Focus |

Microbial genomics

Technical advances in sequencing technologies and new computational developments, alongside continuous reductions in sequencing costs, have democratized microbial genomics, fuelling a rise in the number of available microbial genomes. From microbial evolution to microbial diversity, host–pathogen interactions to disease-causing genetic variation, genomics has provided transformative insights into microbiology. Moreover, genomic technologies show great potential for clinical diagnostics or the real-time detection and surveillance of epidemics. Commissioned by the editors of Nature Reviews Genetics, the articles in this Focus on microbial genomics highlight the impact of high-throughput sequencing on the field of microbiology.

Reviews

Clinical metagenomic next-generation sequencing (mNGS) is rapidly moving from bench to bedside. This Review discusses the clinical applications of mNGS, including infectious disease diagnostics, microbiome analyses, host response analyses and oncology applications. Moreover, the authors review the challenges that need to be overcome for mNGS to be successfully implemented in the clinical laboratory and propose solutions to maximize the benefits of clinical mNGS for patients.

Review Article | | Nature Reviews Genetics

Next-generation sequencing has improved the identification and characterization of antimicrobial resistance. Focusing on sequence-based discovery of antibiotic resistance genes, this Review discusses computational strategies and resources for resistance gene identification in genomic and metagenomic samples, including recent deep-learning approaches.

Review Article | | Nature Reviews Genetics

This article reviews recent advances in ancient pathogen genomics, from methodological improvements in retrieving whole genomes to evolutionary analyses of ancient pathogens that remain relevant to public health. Focusing on the evolutionary history of the plague pathogen Yersinia pestis, the authors present unique insights afforded by the study of ancient pathogen genomes.

Review Article | | Nature Reviews Genetics

News & Comment

From the archive

Next-generation sequencing has the potential to support public health surveillance systems to improve the early detection of emerging infectious diseases. This Review delineates the role of genomics in rapid outbreak response and the challenges that need to be tackled for genomics-informed pathogen surveillance to become a global reality.

Review Article | | Nature Reviews Genetics

Comparing the microbiomes of great apes enables an evolutionary perspective on microbial communities. This approach is revealing not only new insights about humans and what differentiates us from our closest relatives but also the factors that influence microbiome composition and the ways in which microbiomes diverge.

Review Article | | Nature Reviews Genetics

The virulence of viruses is a major determinant of the health burden of viral infections in humans and other species. In this article, Geoghegan and Holmes discuss how largely disparate research fields — theoretical modelling of virulence evolution and experimental dissection of genetic virulence determinants in laboratory model systems — can be bridged by considering real genomic data of viral evolution in a phylogenetic context. They describe the underlying principles of virulence evolution and how they apply to real-world viral infections and outbreaks of global importance.

Review Article | | Nature Reviews Genetics

High-throughput sequencing technologies have enabled comparative analysis of large numbers of diverse bacterial genomes. Such studies are providing insights into the genomic changes that accompany changes in host specificity, with possible implications for controlling transmission of pathogenic bacteria.

Review Article | | Nature Reviews Genetics

Recent microbiome genome-wide association studies have identified numerous associations between human genetic variants and the gut microbiome. Here, the authors review how genetic variation in the host can alter the composition of the gut microbiome towards a disease state, with a focus on disorders of immunity and metabolism.

Review Article | | Nature Reviews Genetics

With the increasing availability of microbial whole genomes, researchers are beginning to carry out genome-wide association studies (GWAS) in bacteria, viruses and protozoa. In this Review, the authors discuss the specific challenges and considerations associated with the application of GWAS methods to microorganisms and consider the future of microbial GWAS in the light of lessons learned from human studies.

Review Article | | Nature Reviews Genetics

Although viral sequences are important in taxonomy, classification has typically also required biological properties, thus excluding viruses that were identified by metagenomics. The proposals in this Consensus Statement, which are supported by the International Committee on Taxonomy of Viruses (ICTV), enable viruses that are discovered by sequence alone to be incorporated into virus classification.

Consensus Statement | Open Access | | Nature Reviews Microbiology

Complex microbial communities shape the dynamics of various environments. In this Review, Knight and colleagues discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets.

Review Article | | Nature Reviews Microbiology