Related presentation: Integrative neuroscience of Paramecium, a swimming neuron (at the Institute for Neural Computation, UCSD). See current offers for Master students.
Protozoa are single-celled eukaryotes that feed on organic matter (such as bacteria). They were formerly considered as microscopic animals (hence the term “protozoa”, first animals), because they display a range of animal-like behaviors (but they are not animals). They move in various ways, hunt, look for mates, escape predators, and so on. Their behavior was described in detail in the early days of microscopy, in the 19th century, in particular by Jennings, who wrote an amazing book about them in 1906 (see the anthology of his works). I am working mostly on Paramecium, a very well-studied ciliate (covered with thousands of cilia) swimming in ponds and lakes all across the world.
Why study protozoa?
There are several reasons why a neuroscientist might get interested in protozoa. First, one can address many of the topics of neuroscience, except in a simpler organism. For example, when Paramecium hits an obstacle, mechanosensitive channels open, depolarize the membrane and trigger a calcium-based action potential. In turn, the action potential triggers a reversal of the swimming direction, followed by a change of direction. This is called the “avoiding reaction”. For this reason, Paramecium was a model organism for neuroscience in the 1970s, which some authors called the “swimming neuron”. I wrote a detailed review on the integrative neuroscience of Paramecium (2).
Paramecium is also sensitive to chemicals, light, gravity, water currents, temperature. It displays adaptation, learning, behavior switching, intrinsic and developmental plasticity, collective behavior (2). More broadly, like other ciliates, Paramecium faces many of the same challenges as animals, except at a microscopic scale: it lives in complex environments, hunts and digests, looks for mates, escapes predators, adapts to changing environments. Typically, neuroscience addresses these questions with reductionist approaches, e.g. looking at visual responses of neurons in the occipital cortex, but as I explain in my book The Brain, In Theory (see also my epistemological work), since behavior and cognition only arise at the level of the system, not of its components, this leads to homuncular explanations (symbols in the brain - who reads them?). In a unicellular organism, this can be studied at the scale of the organism, including the coupling with body and environment, without having to ask how the organism interprets its own activity.
Another reason is that all animals descend from protozoa, most likely marine protists swimming with a flagellum, which transitioned from occasional multicellularity (coming together as part of their behavioral repertoire) to obligate multicellularity. Thus, an animal is in a way a colony of protists that has settled. The significance for neuroscience is that the ancestor of every neuron is a protist, and this gives a very different perspective than connectionism on what a neuron is: a living adaptive system, not a component implementing an operation. Studying protists is a way to understand the logic of cells and neurons in general.
Our research work
Our first project was to develop a biophysical model of the action potential coupled with motility, based on our electrophysiological and behavioral measurements (3). Thus, it is an autonomous model of the swimming neuron, in which the avoiding reaction emerges. The paper comes with movies of swimming paramecia as well as electrophysiological data and code for both the model and the analyses. To do the electrophysiology, we have designed a simple microfluidic device to immobilize cells (1). In collaboration with Alexis Prevost, and Laetitia Pontani (Laboratoire Jean Perrin, a physics lab), we have also empirically characterized the avoiding reaction against obstacles, which is a combination of hydrodynamic interaction and physiological reaction (4).
We have recently discovered that Paramecium engages in foraging behavior, very much like animals (alternating between exploring and stopping for food), and we are working on understanding this behavior and its physiological basis. We believe it involves memory, sensory integration, decision making and complex motor control. We are also interested in adaptation and learning in Paramecium, and more generally any question that links physiology and behavior.
The lab is equipped to do behavioral experiments, culture, electrophysiology, fluorescence microscopy, molecular biology and genetics (in particular RNA interference). We have developed a computational method to track paramecia in 3D from conventional microscope images (5), and we can track trajectories of paramecia for hours.
Contact me if you are interested in a collaboration, an internship, a PhD or a postdoc. Finally, we are happy to help anyone who wants to get started on Paramecium research in their own lab, including hosting visitors in our labs to learn experimental techniques. A good place to start is ParameciumDB, which is a genomics database but also hosts a wiki with experimental techniques.
Relevant publications (chronological order):
- Kulkarni A, Elices I, Escoubet N, Pontani L, Prevost AM, Brette R (2020). A simple device to immobilize protists for electrophysiology and microinjection.
- Brette R (2021). Integrative Neuroscience of Paramecium, a “Swimming Neuron”.
- Elices I, Kulkarni A, Escoubet N, Pontani LL, Prevost AM, Brette R (2022). An electrophysiological and kinematic model of Paramecium, the "swimming neuron".
- Escoubet N, Brette R, Pontani LL, Prevost A (2023). Interaction of the mechanosensitive microswimmer Paramecium with obstacles.
- Hosseini A, Fosse C, Awada M, Stimberg M, Brette R (2025). Single camera estimation of microswimmer depth with a convolutional network.