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The study of microorganisms, the most abundant living entities on Earth, aims to understand their unique biology and the influence they have on human health, disease, and life in general. Here, we highlight work that furthers our understanding of the microbial world.
In hospitals, surfaces present as a reservoir for bacteria pathogens, potentially leading to nosocomial infections. In this work, authors aim to profile extended-spectrum β lactamase- and carbapenemase-carrying bacterial species colonising neonatal hospital wards and causing neonatal sepsis.
Chitwood et al. report on the rapid expansion of a Ural-lineage multidrug resistant strain of Mycobacterium tuberculosis in Moldova. This strain has an estimated reproduction number more than two times greater than otherwise similar drug susceptible strains.
Rise of new viral strains is a major public health challenge, demanding advanced detection and forecasting methods. This study shows how examining communities within networks of viral mutations enables early detection of emerging strains.
Routine sampling of pregnant women at first antenatal care (ANC) visits could be used for malaria surveillance. Here, the authors compare the genetic structure of Plasmodium falciparum parasite populations between samples from first ANC users and children from the community in Mozambique, and show that it can inform about changes in transmission beyond epidemiological data.
Co-infections are much less studied than single pathogen infections. Here, the authors show that co-infection with two unrelated viruses, neurotropic Semliki Forest virus and influenza A virus, exacerbates influenza-related lung pathology and prolongs lung virus replication in a mouse model.
There is limited data on immune factors contributing to SARS-CoV-2 viral clearance in people living with HIV. Here, the authors show that re-emergence of the neutralizing antibody response may be key to clearing persistent SARS-CoV-2 infection in ART-mediated recovery from immunosuppression in advanced HIV disease.
Sturm et. al developed a 2 to 4 h antibiotic susceptibility test based on bacterial vibrations. This diagnostic test applies to the most frequently found gram-negative bacteria in bloodstream infections and demonstrates its potential in contributing to faster treatment decisions.
Catheter-associated urinary tract infections can often lead to secondary bloodstream infections, and catheter-induced bladder inflammation. In this work, authors utilise murine models to probe defective fibrinolysis drives extravascular fibrin formation, potentially predisposing hosts to severe CAUTI.
In this work, authors combine computational models with single-cell and population-level data showing the variability in plasmid copy number within bacterial populations leads to phenotypic diversity. They reveal how multicopy plasmids contribute to bacterial transient antibiotic resistance.
Using unique single mosquito data the authors revisit the core quantitative relationships between sequential stages of Plasmodium parasites in their vector host. Their findings demonstrate the importance of mosquito parasite burden in onward transmission success.
Cerebral malaria can lead to fatal brain swelling. Oelschlegel et al. find infected red blood cells and reduced flow in large draining cerebral veins in mouse model of cerebral malaria, suggesting that impaired venous efflux could cause the swelling.
Phage-plasmids are mobile genetic elements that transfer horizontally between bacterial cells as viruses, and vertically within bacterial lineages as plasmids. Here, Pfeifer & Rocha show that phage-plasmids can mediate gene transfer across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.
The second messenger c-di-GMP regulates various processes in bacteria, including biofilm formation and motility. Here, the authors show that iron regulates c-di-GMP levels in Pseudomonas aeruginosa by modulating the interaction between an iron-sensing protein and a diguanylate cyclase.
Bacteria form matrix-encapsulated communities, called biofilms, which protect resident cells from environmental challenges. Here, the authors show that Vibrio cholerae cells detect environmental threats by sensing a cellular component released through kin cell lysis, which induces formation of biofilms by surviving cells.
Here the authors study recovery from mild to moderate Omicron breakthrough infection at six months post infection. Serum proteomics, PBMC single-cell transcriptomics and clinical parameters indicate slow recovery with coagulation abnormalities and an imbalance of the immune response and metabolism remaining.
Here the authors describe a stabilization technology that engineers crosslinks between tyrosine sidechains into a natively folded vaccine immunogen and show that immunogenicity is improved in small animal models by locking the most potently neutralizing epitopes.
SARS-CoV-2 uses the host endolysosomal system for replication and egress. Here the authors show that SARS-CoV-2 virulence factor ORF3a localizes to the late endocytic compartments of the host cell to disrupt Rab7 GTP to GDP cycling and block lysosome function in cargo degradation, while activated Rab7 promotes virus replication.
Bacterial capsules provide protection against the environment, including host immune systems. Authors swap capsule loci in Klebsiella pneumoniae to reveal the role of these sugar coats against plasmid conjugation and phage infection, showing that the serotype is a key player in regulating conjugation rates, and phage susceptibility.
The relative importance of the various mechanisms that can drive microbial speciation is poorly understood. Here, Stanojković et al. explore the diversification of the soil cyanobacterium Microcoleus, showing that this genus represents a global speciation continuum of at least 12 lineages, with lineage divergence driven by selection, geographical distance, and the environment.
Bacteria have evolved various defence mechanisms to protect themselves against viral infection. Here, Patel et al. identify a type of antiviral defence that blocks virion assembly, thus preventing formation of infectious virions and allowing destruction of the infected cell.
Anaerobic methanotrophic (ANME) archaea are uncultivated microbes that oxidize the greenhouse gas methane and engage in extracellular electron transfer with other microbes, metal oxides, and electrodes. Here, Ouboter et al. observe strong methane-dependent current associated with high enrichment of ANME archaea on the anode, and provide insights into the mechanisms underlying extracellular electron transfer.
Transcriptional regulator MtrR inhibits the expression of the multidrug efflux pump operon mtrCDE in Neisseria gonorrhoeae. Here, Hooks et al. show that hormonal steroids bind to MtrR and decrease its affinity for cognate promoters, thus leading to increased mtrCDE expression and enhanced antimicrobial resistance.
SARS-CoV-2 variants with mutations in spike have emerged during the pandemic. Magaret et al. show that in Latin America, efficacy of the Ad26.COV2.S vaccine against moderate to severe–critical COVID-19 varied by sequence features, antibody escape scores, and neutralization impacting features of the SARS-CoV-2 variant.
Glucose metabolism is crucial for cellular energy regulation and affects the immune response. Here the authors show that nutritional supplementation of mannose may be beneficial during virus infections by rewiring glucose metabolic dysregulation and alleviating inflammatory tissue damage.
Here the authors use dual RNA sequencing to characterize host and parasite gene expression from 136 Malian children with symptomatic Plasmodium falciparum infection. They find that parasitemia levels correlate with neutrophil and T cell levels and that the child’s age correlates with innate immune gene expression as well as gametocyte levels.
The authors identified a series of cytoskeletal proteins involved in the discharge of invasion-related organelles in Toxoplasma gondii. They successfully delineated their functions through the utilization of expansion and cryo-electron microscopy.
A comprehensive analysis found no evidence of m6A modifications in the genome of the cytoplasmic RNA viruses CHIKV and DENV, challenging the current notion that m6A modification is a general feature of cytoplasmic RNA viruses.
The authors show pro-inflammatory responses are needed for Marburg virus control in its natural bat reservoir, and that if reduced, humanlike disease and shedding results, suggesting that natural immunomodulatory stressors may increase spillover risk.
In this work, authors utilise a pan-resistant Pseudomonas aeruginosa in vivo infection model to demonstrate antibiotic re-sensitisation with bacteriophage therapy.
Stupar et al. describe a new role for the Mycobacterium tuberculosis two-component system, TcrXY, in the modulation of up to 70 genes, including two effectors, TarA and TarB which mitigate intracellular redox stress.
Authors present a comparative immunological characterisation of Chlamydia vaccine, CTH522/CAF®01, in mice and humans. Findings suggest the mouse to be a good predictor of human immunity to the Chlamydia vaccine CTH522/CAF®01, and long-lasting protection in the mouse further supports the development of this promising vaccine candidate.
Key cellular processes, such as cell-shape determination, are poorly understood in archaea. Here, Schiller et al. study the model archaeon Haloferax volcanii, which forms rods and disks, and identify a diverse set of proteins important for these processes, including a new actin homolog that plays a role in the formation of disk-shaped cells.
The cell-wall peptidoglycan in model bacteria typically includes 4,3- and 3,3-crosslinks, catalysed by DD- and LD-transpeptidases, respectively. Here, the authors identify and characterise the activity and structure of an LD-transpeptidase that generates a new type of crosslink (1,3).
Genomic surveillance of Plasmodium falciparum could improve monitoring of drug resistance, but implementation has been hampered due to the large and complex genome. Here, de Cesare et al. develop a flexible and cost-effective nanopore sequencing approach to detect drug resistance and diagnostic escape for P. falciparum malaria.
Flavivirus infection or vaccination can induce cross-reactive immune responses. Here, the authors show how previous immunization with the tick-borne encephalitis virus vaccine affects the immune response to the yellow fever vaccine, suggesting that the yellow fever vaccine virus conceals epitopes shared with other flaviviruses in flavivirus-naive but not flavivirus-pre-exposed individuals.
The Wolbachia cifA and cifB genes generate cytoplasmic incompatibility (CI) in insect hosts but the role of cifA is still debated. Here, the authors report the transgenic recapitulation of CI in the major arbovirus vector Aedes aegypti and provide evidence for cifA inhibiting cifB toxicity in the male germline.
Here, the authors provide evidence that, unlike other arboviruses, the initial site of orthobunyavirus replication is the panniculus carnosus muscle layer within the skin. However, virus infection does not damage or kill these cells, allowing them to produce virus over a longer period of time.
Bacteria use various defense systems to protect themselves from phage infection, and phages have evolved diverse counter-defense measures to overcome host defenses. Here, the authors use protein structural similarity and gene co-occurrence analyses for identification of new anti-phage and counter-defense systems.
Previous reports of microbial endemism have been restricted to sub-genus level taxa. Here, Power et al. present evidence supporting that a bacterial genus, Venenivibrio, is endemic to Aotearoa-New Zealand.
Treatment with the clinical stage TGF-β inhibitor galunisertib promotes latency reversal of HIV/SIV. Here, using a treatment regimen similar to the one tested in clinical trials, the authors show how galunisertib affects immune cell function, increases SIV reactivation, and reduces the viral reservoir in macaques.
Measles virus infection causes immunosuppression and it’s unclear whether this can be prevented by antivirals. Here, using a canine distemper virus ferret model, the authors show that measles-like immune amnesia and lethal exacerbated respiratory disease after consecutive respiratory virus infections can be mitigated by oral antiviral therapy initiated at the onset of primary clinical signs.
Bacterial viruses (phages) are generally recognised as rapidly evolving biological entities. Here, Rozwalak et al. analyse DNA sequence datasets generated from ancient palaeofaeces and identify 298 phage genomes from the last 5300 years, including a 1300-year-old phage genome nearly identical to a present-day virus that infects human gut bacteria.
In vitro propagation of the pathogenic bacterium Coxiella burnetii, the causative agent of Q fever, leads to attenuated virulence and lipopolysaccharide (LPS) truncation. Here, Long et al. show that a strain considered to be avirulent (NMII) can be recovered from infected animals, and these isolates display increased virulence and an elongated LPS due to reversion of a 3-bp mutation in a gene.
Cheese fermentation and flavour formation are the result of complex biochemical reactions driven by the activity of multiple microorganisms. Here, the authors identify microbial interactions as a mechanism underlying flavour formation in Cheddar cheese.
Authors apply theory and microbial ecology modelling to a wastewater sample, and show that antimicrobial resistance carrying plasmids interact with a higher number and more diverse range of bacteria than plasmids that do not carry resistance genes.
In this work, the authors identified a hypervirulent carbapenem-resistant Escherichia coli ST410 clone which carries a high pathogenicity island and an O-antigen gene cluster. The findings highlight the ongoing evolution of ST410 towards increased resistance and virulence.
Here the authors screen different lipid nanoparticle (LNP) formulations for intramuscular delivery of plasmid DNA and uptake by antigen-presenting cells. The lead LNP exhibits immunogenicity and protection in small animal models that is comparable to approved SARS-CoV-2 mRNA vaccine formulations.
Wang et al. discovered that AP2XI-2 and AP2XII-1 negatively regulate merozoite-primed pre-sexual commitment in Toxoplasma gondii, and parasites depleted of either AP2XI-2 or AP2XII-1 can serve as a valuable in vitro model for studying merogony.
Here, the authors uncover that, among 92 identified host factors associated with SARS-CoV-2 virions, G3BP1 and G3BP2 are present at the assembly site, incorporated within virions, and unexpectedly promote the production of SARS-CoV-2 virions.
The ecology of Ebola virus (EBOV) is still largely unclear. Here, the authors show that Angolan freetailed bats are selectively permissive to EBOV infection, but not to other filoviruses, and demonstrate EBOV placental tissue tropism indicating potential horizontal and vertical transmission between conspecifics.
What a microbial strain is and how many strains make up a natural bacterial population remain elusive concepts. Here, Viver et al. analyse Salinibacter ruber isolates and metagenomes from two solar salterns, revealing gaps within the species sequence space that they use to define and quantify sub-species categories, such as genomovars and strains, that co-exist in a saltern pond.
The type VI secretion system (T6SS) of Gram-negative bacteria is typically anchored to the cell envelope through a membrane complex (MC), but Bacteroidota appear to lack genes encoding canonical MC components. Here, Bongiovanni et al. identify the Bacteroidota MC and study its biogenesis and connections with the conserved T6SS components.
A defining feature of retroviruses compared to other +ssRNA viruses is reverse transcription. Here, Köppke et al. show that retroviruses (e.g. HIV-1) can produce viral proteins even in the absence of reverse transcription.
Cryo-EM structures of the polymerase of Tilapia Lake virus (Amnoonviridae), a fish pathogen, show that it has the same domains and functions similarly to the distantly related influenza virus (Orthomyxoviridae) polymerase, despite being only 60% the size.
The archaeal ancestor of eukaryotes belonged to the phylum Asgardarchaeota, or Asgard archaea. Here, the authors use ancestral sequence reconstruction and experimentally determine the optimal GDP-binding temperature of a translation elongation factor from ancient and extant Asgard archaea, to infer optimal growth temperatures for eukaryotes’ ancestors.
Molecular diagnostics for tuberculosis have focused on predicting drug susceptibilities in a binary manner (i.e., strains are either susceptible or resistant). Here, CRyPTIC Consortium researchers use whole genome sequencing and a quantitative assay to identify associations between genomic mutations and minimum inhibitory concentrations in over 15,000 Mycobacterium tuberculosis clinical isolates.