Review Articles

  • Review Article |

    In this Review, Rokas, Wisecaver and Lind discuss the diversity in the structure and content of fungal metabolic gene clusters, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations.

    • Antonis Rokas
    • , Jennifer H. Wisecaver
    •  & Abigail L. Lind
  • Review Article |

    Viral infection is a major contributor to the global cancer burden. In this Review, Krump and You explore the molecular mechanisms of viral oncogenesis in humans. They highlight how viral manipulation of host cellular signalling, DNA damage responses, immunity and microRNA targets promotes the initiation and development of cancer.

    • Nathan A. Krump
    •  & Jianxin You
  • Review Article |

    In this Review, Gilbert and Stephens outline the history of the field of microbiology of the built environment and discuss insights into microbial ecology, adaptation and evolution. They consider the implications of this research, specifically, how it is changing the types of materials we use in buildings and how our built environments affect human health.

    • Jack A. Gilbert
    •  & Brent Stephens
  • Review Article |

    Many phages use tails to attach to and penetrate the cell envelope of their bacterial hosts. In this Review, Brouns and colleagues explore recent structural and mechanistic insights into the interaction of phage tails with receptors on the bacterial surface.

    • Franklin L. Nobrega
    • , Marnix Vlot
    • , Patrick A. de Jonge
    • , Lisa L. Dreesens
    • , Hubertus J. E. Beaumont
    • , Rob Lavigne
    • , Bas E. Dutilh
    •  & Stan J. J. Brouns
  • Review Article |

    Archaea have been found in biofilms in a variety of habitats. In this Review, Albers and colleagues explore the different stages of archaeal biofilm development and highlight the similarities and differences between archaea and bacteria. They also consider their role in different industrial processes.

    • Marleen van Wolferen
    • , Alvaro Orell
    •  & Sonja-Verena Albers
  • Review Article |

    In this Review, Brun and colleagues summarize our understanding of the mechanisms governing bacterial adhesion at the single-cell level, including the physical forces experienced by a cell before reaching the surface, the first contact with a surface and the transition from reversible to permanent adhesion.

    • Cecile Berne
    • , Courtney K. Ellison
    • , Adrien Ducret
    •  & Yves V. Brun
  • Review Article |

    One factor contributing to the emergence of antimicrobial resistance is the capacity of bacteria to rapidly export drugs through the intrinsic activity of efflux pumps. This Review describes recent insights into the structure, function and regulation of efflux pumps.

    • Dijun Du
    • , Xuan Wang-Kan
    • , Arthur Neuberger
    • , Hendrik W. van Veen
    • , Klaas M. Pos
    • , Laura J. V. Piddock
    •  & Ben F. Luisi
  • Review Article |

    Bacterial RNA-binding proteins (RBPs) directly associate with and influence the fate of virtually all cellular transcripts. In this Review, Holmqvist and Vogel discuss our current understanding of the molecular interactions between specific RBPs and RNA during transcription, protein synthesis and RNA decay.

    • Erik Holmqvist
    •  & Jörg Vogel
  • Review Article |

    The seabed is a hostile environment for most microorganisms, and unique microbial communities are found in deeply buried marine sediments. In this Review, Orsi highlights which and how microorganisms survive and the differences between oxic and anoxic subseafloor sediments.

    • William D. Orsi
  • Review Article |

    Cyanobacteria can form large blooms that threaten the water quality of lakes and seas. In this Review, Huisman and colleagues discuss bloom formation, the impact of eutrophication and climate change, and measures to prevent and control cyanobacterial blooms.

    • Jef Huisman
    • , Geoffrey A. Codd
    • , Hans W. Paerl
    • , Bas W. Ibelings
    • , Jolanda M. H. Verspagen
    •  & Petra M. Visser
  • Review Article |

    Culturomics was developed to culture and identify unknown bacteria that inhabit the human gut. In this Review, Raoult and colleagues discuss the development of culturomics and how it has extended our understanding of bacterial diversity, and highlight the potential implications for human health.

    • Jean-Christophe Lagier
    • , Grégory Dubourg
    • , Matthieu Million
    • , Frédéric Cadoret
    • , Melhem Bilen
    • , Florence Fenollar
    • , Anthony Levasseur
    • , Jean-Marc Rolain
    • , Pierre-Edouard Fournier
    •  & Didier Raoult
  • Review Article |

    The first line of host defence against both encroaching commensal bacteria and invading enteric pathogens is the intestinal mucosal barrier, which is composed of epithelial cells and a host-secreted mucous layer. In this Review, Martens and colleagues discuss the complex interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier.

    • Eric C. Martens
    • , Mareike Neumann
    •  & Mahesh S. Desai
  • Review Article |

    In this Review, Burnham and Hendrixson explore the unique combination of determinants of Campylobacter jejuni biology that together establish commensalism in many animal hosts and promote diarrhoeal diarrheal disease in humans, including cellular shape and architecture, genotypic and phenotypic diversity, a multi-functional flagellum and metabolic requirements for growth.

    • Peter M. Burnham
    •  & David R. Hendrixson
  • Review Article |

    Virulence plasmids have a major role in the development of disease that is caused by enteric bacterial pathogens. In this Review, Pilla and Tang discuss virulence plasmids in enteric pathogens, outline the mechanisms by which they are maintained in bacterial populations and speculate on how these might contribute their propagation and success.

    • Giulia Pilla
    •  & Christoph M. Tang
  • Review Article |

    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.

    • Rob Knight
    • , Alison Vrbanac
    • , Bryn C. Taylor
    • , Alexander Aksenov
    • , Chris Callewaert
    • , Justine Debelius
    • , Antonio Gonzalez
    • , Tomasz Kosciolek
    • , Laura-Isobel McCall
    • , Daniel McDonald
    • , Alexey V. Melnik
    • , James T. Morton
    • , Jose Navas
    • , Robert A. Quinn
    • , Jon G. Sanders
    • , Austin D. Swafford
    • , Luke R. Thompson
    • , Anupriya Tripathi
    • , Zhenjiang Z. Xu
    • , Jesse R. Zaneveld
    • , Qiyun Zhu
    • , J. Gregory Caporaso
    •  & Pieter C. Dorrestein
  • Review Article |

    Flores and O’Neill review novel approaches to control mosquito-transmitted diseases, with a focus on control methods that are based on the release of mosquitoes, including the release of Wolbachia-infected mosquitoes, and strategies to genetically modify the vector.

    • Heather A. Flores
    •  & Scott L. O’Neill
  • Review Article |

    Ubiquitin-like protein ISG15 is an interferon-induced protein that has been implicated as a central player in the host antiviral response. In this Review, Perng and Lenschow provide new insights into how ISG15 restricts and shapes the host response to viral infection and the viral immune-evasion strategies that counteract ISG15.

    • Yi-Chieh Perng
    •  & Deborah J. Lenschow
  • Review Article |

    Implant infections are often resistant to treatment and immune responses owing to the formation of biofilms. In this Review, Arciola, Campoccia and Montanaro summarize the strategies that pathogens such as staphylococci use to infect implants and novel treatment approaches.

    • Carla Renata Arciola
    • , Davide Campoccia
    •  & Lucio Montanaro
  • Review Article |

    As an obligate human pathogen, Mycobacterium tuberculosis has evolved to survive and thrive in biochemically challenging niches in its host. Ehrt, Schnappinger and Rhee review the unique metabolic features that enable M. tuberculosis pathogenesis and persistence but also represent drug targets.

    • Sabine Ehrt
    • , Dirk Schnappinger
    •  & Kyu Y. Rhee
  • Review Article |

    In this Review, Jennings and colleagues discuss interactions involving host and bacterial glycans that have a role in bacterial pathogenesis. They also highlight recent technological advances that have illuminated the glycoscience of microbial pathogenesis.

    • Jessica Poole
    • , Christopher J. Day
    • , Mark von Itzstein
    • , James C. Paton
    •  & Michael P. Jennings
  • Review Article |

    In recent years, several non-polio enteroviruses (NPEVs) have emerged as serious public health concerns. In this Review, van Kuppeveld and colleagues summarize recent insights from enterovirus research, with a special emphasis on NPEVs, and reflect on how recent discoveries may help in the development of new antiviral strategies.

    • Jim Baggen
    • , Hendrik Jan Thibaut
    • , Jeroen R. P. M. Strating
    •  & Frank J. M. van Kuppeveld
  • Review Article |

    Carriage of Streptococcus pneumoniae on the mucosa of the upper respiratory tract is the prerequisite for transmission and tissue invasion. In this Review, Weiser, Ferreira and Paton summarize the mechanisms that allow pneumococci to transmit and progress from colonizer to pathogen.

    • Jeffrey N. Weiser
    • , Daniela M. Ferreira
    •  & James C. Paton
  • Review Article |

    Autophagy is crucial for innate and adaptive antiviral immunity; in turn, viruses evade and subvert autophagy to support their replication and pathogenesis. In this Review, Choi, Bowman and Jung discuss the molecular mechanisms that govern autophagy during host–virus interactions.

    • Younho Choi
    • , James W. Bowman
    •  & Jae U. Jung
  • Review Article |

    Bacterial microcompartments are self-assembling organelles that consist of an enzymatic core that is encapsulated by a selectively permeable protein shell. In this Review, Kerfeld and colleagues discuss recent insights into the structure, assembly, diversity and function of bacterial microcompartments.

    • Cheryl A. Kerfeld
    • , Clement Aussignargues
    • , Jan Zarzycki
    • , Fei Cai
    •  & Markus Sutter
  • Review Article |

    Much of the molecular virology of rabies virus has been well characterized, and we are gaining a better understanding of how infection dynamics and immune status relate to transmission. In this Review, Schnell and colleagues explore rabies virus transmission, enzootic maintenance and epizootic spread, as well as molecular evolutionary dynamics, host adaptation and the origins of rabies virus.

    • Christine R. Fisher
    • , Daniel G. Streicker
    •  & Matthias J. Schnell
  • Review Article |

    Pseudomonas syringae uses a multitude of virulence factors to infect plants. In this Review, Xin and colleagues highlight key virulence strategies — immune suppression and water soaking — that allow this bacterium to become a successful pathogen under the right environmental conditions.

    • Xiu-Fang Xin
    • , Brian Kvitko
    •  & Sheng Yang He
  • Review Article |

    The causative agents of tuberculosis are a group of closely related bacteria known as the Mycobacterium tuberculosis complex (MTBC). In this Review, Gagneux discusses recent insights into the origin of the MTBC, its molecular evolution and population genetic characteristics, and the evolution of antibiotic resistance.

    • Sebastien Gagneux
  • Review Article |

    Hopanoid lipids are structurally and functionally related to sterols, which are important building blocks of membranes. In this Review, Newman, Silipo and colleagues explore the diversity of bacterial hopanoids and their roles in stress adaptation and plant symbiosis.

    • Brittany J. Belin
    • , Nicolas Busset
    • , Eric Giraud
    • , Antonio Molinaro
    • , Alba Silipo
    •  & Dianne K. Newman
  • Review Article |

    In this Review, Bartenschlager and colleagues discuss how Flaviviridae viruses rewire cellular pathways and co-opt organelles. They compare strategies employed by flaviviruses with those employed by hepaciviruses and discuss the importance of these virus–host interactions in the context of viral replication and antiviral therapies.

    • Christopher J. Neufeldt
    • , Mirko Cortese
    • , Eliana G. Acosta
    •  & Ralf Bartenschlager
  • Review Article |

    The host-adapted human pathogen Neisseria gonorrhoeae is the causative agent of gonorrhoea. In this Review, Quillin and Seifert provide an overview of the bacterial factors that are important for the different stages of pathogenesis, including transmission, colonization and immune evasion, and discuss the problem of antibiotic resistance.

    • Sarah Jane Quillin
    •  & H Steven Seifert
  • Review Article |

    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.

    • David T. Riglar
    •  & Pamela A. Silver
  • Review Article |

    Nitrogen-transforming microorganisms shape global biogeochemical nutrient cycles. In this Review, Kuypers, Marchant and Kartal explore the vast diversity of these microorganisms and their enzymes, highlighting novel pathways, and discuss how nitrogen-transforming microorganisms form complex nitrogen-cycling networks in different environments.

    • Marcel M. M. Kuypers
    • , Hannah K. Marchant
    •  & Boran Kartal
  • Review Article |

    Rhizobia can exist as both free-living soil microbiota and plant-associated endosymbionts, which form N2-fixing root nodules. In this Review, Poole, Ramachandran and Terpolilli explore the drastic lifestyle shift that underlies this transition and the associated plant–bacteria interactions.

    • Philip Poole
    • , Vinoy Ramachandran
    •  & Jason Terpolilli
  • Review Article |

    Bacteria and archaea have intracellular cytoskeletons built from dynamic protein filaments. In this Review, Wagstaff and Löwe discuss how these linear protein polymers are used to organize other molecules in prokaryotic cells.

    • James Wagstaff
    •  & Jan Löwe
  • Review Article |

    Haldar and colleagues discuss markers and mechanisms of resistance to artemisinins and artemisinin-based combination therapies. They describe the identification of Plasmodium falciparum Kelch 13 as the primary and, to date, sole causative marker of artemisinin resistance in P. falciparum and explore two proposed resistance mechanisms. They emphasize continuing challenges to improve detection strategies and new drug development strategies.

    • Kasturi Haldar
    • , Souvik Bhattacharjee
    •  & Innocent Safeukui
  • Review Article |

    Our skin is home to millions of bacteria, fungi and viruses that comprise the skin microbiota. In this Review, Byrd and colleagues discuss recent insights into skin microbial communities, including their composition in health and disease, dynamics between species and interactions with the immune system.

    • Allyson L. Byrd
    • , Yasmine Belkaid
    •  & Julia A. Segre
  • Review Article |

    The interplay between nutrient intake, gut microbial metabolism and microorganism-driven engagement of host receptors contributes to the pathogenesis of cardiovascular disease. In this Review, Brown and Hazen discuss the gut microbial mechanisms that drive cardiovascular disease, with special emphasis on therapeutic interventions.

    • J. Mark Brown
    •  & Stanley L. Hazen
  • Review Article |

    Recently, virulence mechanisms beyond canonical drug resistance were uncovered that enable Acinetobacter baumannii to thrive in the health-care environment and cause infections in critically ill patients. Harding, Hennon and Feldman explore the molecular features that promote environmental persistence and the most recently identified virulence factors that enable successful human infection.

    • Christian M. Harding
    • , Seth W. Hennon
    •  & Mario F. Feldman
  • Review Article |

    In this Review, Husnik and McCutcheon discuss how horizontally transferred genes from bacteria become functional in eukaryotes and classify horizontal gene transfer events into two broad types: those that maintain pre-existing functions and those that add new functionality to the recipient, including altered host nutrition, protection and adaptation to extreme environments.

    • Filip Husnik
    •  & John P. McCutcheon
  • Review Article |

    One of the most prominent features of archaea is the extraordinary diversity of their viruses. In this Review, Prangishvili et al. summarize their morphological diversity, the molecular biology of their life cycles and virus–host interactions, and discuss their evolution and their role in the global virosphere.

    • David Prangishvili
    • , Dennis H. Bamford
    • , Patrick Forterre
    • , Jaime Iranzo
    • , Eugene V. Koonin
    •  & Mart Krupovic
  • Review Article |

    The Archaea was recognized as a third domain of life 40 years ago. In this Review, Eme et al. outline a brief history of the changing shape of the tree of life and examine how the recent discovery of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of the eukaryotic cell.

    • Laura Eme
    • , Anja Spang
    • , Jonathan Lombard
    • , Courtney W. Stairs
    •  & Thijs J. G. Ettema
  • Review Article |

    Co-infection with Mycobacterium tuberculosis is the leading cause of death in individuals infected with HIV-1. In this Review, Bell and Noursadeghi describe the epidemiological associations between the two pathogens, selected interactions of each pathogen with the host and our current understanding of how they affect the pathogenesis of tuberculosis and HIV-1/AIDS in individuals with co-infection.

    • Lucy C. K. Bell
    •  & Mahdad Noursadeghi
  • Review Article |

    Seasonal influenza viruses continue to cause epidemics each year. In this Review, Petrova and Russell discuss recent advances in understanding the molecular determinants of influenza virus immune escape, sources of evolutionary selection pressure, population dynamics of influenza viruses and prospects for better influenza virus control.

    • Velislava N. Petrova
    •  & Colin A. Russell
  • Review Article |

    Staphylococcus aureus is a facultative pathogen that colonizes the human nares. In this Review, Peschel and colleagues discuss the mechanisms that are used by S. aureus to prevail in the human nose and the counter-strategies that are used by other commensals to interfere with its colonization.

    • Bernhard Krismer
    • , Christopher Weidenmaier
    • , Alexander Zipperer
    •  & Andreas Peschel
  • Review Article |

    The ability of Candida albicans to form biofilms is a major cause of disseminated bloodstream infections. Here, Nobile and colleagues review our current understanding of the processes involved in the formation of C. albicans biofilms, the core transcriptional network that regulates biofilm development, and polymicrobial biofilms that are formed by C. albicans and certain bacterial species.

    • Matthew B. Lohse
    • , Megha Gulati
    • , Alexander D. Johnson
    •  & Clarissa J. Nobile
  • Review Article |

    In this Review, Stoodley and colleagues discuss current therapeutic strategies and those under development for the treatment of pathogenic biofilms. They explore novel technologies that promise to enhance the efficacy of current therapeutics or provide novel effects and argue that treating biofilm infections requires combination therapies.

    • Hyun Koo
    • , Raymond N. Allan
    • , Robert P. Howlin
    • , Paul Stoodley
    •  & Luanne Hall-Stoodley
  • Review Article |

    Aspergillus fumigatus is an environmental fungus that can cause life-threatening disease. In this Review, van de Veerdonk and colleagues describe how A. fumigatus adapts to environmental change, mechanisms of host defence and our current knowledge of the interplay between the host immune response and the fungus.

    • Frank L. van de Veerdonk
    • , Mark S. Gresnigt
    • , Luigina Romani
    • , Mihai G. Netea
    •  & Jean-Paul Latgé
  • Review Article |

    Apicomplexa include important human pathogens and possess a unique cellular machinery that promotes gliding motility and is called the glideosome. In this Review, Soldati-Favre and colleagues discuss the principles that govern gliding motility, the characterization of the molecular machinery that comprises the glideosome, and its impact on parasite invasion and egress from infected cells.

    • Karine Frénal
    • , Jean-François Dubremetz
    • , Maryse Lebrun
    •  & Dominique Soldati-Favre
  • Review Article |

    Soil contains a vast diversity of microorganisms that can directly or indirectly modulate soil processes and terrestrial ecosystems. In this Review, Fierer summarizes the challenges in characterizing the composition and functions of the soil microbiome, and discusses key future research directions.

    • Noah Fierer