S. Cerevisiae, also known as baker’s yeast, are picked-up, measured and then deposited in a line with a FluidFM micropipette. The cells stay fully viable through this procedure. 


Single cell force spectroscopy (SCFS) promises critical insights for microbial biofilm formation, anti-microbial surfaces and more. So far, the time-consuming immobilization to the AFM cantilever severely limited the number of studied cells. FluidFM offers much easier manipulation and hence much higher measurement throughput for microbes such as yeast, algae and bacteria. 

Odoo • Text and Image
Odoo • Text and Image
Odoo • Text and Image
Odoo • Text and Image

Pick a microbe with negative pressure, measure, release it again with a positive pressure pulse or by a short cleaning procedure.



20 to 200







Microbes are fundamental to any ecosystem and both are key factors, clinically and industrially; be it as pathogens, symbionts or production organisms. As for eukaryotes, mechanical studies can give valuable insights also for microbes, extending the body of knowledge gained through classical biological research methods.

Biofilm formation of microbes relies on adhesion, where they need to adhere both to a substrate and to each other to thrive. These biochemical adhesion mechanisms can be addressed in the design of implants as well as anti-microbial surfaces – if they are well understood.

Cell-cell heterogeneity is prevalent in microbes, possibly a mechanism to adapt quickly to changing environments. To study this heterogeneity many single cell measurements are required per condition.

So far, single cell force spectroscopy has been a tool to study cell mechanobiology and biophysics of microbes, yet with a typical throughput of 2-3 measured cells per day, the resulting data is limited.

FluidFM now offers a much more accessible and faster method to gain such data measuring dozens to hundreds of cells a day.

Get sound statistics within one day instead of weeks or months.

Fluorescent CRISPR-Cas9 complexes injected into mouse primary hepatocytes with the FluidFM Bio-CRISPR.

Pathogenic S. pyogenes bacteria adhesion is measured with a FluidFM nanopipette. The bacteria chains detach in a zipper-like movement. To better hold this organism, the size of the nanopipette opening was enlarged with focused ion beam (FIB). Courtesy E. Potthoff, ETH Zurich  


The straight-forward handling of microbes and reusable measurement probes make FluidFM ideal for single microbe force spectroscopy studies.

FluidFM increases measurement throughput 10-fold, allowing to gain statistically significant insights faster and for more organisms. The versatile method allows to study 20-200 individual cells a day.


Microscopic organisms come in a wealth of shapes and sizes. FluidFM is a versatile tool to pick and measure many of them. Be it microscopic algae, bacteria, fungi or protozoa; FluidFM can address organisms from a few nm to dozens of micrometers. While the easiest handling can be expected for spherical microorganisms, microbes of other shapes, such as E. coli, have also been addressed by our customers. Here, focused ion beam (FIB) allows the probe opening to be tailored to the microbe geometry.
Ask our experts how FluidFM can address your microbe of interest.

20 to 200 cells per day

The purely physical method of immobilizing the microbes onto the FluidFM cantilever makes it reversible. For non or lightly adherent cells, such as yeast, algae or protozoa, this allows the analysis of many individual cells in quick succession. It has been reported that 200 and more cells have been measured per experiment day in this way.
For strongly adherent cells, a washing procedure is typically required between two sub-sequent measurements, as they quickly adhere to the FluidFM probe as well. Thus, 20 or more cells can be measured per day – still 10 times more than with classical single cell force spectroscopy. 

100s of cells with one FluidFM probe

One FluidFM probe typically lasts for several SCFS measurement days, meaning that the same FluidFM probe can be used for dozens to hundreds of cells – making it very cost-effective.

Pick from substrate or attract from solution

FluidFM probes can pick-up microorganisms directly from a substrate. Alternatively, the microbes can be attracted from a solution via liquid influx to the aperture of the FluidFM probe and held tightly there. This method is also recommended in cases where the long-term adhesion of a microbe to a substrate is too strong to quantify, and hence shorter-term interactions are studied.

Microbes stay fully viable

The reversible immobilization by the FluidFM probe does not harm the microorganisms in any way: they stay fully viable. After a measurement, the same microbe can be tracked and repeatedly measured over time. Alternatively, it can be isolated into a separate well to form a new colony or be analyzed with other methods (e.g. by PCR).

Access single microbe mechanics.    

Get in touch with us to find out more about how FluidFM can help your research.  

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FluidFM is regularly applied to study microbes. Below, we highlight 3 of the most relevant publications; many more can be found in our publications section.

Quantify and optimize bacterial adhesion

Bacteria biofilms are the driving engine in biofilm-reactors e.g. to produce ethanol. In this study researchers from the University of Kaiserslautern apply FluidFM to study bacterial adhesion to typical reactor material such as stainless steel. Not only do they present a new method how to optimize the measurement parameters, they also show that using FluidFM leads to comparable results as with traditional SCFS, where a cell is glued to an AFM probe.

L. Hofherr, C. Müller-Renno, C. Ziegler. FluidFM as a tool to study adhesion forces of bacteria - Optimization of parameters and comparison to conventional bacterial probe Scanning Force Spectroscopy. (2020). PLOS ONE. doi: 10.1371/journal.pone.0227395

Biofilm formation

Candida albicans is notorious as the most common cause for fungal infections in humans. Candida biofilms e.g. on implants are of special concern as they tend to be persistent and drug tolerant. Scientists from both UC Louvain and ETH Zurich used FluidFM to identify a new target mechanism to treat infections associated to Candida biofilms.

J. Dehullu, J.A. Vorholt, P.N. Lipke & Y.F. Dufrêne. Fluidic Force Microscopy Captures Amyloid Bonds between Microbial Cells. (2019). Trends in Microbiology. doi: 10.1016/j.tim.2019.06.001

Bacteria repellent coating

Millions of dental implants are placed every year, where the infection of the implant site is a major risk. By preventing biofilm formation on the implant, the infection risk can be minimized. In this study, researchers from the Hannover Medical School apply a new liquid infused surface layer to titanium and then quantify biofilm formation and adhesion of S. oralis on it. They conclude reduced bacterial adhesion is the key factor which allows the treated surface to repel biofilms with help of shear flows in the oral cavity.

K. Doll, I. Yang, E. Fadeeva, N. Kommerein, S. P. Szafranski, G. B. der Wieden, A. Greuling, A. Winkel, B. N. Chichkov, N. S. Stumpp & M. Stiesch. Liquid-infused structured titanium surfaces: Antiadhesive mechanism to repel Streptococcus oralis biofilms. (2019) ACS Appl. Mater. Interfaces. doi: 10.1021/acsami.9b06817

Quantify bacterial adhesion with colloids

Scientist at ETH Zurich quantified the hydrophobic adhesion properties of 28 bacteria strains taken from leaf isolates. They developed a modular FluidFM approach where colloidal, hydrophobic probes were brought in contact with the isolated bacteria on a PLL coated glass substrate. With 700 individual bacteria measured, this very extensive single cell force spectroscopy study allowed to observe cell-cell heterogeneity. The differences between the strains regarding hydrophobic interactions covered 3 orders of magnitude and correlated well with bacteria retention in planta.

M. Mittelviehfhaus, D.B. Müller, T. Zambelli & J.A. Vorholt. A modular atomic force microscopy approach reveals a large range of hydrophobic adhesion forces among bacterial members of the leaf microbiota. (2019) The ISME Journal. doi: 10.1038/s41396-019-0404-1