News & Views in 2019

Complementary genomic frameworks for taxonomic classification of viruses infecting bacteria and archaea reveal evolutionary drivers, mosaicism and perspective on the genetic diversity of the tiniest, most abundant biological entities on Earth.

Eukaryotes evolved from a symbiosis involving Alphaproteobacteria and archaea phylogenetically nested within the Asgard clade. Two recent studies explore the metabolic capabilities of Asgard lineages, supporting refined symbiotic metabolic interactions that might have operated at the dawn of eukaryogenesis.

Biofilms are communities of bacteria that accumulate on surfaces such as replacement joints or intravenous catheters. By silencing a key communication system, Staphylococcus aureus builds tightly packed biofilms that can withstand attack by host immune cells.

Microscopy and genomic analyses reveal an intriguing symbiosis between eukaryotic protists and Deltaproteobacteria in anoxic marine sediments that involves division of labour and interspecies hydrogen transfer, and enables collective magnetotactic motility by the consortium.

The rapidly dividing bacterium Vibrio natriegens holds promise for transforming traditional molecular biology and biotechnology processes. New work demonstrates that CRISPR interference technology is a robust tool for rapid, genome-wide screens in V. natriegens, facilitating future bioengineering efforts.

A recent study finds that viruses cooperate altruistically to overcome innate host immunity and that this can be explained in the same way we explain altruism between animals.

A class of drugs approved to treat schizophrenia can cause rapid loss of the pilus, an essential virulence factor necessary for the disease-causing properties in the strict human pathogen Neisseria meningitidis.

Differences in microbial genomes can result in vastly different phenotypes and functions. Consequently, it is critical to understand the genome variations that differentiate microbial strains. Here, we discuss recent exciting advances that enable structural variant measurement, their associated phenotypes and the horizon for future discovery.

The secondary metabolite cepacin A is the essential compound made by Burkholderia ambifaria needed for biocontrol of plant pathogens. In this organism, genes responsible for virulence and for cepacin A biosynthesis reside on different replicons, allowing for the engineering of avirulent mutants that retain their biocontrol properties.

Inflammatory molecules evolved partly to protect hosts from viruses, but increasing evidence suggests that they cause disease pathology and chronic conditions, and play a role in aging. By mitigating these effects, bats are able to both tolerate viral infections and live well beyond expectations.

A large-scale comparative genomic survey of Cryptosporidium species and subtypes reveals a cryptic anthroponotic Cryptosporidium parvum branch and a large, recent superclade of species and subtypes that undergo genetic exchange, potentially facilitating host associations.

Computational analysis of fungal genomes revealed that some early-branching fungi use selenocysteine, the selenium-containing amino acid, that was thought to be missing from proteins in this lineage.

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.

Three recent metagenomic studies analyse methanogenesis-related genes in previously uncharacterized, sediment-inhabiting archaeal lineages. They elucidate the metabolic capacity encoded in the genomes of these lineages, yet how these organisms harness energy is still a mystery.

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.

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).

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.

Severe fever with thrombocytopenia virus is an emerging, highly lethal tick-borne pathogen with growing impact. In this issue of Nature Microbiology, two papers make major progress towards a better understanding of its so far incompletely understood mechanisms of virulence.

Bacteria have previously been assumed to cope with environmental stress by tuning their total number of active ribosomes. Instead, a study in this issue of Nature Microbiology shows that from a heterogeneous pool of ribosomes, Vibrio vulnificus uses ribosomes with a particular ribosomal RNA variant to translate upregulated stress response mRNAs.

Molecular players involved in systemic and acute infections are relatively easy to pinpoint, whereas bacterial resilience during chronic infections remains less well understood. Pseudomonas aeruginosa encodes a quorum-regulated virulence factor, TesG, that promotes chronic lung infection by suppressing host inflammatory responses.