Reviews & Analysis

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  • CRISPR–Cas systems provide resistance against foreign mobile genetic elements and have a wide range of genome editing and biotechnological applications. In this Review, Wang, Pausch and Doudna examine recent advances in understanding the molecular structures and mechanisms of enzymes comprising bacterial RNA-guided CRISPR–Cas immune systems and deployed for wide-ranging genome editing applications.

    • Joy Y. Wang
    • Patrick Pausch
    • Jennifer A. Doudna
    Review Article
  • The anti-tuberculosis drug candidate pipeline is promising, but the recent breakthroughs are challenged with the need to prioritize drug combinations for clinical trials and revamping trial designs to accelerate regimen development. In this Review, Dartois and Rubin explore treatment challenges, drug development priorities, and approaches — from basic research to preclinical evaluation — that lead to the selection of drug combinations earlier in the discovery cascade to accelerate the approval of shorter treatment regimens.

    • Véronique A. Dartois
    • Eric J. Rubin
    Review Article
  • In this Review, Greening and Grinter describe the microorganisms and enzymes that use atmospheric trace gases, including hydrogen, carbon monoxide and methane, during growth and survival. They highlight important ecological and biogeochemical roles for these processes in diverse environments, including ecosystem resilience under changing conditions.

    • Chris Greening
    • Rhys Grinter
    Review Article
  • In this Review, Aldridge and colleagues describe different types of mycobacterial heterogeneity and discuss how cell-to-cell heterogeneity and environmental heterogeneity are generated and regulated in response to environmental cues.

    • Eun Seon Chung
    • William C. Johnson
    • Bree B. Aldridge
    Review Article
  • In this Review, Lamers and Haagmans explore recent clinical and experimental advances in understanding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis, interactions with host cells and the involvement of the immune system in the development of severe disease. Specifically, they focus on mechanisms underlying the development of COVID-19-associated acute respiratory distress syndrome.

    • Mart M. Lamers
    • Bart L. Haagmans
    Review Article
  • The impacts of fungal infections on human health are of increasing concern, and resistance of pathogenic fungi to all licensed systemic antifungals has been documented. In this Review, Fisher, Verweij and colleagues discuss the research and innovation topics that are needed to understand and minimize the occurrence and impact of antifungal resistance.

    • Matthew C. Fisher
    • Ana Alastruey-Izquierdo
    • Paul E. Verweij
    Review Article
  • The human gut microbiota produces an extensive array of carbohydrate-active enzymes to degrade carbohydrates derived from the diet, host and other microorganisms. Withers and colleagues discuss the vast diversity and activities of these enzymes and their potential applications.

    • Jacob F. Wardman
    • Rajneesh K. Bains
    • Stephen G. Withers
    Review Article
  • In this Review, Wang and colleagues review the strategies microbial pathogens use to evade plant immunity for successful infection. They highlight how microbial effectors manipulate host cellular processes involved in immune sensing, signal integration and defence execution and how to exploit this knowledge to engineer crop resistance.

    • Yan Wang
    • Rory N. Pruitt
    • Yuanchao Wang
    Review Article
  • Chemotaxis is one of the best studied bacterial behaviours, but the underlying mechanisms are much better understood than the reasons and consequences of chemotaxis. In this Review, Keegstra et al. discuss the costs and benefits both for individual bacteria and whole populations.

    • Johannes M. Keegstra
    • Francesco Carrara
    • Roman Stocker
    Review Article
  • Combining several antibiotics, either in mixtures or sequential order, is proposed to increase treatment efficacy and reduce resistance evolution. In this Review, Andersson and colleagues discuss the effects of antibiotic combinations, the directional effects of previous antibiotic treatments and the role of stress-response systems as well as the interactions between drugs and resistance mutations.

    • Roderich Roemhild
    • Tobias Bollenbach
    • Dan I. Andersson
    Review Article
  • Soil microorganisms shape global element cycles in life and death. In this Review, Sokol and colleagues explore how the biogeochemical cycling of organic matter depends on both living and dead soil microorganisms, their functional traits, and their interactions with the soil matrix and other organisms. They also discuss incorporating microbial life and death into trait-based models that predict soil biogeochemical dynamics.

    • Noah W. Sokol
    • Eric Slessarev
    • Jennifer Pett-Ridge
    Review Article
  • To maintain genome integrity and ensure cell survival, bacteria have evolved several DNA repair pathways to repair different types of DNA damage and non-canonical bases, including strand breaks, nucleotide modifications, cross-links, mismatches and ribonucleotide incorporations. In this Review, Wozniak and Simmons provide a contemporary discussion of the excision-based mechanisms bacteria use to repair the diverse set of lesions they encounter.

    • Katherine J. Wozniak
    • Lyle A. Simmons
    Review Article
  • 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