The formation of multicellular microbial communities, called biofilms, starts from the adhesion of a few planktonic cells to the surface. The transition from a free-living planktonic lifestyle to a sessile, attached state is a multifactorial process that is determined by biological, chemical and physical properties of the environment, the surface and the bacterial cell. The initial weak, reversible interactions between a bacterium and a surface strengthen to yield irreversible adhesion. In this Review, we summarize our understanding of the mechanisms governing bacterial adhesion at the single-cell level, including the physical forces experienced by a cell before reaching the surface, the first contact with a surface and the transition from reversible to permanent adhesion.

Bacterial adhesion at the single-cell level

Microbial roles in cancer formation, diagnosis, prognosis, and treatment have been disputed for centuries. Recent studies have provocatively claimed that bacteria, viruses, and/or fungi are pervasive among cancers, key actors in cancer immunotherapy, and engineerable to treat metastases. Despite these findings, the number of microbes known to directly cause carcinogenesis remains small. Critically evaluating and building frameworks for such evidence in light of modern cancer biology is an important task. In this Review, we delineate between causal and complicit roles of microbes in cancer and trace common themes of their influence through the host's immune system, herein defined as the immuno-oncology-microbiome axis. We further review evidence for intratumoral microbes and approaches that manipulate the host's gut or tumor microbiome while projecting the next phase of experimental discovery.

The microbiome and human cancer.

Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology

Bacteria within communities can interact to organize their behavior. It has been unclear whether such interactions can extend beyond a single community to coordinate the behavior of distant populations. We discovered that two Bacillus subtilis biofilm communities undergoing metabolic oscillations can become coupled through electrical signaling and synchronize their growth dynamics. Coupling increases competition by also synchronizing demand for limited nutrients. As predicted by mathematical modeling, we confirm that biofilms resolve this conflict by switching from in-phase to antiphase oscillations. This results in time-sharing behavior, where each community takes turns consuming nutrients. Time-sharing enables biofilms to counterintuitively increase growth under reduced nutrient supply. Distant biofilms can thus coordinate their behavior to resolve nutrient competition through time-sharing, a strategy used in engineered systems to allocate limited resources.

/pdf/coupling-between-distant-biofilms-and-emergence-of-nutrient-cj4ibbv51m.pdf

Coupling between distant biofilms and emergence of nutrient time-sharing.

Cell migration is a pervasive process in many biology systems and involves protrusive forces generated by actin polymerization, myosin dependent contractile forces, and force transmission between the cell and the substrate through adhesion sites. Here we develop a computational model for cell motion that uses the phase-field method to solve for the moving boundary with physical membrane properties. It includes a reaction-diffusion model for the actin-myosin machinery and discrete adhesion sites which can be in a “gripping” or “slipping” mode and integrates the adhesion dynamics with the dynamics of the actin filaments, modeled as a viscous network. To test this model, we apply it to fish keratocytes, fast moving cells that maintain their morphology, and show that we are able to reproduce recent experimental results on actin flow and stress patterns. Furthermore, we explore the phase diagram of cell motility by varying myosin II activity and adhesion strength. Our model suggests that the pattern of the actin flow inside the cell, the cell velocity, and the cell morphology are determined by the integration of actin polymerization, myosin contraction, adhesion forces, and membrane forces.

http://absimage.aps.org/image/MAR14/MWS_MAR14-2013-000482.pdf

Coupling actin flow, adhesion, and morphology in a computational cell motility model

Species-Independent Attraction to Biofilms through Electrical Signaling

Microbial ecologists are increasingly turning to small, synthesized ecosystems1-5 as a reductionist tool to probe the complexity of native microbiomes6,7. Concurrently, synthetic biologists have gone from single-cell gene circuits8-11 to controlling whole populations using intercellular signalling12-16. The intersection of these fields is giving rise to new approaches in waste recycling17, industrial fermentation18, bioremediation19 and human health16,20. These applications share a common challenge7 well-known in classical ecology21,22-stability of an ecosystem cannot arise without mechanisms that prohibit the faster-growing species from eliminating the slower. Here, we combine orthogonal quorum-sensing systems and a population control circuit with diverse self-limiting growth dynamics to engineer two 'ortholysis' circuits capable of maintaining a stable co-culture of metabolically competitive Salmonella typhimurium strains in microfluidic devices. Although no successful co-cultures are observed in a two-strain ecology without synthetic population control, the 'ortholysis' design dramatically increases the co-culture rate from 0% to approximately 80%. Agent-based and deterministic modelling reveal that our system can be adjusted to yield different dynamics, including phase-shifted, antiphase or synchronized oscillations, as well as stable steady-state population densities. The 'ortholysis' approach establishes a paradigm for constructing synthetic ecologies by developing stable communities of competitive microorganisms without the need for engineered co-dependency.

/pdf/a-stabilized-microbial-ecosystem-of-self-limiting-bacteria-1ci74lazeo.pdf

A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis.

Communities of bacteria and other microbes live in every ecosystem on Earth, including in soil, in hydrothermal vents, on the surface of plants and in the human gut. They often attach to solid surfaces and form dense colonies called biofilms. Most biofilms found in nature are comprised of many different species of bacteria. How the bacteria interact shapes the internal structures of these communities. Many previous studies have focused on the molecules that bacteria use to relate to each other, for example, some bacteria exchange nutrients or release toxins that are harmful to their neighbors. However, it is less clear how direct physical contacts between bacteria affect the whole community. Escherichia coli is a rod-shaped bacterium that is a good swimmer, but has a hard time moving on solid surfaces. Therefore, when a droplet of liquid containing these bacteria is placed in a Petri dish containing a jelly-like substance called agar, the droplet barely expands over a 24-hour period. On the other hand, a droplet containing another rod-shaped bacterium known as Acinetobacter baylyi expands rapidly on agar because these bacteria are able to crawl using microscopic “legs” called pili. Here, Xiong et al. set out to investigate how a colony containing both E. coli and A. baylyi developed on a solid surface. The experiments showed that when a droplet of liquid containing both species was placed on agar, both species grew and spread rapidly, as if the E. coli hitchhiked on the highly motile A. baylyi cells. Furthermore, the growing colony developed a complex flower-like shape. Xiong et al. developed mathematical models that took into account how quickly each species generally grows, their ability to move, the friction between cells and the agar, and other physical properties. The models predicted that the E. coli cells that accumulate at the expanding boundary of the colony make the boundary unstable, leading to the flower-like patterns. Further analysis suggested that similar patterns may form in other situations when motile and non-motile species of bacteria are together. These findings may help us understand the origins of the complex structures observed in many naturally occurring communities of bacteria.

Flower-like patterns in multi-species bacterial colonies

Biochemical adaptation is one of the basic functions that are widely implemented in biological systems for a variety of purposes such as signal sensing, stress response and homeostasis. The adaptation time scales span from milliseconds to days, involving different regulatory machineries in different processes. The adaptive networks with enzymatic regulation (ERNs) have been investigated in detail. But it remains unclear if and how other forms of regulation will impact the network topology and other features of the function. Here, we systematically studied three-node transcriptional regulatory networks (TRNs), with three different types of gene regulation logics. We found that the topologies of adaptive gene regulatory networks can still be grouped into two general classes: negative feedback loop (NFBL) and incoherent feed-forward loop (IFFL), but with some distinct topological features comparing to the enzymatic networks. Specifically, an auto-activation loop on the buffer node is necessary for the NFBL class. For IFFL class, the control node can be either a proportional node or an inversely-proportional node. Furthermore, the tunability of adaptive behavior differs between TRNs and ERNs. Our findings highlight the role of regulation forms in network topology, implementation and dynamics.

/pdf/adaptation-with-transcriptional-regulation-2t3hpaoudg.pdf

Liyang Xiong

Papers

Species-Independent Attraction to Biofilms through Electrical Signaling

A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis.

Flower-like patterns in multi-species bacterial colonies

Adaptation with transcriptional regulation.

Coexistence and Pattern Formation in Bacterial Mixtures with Contact-Dependent Killing.