Microbiome research is often conducted in highly-regulated industries, such as foods, supplements, and pharmaceuticals, and various standards and regulations will apply.
This article explores key factors for setting up a microbiome lab, including commonly used equipment and software and compliance considerations.
Key equipment required for a microbiome lab
Microbiome research involves examining the microbiome composition in different parts of the body; for example, oral, nasal, skin, and gastrointestinal. The human microbiome is closely linked to health, and by understanding how the microbiome works, researchers can develop new ways to prevent and treat conditions and diseases. For example, probiotic supplements help restore a healthy balance of gut microbes, and microbiota transplants have been used to treat intestinal infections.
Researchers typically use DNA sequencing to identify which microbes are present in a sample. The below list reveals the equipment usually found in microbiome labs.
Quantitative PCR instrument
Quantitative polymerase chain reaction (qPCR) instruments are used to study the structure and function of microbial communities. qPCR involves amplifying target DNA and quantifying the concentration of that DNA in the sample. Researchers use this technique to measure the absolute abundance of specific microbes in a sample. Quantitative PCR is a more useful method than standard PCR, which only reveals the relative abundance of each microbe.
Anaerobic chambers
Anaerobic chambers are used to study anaerobic bacteria. This class of bacteria makes up most of the human gut microbiome. These bacteria cannot grow in the presence of oxygen, so they must be cultured in an oxygen-free environment. The anaerobic chamber is sealed and filled with carbon dioxide, allowing the bacteria to grow.
Biological safety cabinet
Biological safety cabinets are designed to protect users and valuable research materials from airborne pathogens and contaminants. There are different classes of cabinets depending on the level of protection required. For example, Class 1 cabinets protect users but not samples and may be used with low or moderate risk biological agents.
Laminar flow fume hood
Laminar flow fume hoods protect products or processes from particulates in the environment by trapping them in a HEPA filter. This is important in microbiome research, as one of the primary techniques, DNA extraction, involves harmful reagents. They are available in either a vertical or horizontal airflow configuration. Vertical laminar flow hoods are suitable for tall or large workspaces, and when large equipment is required. Horizontal laminar flow hoods are suitable for low-turbulence applications, such as those using small equipment.
Autoclave
An autoclave uses heat and pressure to kill pathogens and sterilize instruments, making it an essential tool for preventing contamination and the spreading of harmful bacteria.
Ultra-low freezer
Ultra-low freezers store samples of bacteria and other microorganisms at extremely low temperatures, typically between -20 to -80 degrees Celsius. Ultra-low freezers are ideal for minimizing the risk of sample degradation of microbes.
Incubator
An incubator provides a controlled environment with ideal conditions for working with microbiological cultures. The ability to regulate temperature, humidity, and CO2 and O2 levels enable researchers to optimize specific microorganisms' growth. For example, bacteria in the human microbiome thrives at temperatures similar to those of the human body (around 37°C).
Orbital shaker
Orbital shakers use gentle vibrations to evenly agitate fluid samples, facilitating the growth of aerobic or anaerobic microorganisms and promoting faster and more efficient nutrient uptake.
Microbiome lab compliance and regulation considerations
Since the work in microbiome labs is often linked to pharmaceuticals, some regulations will be similar to those that apply to biopharma labs. Microbiome research plays a role in other industries, too, including agriculture and food. Bodies such as the EMA and NIST have called for the standardization of sample collection procedures, reference materials, and data.
Here are some of the key players involved in the oversight of microbiome research in the United States.
FDA
Many microbiome-related products are linked to the food and drug industries and are regulated by the FDA. To this end, the agency has issued several guidelines for companies working in this field. For example, all studies involving human subjects must be pre-approved by an institutional review board (IRB), also called an independent ethics committee (IEC). While many institutions engaging in research involving human subjects will have their own registered IRB, the FDA allows an “outside” IRB to review studies.
Additionally, all research products must undergo strict quality control procedures to ensure their purity and efficacy. Key documents relevant to microbiome labs include Developing and Manufacturing Drugs Including Biologics and the Code of Federal Regulations (parts 600 and 601). These measures help to ensure that any therapeutics or supplements derived from microbiome research are safe and effective for public use.
NIST
The National Institute of Standards and Technology (NIST) has played a key role in developing standards related to microbiome research. The NIST Biosystems and Biomaterials Division works with the International Organization for Standardization (ISO), Clinical Laboratory Standards Institute (CLSI), and others to develop standards for biotechnology research. Key ISO standards include ISO 20688-1:2020 (nucleic acid synthesis), ISO 5058-1:2021 (genome editing), and ISO 20395:2019 (qPCR and dPCR). MM09-A2 (nucleic acid sequencing methods) is an important CLSI document. Additionally, NIST has developed reference materials to help microbiome researchers with tasks such as whole-genome-sequencing and Metagenomic Next Generation Sequencing (mNGS).