- Advanced Functional Testing
Shotgun Metagenomics Gut Microbiome Test
A broader, more detailed view of your gut’s microbial ecosystem.
Rather than looking for a limited list of organisms, shotgun metagenomic testing analyzes microbial DNA in a stool sample to identify a wide range of species, assess diversity, and reveal the community’s genetic potential — from nutrient metabolism to histamine and hydrogen sulfide production.
"I've tried every probiotic and gut protocol out there. Nothing tells me what's actually living in my gut."
Most stool tests look for a defined list of organisms. They can tell you whether a specific pathogen is present, but not how diverse your microbiome is, which beneficial species are missing, or what your microbes are capable of doing.
Shotgun metagenomics was built for this gap. It sequences all of the microbial DNA in your sample — giving a species-level picture of your gut community and the genes that drive what it does.
Understanding the Test
What is Shotgun Metagenomic Testing?
Shotgun metagenomic gut microbiome testing offers a broader, more detailed view of the gut’s microbial ecosystem than culture-based testing or targeted PCR panels. Rather than looking for a limited list of organisms, it analyzes microbial DNA in a stool sample to identify a wide range of species, assess diversity, and reveal the community’s genetic potential.
Shotgun sequencing helps identify bacteria associated with butyrate production, explore microbes involved in producing compounds related to GABA and dopamine, and detect organisms that may produce inflammatory compounds
Microbiome researcher Dr. Jason Hawrelak and microbiologist Kiran Krishan favor this approach for evaluating microbiome composition because it provides greater species-level detail than conventional 16S sequencing and can offer insights into pathways involved in processes such as oxalate breakdown, histamine production, and hydrogen sulfide production.
These findings can help inform individualized nutrition and gut-support strategies. Targeted pathogen testing and other stool markers also remain valuable when infection, inflammation, or digestive dysfunction is suspected.
What the BiomeFx measures
Deep Shotgun Metagenomics
Richness and balance of your gut community
Bacteria, archaea and fungi at the species level
Akkermansia, Faecalibacterium, Bifidobacterium
Oxalate breakdown, histamine, hydrogen sulfide
Short-chain fatty acids and nutrient metabolism
Overgrowth of potentially harmful organisms
Symptoms beyond the gut
These are the symptoms many people never connect to their gut microbiome — but that a full-picture stool test can help explain.
- Brain fog
- Anxiety
- Low Mood
- Fatigue
- Skin Issues
- Joint Pain
- Low immunity
- Hormones Imbalance
- Food Senstivities
- Oxalate Issues
Your gut microbes talk to your whole body. They help produce short-chain fatty acids, influence inflammation, and interact with the gut–brain axis — which is why an imbalanced microbiome can show up as mood, energy and skin symptoms as often as digestive ones.
Could This Be You?
Signs your microbiome needs a closer look
Digestive symptoms
Often linked to imbalanced fermentation and low diversity
Shifts in microbial balance affect motility and stool form
Some gut microbes carry genes for histamine production
Hydrogen sulfide pathways can be assessed in your report
Without knowing what’s missing, supplements are guesswork
What Shotgun Metagenomics Detects
Six categories.
One detailed picture.
By sequencing all of the microbial DNA in your sample, this test shows who is living in your gut, how diverse the community is, and which genes your microbes carry — insight into what they may be capable of doing.
Diversity & Richness
A diverse microbiome is a resilient one. Low diversity is linked to inflammation, food sensitivities and slower recovery after antibiotics.
- Alpha diversity
- Beta diversity
- Gut microbiome index
Keystone & Beneficial Species
Species that protect the gut lining and calm inflammation. When they’re low, the whole ecosystem tends to destabilize.
- Akkermansia
- Faecalibacterium
- Bifidobacterium
Phylum Balance
Broad shifts in the major bacterial groups can reflect diet, blood-sugar regulation and how efficiently you extract energy from food.
- Firmicutes
- Bacteroidetes
- F/B ratio
Functional Pathways
Microbial genes that point to what your gut community may be capable of producing or breaking down.
- Oxalate breakdown
- Histamine
- Hydrogen sulfide
Metabolic & Hormone Functions
Short-chain fatty acids fuel your colon cells; the estrobolome influences how estrogen is recycled.
- Butyrate
- Acetate
- Estrobolome
Pathogens, Yeast & Parasites
Opportunistic bacteria, fungi and parasites that can drive bloating, inflammation and digestive symptoms.
- Candida
- Blastocystis
- Bilophila
- C. difficile
From the Lab
Why BiomeFx is different
BiomeFx goes beyond identifying which microbes are present. Deep shotgun sequencing profiles the whole community and looks at what it is doing — the activity that links your microbiome to your health.
What sets it apart
- Advanced whole-genome sequencing (deep shotgun metagenomics)
- Strain-level detection across all microbial domains
- Comprehensive stool DNA profiling, 300–500+ organisms
- Beyond functional analysis — the microbiome’s theater of activity — revealing microbial health impact
- Evaluates 20+ microbial pathways and activities
- Assesses metabolites, dysbiosis, pathogens, interactions
20+ microbial pathways and activities assessed, such as:
- Metabolite production
- Dysbiosis ratios
- Pathway-specific insights
- Health-related associations
- Keystone species
- Pathogen balance
- Microbial interactions
The Sequencing Difference
Why shotgun sequencing
goes deeper
Culture-based stool tests can only grow organisms that survive in a lab dish — and most gut microbes don’t. 16S sequencing reads a single marker gene, which usually identifies bacteria to the genus level but rarely to the species.
Shotgun metagenomics reads all of the microbial DNA in your sample. That means species-level identification across bacteria, archaea and fungi — and a look at the genes that drive function, such as the pathways involved in oxalate breakdown, histamine production and hydrogen sulfide production.
It’s important to remember that genes show potential, not proof. A pathway being present doesn’t confirm a metabolite is being produced. I always interpret these findings alongside your symptoms, history and other labs.
Level of detail — visualized
Solid = typically resolved · Faint = limited or partial · Dashed = not assessed
identification, not just genus
insight into what microbes may be capable of doing
bacteria, archaea, fungi and parasites in one test
a small stool sample, collected in minutes
The gut-brain axis — how gut dysfunction shows up in your mind
Low serotonin and GABA from dysbiosis
Direct gut-to-brain communication pathway
Elevated zonulin and immune activation
Pathogens, overgrowths, or bacterial imbalance
The Gut-Brain Connection
Your gut is your second brain
This is not a metaphor. Your gut and brain are in constant two-way communication through the vagus nerve — and the state of your gut microbiome directly influences neurotransmitter production, stress response, and mood regulation.
This is why I use the GI Map with clients dealing with anxiety, OCD, ADHD, and depression just as often as with those dealing with digestive complaints. In many cases the gut is the origin of symptoms that have been treated as purely mental health issues for years.
- Dysbiosis directly lowers serotonin production — affecting mood, anxiety levels, and sleep quality in ways that no antidepressant can fully compensate for if the gut imbalance is never corrected.
- Elevated zonulin allows bacterial toxins called LPS into the bloodstream — where they cross the blood-brain barrier and drive neuroinflammation, brain fog, and cognitive symptoms.
- H. pylori depletes zinc and B12 — two nutrients absolutely critical for mental health, mood stability, and neurological function.
GI Map vs. Standard Testing
Why a standard stool test
is not enough
Standard gastroenterology testing often misses the mark. The GI Map is
designed to find the functional imbalances that cause chronic everyday symptoms.
Standard Stool / GI Test
- Uses culture-based methods that miss many organisms entirely
- Does not test for zonulin or intestinal permeability
- Does not map microbiome balance or dysbiosis
- Misses low-level parasitic infections that PCR often detects
- Does not include digestive enzyme markers or immune function
- Results interpreted with no nutrition or root-cause context
GI Map with Zonulin
- PCR DNA technology detects organisms at extremely low levels
- Includes zonulin — the only validated marker for leaky gut
- Maps full microbiome including beneficial and harmful bacteria
- Detects parasites, fungi, and viruses in one single test
- Includes pancreatic elastase, secretory IgA, and calprotectin
- Results interpreted with full functional nutrition context and a treatment plan
How It Works
Simple at-home collection.
Life-changing results.
The GI Map is a home collection stool test — no clinic visit, no prep procedure, no
discomfort. Here is exactly what working with Samantha looks like from start to finish.
01
Free Discovery Call
We talk through your symptoms, history, and health goals to confirm whether GI Map testing is the right starting point for you.
02
Consultation and Lab Order
After your initial intake session, I order the GI Map kit directly through Diagnostic Solutions. Your collection kit is mailed to your home with clear instructions.
03
Home Collection and Return
You collect a single stool sample at home following the simple instructions provided. The kit ships back to the lab in the pre-paid return packaging.
04
Your Treatment Plan
Once results are in I build your personalized treatment plan. We meet to review every finding together and begin your nutrition, supplement, and lifestyle protocol. Monthly follow-up sessions keep your plan on track.
years in practice
Why Work With Samantha
The GI Map is a tool.
The plan is what heals you.
A detailed stool test report means nothing without someone who knows how to read it in the context of your full health picture. I don’t just look at what the test flagged — I look at how your gut findings connect to your mental health symptoms, nutrient status, hormone levels, and daily life.
I’m Samantha Gilbert, a Certified Functional Nutrition Counselor with over 18 years of experience. The gut-brain connection is central to my practice. Many of my clients dealing with anxiety, OCD, ADHD, and depression find that healing their gut is the missing piece they never knew to look for.
- I connect your gut findings to your whole picture — including mental health, hormone balance, methylation, zinc and copper status, and nutrient absorption.
- I build a specific, actionable plan — targeted foods, therapeutic supplements, and lifestyle shifts based directly on your results, not a generic gut protocol.
- All sessions are fully virtual — I work with clients across the US and internationally. Wherever you are, we can work together.
Common Questions
Everything you need to
know before you start
What is the GI Map test and what does it measure?
The GI Map is a specialty stool test that uses quantitative PCR technology — DNA analysis — to detect and measure over 50 markers in your gut. This includes bacterial pathogens like H. pylori, parasites, fungi, your overall microbiome balance, digestive enzyme levels, immune markers, and zonulin for intestinal permeability. It gives a complete picture of your gut health that standard stool tests cannot come close to matching.
How is the GI Map different from a stool test my doctor orders?
Standard stool tests use culture-based methods that miss many organisms entirely — they can only detect what physically grows in a lab culture. The GI Map uses PCR DNA technology that identifies the genetic fingerprint of organisms, making it far more sensitive and accurate. It also includes zonulin, microbiome balance markers, immune function, and digestive enzyme levels that conventional testing simply does not offer.
Can gut issues really cause anxiety, brain fog, and mood problems?
Absolutely — and this is often the most important thing my clients learn. Around 90% of your serotonin is produced in the gut. Dysbiosis disrupts that production. Elevated zonulin allows bacterial toxins to enter the bloodstream and cross the blood-brain barrier, driving neuroinflammation. H. pylori depletes zinc and B12, both of which are critical for mental health. In my practice, the GI Map regularly uncovers the gut root of symptoms that have been treated as purely psychological for years.
How long does it take to get results?
Once the lab receives your sample, results are typically ready within 2 weeks. After that, I review your full report and build your personalized treatment plan. We then meet to go through everything together — I explain exactly what each finding means for your specific situation and walk you through your nutrition, supplement, and lifestyle recommendations in detail.
Do you only order the GI Map, or do you combine it with other tests?
It depends entirely on your symptoms and history. Some clients start with the GI Map alone. Others benefit from combining it with additional testing — such as the DUTCH hormone test, urine kryptopyrrole for Pyrrole disorder, or bloodwork for zinc, copper, and nutrient status. During your initial consultation we decide together which combination of tests will give us the most useful starting picture for your specific situation.
What is zonulin and why does it matter?
Zonulin is a protein that regulates the tight junctions in your intestinal wall — the microscopic gates that control what passes from your gut into your bloodstream. When zonulin is elevated, those junctions are too open, allowing toxins, bacteria, and undigested food particles to leak through. This is known as intestinal permeability or leaky gut, and it drives systemic inflammation that shows up far beyond the gut — in your joints, skin, brain, and mood.
How do I collect the sample? Is it difficult?
Not at all. Your GI Map kit arrives by mail and includes everything you need — collection tubes, a sample collection device, clear step-by-step instructions, and a pre-paid return shipping label. You collect a small stool sample at home at your convenience, place it in the provided tube, and mail it back to the lab. The whole process takes a few minutes and most clients find it very straightforward.
Is the GI Map covered by insurance?
Not typically. It is a specialty functional lab test ordered outside the conventional medical system and is an out-of-pocket cost. During your free discovery call I will walk you through current pricing and help you decide whether GI Map testing is the right first step based on your symptoms and history, or whether other tests should take priority.
I live outside the United States. Can I still do this test?
Yes. I work with international clients regularly. The GI Map kit can be mailed to a US address — such as a UPS mailbox or a friend or family member in the states — and then shipped back to the lab from within the US. I have several clients in Canada, including many in Vancouver, BC, who have set this up without issue. If you live in a country where the test can be ordered through a local provider, we can often arrange that. Reach out during your discovery call, and we will find the best solution for your situation.
What happens after I get my GI Map results?
Once all your results are in I build your personalized starting treatment plan. We meet to review your findings together — I translate the data into a specific, practical plan covering foods, targeted supplements, and lifestyle changes. From there we meet monthly with updates as your gut heals and your symptoms improve, and you can message me between sessions for additional support whenever you need it. You are never left to figure things out on your own.
Two stool tests, complementary information
Broad view of the whole microbial community: species, diversity and functional potential
Targeted qPCR for specific pathogens, parasites and fungi, plus digestion, inflammation and immune markers
A Broader Perspective
Why I often pair it with the GI-MAP
For these reasons, I often pair the BiomeFx stool test with the GI-MAP stool test to gain a broader perspective on my clients’ gut health. These tests provide complementary information, helping me explore patterns that might not be apparent from a single test alone.
The goal isn’t simply to collect more data — it’s to understand which findings may be relevant to each client’s symptoms and nutritional needs.
- BiomeFx shows the composition, diversity and genetic potential of your microbiome.
- The GI-MAP looks for a defined list of organisms and measures markers like pancreatic elastase, calprotectin and secretory IgA.
- Together they help me see patterns a single test can miss. Learn about the GI-MAP →
Shotgun Metagenomics vs. Standard Testing
Why a standard stool test
doesn’t show the full picture
Conventional stool testing is designed to find obvious infections. Shotgun metagenomics is designed to map the whole ecosystem.
Culture / 16S Testing
- Culture misses the many microbes that can’t grow in a lab dish
- 16S usually stops at the genus level, not species
- Little or no insight into microbial genes and function
- Doesn’t assess oxalate, histamine or hydrogen sulfide pathways
- Results interpreted with no nutrition or root-cause context
Shotgun Metagenomics
- Sequences all microbial DNA in the sample
- Species-level identification across bacteria, archaea and fungi
- Measures diversity and keystone species
- Insight into oxalate, histamine and hydrogen sulfide pathways
- Results interpreted with full functional nutrition context and a treatment plan
How It Works
Simple at-home collection.
A deeper understanding.
Your kit arrives by mail with everything you need. Here is exactly
what working with Samantha looks like from start to finish.
01
Free Discovery Call
We talk through your symptoms, history and health goals to confirm whether shotgun metagenomic testing is the right starting point for you.
02
Consultation and Lab Order
After your initial intake session, I order your BiomeFx kit. It’s mailed to your home with collection tubes, clear instructions and a pre-paid return label.
03
Home Collection and Return
You collect a small stool sample at home, place it in the provided tube and mail it back. The whole process takes just a few minutes.
04
Your Treatment Plan
Results typically arrive in about 2 weeks. We review every finding together and I build your personalized nutrition, supplement and lifestyle plan.
years in practice
Why Work With Samantha
The test reveals patterns.
Context makes them meaningful.
I interpret the results alongside each client’s health history, diet, symptoms, and other relevant laboratory findings, rather than treating any one result as a diagnosis or a complete explanation. This context helps me develop a more individualized nutritional therapy plan.
I’m Samantha Gilbert, a Certified Functional Nutrition Counselor with over 18 years of experience. The gut–brain connection is central to my practice, and many of my clients dealing with anxiety, OCD, ADHD and depression find that their gut is a missing piece.
- I connect your microbiome findings to your whole picture — including mental health, hormone balance, methylation, zinc and copper status, and nutrient absorption.
- No one-size-fits-all probiotics — your plan is based on what your microbiome actually shows, not a generic gut protocol.
- All sessions are fully virtual — I work with clients across the US and internationally.
Common Questions
Everything you need to
know before you start
What is shotgun metagenomic testing?
It’s a stool test that analyzes all of the microbial DNA in your sample to identify a wide range of species, assess diversity, and reveal the genetic potential of your gut community. It offers more species-level detail than culture-based testing or conventional 16S sequencing.
How is BiomeFx different from the GI-MAP?
Both tests use a stool sample, but they provide different types of information about your gut.
BiomeFx takes a broader look at your gut’s microbial community. It uses shotgun metagenomic sequencing to analyze microbial DNA, providing information about the types of microbes present, their relative abundance, and the diversity of your microbiome. It also examines microbial genes to help estimate what your microbes may be capable of doing, such as participating in nutrient metabolism and producing certain compounds. These are insights into functional potential, not direct measurements of everything happening in your gut.
The GI-MAP takes a more targeted approach. It uses quantitative PCR (qPCR) to look for a defined list of organisms, including selected bacteria, parasites, viruses, and fungi. It also measures markers related to digestion, inflammation, and immune activity, such as pancreatic elastase, calprotectin, and secretory IgA.
How is the sample collected?
Your BiomeFx kit arrives by mail and includes everything you need — collection tubes, a sample collection device, clear step-by-step instructions, and a pre-paid return shipping label. You collect a small stool sample at home at your convenience, place it in the provided tube, and mail it back to the lab. The whole process takes a few minutes and most clients find it very straightforward. I’ll advise you on how to prepare for the test, and if anything about your current supplements or medications needs to be considered first.
How long does it take to get results?
Turnaround time is typically 2 weeks. Once received, we’ll book an appointment to review your results.
Is this test covered by insurance?
Not typically. It is a specialty functional lab test ordered outside the conventional medical system and is an out-of-pocket cost. During your free discovery call I will walk you through current pricing and help you decide whether BiomeFx testing is the right first step based on your symptoms and history, or whether other tests should take priority.
Does a functional pathway mean my microbes are producing that compound?
Not necessarily. Shotgun metagenomics shows genetic potential — the genes your microbes carry — not actual metabolite production. That’s why I interpret pathway findings such as histamine or hydrogen sulfide alongside your symptoms, diet and other lab results rather than treating them as a diagnosis.
Do you only order BiomeFx, or combine it with other tests?
I often pair BiomeFx with the GI-MAP with Zonulin because the two provide complementary information. Depending on your symptoms, I may also recommend tests such as the Organic Acids test or the Methylation Profile.
Ready to find out what's
really going on in your gut?
Book your free 20-minute discovery call with Samantha. We will talk through your symptoms and history and figure out whether GI Map testing is the right next step for you.