Your Gut Is Not Generic: How Personalized Microbiome Therapy Is Changing the Way We Treat Digestive Health
Updated: Aug 26
Most probiotics are designed for the average person. There is only one problem: the average person does not exist.
Created by Christopher Caffrey, ACNP, PMHNP, Functional Medicine-trained
August 23rd, 2026
Key Takeaways:
Your microbiome is highly individual. Two people with the same symptoms can have very different bacterial patterns, which is why a one-size-fits-all probiotic may not make sense.
Flore uses deeper microbiome testing to personalize treatment. Whole-genome sequencing looks beyond broad bacterial categories and can provide a more detailed picture of which microbes and functions are present.
The goal is not just to test your gut—it is to act on the results. Flore uses the data to create a personalized synbiotic formula with selected probiotics and prebiotics, then reassesses over time.
The science is promising, but it is still evolving. Early studies and real-world data suggest potential benefits, but personalized microbiome therapy is not yet proven to treat every digestive condition.
The patient still matters more than the test. Microbiome results should be interpreted alongside symptoms, diet, medications, labs, medical history, and other clinical findings—not used in isolation.
Walk into almost any pharmacy and look at the probiotic section.
There may be 30 bottles staring back at you. One promises digestive support, another immune support. One has 10 billion CFUs, another has 50 billion. One contains five strains, another contains 17, and somewhere in the middle there is inevitably a refrigerated bottle costing $79 that appears to require a graduate degree to understand.
So you choose one.
Maybe your friend recommended it. Maybe the Amazon reviews were good. Maybe the label looked particularly scientific. Then you take it and hope. That is essentially how probiotic therapy has been practiced for years.
At Flexup Wellness, I think we can do better.
That is why I am introducing Flore personalized microbiome management as an optional add-on to select Flexup Wellness Partnerships.
Flore uses whole-genome microbiome sequencing, bioinformatics, clinical information, and artificial-intelligence-supported formulation technology to analyze your individual gut ecosystem and create a personalized combination of probiotics and prebiotics based on what is actually found.
Instead of asking, “What probiotic is good for gut health?” we can begin asking, “What does your microbiome look like, and what might this particular ecosystem need?”
That is a very different question, and it represents where I think functional medicine is heading.
First, What Exactly Is the Microbiome?
Your gastrointestinal tract contains a massive ecosystem of microorganisms, including bacteria, viruses, fungi, archaea, and other organisms. Collectively, this ecosystem is referred to as the gut microbiome.
These organisms are not simply passengers traveling through your intestine. They interact with food, produce metabolites, influence intestinal barrier function, communicate with immune cells, affect bile acids, participate in vitamin metabolism, and interact with the nervous system.
Some bacteria ferment dietary fiber and produce short-chain fatty acids such as butyrate, acetate, and propionate. These metabolites can influence intestinal cells, immunity, inflammation, and metabolism. Other organisms may become problematic when they become disproportionately abundant or when the surrounding ecosystem becomes disturbed.
The important word here is ecosystem.
Think less about your gut like a bag containing individual bacteria and more like a rainforest. A rainforest is not healthy because one particular tree is present. It is healthy because thousands of organisms coexist in a complex, relatively stable system.
If you remove enough species, introduce the wrong organisms, alter the soil, change the rainfall, and set half the forest on fire, throwing three new trees into the middle probably will not restore the ecosystem.
Yet that is essentially what we sometimes do with probiotics. Someone has bloating or IBS and we say, “Here are six bacteria. Good luck.”
Sometimes it helps. Sometimes it does nothing. Sometimes symptoms actually get worse. The variability should not surprise us.
Your Microbiome Is Highly Individual
Two people can eat similar diets, weigh the same amount, and have very different microbial ecosystems.
Your microbiome is shaped by genetics, diet, antibiotic exposure, medications, infections, age, exercise, stress, sleep, alcohol, bowel motility, geography, environmental exposures, and even the people and animals you live with.
Even identical twins do not maintain identical microbiomes.
This is one reason I have never loved the question, “What is the best probiotic?” Best for whom?
There is no universally ideal probiotic any more than there is one universally ideal diet or medication. And even within the same bacterial species, strain matters.
That point is extremely important.
Lactobacillus rhamnosus is not one interchangeable organism. Different strains of L. rhamnosus can behave differently and have different clinical evidence. Think of the species name as the family name. Two people named Smith may share a surname, but one might be a neurosurgeon and the other may struggle to assemble an IKEA bookshelf. The family name does not tell you what that individual can do.
This is also why the American Gastroenterological Association has emphasized that probiotic effects should be evaluated at the strain and strain-combination level, rather than simply treating every probiotic as equivalent.[1]
So What Is Flore?
Flore takes the usual probiotic model and essentially works backward.
Instead of manufacturing one probiotic formula and selling it to everyone, Flore begins with information about you.
A stool sample undergoes whole-genome shotgun metagenomic sequencing through a CLIA-certified, CAP-accredited laboratory. This analysis examines microbial DNA at considerably greater resolution than many older microbiome testing methods.[2]
Flore then combines that microbiome information with clinical and symptom data to help develop a personalized synbiotic.
A synbiotic simply means probiotics plus prebiotics.
The probiotics are live microorganisms selected for specific functions. The prebiotics are compounds designed to support particular organisms or microbial functions.
Flore currently draws from a library of up to 68 curated probiotic strains and more than 40 prebiotic ingredients, rather than giving every patient exactly the same formulation.[3]
The result can be manufactured specifically for the individual patient as a capsule or powder.
This is the part I find most useful.
The process is not simply:
Test your stool → receive a 47-page report → stare at it wondering what to do next.
The intention is:
Test → interpret → formulate → intervene → reassess.
That closes a loop that many microbiome tests leave open.
Why Whole-Genome Sequencing Matters
Not every microbiome test is doing the same thing. Many older approaches use 16S ribosomal RNA sequencing. This technique can be useful for identifying broad bacterial groups, but its resolution is limited.
Whole-genome shotgun sequencing reads far more microbial DNA. That allows greater species- and strain-level resolution while also examining microbial genes that may provide clues about what the community is capable of doing.[4]
Imagine looking at a city from an airplane. A lower-resolution test might tell us:
“There are houses, businesses, and roads.” Whole-genome sequencing moves us closer to: “That building is a bakery, that one is a pharmacy, and someone appears to be running an illegal casino behind the laundromat.” We get a more detailed map. That does not mean the map tells us everything.
A stool sample is still a snapshot. Diet changes the microbiome. Antibiotics change it. Medications change it. Bowel transit time affects it. Your microbial ecosystem can look different months from now than it does today.
So I do not consider microbiome testing a permanent diagnosis of who you are.
I consider it a biological snapshot that can help us make better decisions.
Where Artificial Intelligence Comes In
Whole-genome sequencing produces an enormous amount of data. No clinician is going to sit at a desk with a yellow legal pad and manually compare thousands of organisms, microbial pathways, symptoms, previous outcomes, and dozens of potential probiotic strains.
This is exactly the type of problem where computational tools become useful.
Flore Clinical uses a clinical intelligence system built from paired microbiome sequencing, clinical information, and previous treatment outcomes to help identify patterns and generate formulation recommendations.[5]
Artificial intelligence can recognize relationships within datasets that are simply too large for a human to calculate manually. But I want to be clear about what AI is not doing. It is not magically looking at your stool and diagnosing every problem in your body. That would make a fantastic commercial. It would make terrible medicine.
Your symptoms still matter. Your medications matter. Your medical history matters. Your diet matters. Previous treatment responses matter. And established gastrointestinal diagnoses still matter. AI should expand clinical judgment. It should not replace it.
That is how I intend to use it at Flexup Wellness.
Why This Is Different From Buying a Good Probiotic
You might reasonably ask, “I already take a high-quality probiotic. Why would I need this?” You may not.
There are excellent conventional probiotics available, and I use them. A well-studied strain can be perfectly appropriate when there is a clear reason for using it.
The problem is assuming that more organisms, more strains, and more CFUs automatically equal a better treatment. They do not.
The probiotic literature is notoriously inconsistent. Different trials use different strains, combinations, doses, and patient populations, often producing conflicting results.
The American Gastroenterological Association has therefore been appropriately cautious about broadly recommending probiotics for many gastrointestinal disorders.[1]
Ironically, I think that criticism strengthens the case for personalization.
If dozens of studies use dozens of different probiotic combinations and produce inconsistent results, perhaps the question “Do probiotics work?” is simply too crude.
Which probiotic?
Which strain?
Which patient?
Which microbiome?
Which symptom pattern?
Which diet?
Which dose?
For how long?
Personalized microbiome therapy is an attempt to ask a better question.
What Are We Actually Trying to Change?
The goal is not to create a microbiome containing only bacteria someone labeled “good.” Your gut is not Sesame Street. Bacteria do not walk around wearing shirts identifying the good guys and bad guys.
An organism's behavior can depend on abundance, neighboring microbes, diet, intestinal environment, immune function, and host physiology. The goal is therefore to encourage a more functional and resilient microbial ecosystem.
Depending on the person, that may mean supporting:
greater microbial diversity
healthier short-chain-fatty-acid production
more favorable intestinal-barrier signaling
improved bowel regularity
healthier fermentation patterns
competition against potentially problematic organisms
improved digestion
healthier immune interactions
and potentially more favorable gut-brain signaling
Sometimes the goal is adding organisms. Sometimes it is feeding organisms already present. And sometimes the answer is not a probiotic at all.
It may be improving dietary fiber, treating constipation, increasing plant diversity, addressing SIBO, managing bile-acid diarrhea, evaluating celiac disease, or correcting another underlying gastrointestinal problem. The microbiome is part of the patient. It is not the entire patient.
What Symptoms Might Personalized Microbiome Therapy Help?
This is where we need to distinguish between symptoms we may reasonably target and diseases we can claim to treat. Flore is not an FDA-approved treatment for IBS, depression, autoimmune disease, SIBO, or inflammatory bowel disease.
But microbiome-directed strategies may be reasonable to consider in people experiencing:
bloating
excessive gas
constipation
irregular bowel movements
loose stools
abdominal discomfort
post-antibiotic digestive changes
difficulty tolerating conventional probiotics
food intolerance patterns
digestive symptoms associated with altered gut-brain signaling
and certain patterns of fatigue or brain fog that occur alongside gastrointestinal dysfunction
There is also increasing research into the relationships between the microbiome and metabolism, immune regulation, mood, stress responses, sleep, and neurological function. That does not mean a custom probiotic treats anxiety because “anxiety comes from the gut.”
Human biology is not that simple.
But the microbiota-gut-brain axis is a legitimate area of modern neuroscience and gastroenterology, and strain-specific probiotic research has produced some interesting results in mood and anxiety disorders, although findings remain inconsistent.[6]
This is an area where I am interested without pretending the scientific argument is finished.
Is There Evidence Behind Flore Specifically?
Yes, although this is where precision matters. Flore, previously known as Sun Genomics, has published peer-reviewed research involving personalized synbiotics.
A 2024 study published in mSystems, a journal of the American Society for Microbiology, evaluated precision synbiotics in children and adults with autism spectrum disorder. Researchers performed deep metagenomic sequencing and created personalized synbiotic formulations based on each participant's microbiome and clinical information.[7]
Among participants completing the intervention, investigators observed increases in microbial diversity, changes in microbial composition and metabolic pathways, and improvements in gastrointestinal discomfort. Some behavioral measures also improved.[7]
That is encouraging. But it was an open-label study, not a randomized placebo-controlled trial. Participants knew they were receiving treatment, and several study authors were employees of Sun Genomics. Those limitations do not invalidate the findings. They tell us how much certainty we should assign to them.
I would call this promising clinical evidence, not definitive proof.
Flore itself acknowledges that published randomized controlled trials of its personalized formulas are not yet available.[8]
That honesty matters to me.
Real-World Data Is Interesting Too
Flore has also accumulated something traditional probiotic companies rarely have: paired microbiome and symptom information from a large number of people.
The company reports having produced approximately 40,000 personalized formulations based on more than 23,000 sequenced microbiomes.[3]
In one observational analysis involving 651 individuals with paired testing and symptom surveys, Flore reported that 47.4% of tracked symptom instances resolved between baseline and follow-up.[8] That is interesting. It is not equivalent to a randomized trial.
People change diets, begin medications, stop medications, exercise, sleep differently, and experience natural fluctuations in symptoms. Without a control group, we cannot conclude that the personalized probiotic caused every improvement. But large real-world datasets can identify patterns. Those patterns can then generate better clinical trials.
That combination—real-world data, advanced sequencing, and AI-assisted pattern recognition—is one reason this area has so much potential.
Why Retesting Matters
One of the features I like most is that the initial microbiome test does not have to be the finish line. It can be the baseline. If we introduce an intervention intended to change the microbial ecosystem, eventually I want to know whether the ecosystem actually changed.
Flore can incorporate repeat sequencing so that microbial changes can be reassessed and the formulation adjusted when appropriate.[9]
That creates a simple feedback loop:
Measure → intervene → reassess → refine.
That is also how I approach other areas of functional medicine.
We do not start testosterone and never recheck testosterone.
We do not treat insulin resistance and never repeat metabolic markers.
We do not start a weight-management program and never look at body composition.
Why should microbiome management be different?
If we are going to call something personalized medicine, there should ideally be a way to assess whether the personalization moved the biology in the direction we intended.
Why Your Gastroenterologist Probably Hasn't Offered This
You may have seen a gastroenterologist for years and never been offered whole-genome microbiome sequencing. That does not mean your gastroenterologist is behind the times. Conventional gastroenterology is primarily designed to diagnose and treat established gastrointestinal diseases.
If I am concerned about colon cancer, I want a colonoscopy.
If I suspect inflammatory bowel disease, I want appropriate endoscopy, imaging, pathology, and laboratory evaluation.
If you may have celiac disease, microbiome sequencing does not replace appropriate celiac testing.
Where microbiome analysis becomes interesting is the large space between:
“We did not find anything dangerous.”
and
“I actually feel well.”
The colonoscopy can be normal. Imaging can be normal. Blood work can be reassuring. A diagnosis of IBS may be entirely appropriate. But the patient may still have bloating, irregular bowel movements, food intolerance, and significant symptoms.
Microbiome testing remains outside routine allopathic care partly because its clinical utility has not yet been standardized enough for broad guideline-based adoption.
I understand that hesitation.
But I also think there is an important difference between:
“This is not yet standard care.”
and
“This information has no value.”
Functional medicine often works in that middle ground—without replacing appropriate conventional diagnostics.
How Flore Fits Into a Flexup Wellness Partnership
Flore will be offered as an optional personalized microbiome-management add-on for appropriate patients participating in Flexup Wellness Partnerships.
It is not something every patient automatically needs. I prefer it that way. Personalized medicine should not begin by giving every person the same expensive test.
If your symptoms, history, previous treatments, or goals suggest that deeper microbiome analysis could meaningfully influence our strategy, we can discuss whether it makes sense.
The process may include:
review of your gastrointestinal history
review of previous testing
assessment of symptoms and dietary patterns
whole-genome microbiome sequencing
interpretation of the findings within your clinical context
an individualized probiotic and prebiotic formulation
monitoring of tolerance and symptom changes
dietary changes designed to support the microbial ecosystem
and repeat testing when clinically useful
The technology provides information. I provide the clinical context. That combination is where the value lies.
The Microbiome Is Not Just About Probiotics
You cannot supplement your way out of a diet that starves your microbiome.
Your microbes eat what you eat.
If your diet contains very little fermentable fiber, resistant starch, polyphenols, or plant diversity, swallowing the world's most sophisticated personalized probiotic every morning may not overcome the environment you create the other 23 hours and 59 minutes of the day.
That means microbiome management may also involve:
fiber and plant diversity
resistant starch
polyphenol-rich foods
fermented foods when tolerated
adequate protein
meal timing
reducing excess alcohol
reducing ultra-processed foods
exercise
sleep
stress
bowel motility
medication review
and antibiotic stewardship
That is what makes this functional medicine rather than supplement medicine. The probiotic is one lever. The ecosystem is the target.
What Would Success Actually Look Like?
Success is not a stool report filled with green numbers.
I care whether you feel better.
Depending on why we started, improvement might mean less bloating, more predictable bowel movements, less constipation or urgency, better tolerance of foods, reduced abdominal discomfort, improved recovery after antibiotics, or fewer episodes of digestive instability.
Then, when appropriate, we can compare those clinical changes with repeat microbiome testing. The two should be interpreted together. If your microbiome report looks spectacular but you feel terrible, I am not going to congratulate the report.
The patient outranks the test.
That principle applies to almost every diagnostic tool I use.
Why Pricing Is Individualized
Flore personalized microbiome management will not have one universal price because the treatment itself is not universal.
Pricing may vary depending on the complexity of testing, the number and type of probiotic and prebiotic ingredients used, whether reformulation is required, and how long treatment is appropriate.
Some patients may need a relatively focused intervention.
Others may benefit from a longer strategy that includes repeat testing and reformulation.
For that reason, pricing through Flexup Wellness is patient-dependent.
If the therapy is individualized, the treatment plan—and therefore its cost—may be individualized as well.
Is This the Future of Gastrointestinal Medicine?
I think some version of it probably is. Not necessarily today's exact tests. Not necessarily today's exact algorithms. And not necessarily Flore forever.
But the idea that we will continue treating the microbiome as though everyone has essentially the same ecosystem seems increasingly unlikely.
Sequencing is becoming more sophisticated. Datasets are getting larger. Artificial intelligence can identify patterns humans cannot reasonably calculate manually. Researchers are moving beyond simply asking which organisms are present and toward understanding what those organisms are actually doing.
We are beginning to see research into strain-level treatments, next-generation probiotics, bacteriophages, microbial metabolites, postbiotics, engineered microorganisms, and targeted ecosystem restoration.
What looks futuristic today may eventually become fairly ordinary. That does not mean every new microbiome technology will survive scrutiny. Some will not.
But I would be surprised if precision microbiome medicine simply disappears.
Where I Land
I do not believe every gastrointestinal symptom is caused by the microbiome.
I do not think every patient needs microbiome sequencing.
And I certainly do not think a personalized probiotic replaces good gastroenterology.
If you have gastrointestinal bleeding, unexplained anemia, significant weight loss, inflammatory bowel disease, celiac disease, pancreatic disease, or another serious gastrointestinal condition, we need to identify and treat the actual disease.
But I also do not think we should ignore an enormous biological ecosystem simply because our understanding of it is incomplete.
The microbiome influences digestion, metabolism, immune signaling, intestinal barrier physiology, and the gut-brain axis. We now have tools capable of examining that ecosystem at a level of detail that would have been difficult to imagine not very long ago.
What interests me about Flore is not simply that it produces a sophisticated microbiome report.
It attempts to turn that information into an individualized intervention.
That creates a feedback loop I find genuinely useful:
Measure your biology. Understand the pattern. Build a strategy. Intervene. See how you respond. Measure again when appropriate. Then refine.
That is the direction I want Flexup Wellness to move. Healthcare has spent a very long time treating the average patient.
I am much more interested in treating the person sitting in front of me.
And when it comes to your microbiome, there may be no such thing as average.
References
1. Su GL, Ko CW, Bercik P, et al. AGA Clinical Practice Guidelines on the Role of Probiotics in the Management of Gastrointestinal Disorders. Gastroenterology. 2020;159(2):697-705. doi:10.1053/j.gastro.2020.05.059.
2. Flore. At-Home Gut Microbiome Test: Whole-Genome Shotgun Metagenomic Sequencing. Flore describes sequencing through CLIA-certified, CAP-accredited laboratories with strain-level microbial analysis. Accessed August 2026.
3. Flore. About Flore: Personalized Microbiome-Tested Probiotics. Flore reports a formulation library containing up to 68 curated probiotic strains and more than 40 targeted prebiotics, with approximately 40,000 personalized formulations produced. Accessed August 2026.
4. Flore. How Does an At-Home Microbiome Test Work? Discussion of whole-genome shotgun metagenomic sequencing compared with 16S rRNA sequencing. Accessed August 2026.
5. Flore Clinical. The Central Intelligence Engine. Flore describes an AI-supported clinical intelligence platform using paired microbiome sequencing, clinical information, and outcome data to inform individualized formulations. Accessed August 2026.
6. Rahmannia M, Poudineh M, Mirzaei R, et al. Strain-specific effects of probiotics on depression and anxiety: a meta-analysis. Gut Pathogens. 2024;16:46.
7. Phan J, Calvo DC, Nair D, Jain S, et al. Precision synbiotics increase gut microbiome diversity and improve gastrointestinal symptoms in a pilot open-label study for autism spectrum disorder. mSystems. 2024;9(5):e00503-24. doi:10.1128/msystems.00503-24. PMID: 38661344.
8. Flore. The Evidence Behind Flore / Personalized Probiotic Evidence. Flore reports observational outcome data and notes that published randomized controlled trials of its personalized formulas are not yet available. Accessed August 2026.
9. Flore. Test to Treat: The Microbiome Test That Comes With a Treatment. Description of the test → personalized synbiotic → retesting model. Accessed August 2026.
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