Our understanding of how the gut microbiome interacts with its human host has been restrained by limited access to longitudinal datasets to examine stability and dynamics, and by having only a few ...isolates to test mechanistic hypotheses. Here, we present the Broad Institute-OpenBiome Microbiome Library (BIO-ML), a comprehensive collection of 7,758 gut bacterial isolates paired with 3,632 genome sequences and longitudinal multi-omics data. We show that microbial species maintain stable population sizes within and across humans and that commonly used 'omics' survey methods are more reliable when using averages over multiple days of sampling. Variation of gut metabolites within people over time is associated with amino acid levels, and differences across people are associated with differences in bile acids. Finally, we show that genomic diversification can be used to infer eco-evolutionary dynamics and in vivo selection pressures for strains within individuals. The BIO-ML is a unique resource designed to enable hypothesis-driven microbiome research.
Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying ...its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.
Animal medication is a behavioral strategy to resist enemies based on the use of substances from the environment. While it has been observed in several animals, whether invasive species can use ...medication to resist new enemies during its expansion is unknown. Here, we show that the worldwide invasive pest Drosophila suzukii performs trans-generational prophylactic medication by adapting its oviposition behavior in the presence of enemies. We find that flies preferentially lay their eggs on media containing atropine - an entomotoxic alkaloid - in the presence of parasitoids. We further show that flies developing on atropine more efficiently resist parasitization by parasitoids. Finally, we find that developing in hosts reared on atropine strongly impacts the life-history traits of parasitoids. This protective behavior is reported for the first time in a pest and invasive species, and suggests that animal medication may be an important driver of population dynamics during invasions.
Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host ...populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.
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•Thousands of gut bacterial genomes from worldwide human populations were sequenced•HGT occurs at high frequency in the gut microbiome of individual persons•HGT occurs more frequently in the microbiome of industrialized and urban populations•Transferred gene functions in the microbiome reflect the lifestyle of the host
A worldwide microbiome analysis from 15 populations along the industrialization gradient reveals that horizontal gene transfer occurs on short timescales and that microbiomes continuously acquire new functionality based on host lifestyle.
One of the main objectives of the APPLET project was to quantify the variability of concrete properties to allow for a probabilistic performance-based approach regarding the service lifetime ...prediction of concrete structures. The characterization of concrete variability was the subject of an experimental program which included a significant number of tests allowing the characterization of durability indicators or performance tests. Two construction sites were selected from which concrete specimens were periodically taken and tested by the different project partners. The obtained results (mechanical behavior, chloride migration, accelerated carbonation, gas permeability, desorption isotherms, porosity) are discussed and a statistical analysis was performed to characterize these results through appropriate probability density functions.
Laser diode stacks are interesting laser sources for active imaging illuminators. They allow the accumulation of large amounts of energy in multi-pulse mode, which is best suited for long-range image ...recording. Even when the laser diode stacks are equipped with fast-axis collimation (FAC) and slow-axis collimation (SAC) micro-lenses, their beam parameter products BPP are not compatible with direct use in highly efficient and compact illuminators. This is particularly true when narrow divergences are required such as for long-range applications. A solution to overcome these difficulties is to enhance the poor slow-axis BPP by virtually restacking the laser diode stack. We present a beam shaping and homogenization method that is low-cost and efficient and has low alignment sensitivity. After conducting simulations, we have realized and characterized the illuminator. A compact long-range laser illuminator has been set up with a divergence of 3.5×2.6mrad and a global efficiency of 81%. Here, a projection lens with a clear aperture of 62mm and a focal length of 571mm was used.
•The presented laser diode illuminator allows narrow beam divergence in a compact size.•A low cost, efficient and low alignment sensitivity beam shaping method is described.•The illumination beam profile is homogeneous and matched to the detector geometry.•A fully complete study is proposed including theory, simulation and experimentation.
Acute kidney injury (AKI) is a major complication in patients with liver disease. Although hepatorenal syndrome is frequently involved, bile cast nephropathy, characterized by tubular bile cast ...formation, has been scarcely described in the setting of severe liver failure. Few renal histology studies are available in these patients. We describe a case of bile cast nephropathy in a patient with obstructive cholestasis caused by stones in the common bile duct. The kidney biopsy confirmed this diagnosis, with several green casts in tubular lumens, tubular injury, and bilirubin composition of the tubular casts with Hall stain. The patient had no confounding cause of kidney failure, and complete kidney recovery followed removal of the bile duct obstruction. This case shows that severe cholestasis is sufficient to cause AKI, and that AKI can be reversible after treatment of the biliary obstruction.
Abstract This study assessed the relationship between altered cardiac function and the development interstitial pulmonary edema in SCUBA divers. Fifteen healthy males performed a 30-min SCUBA dive in ...open sea. They were instructed to fin for 30 min and were wearing wet suits. Before and immediately after immersion, cardiac indices and extravascular lung water were measured using echocardiography and lung ultrasound respectively. The mean ultrasound lung comet score rose from 0 to 4.6 ± 3.4. The diameter of the inferior caval vein increased by 47 ± 5.2%, systolic pulmonary artery pressure increased by 105 ± 8.6%, left atrial volume increased by 18.0 ± 3.3% and left ventricle end-diastolic volume increased by 10 ± 2.4% suggesting both right and left ventricular filling pressures were elevated. Doppler studies showed an increased mitral E peak (+2.5 ± 0.3%) and E/A ratio (+22.5 ± 3.4%) with a decreased mitral A peak (-16.4 ± 2.7%), E peak deceleration time (-14.5 ± 2.4%) consistent with rapid early left ventricular filling but without a change in left ventricular stroke volume. There was an increase in right/left ventricle diameter ratio (+33.6 ± 4.8%) suggesting a relative increase in right sided heart output compared to the left. Furthermore, the lung comet score correlated significantly with inferior caval vein diameter, systolic pulmonary artery pressure, right/left ventricle diameter ratio and E-wave deceleration time. In conclusion, the altered right/left heart stroke volume balance could play an essential role in the development of immersion pulmonary edema. Our findings have important implications for the pathogenesis of cardiogenic pulmonary edema.
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