Latest Reviews

  • Perspective |

    In this Opinion article, Sonnenburg and Sonnenburg explore whether individuals in the industrialized world may be harbouring a microbial community that is now incompatible with human biology, and they hypothesize that the modern, industrial lifestyle has contributed to alterations in the microbiota that may be linked to the deterioration of human health.

    • Erica D. Sonnenburg
    •  & Justin L. Sonnenburg
  • Publisher Correction |

    • Nathalie Q. Balaban
    • , Sophie Helaine
    • , Kim Lewis
    • , Martin Ackermann
    • , Bree Aldridge
    • , Dan I. Andersson
    • , Mark P. Brynildsen
    • , Dirk Bumann
    • , Andrew Camilli
    • , James J. Collins
    • , Christoph Dehio
    • , Sarah Fortune
    • , Jean-Marc Ghigo
    • , Wolf-Dietrich Hardt
    • , Alexander Harms
    • , Matthias Heinemann
    • , Deborah T. Hung
    • , Urs Jenal
    • , Bruce R. Levin
    • , Jan Michiels
    • , Gisela Storz
    • , Man-Wah Tan
    • , Tanel Tenson
    • , Laurence Van Melderen
    •  & Annelies Zinkernagel
  • 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
  • Consensus Statement | | open

    Antibiotic persistence contributes to the survival of bacteria during antibiotic treatment. In this Consensus Statement, scientists working on the response of bacteria to antibiotics define antibiotic persistence and provide practical guidance on how to study bacterial persisters.

    • Nathalie Q. Balaban
    • , Sophie Helaine
    • , Kim Lewis
    • , Martin Ackermann
    • , Bree Aldridge
    • , Dan I. Andersson
    • , Mark P. Brynildsen
    • , Dirk Bumann
    • , Andrew Camilli
    • , James J. Collins
    • , Christoph Dehio
    • , Sarah Fortune
    • , Jean-Marc Ghigo
    • , Wolf-Dietrich Hardt
    • , Alexander Harms
    • , Matthias Heinemann
    • , Deborah T. Hung
    • , Urs Jenal
    • , Bruce R. Levin
    • , Jan Michiels
    • , Gisela Storz
    • , Man-Wah Tan
    • , Tanel Tenson
    • , Laurence Van Melderen
    •  & Annelies Zinkernagel
  • 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
  • Analysis |

    In this Analysis article, Flemming and Wuertz calculate the total number of bacteria and archaea on Earth and estimate the fraction that lives in biofilms. They propose that biofilms are the most prominent and influential type of microbial life.

    • Hans-Curt Flemming
    •  & Stefan Wuertz
  • 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
  • Progress |

    Previously, Zika virus was thought to cause mild infection, and serious complications only recently emerged. Liu, Shi and Qin discuss how the virus has evolved during its recent global spread and consider how these changes might be linked to pathogenesis.

    • Zhong-Yu Liu
    • , Wei-Feng Shi
    •  & Cheng-Feng Qin
  • 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
  • Perspective |

    Studies of ancient DNA and endogenous viral elements have revealed extraordinary conservation of virus genome sequences over thousands or millions of years. In this Opinion article, Simmonds, Aiewsakun and Katzourakis describe a niche-filling model that describes how viruses can rapidly evolve to adapt to new host environments while their longer-term evolution is increasingly driven by their hosts.

    • Peter Simmonds
    • , Pakorn Aiewsakun
    •  & Aris Katzourakis
  • 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
  • Consensus Statement | | open

    This Consensus Statement presents the barriers that currently prevent the timely development and implementation of novel and rapid antimicrobial susceptibility testing platforms, including the costs involved, uptake of new tools, legal and regulatory aspects, difficulties conducting clinical trials and quality control, and presents possible solutions.

    • Alex van Belkum
    • , Till T. Bachmann
    • , Gerd Lüdke
    • , Jan Gorm Lisby
    • , Gunnar Kahlmeter
    • , Allan Mohess
    • , Karsten Becker
    • , John P. Hays
    • , Neil Woodford
    • , Konstantinos Mitsakakis
    • , Jacob Moran-Gilad
    • , Jordi Vila
    • , Harald Peter
    • , John H. Rex
    •  & Wm. Michael Dunne Jr
  • 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
  • Progress |

    Marine oxygen minimum zones are expanding globally as a result of rising temperatures. In this Progress article, Bertagnolli and Stewart describe the ecological and functional diversity of the microbial communities that inhabit these zones and their contribution to biogeochemical cycles.

    • Anthony D. Bertagnolli
    •  & Frank J. Stewart
  • 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
  • Analysis |

    Candidate phyla radiation (CPR) bacteria and DPANN archaea are massive radiations of organisms recently identified. In this Analysis, Castelle et al. explore the metabolic potential of CPR and DPANN radiation, focusing in particular on metabolic gaps and unexpected biological features that are unusual outside of these groups.

    • Cindy J. Castelle
    • , Christopher T. Brown
    • , Karthik Anantharaman
    • , Alexander J. Probst
    • , Raven H. Huang
    •  & Jillian F. Banfield
  • Progress |

    In this Progress article, McGinn and Marraffini review recent studies that have advanced our understanding of the molecular mechanisms of spacer integration, protospacer capture and primed spacer acquisition, and discuss the future of the field.

    • Jon McGinn
    •  & Luciano A. Marraffini
  • 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
  • Progress |

    Canonical two-component systems catalyse autophosphorylation of the histidine kinase, transfer of the phosphoryl group to the regulator and dephosphorylation of the phosphoregulator. In this Progress article, Jacob-Dubuisson and colleagues highlight recent structural insights into the signalling and catalytic mechanisms of sensor histidine kinases.

    • Françoise Jacob-Dubuisson
    • , Ariel Mechaly
    • , Jean-Michel Betton
    •  & Rudy Antoine
  • 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