Biosensors and Bioreactors, in microbial context!

I was recently engrossed in a review article of different biosensors, which had immense value in pathogen detection. In my field of work with metagenomics, bioreactors often replace animal models to monitor chemical changes including those from pathogenic microbial growth. So I began wondering, how do these techniques compliment each other, and what sort of commercial choices already exist in the market today!

So, what is a biosensor?

Biosensors are analytical devices that combine a biological component with a physicochemical detector. In the context of microbiology, a biosensor is a device that can signal the presence of disease-causing microbes in a sample such as water, or in blood serum, to help diagnose infections.

Types of biosensors

Types of biosensors

There are multiple types of biosensor devices such as enzyme-based, tissue-based, immunosensors, DNA biosensors, and thermal and piezoelectric biosensors. Here, I focus on DNA-based pathogen-detecting biosensors, the most common of which are lab-on-a-chip types of devices that use microfluidics to sense changes in chemical activity.

We can use DNA from certain pathogens to flag foods as unhygienic, for example through the detection of bacterial species like E. coli or *Staphylococcus aureus*.

A lab-on-a-chip (LOC) device involves following process:

LOC workflow

1. Sample input

2. A large number of micro-pumps and micro-valves on the chip to precisely control the flow direction and flow rate of microfluids

3. Sample preparation, including pathogen capture, cell lysis, nucleic acid extraction, and purification. This part often requires external electric fields, magnetic fields, or ultrasonic sound waves.

4. Nucleic acid amplification. In addition to traditional PCR, various emerging isothermal nucleic acid amplification techniques have been applied to LOC equipment, where the temperature of the reaction process is controlled by a temperature controller.

5. Sample detection using sensors such as fluorescence or electrochemical biosensors, among others.

Fun fact: I once participated in a project where we built an automated drug dosage monitoring system using a chemical compound as a biomarker for epileptic seizures.

A microfluidic biosensor I made for epileptic patients

This model revolved around the idea that fluctuations of certain chemicals in the blood can be uniquely associated with disease onset. It is true that such devices in the future can aid in more personalized medicine delivery.

However, today, most traditional detection methods are expensive, time-consuming, and often unfeasible in practice without sophisticated instruments and trained operators. Point-of-care testing (POCT) can be used to detect microorganisms rapidly on-site and greatly improve the efficiency of microbial detection. Lab-on-a-chip (LOC) is an emerging POCT technology with great potential, as it integrates most of the experimental steps carried out in the laboratory into a single monolithic device.

Pros and cons

Ongoing research already shows detection limits as low as 10 cells of pathogenic bacteria within an hour of application. At the same time, there are limitations, such as the requirement for advanced DNA extraction and purification as a precursor to biosensor application.

Although these devices are useful in detecting food poisoning and monitoring hygiene, these bulky pre-processing steps make them unable to fully meet the requirements of a POCT kit. This brings us to bioreactors.

What is a bioreactor?

A bioreactor is a vessel in which a biological reaction or chemical change can take place. The biological systems involved include enzymes, microorganisms, animal cells, plant cells, and tissues.

SHIME bioreactor system

So why do we need these large contraptions?

Unlike small-scale biosensors, a bioreactor can be scaled to large industrial-level production of chemical compounds, or for cultivating tissues/cells and monitoring chemical reactions. More interestingly, a bioreactor can be optimized for specific growth conditions that are favourable for certain microbes using pH, temperature, nutrients, and aeration.

Specifically, in the context of the human gut, we can develop an in vitro gastrointestinal system that can be used to study digestion, nutrient absorption, and the gut microbiome without the need for human or animal trials. This aligns with ethical principles of animal welfare, as laid down by William Russell and Rex Burch in 1959. These principles are known as the 3Rs: reduction, refinement, and replacement, promoting more humane methods to generate experimental data.

A gut bioreactor can be of four main types:

1. Complex Multi-Compartment Simulators These model multiple regions of the gut, including the stomach, small intestine, and colon, simultaneously to study the entire digestive process.
2. Specialized Colon Models These focus specifically on the colon, where the majority of microbial activity occurs.
3. Gut-on-a-Chip systems These involve microfluidic systems using living human cells to observe host–microbe interactions.
4. Specialized or Species-Specific Simulators These are designed to study species–species interactions or replicate specific biomechanical or chemical processes in the digestive system.

I have collected some examples for each of these four bioreactor groups, with one of the most popular being a complex compartment machine known as SHIME, developed by ProDigest:

SHIME® (Simulator of the Human Intestinal Microbial Ecosystem): Mimics the entire gastrointestinal tract and allows long-term studies of the microbiota.

There are multiple extensions of the SHIME system, such as:

• M-SHIME® (Mucosal-SHIME): Includes mucin-covered beads to simulate the mucus layer, allowing the study of bacteria that adhere to the intestinal wall.
• Toddler SHIME®: Specifically adapted to mimic a toddler’s gut conditions and microbiota.

We can also have SHIME coupled with computer-controlled systems such as:

• TIM (TNO Gastro-Intestinal Model): A highly dynamic, computer-controlled system.
• TIM-1: Simulates the stomach and small intestine, focusing on digestion and absorption.
• TIM-2: Focuses on the proximal colon, incorporating dynamic peristaltic movements and a dialysis membrane for removing metabolites.
• SIMGI (Simulator Gastro-Intestinal): A fully automated, five-compartment system similar to SHIME, including simulated peristaltic movements in the stomach module.

2. Specialized Colon Models

• PolyFermS (Polyfermentor Intestinal Model): Extension of SHIME, Uses immobilized fecal microbiota in gel beads and allows parallel operation of multiple reactors to compare treatments.
• **Mini Colon Model (MiCoMo):** A relatively low-cost benchtop device consisting of replicate bioreactors that run independently, enabling high-throughput and multiplexing without requiring a full anaerobic chamber.
• **Robogut:** Capable of maintaining precise, automated control of environmental conditions like pH and anaerobiosis, ensuring reproducibility.
• **PETR (Peristaltic Mixed Tubular Bioreactor):** Designed to mimic peristalsis using a mechanically massaged single-tube design, along with an integrated dialysis system to absorb metabolites and water, providing realistic transit times.

3. Gut-on-a-Chip

• SIFR (Screening Intelligent Fecal Research): An ex vivo technology that allows high-throughput screening of gut microbiota modulation.

4. Specialized & Species-Specific Simulators

• DGM (Dynamic Gastric Model): Focuses on replicating the mechanical, physical, and chemical processing of food in the stomach.
• Animal Simulators (SPIME, SCIME, SFIME): Adapted from the SHIME platform to simulate gastrointestinal ecosystems of animals such as pigs, dogs, and cats.

Which is more suitable for microbial research?

Ultimately, the choice of experiment determines which biomechanical method best suits a research investigation. Bioreactors can act as an all-in-one solution to generate and monitor biological processes in a controlled environment, whereas biosensors are used to detect the presence of specific chemical compounds or pathogens. In more advanced systems, biosensors are often integrated into bioreactors to continuously enable monitoring and identification.