Bulletin of the American Physical Society
APS March Meeting 2017
Volume 62, Number 4
Monday–Friday, March 13–17, 2017; New Orleans, Louisiana
Session H49: Physical Perspectives on the Microbiota of Humans and other AnimalsInvited
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Sponsoring Units: DBIO Room: 396 |
Tuesday, March 14, 2017 2:30PM - 3:06PM |
H49.00001: Probing Microbial Interactions with the Mucus Barrier Invited Speaker: Katharina Ribbeck Mucus is a biological gel that lines all wet epithelia in the body, including the mouth, lungs, and digestive tract, and has evolved to protect us from pathogenic invasion. Microbial pathogenesis in these mucosal systems, however, is often studied in mucus- free environments, which lack the geometric constraints and microbial interactions that are found in natural, three-dimensional mucus gels. To bridge this gap, my laboratory has developed a model test systems based on purified mucin polymers, the major gel-forming constituents of the mucus barrier. We use this model to understand how the mucus barrier influences bacterial virulence, and moreover, to elucidate strategies used by microbes to overcome the normal protective mucus barrier. I will discuss data showing that the mucus environment has a significant impact on the physiological behavior of microbes, including surface attachment, quorum sensing, the expression of virulence genes, and biofilm formation. The picture is emerging that mucins are key host players in the regulation of microbial virulence and are critical to consider when studying mucosal pathogenesis. Our work may also be the basis for the design of synthetic gels that mimic the basic selective properties and virulence-neutralizing capacity of mucus gels. [Preview Abstract] |
Tuesday, March 14, 2017 3:06PM - 3:42PM |
H49.00002: Statistical Physics Approaches to Microbial Ecology Invited Speaker: Pankaj Mehta The unprecedented ability to quantitatively measure and probe complex microbial communities has renewed interest in identifying the fundamental ecological principles governing community ecology in microbial ecosystems. Here, we present work from our group and others showing how ideas from statistical physics can help us uncover these ecological principles. Two major lessons emerge from this work. First, large, ecosystems with many species often display new, emergent ecological behaviors that are absent in small ecosystems with just a few species. To paraphrase Nobel laureate Phil Anderson, "More is Different", especially in community ecology. Second, the lack of trophic layer separation in microbial ecology fundamentally distinguishes microbial ecology from classical paradigms of community ecology and leads to qualitative different rules for community assembly in microbes. I illustrate these ideas using both theoretical modeling and novel new experiments on large microbial ecosystems performed by our collaborators (Joshua Goldford and Alvaro Sanchez). [Preview Abstract] |
Tuesday, March 14, 2017 3:42PM - 4:18PM |
H49.00003: Dynamic processes of the microbiota - from metagenomics to biofilms Invited Speaker: Ned Wingreen The extent, origin, and impact of microbial diversity is a central question in biology. We expect that physical processes contribute to this diversity, but we are only beginning to explore the nature of these interactions. I will briefly discuss two approaches to this question, one based on metagenomics the other on observation of bacterial biofilms. First, I will address the challenge of identifying the constituents of microbial systems by presenting a new approach to analyzing community sequencing data that identifies microbial subpopulations while avoiding problematic clustering-based methods. Using data from a time-series study of human tongue microbiota, we were able to resolve within the standard definition of a ``species'' up to 20 ecologically distinct subpopulations with tag sequences differing by as little as one nucleotide (99.2{\%} similarity). This fine resolution allowed us decouple sequence similarity from dynamical similarity, and to resolve dynamics on multiple time scales, including the slow appearance and disappearance of strains over months. Second, I will present recent results on the growth and competition of bacteria within biofilms. We imaged the growth of\textit{ living} biofilms of \textit{Vibrio cholerae }from single founder cells to ten thousand cells at single cell spatial resolution and with temporal resolution of one cell cycle. We discovered a transition from a branched 2D colony to a dense 3D cluster, in which cells at the biofilm center exhibit collective vertical alignment and local nematic packing. Our results suggest that biofilm cells exploit mechanics to simultaneously achieve strong surface adhesion, access to 3D space, resistance to invasion, and dominance over surface territory. [Preview Abstract] |
Tuesday, March 14, 2017 4:18PM - 4:54PM |
H49.00004: Spatiotemporal microbiota dynamics from quantitative in vitro and in silico models of the gut Invited Speaker: Terence Hwa The human gut harbors a dynamic microbial community whose composition bears great importance for the health of the host. Here, we investigate how colonic physiology impacts bacterial growth~behaviors, which ultimately dictate the gut microbiota composition. Combining measurements of bacterial growth physiology with analysis of published data on human physiology into a quantitative modeling framework, we show how hydrodynamic forces in the colon, in concert with other physiological factors, determine the abundances of the major bacterial phyla in the gut. Our model quantitatively explains the observed variation of microbiota composition among healthy adults, and predicts colonic water absorption (manifested as stool consistency) and nutrient intake to be two key factors determining this composition. The model further reveals that both factors, which have been identified in recent correlative studies, exert their effects through the same mechanism: changes in colonic pH that differentially affect the growth of different bacteria. Our findings show that a predictive and mechanistic understanding of microbial ecology in the human gut is possible, and offer the hope for the rational design of intervention strategies to actively control the microbiota. [Preview Abstract] |
Tuesday, March 14, 2017 4:54PM - 5:30PM |
H49.00005: Community assembly of the worm gut microbiome Invited Speaker: Jeff Gore It has become increasingly clear that human health is strongly influenced by the bacteria that live within the gut, known collectively as the gut microbiome. This complex community varies tremendously between individuals, but understanding the sources that lead to this heterogeneity is challenging. To address this challenge, we are using a bottom-up approach to develop a predictive understanding of how the microbiome assembles and functions within a simple and experimentally tractable gut, the gut of the worm \textit{C. elegans}. We have found that stochastic community assembly in the \textit{C. elegans }intestine \quad is sufficient to \quad 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. We have also characterized all pairwise interspecies competitions among a set of eleven bacterial species, illuminating the rules governing interspecies community assembly. These results demonstrate the potential importance of stochastic processes in bacterial community formation and suggest a role for \textit{C. elegans} as a model system for ecology of host-associated communities. [Preview Abstract] |
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