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Here, the authors identify distinct gut microbiome and metabolome signatures in microscopic colitis, a condition causing chronic diarrhea, highlighting pro-inflammatory species and metabolites as potential non-invasive biomarkers and therapeutic targets.

Polygenic risk scores can help identify individuals at higher risk of type 2 diabetes. Here, the authors characterise a multi-ancestry score across nearly 900,000 people, showing that its predictive value depends on demographic and clinical context and extends to related traits and complications.

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.

Plant litter additions enhance soil microbial functional potentials for carbon and nitrogen cycling in high-Arctic ecosystems, based on a four-year experiment simulating vegetation expansion under climate warming.

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 gut microbiomes of urban-industrialized societies differ from those of traditional rural societies and hunter-gatherers. Here the authors perform a comparative analysis of available and new gut microbiome data to provide fresh insight into these differences.

Analysing pesticide residues in pollen and nectar collected by three bee species along a land-use gradient, the authors show that extensive foragers like Apis mellifera have higher pesticide risk than species that forage at intermediate or limited ranges, irrespective of landscape context.

A conserved network of bacteria and fungi underpins cadaver decomposition despite selection effects of location, climate and season.

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.

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

Faecal metagenomes and machine learning reveal a panel of 31 multikingdom microbiome markers and microbiome functions that are associated with autism spectrum disorder in male and female children.

A multi-omics investigation at Sweden’s Stordalen Mire shows that microbial dynamics and metabolites must be taken into account to predict ecosystem responses to environmental change.

Re-exposure to a high-fat diet in mice led to emergency myelopoiesis and increased neutrophils in the blood, which infiltrated plaques and released neutrophil extracellular traps, exacerbating atherosclerosis.

Many large mammals became extinct worldwide at the end of the Pleistocene epoch, around 12,000 years ago. Here, it is shown that smaller mammals, which often provide much more comprehensive fossil records than large mammals, were much less likely to respond to the Pleistocene–Holocene transition by becoming extinct. Instead, diversity and evenness suffered, so that less abundant species became rarer, with more generalist 'weedy' species becoming more common.

Gut microbes influence our health and may contribute to human adaptation to different lifestyles. Here, the authors describe the gut microbiome of a community of hunter-gatherers and identify unique features that could be linked to a foraging lifestyle.

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.

Lolamicin, a novel antibiotic developed from a pyridinepyrazole precursor, exhibits potent activity against a broad range of Gram-negative multidrug-resistant clinical isolates, and good efficacy in mouse models of infection without inducing gut dysbiosis.

Here, by performing an integrative multi-omics analysis coupled to clinical features of COVID-19 patients prospectively followed for up to 6 month, the authors identify specific gut microbiome patterns associated with disease severity and development of post-acute COVID-19 syndrome.

Metagenomic analyses reveal that microbial genomes undergo a community-wide transition in size and GC content across a narrow depth range, indicating that nutrient limitation is a major driver in marine microbial genomic and proteomic evolution.

A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.

Fecal microbiota transplantation (FMT) is effective in treating recurrent Clostridium difficile infection (CDI). Here, the authors show that the composition of the gut fungal microbiota of donors and recipients, and especially the abundance of Candida, correlates with FMT outcome in CDI patients.

Stagaman et al. investigate the associations between early idiopathic Parkinson’s disease (PD) and the diversity and composition of both saliva and stool microbiomes in a large, geographically diverse US cohort. Abundances of saliva microbes, particularly Prevotella, Neisseria, and Streptococcus OTUs, best distinguish between controls and cases.

Bacterial AB₅ toxins, such as cholera toxin, bind to oligosaccharides on the host cell surface and play key roles in the pathogenesis of diarrheal disease. Here, Patry et al. show that these toxins bind also to bacterial oligosaccharides and inhibit the growth of Campylobacter jejuni and gut commensal bacteria.

HLA peptidomic analysis identifies recurrent intracellular bacteria-derived peptides presented on HLA-I and HLA-II molecules in melanoma tumours, revealing how bacteria can modulate immune functions and responses to cancer therapies.

Genome-wide association analyses of 41,917 bipolar disorder cases and 371,549 controls of European ancestry provide new insights into the etiology of this disorder and identify novel therapeutic leads and potential opportunities for drug repurposing.

An oral inulin allergen gel restores the microbiota of allergic mice and suppresses undesired immune responses to achieve allergen-specific oral tolerance, effectively overcoming food allergy.

Here, the authors show that SARS-CoV-2 infection causes gut microbiome dysbiosis and gut epithelial cell alterations in a mouse model, and correlate dysbiosis observed in COVID-19 patients with blood stream infections, matching reads of bacterial sequences from stool samples to organisms found in the blood.

DNA analysis of 6 individuals from eastern and south-central Africa spanning the past approximately 18,000 years, and of 28 previously published ancient individuals, provides genetic evidence supporting hypotheses of increasing regionalization at the end of the Pleistocene.

Here, using fecal metagenomics data of 2,320 individuals, the authors develop a microbiome-based machine learning approach showing high accuracy for multi-class disease diagnosis, highlighting its potential application in improving noninvasive diagnostics and monitor responses to therapy.

Analysis of a CO₂-driven geyser over a complete eruption cycle showed temporal changes in microbial community composition and function, associated with eruption phase and aquifer water depth, and revealed a putative archaeal symbiosis.

MultiSTAAR provides a general and flexible statistical framework for functionally informed multi-trait rare variant analysis of biobank-scale sequencing studies by jointly analyzing multiple traits and incorporating annotation information.

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.

The archaeological site Shinfa-Metema 1 in the lowlands of northwest Ethiopia provides early evidence of intensive riverine-based foraging aided by the likely adoption of the bow and arrow.

Ready access to diagnostic tests that work well under remote field conditions is a major barrier to improving the health of people in the developing world. Here, Curtis Chin and his colleagues have developed a chip-based, microfluidic device and handheld reader for the simultaneous and rapid diagnosis of HIV and syphilis that uses only 1 μl of unprocessed whole blood and that was successfully field tested in Rwanda.

Polymer brushes are often used to functionalise surfaces. Here, the authors report on the creation of high-density, regenerating hyaluronan brushes using hyaluronan synthase enzymes which can be patterned by photo-deactivation and demonstrate biocompatibility and resistance to biofilm formation.

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.

Using data from the Tara Pacific expedition, this study shows that a key driver of variation in coral telomere DNA length across the Pacific Ocean is the history of water temperature. The telomere lengths of short-lived, stress-sensitive Pocillopora colonies are more sensitive to seasonal temperature variations than those of long-lived and stress-resistant Porites colonies.

The Human Breast Cell Atlas identifies 12 major breast cell types and 58 biological cell states, revealing abundant pericyte, endothelial and immune cell populations, and highly diverse luminal epithelial cell states.

Using genome-wide meta-analyses of clinical measures of depression and biobank data, the authors investigate symptom-specific genetic associations between depression and subsequent risk for Alzheimer’s disease, finding an absence of a putative genetic overlap between disorders.

Enterococci enhance the fitness and pathogenesis of Clostridioides difficile in the gut by altering the amino acid composition and providing signals that increase its virulence towards the host.

Mutations in histone acetyltransferases (HATs) CREBBP and EP300 are generally thought to lead to decreased function or absence of protein product. Here the authors describe a gain of function of several CREBBP mutations leading to baseline hyper-acetylation, increased homologous recombination and potential synergy between radiation and HAT inhibition in CREBBP/EP300 mutant tumors.