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Multiomics reveals that almost half of gut microbiome diversity in humans can be explained by 40 blood metabolites.

Here, the authors use detailed temporal nutrition intake data captured through real-time food logging via a smartphone app and gut microbiota profiles from ~1,000 participants of a digital cohort on personalized nutrition to associate dietary regularity and quality with gut microbiome diversity.

Here, the authors show that pre-infection gastrointestinal microbial composition predicts parasite levels in rhesus macaques infected with P. fragile and humans infected with P. falciparum in a controlled human malaria infection (CHMI) study.

Fine-scale field analysis and modelling of the spatial dynamics of infection of Darwin’s frogs with Batrachochytrium dendrobatidis fungus identifies highly localized transmission dynamics that generate clustered epidemics and can drive collapse of local subpopulations.

AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect prediction and enables comprehensive genomic analysis.

Here, the authors analyze longitudinal stool microbiome and illness data from Gambian children enroled in a randomised, double-blind iron supplementation trial, showing that those who remained infection-free exhibit higher abundance of Prevotella stercorea, while Escherichia coli and other opportunistic pathogens are enriched in those who developed infection.

Andrew Feinberg, John Goutsias and colleagues derive potential energy landscapes from bisulfite sequencing data and quantify DNA methylation stochasticity genome-wide using Shannon's entropy, identifying an association between entropy and chromatin structure. Their analysis highlights the information-theoretic nature of the epigenome and provides a methodology for studying its role in disease and aging.

Here, the authors present an update to a widely used curatedMetagenomicData (cMD) database and use it to create a catalog of microbiome-phenotype associations (age, sex, body mass index), and develop an oral enrichment score in the gut microbiome independently of age.

McGrail and colleagues report that high intratumoral bacteria abundance is associated with an immunosuppressive microenvironment and resistance to immune checkpoint blockade in head and neck squamous cell carcinoma.

cfDNA fragmentomics is a potential clinically applicable method for identifying cancer. Here, the authors assess fragmentomics analysis methods and their application to commercial targeted sequencing panels.

Humanity’s Last Exam, a multi-modal benchmark at the frontier of human knowledge, is designed to be an expert-level closed-ended academic benchmark with broad subject coverage.

Five-year survival data and biomarker analysis of the PRADO extension cohort of the phase 2 OpACIN-neo trial, in which patients with high-risk stage III melanoma received neoadjuvant ipilimumab and nivolumab and underwent pathologic response-directed surgery and adjuvant therapy, show 71% event-free survival and 88% overall survival, with tumor mutational burden, IFNγ signature and PD-L1 expression associated with favorable outcomes.

Using multiple visualization and profiling methods, Gigi et al. characterize the microbiome diversity of 322 brain tumors including brain metastases and glioblastomas.

Cities are engines of innovation and economic growth, but they also struggle with segregation, which works against both. This study finds rings of isolation around US cities and pockets of segregation within them, a pattern persistent over time and intensified since the pandemic.

Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.

A survey of T cell repertoire evolution in the tumors, healthy tissue and blood of patients with early-stage untreated lung cancer offers an opportunity to monitor and identify neoantigen-specific T cells for personalized immunotherapy.

Sears and colleagues found that ongoing replication stress pathways and T cell clonal responses differentiate liver and lung recurrence and are associated with different clinical outcomes in the context of pancreatic ductal adenocarcinoma.

Immune lymphocyte estimation from nucleotide sequencing (ImmuneLENS) infers B cell and T cell fractions from whole-genome sequencing data. Applied to the 100,000 Genomes Project datasets, circulating T cell fraction provides sex-dependent and prognostic insights in patients.

Variation in the gut microbiome can reflect host lifestyle, behaviour, and influence blood-based biomarkers. Here the authors examine associations between the microbiota and 150 host phenotypic features in a large cohort of >3,000 individuals.

This network meta-analysis of 183 trials of well-being interventions from across disciplines found that yoga, mindfulness, compassion, exercise and positive psychology improved adult well-being, with combined exercise and psychological approaches showing the largest effects.

Resistance to therapy can be driven by intratumoral heterogeneity. Here, the authors show that drug tolerant persistent cell populations emerge during treatment, and these emergent populations arise through epigenetically mediated cell state transitions rather than sub population selection.

Colorectal cancer is often diagnosed at later stages, leading to poor prognosis. Here, the authors utilise analysis of rectal mucus specimens using host and microbial analysis to detect cancer lesions.

Ke et al. investigated the association between trauma exposure and post-traumatic stress disorder symptoms and the gut microbiome and dietary pattern of a cohort of women enrolled in a longitudinal study in the United States.

cellSTAAR advances noncoding rare variant association analysis by integrating single-cell genomics data.

Aligning foundation models with human judgments enables them to more accurately approximate human behaviour and uncertainty across various levels of visual abstraction, while additionally improving their generalization performance.

A common but untested expectation is that nutrient enrichment causes biotic homogenization. However, a globally standardized nutrient addition experiment in grasslands shows proportionally similar species loss across scales and no biotic homogenization after up to 14 years of treatment.

Coastal upwelling sustains some of the most productive ocean regions. Here, the authors find that spatial patterns and temporal changes in nutrient supply explain marine microbial community structure and diversity in the Southern California Current region.

Increasing compositional uniqueness of the gut microbiome, and corresponding changes in microbial metabolites in the blood, are identified as a signature of healthy ageing in humans.

The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitating the discovery of potential effects of genetic variants, including variants associated with disease, on genome structure and function.

An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the identification of new species associated with the development of cancer.

Analysis of Triton, a high-resolution dataset documenting the macroperforate planktonic foraminifera fossil record, reveals a global climate-linked equatorward shift of ecological and morphological community equitability over the past 8 million years.

Malignant cells with mesenchymal features display increased chromatin accessibility, particularly in the pericentromeric and centromeric regions, in turn resulting in delayed mitosis and catastrophic cell division.

Antimicrobial resistance genes that have been mobilized between bacterial species represent a subset of the naturally occurring resistome. Here, the authors compare the abundance, diversity and geographical patterns of acquired resistance genes with latent resistance genes in global sewage metagenomes.

As phase 1 of the Earth Microbiome Project, analysis of 16S ribosomal RNA sequences from more than 27,000 environmental samples delivers a global picture of the basic structure and drivers of microbial distribution.

Solid organ transplant recipients are at increased risk of infectious disease and have unique molecular pathophysiology. Here the authors use host-microbe profiling to assess SARS-CoV-2 infection and immunity in solid organ transplant recipients, showing enhanced viral abundance, impaired clearance, and increased expression of innate immunity genes.

Measures of biodiversity and ecosystem functioning show variable responses to perturbations, complicating the prediction of responses to global change. This study shows that the variability of community-level responses itself is predictable and can be used to study species’ responses to perturbations and contributions to functions.

Through metagenomics, Bray et al. identified Klebsiella pneumoniae interacting microbiota partners in the gut, and a transposon mutagenesis screen revealed a role for its T6SS in gut colonization, with t6ss transcription only occurring in vitro under GI-mimetic conditions.

Population genomic analyses identify multiple effect loci in the common bean genome that influence seed components and metabolites that consequently affect the human gut microbiome.

RNA sequencing data and tumour pathology observations of non-small-cell lung cancers indicate that the immune cell microenvironment exerts strong evolutionary selection pressures that shape the immune-evasion capacity of tumours.

Brain-machine interfaces are hindered by neuroinflammation. Here, the authors found that bacterial sequences invade the brain post-microelectrode implantation. Antibiotic-treated mice showed reduced bacterial presence and altered neuroinflammatory profile, temporarily improving recording performance.

Transmission of influenza A viruses (IAV) between hosts and replication within host impose genetic bottlenecks, constraining viral diversity and adaptation. Here, Amato et al. perform site-specific inoculation of barcoded IAV of ferrets and track viral diversity as infection spreads to the lower respiratory tract and conclude that narrow population bottlenecks are an important feature of the within-host infection dynamics.

Little is known about how climate change impacts glacier-fed streams (GFSs) microbiomes. Here, using a modelling framework based on global GFS metagenomic, climatic and environmental data the authors predict future increases in GFS bacterial biomass and diversity, but potential loss of clades adapted to extreme conditions.

Using metagenomics, culture and machine learning approaches, the authors characterized the resistome of preterm infants that received antibiotics and found that they have an enriched gut antibiotic resistome with distinct assembly patterns and prolonged carriage of multidrug-resistant bacteria, compared with healthy infants that did not receive antibiotics.

Imaging mass cytometry profiling of 693 breast tumors identified 10 recurrent tumor microenvironment spatial structures. These structures were enriched in different molecular subtypes and can be associated with genomic profiles and outcomes.

Latitudinal ecosystem boundaries in the global upper ocean may be driven by many factors. Here the authors investigate pole-to-pole eukaryotic phytoplankton metatranscriptomes, gene co-expression networks, and beta diversity, finding that geographic patterns are best explained by temperature gradients.