Articles in 2019

Quantitative stable isotope probing and gene expression analyses in anoxic Namibian shelf sediments reveal that representatives of the Asgard candidate phylum Candidatus Lokiarchaeota are capable of homoacetogenesis, a metabolic strategy of high energetic efficiency that may explain how these archaea thrive in the energy-limited seafloor subsurface environment.

Galacturonic acid produced by Bacteroides thetaiotamicron is shown to be sensed by enterohaemorrhagic Escherichia coli and Citrobacter rodentium to initiate an infection program that includes its use as a carbon source and regulation of the type III secretion system, leading to colitis and inflammation.

High-throughput chromosomal conformation capture identified changes in the gut microbiome over 10 years, including substantial exchange of accessory elements and adaptive evolution in core genomes.

The lipopolysaccharide of the intracellular pathogen Shigella, in particular its O antigen, interacts with caspases and blocks their activation to prevent apoptosis.

Two recent studies reveal a virus anti-defence strategy whereby large, ‘jumbo’ phages protect themselves from both restriction endonucleases and DNA-targeting CRISPR–Cas systems, but not from RNA-targeting ones, by encapsulating the phage genome inside the cell in a ‘nucleus’-like shell that is impenetrable for CRISPR effectors.

Metabolic adaptation plays a key role in determining the composition of microbial ecosystems. A new study shows that in the inflamed gut, pathogenic Enterobacteriaceae can reprogramme their metabolism towards diet-derived l-serine utilization to outcompete the resident microbiota and cause disease.

Baloxavir marboxil (BXM) represents a promising advance in antiviral chemotherapies for influenza infections. Identification of transmissible BXM-resistant strains in Japan may hit pause on widespread adoption of this therapy and could lead to revision of surveillance practices for emerging viruses.

Adding a flap on the top of an insecticide-treated bednet helps to intercept blood-seeking mosquitoes and allows a wider range of insecticides to be used together. Net buyers must now make a challenging decision for each target area: which net product will be most cost-effective, given the resistance in local vectors?

Nature Microbiology will offer authors the option of publishing a peer-review file that includes anonymous peer-review reports, author responses and our decision letters. We will also request that articles include more source data and are more transparent in reporting data availability.

The host protein cyclophilin A binds to the HIV-1 capsid and its role in infection has long been enigmatic. A new study shows that this interaction protects the virus from inhibition by TRIM5α in physiologically relevant primary human cells.

As microbiome science expands, academic centres scramble to fill many needs, from service provider to industry liaison. A newly created network aims to share strategies and accelerate knowledge transfer, and invites others to join the efforts.

This Review summarizes mechanisms by which hosts recognize pathogens and their effectors, and trigger downstream immune pathways.

Shotgun metagenomic sequencing (using the MinION platform) of mock microbial communities and faecal samples from healthy and ill preterm infants can be used to identify pathogens and their antimicrobial resistance gene profiles in real time, indicating the potential for translation into clinical settings.

Herpesviruses are shown to specifically block innate antiviral responses by inducing the aggregation of key signalling molecules nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) essential modulator (NEMO) and receptor-interacting protein kinase 1 (RIPK1) and their degradation by selective autophagy, thereby blocking the activation of NF-κB and the induction of necroptosis, respectively.

The comparison of the ability of native and engineered gene clusters transferred into bacteria that live on or inside cereal roots to regulate nitrogenase activity reveals different strategies to control nitrogen fixation in rhizobia and paves the way to engineer a bacterium able to deliver high nitrogen fluxes to crops.

The structure of the FlaG–FlaF complexes from Sulfolobus acidocaldarius, combined with mutational and biochemical studies, suggests that these proteins form a heterotetrameric complex in which FlaF regulates the filamentation of FlaG and anchoring of the archaellum to the S-layer, thereby modulating motility.

Reactive oxygen species produced by macrophages following infection with Staphylococcus aureus attack bacterial iron–sulfur cluster-containing proteins, thereby leading to alterations in bacterial metabolism that increase their tolerance to antibiotics.

Metagenomic sequencing of near-surface marine viral communities sampled monthly over 5 years revealed that overall communities were stable over time, although minor population variants were more variable, which is consistent with Red Queen-like dynamics.

This study reports that flavivirus transmission by mosquitoes to mice is increased if mosquitoes feed subsequently on non-infectious blood, possibly because feeding causes microperforations in the gut. Modelling shows this could explain how A. aegypti can sustain an explosive epidemic such as Zika virus despite its perceived poor vector competence.

This paper identifies a Serratia jumbo phage that, on infection, leads to the formation of a nucleus-like structure that protects phage DNA from CRISPR–Cas defence systems. However, the phage is still susceptible to CRISPR–Cas RNA targeting in the cytoplasm.