Editorial: From Genes to Species: Novel Insights from Metagenomics

The majority of microbes in many environments are considered " as yet uncultured " and were traditionally considered inaccessible for study through the microbiological gold standard of pure culture. The emergence of metagenomic approaches has allowed researchers to access and study these microbes in a culture-independent manner through DNA sequencing and functional expression of metagenomic DNA in a heterologous host. Metagenomics has revealed an extraordinary degree of diversity and novelty, not only among microbial communities themselves, but also within the genomes of these microbes. Metagenomic analysis can involve sequence-based or functional approaches (or a combination of both). The continuous improvements to DNA sequencing technologies coupled with dramatic reductions in cost have allowed the field of metagenomics to grow at a rapid rate. Many novel insights on microbial community composition, structure, and functional capacity have been gained from sequence-based metagenomics. Functional metagenomics has been utilized, with much success, to identify many novel genes, proteins, and secondary metabolites such as antibiotics with industrial, biotechnological, pharmaceutical, and medical relevance. Future improvements and developments in sequencing technologies, expression vectors, alternative host systems, and novel screening assays will help advance the field further by revealing novel taxonomic and genetic diversity. This Research Topic aims to showcase the utility of metagenomics to gain insights on the microbial and genomic diversity in different environments by revealing the breadth of novelty that was in the past, largely untapped. This Research Topic comprises 19 submissions from experts in the field and covers a broad range of themes and article types (Review, Methods, Perspective, Opinion, and Original Research articles). We have broadly grouped the articles under four themes; functional metagenomics, targeted metagenomics, sequence-based metagenomics, and host-associated. We begin with a number of articles focusing on functional metagenomics. A review by Coughlan et al. gives an overview of metagenomics and focuses on the utility of functional metagenomics for the discovery of proteins and antimicrobial compounds with relevance to the food and pharmaceutical industries. Continuing this theme Uchiyama et al. report the discovery of a glucose-tolerant β-glucosidase from screening ∼10,000 clones from a metagenomic library created from Kusaya gravy (a traditional Japanese fermentate made from fish). β-glucosidases are often sensitive to glucose inhibition, therefore glucose-tolerant variants are desirable to improve enzymatic efficiency. Mirete et al. also used a functional metagenomic approach to identify novel salt tolerance genes from brine and rhizosphere-associated communities in a hypersaline saltern. A number of the genes had …