Introduction to Microbiome Research
The microbiome, composed of bacteria, viruses, fungi, and other microorganisms, plays a vital role in a wide range of processes in human health, agriculture, and environmental sciences.
Microbiome research and analysis has rapidly increased in recent years. In humans, the gut microbiome influences digestion, immune function, mental health, and even susceptibility to diseases such as obesity, diabetes, and inflammatory bowel conditions. Microbiomes contribute to soil fertility, plant health, and pollution degradation in environmental and agricultural sciences.
Understanding the trillions of microorganisms that inhabit our bodies and surroundings is proving essential for human well-being. As research in this field grows, so does the need for effective and standardized methods of microbiome sample collection.
Advancements in next-generation sequencing (NGS) and bioinformatics allow researchers to analyze microbial communities at an unprecedented level, leading to breakthroughs in healthcare, agriculture, and biotechnology. However, these sophisticated analyses require high-quality sample collection and extraction to ensure accurate results.
Microbiome Analysis Methods
There are several different types of nucleic acid-based microbiome analysis. Each analysis method has its strengths and limitations, and researchers often use a combination of methods to give a comprehensive picture of the community.
The three most commonly used methods are:
1. Amplicon Sequencing (16S rRNA, ITS, 18S rRNA)
Targeted sequencing of the 16s rRNA in bacteria and ITS and 18S rRNA genes in fungi is cost-effective. These genes are highly conserved but have diverged over time and, so, can be used to provide a “barcode” that can be assigned to specific taxonomies or counted to identify the frequency of each member of the microbial community. This method is widely used but can be limited in resolution; in some cases, distinguishing species is impossible.
2. Shotgun Metagenomics (Whole-Genome Shotgun Sequencing)
Untargeted, shotgun sequencing methods capture all microbial genomes present within a sample. Metagenomic shotgun assemblies are either performed de novo, based on reference genomes, or using a hybrid of both methods. All types of microorganisms can be sequenced, not just bacteria and fungi. This method can identify species, strains, and functional genes but requires significant computational resources for analysis.
3. Metatranscriptomics
Sequencing the RNA of a microbial community can give information on the diversity of the active genes present, quantify their expression levels, and monitor how these levels change in different conditions. The advantage of metatranscriptomics is that it can provide information about differences in the active functions of microbial communities that would otherwise appear to have a similar makeup. However, it is a more expensive and complex analysis than DNA-based methods.
How to Collect Microbiome Samples
Extracting DNA and RNA from complex microbiome samples can be challenging due to low yields in some sample types such as skin or environmental swabs, and the presence of inhibitors and background DNA and RNA from host organisms. Careful sample collection is crucial for obtaining accurate and reproducible data.
Enabling donors to collect samples at home removes the need to travel to a clinic or laboratory, which is particularly beneficial for individuals with mobility issues, busy schedules, or living in remote areas.
Collecting samples at home can also significantly reduce the costs associated with sample collection by eliminating the need for dedicated space and staff to handle sample collection in a clinical setting. Sample collection by study participants requires simple, straightforward protocols that non-professionals can follow.
What to consider when collecting microbiome samples
Sample type: Sample types vary widely depending on the microbiome to be studied. Key issues revolve around the complexity of the sample matrix, the presence of inhibitors, and the relative biomass of microbial cells. Specialized collection and extraction kits tailored to each sample type can be used to overcome these challenges.
Maintaining nucleic acid stability: Using a stabilization reagent to preserve the nucleic acids present in a sample ensures that the sample reflects the microbiome at the time of sampling and is not affected by nucleic acid degradation or overgrowth of particular species.
Contamination Prevention: Using sterile, single-use collection tools ensures you are not introducing microbial nucleic acids from the sample collection apparatus into your samples.
Storage & Transport: If collection tubes and sample packaging are sufficiently robust, stabilized samples can be sent to the laboratory for processing using regular mail, a straightforward and cost-effective method of sample transport. Using stabilization reagents prevents the need for expensive low temperature sample storage and transport.
Standardized Protocols: Adopting validated protocols for sample collection enhances reproducibility and data accuracy. Choosing simple protocols that minimize the risk of contamination and can be easily followed by participants without laboratory training, will give the best results.
What to consider when collecting microbiome samples
Below we have outlined the key considerations for sample collection of three of the most commonly studied microbiomes, with links to example products from the Isohelix product portfolio that can be used for these sample types:
1. Collecting DNA from Human Gut Microbiome Samples
Sample Type: Fecal samples or rectal swabs
Collection Method: The simplest method, as employed by the Isohelix StoolFix Gut Microbiome stabilization kit (STF), is to brush the outside of a stool sample with a swab such as the Isohelix SK Swab before placing the swab into an Isohelix StoolFix Gut Microbiome DNA Stabilization Kit tube containing stabilization solution. This method requires minimal sample handling and uses a non-toxic stabilization buffer inside an easy-to-use collection device that can be used within the laboratory or at remote patient collection sites.
Best Practice: Avoid contamination by following instructions carefully and ensuring samples are correctly sealed before shipment.
2. Oral Microbiome Samples
Best Practice: Refrain from eating, drinking, or brushing teeth for at least one hour before collection.
Sample Type: Saliva, tongue swabs, or dental plaque
Collection Method: Use saliva collection tubes or sterile swabs to capture microbiome samples from the mouth. The GeneFix Saliva Microbiome DNA Collector (MFX) is an easy to use oral microbiome DNA collection kit that has been optimized for the collection of samples using saliva. Alternatively, Isohelix SK Swabs can be used to swab the mouth; a range of Isohelix stabilization kits are available for swabs.
3. Skin Microbiome
Sample Type: Skin swabs
Collection Method: Isohelix SK Swabs can be used to collect samples from the skin for microbiome sampling. Various stabilization options are available to preserve swab samples.
Best Practice: Avoid using soaps or lotions for several hours before collection to prevent altering the microbial composition.
4. Environmental samples
Sample Type: Soil, water, surface swabs, or air samples
Collection Method: Different protocols can be followed, depending on the environment to be sampled. Isohelix SK Swabs can be used to collect samples from environmental surfaces. Various stabilization options are available to preserve swab samples.
Best Practice: Use aseptic techniques to prevent contamination during collection.
Conclusion
Microbiome research is revolutionizing our understanding of health, disease, and ecosystems. With the increasing significance of this field, proper sample collection methods are essential for generating reliable and reproducible data. By considering high-quality collection solutions like those from Isohelix and following best practices in sample collection, researchers can continue to unlock the microbiome’s vast potential for improving health and sustainability.
Microbiome research is revolutionizing our understanding of health, disease, and ecosystems. With the increasing significance of this field, proper sample collection methods are essential for generating reliable and reproducible data. By considering high-quality collection solutions like those from Isohelix and following best practices in sample collection, researchers can continue to unlock the microbiome’s vast potential for improving health and sustainability.
We are constantly adding to the information on microbiomics on our website. See below for some of our resources:
Product details and how to order Isohelix products :
Microbiomics articles:
- How Isohelix swabs were used to study the microbiomes of astronauts
- The microbiome and its role in Sake brewing
- Microbiome DNA sampling and analysis
Microbiomics Application Notes
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