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In a phase 2 trial evaluating healthy donor fecal microbial transplantation plus either anti-PD-1 in patients with non-small cell lung cancer or anti-PD-1 and anti-CTLA-4 in patients with melanoma, encouraging efficacy was seen in both cohorts, with responses linked to significantly greater loss of baseline bacterial species.

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

Here, using samples from ~1,100 individuals, the authors define the nasal microbiome linked to Staphylococcus aureus colonization, identifying seven communities- either S. aureus-dominated or dominated by other bacteria.

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.

Metagenomes from prairie soils in Kansas, USA, show how historical exposure to water stress impacts soil microorganisms and subsequently drought responses in plants.

Therapeutic options for patients with renal medullary carcinoma (RMC) are limited. Here the authors report the results of a phase II clinical trial of anti-PD1 nivolumab plus anti-CTLA4 ipilimumab in RMC, associating the activation of a myeloid mimicry program in tumor cells to the rapid disease progression and hyper-progression observed in treated patients.

Soil microbial populations bloom and then die-off in ecosystems with seasonal snowpack. This study showed that distinct taxa utilize different N sources for growth or energy during the microbial bloom and alter the fate of N after snowmelt.

Schisantherin A (Sin A), a bioactive lignan from Schisandra chinensis, alleviates obesity and liver fat accumulation in mice, but the mechanisms are incompletely understood. Here the authors show that Sin A mitigates obesity and related metabolic disorders by elevating circulating conjugated bile acids, which in turn modulate adipose tissue thermogenesis in mice.

Here, by integrating faecal metabolomics, metagenomics, and habitual dietary data of two large human cohorts, the authors show that faecal metabolites reflect diet and gut microbiome interactions, predict dietary patterns, and indicate cardiovascular risk, offering insights for diet-based health interventions.

The potential roles of viruses in microbial-induced permafrost thaw, which is accelerated by climate change, are unclear. Here, Trubl et al. sample a permafrost thaw gradient and identify thousands of new viruses carrying genes with metabolic-related functions, which might influence the fate of stored carbon.

An exploratory analysis of the phase 3 ECOSPOR III trial shows that a higher dosage of the oral microbiome therapeutic VOWST led to enhanced pharmacokinetics, increased species engraftment and altered microbiome and metabolite profiles, providing mechanistic insights into how it may prevent Clostridioides difficile infection recurrence.

The microbiomes associated with reef corals are complex and diverse. Here, the authors investigate fire coral clones naturally occurring in distinct habitats as a model system to disentangle the contribution of host genotype and environment on their microbiome, and predict genomic functions based on taxonomic profiles.

A metric to measure coral thermal tolerance to cold stress was developed alongside heat tolerance, revealing species-specific thermal limits and microbial patterns that improve assessment of coral resilience under climate change.

The microbiota may mediate the differential responses to oral cholera vaccine (OCV). Here, the authors reveal that the presence of sphingolipid-producing bacteria is associated with the development of protective immune responses after OCV.

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.

Colorectal cancer has high recurrence and metastasis rates making treatment difficult. Here, the authors report on peptide modified cell membrane coated cobalt based metal-organic frameworks which degrades and forms, in situ, photothermal materials with H₂S, allowing for immune-photothermal therapy.

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.

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.

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.

Metagenomic analysis of the gut microbiome of people with human immunodeficiency virus (HIV), from three distinct cohorts, revealed infection- and antiretroviral drug-linked alterations, which may contribute to HIV-associated non-infectious comorbidities.

Current first-line treatments of pediatric UC maintain a 6-month remission in only half of the patients. Here, applying multi-omics on intestinal biopsies from treatment-naïve children, the authors show that relapse-prediction using separate omics data is outperformed by a robust machine learning approach combining microbiomes and epigenomes.

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.

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.

Analysis of crop yields, farmer income and bird species abundances identifies multiple positive outcomes of a large-scale Indian government-incentivized agroecology initiative.

Here, the authors present ConQuR, a conditional quantile regression method that removes microbiome batch effects through non-parametric modeling of complex microbial read counts, while preserving the signals of interest.

Here, the authors present a metagenomic catalogue of the early-life human gut virome including 160,478 non-redundant DNA and RNA viral sequences from 8,130 gut virus-like particles enriched or bulk metagenomes in the first three years of life.

Longitudinal profiling of the nasal and faecal microbiomes of 66 dairy farmers and 166 dairy cows over a year-long period shows that microbes acquired from cow microbiomes introduce clinically relevant antimicrobial resistance genes to farmer guts.

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

The role of ecological factors in modulating the spread of antibiotic-resistance bacteria in the gut remains unclear. Here, the authors use anaerobic microcosms to study the population growth of four clinical E. coli strains in the gut microbiome.

Variation in vegetation and climate affects the long-term changes in bird communities in intensive-agriculture habitats, but not in diversified-agriculture or natural-forest habitats, by changing the local colonization and extinction rates.

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

Agricultural land-use change affects belowground biodiversity. Here, the authors compare soil microbial communities from natural ecosystems and agricultural systems, finding that agricultural conversion leads to taxonomic and functional homogenisation.

Bleaching threatens corals worldwide as the oceans warm from climate change. Here the authors provide insight into intergenerational acclimatization potential by identifying metabolomic signatures of coral resistance to bleaching at all stages of development, including in the new generation.

The authors document unexpectedly high levels of biodiversity in algal habitats between the coral reefs in the Great Barrier Reef.

Multi-modal analysis of genomically unstable ovarian tumours characterizes the contribution of anatomical sites and mutational processes to evolutionary phenotypic divergence and immune resistance mechanisms.

Single-cell and spatial transcriptomics analysis of stricturing Crohn’s disease highlights cellular heterogeneity in fibrotic tissue and identifies neighborhoods of fibroblasts and immune cells contributing to this severe disease complication.

The analysis of field-caught Aedes aegypti from Brazil through 16S rRNA amplicon-sequencing (V3-V4 region) evidenced that Wolbachia wMel strain reduces the bacterial diversity of mosquito’s midgut and reshapes microbial interactions.

Inflammatory bowel disease (IBD) is a chronic immune-mediated condition. This study presents a drug-free treatment strategy for IBD that targets bacterial adhesion, utilizing mannan oligosaccharide-loaded porous microgels to selectively capture adherent-invasive E. coli and competitively inhibit bacterial colonization on the gut epithelium.