BiomeFx

Functional Microbiome Stool Analysis

Rethinking How We Test

Star Edwards, MS, RDN/LD

Learning & Development Manager
Topics:
• Rethinking How We Test with Functional Microbiome Analysis
• Why BiomeFx?
• Report Overview & Insights
• Which Patients Will Benefit
• Leveraging Results to Create Protocols Your Patients Will Follow
• 16s vs. Whole Genome Sequencing Technology
• Special Offer
Highlights
• Functional Microbiome Analysis Stool Test
• Provides valuable insight into the gut microbial ecosystem
• Whole Genome Sequencing powered by CosmosID
• Most accurate testing on the market with 99.9% specificity and
>95.7% sensitivity
• Customized nutrition, lifestyle, and supplement recommendations
Functional Microbiome
Analysis
• Paints a picture of the overall strength, resiliency, and
health of the microbiome
• Insight into how the patient’s diet is impacting the
microbiome
• This valuable insight directs treatment plans that restore
balance to the microbiome and builds strength and
resiliency
 FMA vs. Traditional Testing
Purpose Approach Result

Traditional Stool Tests Diagnose a specific Probing for specific Diagnosis, prescription
health condition markers (usually with medications, natural
16s or culture). antimicrobials, and
Reports a list of those occasional attempt to
markers. reseed with probiotics
Two Different (who do we need to
Tools: eliminate?)

Functional Microbiome Gain information about Reports functions of Recommend diet,

Analyses the overall strength microbes, patterns of lifestyle & supplement
and resiliency of the those functions, & protocols to rebuild the
microbiome microbial mapping. strength and resiliency
Broader reporting of of the microbiome
who is in the gut with (who do we need to
whole genome support by increasing
sequencing. or balancing?)
 Traditional

TWO DIFFERENT
TOOLS . BiomeFx
FMA
Why BiomeFx?
The health of our microbiome impacts our
overall health:

• Produces postbiotics and performs

functions that benefit our health

• Contributes to a well-functioning
intestinal barrier

• Has a low inflammatory load

• Builds a more resilient environment

less likely to experience chronic disease
Dysbiosis Risk Factors
• Medications & natural • Lack of sleep
antimicrobials
• Intense exercise
• Infections • Saturated fats and the Standard
• Excessive alcohol American Diet
• Environmental toxins like
• Smoking
glyphosate
• Stress
Why BiomeFx?
• These risk factors impact the
balance of microbes in the gut and
lead to dysbiosis
• Because different types of bacteria
perform different functions, the
postbiotics and functions being
performed in the gut are also
altered
• The only way to know how the
microbiome has been impacted ,
and therefore, how to restore
balance, is through a Functional
Microbiome Analysis
Microbiome Impact
• Metabolic dysfunction
• Autoimmunity
• Skin conditions
• Nervous system
disorders
• Hormone balance
• Liver health and function
Why BiomeFx?

Most patients have been exposed to

dysbiosis risk factors that impact overall
health. Using award-winning whole-genome
sequencing with unrivaled sensitivity and
precision, BiomeFx offers valuable insight
into your patient’s microbial ecosystem and
a roadmap to restore balance and build
resiliency in the microbiome, influencing
health systemically.
 The BiomeFx Advantage
1. ACCURACY (whole genome
sequencing)

2. > 20 FUNCTIONS of microbes

measured

3. EASY stool collection and return

4. DIETARY INSIGHTS
Report Insights
1. Who is in the gut
2. What they are doing there
3. If there is balance
4. How to restore balance,
strength and resiliency to
the microbial ecology
Report Sections
§ Overall Diversity, Stability & § Functional Keystone Species
Resilience
§ Short-Chain Fatty Acid
§ Gut Microbial Composition Producers
§ Dysbiosis Ratios § Functional Analysis
§ Pathobiome § Vitamin Biosynthesis
Report Summary
• Summarizes details of report
• Overview of the general health,
strength & resiliency of the
microbiome
• At-a-Glance out-of-range Pathogens,
Keystone Species, & Functions
• Tip: pull up with Report
Recommendations to create
patient diet, supplement, and
lifestyle protocols
 Alpha & Beta Diversity
§ Alpha Diversity - Quantity
§ How many species in patient’s
gut compared to healthy US
gut

§ Beta Diversity - Quality

§ How the species identified in
the gut compares to the
species in the healthy US gut
 Gut Microbial Composition -
Phylum
§ Who is taking up the most real
estate in the patient’s
microbiome vs. who should be
there?
Clinical Pearls – Phylum Level
Gut Composition
§ Bacteroidetes should take up the most real estate in
the gut. If we glance at it here and see that it
doesn’t, we know that our patient is struggling with
significant dysbiosis.
§ Firmicutes contains the most keystone species but
there are plenty of opportunistic groups residing in
this phyla also.
§ Actinobacteria is where Bifdo species reside.

§ Verrucomicrobia is where Akkermansia muciniphilia

lives.
§ Proteobacteria is the most inflammatory (LPS). Aim
for <2.739% overall relative abundance.
Clinical Pearls – Phylum Level
Gut Composition
§ Euyrarchaeota are methane producers (think
constipation).
§ Synergistetes often correlates with oral
dysbiosis, gingivitis, and poor stomach acid.
§ Ascomycota is the phylum for yeasts, fungi, and
mold.
§ Spirochaetes is where Borrelia (Lyme) and
Syphilis live
§ Fusobacteria is very inflammatory and often
associated with IBD and colorectal cancer.
Dysbiosis Ratios

§ Elevated ratios for these bacterial

phyla or genera point to dysbiosis
associated with a range of health
conditions:

Ø Firmicutes:Bacteroidetes (F/B)
Ø Proteobacteria:Actinobacteria (P/A)
Ø Prevotella:Bacteroides (P/B)
 Proteobacteria:Actinobacteria
§ Proteobacteria – most pathogenic phylum (gram-
negative, contains LPS). May secrete ammonia to
increase the alkalinity of the intestines.
§ Actinobacteria – contains strong butyrate producers
and certain bacteria in this phylum are associated
with improved cognition, memory and social skills.
§ Elevated ratio linked to intestinal permeability,
inflammation, dysbiosis, increased risk for chronic
disease.
 Pathobiome

§ Pathogen Control Index

§ Pathogen Species
§ Bacteria
§ Viruses
§ Protists
§ Fungi
§ Virulence Factors
 Keystone Species
§ Beneficial bacteria that have a
disproportionately large effect on
both their habitat and the status
of other microbial communities
of the gut
§ Short-Chain Fatty Acid producers
§ Create an environment that is
unfriendly to pathogens yet
allows good microbes to thrive
Functional Analysis
§ Mines sample for genes known to contribute to
the production of metabolically important
functions:
§ Saccharolytic fermentation: butyrate, propionate,
acetate, lactate
§ Proteolytic fermentation: polyamines, phenols,
ammonia, hydrogen sulfide, methane
§ Hormones & Neurotransmitters: GABA,
glutathione, histamine, indole, estrobolome
§ Vitamin Biosynthesis: Thiamin, Riboflavin,
Pantothenic acid, Pyridoxine (Vitamin B6), Biotin,
Folate, Cobalamin (Vitamin B12), Vitamin K2
Menaquinone
Saccharolytic & Proteolytic Fermentation

§ Gut bacteria feed on the food we consume and give off by-products
(postbiotics)
§ Saccharolytic Fermentation – fermentation of non-digestible
carbohydrates
Ø By-products tend to be more helpful (SCFA)
§ Proteolytic Fermentation – fermentation of protein
Ø By-products tend to be more inflammatory, especially in high amounts
(ammonia, sulfides, methane)
§ This section can be very valuable for directing a patient’s diet
 Short-Chain Fatty Acid
Production

§ Measures the genes

in the sample that
code for SCFA
production
 Ammonia Production
§ Elevated ammonia can be toxic to the gut, the liver, and the brain
§ Occurs when there is an overgrowth of ammonia producers with
excessive dietary protein intake (especially glutamine), and liver or
kidney dysfunction
 Hydrogen Sulfide Production
§ Sulfate-reducing bacteria convert dietary sulfur and taurine to
H2S
§ Toxic compound that impairs intestinal detox pathways and can
cause gas that smells like rotten eggs
§ Associated with high-protein, low-fiber diets
Methane Producers
§ Methane slows the intestinal transit and affects gut motility
§ Indirectly associated with digestive issues
Most Common BiomeFx Patterns

• Inflammation

• Constipation (possibly SIBO

or IBS-C)

• Yeast overgrowth
• Digestive efficiency in colon
Clinical Pearls - SIBO
§ Disclaimer: BiomeFx does not § Hydrogen Sulfide production
diagnose SIBO patterns:
§ Methane production patterns: Ø Desulfovibrio (family level
“fingerprint section”)
Ø Euyrachaeota (phylum level)
Ø Bilophilia wadsworthia (pathogenic
Ø Methanobacter (family level) bacteria)
Ø Methane production (functions Ø Hydrogen Sulfide production
section) (functions section)
Ø Acetate at decent levels but
butyrate low
§ Bilophilia Wadsworthia
Clinical Pearls – IBS-C
• Most common functional GI disorder
• No lab test that can definitively diagnose
IBS-C
• Microorganism patterns in stool tests
provides valuable information
• Euyrarchaeota
• Methanobacter
• Methanogens
• Fusobacteria
GABA Production
§ Neurotransmitter produced by bacteria
§ Known to have a calming effect on the
brain and may improve mood and
sleep
§ Bacillus subtilis, E. coli, Lactobacillus
rhamnosus, Bifidobacterium dentium,
and several species of Bacteroides can
produce GABA within the gut
Histamine Production
§ Produced by certain microbes as a result of histidine (amino acid)
metabolism
§ Histamine produced in the gut may elicit an immune response in
other areas of the body, as histamine can enter the bloodstream
through a weakened gut barrier
 Estrobolome
§ 60 genera of bacteria that
can recycle or deconjugate
inactivated estrogens for
reabsorption (reactivation)
into circulation by producing
Beta-glucuronidase enzymes
§ Elevated estrobolome can
contribute to estrogen
dominance
 Vitamin Biosynthesis
§ Gut bacteria synthesize
vitamins in the colon and our
symbiotic relationship allows us
to absorb and utilize these
vitamins
§ Measurement of the genes in
the sample from bacteria who
code for vitamin biosynthesis
 Who Is A Good Candidate?
Patients:
• Who are most serious about healing
their leaky gut
• For which more specific information and
direction for creating personalized
protocols that support the overall
microbiome is needed
• Who have been exposed to dysbiosis
risk factors and have symptoms and
health conditions that may be rooted in
dysbiosis
Leveraging Results to Create
Protocols Your Patients Will Follow

1. BiomeFx.com

2. Clinical
Consultations
Report Recommendations

§ Nutrition, lifestyle, and

supplement recommendations
for each marker of the test

§ BiomeFx.com > Education >

Report Recommendations
Report Recommendations
Example
§ C. diff – high

§ Akkermansia – low

§ GABA - low
Report Recommendations –
C. Diff
Report Recommendations –
Akkermansia
Report Recommendations -
GABA
Personalized Patient
Recommendations
Diet Recommendations Supplement Recommendations Lifestyle Recommendations

C. diff - High Green bananas Chicory Bacillus clausii Take spore-based probiotics along
Leeks Dandelion root RESTORFLORA OR MSB with antibiotics if you need to take
Asparagus Avoid processed sugar IgG antibiotics.
Onions MEGAIGG2000
Garlic Avoid smoking cigarettes
Artichokes
Wash hands thoroughly
Akkermansia - Cranberry polyphenols Cranberry polyphenols Consider intermittent fasting
Low Reduce sugar intake MEGAMUNE Moderate exercise 2-3 x a week
Prebiotic fibers FOS, GOS, XOS Avoid prolonged exposure to cold
MEGAPRE temps.
GABA - Low Asparagus Green tea Vitamin B6 Stress-reducing activities like yoga,
Beets Meat 5-HTP deep breathing, massage, or
Bone broth Mushrooms Oligosaccharides XOS, GOS, & FOS acupuncture
Broccoli Onion Mushroom powders
Carrots Peas and tomatoes Bacillus spore-based probiotics 7-9 hrs of sleep each night as
Cheese Avoid MSG impaired sleep is associated with low
Corn Limit caffeine GABA production
Eggs Limit high fat foods
Unrivaled Technology
16s (Amplicon)
All bacteria have the 16s rRNA
gene
§ This gene contains 9
variable regions
§ 1 or 2 hypervariable regions
of the 16s gene are
amplified using PCR
16 s (Amplicon) Limitations

§ Only a few pieces to the puzzle

§ Not accurate beyond genus level
§ 14.7% specificity and 90.8% sensitivity at
the species level*
§ Cannot identify viruses, fungi, or protists

* Analysis of sequencing strategies and tools for taxonomic annotation: Defining

standards for progressive metagenomics, Escobar-Zepeda (2018) Nature Scientific
Reports. https://www.nature.com/articles/s41598-018-3-515-5
Taxonomic Hierarchy
Whole Genome Sequencing

• End-to-end sequencing of DNA

• Complete puzzle
• Accurately identifies at species and
strain levels
• Identifies bacteria, virus, fungi, and
protists
 10,000 x more data
300 base pairs vs. 3,000,000 base pairs
Whole Genome Sequencing
with CosmosID
World’s largest microbe database:

• 10 + years curating data

• 150,000 genomes & gene sequences
• Human Microbiome Project &
American Gut Project
Mosaic Challenge

https://www.cosmosid.com/cosmosid-is-the-top-performer-in-
janssens-mosaic-strain-challenge-and-precisionfdas-cfsan-pathogen-
detection-challenge/
 The BiomeFx Difference
How does BiomeFx compare to tests like GI Map and GI Effects?
1. Purpose:
§ GI Map & GI Effects: While not diagnostic, the paradigm behind using these tests is comparable to that of traditional stool
tests (see slides 5&6): a list of specific markers probed for, with the question, “who needs to be eradicated?” These tests
usually result in antimicrobials. While sometimes necessary, this can result in overall harm to the microbiome. These test have
no or a very limited functional microbiome analysis section to report the functions of the microbes in the gut and how to
rebuild strength and resiliency in the microbiome.
§ BiomeFx The paradigm behind this test is analyzing the overall strength and resiliency of the microbiome by looking for genes
that code for specific functions, and answers the question, “how can I support and rebuild the microbiome with diet, lifestyle,
and supplement protocols?” The functional analysis includes genes from all the microbes found in the patient’s sample rather
than probing for and reporting only specific microbes.
2. Technology (the last time I checked):
1. GI Map: 16s and 23s
2. GI Effects: 16s, mass spectrometry and microscopy
3. BiomeFx: whole genome sequencing
BiomeFx Making a Difference

From a Client Survey:

I have been using other companies for stool testing with my clients, this was the first time I tried
BiomeFX. It wasn't long before I saw why so many of my colleagues are switching to them! The
comprehensive test covers a broad scope of gut microbes and it is super easy to decipher results
once they're back from lab.
When one of their in-house doctors reached out about reviewing the test and making
recommendations on how to best use these findings (and what changes might be necessary) in
order help me better serve clients - that's when I knew this company would become an
indispensable part my practice moving forward. BiomeFX stool tests are my new go-to - the
diagnostic power of this test is truly impressive, and it could not be simpler to use in practice! I am
so excited about using BiomeFX because each gut profile has excellent detail that allows me to
create a customized treatment plan for every client.
Summary

BiomeFx is a FMA that analyzes who is in the gut,

what they are doing there, and provides next-step
treatment guidance to restore balance to the gut,
therefore improving overall health, and strength and
resiliency to the gut microbiome.
Vaginal FMA Health Kit
Ø Gut bacteria easily contaminate
vaginal microbiome
Ø Gut dysbiosis can lead to vaginal
dysbiosis
Ø Vaginal health conditions – consider
stool and vaginal tests
Ø Type III and IV CSTs associated with
microbes that may have originated
in the gut
Special Offer

Coupon Code:

TS-BHRT-WEB-
AUG22

15% off
QUESTIONS?
BiomeFx.com