Reviews & Analysis

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  • Osteomyelitis is an infection of bone that arises when a pathogen colonizes bone tissue owing to injury or surgery. In this Review, Masters and colleagues explore the microbial pathogenesis, immunity and clinical management of bone infections.

    • Elysia A. Masters
    • Benjamin F. Ricciardi
    • Gowrishankar Muthukrishnan
    Review Article
  • Differential availability of oxygen, nutrients and other resources leads to metabolic and structural heterogeneity in multicellular systems, including in biofilms. In this Review, Jo et al. discuss how chemical and physical gradients can affect the physiology of microbial biofilms.

    • Jeanyoung Jo
    • Alexa Price-Whelan
    • Lars E. P. Dietrich
    Review Article
  • The distinct spatial patterning of microorganisms during infection can influence infection outcomes. In this Review, Azimi et al. detail the microbiogeography of human infections and discuss approaches to study the processes that influence polymicrobial patterning.

    • Sheyda Azimi
    • Gina R. Lewin
    • Marvin Whiteley
    Review Article
  • The ocean is home to a diverse and metabolically versatile microbial community that performs the complex biochemical transformations that drive the nitrogen cycle. In this Review, Hutchins and Capone explore the latest developments in our understanding of the role of microorganisms in the marine nitrogen cycle, including new taxa, pathways, methods and concepts. They also discuss opportunities to understand and better predict the effects of humans and global change.

    • David A. Hutchins
    • Douglas G. Capone
    Review Article
  • Chronic infections caused by microbial biofilms represent an important clinical challenge owing to the recalcitrance of microbial biofilms to antimicrobials and the immune system, causing persistence and clinical recurrence of these infections. In this Review, Ciofu and colleagues discuss our current understanding of the mechanisms of tolerance of such biofilms to the immune system as well as of tolerance and resistance to antimicrobials.

    • Oana Ciofu
    • Claus Moser
    • Niels Høiby
    Review Article
  • We take up a multitude of foreign substances, so called xenobiotics, such as medications, food additives and pollutants, which affect the composition and function of the gut microbiota. In this Review, Lindell, Zimmermann-Kogadeeva and Patil discuss these reciprocal interactions and their mechanisms.

    • Anna E. Lindell
    • Maria Zimmermann-Kogadeeva
    • Kiran R. Patil
    Review Article
  • Microbiome-based therapeutics hold great promise for reducing disease susceptibility and enhancing disease resistance. In this Review, Sorbara and Pamer explore the major bacterial phyla associated with health benefits and the potential of microbiome-based therapeutics, including faecal microbiota transplantation, bacterial consortia, engineered symbiotic bacteria, diet and prebiotics, and microbiome-derived proteins and metabolites. They also discuss the challenges confronting therapeutic development as well as the regulatory hurdles for clinical trials and manufacturing.

    • Matthew T. Sorbara
    • Eric G. Pamer
    Review Article
  • The role of CRISPR–Cas systems in defence against mobile genetic elements is well established, but there is increasing evidence that these systems have alternative functions beyond adaptive immunity. In this Review, Staals, van der Oost and colleagues explore these non-canonical functions of CRISPR–Cas systems with relevant consequences for CRISPR-based genome editing applications.

    • Prarthana Mohanraju
    • Chinmoy Saha
    • John van der Oost
    Review Article
  • In this Review, Harvey and Holmes explore our changing understanding of the structure, diversity and evolution of the animal virome. They also outline the factors that determine the phylogenetic diversity and genomic structure of animal viruses on evolutionary timescales and show how these impact assessment of the risk of disease emergence.

    • Erin Harvey
    • Edward C. Holmes
    Review Article
  • Toxin–antitoxin systems are composed of a toxin that inhibits an essential cellular process and an antitoxin that counteracts its cognate toxin. In this Review, Van Melderen and colleagues summarize the recent progress in understanding the biology and evolution of these small genetic elements, and discuss how genomic conflicts could shape the diversification of toxin–antitoxin systems.

    • Dukas Jurėnas
    • Nathan Fraikin
    • Laurence Van Melderen
    Review Article
  • 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.

    • Shannon L. Kordus
    • Audrey K. Thomas
    • D. Borden Lacy
    Review Article
  • 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.

    • Manuel Ruiz-Aravena
    • Clifton McKee
    • Raina K. Plowright
    Review Article
  • 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.

    • Brian J. Arnold
    • I-Ting Huang
    • William P. Hanage
    Review Article
  • 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.

    • Wen-Sheng Shu
    • Li-Nan Huang
    Review Article
  • 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.

    • D. G. Joakim Larsson
    • Carl-Fredrik Flach
    Review Article
  • 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.

    • Jiawei Sun
    • Steven T. Rutherford
    • Kerwyn Casey Huang
    Review Article
  • 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.

    • Rachel E. Baker
    • Ayesha S. Mahmud
    • C. Jessica E. Metcalf
    Review Article
  • 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.

    • Roger E. Summons
    • Paula V. Welander
    • David A. Gold
    Review Article
  • 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.

    • Anelize Bauermeister
    • Helena Mannochio-Russo
    • Pieter C. Dorrestein
    Review Article
  • 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.

    • Navish Wadhwa
    • Howard C. Berg
    Review Article