Microbiome Testing vs. Genetic Testing: Which is Better for Nutrition Insights?
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This is an exciting time for personalized health and nutrition. Real optimism abounds that the scientific community is on the verge of unlocking meaningful advancements that will forever change how we approach longevity, diet, and self care. But even with the horizon as bright as it is, the technology we have available today can help those struggling with diet move past one size fits all dogma and into a routine that works best for their needs.
Today, I want to zoom in on the topic of personalized nutrition and compare at-home microbiome tests vs. genetic tests for consumers looking to make an educated decision.
Charts can be a useful way to draw top level comparisons, so our team put together a TLDR table below.
Quick view
| DNA | Microbiome | |
|---|---|---|
| FSA/HSA | Often, yes | Often, yes |
| Typical cost | $99 – 300 | $150 – 400+ |
| Scientific Consensus | More established – decades of research | Emerging – rapidly growing |
| Reproducibility | High | Lower – results can vary wildly |
| Precision nutrition | Useful for setting a baseline | Very limited consensus for nutrition |
| Test frequency | Once in a lifetime (or a handful for different products) | Repeated – once every 3-6 months |
| Interpretation | Based on known SNPs and association with traits | Based on bacterial diversity |
| Use case | Foundational nutrition guidance | Adaptive dietary tweaks |
| Biological basis | DNA – fixed genome | Gut bacteria – dynamic and influenced by environment |
| Sample type | Cheek swab | Stool sample |
| Time horizon | Long term predisposition | Snapshot of gut health |
Are both *technically* DNA tests?
You could argue that microbiome testing and genetic testing are both DNA tests, it’s just that traditional genetic tests sequence your genetics (human DNA), whereas microbiome tests sequence the DNA of your microbiome, the trillions of bacteria that populate your gut. One distinction is that companies like Viome sequence microbiome RNA, which differs from looking at the DNA of bacteria because RNA is able to zoom in exclusively on living bacteria, whereas DNA also sequences dead species of bacteria.
For an in-depth look at the types of genetic tests available to consumers and which to choose, check out our recent post on Whole Genome Sequencing.
Genetic tests usually involve a cheek swab and are more proven in terms of stability, reproducibility, and long-standing research. For example, most people have no idea just how extensive GWAS research is, how long it’s been around, and the fact that it has been validated across ethnic groups.
By contrast, microbiome tests require capturing a still sample and hold more promise for real-time, adaptive nutrition—but the science is newer and still catching up.
And this is how I have always viewed the personalized nutrition space – build on the foundation of genetics with microbiome testing and advanced blood work as add-ons. Now, admittedly, I am biased because of my involvement with Gene Food, but I chose to build a nutrigenomics platform for a reason – genetic results are immutable. That isn’t to say that interpretation stays static, because it evolves as research emerges, but it’s easier to interpret testing that is inherently dynamic (like microbiome and blood work) when you first have genetic data in hand.
In this sense, DNA testing, including DNA diet testing, is a nice tool to get more out of your subsequent microbiome and blood testing.
Get Started With Personalized Nutrition
Gene Food uses a proprietary algorithm to divide people into one of twenty diet types based on genetics. We score for cholesterol and sterol hyperabsorption, MTHFR status, histamine clearance, carbohydrate tolerance, and more. Where do you fit?
Using heart health as an example
Genetic testing is a far better solution for crafting a long-term heart healthy diet than is microbiome testing.
Heart disease is the number one cause of death in America, and genetics play an important role in assigning risk. Many of our customers come to us because they want to understand their baseline risk genetically so they can establish a template for eating that is heart healthy.
Genetics, and especially polygenic risk scoring, offer an excellent tool for setting a baseline for precision nutrition. For example, the ketogenic diet is heavily marketed, but many of us can’t achieve a state of nutritional ketosis no matter how much fat we eat. Tools like ours can evaluate a user for relatively common SNPs in the PPARA gene to determine whether that person can reap the benefits of a ketogenic diet. In individuals who metabolize saturated fat poorly, a high-fat ketogenic diet is one of the worst diets they could follow, and one that can do long term damage. Scientifically backed markers like PPARA, and others, are the reason many advanced labs and health systems use nutrigenomics testing in their protocols (Boston Heart Diagnostics and the Cleveland Clinic are two notable examples).
Eggs, and by association plant sterols, are another controversial nutrition topic where genetic testing can shed light. The underreported issue of plant sterol absorption has recently made its way to the Wall Street Journal, and we are starting to understand that hyperabsorption is more prevalent in children and adults than previously recognized. (R) (R)
Fundamentally, this is an area where genetic testing is crucially important because of the role that variants in the ABCG5/8 genes play in cholesterol and sterol absorption.
By contrast, microbiome testing has very little to offer in terms of heart healthy eating. Innovative at-home tests like Viome, which I have tried, can offer insight into TMA levels, which impact a little known marker of cardiovascular health called TMAO, but the lipid community will be the first to admit that TMAO is not a reliable biomarker at this stage of the game. When I have had the chance to interview lipid expert Dr. Tom Dayspring, he has been quite critical of TMAO as a diagnostic tool.
Gut health
Microbiome testing offers real time insights into the state of the gut which genetic tests can’t evaluate.
Of course, a microbiome test, rather than identifying predispositions, will offer actual insight into the real time state of a user’s gut health. Genetic tests cannot do this.
For example, when I dig into my Viome results, there are several interesting evaluations related to gut health, the problem, and this is based in the fact that microbiome research is in its infancy, is the data is very “zoomed out,” meaning I am classed in a risk zone, but with no data as the actual strains populating my gut.
Nonetheless, there are some fascinating reports that can’t be learned from genetic testing, such as: butyrate production, lipopolysaccharides and inflammation (leaky gut), putrescine and protein fermentation, and many others. As I have written before, putrescine and protein fermentation are especially interesting at a time when the all-meat carnivore diet has become so popular in internet circles.
Business model
Last, a quick note on the respective business models of microbiome testing versus genetic testing. Some of the buzz the microbiome space has attracted, especially from investors, is based on the necessity of repeat testing and the potential that brings to sell lifelong, or at least long term, supplement and prebiotic plans to costumers. Subscription models that offer stable recurring revenue are preferred by investors, and friends of mine who run microbiome startups are especially excited about the potential for prebiotic products that help balance gut health that has fallen out of balance.
Now to be fair, these products are not snake oil, they are often clinically validated and may soon be covered by insurance. That, and genetic testing can help dial in supplement protocols as well, with markers like MTHFR achieving wide notoriety in functional health circles. Nonetheless, consumers should be aware of the business pressures that give rise to different business models in this space and do their best to sift through the noise to the substance, which should be the science.
