Review Articles in 2021

Clostridioides difficile produces up to three different toxins, which are key to the pathogenesis of C. difficile infection of the colon. In this Review, Kordus, Thomas and Lacy discuss the structure and function of these toxins and how this information informs new therapeutic approaches.

Bats harbour a multitude of coronaviruses and owing to their diversity and wide distribution are prime reservoir hosts of emerging viruses. Ruiz-Aravena, McKee and colleagues analyse the currently available information on bat coronaviruses and discuss their role in recent and potential future spillovers.

Bacterial DNA transfers between cells in numerous ways and becomes integrated into the genome, with diverse consequences for bacterial genomes. In this Review, Arnold, Huang and Hanage discuss the underlying theory used to infer the selective forces acting on transferred DNA and how they shape patterns of genomic variation.

Microbial life can thrive in extreme environments such as terrestrial hot springs and deep sea hydrothermal vents, glaciers and permafrost, hypersaline habitats, acid mine drainage and the subsurface. In this Review, Shu and Huang explore the diversity, functions and evolution of bacteria and archaea inhabiting Earth’s major extreme environments.

In this Review, Larsson and Flach discuss the drivers of and bottlenecks for environmental evolution and transmission of antibiotic resistance, and they explore environmental surveillance strategies that could complement clinical surveillance systems.

In this Review, Huang and colleagues explore the emerging physical and mechanical properties of the Gram-negative outer membrane. They discuss recent studies that revealed key molecular factors and interactions that give rise to the spatial organization, limited diffusivity and stress-bearing capacity of the outer membrane.

Global change, including climate change, urbanization and global travel and trade, has affected the emergence and spread of infectious diseases. In the Review, Baker, Metcalf and colleagues examine how global change affects infectious diseases, highlighting examples ranging from COVID-19 to Zika virus disease.

Lipid biomarkers provide insights into the nature and history of the Earth’s microbial life. In this Review, Summons et al. discuss how advances in molecular biology have helped elucidate lipid biomarker origins and afforded robust interpretations of fossil lipids, and explore key examples of how genomics-enabled advances in lipid biomarker science are illuminating the history of microbial life on the Earth.

Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota and to understand the functional role of these microbial metabolites. In this Review, Dorrestein and colleagues review common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis.

In this Review, Wadhwa and Berg explore the most common bacterial motility mechanisms and summarize the current understanding of the molecular machines that enable bacteria to swim in aqueous media and move on solid surfaces.

Elucidating the structure and function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is vital for understanding the molecular mechanisms of viral replication and COVID-19 pathogenesis, and could lead to the development of novel therapeutics. In this Review, Yang and Rao delineate the structural features of SARS-CoV-2 from the whole viral particle to the individual viral proteins and discuss their functions as well as their potential as targets for therapeutic interventions.

In this Review, Perry, Meirelles and Newman review the growing body of evidence that microbial secondary metabolites can modulate susceptibility to commonly used antibiotics, focusing on the mechanisms and why this phenomenon occurs, and they discuss the implications for the diagnosis of antibiotic resistance and therapeutic strategies.

Linking genotype to phenotype is particularly challenging for viruses because of their small size, sparse phenotypic data and interlinked viral, host and environmental factors. In this Review, DeLong and colleagues discuss traits of virions and virocells and phenotypic plasticity.

Human papillomaviruses (HPVs) are a diverse group of viruses that replicate in specific anatomical niches of the stratified epithelia. Most HPVs cause asymptomatic infections, some cause benign, proliferative lesions on the skin and mucosa, and others are associated with the development of cancer. In this Review, McBride explores the diversity, evolution, infectious cycle, host interactions and disease association of HPVs.

The order and timing of the arrival (priority effects) of members of a microbiome can influence microbiome composition and function. In this Review, Debray and colleagues provide an overview of the mechanisms of priority effects, highlight examples in host-associated and environmental communities, and discuss methods to detect priority effects in microbial communities.

Infections during pregnancy can be associated with devastating outcomes for the pregnant mother and developing fetus. In this Review, Megli and Coyne discuss placental defences and provide an overview of how various viral, bacterial and parasitic pathogens traverse the maternal–fetal interface and cause disease.

In this Review, Chevallereau et al. explore the composition and evolution of phage communities as well as their roles in controlling the population and evolutionary dynamics of bacterial communities. They highlight the need for greater ecological realism in laboratory studies to capture the complexity of microbial communities that thrive in natural environments.

In this Review, Avalos and colleagues discuss different aspects of microbial physiology that can have an impact on engineered metabolic pathways, and they describe instances in which natural or engineered physiological traits in host organisms have been harnessed to benefit engineered metabolic pathways for chemical production.

In this Review, Lovley and Holmes discuss the physiological and phylogenetic diversity of electroactive microorganisms, and their mechanisms for extracellular electron transfer in various electromicrobiomes.

A hallmark of retroviral replication is establishment of the proviral state, wherein a DNA copy of the viral RNA genome is stably incorporated into a host cell chromosome by the viral enzyme integrase. In this Review, Maertens, Engelman and Cherepanov explore the structure and function of retroviral integrase and how this knowledge is informing the development of integrase inhibitors for the treatment of HIV infection.