Reviews & Analysis

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  • A statistical framework that integrates data from a fine-scale targeted testing scheme and regular randomized surveillance surveys provides unbiased and fine-grained estimates of key SARS-CoV-2 epidemiological parameters that are critical for real-time policy decision-making.

    • Hagai Rossman
    • Eran Segal
    News & Views
  • The development of the infant gut microbiota into an adult configuration is heavily influenced by lifestyle. A large study of children from The Gambia reveals how the microbiota assembles in children with a non-industrial lifestyle.

    • Matthew M. Carter
    • Matthew R. Olm
    • Erica D. Sonnenburg
    News & Views
  • Construction of a global catalogue of human gut archaeal genomes and their viruses provides insights into the structure, composition and function of the human gut archaeome.

    • Patricia Geesink
    • Thijs J. G. Ettema
    News & Views
  • Immunologic recognition of bacterial products during skin infection triggers a cytokine and chemokine response that facilitates neutrophil recruitment to the site of infection. Staphylococcus aureus phenol-soluble modulins can function as early chemoattractants to directly recruit neutrophils and alert the host to infection.

    • Leslie A. Fogel
    • Juliane Bubeck Wardenburg
    News & Views
  • Cooperative interaction between low-abundance gut bacteria is required to convert l-carnitine to TMAO via a multi-step pathway, which leads to an increased risk of cardiovascular disease.

    • Joanna Coker
    • Livia S. Zaramela
    • Karsten Zengler
    News & Views
  • Gut microbiome development in full-term infants has important implications for health and disease, but less is known for preterm infants. Here the authors summarize current knowledge in preterm infants, compare this to what is known for full-term babies, and discuss potential diagnostics and interventions to improve outcomes for preterm infants.

    • David B. Healy
    • C. Anthony Ryan
    • Eugene M. Dempsey
    Perspective
  • Shigella uses the OspC3 type III secretion system effector to catalyze ADP riboxanation of caspases-4 and 11, preventing lipopolysaccharide recognition and pyroptotic death of the infected cell.

    • Bo Wei
    • Edward A. Miao
    News & Views
  • Advances in CRISPR–Cas tools coupled with innovative screening and bioinformatic pipelines make it possible to conduct strain-specific and site-specific genome editing within a microbial community without the need for prior culturing or engineering.

    • Connie W. Y. Ha
    • Suzanne Devkota
    News & Views
  • Bacteriophages fight back with the double whammy of an anti-CRISPR protein and integration into the CRISPR array to protect themselves from the CRISPR–Cas9 immune system of Streptococcus pyogenes.

    • Joseph Bondy-Denomy
    News & Views
  • A network science framework for understanding and predicting human and animal susceptibility to viral infections is proposed.

    • Gregory F. Albery
    • Daniel J. Becker
    • Colin J. Carlson
    Perspective
  • The mammalian immune system has evolved to tolerate commensal microbes that inhabit our mucosal surfaces. Two recent studies explore how intestinal immunity achieves this state of tolerance and show that IgA enforces commensalism of pathobiont Candida species.

    • Ivy M. Dambuza
    • Gordon D. Brown
    News & Views
  • Diverse CRISPR–Cas systems protect prokaryotes against invasive genetic elements like phages. A new study finds that evolution has fused a multi-subunit CRISPR complex into a single protein that cuts RNA and interacts with an ancillary caspase-like peptidase, which may trigger cell suicide.

    • Megan L. Hochstrasser
    • James K. Nuñez
    News & Views
  • Mimicking microbial degradation of sinking marine particles in the laboratory reveals a complex relationship between settling and decomposition rates that informs our view on how the ocean’s biological carbon pump is controlled.

    • Philip W. Boyd
    • Fraser Kennedy
    News & Views
  • Dysbiosis of the gut mycobiota is associated with increased mortality after allogenic hematopoietic cell transplantation.

    • Jianfeng Lin
    • Scott G. Filler
    News & Views
  • A complex network of fungal transcription factors regulates plant invasion by Magnaporthe oryzae.

    • Jessica Cooper
    • Nicole Donofrio
    News & Views
  • Cell entry mechanisms of the non-enveloped viruses bluetongue and rhesus rotavirus are delineated using structural and molecular biology.

    • Yves Gaudin
    News & Views
  • Systematic single-cell analyses of human cytomegalovirus infection reveal that host factors modulate the progression of infection, but the course of viral infection itself is determined by virus genes.

    • Laurent Perez
    News & Views
  • Infections caused by antibiotic-resistant bacteria are increasingly prevalent and difficult to treat. A new study identifies the unique vulnerabilities of a class of antibiotic-resistant mutants at the genomic scale, giving new insights into drugs that can be used in combination with antibiotics to suppress resistance.

    • Anupama Khare
    News & Views
  • Roles for dimethylsulfoniopropionate-based infochemical signalling in ocean microbiome ecosystems are reported in a pair of Nature Microbiology papers.

    • Virginia P. Edgcomb
    News & Views
  • Breastmilk contains human milk oligosaccharides that promote the growth of Bifidobacterium species in the infant gut. These beneficial bacteria can produce aromatic lactic acids that may impact immune function in early life.

    • Christopher J. Stewart
    News & Views