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Here, the authors show that the skin microbiome of a remote hunter-gatherer Yanomami community harbors environmental microbes that help maintain skin barrier integrity and combat oxidative stress—functions that are reduced by industrial lifestyles.

Mesocosm experiments revealed that both phytoplankton community composition and cellular acclimation influence marine particulate C:N:P ratios, with community shifts more sensitive to nitrogen supply and acclimation to the nutrient N:P supply ratio

Wildfires have caused widespread and increasingly severe losses within timber-producing forests in recent decades, according to maps of logging activity and wildfires.

Whether multimorbidity accelerates brain Aβ deposition in humans remains largely unknown. Here, the authors demonstrate that higher self-reported multimorbidity burden predicts increased brain Aβ accumulation rates in the ADNI cohort.

The microstructure of natural materials such as bone and wood makes them strong and tough. Chemists are also good at crystallizing fine particles, but a flexible adhesive is needed to bind them together. Daedalus thinks he has the answer.

In this study, the authors analyse 2,409 nasopharyngeal swabs from 300 infants in Botswana to investigate the impacts of respiratory virus infection on the colonisation dynamics of bacterial respiratory pathobionts.

Wastewater treatment plants are important reservoirs of antibiotic resistance genes (ARGs). Here, the authors analyze ARGs in a global collection of samples from wastewater treatment plants across six continents, providing insights into biotic and abiotic mechanisms that appear to control ARG diversity and distribution.

Taxonomic compositions in bathtub faucet water microbiomes showed household individuality, with differences in the prevalences of non-tuberculous mycobacterial species. A similar antimicrobial resistome was detected.

Here, using metagenomic profiling in 180 individuals from the Democratic Republic of the Congo, the authors find associations between the gut microbiome and konzo, a neurodegenerative disease that mostly affects children and is caused by the consumption improperly processed cassava.

Multiple computational approaches have been developed for the deconvolution of cells in the tumour microenvironment (TME) using bulk RNA-seq data. Here, the authors use breast cancer single-cell RNA-seq data to produce simulated bulk data, with which they compare the performance of nine TME deconvolution methods.

Timber plantations in temperate countries are twice as likely to be destroyed by wildfires compared to natural wood-producing forests under similar conditions. The increasing threat of wildfires in the future will threaten global wood security.

Exploring pollen records from 13 South Pacific islands, the authors find that floristic homogenization commenced following human arrival beginning around 3,000 years ago.

Global sampling of microbial communities associated with wastewater treatment plants and application of ecological theory revealed a small, core bacterial community associated with performance and provides insights into the community dynamics in this environment.

Statistical analyses of a metagenomics-sequenced human cohort identify a relatively minor role for genetics in determining microbiome composition and show that several human phenotypes are as strongly associated with the gut microbiome as with host genetics.

Using a cohort of nearly 1,000 genetically diverse mice undergoing dietary restriction over the lifespan, the authors reveal numerous insights into the interactions between the gut microbiome, host genome, diet, health and longevity.

Sedimentary DNA can be used to infer how organisms responded to changing environmental conditions over millennia. Here, the authors use sedimentary DNA of micro-eukaryotes in low-elevation (human-impacted) and high-elevation (more pristine) lakes to show how human influences have altered lake community composition in the Anthropocene.

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.

The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.

Using ethnically and geographically diverse metagenomic data, the authors identify microbiota alterations associated with inflammatory bowel disease (IBD). They discover universal IBD-associated bacteria, which serve as the basis for a multibacteria biomarker panel that could support a noninvasive tool for IBD diagnosis.

Large-scale network analysis of invertebrate communities across >500 arable farms in the United Kingdom reveals that genetic modification for herbicide tolerance has little influence on overall network structure, which is largely shaped by crop type.

A genomic study of 125 individuals from the Carpathian Basin (4800–3900 BCE) reveals different kinship systems in nearby Copper Age communities, and highlights both genetic continuity and contrasting patterns of social organization.

Little is known about the microbiota of marine mammals, despite the crucial ecological roles played by these animals. Here, Bik et al. describe the bacterial communities associated with various body sites in dolphins and sea lions, as well as the microbiota of their dietary fish and adjacent seawater.

In a double-blind, randomized, placebo-controlled trial, dapagliflozin, as an adjunct to insulin, resulted in significant reductions in glomerular filtration rate and measures of glycemia when compared to placebo in youth with type 1 diabetes.

In this work, authors assess airway microbiome dynamics to show bacterial pneumonia in critically ill COVID-19 patients is significantly associated with death, corticosteroid treatment, disruption of the lung microbiome and a distinct pulmonary host response.

Invertebrate and microbe communities support reef ecosystems and coral health. Here, the authors characterize these communities from degraded and healthy reefs, showing that transplanting these healthy communities improved coral health at degraded reefs.

Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

Autism spectrum disorder (ASD) is characterized by heterogeneous phenotypes. Disruption of the gut–brain axis (GBA) has been implicated in ASD although with limited reproducibility across studies. In this study, the authors propose a framework to leverage multi-omic datasets and investigate how the GBA influences ASD.

Reduced dietary fibre together with mutations in the host mismatch repair machinery promote colon carcinogenesis by increasing inflammation, nitrate-fuelled growth of colibactin-producing Escherichia coli and colibactin-dependent genotoxic tissue damage.

Picks include a rogue gene-editor, a wunderkind physicist and a DNA detective who helped catch a serial killer.

Metagenomic analyses of European pig and poultry farms show differing resistome profiles and an association with country-level antibiotic use.

Tumour samples are heterogeneous and are comprised of multiple cell types in addition to cancer cells. Here, the authors devised a method to estimate the relative levels of haematopoietic cells in breast cancer samples and demonstrate that this correlates with prognosis.

Here, using murine models of prostate cancer, the authors show that reduced fecal microbiota alpha-diversity correlates with increased prostate tumor burden, and that Omega-3 prebiotic supplementation reduces prostate cancer up-grading associated with a reduction of gut Ruminococcaceae and fecal butyrate levels.

Time-resolved drone imaging of potato crop development and seed tuber microbiome data can be used to predict potato vigour, or growth potential, in next-season crops in trial fields.

Levantine Phoenicians made little genetic contribution to Punic settlements in the central and western Mediterranean between the sixth and second centuries bce; instead, the Punic people derived most of their ancestry from a genetic profile similar to that of Sicily and the Aegean, with notable contributions from North Africa as well.

The biogeography of viral communities in extreme environments remains understudied. Here, the authors use metagenomic sequencing on 90 acid mine drainage sediments sampled across Southern China, showing the predominant effects of prokaryotic communities and the influence of environmental variables on viral taxonomy and function.

Gao and colleagues explore soluble biomarkers, immune cell subsets, viral antibody responses and plasma proteomics to better define and understand long COVID in two independent cohorts.

By analysing plant and nematode DNA from sites all around the Arctic, it is shown that vegetation before about 10,000 years ago contained more forbs (non-graminoid herbaceous vascular plants) than previously believed, which changes our understanding about the functioning of the diverse northern ecosystem that existed at this time.

Analyses of genome and exome sequencing data identify rare coding and structural variants associated with atrial fibrillation and highlight genetic links between atrial fibrillation and cardiomyopathies.

How maternal factors influence a newborn’s microbiota remains unclear. Here, the authors examined the buccal, rectal, and stool microbiotas of newborns within three days of birth and explore the impact of over 200 maternal factors on the newborns’ microbiotas.

Livestock play a role in maintaining antibiotic resistance reservoirs. Here, Liu et al. use metagenomics to study the dynamics of antibiotic resistance genes (ARGs) in the gut of dairy cattle during early life, showing that colostrum is a potential source of ARGs and ARG abundance declines during nursing covarying with dietary transition.

De novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution reveal considerable diversity in the size and structure of the human Y chromosome.

Tisza et al. carry out a sequencing-based analysis of wastewater samples from major cities, to detect and quantify hundreds of distinct pathogenic viruses, finding striking correlations between virus abundance and local clinical cases.

Micronutrient supplements are key to global efforts to address child malnutrition. Here, in a cohort of children, previously enrolled into a large cluster randomized controlled trial of micronutrient supplementation in Pakistan, Popovic et al. find that vitamins and iron increase carriage of protozoa and fungi in the gut, potentially disrupting the bacterial microbiome.