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Background Both testicular germ cell tumours (TGCT) and neurodevelopmental disorders are associated with urogenital malformations. Few studies have investigated the association between psychiatric disorders and TGCT. We investigated whether history of any psychiatric or neurodevelopmental disorder is associated with increased risk or mortality of TGCT. Method This is a nested case–control study including 6166 TGCT patients diagnosed during 1992–2014, individually matched for age and calendar period to 61,660 controls. We calculated odds ratios (ORs) for the association between type of psychiatric diagnoses and TGCT risk. Among the cases, we used a cohort design and calculated hazard ratios (HRs) of the association between psychiatric diagnose and all-cause and TGCT-specific death. Results History of a neurodevelopmental disorder (attention deficit hyperactivity disorder, autism spectrum disorder and intellectual disabilities) was associated with an increased risk of seminoma (OR: 1.54; 1.09–2.19). Seminoma patients with neurodevelopmental disorders were younger (34 versus 38 years, p = 0.004) and had more stage IV disease (5.4% versus 1.2%) than those without. Psychiatric history overall was not associated with TGCT. Patient history of any psychiatric disorder was associated with an increased all-cause and TGCT-specific death. Conclusions We report an association between neurodevelopmental disorders and testicular seminoma, and an increased TGCT-specific mortality for TGCT patients with psychiatric disorders.

Background: The COVID-19 global pandemic greatly impacted lifestyles and physical activity routines. This study explored how the COVID-19 pandemic impacted participant experience and motivation in ecofit, a large, community-based, multicomponent intervention that supports aerobic and resistance-based physical activity using publicly available, outdoor exercise facilities and smartphone technology. Methods: Fifteen participants from the intervention arm of the study were interviewed. Audiotaped telephone interviews were transcribed verbatim and analyzed by a researcher uninvolved in the intervention. Through an inductive thematic approach, data were coded and organized into themes. The quantitative measure of participant smartphone application engagement was used as a classification during analysis. Results: Several themes representing participants’ experience of the COVID-19 pandemic in their engagement with ecofit, overall physical activity levels, motivation to exercise, and perception and usage of outdoor gym facilities were identified. Conclusion: The impact of the COVID-19 pandemic on clinical trials is beginning to emerge. Although the present study showed a mixed impact of the pandemic on participation in the ecofit program, the overall implications for the intervention are yet to be determined. Interestingly, although a large review found a negative impact of COVID-19 on physical activity, this sample reported an overall increase.

Fungal mineral weathering processes regulate the bioavailability of inorganic nutrients from mineral surfaces to organic matter and increase the bioavailable fraction of nutrients. Fungal mineral weathering strategies can be classified as biomechanical (direct) or biochemical (indirect). In the case of fungal uptake of mineral nutrients through indirect weathering, it is widely hypothesized that uptake of mineral derived nutrients occurs through organic acid chelation, but such processes have not been directly visualized. This is in part due to challenges in probing the complex and heterogeneous soil environment. Here, using an epoxy-based mineral doped soil micromodel platform that we developed, which mimics soil mineralogy and structure, it permitted us to visualize and spatially probe the molecular mechanisms of mineral weathering. Mass spectrometry imaging revealed differences in the distribution of fungal exudates, citric acid and tartaric acid, on the soil micromodels in presence of minerals. Citric acid was detected closer to the nutrient rich inoculation point, whereas tartaric acid was highly abundant away from inoculation point. This suggested that the organic acid exuded by the fungi depended on the proximity from the carbon rich organic substrate at the point of inoculation. Using a combination of X-ray fluorescence and X-ray near edge structure analysis, we identified citric acid- and tartaric acid-bound K within fungal hyphae networks grown in the presence of minerals. Combined our results provide direct evidence that fungi uptake and transport mineral derived nutrient organic acid chelation. The results of this study provided unprecedented visualization of fungal weathering of soil minerals and hyphal K+transport, while resolving the indirect weathering mechanism of fungal K uptake from mineral interfaces.

Two factors that are well-known to influence soil microbiomes are the depth of the soil as well as the level of moisture. Previous works have demonstrated that climate change will increase the incidence of drought in soils, but it is unknown how fluctuations in moisture availability affect soil microbiome composition and functioning down the depth profile. Here, we investigated soil and wheatgrass rhizosphere microbiomes in a single common field setting under four different levels of irrigation (100%, 75%, 50%, and 25%) and three depths (0-5 cm, 5-15 cm, and 15-25 cm from the surface). We demonstrated that there is a significant interactive effect between depth and irrigation, where changes in soil moisture more strongly affect soil microbiomes at the surface layer than at deeper layers. This was true for not only microbiome community composition and diversity metrics, but also for functional profiles (transcriptomic and metabolomic datasets). Meanwhile, in rhizosphere communities the influence of irrigation was similar across the different depths. However, for the ‘Alkar’ wheatgrass cultivar, the rhizosphere microbial communities responded more strongly to changes in irrigation level than did the communities for the ‘Jose’ cultivar rhizosphere. The lessened response of deeper soil microbiomes to changes in irrigation may be due to higher incidence of slow-growing, stress-resistant microbes. These results demonstrate that the soil microbiome response to moisture content is depth-dependent. As such, it will be optimal for soil microbiome studies to incorporate deeper as well as surface soils, to get a more accurate picture of the soil microbiome response to stress.

Background Microbiomes contribute to multiple ecosystem services by transforming organic matter in the soil. Extreme shifts in the environment, such as drying-rewetting cycles during drought, can impact the microbial metabolism of organic matter by altering microbial physiology and function. These physiological responses are mediated in part by lipids that are responsible for regulating interactions between cells and the environment. Despite this critical role in regulating the microbial response to stress, little is known about microbial lipids and metabolites in the soil or how they influence phenotypes that are expressed under drying-rewetting cycles. To address this knowledge gap, we conducted a soil incubation experiment to simulate soil drying during a summer drought of an arid grassland, then measured the response of the soil lipidome and metabolome during the first 3 h after wet-up. Results Reduced nutrient access during soil drying incurred a replacement of membrane phospholipids, resulting in a diminished abundance of multiple phosphorus-rich membrane lipids. The hot and dry conditions increased the prevalence of sphingolipids and lipids containing long-chain polyunsaturated fatty acids, both of which are associated with heat and osmotic stress-mitigating properties in fungi. This novel finding suggests that lipids commonly present in eukaryotes such as fungi may play a significant role in supporting community resilience displayed by arid land soil microbiomes during drought. As early as 10 min after rewetting dry soil, distinct changes were observed in several lipids that had bacterial signatures including a rapid increase in the abundance of glycerophospholipids with saturated and short fatty acid chains, prototypical of bacterial membrane lipids. Polar metabolites including disaccharides, nucleic acids, organic acids, inositols, and amino acids also increased in abundance upon rewetting. This rapid metabolic reactivation and growth after rewetting coincided with an increase in the relative abundance of firmicutes, suggesting that members of this phylum were positively impacted by rewetting. Conclusions Our study revealed specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. The drought-induced nutrient limitation was reflected in the lipidome and polar metabolome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long-chain polyunsaturated fatty acids in dry soil suggest that lipids likely play an important role in the drought tolerance of microbial taxa capable of synthesizing these lipids. An increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest a metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions.

Background Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). Results We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. Conclusions Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks.

Arctic permafrost is thawing due to global warming, with unknown consequences on the microbial inhabitants or associated viruses. DNA viruses have previously been shown to be abundant and active in thawing permafrost, but little is known about RNA viruses in these systems. To address this knowledge gap, we assessed the composition of RNA viruses in thawed permafrost samples that were incubated for 97 days at 4°C to simulate thaw conditions. A diverse RNA viral community was assembled from metatranscriptome data including double-stranded RNA viruses, dominated by

Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. This ability is particularly advantageous in impoverished soils because fungal mycelial networks can bridge otherwise spatially disconnected and inaccessible nutrient hot spots. However, the molecular mechanisms underlying fungal mineral weathering and transport through soil remains poorly understood primarily due to the lack of a platform for spatially resolved analysis of biotic-driven mineral weathering. Here, we addressed this knowledge gap by demonstrating a mineral-doped soil micromodel platform where mineral weathering mechanisms can be studied. We directly visualize acquisition and transport of inorganic nutrients from minerals through fungal hyphae in the micromodel using a multimodal imaging approach. We found that Fusarium sp. strain DS 682, a representative of common saprotrophic soil fungus, exhibited a mechanosensory response (thigmotropism) around obstacles and through pore spaces (~12 μm) in the presence of minerals. The fungus incorporated and translocated potassium (K) from K-rich mineral interfaces, as evidenced by visualization of mineral-derived nutrient transport and unique K chemical moieties following fungus-induced mineral weathering. Specific membrane transport proteins were expressed in the fungus in the presence of minerals, including those involved in oxidative phosphorylation pathways and the transmembrane transport of small-molecular-weight organic acids. This study establishes the significance of a spatial visualization platform for investigating microbial induced mineral weathering at microbially relevant scales. Moreover, we demonstrate the importance of fungal biology and nutrient translocation in maintaining fungal growth under water and carbon limitations in a reduced-complexity soil-like microenvironment.

Soil microorganisms provide key ecological functions that often rely on metabolic interactions between individual populations of the soil microbiome. To better understand these interactions and community processes, we used chitin, a major carbon and nitrogen source in soil, as a test substrate to investigate microbial interactions during its decomposition. Chitin was applied to a model soil consortium that we developed, "model soil consortium-2" (MSC-2), consisting of eight members of diverse phyla and including both chitin degraders and nondegraders. A multiomics approach revealed how MSC-2 community-level processes during chitin decomposition differ from monocultures of the constituent species. Emergent properties of both species and the community were found, including changes in the chitin degradation potential of

Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value = .05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.

Soil is known to harbor viruses, but the majority are uncharacterized and their responses to environmental changes are unknown. Here, we used a multi-omics approach (metagenomics, metatranscriptomics and metaproteomics) to detect active DNA viruses and RNA viruses in a native prairie soil and to determine their responses to extremes in soil moisture. The majority of transcribed DNA viruses were bacteriophage, but some were assigned to eukaryotic hosts, mainly insects. We also demonstrated that higher soil moisture increased transcription of a subset of DNA viruses. Metaproteome data validated that the specific viral transcripts were translated into proteins, including chaperonins known to be essential for virion replication and assembly. The soil viral chaperonins were phylogenetically distinct from previously described marine viral chaperonins. The soil also had a high abundance of RNA viruses, with highest representation of Reoviridae. Leviviridae were the most diverse RNA viruses in the samples, with higher amounts in wet soil. This study demonstrates that extreme shifts in soil moisture have dramatic impacts on the composition, activity and potential functions of both DNA and RNA soil viruses., Wu et al. use a multi-omics approach (metagenomics, metatranscriptomics, and metaproteomics) to characterize soil viral responses to soil moisture. The results indicate that extreme shifts in soil moisture have dramatic impacts on the composition, activity and potential functions of both DNA and RNA soil viruses.

Here, we report 36 active-layer and 17 permafrost metagenomes from Utqiaġvik, AK, USA. Samples were collected from different topographical features and depths to study Arctic tundra microbiomes.

Metaproteomics has been increasingly utilized for high-throughput characterization of proteins in complex environments and has been demonstrated to provide insights into microbial composition and functional roles. However, significant challenges remain in metaproteomic data analysis, including creation of a sample-specific protein sequence database. A well-matched database is a requirement for successful metaproteomics analysis, and the accuracy and sensitivity of PSM identification algorithms suffer when the database is incomplete or contains extraneous sequences. When matched DNA sequencing data of the sample is unavailable or incomplete, creating the proteome database that accurately represents the organisms in the sample is a challenge. Here, we leverage a

Plant growth-promoting rhizobacteria (PGPR) play a crucial role in biological control and pathogenic defense on and within plant tissues, however the mechanisms by which plants associate with PGPR to elicit such beneficial effects need further study. Here, we present time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging of Brachypodium distachyon (Brachypodium) seeds with and without exposure to two model PGPR, i.e., Gram-negative Pseudomonas fluorescens SBW25 (P.) and Gram-positive Arthrobacter chlorophenolicus A6 (A.). Delayed image extraction was used to image PGPR-treated seed sections to reveal morphological changes. ToF-SIMS spectral comparison, principal component analysis (PCA), and two-dimensional (2D) imaging show that the selected PGPR have different effects on the host seed surface, resulting in changes in chemical composition and morphology. Metabolite products and biomarkers, such as flavonoids, phenolic compounds, fatty acids, and indole-3-acetic acid (IAA), were identified on the PGPR-treated seed surfaces. These compounds have different distributions on the Brachypodium seed surface for the two PGPR, indicating that the different bacteria elicit distinct responses from the host. Our results illustrate that ToF-SIMS is an effective tool to study plant–microbe interactions and to provide insightful information with submicrometer lateral resolution of the chemical distributions associated with morphological features, potentially offering a new way to study the mechanisms underlying beneficial roles of PGPR.

Background Observations based on the spread of SARS-CoV-2 early into the COVID-19 pandemic have suggested a reduced burden in tropical regions leading to the assumption of a dichotomy between cold and dry and wet and warm climates. Objectives Analyzing more than a whole year of COVID-19 infection data, this study intents to refine the understanding of meteorological variables (temperature, humidity, precipitation and cloud coverage) on COVID-19 transmission in settings that experience distinct seasonal changes. Methods and findings A time stratified case-crossover design was adopted with a conditional Poisson model in combination with a distributed lag nonlinear model to assess the short-term impact of mentioned meteorological factors on COVID-19 infections in five US study sites (New York City (NYC); Marion County, Indiana (MCI); Baltimore and Baltimore County, Maryland (BCM); Franklin County, Ohio (FCO); King County, Washington (KCW)). Higher-than-average temperatures were consistently associated with a decreased relative risk (RR) of COVID-19 infection in four study sites. At 20 degrees Celsius COVID-19 infection was associated with a relative risk of 0.35 (95%CI: 0.20–0.60) in NYC, 1.03 (95%CI:0.57–1.84) in MCI, 0.34 (95%CI: 0.20–0.57) in BCM, 0.52 (95%CI: 0.31–0.87) in FCO and 0.21 (95%CI: 0.10–0.44) in KCW. Higher-than-average humidity levels were associated with an increased relative risk of COVID-19 infection in four study sites. Relative to their respective means, at a humidity level of 15 g/kg (specific humidity) the RR was 5.83 (95%CI: 2.05–16.58) in BCM, at a humidity level of 10 g/kg the RR was 3.44 (95%CI: 1.95–6.01) in KCW. Conclusions The results of this study suggest opposed effects for higher-than-average temperature and humidity concerning the risk of COVID-19 infection. While a distinct seasonal pattern of COVID-19 has not yet emerged, warm and humid weather should not be generally regarded as a time of reduced risk of COVID-19 infections.

Many organisms process carbon and other nutrients to generate energy through aerobic respiration where organic carbon compounds are broken down and oxygen is consumed, producing carbon dioxide and water. Respiration is indicative of active metabolism, and respiration rates are proportional to the amount of living biomass in an ecosystem. Although there are many methods for measuring respiration rates in the laboratory, current systems, such as infrared gas analyzers, are limited in their ability to independently resolve isotopomer fluxes across a range of relevant gases including both CO2 and O2 in real-time. Therefore, monitoring of biological respiration in real time under controlled laboratory conditions would enable better understanding of cellular physiology. To address this challenge, we developed a real time mass spectrometry (RTMS) manifold that simultaneously measures production and consumption of multiple gases and their isotopologues in seconds with the speed and sensitivity necessary to characterize rapidly changing respiration events as they occur. This universal manifold can be fitted to a variety of instruments and affords the same analytical precision and accuracy of the instrument while allowing for the real time measurements. Here, we paired the manifold to a single quad MS with an electron impact (EI) source operated in scan mode to detect extracted target gases by their respective masses (e.g., 12CO2 at mass 44, 13CO2 at 45). We demonstrated applicability of the RTMS instrument to different biological ecosystems (bacterial cultures, plants, and soil), and in all cases, we were able to detect simultaneous and rapid measurements of multiple gases in real time, providing novel insights into complex respiratory metabolism and the influence of biological and environmental factors.

The microbial catabolism of chitin, an abundant and ubiquitous environmental organic polymer, is a fundamental cog in terrestrial and aquatic carbon and nitrogen cycles. Despite the importance of this critical bio-geochemical function, there is a limited understanding of the synergy between the various hydrolytic and accessory enzymes involved in chitin catabolism. To address this deficit, we synthesized activity-based probes (ABPs) designed to target active chitinolytic enzymes by modifying the chitin subunits N-acetyl glucosamine and chitotriose. The ABPs were used to determine the active complement of chitinolytic enzymes produced over time by the soil bacterium Cellvibrio japonicus treated with various C substrates. We demonstrate the utility of these ABPs in determining the synergy between various enzymes involved in chitin catabolism. The strategy can be used to gain molecular-level insights that can be used to better understand microbial roles in soil bio-geochemical cycling in the face of a changing climate.

Communities of soil microorganisms (soil microbiomes) play a major role in biogeochemical cycles and support of plant growth. Here we focus primarily on the roles that the soil microbiome plays in cycling soil organic carbon and the impact of climate change on the soil carbon cycle. We first discuss current challenges in understanding the roles carried out by highly diverse and heterogeneous soil microbiomes and review existing knowledge gaps in understanding how climate change will impact soil carbon cycling by the soil microbiome. Because soil microbiome stability is a key metric to understand as the climate changes, we discuss different aspects of stability, including resistance, resilience, and functional redundancy.We then review recent research pertaining to the impact of major climate perturbations on the soil microbiome and the functions that they carry out. Finally, we review new experimental methodologies and modeling approaches under development that should facilitate our understanding of the complex nature of the soil microbiome to better predict its future responses to climate change.

Background Understanding the structure and drivers of gut microbiota remains a major ecological endeavour. Recent studies have shown that several factors including diet, lifestyle and geography may substantially shape the human gut microbiota. However, most of these studies have focused on the more abundant bacterial component and comparatively less is known regarding fungi in the human gut. This knowledge deficit is especially true for rural and urban African populations. Therefore, we assessed the structure and drivers of rural and urban gut mycobiota. Results Our participants (n = 100) were balanced by geography and sex. The mycobiota of these geographically separated cohorts was characterized using amplicon analysis of the Internal Transcribed Spacer (ITS) gene. We further assessed biomarker species specific to rural and urban cohorts. In addition to phyla which have been shown to be ubiquitous constituents of gut microbiota, Pichia were key constituents of the mycobiota. We found that geographic location was a major driver of gut mycobiota. Other factors such as smoking where also determined gut mycobiota albeit to a lower extent, as explained by the small proportion of total variation. Linear discriminant and the linear discriminant analysis effect size analysis revealed several distinct urban and rural biomarkers. Conclusions Together, our analysis reveals distinct community structure in urban and rural South African individuals. Geography was shown to be a key driver of rural and urban gut mycobiota.

Graphical abstract, Microbial communities organize into spatial patterns that are largely governed by interspecies interactions. This phenomenon is an important metric for understanding community functional dynamics, yet the use of spatial patterns for predicting microbial interactions is currently lacking. Here we propose supervised deep learning as a new tool for network inference. An agent-based model was used to simulate the spatiotemporal evolution of two interacting organisms under diverse growth and interaction scenarios, the data of which was subsequently used to train deep neural networks. For small-size domains (100 µm × 100 µm) over which interaction coefficients are assumed to be invariant, we obtained fairly accurate predictions, as indicated by an average R2 value of 0.84. In application to relatively larger domains (450 µm × 450 µm) where interaction coefficients are varying in space, deep learning models correctly predicted spatial distributions of interaction coefficients without any additional training. Lastly, we evaluated our model against real biological data obtained using Pseudomonas fluorescens and Escherichia coli co-cultures treated with polymeric chitin or N-acetylglucosamine, the hydrolysis product of chitin. While P. fluorescens can utilize both substrates for growth, E. coli lacked the ability to degrade chitin. Consistent with our expectations, our model predicted context-dependent interactions across two substrates, i.e., degrader-cheater relationship on chitin polymers and competition on monomers. The combined use of the agent-based model and machine learning algorithm successfully demonstrates how to infer microbial interactions from spatially distributed data, presenting itself as a useful tool for the analysis of more complex microbial community interactions.

Background Recent evidence has linked the gut microbiome to host behavior via the gut–brain axis [1–3]; however, the underlying mechanisms remain unexplored. Here, we determined the links between host genetics, the gut microbiome and memory using the genetically defined Collaborative Cross (CC) mouse cohort, complemented with microbiome and metabolomic analyses in conventional and germ-free (GF) mice. Results A genome-wide association analysis (GWAS) identified 715 of 76,080 single-nucleotide polymorphisms (SNPs) that were significantly associated with short-term memory using the passive avoidance model. The identified SNPs were enriched in genes known to be involved in learning and memory functions. By 16S rRNA gene sequencing of the gut microbial community in the same CC cohort, we identified specific microorganisms that were significantly correlated with longer latencies in our retention test, including a positive correlation with Lactobacillus. Inoculation of GF mice with individual species of Lactobacillus (L. reuteri F275, L. plantarum BDGP2 or L. brevis BDGP6) resulted in significantly improved memory compared to uninoculated or E. coli DH10B inoculated controls. Untargeted metabolomics analysis revealed significantly higher levels of several metabolites, including lactate, in the stools of Lactobacillus-colonized mice, when compared to GF control mice. Moreover, we demonstrate that dietary lactate treatment alone boosted memory in conventional mice. Mechanistically, we show that both inoculation with Lactobacillus or lactate treatment significantly increased the levels of the neurotransmitter, gamma-aminobutyric acid (GABA), in the hippocampus of the mice. Conclusion Together, this study provides new evidence for a link between Lactobacillus and memory and our results open possible new avenues for treating memory impairment disorders using specific gut microbial inoculants and/or metabolites.

Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin – a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.

Metagenomics is unearthing the previously hidden world of soil viruses1,2. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. To date only one soil viral AMG has been expressed3 and none has a solved structure. Here, we aimed to establish that AMGs on soil viruses actually produce functional, active proteins. We focused on AMGs that potentially encode chitosanase enzymes that metabolize chitin – a common carbon polymer. Glycoside hydrolase family 75 viral chitosanase genes were identified from environmental metagenomes. Several of these were expressed and functionally screened. One expressed protein showing endo-chitosanase activity (V-Csn) was crystalized and structurally characterized at ultra-high resolution, thus representing the first structure of a soil viral AMG product. A structure for an inactive mutant with a bound substrate (chitosan oligomer) was also determined. Conserved active site residues in V-Csn resided in a cleft between two domains. These structures provided details about the active site, and together with structure models determined using AlphaFold2, facilitated understanding of substrate specificity and enzyme mechanism. These findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts. Soil viral chitosanase AMG products that assist chitin decomposition may therefore play a previously unrecognized essential role in soil carbon cycling.

Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (∼0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change. IMPORTANCE Soil viruses are abundant but poorly understood. Because soil viruses regulate the dynamics of their hosts and potentially key processes in soil ecology, it is important to understand them better. Here, we leveraged massive DNA sequencing to unearth previously unknown soil viruses. We found that soil viruses differed across a historical gradient of precipitation. We compared soil viruses from Iowa, which is traditionally wetter, to those from Washington, which is traditionally drier, and from Kansas, which is intermediate. This study provides strong evidence that changes in historical precipitation impact not only the types of soil viruses but also their functional potential.

A strain of obligately anaerobically growing Gram-positive cocci was isolated from a human genito-urinary sample and characterized by a polyphasic approach. Analyses of 16S rRNA gene and whole-genome sequences of this strain S3374T indicated that it belonged to the genus Parvimonas . Overall genome relatedness index calculations confirmed it to be phylogenetically distinct from Parvimonas micra (NCTC 11808T) as its most closely related species with standing in nomenclature, with average nucleotide identity and genome-to-genome distance values of 85.8 and 30.2 %, respectively. Biochemically, strain S3374T was strongly proteolytic and can be differentiated from P. micra (DSM 20468T) by absence of phosphatase activity. The DNA G+C content of strain S3374T was 28.6 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3374T is considered to represent a novel species within the genus Parvimonas , for which the name Parvimonas parva sp. nov. is proposed. The type strain is S3374T (=DSM 110786T=CCOS 1934T=CCUG 74294T). This description adds strain S3374T as a second species to the genus Parvimonas which has so far been monotypic. While the type strain of this genus, P. micra , has a long standing in nomenclature and its role in human health and disease has been studied to some extent, this description of the proposed novel species represented by strain S3374T will allow microbiologists worldwide to identify isolates of P. parva sp. nov., a prerequisite for further investigation of its relevance in the clinical context and beyond.

The “Earthrise” photograph, taken on the 1968 Apollo 8 mission, became one of the most significant images of the 20th Century. It triggered a profound shift in environmental awareness and the potential for human unity—inspiring the first Earth Day in 1970. Taking inspiration from these events 50 years later, we initiated Project Earthrise at our 2020 annual conference of inVIVO Planetary Health. This builds on the emergent concept of planetary health, which provides a shared narrative to integrate rich and diverse approaches from all aspects of society towards shared solutions to global challenges. The acute catastrophe of the COVID-19 pandemic has drawn greater attention to many other interconnected global health, environmental, social, spiritual, and economic problems that have been underappreciated or neglected for decades. This is accelerating opportunities for greater collaborative action, as many groups now focus on the necessity of a “Great Transition”. While ambitious integrative efforts have never been more important, it is imperative to apply these with mutualistic value systems as a compass, as we seek to make wiser choices. Project Earthrise is our contribution to this important process. This underscores the imperative for creative ecological solutions to challenges in all systems, on all scales with advancing global urbanization in the digital age—for personal, environmental, economic and societal health alike. At the same time, our agenda seeks to equally consider our social and spiritual ecology as it does natural ecology. Revisiting the inspiration of “Earthrise”, we welcome diverse perspectives from across all dimensions of the arts and the sciences, to explore novel solutions and new normative values. Building on academic rigor, we seek to place greater value on imagination, kindness and mutualism as we address our greatest challenges, for the health of people, places and planet.

Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. This ability is particularly advantageous in impoverished soils, because fungal mycelial networks can bridge otherwise spatially disconnected and inaccessible nutrient hotspots. However, the molecular mechanisms underlying fungal mineral weathering and transport through soil remains poorly understood. Here, we addressed this knowledge gap by directly visualizing nutrient acquisition and transport through fungal hyphae in a mineral doped soil micromodel using a multimodal imaging approach. We observed thatFusarium sp. DS 682, a representative of common saprotrophic soil fungi, exhibited a mechanosensory response (thigmotropism) around obstacles and through pore spaces (∼12 µm) in the presence of minerals. The fungus incorporated and translocated potassium (K) from K-rich mineral interfaces, as evidenced by visualization of mineral derived nutrient transport and unique K chemical moieties following fungal induced mineral weathering. Specific membrane transport proteins were expressed in the presence of minerals, including those involved in oxidative phosphorylation pathways and transmembrane transport of small molecular weight organic acids. This study establishes the significance of fungal biology and nutrient translocation mechanisms in maintaining fungal growth under water and nutrient limitations in a soil-like microenvironment.

Background Mobile app-based interventions have the potential for wide-reach and therefore may be a useful tool in up-scaling physical activity interventions. In larger-scale interventions, face-to-face assessments are less cost-effective, and researchers often rely on surveys or activity trackers to assess outcomes. However, there is limited evidence of valid muscular fitness assessments that can be self-administered within mHealth interventions. As such, this study will evaluate the concurrent validity of upper and lower body muscular fitness that have been independently assessed by participants via the ecofit app, and face-to-face assessments conducted by a trained researcher. Methods This study compared baseline data from two muscular fitness tests from the ecofit two-armed randomised controlled trial and self-assessed data collected via the ecofit smartphone app (i.e., validated 90-degree push-up and 60-second sit-to-stand test). To assess the concurrent validity, the self-assessed push-up and sit-to-stand tests (i.e., collected via the ecofit app) were correlated using Spearman’s correlation coefficient against the researcher-assessed results (i.e., objective results collected during baseline assessment for the ecofit trial). Bland-Altman plots were also used to allow visualisation of the differences between the self- and research-assessed tests. Results Participants (N = 54) completed the push-up (24.1%) and sit-to-stand (100%) tests within 14-days of receiving the app. The results revealed a strong significant correlation for the push-up test (0.83, pp Conclusion This study provides support for the concurrent validity of self-reported upper and lower body muscular fitness assessments (i.e., the push-up and sit-to-stand tests) in mHealth. While these tests may be a feasible option for large scale physical activity interventions, more research is needed to determine the generalisability of these results.

A novel species within the genus Eikenella is described, based on the phenotypical, biochemical and genetic characterization of a strain of a facultatively anaerobic, Gram-negative rod-shaped bacterium. Strain S3360T was isolated from the throat swab of a patient sampled during routine care at a hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequences) placed the strain in the genus Eikenella , separate from all recognized species but with the closest relationship to Eikenella longinqua (NML 02-A-017T). Eikenella is one of the genera in the HACEK group known to be responsible for rare cases of endocarditis in humans. Until the recent descriptions of Eikenella exigua , Eikenella halliae and Eikenella longinqua , Eikenella corrodens had been the only validly published species in this genus since its description as Bacteroides corrodens in 1958. Unlike these species, strain S3360T is able to metabolize carbohydrates (glucose). The average nucleotide identities of strain S3360T with E. longinqua (NML 02-A-017T) and E. corrodens (NCTC 10596T), the type species of the genus, were 90.5 and 84.7 %, respectively, and the corresponding genome-to-genome distance values were 41.3 and 29.0 %, respectively. The DNA G+C content of strain S3360T was 58.4 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3360T is considered to represent a novel species within the genus Eikenella , for which the name Eikenella glucosivorans sp. nov. is proposed. The type strain is S3360T (DSM 110714T=CCOS 1935T=CCUG 74293T). In addition, an emendation of the genus Eikenella is proposed to include species which are saccharolytic.

Heterogeneous patient populations, complex pharmacology and low recruitment rates in the Intensive Care Unit (ICU) have led to the failure of many clinical trials. Recently, machine learning (ML) emerged as a new technology to process and identify big data relationships, enabling a new era in clinical trial design. In this study, we designed a ML model for predictively stratifying acute respiratory distress syndrome (ARDS) patients, ultimately reducing the required number of patients by increasing statistical power through cohort homogeneity. From the Philips eICU Research Institute (eRI) database, no less than 51,555 ARDS patients were extracted. We defined three subpopulations by outcome: (1) rapid death, (2) spontaneous recovery, and (3) long-stay patients. A retrospective univariate analysis identified highly predictive variables for each outcome. All 220 variables were used to determine the most accurate and generalizable model to predict long-stay patients. Multiclass gradient boosting was identified as the best-performing ML model. Whereas alterations in pH, bicarbonate or lactate proved to be strong predictors for rapid death in the univariate analysis, only the multivariate ML model was able to reliably differentiate the disease course of the long-stay outcome population (AUC of 0.77). We demonstrate the feasibility of prospective patient stratification using ML algorithms in the by far largest ARDS cohort reported to date. Our algorithm can identify patients with sufficiently long ARDS episodes to allow time for patients to respond to therapy, increasing statistical power. Further, early enrollment alerts may increase recruitment rate.

Objectives While outdoor gyms are being rapidly installed around the globe, little is known about their implications on physical activity, and fitness and other health-related outcomes. The primary objective of this systematic review was to examine the effects of outdoor gyms on physical activity, fitness and other health-related outcomes. Secondary objectives were to describe outdoor gym characteristics, user characteristics, and outdoor gym usage. Design Systematic review. Methods Peer-reviewed papers published in English were obtained through online database searches of the following databases; EBSCO, SPORTdiscus, Medline, PsycINFO, Web of Science, Scopus and Informit. Searches covered the periods from database inception to January 2019. Studies that reported on the efficacy of outdoor gym use for physical activity, health-related outcomes or descriptive aspects of outdoor gyms and their users were eligible for inclusion. Results There was some support that outdoor gyms may improve physical activity, fitness and other health-related outcomes, however few experimental studies have been conducted. There was no consistency between outdoor gyms in terms types and number of installed equipment for each facility. Further, this review found discrepancies of whom were the most likely users of outdoor gyms and when they were mainly used. Conclusions This review contributes to the limited evidence on the impact and characteristics of outdoor gyms on physical activity and fitness and health-related outcomes.

Introduction Escherichia coli and Staphylococcus aureus are important causes of severe diseases like blood stream infections. This study comparatively assessed potential differences in their impact on disease severity in local and systemic infections. Methods Over a 5-year interval, patients in whom either E. coli or S. aureus was detected in superficial or primary sterile compartments were assessed for the primary endpoint death during hospital stay and the secondary endpoints duration of hospital stay and infectious disease as the main diagnosis. Results Significance was achieved for the impacts as follows: Superficial infection with S. aureus was associated with an odds ratio of 0.27 regarding the risk of death and of 1.42 regarding infectious disease as main diagnosis. Superficial infection with E. coli was associated with a reduced duration of hospital stay by –2.46 days and a reduced odds ratio of infectious diseases as main diagnosis of 0.04. The hospital stay of patients with E. coli was increased due to third-generation cephalosporin and ciprofloxacin resistance, and in the case of patients with S. aureus due to tetracycline and fusidic acid resistance. Conclusions Reduced disease severity of superficial infections due to both E. coli and S. aureus and resistance-driven prolonged stays in hospital were confirmed, while other outcome parameters were comparable.

The signs of climate change are undeniable, and the inevitable impact for Earth and all its inhabitants is a serious concern. Ice is melting, sea levels are rising, biodiversity is declining, precipitation has increased, atmospheric levels of carbon dioxide and greenhouse gases are alarmingly high, and extreme weather conditions are becoming increasingly common. But what role do microorganisms have in this global challenge? In this Viewpoint article, several experts in the field discuss the microbial contributions to climate change and consider the effects of global warming, extreme weather, flooding and other consequences of climate change on microbial communities in the ocean and soil, on host-microbiota interactions and on the global burden of infectious diseases and ecosystem processes, and they explore open questions and research needs.

Objectives: Crohn’s disease is characterized by a gut dysbiosis with decreased abundance of butyrate producers such as Faecalibacterium prausnitzii. Although F. prausnitzii secretes anti-inflammato...

Inflammatory bowel diseases, which include Crohn’s disease and ulcerative colitis, affect several million individuals worldwide. Crohn’s disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study’s infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi’omics Database (http://ibdmdb.org), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases., The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.

The chemical structure of organic molecules profoundly impacts their interactions with metal ions and mineral phases in soils. Understanding the sources and cycling of metal-chelating compounds is therefore essential for predicting the bioavailability and transport of metals throughout terrestrial environments. Here we investigate the molecular speciation of organic molecules that solubilize trace metals in calcareous soils from Eastern Washington. Ultra-high performance Fourier transform ion cyclotron resonance mass spectrometry at 21 Tesla enabled fast and confident detection and identification of metal chelators that are produced by microbes that inhabit these soils based on screening for features that match diagnostic metal isotope patterns. We compared two approaches, one based on direct infusion using the incorporation of a rare isotope to validate true iron-binding features, and another based on separation with liquid chromatography and detection of isotopologues with coherent elution profiles. While the isotopic exchange method requires significantly shorter analysis time, nearly twice as many features were observed with liquid chromatography mass spectrometry (LCMS), mostly due to the reduction in ion suppression where major features limit the sensitivity of minor features. In addition, LCMS enabled the collection of higher quality fragmentation spectra and facilitated feature identification. Siderophores belonging to four major classes were identified, including ferrioxamines, pseudobactins, enterobactins, and arthrobactins. Each of these siderophores likely derives from a unique member of the microbial community, and each possesses different chemical characteristics and uptake pathways, likely contributing to fierce competition for iron within these soils. Our results provide insight into the metabolic pathways by which microbes that co-inhabit calcareous soils compete for this essential micronutrient.