Reviews & Analysis

Multi-omics reveals how metabolites produced by pioneer bacterial species might alter the neonatal gut environment to an anaerobic state much earlier than was previously thought during the first hours of life.

Urban informal settlements, more commonly known as slums, are hotspots for the environmental transmission of antimicrobial resistance (AMR). Here, the authors discuss the behavioural, environmental and structural reasons for this and propose that improvements in water and waste infrastructure, as well as legal and economic incentives, could limit environmental AMR dissemination.

Recent advances in genome sequencing have started to reveal an increasing diversity and distribution of archaeal genomes across multiple ecosystems. In this Review, Baker and colleagues discuss how these genomes elucidate the metabolic capabilities of the Archaea and their ecological roles, while also expanding our view of the tree of life and of eukaryogenesis.

Flaviviruses, a group of vector-borne RNA viruses that includes dengue virus, West Nile virus, Zika virus and several lesser-known species, often emerge in human populations and cause epidemics. Here, Pierson and Diamond review the basic biology of these viruses, their life cycles, the diseases they cause and available therapeutic options. They also discuss the global distribution of flaviviruses, with a focus on lesser-known species that have the potential to emerge more broadly in human populations.

Here, the International Committee on Taxonomy of Viruses describe a new, expanded virus classification scheme with 15 ranks that closely aligns with the Linnaean taxonomic system and better encompasses viral diversity.

In this Perspective, Lopez-Garcia and Moreira update the Syntrophy hypothesis for the origin of eukaryotes, considering recent advances in the archaeal field about the physiology, metabolism, ecology and evolution of these microbes. They also compare and contrast their model with alternative ones, such as the classical Searcy’s and Hydrogen hypotheses and the more recent Reverse Flow and Entangle–Engulf–Endogenize models, and discuss model predictions and ways to test these.

The combined selective pressures of residing in different protozoan hosts in the environment drives the evolution of virulence in the opportunistic pathogen Legionella pneumophila.

N⁶-methyladenosine (m⁶A) is a widespread modification on cellular RNA that is dynamically regulated involving m⁶A writers, erasers and readers, and can impact many cellular processes and pathways. A recent study demonstrates that viruses can use m⁶A to ensure their RNA avoids innate immune sensing.

Two studies now identify bradyzoite-formation deficient 1 and microrchidia as ‘master regulators’ of the transcriptional events that control developmental life cycle transitions in the protozoan parasite Toxoplasma gondii.

The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.

Resistance to antibiotics is a hot topic in microbiology, but there is much less coverage on resistance to vaccines. The associated risk to disease control has potentially devastating implications, but advances are being made towards smarter vaccine design that reduces the risk of antibiotic-resistant disease.

Bacteriophage therapeutics has emerged as one of the few potential beacons that represent possible solutions to the growing global crisis of antimicrobial resistance. Bringing science to the bedside (and vice versa) will maximize the potential of this compelling opportunity.

Mosquitoes have been known for over a century to transmit viruses such as yellow fever. However, laboratory studies to identify the species capable of natural transmission still fail to explain some outbreaks, such as Zika. Now, this paradox is partially explained by a simple methodological shortcoming.

Antibiotic overuse has led to a rise of multidrug-resistant pathogens and increased morbidity. A new study shows that the microbiome can prime two different host response pathways in the intestine and lungs that protect against an antibiotic-resistant pathogen.