Patrick Sam Guy Chain

Comparative analysis of (meta)genomes necessitates aggregation, integration, and synthesis of well-annotated data using standards. The Genomic Standards Consortium (GSC) collaborates with the research community to develop and maintain the Minimum Information about any (x) Sequence (MIxS) reporting standard for genomic data. To facilitate the use of the GSC’s MIxS reporting standard, we provide a description of the structure and terminology, how to navigate ontologies for required terms in MIxS, and demonstrate practical usage through a soil metagenome example.

The production of a highly specialized cell structure called a spore is a remarkable example of a survival strategy displayed by bacteria in response to challenging environmental conditions. The detailed analysis and description of the process of sporulation in selected model organisms have generated a solid background to understand the cellular processes leading to the formation of this specialized cell. However, much less is known regarding the ecology of spore-formers. This research gap needs to be filled as the feature of resistance has important implications not only on the survival of sporeformers and their ecology, but also on the use of spores for environmental prospection and biotechnological applications.

Identification of microorganisms using nucleic acid sequencing has become a well-established field, with a variety of applications. With rapid changes in both hardware and software technologies over the last decade, the ability for a single microbial type to be identified in a complex sample is becoming easier and more robust with each turn. In this chapter we explore the history of sequencing and the upcoming challenges, and the importance of sequencing to public health and biodefense. We will also look at how sequencing fits with other orthogonal data types and the technology’s current abilities and limitations, as well as taking a forward look at sequencing overall.