Bulletin of the American Physical Society
APS March Meeting 2019
Volume 64, Number 2
Monday–Friday, March 4–8, 2019; Boston, Massachusetts
Session F63: Physics of Microbiomes and Microbial Communities IFocus
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Sponsoring Units: DBIO Chair: Yang-Yu Liu, Harvard University Room: BCEC 259A |
Tuesday, March 5, 2019 11:15AM - 11:51AM |
F63.00001: Observing the interplay between bacterial behaviors and the physical landscape inside the zebrafish gut Invited Speaker: Raghuveer Parthasarathy In any ecosystem, the structure of the landscape and the activities of its organisms influence one another. This is true in the vertebrate gut as well, where vast numbers of microbes cooperate, compete, and influence both normal and disease-related functions of their hosts. In gut ecosystems, however, we know little about spatial structure, bacterial behaviors, and physical forces. Most of our knowledge comes from sequencing-based studies lacking spatial or temporal information, severely limiting our ability to understand, let alone manipulate, the gut microbiome. To address this, my lab applies light sheet fluorescence microscopy to a model system that combines an in vivo environment with a high degree of experimental control: larval zebrafish with defined sets of bacterial species. I will describe this approach and experiments that have revealed how a species can manipulate intestinal mechanics to facilitate invasion; how differences in bacterial behaviors across species correlate with differences in spatial distributions; and how genetic switches and antibiotics can reveal the roles of individual behaviors such as motility in governing community outcomes. In all of these cases, the physical structure of the microbiome emerges as a major determinant of its population dynamics. |
Tuesday, March 5, 2019 11:51AM - 12:03PM |
F63.00002: Growth strategy of microbes on mixed carbon sources Xin Wang, Kang Xia, Xiaojing Yang, Chao Tang A classic problem in microbiology is that bacteria display two types of growth behavior when cultured on a mixture of two carbon sources: in certain mixtures the bacteria consume the two carbon sources sequentially (diauxie) and in other mixtures the bacteria consume both sources simultaneously (co-utilization). The search for the molecular mechanism of diauxie led to the discovery of the lac operon and gene regulation in general. However, questions remain as why microbes would bother to have different strategies of taking up nutrients and in the case of co-utilization what determines the partition and distribution of carbon sources in the cell. Here we show that diauxie versus co-utilization can be understood from the topological features of the metabolic network. A model of optimal allocation of protein resources quantitatively explains why and how the cell makes the choice when facing multiple carbon sources. When two carbon sources are being co-utilized, the model predicts the percentage of each carbon source in supplying the synthesis of every type of amino acid, which is quantitatively verified by experiments. Our work solves a long-standing puzzle and provides a quantitative framework for the carbon source utilization of microbes. |
Tuesday, March 5, 2019 12:03PM - 12:15PM |
F63.00003: A quorum sensing-controlled program of aggregation in V. cholerae Matthew Jemielita, Ned Wingreen, Bonnie Bassler Bacteria communicate and collectively regulate gene expression using the process called quorum sensing (QS). QS relies on population-wide responses to extracellular signal molecules called autoinducers. We demonstrate that, in Vibrio cholerae, QS activates a novel program of multicellularity, which we call aggregation. Aggregation is distinct from the canonical surface-biofilm formation program, which QS represses. Specifically, aggregation is induced by autoinducers, rapidly occurs in cell suspensions, and does not require cell-division, features distinct from those characteristic of V. cholerae biofilm formation. A genetic screen identifies components required for aggregation, revealing proteins involved in V. cholerae intestinal colonization, stress response, as well as a protein that distinguishes the current V. cholerae pandemic strain from earlier pandemic strains. We propose that aggregate formation is important for V. cholerae to transit between the marine niche and the human host. Further exploration of the aggregation process may yield insight into principles that allow bacteria to rapidly build multicellular communities and collectively defend against environmental insults or withstand starvation. |
Tuesday, March 5, 2019 12:15PM - 12:27PM |
F63.00004: Verticalization of bacterial biofilms Farzan Beroz, Jing Yan, Benedikt Sabass, Yigal Meir, Howard A Stone, Bonnie Bassler, Ned Wingreen Biofilms are communities of bacteria adhered to surfaces. Recently, biofilms of rod-shaped bacteria were observed at single-cell resolution and shown to develop from a disordered, two-dimensional layer of founder cells into a three-dimensional structure with a vertically-aligned core. In this talk, I will discuss how verticalization is driven by a series of localized mechanical instabilities on the cellular scale. For short cells, these instabilities are primarily triggered by cell division, whereas long cells are more likely to be peeled off the surface by nearby vertical cells, creating an "inverse domino effect". The interplay between cell growth and cell verticalization gives rise to an exotic mechanical state in which the effective surface pressure becomes constant throughout the growing core of the biofilm surface layer. This dynamical isobaricity determines the expansion speed of a biofilm cluster and thereby governs how cells access the third dimension. In particular, theory predicts that a longer average cell length yields more rapidly expanding, flatter biofilms. We experimentally show that such changes in biofilm development occur by exploiting chemicals that modulate cell length. |
Tuesday, March 5, 2019 12:27PM - 12:39PM |
F63.00005: Light dependent motility of microalgae induces pattern formation in confinement Alexandros Fragkopoulos, Johannes Frey, Flora-Maud Le Menn, Jeremy Vachier, Marco G. Mazza, Oliver Baeumchen A collection of self-propelled particles can undergo complex dynamics due to hydrodynamic and steric interactions. In highly concentrated suspensions, it is possible for such particles to form large-scale concentration patterns, where the active suspension separates into regions of high and low particle concentrations. Here we present that suspensions of Chlamydomonas reinhardtii cells, a unicellular soil-dwelling microalgae and a model organism of puller-type microswimmers, may form patterns of high and low cell density regions in confinement under specific light conditions. We find that there are significant deviations in the motility of the cells under different light intensities and cell densities, which regulate patern formation in such active suspensions. Finally, by performing active Brownian simulations of such active particles with the observed motility characteristics, we show that we can re-create the pattern observed in our experiments. |
Tuesday, March 5, 2019 12:39PM - 12:51PM |
F63.00006: The universal dynamics of the human microbiome Amir Bashan, Travis Gibson, Jonathan Friedman, Vincent Carey, Scott Weiss, Elizabeth Hohmann, Yang-Yu Liu In this talk I will address a simple but fundamental question: are the microbial ecosystems in different people governed by the same host-independent (i.e. “universal”) ecological dynamics? Answering this question determines the feasibility of general therapies and control strategies for the human microbiome. I will introduce our novel methodology that distinguishes between two scenarios: host-independent and host-specific underlying dynamics. This methodology has been applied to study different body sites across healthy subjects. We also analyzed the gut microbial dynamics of subjects with recurrent Clostridium difficile infection and the same set of subjects after fecal microbiota transplantation. The results can fundamentally improve our understanding of forces and processes shaping human microbial ecosystems, paving the way to design general microbiome-based therapies. |
Tuesday, March 5, 2019 12:51PM - 1:03PM |
F63.00007: Deciphering Functional Redundancy in the Human Microbiome Liang Tian, Xuwen Wang, Angkun Wu, Yuhang Fan, Jonathan Friedman, Amber Dahlin, Matthew Waldor, George Weinstock, Scott Weiss, Yang-Yu Liu Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved. The striking conservation of functional capacity implies an ecological property known as functional redundancy. Although this redundancy is thought to underlie the stability and resilience of the human microbiome, its origin is elusive. Here, we decipher the basis for functional redundancy in the human microbiome by analyzing its genomic content network --- a bipartite graph that links microbes to the genes in their genomes. We show that this network exhibits special topological features that favor high functional redundancy. Moreover, we find that the assemblage of microbes plays a more important role than their abundances in determining the high functional redundancy of the human microbiome. We propose a simple genome evolution model to explain the key topological features observed in the real genomic content network. These observations deepen our understanding of species-function relationships, a critical step for developing function-based diagnostics and therapeutics. |
Tuesday, March 5, 2019 1:03PM - 1:15PM |
F63.00008: A numerical model of Vibrio fischeri growth and intraspecific competition Yuexia Lin, Stephanie Nicole Smith, Alecia Septer, Christopher Rycroft, Eva Kanso E. scolopes squids are colonized with V. fischeri bacteria, and this symbiosis serves as a model system for studying host-microbe interactions. Wild-caught adult squids harbor multiple strains of V. fischeri that engage in intraspecific competition during initial host colonization. However, little is known about how competing strains interact at the single-cell level to influence their spatial structure as they coexist. When grown on agar surfaces, two competing strains form segregated spatial patterns that is dependent on their ability to kill one another. We developed an experimentally informed, multi-agent numerical model of cell growth, division, and death in 2D that can simulate intercellular interactions and environmental factors. In particular, the model accounts for intraspecific competition via mutual killing and differences in growth. This computational model is used to explore conditions that allow a diversity of strains to coexist, as well as investigate the spatiotemporal properties of this coexistence. We present results that demonstrate the method’s ability to capture the segregated patterns and their length scales, and explore parameter space that is hard to access in experiments. |
Tuesday, March 5, 2019 1:15PM - 1:27PM |
F63.00009: Machine learning the space-time phase diagram of bacterial swarm expansion Hannah Jeckel, Eric Jelli, Raimo Hartmann, Praveen Singh, Rachel Mok, Jan Frederik Totz, Lucia Vidakovic, Bruno Eckhardt, Jorn Dunkel, Knut Drescher Coordinated dynamics of individual components in active matter are an essential aspect of life. Establishing a comprehensive, causal connection between intercellular and macroscopic behaviors has remained a major challenge due to limitations in data acquisition and analysis techniques suitable for multi-scale dynamics. Here, we combine a high-throughput adaptive microscopy approach with machine learning, to identify key biological and physical mechanisms that determine distinct microscopic and macroscopic collective behavior phases which develop as Bacillus subtilis swarms expand over five orders of magnitude in space. Our experiments and particle-based simulations reveal that the microscopic swarming motility phases are dominated by physical cell-cell interactions. These results provide a unified understanding of bacterial multi-scale behavioral complexity in swarms. |
Tuesday, March 5, 2019 1:27PM - 1:39PM |
F63.00010: Switching and Torque Generation in Swarming Bacteria Katie Ford, Jyot Antani, Aravindh Nagarajan, Madeline Johnson, Pushkar Lele Escherichia coli swarm on semi-solid surfaces with the aid of flagella. It has been hypothesized that swarmer cells overcome the increased viscous drag near surfaces by developing higher flagellar thrust and by promoting surface wetness with the aid of a flagellar switch. The switch enables reversals between clockwise (CW) and counterclockwise (CCW) directions of rotation of the flagellar motor. Here, we measured the behavior of flagellar motors in swarmer cells. Results indicated that although the torque was similar to that in planktonic cells, the tendency to rotate CCW was higher in swarmer cells, surprisingly. Consistent with earlier reports, moisture added to the swarm surface restored swarming in a CCW-only mutant, but not in a FliG mutant that rotated motors CW-only (FliGCW). Fluorescence assays revealed that FliGCW cells grown on agar surfaces carried fewer flagella than planktonic FliGCW cells. The surface-dependent reduction in flagella correlated with a reduction in the number of putative flagellar preassemblies. These results suggest that the conformational dynamics of switch proteins play a role in the proper assembly of flagellar complexes and flagellar export, thereby aiding bacterial swarming. |
Tuesday, March 5, 2019 1:39PM - 1:51PM |
F63.00011: Geometric control of bacterial surface accumulation Rachel Mok, Jorn Dunkel, Vasily Kantsler Controlling and suppressing bacterial accumulation at solid surfaces is essential for preventing biofilm formation and biofouling. Whereas various chemical surface treatments are known to reduce cell accumulation and attachment, the role of complex surface geometries remains less well understood. Here, we report experiments and simulations that explore the effects of locally varying boundary curvature on the scattering and accumulation dynamics of swimming Escherichia coli bacteria in quasi-two-dimensional microfluidic channels. Our experimental and numerical results show that a non-convex periodic boundary geometry can decrease the average cell concentration at the boundary by more than 50% relative to a flat surface. |
Tuesday, March 5, 2019 1:51PM - 2:03PM |
F63.00012: Atomistic modeling of molecule-lipid interactions to understand small-molecule induced outer membrane vesicle biogenesis in Gram-negative bacteria Ao Li, Jeffrey W Schertzer, Xin Yong With the role of packing biochemical cargos, outer membrane vesicles (OMVs) of Gram-negative bacteria have great importance in many disease-related processes. Recent studies have shown a strong link between a self-produced small molecule, Pseudomonas Quinolone Signal (PQS), and OMV biogenesis in Pseudomonas aeruginosa. We conducted all-atom molecular dynamics simulations to elucidate the interactions between PQS and a model outer membrane. We discovered two characteristic states of PQS, namely attachment on the membrane surface and insertion into the Lipid A leaflet. The time-resolved position of PQS and the angle between its heterocyclic ring and alkyl side chain reveal a four-staged dynamical process: flotation, attachment, folding, and insertion. Remarkably, PQS bends its hydrophobic chain into a closed conformation to lower the energy barrier for penetration through the hydrophilic Lipid A head-group zone, which was confirmed by the potential of mean force (PMF) measurements. Simulation with multiple PQS exhibit significant aggregation of these amphiphilic molecules in the surrounding aqueous phase. Yet, both attached and inserted states were simultaneously observed even in the presence of PQS aggregation. These findings provide critical insight into OMV biogenesis. |
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