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Pneumococci can cause a variety of bacterial infections including conjunctivitis. Here, Valentino et al.show that most conjunctivitis-causing pneumococci belong to a closely related group of strains that possess a unique set of putative virulence factors.

Using a globally distributed standardized aerial sampling of fungal spores, we show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude.

The bacterium Helicobacter pylori, often found in the human stomach, can be classified into distinct subpopulations associated with the geographic origin of the host. Here, the authors provide insights into H. pylori population structure by collecting over 1,000 clinical strains from 50 countries and generating and analyzing high-quality bacterial genome sequences.

Jingyu Dai et al. study the role of tree allometry in maintaining a high carbon sequestration. They measure allometry in semi-arid forests using terrestrial laser scanning. They report that tree height as well as canopy area decline to varying degrees among individuals. They provide insights on how trees balance water consumption and carbon assimilation which enhances the survival rate of the forest trees.

Subfunctionalization allows gene paralogues to perform distinct ancestral functions. Now, Glover et al. report the functional divergence of proteins of the TRANSPARENT TESTA GLABRA 1 (TTG1) WD40-repeat family in Arabidopsis, showing that small changes in highly conserved proteins can result in major changes to their functions.

Evaluation of the efficiency of land-use changes and their effect on global carbon storage shows that several land-use and consumption choices relevant to climate policy have greater implications than previously thought.

Although the number of participants is important for phenotypic prediction accuracy in brain-wide association studies using functional MRI, scanning for at least 30 min offers the greatest cost effectiveness.

Wildfires have unknown impacts on soil microbes and biogeochemistry. Using metagenomics across forest burn gradients, here the authors show severity-dependent losses in microbiome diversity and functional shifts that underpin post-fire survival.

To avoid self-fertilization, members of the Solanaceae family, such as Petunia, use a system in which components of S-ribonucleases in pistils are detoxified by a collection of 16–20 different S-locus F-box proteins expressed in non-self pollen.

G-protein-coupled receptors are a large and diverse group of eukaryotic membrane receptors. Here the authors couple GPCRs to dCas9 to link extracellular sensing to genome regulation.

Batrachochytrium dendrobatidis and B. salamandrivoransare both important pathogens of amphibians, but they differ in their host ranges, infection strategies, and host immune responses. Here, Farrer and colleagues compare their genomes and transcriptomes to identify the genetic basis of these differences.

Analysis of more than 1,500 microbial genomes sheds light on the processing of carbon released as permafrost thaws.

Taurine and indicine cattle have different desirable traits making them better adapted to different climates across the world. Here, Low et al. describe a pipeline to produce haplotype-resolved, chromosome-level genomes of Angus and Brahman cattle breeds from a crossbred individual and report on comparisons of the two genomes.

Between 18,475 and 17,350 years ago, the amplitude of variations in atmospheric radiocarbon levels was large, probably in response to solar variability and low atmospheric carbon dioxide concentrations, according to millennial tree-ring chronologies of subfossil larch trees from northeastern Italy.

The prognostic and diagnostic roles of DNA methylation in acute myeloid leukemia remains to be explored. Here, the authors develop DNA methylation-based models for the prediction of five-year survival and clinical molecular subtypes in both pediatric and adult test cohorts.

This study reveals how the pathogen Staphylococcus aureus adapts to the lung microenvironment, rich in host metabolites fumarate and itaconate, by using a key enzyme, FumC, to support its metabolic fitness, survival, and persistence.

Severe sepsis has a high mortality rate. Here, the authors provide genomic, transcriptomic, proteomic and metabolomic data across four sepsis-causing pathogens and identify a signature of global increase in fatty acid and lipid biosynthesis as well as cholesterol acquisition.

Patient-derived xenograft models (PDX) have been extensively used to study the molecular and clinical features of cancers. Here the authors present a cohort of 536 PDX models from 25 cancers, as well as their genomic and evolutionary profiles and their suitability for clinical trials.

A comparison of the evolutionary history and geographical spread of the antimicrobial-resistant pathogen Staphylococcus capitis in neonatal intensive care units indicates that acquisition of antibiotic resistance and increased competitiveness have led to the success of the NRCS-A S. capitis clone.

The neuraminidase-targeting monoclonal antibody FNI9 potently inhibits the enzymatic activity of influenza A and B viruses via receptor mimicry.

Microbes in the cow rumen are crucial for the breakdown of plant material. Here, Stewart et al. assemble over 900 bacterial and archaeal genomes from the cow rumen microbiome, revealing new species and genes encoding enzymes with potential roles in carbohydrate metabolism.

TMAO is known to be atherothrombotic. Here the authors show that i) kidney function is the main determinant of serum TMAO, ii) TMAO increases kidney scarring with TGF-β1 signalling and iii) anti-diabetic drugs with reno-protective properties such as GLP1R agonists reduce plasma TMAO.

Ticks transmit a large number of pathogens that cause human diseases. Here, the authors sequence the genome of the tick Ixodes scapularisand uncover expansion of genes associated with parasitic processes unique to ticks and tick-host interactions.

MCR-1-positive Escherichia coli carriage in humans across China is associated with anthropogenic factors, including meat consumption and aquatic food production.

The Microarray Quality Control consortium pitted 36 teams against each other to evaluate methods for creating genomic classifiers, computational tools for interpreting gene expression profiles. The performance of the classifiers on blinded validation data—and metadata on the analytic methods—reveal the challenges facing the field.

In a combined analysis of two large patient cohorts, three peripheral consensus transcriptomic subtypes of sepsis are identified, which can be linked to an 18-gene classifier associated with different odds of mortality and may offer a way to tailor care for patients with sepsis.

Genome sequencing can be used to infer pathogen transmission dynamics and inform public health responses. Here, the authors sequence >1,200 SARS-CoV-2 samples from Victoria, Australia and find genomic support for the effectiveness of social restrictions in reducing transmission.

Paul Boutros, Robert Bristow and colleagues report a molecular analysis of the spatial heterogeneity of clinically localized, multifocal prostate cancer. They find that multifocal tumors are highly heterogeneous, and they identify a novel recurrent amplification of MYCL1.

Fernando Pardo-Manuel de Villena, Gary Churchill and colleagues provide a high-resolution phylogenetic map of mouse inbred strains based on comparisons to wild-caught mice. They show that the genomes of classical strains are overwhelmingly derived from Mus musculus domesticus whereas wild-derived laboratory strains include a broad sampling of diversity from multiple subspecies with pervasive introgression. The subspecific origin, haplotype diversity and identity-by-descent map of laboratory strains can be visualized at http://msub.csbio.unc.edu/PhylogenyTool.html.

CCR5 is a co-receptor for many transmitted HIV strains. Here, the authors show that biweekly injection of the CCR5-specific antibody Leronlimab protects rhesus macaques against infection following repeated intrarectal challenges of a CCR5-tropic SHIV.

An integrated analysis of de novo and inherited coding variants in 42,607 individuals with autism spectrum disorder identifies 60 risk genes of which five have not previously been associated with neurodevelopmental disorders.

Available wheat genomes are annotated by projecting Chinese Spring gene models across the new assemblies. Here, the authors generate de novo gene annotations for the 9 wheat genomes, identify core and dispensable transcriptome, and reveal conservation and divergence of gene expression balance across homoeologous subgenomes.

Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Here, authors show that pluripotency and self-renewal processes have a high level of regulatory complexity and suggest that genetic factors contribute to cell state transitions in human iPSC lines.

Using different high-resolution satellite datasets, this study analyses gross forest carbon loss associated with forest removal over the tropics during the twenty-first century focusing on regional fluxes and trends, as well as drivers of loss, both aspects rarely studied in previous work.

The Eucalyptus grandis genome has been sequenced, revealing the greatest number of tandem duplications of any plant genome sequenced so far, and the highest diversity of genes for specialized metabolites that act as chemical defence and provide unique pharmaceutical oils; genome sequencing of the sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression.

InstaNovo, a transformer-based model, and InstaNovo+, a multinomial diffusion model, enhance de novo peptide sequencing, enabling discovery of novel peptides, improved therapeutics sequencing coverage and detection of unreported organisms in proteomics studies

Crassulacean acid metabolism (CAM) is a metabolic adaptation of photosynthesis that enhances water use efficiency. Here, via genomic analysis of Kalanchoë, the authors provide evidence for convergent evolution of protein sequence and temporal gene expression underpinning the multiple independent emergences of CAM.

Phage engineered with tail fibers and CRISPR–Cas reduce Escherichia coli load in animals.

The tumour microenvironment is low in glucose and high in the alternative metabolite lactate, which regulatory T cells are shown here to use, maintaining their ability to suppress effector immune cells.

Francis Drobniewski and colleagues report the whole-genome sequencing of 1,000 Mycobacterium tuberculosis strains obtained prospectively from patients over a 2-year period in Samara, Russia, a region with a high incidence of multidrug-resistant (MDR) tuberculosis. They compare these strains to a diverse panel of strains isolated from across the UK and characterize the patterns of the emergence and evolution of drug resistance.

This study reports on excavations of hearths and stone artefacts from 20,000-year-old deposits at Dargan Shelter, which at an elevation of 1,073 m is believed to be the oldest occupied high-altitude site in Australia.

Malaria parasites are protected from febrile temperatures in humans by a heat-shock response that is coordinated by the transcriptional activator PfAP2-HS.

The Omicron variant evades vaccine-induced neutralization but also fails to form syncytia, shows reduced replication in human lung cells and preferentially uses a TMPRSS2-independent cell entry pathway, which may contribute to enhanced replication in cells of the upper airway. Altered fusion and cell entry characteristics are linked to distinct regions of the Omicron spike protein.

In a serological analysis, Bore et al. utilise serum samples, collected from a cohort of individuals associated with bushmeat hunting and butchering, in the forested region of Guinea, a region close to the epicentre of the 2013–2016 West Africa Ebola virus disease epidemic.