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Meeting: Pankaj Mehta
Dept. of Physics, Boston University
Toward a statistical mechanics of microbiomes

A major unresolved question in microbiome research is whether the complex ecological patterns observed in surveys of natural communities can be explained and predicted by fundamental, quantitative principles. Bridging theory and experiment is hampered by the multiplicity of ecological processes that simultaneously affect community assembly and a lack of theoretical tools for modeling diverse ecosystems. In the first part of the talk, I will present a simple ecological model of microbial communities that reproduces large-scale ecological patterns observed across multiple experimental settings including compositional gradients, clustering by environment, diversity/harshness correlations, and nestedness. Surprisingly, our model works despite having a “random metabolisms” and “random consumer preferences”. This raises the natural of question of why random ecosystems can describe real-world experimental data. In the second, more theoretical part of the talk, I will answer this question by showing that when a community becomes diverse enough, it will always self-organize into a stable state whose properties are well captured by a “typical random ecosystems”. If time permits, I will also highlight surprising connections between ecological dynamics, constrained optimization, and kernel-based machine learning methods such as Support Vector Machines.

Josh Goldford
Physics of Living Systems, Massachusetts Institute of Technology

Pankaj Mehta
Dept. of Physics, Boston University
Primer: Introduction to ecological models for microbiomes

This tutorial will provide a brief introduction to key concepts and mathematical models in community ecology, with an eye towards understanding microbiomes. We will introduce Consumer Resource Models (CRMs) and generalized Lotka-Volterra equations, emphasizing overarching ecological concepts, graphical methods, and connections to optimization. The last part of the tutorial will focus on shortcomings of these classical models for understanding microbial systems, and in particular discuss how metabolism naturally couples species and their environments through ubiquitous cross-feeding necessitating modifications of classical ecological models.

Chapters:
00:00 Primer - Pankaj Mehta
28:25 Primer - Josh Golford
52:09 Meeting - Pankaj Mehta