Biology subjects

Gore, J.

Publications and source records attributed to Gore, J..

46 records · Page 3Linked to original sources

bioRxiv2019

Interspecies bacterial competition determines community assembly in the C. elegans intestine

From insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. However, the complexity of these gut microbiomes and their hosts often constrains our ability to understand how these bacterial communities assemble and function. In order to elucidate basic principles of community assembly in a host intestine, we study the assembly of the microbiome of Caenorhabditis elegans with a bottom-up approach. We colonize the gut of the worm C. elegans with 11 bacterial species individually, in all possible pairs, and in selected trios, and we find an organized mixture of coexistence and competitive exclusion that indicates a hierarchical structure in the bacterial interactions. The capacity of a bacterial species fed in monoculture to colonize the C. elegans intestine correlates with its average fraction in co-culture experiments, yet fails to predict its abundance in many two- and three-species microbiomes. Hence, the bacterial fractional abundances in co-culture experiments--pairwise outcomes--are influenced by interspecies interactions. These pairwise outcomes accurately predict the trio outcomes in the worm intestine, further highlighting the importance of pairwise interactions in determining community composition. We also find that the C. elegans gut environment influences the outcome of co-culture experiments, and demonstrate that the low intestinal pH is one of the causes. These results highlight that a bottom-up approach to microbiome community assembly may provide valuable insight into the structure and composition of complex microbial communities.

microbiology↗

bioRxiv2018

Attraction to pheromones in Caenorhabditis elegans can be reversed through associative learning

Despite the ubiquity and importance of chemical signaling, we have only limited insight about the role of learning in the response to pheromones. Here, we demonstrate that responses to pheromones can be reprogrammed through associative learning. In particular, we show that attraction to ascaroside pheromones in the model nematode Caenorhabditis elegans can be reversed by training the animals to associate either a pheromone blend or single synthetic ascarosides with the lack of food. This behavioral plasticity alters worm preference for pheromones following consumption of a food patch, possibly improving foraging in natural environments. By bridging the gap between the current knowledge on the chemical language and the learning abilities of C. elegans, we provide insight on the possible links between learning and chemical signaling in animals.

ecology↗

bioRxiv2018

Mortality causes universal changes in microbial community composition

All organisms are sensitive to the abiotic environment, and a deteriorating environment can lead to extinction. However, survival in a multispecies community also depends upon inter-species interactions, and some species may even be favored by a harsh environment that impairs competitors. A deteriorating environment can thus cause surprising transitions in community composition. Here, we combine theory and laboratory microcosms to develop a predictive understanding of how simple multispecies communities change under added mortality, a parameter that represents environmental harshness. In order to explain changes in a multispecies microbial system across a mortality gradient, we examine its members pairwise interactions. We find that increasing mortality favors the faster grower, confirming a prediction of simple models. Furthermore, if the slower grower outcompetes the faster grower in environments with low or no added mortality, the competitive outcome can reverse as mortality increases. We find that this tradeoff between growth rate and competitive ability is indeed prevalent in our system, allowing for striking pairwise outcome changes that propagate up to multispecies communities. These results argue that a bottom-up approach can provide insight into how communities will change under stress.

ecology↗

bioRxiv2018

Disentangling bacterial invasiveness from lethality in an experimental host-pathogen system

Quantifying virulence remains a central problem in human health, pest control, disease ecology, and evolutionary biology. Bacterial virulence is typically quantified by the LT50 (i.e. the time taken to kill 50% of infected hosts), however, such an indicator cannot account for the full complexity of the infection process, such as distinguishing between the pathogens ability to colonize vs. kill the hosts. Indeed, the pathogen needs to breach the primary defenses in order to colonize, find a suitable environment to replicate, and finally express the virulence factors that cause disease. Here, we show that two virulence attributes, namely pathogen lethality and invasiveness, can be disentangled from the survival curves of a laboratory population of Caenorhabditis elegans nematodes exposed to three bacterial pathogens: Pseudomonas aeruginosa, Serratia marcescens and Salmonella enterica. We first show that the host population eventually experiences a constant mortality rate, which quantifies the lethality of the pathogen. We then show that the time necessary to reach this constant-mortality rate regime depends on the pathogen growth rate and colonization rate, and thus determines the pathogen invasiveness. Our framework reveals that Serratia marcescens is particularly good at the initial colonization of the host, whereas Salmonella enterica is a poor colonizer yet just as lethal once established. Pseudomonas aeruginosa, on the other hand, is both a good colonizer and highly lethal after becoming established. The ability to quantitatively characterize the ability of different pathogens to perform each of these steps has implications for treatment and prevention of disease and for the evolution and ecology of pathogens.

ecology↗

bioRxiv2017

Migration alters oscillatory dynamics and promotes survival in connected bacterial populations

Migration influences population dynamics on networks, thereby playing a vital role in scenarios ranging from species extinction to epidemic propagation. While low migration rates prevent local populations from becoming extinct, high migration rates enhance the risk of global extinction by synchronizing the dynamics of connected populations. Here, we investigate this trade-off using two mutualistic strains of E. coli that exhibit population oscillations when co-cultured. In experiments, as well as in simulations using a mechanistic model, we observe that high migration rates lead to in-phase synchronization whereas intermediate migration rates perturb the oscillations and change their period. Further, our simulations predict, and experiments show, that connected populations subjected to more challenging antibiotic concentrations have the highest probability of survival at intermediate migration rates. Finally, we identify altered population dynamics, rather than recolonization, as the primary cause of extended survival.

ecology↗

bioRxiv2017

Asymmetric migration decreases stability but increases resilience in a heterogeneous metacommunity

Many natural communities are spatially distributed, forming a network of subcommunities linked by migration. Migration patterns are often asymmetric and heterogeneous, with important consequences on the ecology and evolution of the species. Here we investigated experimentally how asymmetric migration and heterogeneous structure affect a simple metacommunity of budding yeast, formed by one strain that produces a public good and a non-producer strain that benefits from it. We find that asymmetric migration increases the fraction of producers in all subpopulations of the metacommunity. Furthermore, asymmetric migration decreases the metacommunitys tolerance to challenging environments, but increases its resilience to transient perturbations. This apparent paradox occurs because tolerance to a constant challenge depends on the weakest subpopulations of the network, while resilience to a transient perturbation depends on the strongest ones.\n\nOne Sentence SummaryAsymmetric migration decreases the stability of experimental yeast metacommunities but increases their resilience to transient shocks.

ecology↗

bioRxiv2017

Co-occurring soil bacteria exhibit a robust competitive hierarchy and lack of non-transitive interactions

Microbial communities are typically incredibly diverse, and this diversity is thought to play a key role in community function. However, explaining how this diversity can be maintained is a major challenge in ecology. Temporal fluctuations and spatial structure in the environment likely play a key role, but it has also been suggested that the structure of interactions within the community may act as a stabilizing force for species diversity. In particular, if competitive interactions are non-transitive as in the classic rock-paper-scissors game, they can contribute to the maintenance of species diversity; on the other hand, if they are predominantly hierarchical, any observed diversity must be maintained via other mechanisms. Here, we investigate the network of pairwise competitive interactions in a model community consisting of 20 strains of naturally co-occurring soil bacteria. We find that the interaction network is strongly hierarchical and lacks significant non-transitive motifs, a result that is robust across multiple environments. Moreover, in agreement with recently proposed community assembly rules, the full 20-strain competition resulted in extinction of all but three of the most highly competitive strains, indicating that higher order interactions do not play a major role in structuring this community. The lack of non-transitivity and higher order interactions in vitro indicates that other factors, such as temporal or spatial heterogeneity, must be at play in enabling these strains to coexist in nature.

ecology↗

bioRxiv2017

Ecological suicide in microbes

The growth and survival of organisms often depend on interactions between them. In many cases, these interactions are positive and caused by a cooperative modification of the environment, such as the cooperative breakdown of complex nutrients in microbes [1]-[3] or the construction of elaborate architectures in social insects [4]. However, organisms can similarly display negative interactions by changing the environment in ways that are detrimental for them, eg by resource depletion or the production of toxic byproducts [5]. Here we find an extreme type of negative interactions, in which bacteria modify the environmental pH to such a degree that it leads to a rapid extinction of the whole population, a phenomenon we call ecological suicide. Modification of the pH is more pronounced at higher population densities, and thus ecological suicide is more likely with increasing bacterial density. Correspondingly, promoting bacterial growth can drive populations extinct whereas inhibiting bacterial growth by the addition of harmful substances - like antibiotics - can rescue them. Moreover, ecological suicide can cause oscillatory dynamics, even in single-species populations. We find ecological suicide in a wide variety of microbes, suggesting that it could play a significant role in microbial ecology and evolution.

systems biology↗

bioRxiv2017

Modifying And Reacting To The Environmental pH Drives Bacterial Interactions

Microbes usually exist in communities consisting of myriad different but interacting species. These interactions are typically mediated through environmental modifications; microbes change the environment by taking up resources and excreting metabolites, which affects the growth of both themselves and also other microbes. A very common environmental modification is a change of the environmental pH. Here we show that changing and reacting to the pH leads to a feedback loop that can determine the fate of bacterial populations. We find experimentally that these pH changes can decide the fate of bacterial populations; they can either facilitate or inhibit growth, and in extreme cases will cause extinction of the bacterial population. Moreover, modifying the pH can determine the interactions between different species. Understanding how single species change the pH and react to it allowed us to estimate their pairwise interaction outcomes. Those interactions lead to a set of generic interaction motifs--bistability, succession, murder suicide, and mutualism--that may be independent of which environmental parameter is modified and thus reoccur in different microbial systems.

microbiology↗

bioRxiv2017

Random Sequences Rapidly Evolve Into De Novo Promoters

How do new promoters evolve? To follow evolution of de novo promoters, we put various random sequences upstream to the lac operon in Escherichia coli and evolved the cells in the presence of lactose. We found that a typical random sequence of ~100 bases requires only one mutation in order to enable growth on lactose by increasing resemblance to the canonical promoter motifs. We further found that ~10% of random sequences could serve as active promoters even without any period of evolutionary adaptation. Such a short mutational distance from a random sequence to an active promoter may improve evolvability yet may also lead to undesirable accidental expression. We found that across the E. coli genome accidental expression is minimized by avoiding codon combinations that resemble promoter motifs. Our results suggest that the promoter recognition machinery has been tuned to allow high accessibility to new promoters, and similar findings might also be observed in higher organisms or in other motif recognition machineries, like transcription factor binding sites or protein-protein interactions.

molecular biology↗