News & Views in 2016

The surprising discovery of viable mutants that retain a peptidoglycan cell wall but lack the essential director of normal cytokinesis, FtsZ, reveals that Escherichia coli can proliferate in a completely unexpected manner.

Deep sequencing of hydrothermal vent and upper ocean water samples further implicate the ocean as a microbial ‘seed bank’. Do these data finally reveal that everything is everywhere? To some extent, but questions remain as to whether these ocean-borne microbes are, in fact, viable and colonize distant locales.

Inspection of more than 286,000 gene families has shed light on the most recent common ancestors of all life. The last universal common ancestor was likely to have been a thermophilic, anaerobic, N₂-fixing organism that used the Wood–Ljungdahl pathway to fix CO₂, using H₂ as an electron donor.

Regulated splicing of some influenza virus RNAs is necessary for the synthesis of various essential proteins. Processing of these transcripts is now found to occur in nuclear speckles, previously considered storage sites for cellular splicing factors.

A combination of metagenomics and stable isotope probing provides new insight into the community-wide degradation of hydrocarbons released during the 2010 Deepwater Horizon oil spill.

Single-particle cryo-electron microscopy is transforming our ability to study the most intimate details of supramolecular multi-protein complexes. The recently observed atomic structure of the T4 phage baseplate paves the way towards understanding the molecular dynamics of other contractile machines such as the bacterial type VI secretion system.

A newly discovered type of bacterial effector produced by the intracellular pathogen Shigella flexneri cooperates with other virulence factors to sabotage host inflammatory responses.

Mice raised under specific pathogen-free conditions in a lab do not model the natural exposure of animals and humans to environmental commensals and pathogens. Now, two studies show that exposing mice to their natural environment, or infecting them with specific pathogens, results in an immune system that better resembles that of adult humans.

Antibiotic therapy is a cornerstone of contemporary medicine. Resistance testing is the gold standard for selecting antibiotics, but in some cases they are surprisingly ineffective. A study now shows that pathogens can form a subset of cells which survive, and even continue to grow in the face of antibiotics.

Human pressures on coral reefs are giving macroalgae a competitive advantage over reef-building corals. These algae support larger, and potentially pathogenic, microbial populations that are metabolically primed for less-efficient, yet faster, carbohydrate remineralization, perpetuating a vicious cycle of reef degradation.

Several microbes produce proteases that cleave antibodies to evade immune recognition. Humans seem to have a receptor on myeloid cells that detects the presence of cleaved antibodies and activates innate immunity.

The plant pathogenic fungus Fusarium oxysporum secretes an effector that is similar to a plant peptide hormone, underscoring the variety of mechanisms that plant pathogens have evolved to tamper with host physiology.

A classical mutant screen and genetic analyses powered by next-generation sequencing reveal that Aspergillus nidulans phytochrome-dependent red light sensing is transmitted via the high-osmolarity-glycerol mitogen-activated protein kinase cascade.

A new large-scale genomics study reports a vastly expanded tree of life that is based on genomic data from over 3,000 species, including many uncultivated and poorly characterized prokaryotes.

Multidrug tolerant bacterial persister cells frequently arise in response to the activation of toxin–antitoxin systems. However, this prevailing view may be less general than assumed. ATP depletion may mediate another route to the persister state for the Gram-positive pathogen Staphylococcus aureus.

A linear-mixed modelling genome-wide association approach for detecting genes and genetic variants underlying antibiotic resistance in bacterial pathogens heralds a new era for microbial genome-wide association studies.

Methylation of HIV RNA has been identified as a way to modulate export of viral transcripts, thereby impacting viral gene expression and particle production. Thus epitranscriptomics adds a new layer of complexity in viral gene expression regulation and also new opportunities for developing therapeutic strategies.

Functional selection of novel antibiotic resistance genes and metagenomic sequencing reveal how antibiotic treatment and bacterial resistance genes interact to shape the fragile microbiome of premature infants.

A viral infection can reduce expression of a host phosphatase that would otherwise dampen the oncogenic activity of a bacterial virulence factor. The results suggest a possible mechanism for cooperation of infections in the development of stomach cancer.

Genomic analysis of Salmonella Enteritidis isolates taken from a single individual with a chronic and relapsing infection reveals how these bacteria have adapted to their host surroundings. Increased within-host fitness comes at the expense of ancillary traits such as virulence.