Latest Reviews

  • Review Article |

    The gut microbiota contributes to host physiology through the production of a myriad of metabolites. In this Review, Bäckhed and colleagues discuss the major classes of microbial metabolites, highlight examples of how microbial metabolites affect host health and provide a potential framework for integration of discovery-based metabolite studies with mechanistic work.

    • Kimberly A. Krautkramer
    • , Jing Fan
    •  & Fredrik Bäckhed
  • Review Article |

    Genome-scale models (GEMs) are mathematical representations of reconstructed networks that facilitate computation and prediction of phenotypes, and are useful tools for predicting the biological capabilities of microorganisms. In this Review, Fang, Lloyd and Palsson discuss the development and the emerging application of GEMs.

    • Xin Fang
    • , Colton J. Lloyd
    •  & Bernhard O. Palsson
  • Review Article |

    The COVID-19 pandemic has prompted unparalleled progress in the development of vaccines and therapeutics in many countries, but it has also highlighted the vulnerability of resource-limited countries in Africa. Margolin and colleagues review global efforts to develop SARS-CoV-2 diagnostics, therapeutics and vaccines, with a focus on the opportunities and challenges in Africa.

    • Emmanuel Margolin
    • , Wendy A. Burgers
    • , Edward D. Sturrock
    • , Marc Mendelson
    • , Rosamund Chapman
    • , Nicola Douglass
    • , Anna-Lise Williamson
    •  & Edward P. Rybicki
  • Review Article |

    Fungi originated in a freshwater environment and their evolution accompanied the rise of algae and land plants. In this Review, Berbee and colleagues examine the fossil and genomic record of ancient fungi and the inferences we can make about their lifestyle.

    • Mary L. Berbee
    • , Christine Strullu-Derrien
    • , Pierre-Marc Delaux
    • , Paul K. Strother
    • , Paul Kenrick
    • , Marc-André Selosse
    •  & John W. Taylor
  • Review Article |

    In this Review, Fan and Pedersen discuss how the gut microbiota and derived microbial compounds may contribute to human metabolic health and to the pathogenesis of common metabolic diseases, and highlight examples of microbiota-targeted interventions aiming to optimize metabolic health.

    • Yong Fan
    •  & Oluf Pedersen
  • Review Article |

    Escherichia coli is a commensal of the vertebrate gut as well as an opportunistic pathogen. In this Review, Denamur and colleagues explore the emergence of virulence during the evolution of E. coli, with a focus on the main ExPEC, InPEC and hybrid clones.

    • Erick Denamur
    • , Olivier Clermont
    • , Stéphane Bonacorsi
    •  & David Gordon
  • Review Article |

    In this Review, Rotello and colleagues discuss the mechanisms by which nanomaterials can be used to target antibiotic-resistant bacterial infections, highlight design elements and properties of nanomaterials that can be engineered to enhance potency, and explore recent progress and remaining challenges for clinical implementation of nanomaterials as antimicrobial therapeutics.

    • Jessa Marie V. Makabenta
    • , Ahmed Nabawy
    • , Cheng-Hsuan Li
    • , Suzannah Schmidt-Malan
    • , Robin Patel
    •  & Vincent M. Rotello
  • Review Article |

    Newly developed antibacterial nanostructured surfaces show excellent prospects as next-generation biomaterials. In this Review, Ivanova, Stoodley and colleagues explore the different mechanisms by which various surface nanopatterns exert the necessary physico-mechanical forces on the bacterial cell membrane that will ultimately result in cell death.

    • Denver P. Linklater
    • , Vladimir A. Baulin
    • , Saulius Juodkazis
    • , Russell J. Crawford
    • , Paul Stoodley
    •  & Elena P. Ivanova
  • Review Article |

    In this Review, Trivedi and colleagues explore the interactions between plants, their associated microbial communities and the environment, and also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits.

    • Pankaj Trivedi
    • , Jan E. Leach
    • , Susannah G. Tringe
    • , Tongmin Sa
    •  & Brajesh K. Singh
  • Review Article |

    Advances in imaging techniques have revealed an unexpected abundance and diversity of organelles in bacteria. In this Review, Greening and Lithgow outline the different types of bacterial organelles and discuss common themes in their formation and function.

    • Chris Greening
    •  & Trevor Lithgow
  • Review Article |

    Mycorrhizas are ubiquitous mutualistic symbioses established between plant roots and soil fungi. In this Review, Bonfante and colleagues explore the origin and evolution of mycorrhizal fungi, the diversity of their interactions with host plants and the potential of application of mycorrhizal symbioses in the development of sustainable agricultural and environmental strategies.

    • Andrea Genre
    • , Luisa Lanfranco
    • , Silvia Perotto
    •  & Paola Bonfante
  • Review Article |

    The archaeal community, the archaeome, is now increasingly recognized as an important component of host-associated microbiomes. In this Review, Moissl-Eichinger and colleagues discuss the diversity and potential roles of the archaea associated with protists, plants and animals, highlighting the potential roles of archaea in human health and disease.

    • Guillaume Borrel
    • , Jean-François Brugère
    • , Simonetta Gribaldo
    • , Ruth A. Schmitz
    •  & Christine Moissl-Eichinger
  • Perspective |

    The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. In this Perspective article, Krupovic, Dolja and Koonin analyse the extant distribution of viruses across the two primary domains of life to infer the LUCA virome.

    • Mart Krupovic
    • , Valerian V. Dolja
    •  & Eugene V. Koonin
  • Review Article |

    Borrelia burgdorferi has a complex life cycle with several different hosts, causing Lyme disease when it infects humans. In this Review, Fikrig and colleagues discuss how B. burgdorferi infects and interacts with its tick vector to ensure onward transmission.

    • Cheyne Kurokawa
    • , Geoffrey E. Lynn
    • , Joao H. F. Pedra
    • , Utpal Pal
    • , Sukanya Narasimhan
    •  & Erol Fikrig
  • Review Article |

    During target protection, a resistance protein physically associates with an antibiotic target to rescue the latter from antibiotic-mediated inhibition. In this Review, O’Neill and colleagues describe the different molecular mechanisms underlying target protection and emphasize the importance of this phenomenon as a cause of clinically significant antibiotic resistance.

    • Daniel N. Wilson
    • , Vasili Hauryliuk
    • , Gemma C. Atkinson
    •  & Alex J. O’Neill
  • Review Article |

    In this Review, Tsai and Cullen discuss how host epigenetic and epitranscriptomic processes regulate viral gene expression at the levels of chromatin and RNA function, respectively, and explore how viruses modify, avoid or utilize these processes in order to promote their replication or persistence.

    • Kevin Tsai
    •  & Bryan R. Cullen
  • Review Article |

    In this Review, Rumbaugh and Sauer discuss the environmental cues and microorganism-derived signals that lead to the biofilm dispersal response, recent findings of matrix-degrading enzymes required for cells to liberate themselves from the biofilm matrix, novel insight into the mechanisms and regulation of dispersal, and the implications of these insights for biofilm control efforts.

    • Kendra P. Rumbaugh
    •  & Karin Sauer
  • Review Article |

    Bats harbour a large number of different viruses, some of which have spilled over to cause human disease. In this Review, Letko, Munster and colleagues discuss the diversity of bat viruses and the factors that determine the emergence of zoonotic viruses from bats.

    • Michael Letko
    • , Stephanie N. Seifert
    • , Kevin J. Olival
    • , Raina K. Plowright
    •  & Vincent J. Munster
  • Review Article |

    Large-scale metagenomic analyses are vastly increasing the rate of discovery of variation within species but they are also leading to scientific and semantic challenges. Bork and colleagues highlight the advances and challenges that are resulting from the use of metagenomic data to study within-species diversity.

    • Thea Van Rossum
    • , Pamela Ferretti
    • , Oleksandr M. Maistrenko
    •  & Peer Bork
  • Review Article |

    Actinobacteria are versatile producers of bioactive natural products. In this Review, van Wezel and colleagues discuss ecological and genomic insights into the mechanisms governing natural product metabolism and how those insights can be translated into approaches for computational and experimental genome mining strategies that yield novel bioactive molecules, in particular antibiotics.

    • Doris A. van Bergeijk
    • , Barbara R. Terlouw
    • , Marnix H. Medema
    •  & Gilles P. van Wezel
  • Review Article |

    In this Review, Lopatkin and Collins discuss key areas of predictive biology that are of growing interest to microbiology, the challenges associated with the innate complexity of microorganisms and the value of quantitative methods in making microbiology more predictable.

    • Allison J. Lopatkin
    •  & James J. Collins
  • Review Article |

    Antibiotic persistence is a threat to effective treatment of bacterial infections. In this Review, Bakkeren, Diard and Hardt discuss the evolutionary forces that have favoured the development of persisters in populations and the consequences for spread of resistance and virulence determinants.

    • Erik Bakkeren
    • , Médéric Diard
    •  & Wolf-Dietrich Hardt
  • Review Article |

    In this Review, Ruff, Greiling and Kriegel discuss the mechanisms through which the microbiota contributes to the predisposition, initiation and perpetuation of immune-mediated diseases, and explore the therapeutic avenues that either target the microbiota, the barrier surfaces or the host immune system to restore tolerance and homeostasis.

    • William E. Ruff
    • , Teri M. Greiling
    •  & Martin A. Kriegel
  • Review Article |

    In this Review Egan, Errington and Vollmer discuss new insights into the molecular mechanisms of peptidoglycan synthesis, sacculus growth regulation and bacterial morphology, as well as how bacteria achieve robust cell wall growth under different conditions and stresses.

    • Alexander J. F. Egan
    • , Jeff Errington
    •  & Waldemar Vollmer
  • Review Article |

    The schooner Tara sailed 140,000 km across the global oceans to sample diverse marine ecosystems and plankton communities. In the Review, members of the Tara Oceans project highlight how resulting data can be used for an integrated understanding of ocean biology.

    • Shinichi Sunagawa
    • , Silvia G. Acinas
    • , Peer Bork
    • , Chris Bowler
    • , Silvia G. Acinas
    • , Marcel Babin
    • , Peer Bork
    • , Emmanuel Boss
    • , Chris Bowler
    • , Guy Cochrane
    • , Colomban de Vargas
    • , Michael Follows
    • , Gabriel Gorsky
    • , Nigel Grimsley
    • , Lionel Guidi
    • , Pascal Hingamp
    • , Daniele Iudicone
    • , Olivier Jaillon
    • , Stefanie Kandels
    • , Lee Karp-Boss
    • , Eric Karsenti
    • , Magali Lescot
    • , Fabrice Not
    • , Hiroyuki Ogata
    • , Stéphane Pesant
    • , Nicole Poulton
    • , Jeroen Raes
    • , Christian Sardet
    • , Mike Sieracki
    • , Sabrina Speich
    • , Lars Stemmann
    • , Matthew B. Sullivan
    • , Shinichi Sunagawa
    • , Patrick Wincker
    • , Damien Eveillard
    • , Gabriel Gorsky
    • , Lionel Guidi
    • , Daniele Iudicone
    • , Eric Karsenti
    • , Fabien Lombard
    • , Hiroyuki Ogata
    • , Stephane Pesant
    • , Matthew B. Sullivan
    • , Patrick Wincker
    •  & Colomban de Vargas
  • Review Article |

    Filoviruses such as Ebola virus pose a substantial health risk to humans. Advances in genomic technologies have enabled the rapid, large-scale generation of virus sequence data at the location of disease outbreaks and thus the use of reverse functional genomics to swiftly characterize the threat of, and treatment for, filovirus disease.

    • Nicholas Di Paola
    • , Mariano Sanchez-Lockhart
    • , Xiankun Zeng
    • , Jens H. Kuhn
    •  & Gustavo Palacios
  • Review Article |

    In this Review, Jones and colleagues describe the extremely diverse Xanthomonas spp. and how these plant pathogens use their extensive repertoire of effectors for virulence and immune evasion. Understanding these prototypical plant pathogens paves the way to combat disease.

    • Sujan Timilsina
    • , Neha Potnis
    • , Eric A. Newberry
    • , Prabha Liyanapathiranage
    • , Fernanda Iruegas-Bocardo
    • , Frank F. White
    • , Erica M. Goss
    •  & Jeffrey B. Jones
  • Review Article |

    New antibacterial agents are urgently needed to address the global increase in resistance. In this Review, Theuretzbacher and colleagues critically review the current published literature and publicly available information on antibacterial agents in all phases of clinical development.

    • Ursula Theuretzbacher
    • , Karen Bush
    • , Stephan Harbarth
    • , Mical Paul
    • , John H. Rex
    • , Evelina Tacconelli
    •  & Guy E. Thwaites
  • Review Article |

    Worldwide amphibian declines caused by pathogenic chytrid fungi are emblematic of the emerging infectious diseases driven by globalization. Fisher and Garner discuss how these wildlife pathogens emerge to drive global declines in amphibian biodiversity and the implications of current research for policy and control measures.

    • Matthew C. Fisher
    •  & Trenton W. J. Garner
  • Review Article |

    Non-tuberculous mycobacteria, such as Mycobacterium abscessus, are an increasing global health burden, in part due their extensive drug resistance. In this Review, Johansen, Herrmann and Kremer discuss the infection process, host interactions, mechanisms of drug resistance and drug development.

    • Matt D. Johansen
    • , Jean-Louis Herrmann
    •  & Laurent Kremer
  • Review Article |

    In this Review, Hatzenpichler et al. introduce next-generation physiology, which is a suite of new techniques that enable investigation into the phenotypes of individual cells in a non-destructive manner. Next-generation physiology complements genomics and culturing and provides new insights into microbiome function.

    • Roland Hatzenpichler
    • , Viola Krukenberg
    • , Rachel L. Spietz
    •  & Zackary J. Jay
  • Review Article |

    Over the past decade, Klebsiella pneumoniae has emerged as a major clinical and public health threat. In this Review, Wyres, Lam and Holt discuss how genomics approaches have advanced our understanding of K. pneumoniae taxonomy, ecology and evolution as well as the diversity and distribution of clinically relevant determinants of pathogenicity and antimicrobial resistance.

    • Kelly L. Wyres
    • , Margaret M. C. Lam
    •  & Kathryn E. Holt
  • Review Article |

    In this Review, van Belkum and colleagues discuss routinely used antimicrobial susceptibility testing (AST) methods, explore current efforts to improve phenotypic AST systems — including new emerging technologies as well as genomic and gene-based antimicrobial resistance detection methods — and highlight the challenges and opportunities for new rapid AST systems.

    • Alex van Belkum
    • , Carey-Ann D. Burnham
    • , John W. A. Rossen
    • , Frederic Mallard
    • , Olivier Rochas
    •  & William Michael Dunne Jr.
  • Review Article |

    In this Review, Berman and Krysan define and distinguish resistance and tolerance, and discuss the current understanding of the molecular, genetic and physiological mechanisms that contribute to those phenomena. Distinguishing tolerance from resistance might provide important insights into the reasons for treatment failure in some settings.

    • Judith Berman
    •  & Damian J. Krysan
  • Review Article |

    Phages are tremendously abundant and are found in every environment where bacteria exist. In this Review, Dion, Oechslin and Moineau explore the diversity of phages at the structural, genomic and community levels as well as their complex evolutionary relationships.

    • Moïra B. Dion
    • , Frank Oechslin
    •  & Sylvain Moineau
  • Review Article |

    Bacteria produce diverse polymers, such as polysaccharides, polyesters, polyphosphates and extracellular DNA. In this Review, Moradali and Rehm discuss the types of bacterial polymers and their role in bacterial physiology and pathogenesis as well as their production and use as novel biomaterials.

    • M. Fata Moradali
    •  & Bernd H. A. Rehm
  • Review Article |

    During intraerythrocytic development, malaria parasites replicate within a membrane-bound parasitophorous vacuole. In this Review, Matz, Beck and Blackman explore the origin, development, molecular composition and functions of the parasitophorous vacuole during blood-stage development. They also discuss the relevance of the malaria parasite’s intravacuolar lifestyle for successful erythrocyte infection and provide perspectives for future research directions.

    • Joachim M. Matz
    • , Josh R. Beck
    •  & Michael J. Blackman
  • Review Article |

    Microbiology and biophysics are converging to advance our understanding of the mechanobiology of microorganisms. In this Review, Dufrêne and Persat discuss the physical forces that bacteria experience in their natural environments and the structures that transmit these forces to a cell. Furthermore, they explore bacterial phenotypes influenced by mechanical inputs, including adhesion, motility and biofilm formation.

    • Yves F. Dufrêne
    •  & Alexandre Persat
  • Review Article |

    Plastic debris in the marine environment provides a durable substrate that can be colonized by microorganisms and supports the growth of microbial biofilms. In this Review, Amaral-Zettler and colleagues explore the microbial ecology of the plastisphere in the context of its diversity and function, as well as suggesting areas for further research.

    • Linda A. Amaral-Zettler
    • , Erik R. Zettler
    •  & Tracy J. Mincer
  • Review Article |

    Plasmodium falciparum and other malaria parasites have complex life cycles, inhabiting different host cells and tissues during their multistage development. In this Review, Marti and colleagues discuss blood-stage parasite development and the newly discovered reservoir in the haematopoietic niche.

    • Kannan Venugopal
    • , Franziska Hentzschel
    • , Gediminas Valkiūnas
    •  & Matthias Marti
  • Review Article |

    In this Review, Perlmutter and Bordenstein discuss our current knowledge of microbial symbionts that inhabit or transmit through the reproductive tissues of arthropods, their modes of transmission, and the physiological and evolutionary outcomes of their symbiotic relationships.

    • Jessamyn I. Perlmutter
    •  & Seth R. Bordenstein
  • Review Article |

    The number and diversity of known CRISPR–Cas systems have substantially increased in recent years. In this Review, Koonin and colleagues provide an updated evolutionary classification of CRISPR–Cas systems and cas genes, with an emphasis on major developments, and outline a complete scenario for the origins and evolution of CRISPR–Cas systems.

    • Kira S. Makarova
    • , Yuri I. Wolf
    • , Jaime Iranzo
    • , Sergey A. Shmakov
    • , Omer S. Alkhnbashi
    • , Stan J. J. Brouns
    • , Emmanuelle Charpentier
    • , David Cheng
    • , Daniel H. Haft
    • , Philippe Horvath
    • , Sylvain Moineau
    • , Francisco J. M. Mojica
    • , David Scott
    • , Shiraz A. Shah
    • , Virginijus Siksnys
    • , Michael P. Terns
    • , Česlovas Venclovas
    • , Malcolm F. White
    • , Alexander F. Yakunin
    • , Winston Yan
    • , Feng Zhang
    • , Roger A. Garrett
    • , Rolf Backofen
    • , John van der Oost
    • , Rodolphe Barrangou
    •  & Eugene V. Koonin
  • Review Article |

    In the outer membrane, trimeric porins control the cellular uptake of small molecules, including nutrients and antibacterial agents. In this Review, Pagès and colleagues discuss advances in our understanding of the roles of general porins in small-molecule translocation in Enterobacteriaceae and consider the crucial contribution of porins in antibiotic resistance.

    • Julia Vergalli
    • , Igor V. Bodrenko
    • , Muriel Masi
    • , Lucile Moynié
    • , Silvia Acosta-Gutiérrez
    • , James H. Naismith
    • , Anne Davin-Regli
    • , Matteo Ceccarelli
    • , Bert van den Berg
    • , Mathias Winterhalter
    •  & Jean-Marie Pagès
  • Review Article |

    Secreted siderophores help bacteria to take up iron from the environment. In this Review, Kramer, Özkaya and Kümmerli discuss the functions and implications that siderophores have for social interactions between bacterial cells and the resulting consequences for communities and hosts.

    • Jos Kramer
    • , Özhan Özkaya
    •  & Rolf Kümmerli
  • Viewpoint |

    In this Viewpoint article, seven experts discuss the challenges that are contributing to the decline in antibiotic drug discovery and development, and the international and national initiatives aimed at incentivizing research and the development of new antibiotics to improve the economic feasibility of antibiotic development.

    • Christine Årdal
    • , Manica Balasegaram
    • , Ramanan Laxminarayan
    • , David McAdams
    • , Kevin Outterson
    • , John H. Rex
    •  & Nithima Sumpradit
  • Review Article |

    With rising rates of antibiotic resistance, it is essential that new antibiotics are developed. In this Review, Theuretzbacher et al. take stock of the preclinical antibiotic pipeline and discuss challenges and opportunities for the discovery and development of novel antibacterial therapies.

    • Ursula Theuretzbacher
    • , Kevin Outterson
    • , Aleks Engel
    •  & Anders Karlén
  • Review Article |

    Mycobacterium tuberculosis has a distinctive cell envelope that contributes to its resistance against the human immune system and antibiotic therapy. In this Review, Dulberger, Rubin and Boutte discuss mycobacterial cell envelope dynamics and their relevance for infection and drug treatment.

    • Charles L. Dulberger
    • , Eric J. Rubin
    •  & Cara C. Boutte