PCR (qPCR) and next-generation sequencing (NGS) of bacterial isolates can potentially be replaced by diagnostic shotgun metagenomics. However, the methods for pre-analytical sample preparation are often optimized for qPCR, and do not necessarily perform equally well for qPCR and sequencing. The present study investigates, through ...

December 2015 | Volume 2 | Issue 6 | Page 96 Abstract | Next generation sequencing (NGS) opened up a plethora of new research possibilities in biology and medicine. Metagenomics is one of these emerging NGS applications and offers the opportunity to study i.e. whole ecosystems. Basically, the metagenomics approach is similar to well-known shotgun-sequencing, though on a much bigger scale. For i...

BACKGROUND The Human Microbiome Project has ushered in a new era for human metagenomics and high-throughput next-generation sequencing strategies. CONTENT This review describes evolving strategies in metagenomics, with a special emphasis on the core technology of DNA pyrosequencing. The challenges of microbial identification in the context of microbial populations are discussed. The developme...

BACKGROUND Rodents are major reservoirs of pathogens responsible for numerous zoonotic diseases in humans and livestock. Assessing their microbial diversity at both the individual and population level is crucial for monitoring endemic infections and revealing microbial association patterns within reservoirs. Recently, NGS approaches have been employed to characterize microbial communities of di...

Metagenomics is an emerging methodology for the direct genomic analysis of a mixed community of uncultured microorganisms. The current analyses of metagenomics data largely rely on the computational tools originally designed for microbial genomics projects. The challenge of assembling metagenomic sequences arises mainly from the short reads and the high species complexity of the community. Alte...

Diagnostic metagenomics is a rapidly evolving laboratory tool for culture-independent tracing of foodborne pathogens. The method has the potential to become a generic platform for detection of most pathogens and many sample types. Today, however, it is still at an early and experimental stage. Studies show that metagenomic methods, from sample storage and DNA extraction to library preparation a...

Functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted DNA of mixed microbial populations. A functional approach relies on the construction and screening of metagenomic libraries-physical libraries that contain DNA cloned from environmental metagenomes. The information obtained from functional metagenomics can help in future annotatio...

More than 99% of identified prokaryotes, including many from the marine environment, cannot be cultured in the laboratory. This lack of capability restricts our knowledge of microbial genetics and community ecology. Metagenomics, the culture-independent cloning of environmental DNAs that are isolated directly from an environmental sample, has already provided a wealth of information about the u...

Metagenomics is the study of genomes directly sequenced from an environment. The goal of metagenomics is to understand the ecosystems by identifying the community members and the genes in the environment, and microbial organisms are a main target of the research [2] [3]. Microbial metagenomics enables to access uncultured microbial organisms, thus obtained sequences are composed of various spec...