BD Accuri News

Identifying the Microbes in Your Gut

Gemma Walton, PhD, and Sandra Tejero, PhD, are researchers in the Food and Nutritional Sciences Department at the University of Reading, UK. Their research interests include gut microbiology, prebiotics and probiotics, and the role of gut bacteria in health and disease. They told us how they adapted the Flow-FISH methodology to identify gut microbes using the BD Accuri™ C6 flow cytometer.*


Q: Would you tell us about your research program?

Drs. Walton & Tejero: We work in the field of gut microbiology. We all have billions of bacteria residing within our gastrointestinal tracts that influence our health. We run several different human intervention studies and in vitro assays to study the impact of different intervention strategies (such as prebiotics, probiotics, and antibiotics) on the bacteria within us, and their subsequent impact on human health.

Q: How do you use the BD Accuri C6 in your research?

Drs. Walton & Tejero: Our goal is to use the BD Accuri C6 to enumerate different bacterial groups within complex mixed samples (such as feces) using fluorescence in situ hybridization (FISH). The FISH method uses fluorescently labeled oligonucleotide probes, targeting bacterial nucleic acid sequences to enable specific hybridization to bacterial groups of interest. The use of fluorescence means that samples can be quantified visually using microscopy. Though well established, FISH by microscopy is time consuming and can be subjective, particularly with inexperienced counters.

Flow cytometry offers a faster and more attractive solution. Flow-FISH can achieve higher sample throughput at a greater sensitivity compared to microscopy, while providing additional information on cell size. Using FISH, background fluorescence can be an issue, so currently we are comparing Flow-FISH data with microscopy data to optimize the method. Furthermore, the use of flow cytometry threshold values assists in eliminating some background particles.

We also use the BD Accuri C6 with the BD™ Cell Viability Kit (Cat. No. 349483), which contains propidium iodide (PI) and thiazole orange (TO), to examine live and dead bacterial cell populations within samples.** Finally, we have been using the BD Accuri C6 for immunological analysis, including identification of human peripheral blood cell populations.

Q: Why did you choose the BD Accuri C6?

Drs. Walton & Tejero: The BD Accuri C6 is a very robust and portable instrument. We will have many students using this equipment; therefore ease of use makes it a good option. Furthermore, the equipment maintenance steps are easy and quick to perform, with a simple startup, and fast cleaning and shutdown process. The non-pressurized system means that we are able to adapt to the different tubes presented to us by students wishing to use the machines.

One of the machine's acquisition options enables volumetric measurements. This means that we can obtain absolute counts within a set volume of sample, which is essential for accurate quantification. The four fluorescence detectors with optical filters enable simultaneous analysis of different bacterial groups through the use of different microbial probes.

Q: What does BD Accuri's motto, "Flow cytometry within reach™," mean to you?

Drs. Walton & Tejero: The BD Accuri C6 is able to fit many different applications, and its ease of use makes it accessible and straightforward to use, even to those without a strong background in flow cytometry. The [BD CSampler™] autosampler system means that the system can be left to run, freeing up users for other tasks.

Read the September 2012 BD Accuri™ News feature about microbiology on the BD Accuri C6 »

View sample microbiology data on the BD Accuri C6 »



*Drs. Walton and Tejero’s collaborators on the flow cytometry suite team include Dr. Adele Costabile, Dr. Sofia Kolia, and Dr. Caroline Childs (who is now at University of Southampton).

**Gatza E, Peña PV, Srienc F, Overton T, Lavarreda CA, Rogers CE. Bioprocess monitoring with the BD Accuri™ C6 flow cytometer. BD Biosciences White Paper, April 2012. Available at: