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Microscopy and 16S rRNA sequencing suggest that there is a limited bacterial presence in the human fetal intestine, with one enriched Micrococcus species exhibiting immunomodulatory activity ex vivo.

Despite growing interest in environmental metabolomics, we lack conceptual frameworks for considering how metabolites vary across space and time in ecological systems. Here, the authors apply (species) community assembly concepts to metabolomics data, offering a way forward in understanding the assembly of metabolite assemblages.

Data from more than 9,700 human stool and oral metagenomes has been used to decipher the strain transmission patterns of the human microbiome from mother to infant, within households and within populations.

Microbial carbon use efficiency has an important role in soil C cycling. Here the authors test the interactive effects of temperature and moisture and manipulate microbial community composition in soil microcosms, showing a positive relationship between microbial diversity and CUE that is contingent on abiotic conditions.

Mesoscal eddies influence the distribution of marine diazotrophs in the North Atlantic, highlighting the potential role of particle-associated non-cyanobacterial diazotrophs (NCDs) on their contribution to nitrogen and carbon cycles.

Simpson and colleagues systematically interrogate the influence of dietary carbohydrate type and quality on the obesogenic impact of protein-diluted diets in mice.

Qi Zhang, Zhenyan Zhang et al. show that the numbers and relative abundance of antibiotics-resistance genes increase during a cyanobacterial bloom in Lake Taihu of China. This correlation provides insights to the ecologists and the policy makers who manage the quality of fresh water.

The microbiota of centenarians (aged 100 years and older) comprise gut microorganisms that are capable of generating unique secondary bile acids, including isoallolithocholic acid, a bile acid with potent antimicrobial effects against Gram-positive—but not Gram-negative—multidrug-resistant pathogens.

Here, via a metagenomics analysis of population-based and disease cohorts, Vich Vila et al. study the impact of 41 commonly used medications on the taxonomic structures, metabolic potential and resistome of the gut microbiome, underscoring the importance of correcting for multiple drug use in microbiome studies.

Alterations to the microbiome are now associated with various diseases. Here the authors analyze microbiomes from a large population based cohort and show positive correlations between abundance of Streptococcus spp. and osteoarthritis-related knee pain.

Integrated analysis of microbiome and host cell transcriptional data on clinically annotated cohorts of patients with melanoma who were treated with anti-programmed cell death protein-1, uncovers new associations of streptococcus species with immune-related adverse effects and finds consistent microbiome associations with clinical outcomes.

A diverse intestinal microbiota is required for mice to undergo extinction-related neuronal plasticity and normal fear extinction learning.

Herold et al. present an integrated meta-omics framework to investigate how mixed microbial communities, such as oleaginous bacterial populations in biological wastewater treatment plants, respond with distinct adaptation strategies to disturbances. They show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity.

The success rate of chimeric antigen receptor T cell therapy is high in blood cancers, yet individual patient characteristics might reduce therapeutic benefit. Here authors show that therapeutic response in multiple myeloma, acute lymphoblastic leukemia and non-Hodgkin lymphoma, and occurrence of severe cytokine release syndrome in multiple myeloma are associated with specific gut microbiome alterations.

Methane emissions are determined by the balance of microbial methane production relative to consumption. Warming drives larger increases in methane production than consumption in experimental ponds, suggesting that natural ecosystems may represent a positive feedback under climate change.

Using genome-resolved metagenomics for 41 Arctic seawater samples, this ecogenomic analysis of 530 metagenome-assembled genomes (MAGs) from the polar Arctic Ocean reveals uncultured Arctic bacterial and archaeal MAGs, their gene expression patterns, habitat preferences and metabolic potential.

Knowing which species traits may confer resilience to human-mediated stressors will help predict future impacts on biodiversity. Here, Mellin et al. show that large bodied fish with small geographic ranges are disproportionately affected by the negative impacts of human disturbance and climate variability.

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.

Longitudinal multi-omic analysis of 114 healthy infants from birth to 12 months of age showed that first viral encounters are associated with airway inflammation, changes in respiratory microbiota and later susceptibility to clinical respiratory tract infections.

Transfer of a host’s microbiota by faecal microbiota transplantation has shown benefit in the context of recurrent Clostridioides difficle infection. Here the authors shows the inflammatory status of the recipient can impact on engraftment and the efficacy of the introduced microbiota in a model of C.difficile infection.

Here, the authors characterize gut viromes in a cohort of individuals with metabolic syndrome, which they find associated with a highly widespread family of gut bacteriophages they name Candidatus Heliusviridae.

Sampling plants and lichens from across boreal North America and Eurasia, the authors show that the composition and diversity of symbiotic fungal endophyte communities are controlled primarily by host associations, not environmental filtering.

Using metabolomics and shotgun metagenomics on stool samples from individuals with and without inflammatory bowel disease, metabolites, microbial species and genes associated with disease were identified and validated in an independent cohort.

The structure and distribution of strain-level diversity in host-associated bacterial communities is largely unexplored. Here, Ellegaard and Engel analyze strain level diversity of the honey bee gut microbiota, showing that bees from the same colony differ in strain but not phylotype composition.

Arabidopsis thaliana plants lacking the rbohD gene, which encodes the NADPH oxidase RBOHD, have an altered leaf microbiome including an enrichment of opportunistic pathogens, indicating that RBOHD is essential for maintaining leaf microbiota homeostasis.

Chronic obstructive pulmonary disease (COPD) is a progressing disease, with lung but not gut microbiota implicated in its etiology. Here the authors compare the stool from patients with COPD and healthy controls to find specific gut bacteria and metabolites associated with active disease, thereby hinting at a potential role for the gut microbiome in COPD.

Disordered nanoscale striations on petals, tepals and bracts have evolved multiple times among flowering plants and provide a salient visual signal to foraging bumblebees (Bombus terrestris).

Conducting a series of removal experiments using synthetic leaf-inhabiting bacterial communities, the authors identify several keystone strains and show that priority effects drive phyllosphere community assembly.

The potential recovery of the human gut microbiota after an antibiotic treatment, and its effects on our health, are poorly understood. Here, the authors use a mouse model mimicking paediatric antibiotic use to shed new light into these processes.

The authors defined rat microbial biogeography by re-analyzing publicly available RNA sequencing data from 11 organs of juvenile, adolescent, adult and aged Fisher 344 rats.

Single-cell mass cytometry was applied to comprehensively characterize postmortem and fresh human microglia. Using a hybrid workflow for multidimensional data analysis, a core signature and regional heterogeneity were identified.

Here, by analyzing 250 species of animals covering a large taxonomic spectrum, the authors show that archaea are common constituent of the animal gut throughout the animal kingdom, and identify six main genera/families of gut archaea revealing their abundance and diversity to be driven by host diet, evolutionary history and physiology.

A microfluidic intestine-on-a-chip that allows the control of physiologically relevant oxygen gradients, enables the extended coculture of living human intestinal epithelium with stable communities of aerobic and anaerobic human gut microbiota.

A reconstruction of the genomic history of japonica and indica rice over 9,000 yr with geographic, environmental, archaeobotanical and paleoclimate data.

Analysis of 60 sites in three ocean basins suggests that overgrowth of fleshy algae on coral reefs supports higher microbial abundances dominated by copiotrophic, potentially pathogenic bacteria via the provision of dissolved inorganic carbon.

Little is known about the microbiota of marine mammals, despite the crucial ecological roles played by these animals. Here, Bik et al. describe the bacterial communities associated with various body sites in dolphins and sea lions, as well as the microbiota of their dietary fish and adjacent seawater.

Habitat factors such as current velocity and water depth play a key role in the survivorship of the endangered coral Acropora palmata and its microbiome, according to surveys at coral restoration sites.

Infant nutrition and maternal weight gain during pregnancy impact early-life acquisition and function of the gut microbiome .

Soil weathering, rather than short-term warming, controls microbial community composition, nutrient availability and soil carbon content, according to observations from a 3-Myr-old soil chronosequence preserved in river terraces in California.

High-resolution meta-analysis of cheese microbiomes and corresponding volatilomes provide technological and ecological insights for improving cheese production.

Power et al. catalogue the microbial biodiversity and physicochemistry of around 1000 hotsprings across New Zealand, providing insights into the ecological conditions that drive community assembly in these ecosystems.