Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable ...avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. This protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.
A fitness landscape is a map between the genotype and its reproductive success in a given environment. The topography of fitness landscapes largely governs adaptive dynamics, constraining ...evolutionary trajectories and the predictability of evolution. Theory suggests that this topography can be deformed by mutations that produce substantial changes to the environment. Despite its importance, the deformability of fitness landscapes has not been systematically studied beyond abstract models, and little is known about its reach and consequences in empirical systems. Here we have systematically characterized the deformability of the genome-wide metabolic fitness landscape of the bacterium Escherichia coli. Deformability is quantified by the noncommutativity of epistatic interactions, which we experimentally demonstrate in mutant strains on the path to an evolutionary innovation. Our analysis shows that the deformation of fitness landscapes by metabolic mutations rarely affects evolutionary trajectories in the short range. However, mutations with large environmental effects produce long-range landscape deformations in distant regions of the genotype space that affect the fitness of later descendants. Our results therefore suggest that, even in situations in which mutations have strong environmental effects, fitness landscapes may retain their power to forecast evolution over small mutational distances despite the potential attenuation of that power over longer evolutionary trajectories. Our methods and results provide an avenue for integrating adaptive and eco-evolutionary dynamics with complex genetics and genomics.
A major open question in microbial community ecology is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by ...this challenge, we investigate whether communities assembled in pairs of nutrients can be predicted from those assembled in every single nutrient alone. We find that although the null, naturally additive model generally predicts well the family-level community composition, there exist systematic deviations from the additive predictions that reflect generic patterns of nutrient dominance at the family level. Pairs of more-similar nutrients (e.g. two sugars) are on average more additive than pairs of more dissimilar nutrients (one sugar-one organic acid). Furthermore, sugar-acid communities are generally more similar to the sugar than the acid community, which may be explained by family-level asymmetries in nutrient benefits. Overall, our results suggest that regularities in how nutrients interact may help predict community responses to dietary changes.
The popularity of rideshare electric scooters is due to their availability, accessibility, and low cost. The recent increase in electric scooter use has raised concerns regarding the safety of both ...riders and pedestrians. Previous studies characterize the incidence and pattern of injury for riders, but there is a lack of literature concerning electric scooters' impact on pedestrians. Pedestrians injured by electric scooters face potential financial burdens from hospitalization costs, medical interventions, taking time off from work, and rehabilitation therapies. Based on prior studies, pedestrians who are most prone to injuries sustained by pedestrian transportation include individuals with vision and/or hearing impairment, young children, the elderly, and people distracted by mobile devices. We present a case involving a sixty-year-old female pedestrian who presented to the emergency department with an acute lumbar compression fracture after a collision with an electric scooter. This study highlights the safety risks and incidence of injuries for pedestrians associated with electric scooters, which can help shape public policy to ensure the safety of both riders and pedestrians.
•Well-documented adverse-pressure-gradient TBLs database.•Characterization of approximately-constant and non-constant βhistories.•Two large-scale phenomena connected with the Re and βeffect are ...identified.•No complete self-similarity is observed within the approximately-constant βregion.
A new experimental database of adverse-pressure-gradient (APG) turbulent boundary layers (TBLs) obtained through hot-wire anemometry and oil-film interferometry covering a momentum–loss Reynolds number 450<Reθ<23450 and Clauser pressure-gradient-parameter range up to β≈2.4 is presented. Both increasing and approximately constant β distributions with the same upstream history are characterised. Turbulence statistics are compared among the different pressure-gradient distributions with additional numerical and experimental zero-pressure-gradient (ZPG) TBL data. Cases at approximately constant β, which can be considered as canonical representations of the boundary layer under a certain pressure-gradient magnitude, exhibit skin-friction and shape-factor curves consistent with the ones proposed by Vinuesa et al. (2017). These curves show a similar scaling behaviour as those proposed by Nagib et al. (2007) for ZPG TBLs. The pre-multiplied power-spectral density is employed to study the differences in the large-scale energy content throughout the boundary layer. Two different large-scale phenomena are identified, the first one related to the pressure gradient and the second one (also present in high-Re ZPG TBLs) due to the Reynolds number. Recently proposed scaling laws by Kitsios et al. (2016) and Maciel et al. (2018) are tested over a wider Reynolds-number range and for different β cases. The mean velocity and streamwise velocity fluctuation profiles are found to be dependent on the upstream development. The mean velocity profile is found to be self-similar only in the outer region, in agreement with classical theory. The mean and higher-order statistics of the new APG TBL database are made available under www.flow.kth.se.
The taxonomic composition of microbial communities can vary substantially across habitats and within the same habitat over time. Efforts to build quantitative and predictive models of microbial ...population dynamics are underway, but fundamental questions remain. How different are population dynamics in different environments? Do communities that share the same taxa also exhibit identical dynamics? In vitro communities can help establish baseline expectations that are critical towards resolving these questions in natural communities. Here, we applied a recently developed tool, Dissimilarity-Overlap Analysis (DOA), to a set of experimental in vitro communities that differed in nutrient composition. The Dissimilarity and Overlap of these communities are negatively correlated in replicate habitats, as one would expect if microbial population dynamics were on average strongly convergent (or "universal") across these replicate habitats. However, the existence of such a negative correlation does not necessarily imply that population dynamics are always universal in all communities. Even in replicate, identical habitats, two different communities may contain the same set of taxa at different abundances in equilibrium. The formation of alternative states in community assembly is strongly associated with the presence of specific taxa in the communities. Our results benchmark DOA, providing support for some of its core assumptions, and suggest that communities sharing the same taxa and external abiotic factors generally (but not necessarily) have a negative correlation between Dissimilarity and Overlap.
Understanding the ecological and evolutionary processes determining the outcome of biological invasions has been the subject of decades of research with most work focusing on macro-organisms. In the ...context of microbes, invasions remain poorly understood despite being increasingly recognized as important. To shed light on the factors affecting the success of microbial community invasions, we perform simulations using an individual-based nearly neutral model that combines ecological and evolutionary processes. Our simulations qualitatively recreate many empirical patterns and lead to a description of five general rules of invasion: (1) larger communities evolve better invaders and better defenders; (2) where invader and resident fitness difference is large, invasion success is essentially deterministic; (3) propagule pressure contributes to invasion success, if and only if, invaders and residents are competitively similar; (4) increasing the diversity of invaders has a similar effect to increasing the number of invaders; and (5) more diverse communities more successfully resist invasion.
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•Cellulose, hemicelluloses and lignin were separated in a single reaction.•Water/1-butanol/catalyst media were employed for vine shoot fractionation.•Optimal conditions for lignin and ...cellulose recovery were identified.•The recoverd lignin showed 85% purity, and the solid contained 75% cellulose.•Furans were produced from the aqueous phase obtained in fractionation.
Vine shoots were subjected to a mild aqueous extraction (to remove water-soluble extractives), and the extracted solids were reacted in catalyzed media (containing water and 1-butanol) to achieve the one-stage solubilization of lignin and hemicelluloses, yielding a cellulose-rich solid. Operating in a microwave-heated reactor under optimized conditions (190 °C in media containing 2% of catalyst and 52% 1-butanol), 67.8% lignin was dissolved, and solids containing 75% cellulose were obtained. Lignin was recovered from the reaction medium and characterized, whereas the hemicellulose-derived products present in the aqueous phase (obtained under conditions leading to maximum concentrations of 17.7 g pentoses/L) were converted into furfural at 64.6% molar yield by acidic processing in the presence of recycled 1-butanol.
Predictively linking taxonomic composition and quantitative ecosystem functions is a major aspiration in microbial ecology, which must be resolved if we wish to engineer microbial consortia. Here, we ...have addressed this open question for an ecological function of major biotechnological relevance: alcoholic fermentation in wine yeast communities. By exhaustively phenotyping an extensive collection of naturally occurring wine yeast strains, we find that most ecologically and industrially relevant traits exhibit phylogenetic signal, allowing functional traits in wine yeast communities to be predicted from taxonomy. Furthermore, we demonstrate that the quantitative contributions of individual wine yeast strains to the function of complex communities followed simple quantitative rules. These regularities can be integrated to quantitatively predict the function of newly assembled consortia. Besides addressing theoretical questions in functional ecology, our results and methodologies can provide a blueprint for rationally managing microbial processes of biotechnological relevance.
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