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Environmental drivers of soil carbon and its sensitivity to warming are poorly understood. The authors compare soil samples of paired urban and natural ecosystems and show that under warming, the microbiome is an essential driver of soil carbon in urban greenspace compared with natural ecosystems.

Here, the authors use fecal immunochemical test (FIT) samples from around 1000 individuals to characterize their gut virome, showing a diverse viral community, indicative of the individual lifestyle (smoking, fiber consumption and physical activity), thus highlighting FIT samples as a useful alternative for virome analyses.

The reasons why malaria manifests with a variety of well-recognized clinical phenotypes remain poorly understood. Here, using distinct rodent models, the authors reveal that the microbiota colonizing the lung promotes respiratory distress syndrome and mortality during malaria infections.

Familial dysautonomia is a rare genetic disease caused in part by neurodegeneration. Here, the authors show that the gut-metabolism axis is altered in both patients and transgenic mice and that disease pathology is ameliorated by controlling microbiome divergence.

Here, the authors compare the fecal microbial community of individuals in the U.S., Uganda, and Botswana, and identify significant bacterial taxa alterations with both treated and untreated HIV infection although with a high degree of uniqueness in each cohort, and also significant differences between populations that report men who have sex with men (MSM) behavior and non-MSM populations.

The fate of soil carbon depends on microbial processes, but whether different microbial taxa have individualistic effects on carbon fluxes is unknown. Here the authors use 16 S amplicon sequencing and stable isotopes to show how taxonomic differences influence bacterial respiration and carbon cycling across four ecosystems.

The establishment and composition of the host microbiota is known to impact the function of the host immune response. Here the authors show that mode of delivery may impact the intestinal microbiota composition from birth and modulate the response to routine childhood vaccines.

A secreted protein effector from the fungal pathogen Verticillium dahliae has bactericidal properties. It allows the pathogen to modify the root microbiome in tomato and cotton, specifically eliminating plant-protective bacteria, to increase its own virulence.

Land degradation in drylands impacts livelihoods and productivity and is affected by biocrusts that stabilize the soil. Long-term experiments show that biocrust recovery from disturbance is faster than expected, but stopped under warming, with warming alone causing loss of biocrust groups and soil stability.

The gut microbiomes of Irish Travellers, an ethnically distinct subpopulation of Ireland, have similarity to the microbiomes of non-industrialized populations, but externally imposed lifestyle changes may alter their microbiota, with potential health sequelae.

The Ross Ice Shelf is the most extensive ice shelf of Antarctica and isolates the underlying ocean from sunlight. Here the authors use multi-omics to unravel the phylogenetic and functional diversity of microbial life in this ecosystem.

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 ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. Here, Clerc et al. show that marine bacteria are strongly attracted to algal polysaccharides, and this chemotactic behaviour is enhanced by dimethylsulfoniopropionate (DMSP), a ubiquitous algal metabolite.

A survey of 119 countries shows that education is the strongest predictor of climate change awareness around the world. The results suggest that improving understanding of local impacts is vital for public engagement.

Opportunistic plant pathogen Xanthomonas secretes leaf-degrading enzymes through the type-2 secretion systems that cause disease and thereby trigger changes in leaf microbiome composition.

Anaerobic gut fungi are a functionally important component of mammalian herbivores’ microbiomes. Here, the authors surveys anaerobic gut fungi in 34 species of ruminants and hindgut fermenters, assessing their patterns and identifying 56 novel genera.

Elevational trends in biodiversity and ecosystem functions across natural and anthropogenic habitats on Mount Kilimanjaro show that the effects of land use are strongly mediated by climate.

Leaf-feeding insect microbiomes could be influenced by the soil, the plant, or a product of the two. Here, the authors conduct a series of experiments to show that an herbivorous insect predominantly acquires its microbiome from the soil rather than the plant, and that these insect microbiomes reflect soil legacies of earlier growing plants.

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.

Multiomics reveals that almost half of gut microbiome diversity in humans can be explained by 40 blood metabolites.

Tyrosine kinase inhibitors (TKIs) have improved the clinical outcomes of patients with metastatic renal cell carcinoma (mRCC), however TKI-related diarrhoea is a common and serious adverse effect. Here the authors show in a randomized clinical trial that faecal microbiota transplantation from healthy donors can improve TKI-induced diarrhoea in patients with mRCC.

In this work, authors show that exacerbations of respiratory symptoms in persons with cystic fibrosis (CF) were associated with either CF pathogen-driven or anaerobe-based changes in airway bacterial community structure.

The authors profile stool metagenomics and plasma metabolomics in Tanzanian individuals and uncover a gradient of gut microbial profiles, from rural through urban Tanzania towards Western populations. Integration with ex vivo blood microbial stimulations reveals immune responses associated with histidine and arginine pathways, mediated by Bifidobacterium longum and Akkermansia muciniphila.

Bacteria–bacteria interactions and resultant microbiota changes were characterized using a synthetic phyllosphere community in planta.

Metagenomic analysis of the gut virome along the mammalian gastrointestinal tract of two mammalian species reveals the biogeography of bacteriophage, including region- and species-specific variations in virome composition.

Utilising various Campylobacter vaccination regimens, the authors explore the effect of vaccination on Campylobacter-associated diarrhoea, mortality, and growth kinetics in vaccinated infant rhesus macaques.

The flexibility of corals to associate with different bacteria in different environments has not been systematically investigated. Here, the authors study bacterial community dynamics for two coral species and show that bacterial community structure responds to environmental changes in a host-specific manner.

Using stable isotope probing to quantify growth and carbon assimilation rates of soil microbes along an elevation gradient, the authors show that these traits are more constrained by evolutionary history than environmental variation.

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.

Study of the genetically diverse Collaborative Cross (CC) mouse system reveals that early life history impacts mouse gut microbiome composition and although dietary changes have only a moderate effect on the microbiome, it does shape the gut metabolome.

Faecal carbon:nitrogen measurements and manipulation of nitrogen availability via diet and host secretions in a murine model suggest that intestinal nitrogen limitation occurs due to host absorption and microbial use, leading to benefits for specific taxa.

Early postnatal colonization has been described to be critical for the long-term microbiota composition and health. Here, via multi-omics approach, the authors investigate the impact of the developing host hepatic metabolism on the murine intestinal microbiota composition with comparative analysis at immediate postnatal period, early infancy and weaning and adulthood.

Inflammatory bowel disease (IBD) has been linked to host-microbiota interactions. Here, the authors investigate mucosa-associated microbiota using endoscopically-targeted biopsies from inflamed and non-inflamed colon in patients with Crohn’s disease and ulcerative colitis, finding associations with inflammation and host epigenomic alterations.

Due to a microbiota-dependent increase in intestinal permeability with age, the gut metabolite N⁶-carboxymethyllysine accumulates in the microglia of mouse and human brains. As a result, microglia display increased oxidative stress and mitochondrial dysfunction.

Many microbiome differential abundance methods are available, but it lacks systematic comparison among them. Here, the authors compare the performance of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample groups, and show ALDEx2 and ANCOM-II produce the most consistent results.

Integration of longitudinal gut metagenomic datasets from children in Finland, Estonia and Russian Karelia reveals high strain-level diversity, which consequently impacts the functional capabilities of the early life microbiome.