Volume 4 Issue 4, April 2019

Megaphages, the largest phage genomes sequenced to date, are abundant in faecal microbiomes from humans, baboons and pigs, leading us to question whether there is an upper limit to the size of viruses relative to their hosts.

Animal studies have strongly implicated the gut microbiome as a key regulator of brain and behaviour. Recent work using two large population cohorts and bioinformatics tools has strengthened the link between microbial disturbances and depression (or quality of life in general).

Rapid diagnostic tests capable of detecting any potential pathogen are needed to improve the efficacy of antimicrobial therapy and inform antimicrobial stewardship efforts. A new metagenomics-based test that detects microbial DNA in human blood can identify a diverse array of pathogens from any source in the body.

Eradicating the viral reservoir remains a formidable barrier to curing human immunodeficiency virus (HIV). The first challenge is to characterize the cells and tissues where HIV hides. In this issue of Nature Microbiology, urethral macrophages are shown to retain infectious HIV particles, prompting us to rethink strategies to eliminate the reservoir.

Innovations in teaching STEM subjects can help build critical science literacy and address global economic needs. Virology teachers and researchers are actively developing and integrating innovative educational materials for students, creating engaging teaching programs and improving information platforms for the general public.

This Review describes the potential opportunities for finding new uses as antimicrobials for existing drugs, the approaches used for screening and the scientific, intellectual property and regulatory challenges to be overcome.

A member of the importin-β protein family, transportin 1, binds to influenza A virus matrix protein M1 and promotes its removal from the viral ribonucleoproteins (vRNPs), enabling disassembly of vRNP bundles, vRNP interaction with importin-α/β and entry into the nucleus.

Classically, peptidoglycan (PG) synthesis was thought to be mediated solely by class A penicillin-binding proteins (PBPs) and related enzymes, a view changed by the identification of RodA as a PG polymerase. Now FtsW is also shown to polymerize PG, in a process that requires complex formation with a partner class B PBP.

A metagenome-based survey of archaeal genomes encoding methyl-coenzyme M reductase (MCR)—a key enzyme for methanogenesis and anaerobic methane oxidation—reveals that MCR-based metabolism is common and diverse in archaea, and may be coupled to dissimilatory sulfate reduction in single organisms.

A search for methyl-coenzyme M reductase complex (MCR) and MCR-like homologues—which govern methane and short-chain alkane metabolism—across publicly available metagenomes reveals that these metabolic pathways are widespread and diverse in archaea, and may in some organisms be linked to alkane and/or fatty acid oxidation.

Metagenomics analyses of a hot spring in Yellowstone National Park reveal previously uncharacterized archaeal populations, including one with the genomic capacity to potentially couple anaerobic methane metabolism and dissimilatory sulfur reduction in a single organism.

Correlation of microbiome features with host quality of life and depression identified specific taxa and microbial pathways in two independent, large population cohorts, identifying links between microbial neuroactive potential and depression.

Suppressive combination antiretroviral therapy fails to eradicate HIV-1 latent reservoirs in poorly characterized cell compartments. Here, urethral macrophages, but not urethral T cells, are shown to contain integrated HIV-1 DNA and to be able to release infectious HIV-1 following reactivation with lipopolysaccharide.

A Drosophila melanogaster systemic infection model for the microsporidian Tubulinosema ratisbonensis reveals that the parasite hijacks host phosphatidic acid, which is a limiting precursor for synthesis of parasite membranes and therefore proliferation.

Type III-A CRISPR–Cas systems use a non-specific RNase, Csm6, to mediate immunity against plasmids when transcription across the target is low. This results in non-specific degradation of host and plasmid transcripts, leading to growth arrest and preventing plasmid replication.

Assessment of metagenomic sequencing of cell-free DNA directly from patient samples as a diagnostic for infections.

The structure of adeno-associated virus (AAV) type 2 in complex with its receptor, AAVR, provides new insights on the molecular mechanism of AAV entry into host cells and will serve to optimize the design of AAV vectors for gene therapy.

By combining a yeast single-cell RNA-seq method that counts transcript start sites in a strand- and isoform-specific manner with index sorting, the authors uncover a linear relationship between cell size and RNA content and extreme cell heterogeneity in the expression of metabolic genes.

Here the authors discover megaphages, or Lak phages, with genomes >540 kilobases in length in the gut microbiomes of a range of hosts, identify Prevotella as the bacterial host and suggest that these phages are common members of the mammalian gut microbiome.

Bacterial DNA from Listeria monocytogenes infection is packaged within extracellular vesicles and induces paracrine cGAS–STING signalling in bystander cells to subvert host responses.

Leishmania exosomes function as viral envelopes for Leishmania RNA virus 1 (LRV1) and facilitate LRV1 transmission, resulting in more aggressive mucocutaneous disease triggered in response to the double-stranded RNA virus in the mammalian host.