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The study of microbiology is undergoing a renaissance owing to the development and application of a diverse range of new technologies. A little more than a decade ago, the visualization of fundamental subcellular structures and processes was almost impossible; now, following the successful marriage of biophysics and microbiology, the number of single-molecule studies in living cells is growing at a rapid pace. Increasingly sophisticated sequencing approaches, coupled with improved analytical and computational tools, allow us to rapidly indentify pathogens, track infectious disease outbreaks and identify links between microorganisms and disease. Furthermore, innovative micro-scale engineering has facilitated the simulation of microbial environments with remarkable precision and has opened the door to understanding microbial heterogeneity at an unprecedented level of detail. In this series of articles, Nature Reviews Microbiology explores some of the most recent technological developments and their applications, highlighting the ways in which this powerful toolkit is changing the face of modern-day microbiology.
Advances in synthetic biology allow the generation of ever more sophisticated engineered bacteria. In this Review, Riglar and Silver showcase recent highlights in engineered bacterial therapeutics and diagnostics and discuss how best to develop them for clinical application.
In this Review, Pedra and colleagues describe the advances and challenges in the genetic engineering of obligate intracellular bacteria, and highlight examples of how the use of genetically manipulated pathogens has improved our understanding of microbial pathogenesis and host–pathogen interactions.
In this Review, Puschnik and colleagues discuss the technical aspects of using CRISPR–Cas technology in genome-scale knockout screens to study virus–host interactions, and they compare these screens with alternative genetic screening technologies.
Sequencing viral DNA and RNA is an important part of clinical practice, although, so far, mostly subgenomic fragments have been sequenced. In this Opinion article, Houldcroft, Beale and Breuer highlight the potential that sequencing whole viral genomes has for clinical applications.
In this Opinion article, Kreft and colleagues discuss how the combination of individual-based observations with individual-based models (IBMs) can lead to the new approach of microbial individual-based ecology (μIBE). They illustrate this point by describing how IBMs help to explore competitive and cooperative microbial interactions, which include the emergence of spatial patterns in biofilms and bacteria–phage dynamics.
In this Review, Oikonomou and Jensen discuss how electron cryotomography has provided structural and mechanistic insights into the physiology of bacteria and archaea, from morphogenesis to subcellular compartmentalization and from metabolism to complex interspecies interactions.
Transposon insertion sequencing (TIS) enables genome-wide definition of loci that are required for growth in diverse conditions. In this article, Waldor and colleagues discuss the benefits and limitations of different experimental approaches to TIS analyses.
Stocker and colleagues review how combining dynamic imaging techniques with microfluidics has furthered our understanding of the hydrodynamic signature of individual microorganisms, the mechanics of their locomotion, and the effects of surfaces, fluid flow and crowded habitats on microbial motility.
The first bacterial genome sequence was published 20 years ago. In this Timeline, Loman and Pallen review the first two decades of bacterial genome sequencing, discussing how advances in sequencing technologies and bioinformatics have furthered our understanding of the biology, diversity and evolution of bacteria.
In this Review, Sourjik and Typas describe the principles of protein–protein interaction networks and the current experimental approaches used to probe these networks in bacteria. They consider how these techniques have led to an increased understanding of the chemotaxis and cell cycle networks inEscherichia coli, highlighting the applicability of such methods to understanding diverse bacterial processes.
Crabb and colleagues discuss the molecular genetics systems that are currently available forPlasmodium falciparum and Plasmodium berghei, including conditional systems and gene editing tools, and examine the insights that have been gained into the function of genes that are important during the blood stages of the parasites.
Marine viruses have important roles in modulating the dynamics of microbial life in the global oceans. Brum and Sullivan discuss the recent technological advances that are facilitating an accelerated pace of discovery in marine virology, including metagenomics and several cultivation-dependent and cultivation-independent tools.
Although studies in 2D cell culture systems have provided great insights into the biology and pathogenesis of HIV-1 infection, such studies cannot account for many aspects of host physiology that affect HIV-1in vivo. Fackler et al. discuss the development and application of more integrative studies, including organotypic 3D culture systems, small-animal models and advanced live-cell imaging, and the impact of such studies on our understanding of the mechanisms of HIV-1 spread.
Here, Gahlmann and Moerner describe single-molecule imaging in live bacterial cells, which has transformed the study of bacterial cell biology. They discuss the insights that have been gained about the bacterial cytoskeleton, nucleoid organization and chromosome segregation and partitioning, as well as transcription and translation.
The combination of transposon mutagenesis with next-generation sequencing has emerged as a useful tool for identifying putative gene function in a high-throughput manner. Here, van Opijnen and Camilli describe the four main techniques that are used for this purpose, with a focus on their application for uncovering bacterial gene function.
In vitrosingle-molecule technologies have emerged as powerful tools for the study of complex biological phenomena. Here, Robinson and van Oijen summarize the latest insights that fluorescence-based single-molecule studies have provided for DNA replication, transcription and translation in bacterial cells.
Microorganisms can form complex, spatially organized communities that are coordinated by both physical and chemical intercellular interactions, as well as by other molecules present in the surrounding environment. Here, Whiteley and colleagues describe a number of microscale techniques for reproducing small bacterial communities in the laboratory. They also discuss the analytical tools available to monitor the impact of spatial organization on both bacterial behaviour and the generation of phenotypic heterogeneity.
In this Progress article, Collins and colleagues discuss how CRISPR-based analyses in genetically intractable microorganisms, including mycobacteria, fungi and parasites, have enabled the discovery of novel gene functions, the investigation of genetic interaction networks and the identification of virulence factors.