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The authors evaluated and integrated compositional and functional microbiota data using fecal samples taken from healthy individuals and multimodal neuroimaging.

Obtaining data on antimicrobial resistance (AMR) from healthy human populations is difficult. Here, Hendriksen et al. use metagenomic analysis to obtain AMR data from untreated sewage from 79 sites in 60 countries, finding correlations with socio-economic, health and environmental factors.

On the basis of a soil-conditioning experiment, the authors show that while alien plant species are not more competitive than natives when growing in other native soil legacies or non-conditioned soils, they outcompete natives under soil legacies from other alien species, their growth being less negatively affected than those of native species. This points to an invasional meltdown as invasive species increase in presence and abundance.

Land use intensification could make soil food webs less able to recover from drought. Here, the authors find that intensive grassland management impairs recent photosynthate flux to roots and soil biota after drought, whereas extensive grassland management buffers the legacy of drought.

A genome-wide association study including over 76,000 individuals with schizophrenia and over 243,000 control individuals identifies common variant associations at 287 genomic loci, and further fine-mapping analyses highlight the importance of genes involved in synaptic processes.

Microbial communities are responsible for biological wastewater treatment. Here, Dueholm et al. generate more than 5 million high-quality, full-length 16S rRNA gene sequences from wastewater treatment plants across the world to construct a database with a comprehensive taxonomy, providing insights into diversity and function of these microbial communities.

Here the authors show that mice exposed to a variety of pathogens initially have impaired innate type 2 responses to lung allergens, but reactivity resets over time, indicating that microbial experience does not stably inhibit innate immunity to allergens.

Long et al. examined the gut microbiome of C57BL/6 mice from two production sites of three different vendors upon receipt, and as the mice adapted to the new vivarium at the University of Connecticut Health Center. Bacterial proportional abundance varied among mice from each vendor, and mice from all vendors exhibited changes in microbial profiles over time. These findings support the need to consider the microbiome as a potential source of variation in mouse studies.

The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.

Delivery via caesarean section, maternal antibiotic prophylaxis and colonization by opportunistic pathogens associated with the hospital environment affect the composition of the gut microbiota of children from birth until infancy.

Wastewater is a promising source of data for continuous monitoring of pathogens in communities, but analysis protocols and methods are still being established. Here, the authors develop sequencing and analysis protocols and use them to evaluate the microbial content of longitudinal wastewater samples from Miami-Dade County, USA.

The skin microbiome in patients prone to atopic dermatitis is enriched in Streptococcus and Gemella, and is associated with an adaptive immune response, an altered eukaryotic community and a functional shift in the microbiome-wide gene repertoire.

A characteristic of costal-pelagic fishes is their large population size fluctuations, yet the drivers remain elusive. Here, the authors analyze a 45-year timeseries of nitrogen stable isotopes measured in larvae of Northern Anchovy and find that high energy transfer efficiency from the base of the food web up to young larvae confers high survival and recruitment to the adult population.

This study examines how the tropicalisation of shallow reefs changes functional niches for fishes in Japan and Australia. They discover that functional niches in tropical-temperate transitional communities are asynchronously invaded by tropical species, mediated more by habitat availability than competition with resident temperate species.

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 pathogen Batrachochytrium dendrobatidis (BD) associated with widespread amphibian declines is present in Europe but has not consistently caused disease-induced declines in that region. Here, the authors suggest that an endemic strain of BD with low virulence may protect the hosts upon co-infection with more virulent strains.

The authors demonstrate in a mouse model that Western-style diets synergize with antibiotics to impair microbiota function. In turn, Klebsiella oxytoca promotes post-antibiotic microbiota recovery and removal of the pathogen Klebsiella pneumoniae.

Elevated CO₂ increases plant biomass, providing a negative feedback on global warming. Nutrient availability was found to drive the magnitude of this effect for the majority of vegetation globally, and analyses indicated that CO₂ will continue to fertilize plant growth in the next century.

This study shows that the biological impact and footprint of a leakage from a controlled sub-seabed release of carbon dioxide is confined to a few tens of metres, and identifies monitoring strategies for full-scale carbon storage operations.

Metagenomic and 16S rRNA amplicon sequencing of coastal subsurface microbiomes reveals a decoupling between a stable functional structure and highly variable taxonomic composition and also sheds light on the processes driving taxonomic variability.

Compiled data on litterfall and litter in eucalypt forests and woodlands for the Australian continent shows that litter mass can be robustly predicted using just three independent variables – time, aridity and litterfall quality

It is unclear whether stream detritivore diversity enhances decomposition across climates. Here the authors manipulate litter diversity and examine detritivore assemblages in a globally distributed stream litterbag experiment, finding a positive diversity-decomposition relationship stronger in tropical streams, where detritivore diversity is lower.

There are many open questions about biogeochemical function in peatlands. Here, the authors investigate the nitrogen cycle of tropical peatlands, finding that a surprisingly high fraction of nitrous oxide production is abiotic and that denitrification is a coupled abiotic-biotic process.

A prospective analysis of gut microbiome signatures in patients treated with neoadjuvant immunocheckpoint blockade for high risk resectable metastatic melanoma identifies new links between microbiota signatures, dietary intake and systemic inflammation in shaping the response and toxicity to immunotherapy.

The use of mechanical energy in wastewater treatment has been associated with accelerating physical mixing in compartments, and its effect on microbial activities has not been explored. The implementation of the developed mechano-driven bio-denitrification approach in real wastewater treatment provides a new method for wastewater denitrification.

Cell Painting is a high-content screening assay that uses multiplexed fluorescent dyes for image-based profiling of ∼1,500 morphological features. Image analysis with CellProfiler automatically identifies and extracts data from individual cells.

Mitsuokella jalaludinii and Anaerostipes rhamnosivorans degrade dietary phytate via synergistic interactions in the gut to produce the beneficial short-chain fatty acid propionate.

Small-scale farmers in Southeast Asia are increasingly turning to monocultures of oil palm and rubber to maximize income. Clough and colleagues demonstrate that this land-use change in Indonesia comes at a cost to a wide array of ecosystem functions and biodiversity.

Dissolved organic matter in the Fennoscandian Shield deep continental bedrock fracture waters of varying characteristics and ages carries a strong terrigenous signature, and only a small proportion of this potential energy source links to the deep biosphere microbial community.

Bowie et al. investigate the urinary microbiome in a large cohort of community dwelling men age 65 and older from the Osteoporotic Fractures in Men Study (MrOS) study. They identify several associations with the diversity of the urinary microbiome and benign prostatic hyperplasia, age, and body mass index.

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.

A new study examines microbiome-generated ethanol in individuals with and without nonalcoholic fatty liver disease (NAFLD), concluding that microbial ethanol might contribute to pathogenesis in some patients with NAFLD.

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.

Gold nanoparticles typically considered inert in oxic waters accumulate in freshwater wetland subaquatic plants and are completely biotransformed to oxidized Au species by the associated cyanogenic biofilm.