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Warming temperatures and interactions between plants are the main drivers of changes in Arctic plant communities in response to climate change, and there is no evidence of overall biotic homogenization.

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.

Florfenicol treatment substantially increased the abundance and mobility of antibiotic resistance genes (ARGs) in the common carp gut microbiome. The resistome and mobilome profiles failed to return to baseline after the mandated withdrawal time, indicating that this period is insufficient to mitigate the risk of ARG transmission to consumers.

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.

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.

Leveraging metabarcoding and metagenomics, a survey of bacteria in the benthic microbiome across 152 glacier-fed streams (GFSs) provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem.

The gut microbiome has been associated with pancreatic cancer. This Review summarizes the latest findings of microbiota association studies of tumours of the pancreas and outlines the mechanisms as to how the microbiome influences pancreatic cancer and the clinical potential of harnessing the microbiome in pancreatic cancer.

Antimicrobial resistance has evolved over decades due to widespread antimicrobial use, with resistance genes now circulating across humans, animals and the environment, creating complex cross-sector connectivity challenges. This Perspective advocates for genomics-based studies of AMR connectivity to enable coordinated global action and investment under the One Health framework.

The oral antibiotic adsorbent DAV132 can reduce fecal concentrations of antibiotics while preserving their pharmacokinetic properties. Here, in a randomized trial in healthy volunteers treated with antibiotics, the authors show that DAV132 does not affect plasma concentrations of the antibiotics but preserves microbiome diversity and composition, with implications for cancer immunotherapy.

Analysing data from 64,305 Holocene pollen samples worldwide, the authors reveal regionally variable long-term diversity trends associated with human impact over the last 8,000 years.

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.

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.

Across large spatial scales, climate is more important than soil conditions for plant adaptation and variation in root-associated filamentous eukaryotic communities.

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.

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

Sponges are early-diverging marine organisms that establish complex symbioses with microorganisms. Here, Thomas et al.analyse the microbial communities associated with 81 species of sponges from around the world, shedding light on the ecological and evolutionary drivers of these host-microbe associations.

Here, Manghi et al. identify potential salivary microbial biomarkers for autism through a large-scale metagenomic analysis of 2,000 families, revealing shifts in neurotransmitter-related pathways

Kidney shortages limit treatment options for patients with end-stage kidney disease, prompting exploration of xenotransplantation. Here, the authors show that a genetically modified pig kidney sustained essential functions in a living human for 51 days, informing future clinical strategies.

Here, the authors show that elevating fiber intake in humans alters their gut microbiota, which, upon transplantation into mice, enhances intestinal mucus function, and identify a crucial role played by the commensal bacterium Blautia and its fermentation products.

Here, the authors profile the gut phageome of individuals recruited into two double-blind randomized trials of Fecal Microbial Transplantation for ulcerative colitis, showing that phage communities are stable in health, dysbiotic in ulcerative colitis, modulated by antibiotics and by fecal transplants, with one Oscillospiraceae phage being associated with disease remission.

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.

Fetal meconium does not have a detectable microbiota, as shown using 16S rRNA sequencing and culture of rectal swabs collected during elective breech caesarean sections without labour and before antibiotics, indicating that colonization occurs during and after birth.

The taxonomic and functional diversity of marine microbial communities are shaped by both environmental and biotic factors. Here, the authors investigate the functional biogeography of epipelagic prokaryotic communities along a 13,000-km transect in the Southern and Atlantic Oceans, showing finely tuned genetic adaptations to regional conditions.

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.

Microbes inhabit built environments and could contribute to degradation of surfaces especially in damp conditions. Here the authors explore how communities of microbes and their metabolites affect four types of built surfaces under varying environmental conditions.

Circulating microbiome has been very little studied for blood malignancies. Here, the authors show specific microbiome signatures in the blood are associated with different types of myeloid malignancies and specific genetic mutations.

In a randomized phase 1 trial, the addition of a live Clostridium species-containing product to a tyrosine kinase inhibitor and anti-programmed cell death protein 1 treatment combination did not increase bacterial abundance of Bifidobacterium spp. but enhanced clinical responses in participants with metastatic renal cell carcinoma.

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.

There are stable relationships between diet and microbiome in humans and lab animals. A study on African buffalo finds that diet influences microbiome variation and enterotype formation. Three pathogens may associate with microbiome depending on host diet, suggesting nutrition impacts relationships between gut microbiome and host health.

Faecal microbiota transplantation (FMT) can be used to treat established colitis. Here the authors profile transcriptional changes in humans after FMT and how this relates to colitis remission identifying a role for GBP5, and this protein is validated in a loss-of-function mouse model.

The major nutrients nitrate and phosphate have one of the strongest correlations in the sea, with a slope similar to the average nitrogen to phosphorus content of plankton biomass (16:1). Why this global relationship exists, despite the wide range of nitrogen to phosphorus ratios at the organism level, is unknown. Here, an ocean circulation model and observed nutrient distributions have been used to show that the covariation of dissolved nitrate and phosphate is maintained by ocean circulation.

A benchtop fusion reactor, called the Thunderbird Reactor, is described, showing that electrochemically loading a metal lattice with deuterium could enhance nuclear fusion rates when that metal is also bombarded by deuterium ions.

The combination of chemotherapy and broad-spectrum antibiotics induces gut microbiota (GM) dysbiosis in acute myeloid leukaemia (AML) leading to additional complications. Here, the authors report the efficacy in GM restoration and safety of autologous faecal microbiota transfer in treated AML patients in a phase II clinical trial.

Phage immunoprecipitation sequencing illustrates the wide breadth of systemic microbiota-specific antibody responses, which are more longitudinally stable than gut microbiome species abundances in a cohort of healthy individuals.

A disturbed microbial network characterizes relapsing refractory Crohn’s disease and antedates disease recurrence after surgical removal of the active disease segment.

Sponges live in symbiosis with diverse microorganisms. This study uses metabolic modelling to show that the microbial symbionts rely on sponge-derived metabolites to maintain community stability and facilitate elemental cycling, and identifies a key microbial clade that drives cross-feeding processes.

Plant-beneficial bacteria provide multiple benefits to plants. This study constructs a database to couple microbial taxonomy with their plant-beneficial traits, and predicts that fossil-fuel-dependent scenarios could potentially lead to a marked decline of plant-beneficial bacteria abundance in global soils.

Of 248 marine heatwaves between 1993 and 2019 in North American and European seas, the effects on fish biomass were often minimal, and the heatwaves were not consistently associated with tropicalization or deborealization.

Tracking the behaviour of normal versus microbiome-free honeybees in experimental colonies, the authors show that gut microbiota colonization was associated with an increase in the rate and specificity of social interactions among bees and higher abundances of brain metabolites linked to these interactions.

Marine host-associated microbiomes retain a tremendous pool of genetic diversity, which is key to the health of marine ecosystems. This study on reef sponges shows that genomic diversification of individual microbiomes follows different rules at strain- and intrastrain-levels.

Phytopathogenic fungi threaten global food security but their global diversity and biogeography are underexplored. Using more than 20,000 globally distributed samples, this study builds a global atlas of phytopathogenic fungi, and predicts that that their diversity and invasion potential will increase globally by the end of this century, especially in forest and cropland ecosystems.

Here, via metagenomics and ITS2 sequencing analysis of children's stool samples from three months to four years, the authors show that the fungal composition changes and relative abundance increases at weaning, but unlike bacteria, the overall levels of fungal diversity do not change substantially over time.

The environmental microbiota can have important implications for our well-being. Here, the authors describe the composition of microbiomes from diverse buildings, including samples from clinical environments, and show that cleaner environments are associated with a loss of microbial diversity and an increase in genes associated with antibiotic resistance.

In a large multicentric study of patients with advanced NSCLC undergoing anti-PD-1 therapy, the relative abundance of intestinal Akkermansia spp. was shown to associate with changes in the gut microbiome ecosystem and clinical outcomes.