Review Articles

  • Review Article |

    TRIM5 is a potent restriction factor for HIV-1 and other retroviruses. In this Review, Ganser-Pornillos and Pornillos provide an overview of the current state of knowledge of the molecular mechanism of TRIM5-mediated restriction, highlight recent advances and discuss implications for the development of capsid-targeted antiviral therapeutics.

    • Barbie K. Ganser-Pornillos
    •  & Owen Pornillos
  • Review Article |

    Metagenomic studies are beginning to clarify the huge phylogenetic and functional diversity of plant viruses and their importance for ecosystem stability. In this Review, Varsani and colleagues discuss evolutionary relationships between plant viruses, their vectors and host plants.

    • Pierre Lefeuvre
    • , Darren P. Martin
    • , Santiago F. Elena
    • , Dionne N. Shepherd
    • , Philippe Roumagnac
    •  & Arvind Varsani
  • Review Article |

    Coral reefs are threatened by climate change; one avenue to address this threat is to understand and manipulate the microbial partners of corals. In this Review, van Oppen and Blackall discuss the bacteria found in the coral microbiome and their roles.

    • Madeleine J. H. van Oppen
    •  & Linda L. Blackall
  • Review Article |

    Perturbations in the intestinal microbiome are implicated in inflammatory bowel disease (IBD). In this Review, Xavier and colleagues highlight current knowledge of gut microbial factors linked to IBD pathogenesis and discuss how multiomics data from large-scale population studies in health and disease have been used to identify specific microbial strains, transcriptional changes and metabolic alterations associated with IBD.

    • Melanie Schirmer
    • , Ashley Garner
    • , Hera Vlamakis
    •  & Ramnik J. Xavier
  • Review Article |

    In this Review, Andersson and colleagues outline factors to consider when studying and defining heteroresistance, and they explore the different genetic mechanisms underlying heterogeneity in antibiotic resistance phenotypes, the impact of such mechanisms on the efficacy of treatment and the methods and difficulties in diagnosing heteroresistance in clinical bacterial isolates.

    • Dan I. Andersson
    • , Hervé Nicoloff
    •  & Karin Hjort
  • Review Article |

    Whole genome sequencing (WGS) offers new opportunities in the clinical management and surveillance of Mycobacterium tuberculosis. In this Review, Meehan and colleagues explore the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.

    • Conor J. Meehan
    • , Galo A. Goig
    • , Thomas A. Kohl
    • , Lennert Verboven
    • , Anzaan Dippenaar
    • , Matthew Ezewudo
    • , Maha R. Farhat
    • , Jennifer L. Guthrie
    • , Kris Laukens
    • , Paolo Miotto
    • , Boatema Ofori-Anyinam
    • , Viola Dreyer
    • , Philip Supply
    • , Anita Suresh
    • , Christian Utpatel
    • , Dick van Soolingen
    • , Yang Zhou
    • , Philip M. Ashton
    • , Daniela Brites
    • , Andrea M. Cabibbe
    • , Bouke C. de Jong
    • , Margaretha de Vos
    • , Fabrizio Menardo
    • , Sebastien Gagneux
    • , Qian Gao
    • , Tim H. Heupink
    • , Qingyun Liu
    • , Chloé Loiseau
    • , Leen Rigouts
    • , Timothy C. Rodwell
    • , Elisa Tagliani
    • , Timothy M. Walker
    • , Robin M. Warren
    • , Yanlin Zhao
    • , Matteo Zignol
    • , Marco Schito
    • , Jennifer Gardy
    • , Daniela M. Cirillo
    • , Stefan Niemann
    • , Inaki Comas
    •  & Annelies Van Rie
  • Review Article |

    In this Review, Reyes-Lamothe and Sherratt describe the contributions of chromosome structure and nucleoid folding to cell cycle regulation, detail the cellular processes involved in the initiation of DNA replication and DNA segregation and explore how those processes are linked to cell growth and cell division.

    • Rodrigo Reyes-Lamothe
    •  & David J. Sherratt
  • Review Article |

    In this Review, Mitchell and Silhavy explore the cellular envelope stress response pathways and discuss what occurs when these pathways are aberrantly activated. They also discuss how recent insights into stress response activation have highlighted the extreme toxicity of unfolded outer membrane proteins.

    • Angela M. Mitchell
    •  & Thomas J. Silhavy
  • Review Article |

    Lipopolysaccharide is a key component of the Gram-negative cell envelope and functions, for example, as a permeability barrier or determinant of host immune responses. In this Review, Simpson and Trent guide us through lipopolysaccharide biogenesis and modifications and their functional and therapeutic implications.

    • Brent W. Simpson
    •  & M. Stephen Trent
  • Review Article |

    Type IV pili (T4P) are dynamic filaments on the surface of many bacteria with essential roles in colonization and pathogenesis. In this Review, Craig, Forest and Maier examine the T4P architecture, present molecular models for T4P dynamics and highlight recent insights into T4P retraction.

    • Lisa Craig
    • , Katrina T. Forest
    •  & Berenike Maier
  • Review Article |

    Vertebrate genomes typically contain thousands of loci composed of ancient retroviral sequences, known as endogenous retroviruses (ERVs). In this Review, Johnson describes ERV origins, their diversity and their relationships to retroviruses and discusses the potential for ERVs to reveal virus–host interactions on evolutionary timescales. He also describes examples of cellular functions, including protein-coding genes and regulatory elements that have evolved from ERVs.

    • Welkin E. Johnson
  • Review Article |

    Most bacteria live in fluctuating environments that can have complex topographies and multiple species present. In this Review, Mukherjee and Bassler discuss how factors such as flow, geometry, biofilms and the presence of the host microbiota influence bacterial quorum sensing.

    • Sampriti Mukherjee
    •  & Bonnie L. Bassler
  • Review Article |

    Many symbioses depend on the acquisition of microbial symbionts from the environment. In this Review, Raina and colleagues argue that chemotaxis and motility are widespread but overlooked mechanisms that enable symbionts to find and/or colonize their hosts.

    • Jean-Baptiste Raina
    • , Vicente Fernandez
    • , Bennett Lambert
    • , Roman Stocker
    •  & Justin R. Seymour
  • Review Article |

    In this Review, Grossart and colleagues conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. They focus on currently unexplored aquatic fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.

    • Hans-Peter Grossart
    • , Silke Van den Wyngaert
    • , Maiko Kagami
    • , Christian Wurzbacher
    • , Michael Cunliffe
    •  & Keilor Rojas-Jimenez
  • Review Article |

    Electroactive microorganisms can transfer electrons to or take them up from electrodes, and they are used in applications such as microbial fuel cells. In this Review, Logan and colleagues discuss the diversity of exoelectrogenic and electrotrophic microorganisms and their functions.

    • Bruce E. Logan
    • , Ruggero Rossi
    • , Ala’a Ragab
    •  & Pascal E. Saikaly
  • Review Article |

    In this Review, Bush and Bradford describe medically relevant β-lactamase families and various combinations of a β-lactam with a β-lactamase inhibitor that have been developed, or that are being developed, to counteract these enzymes.

    • Karen Bush
    •  & Patricia A. Bradford
  • Review Article |

    Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen both within hospitals and in the community. In this Review, Fowler and colleagues provide an overview of basic and clinical MRSA research and explore the epidemiology, transmission, genetic diversity, evolution, surveillance and treatment of MRSA.

    • Nicholas A. Turner
    • , Batu K. Sharma-Kuinkel
    • , Stacey A. Maskarinec
    • , Emily M. Eichenberger
    • , Pratik P. Shah
    • , Manuela Carugati
    • , Thomas L. Holland
    •  & Vance G. Fowler Jr
  • Review Article |

    Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract disease in young children and elderly people. In this Review, Battles and McLellan summarize our current understanding of RSV entry, describe progress on the development of new interventions and conclude with a perspective on gaps in our knowledge that require further investigation.

    • Michael B. Battles
    •  & Jason S. McLellan
  • Review Article |

    Combinations of antibiotics and of antibiotics with non-antibiotic activity-enhancing compounds offer a productive strategy to address the widespread emergence of antibiotic-resistant strains. In this Review, Tyers and Wright outline a theoretical and practical framework for the development of effective drug combinations.

    • Mike Tyers
    •  & Gerard D. Wright
  • Review Article |

    Methane metabolism has a central role in the global carbon cycle. In the Review, Tyson and colleagues discuss the enzymatic pathways responsible for archaeal methane metabolism and highlight the evolutionary relationships of key enzymes with recently discovered alkane-oxidizing archaea.

    • Paul N. Evans
    • , Joel A. Boyd
    • , Andy O. Leu
    • , Ben J. Woodcroft
    • , Donovan H. Parks
    • , Philip Hugenholtz
    •  & Gene W. Tyson
  • Review Article |

    In this Review, Brennan and Garrett discuss the multifaceted associations of Fusobacterium nucleatum with its human host that range from symbiotic in oral biofilms to potential infectious pathogen at several sites and cancer-promoting member of the microbiota in the gut.

    • Caitlin A. Brennan
    •  & Wendy S. Garrett
  • Review Article |

    In this Review, Nancy P. Keller describes the classification and genetics of secondary metabolites and biosynthetic gene clusters, cluster regulation and the ecological roles of secondary metabolites, and she explores avenues for the discovery of new fungal metabolites and current challenges in their identification.

    • Nancy P. Keller
  • Review Article |

    Coronaviruses have a broad host range and distribution, and some highly pathogenic lineages have spilled over to humans and animals. Here, Cui, Li and Shi explore the viral factors that enabled the emergence of diseases such as severe acute respiratory syndrome and Middle East respiratory syndrome.

    • Jie Cui
    • , Fang Li
    •  & Zheng-Li Shi
  • Review Article |

    Eukaryotic viruses have evolved a variety of ways to manipulate the cellular translation apparatus. In this Review, Jaafar and Kieft present important examples of viral RNA-based strategies to exploit the cellular translation machinery.

    • Zane A. Jaafar
    •  & Jeffrey S. Kieft
  • Review Article |

    Influenza A viruses cause pandemics when they cross between species. In this Review, Barclay and colleagues examine the host barriers that influenza A viruses must overcome to initiate a pandemic in humans and describe how, on crossing the species barrier, the virus mutates to establish new interactions with the human host.

    • Jason S. Long
    • , Bhakti Mistry
    • , Stuart M. Haslam
    •  & Wendy S. Barclay
  • Review Article |

    Fungi are enormously diverse, not the least in potential genetic markers that can be used for high-throughput sequencing studies of the mycobiome. In this Review, Nilsson and colleagues provide advice for leveraging next-generation technologies to explore mycobiome diversity in different habitats.

    • R. Henrik Nilsson
    • , Sten Anslan
    • , Mohammad Bahram
    • , Christian Wurzbacher
    • , Petr Baldrian
    •  & Leho Tedersoo
  • Review Article |

    Cyanobacteria have evolved a number of photoreceptor-controlled mechanisms that enable them to sense and respond to environmental light conditions. In this Review, Kehoe and Wiltbank examine physiological responses that are controlled by members of the phytochrome photoreceptor superfamily and discuss the signal transduction pathways through which these photoreceptors operate.

    • Lisa B. Wiltbank
    •  & David M. Kehoe
  • Review Article |

    Bacterial membrane vesicles can transfer material between cells and function as decoys for antibiotics and phages. This Review provides an overview of different vesicle types, including classic outer-membrane vesicles and newly identified types that are induced by phage-derived autolysins.

    • Masanori Toyofuku
    • , Nobuhiko Nomura
    •  & Leo Eberl
  • Review Article |

    Light controls important physiological and morphological responses in fungi. In this Review, Yu and Fischer review the structural basis for light sensing in filamentous fungi and explore the light signalling mechanisms for blue-light photoreceptors, green-light photoreceptors and red-light photoreceptors.

    • Zhenzhong Yu
    •  & Reinhard Fischer
  • Review Article |

    Most infections with enterococci involve the formation of biofilms, which further increases the antibiotic tolerance and resistance of these priority pathogens. In this Review, Kline and colleagues summarize how enterococci form biofilms, including polymicrobial biofilms, and highlight new treatment options.

    • Jun-Hong Ch’ng
    • , Kelvin K. L. Chong
    • , Ling Ning Lam
    • , Jun Jie Wong
    •  & Kimberly A. Kline
  • Review Article |

    The dynamic and polymicrobial oral microbiota is a direct precursor of diseases such as dental caries and periodontitis. In this Review, Lamont, Koo and Hajishengallis discuss the mechanisms by which oral microbial communities develop and become functionally specialized. They also examine the progression of polymicrobial communities towards pathogenicity.

    • Richard J. Lamont
    • , Hyun Koo
    •  & George Hajishengallis
  • 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