MCSPACE: inferring microbiome spatiotemporal dynamics from high-throughput co-localization data.

Recent advances in high-throughput approaches for estimating co-localization of microbes, such as SAMPL-seq, allow characterization of the biogeography of the gut microbiome longitudinally and at unprecedented scale. However, these high-dimensional data are complex and have unique noise properties. To address these challenges, we developed MCSPACE, a probabilistic AI method that infers from microbiome co-localization data spatially coherent assemblages of taxa, their dynamics over time, and their responses to perturbations.

On the possibility of engineering social evolution in microfluidic environments.

Many species of microbes cooperate by producing public goods from which they collectively benefit. However, these populations are under the risk of being taken over by cheating mutants that do not contribute to the pool of public goods. Here we present theoretical findings that address how the social evolution of microbes can be manipulated by external perturbations to inhibit or promote the fixation of cheaters.

Tissue Failure Propagation as Mediated by Circulatory Flow.

Aging is driven by subcellular processes that are relatively well understood. However, the qualitative mechanisms and quantitative dynamics of how these micro-level failures cascade to a macro-level catastrophe in a tissue or organs remain largely unexplored. Here, we experimentally and theoretically study how cell failure propagates in an engineered tissue in the presence of advective flow.

Evolution of chemotactic hitchhiking.

Bacteria typically reside in heterogeneous environments with various chemogradients where motile cells can gain an advantage over nonmotile cells. Since motility is energetically costly, cells must optimize their swimming speed and behaviour to maximize their fitness. Here, we investigate how cheating strategies might evolve where slow or nonmotile microbes exploit faster ones by sticking together and hitching a ride.

Evolution of specialized microbial cooperation in dynamic fluids.

Here, we study the evolution of specialization using realistic computer simulations of bacteria that secrete two public goods in a dynamic fluid. Through this first-principles approach, we find physical factors such as diffusion, flow patterns and decay rates are as influential as fitness economics in governing the evolution of community structure, to the extent that when mechanical factors are taken into account, (a) generalist communities can resist becoming specialists despite the invasion fitness of specialization; (b) generalist and specialists can both resist cheaters despite the invasion fitness of free-riding; and (c) multiple community structures can coexist despite the opposing force of competitive exclusion. Our results emphasize the role of spatial assortment and physical forces on niche partitioning and the evolution of diverse community structures.

Shearing in flow environment promotes evolution of social behavior in microbial populations.

How producers of public goods persist in microbial communities is a major question in evolutionary biology. Cooperation is evolutionarily unstable, since cheating strains can reproduce quicker and take over. Spatial structure has been shown to be a robust mechanism for the evolution of cooperation.