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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.

The SWEET project is a multicenter, randomized, controlled trial that shows that long-term consumption of sweeteners and sweetness enhancers improves body weight control and elicits beneficial gut microbiota changes in adults with overweight or obesity.

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.

Non-antibiotic drugs from a wide range of therapeutic classes can alter the ability of gut commensals to resist invasion by enteropathogens, a previously underappreciated side effect of such drugs.

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.

Spatial cell distribution within a tissue microenvironment is a rapidly advancing field. Here, authors assess three commercially available single-cell resolution spatial transcriptomics approaches (CosMx, MERFISH, and Xenium) to inform which technology outperforms for immune profiling of solid tumors using patient samples.

The response of marine fish assemblages to global change is not fully understood. Analysing a 29-year time-series, Magurran et al.show that despite little change in species richness, high species turnover is leading to North Atlantic groundfish assemblages becoming spatially homogenized, likely as a result of climatic change.

In participants from a randomized controlled trial, doxy-PEP use over 6 months minimally affected the gut microbiome’s taxonomic composition but increased the abundance and active expression of tetracycline antibiotic resistance genes.

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.

Tropical Pacific islands enhance phytoplankton biomass, productivity and biodiversity at both local and basin scales, according to ocean colour satellite observations used to identify island-enriched waters.

Here, the authors analysed 1374 single-cell genomes from Subglacial Lake Mercer in Antarctica’s deep biosphere and report that microbes in this habitat are mostly novel and genetically isolated, exhibiting chemosynthetic and heterotrophic lifestyles shaped by oxygen availability.

Early life microbiome is affected by factors such as mode of delivery, gestational age at birth and feeding regime. Here, the authors show that gestational age at birth still imprints on the microbiome at four years of age, suggesting a link between altered microbiome in prematurity and long term health implications.

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.

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.

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.

Humans tend to adopt one of a limited number of different bacterial community structures in the gut, known as enterotypes. Moeller et al.now show that these microbial fingerprints are conserved in chimpanzees, and that individuals can switch between enterotypes over periods of several years.

Gene expression profiles can classify breast cancer into five clinically relevant subtypes. Here, the authors perform an in-depth quantitative profiling of the proteome of 45 breast tumors, and show they can recapitulate the transcriptome-based classifications and identify many potentially antigenic tumour-specific peptides.

The advantage of living in cities compared with rural areas with respect to height and BMI in children and adolescents has generally become smaller globally from 1990 to 2020, except in sub-Saharan Africa.

Here, in a cohort of nearly 1000 infants, the authors characterize the gut microbiota development in the first 2 years of life and develop a gut microbiota wellbeing index (MWI) using clustering and trajectory modelling, showing that infants’ microbiota development follows distinct trajectories, dependent on infant exposures, which are predictive of later health outcomes.

Anthropogenic eutrophication is a driver of plant community shifts in many grassland ecosystems. Here, the authors use data from a globally distributed experiment to assess how nutrient addition affects multiple facets of grassland ecological stability and their correlations.

Anaerobic digesters play an important role in biodegradation. In the MiDAS 5 project, the authors use global 16S rRNA sequencing to expand the microbial reference database, improving taxonomic classification and revealing how environmental factors and geography shape microbial communities in anaerobic digesters.

Claudin-low tumors are a rare aggressive subtype of breast cancers. In this study, the authors use a multiomics approach to demonstrate that these tumors are heterogeneous and comprise three main subgroups that emerge from different evolutionary processes.

Lakes play an important role in the global carbon cycle and understanding their organic matter cycling is vital. Kellerman et al.apply an ultrahigh-resolution technique to 120 lakes across Sweden and show that the molecular composition is shaped by water dynamics and temperature.

Bifidobacterium species associated with breastfeeding can convert aromatic amino acids into their respective aromatic lactic acids via a previously uncharacterized aromatic lactate dehydrogenase, which may impact immune function in infants.

Using metagenomics and metatranscriptomics, up to 16 strains of intracellular, sulfur-oxidizing symbiotic bacteria were identified in individual mussels with different functions, indicating that high strain diversity is present in symbioses.

Phylogenomic analysis of 7,923 angiosperm species using a standardized set of 353 nuclear genes produced an angiosperm tree of life dated with 200 fossil calibrations, providing key insights into evolutionary relationships and diversification.

A region on chromosome 19p13 is associated with the risk of developing ovarian and breast cancer. Here, the authors genotyped SNPs in this region in thousands of breast and ovarian cancer patients and identified SNPs associated with three genes, which were analysed with functional studies.

Previous studies suggested a role for CARD9 pathway in atherosclerosis but the underlying mechanisms remain poorly understood. Here, the authors show that the pro-atherogenic effects of Card9 deficiency are mediated by CD36-dependent defective autophagy that can be reversed by rapamycin and metformin.

The combination of neoadjuvant nivolumab, ipilimumab and chemotherapy showed promising efficacy in patients with resectable non-small cell lung cancer, with higher tumor immune cell infiltration and tertiary lymphoid structures after treatment compared with neoadjuvant nivolumab plus chemotherapy.

Genetics factors involved in rhizosphere microbiomes assembly remain largely elusive. Here, the authors integrate microbiomics and quantitative plant genetics to reveal genetic loci associated with specific microbes and rhizobacterial traits underlying microbiome assembly in tomato.

Authors utilise a murine model of infection to provide mechanistic insight into how antimicrobial therapy may be a predisposing risk factor for hospital-acquired pneumonia. They show that antibiotic-induced microbiota perturbations compromise inflammatory monocytes and thereby impair antibacterial defence.

Paul Pharoah and colleagues report the results of a large genome-wide association study of ovarian cancer. They identify new susceptibility loci for different epithelial ovarian cancer histotypes and use integrated analyses of genes and regulatory features at each locus to predict candidate susceptibility genes, including OBFC1.

Stig Bojesen, Georgia Chenevix-Trench, Alison Dunning and colleagues report common variants at the TERT-CLPTM1L locus associated with mean telomere length measured in whole blood. They also identify associations at this locus to breast or ovarian cancer susceptibility and report functional studies in breast and ovarian cancer tissue and cell lines.

In this large-scale metagenomics study encompassing 3,483 human host-derived samples from seven body sites, researchers identify 583 unreported single-genome bins and report 314 metagenome-disease as well as 814 biosynthetic gene-disease associations.