Biology subjects

Jeff Gore

Publications and source records attributed to Jeff Gore.

3 recordsLinked to original sources

bioRxiv2016

Community structure follows simple assembly rules in microbial microcosms

IntroductionMicrobes typically form diverse communities of interacting species, whose activities have tremendous impact on the plants, animals, and humans they associate with1-3, as well as on the biogeochemistry of the entire planet4. The ability to predict the structure of these complex communities is crucial to understanding, managing, and utilizing them5. Here, we propose a simple, qualitative assembly rule that predicts community structure from the outcomes of competitions between small sets of species, and experimentally assess its predictive power using synthetic microbial communities. The rule's accuracy was evaluated by competing combinations of up to eight soil bacterial species, and comparing the experimentally observed outcomes to the predicted ones. Nearly all competitions resulted in a unique, stable community, whose composition was independent of the initial species fractions. Survival in three-species competitions was predicted by the pairwise outcomes with an accuracy of ~90%. Obtaining a similar level of accuracy in competitions between sets of seven or all eight species required incorporating additional information regarding the outcomes of the three-species competitions. Our results demonstrate experimentally the ability of a simple bottom-up approach to predict community structure. Such an approach is key for anticipating the response of communities to changing environments, designing interventions to steer existing communities to more desirable states, and, ultimately, rationally designing communities de novo6,7.

Ecology↗

bioRxiv2016

Stochastic Assembly Produces Heterogeneous Communities in the C. elegans Intestine

Author SummaryHost-associated bacterial communities vary extensively between individuals, but it can be very difficult to determine the sources of this variation. In this manuscript, we demonstrate experimentally how randomness in colonization can result in large differences in the composition of host-associated bacterial communities, using the nematode worm C. elegans as a tractable host model. Here, the amount of variation between individual communities is a function of two rates relevant to how bacteria colonize the host intestine, the colonization rate and the birth rate. We can therefore control the degree of variation between communities by controlling the colonization rate, using the amount of bacteria presented to the worms to control the rate at which migrants enter the intestine. When worms are fed with two neutrally-competing fluorescently labeled bacterial strains at low colonization rates, we are able to produce noise-induced bistability in this system, where each community is dominated by bacteria of only one color. These results demonstrate the potential importance of noise as a driver of variation between communities and highlight the utility of the simple model organism C. elegans for studying questions relevant to host-associated microbial communities.\n\nAbstractHost-associated bacterial communities vary extensively between individuals, but it can be very difficult to determine the sources of this heterogeneity. Here we demonstrate that stochastic bacterial community assembly in the C. elegans intestine is sufficient to produce strong inter-worm heterogeneity in community composition. When worms are fed with two neutrally-competing fluorescently labeled bacterial strains, we observe stochastically-driven bimodality in community composition, where approximately half of the worms are dominated by each bacterial strain. A simple model incorporating stochastic colonization suggests that heterogeneity between worms is driven by the low rate at which bacteria successfully establish new intestinal colonies. We can increase this rate experimentally by feeding worms at high bacterial density; in these conditions the bimodality disappears. These results demonstrate that demographic noise is a potentially important driver of diversity in bacterial community formation and suggest a role for C. elegans as a model system for ecology of host-associated communities.

Microbiology↗

bioRxiv2014

Phenotypic heterogeneity implements a game theoretic mixed strategy in a clonal microbial population

Genetically identical cells in microbial populations often exhibit a remarkable degree of phenotypic heterogeneity even in homogenous environments. While such heterogeneity is often thought to be a bet-hedging strategy against unpredictable environments, evolutionary game theory also predicts phenotypic heterogeneity as a stable response to evolutionary \"hawk-dove\" games, in which rare strategies are favored over common ones. Here we provide experimental evidence for this game theoretic explanation in the context of the well-studied yeast GAL network. In an environment containing the two sugars glucose and galactose, the yeast GAL network displays stochastic bimodal activation. We show that genetic mutants playing the \"pure\" strategies of GAL-ON or GAL-OFF can each invade the opposite strategy when rare, indicating a hawk-dove game between the two. Consistent with the Nash equilibrium of an evolutionary game, the stable mix of pure strategists does not necessarily maximize the growth of the overall population. We also find that the wild type GAL network can invade populations of both pure strategists while remaining uninvasible by either. Taken together, our results provide experimental evidence that evolutionary hawk-dove games between identical cells can explain the phenotypic heterogeneity found in clonal microbial populations.

Systems Biology↗