Microbiome Testing: Is A Gut Test Worth The Wait?



If you do a little shopping around, you may notice that the processing time for microbiome testing varies. Anywhere from 1 - 6 weeks.

This distinction is important to make.

Processing time depends on the type of stool test that you do. Some stool tests are comprehensive and more accurate than others.

These 3 types of stool tests have different processing times

PCR microbiome testing has a rapid processing time. You may receive your results in 1 - 2 weeks. But it must be ordered through your healthcare provider and it’s limited to specific set microbes that the test looks for. It also doesn’t necessarily give a function analysis.

16S sequencing is another technology used by companies offering microbiome testing. Processing time may range from 2 - 3 weeks. Even though 16S offers a more rapid processing time and tends to be more affordable, it’s not a technology that we recommend.

In the case of 16S, you get what you pay for.

With false positives and low accuracy, 16S technology only looks at bacteria and 0.01% of the bacterial genome - whereas shotgun metagenomics assess 100% of the bacterial genome.

Tiny Health uses shotgun metagenomics, the most advanced sequencing technology in microbiome research.

Although processing times are longer, shotgun metagenomic sequencing gives you the most accurate and comprehensive overall picture of gut health. This type of microbiome testing provides strain-level resolution, which is as accurate as you can get. And it reveals the potential metabolic function of bacteria. Such as the ability to break down special milk sugars, known as HMOs, or to produce protective short-chain fatty acids.

The benefit of microbiome testing during a baby’s first 1,000 days

Tiny Health gut tests work best when multiple samples are taken over time. Especially within a baby’s first 1,000 days, which includes 9 months of pregnancy and a baby’s first two years.

This gives parents a clear understanding of gut and immune development.

It can show any underlying gut imbalances that may need to be addressed - before there’s a problem. Or even when symptoms have temporarily cleared, gut testing can pinpoint the root cause of common troubles like silent reflux or eczema.

If a baby’s immune system isn’t set up correctly in early life, which may be related to low levels of specific good  bacteria, it may trigger a series of immune-mediated issues. Specifically, allergic conditions such as eczema and food allergies.

This is where microbiome testing comes in.

The first test you do with Tiny Health is called the “baseline sample.” Ideally, we capture your baseline sample before any big changes in diet or supplementation. The baseline sample gives insight into the status of overall microbiome health.

It’s worth pointing out that baseline sampling is most helpful when testing the microbiome of older children and adults. It’s less significant with babies, since the baby gut microbiome changes so dramatically over the course of the first year.

Regardless of age, after a baseline sample, additional tests can help parents pivot when there has been antibiotic exposure, the addition of supplements, or when beginning solid foods.

How to use test results when life goes on during processing time

A baby’s first 1,000 days pass quickly. And while shotgun metagenomic sequencing is the gold standard for microbiome testing, processing time can sometimes take up to 4 weeks.

A lot can change in 4 weeks.

For example:

  • Did you start a probiotic? With your microbiome test results, you can now know if it contains the species that your baby needs.
  • Was there exposure to antibiotics? To help with antibiotic recovery, it’s best to find out if your baby has any evidence of an antibiotic resistance signature as soon as possible.
  • Started solids? Solid foods can increase diversity of the gut. Having the pre-solids sample helps us to capture any earlier microbiome signatures that may be lost once solids start.

With a baseline sample, you’re equipped to understand and smoothly navigate these changes.