BiomeFx Report Glossary of Terms
Notes:
▪ For additional information and definitions, see the Interpretation Guide and Sample Report at
BiomeFx.com (under the “Education” tab).
▪ Coming soon: An encyclopedia of the microbes found in the phyla and family level composition
sections and their known functions.
▪ To search within this document, push control + F and enter your search term in the search bar.
TERM DEFINITION
1° (Primary) bile acids Bile acids synthesized by the liver.
2° (Secondary) bile acids Bile acids resulting from bacterial actions in the colon.
Absolute values The distance from zero that a number is on the number line,
without considering direction (to remove any negative sign in
front of a number).
Acetate A short-chain fatty acid produced by gut bacteria through the
fermentation of prebiotic fibers like inulin.
Alpha Diversity The number of different species of bacteria in the patient’s gut
compared to the number of species in the US Healthy
Population. This is a quantitative measure.
Amines Derivatives of ammonia. Involved in the creation of amino acids,
the building blocks of proteins. Amines participate in important
metabolic and physiological functions.
Amino acid Building blocks of proteins. Function to build muscles, cause
chemical reactions, transport nutrients, prevent illness, and
carry out other functions.
Ammonia A gas produced by gut bacteria.
AMR Acronym for Antimicrobial Resistance. Occurs when bacteria,
viruses, fungi, and parasites change over time and no longer
respond to antimicrobials produced by microorganisms or
antibiotic medicines.
AMR Richness or Index AMR stands for Antimicrobial Resistance. Microbes within the
same ecosystem compete through production of natural
antimicrobials and genes. This competition creates resilience.
The AMR Index indicates the distance between the patient’s
sample and the average healthy microbiome.
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Antibiotic Resistance Genes Genes produced my microbes so that they are no longer
affected by antimicrobials produced by microorganisms or
antibiotic medicines.
Arabinoxylan A type of dietary fiber found in cereal grains including rye,
wheat, barley, oats, rice, maize, millet, as well as psyllium, flax
seed, bamboo shoots, and rye grass.
Arginine An amino acid used in the biosynthesis of proteins. Found in red
meat, poultry, fish, and dairy products.
B-glucuronidase An enzyme produced by the intestinal epithelium and certain
intestinal bacteria. B-glucuronidase breaks bonds between
glucuronic acid and toxins in the intestines. The binding of toxins
in the gut is protective because it blocks their absorption and
facilitates excretion. Higher levels of B-glucuronidase may be
associated with higher circulating estrogens and lower fecal
excretion of estrogen in premenopausal women.
Beta Diversity How the specific species of bacteria in a patient’s gut compares
to the specific species of bacteria in the US Healthy Population.
This is a qualitative measure.
Cell surface carbohydrates Surface carbohydrates on a cell. Serve as points of attachment
for other cells, including infectious bacteria and viruses, toxins,
and hormones.
Cell surface proteins Proteins that are embedded in or span the layer of cell
membranes and influence the way in which a cell interacts with
the environment, including other cells.
Cell turnover When dead cells are replaced with younger cells.
Deconjugate To disrupt a system of conjugated double bonds leading to loss
of conjugation (to break apart).
Dendritic Cells Specialized immune cells that act as messengers between the
innate and adaptive immune system.
Dietary Fiber Carbohydrates that are edible but not digestible by humans.
Fiber is passed through the digestive system but not absorbed
and metabolized.
Diversity The variety of species of bacteria in the microbiome.
Dopamine A neurotransmitter that plays a role in how we feel pleasure.
Dysbiotic Gut Disruption in the normal, healthy balance of microbes in the
microbiome, resulting in changes in the functions and metabolic
activities being performed.
Endocrine gland Glands that make up the endocrine system and produce
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hormones. Endocrine glands include pituitary, thyroid, thymus,
and adrenal glands.
Endogenously Originating from within the body.
Enterocytes Cells of the intestinal lining.
Environmental Toxins Toxins in the environment (air, drinking water, and food) that
often have a cumulative and delayed effect. These can include
heavy metals like lead, mercury, and arsenic, insecticides and
pesticides, chemicals found in plastic, and more.
Enzyme A substance that acts as a catalyst in living organisms,
accelerating chemical reactions.
Estrogen dominance A type of hormonal imbalance in which the body produces too
much estrogen.
Fat-soluble vitamin Vitamins that are absorbed along with fats in the diet and stored
in the body’s fatty tissue and liver. Vitamins A, D, E, and K are
fat-soluble.
FOS (Fructooligosaccharides) Non-digestible carbohydrates considered a prebiotic. Found
naturally in kiwi fruit, chicory, onions, asparagus, and more.
Functional Analysis Assessment of the metabolic functions being carried out by
microbes in the gut. For example, production of short-chain fatty
acids, ammonia, hydrogen sulfide, methane, and
neurotransmitters, estrogen recycling, and vitamin biosynthesis
are included in the Functional Analysis.
Genome All genetic information of an organism.
Gluconeogenesis The process by which non-carbohydrate precursors produce
glucose for energy.
Glutamine The most abundant naturally occurring, nonessential amino acid
in the human body, and one of the few amino acids that can
directly cross the blood-brain barrier. Glutamine plays a role in
protein synthesis, lipid synthesis, cellular energy, regulation of
acid-base balance in the kidneys, the integrity of the intestinal
mucosa, and more. Humans obtain glutamine through
catabolism of proteins in foods they eat chicken, beef, and eggs.
L-glutamine is a popular nutrition supplement.
GOS Non-digestible carbohydrates considered a prebiotic. Found
(Galactooligosaccharides) naturally in cow’s milk, yogurt, artichoke, lentils, lentils, and
more.
Gram-negative bacteria Bacteria that have a thin peptidoglycan layer and an outer lipid
membrane. Contain LPS (lipopolysaccharide).
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Gram-positive bacteria Bacteria that have a thick peptidoglycan layer and no outer lipid
membrane.
Gut Associated Lymphoid Tissue in the gut consisting of immune cells.
Tissues (GALT)
Gut Microbiome Index Overall score of gut microbiome health. The Gut Microbiome
Index considers the following scores: Alpha Diversity, Beta
Diversity, Pathogen Occurrence and Resistome Occurrence.
Gut motility Stretching and contracting of the muscles in the gastrointestinal
system (peristalsis) that enable food to move through the
digestive tract.
Histamine A chemical found in some of the body’s cells that causes many
of the symptoms of allergies. Histamine also helps regulate
physiological function in the gut and acts as a neurotransmitter
for the brain, spinal cord, and uterus.
Histone deacetylases Enzymes that remove acetyl groups from lysine residues,
(HDACs) resulting in repression of gene expression.
Hormone Chemical messengers that are secreted directly into the blood,
which carries them to organs and tissues of the body to exert
their functions.
Hydrogen sulfide / H2S A toxic compound produced by sulfate-reducing bacteria from
dietary sulfur and taurine. Hydrogen sulfide can impair intestinal
detoxification pathways.
Hydrolytic enzymes As it pertains to virulence, enzymes that contribute to host tissue
invasion by digesting or destroying cell membranes and by
degrading host surface molecules.
Immunomodulation Modification of the immune system.
Inflammatory disease Disease or disorder characterized by inflammation occurring
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when the immune system attacks the body’s own tissues.
Examples include allergies, asthma, autoimmune diseases,
Celiac disease, and inflammatory bowel disease.
Insulin sensitivity Insulin sensitivity is how sensitive the body's cells are to insulin.
High insulin sensitivity allows the cells of the body to use blood
glucose more effectively, reducing blood sugar.
Intestinal Barrier Function The intestinal barrier functions as a structure that allows for the
uptake of essential nutrients and immune homeostasis, while
restricting pathogenic organisms, toxins, and undigested food
particles from passing into the bloodstream.
Intestinal detoxification Intestinal epithelial cells have a detoxification system, which
serves as a chemical barrier in the gut. Toxic xenobiotics are
metabolized by detoxification enzymes, and the resultant less-
harmful compounds are efficiently excreted from the cells to the
intestinal lumen.
Intestinal pH PH is a scale of acidity from 0 to 14. It tells how acidic or
alkaline a substance is. Optimal pH in the digestive system
helps to digest food and minimize pathogens.
Intestinal transit Time it takes for food to travel from your mouth through your
digestive tract to your anus.
Inulin A type of dietary fiber found in Jerusalem artichoke, leeks,
bananas, jicama, and more.
Keystone Species Beneficial bacteria that have a disproportionately large effect on
both their habitat and the status of other microbial communities
of the gut. These species create an environment that is
unfriendly to pathogens yet allows good gut microbes to thrive.
Low levels are associated with obesity, diabetes, liver disease,
cardiometabolic disease, low-grade inflammation, IBS, Crohn’s,
Celiac Disease, chronic constipation, allergies and asthma,
chronic fatigue, and more.
Latent infection The presence of a pathogen without symptoms. This may occur
during incubation periods, or when viruses lie dormant within
cells as part of their life cycle.
Lipogenesis Formation of fat in the body for storage.
Macrophages Immune cells that are highly specialized in removal of dying or
dead cells and cellular debris.
Metabolic imbalances Metabolism is the chemical processes that occur within a living
organism in order to maintain life. Imbalances in these
processes are termed metabolic imbalances. Examples include
dysregulated blood sugar, electrolyte imbalances, and acid-base
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imbalances.
Metabolism The chemical processes that occur within a living organism in
order to maintain life, including the conversion of food to energy,
the conversion of food to building blocks (for proteins, lipids, and
some carbohydrates), and the elimination of metabolic wastes.
Metabolite An intermediate or end product of metabolism.
Microbes Bacteria, fungi, protozoa, and viruses.
Microbial genes The genetic information possessed by microbes.
Microbiome (gut microbiome) The collection of microbes that reside within the human gut.
Microbes include bacteria, fungi, parasites, and viruses.
My Sample Relative Relative species abundance is a component of biodiversity and
Abundance (%) refers to how common or rare a species is relative to other
species in a defined location or community. Relative abundance
is the percent composition of an organism of a particular kind
relative to the total number of organisms in the area.
Neurotransmitters Chemical messengers that transmit a signal from a neuron
(nerve cells) across a synapse (neuronal junction) to a target
cell, which may be another neuron, a muscle cell, or a gland
cell.
Oxidative stress Free radicals are by-products of metabolic processes including
ATP or energy production. Antioxidants neutralize or remove
free radicals. Oxidative stress occurs when there is an
imbalance of free radicals and antioxidants. Oxidative stress can
cause cell and tissue damage and plays a role in the aging
process.
P-cresol A by-product of tyrosine metabolism by gut bacteria that can be
toxic to intestinal cells and impair intestinal barrier function.
Tyrosine is an amino acid the body makes from the amino acid
phenylalanine. It is needed to produce neurotransmitters
including epinephrine, norepinephrine, and dopamine.
Pathogen Control Index Low levels of pathogens can be normal and characteristic of a
healthy, diverse gut microbiome. Increased levels of pathogens
could indicate that a pathogen is playing a role in
symptomatology. The Pathogen Control Index is a measure of
the number of pathogens in the patient’s microbiome compared
to the number of pathogens in the US Healthy Population’s
microbiome. The more pathogens that are present, the more the
score drops.
Pathogenicity The property of causing disease.
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Pathogens Viruses, bacteria, fungi, protozoa, and worms that can cause
disease. It’s often normal for low levels of pathogens to inhabit
the microbiome, but in greater quantities can lead to illness.
PCo Principal Coordinate Analysis at the 1st axis. A way to visualize
dis-similarity data. We are plotting the dissimilarity matrix of the
Bray-Curtis beta diversity. The PCoA produces orthogonal axes
to summarize the variability in the data set.
PCoA2 Principal Coordinate Analysis at the 2nd axis. A way to visualize
dis-similarity data. We are plotting the dissimilarity matrix of the
Bray-Curtis beta diversity. The PCoA produces orthogonal axes
to summarize the variability in the data set.
Peptides Short chains of amino acids (the body’s basic building blocks)
held together by peptide bonds. Peptides act as transporters,
enzymes, hormones, structural elements (part of the muscle, for
example), and link together to form protein.
Percentile A score below which a given percentage of scores in its
frequency distribution falls or a score at or below which a given
percentage falls. For example, the 50th percentile is the score
below which or at or below which 50% of the scores in the
distribution may be found.
Phenol Compounds resulting from the fermentation of amino acids such
as tryptophan and tyrosine by bacteria like E. coli. Phenols are
cytotoxic and may cause damage to the gut, skin, vascular
system, kidney, and more.
Phylum The third broadest taxonomic rank of organisms in biology.
Taxonomy names and classifies groups of organisms based on
shared characteristics.
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Polyamines A type of amine that possesses more than one amine
functionality.
Polysaccharides A large molecule made of many smaller monosaccharides, or
simple sugars like glucose. Examples of polysaccharides
include cellulose found in legumes and resistant starch found in
plantains.
Postbiotic By-products secreted by live bacteria after they ferment dietary
components from the human diet. Examples include enzymes,
short-chain fatty acids.
Prebiotic Fibers Dietary fibers that are resistant to digestion and feed bacteria in
the gut. Food sources of prebiotic fiber include chicory root,
oatmeal, asparagus, and Jerusalem Artichoke.
Prefrontal cortex A part of the brain located at the front of the frontal
lobe. Implicated in a variety of complex behaviors,
including planning, and greatly contributes to
personality development.
Presynaptic nerve terminal A specialized area
within the axon
(nerve fiber) of the
presynaptic cell
(cell that releases
neurotransmitters
to stimulate the
postsynaptic cell)
that contains
neurotransmitters
enclosed in small membrane-bound spheres.
Proteolytic fermentation Fermentation of protein by gut bacteria. Bacteria utilize protein
in the human diet to ferment and produce by-products like
ammonia and hydrogen sulfide that are generally viewed as
more toxic, especially in high amounts.
Protists Microscopic, one-celled organisms. A type of parasite (organism
that lives on or in a host organism and obtains its food from or at
the expense of its host).
Psychobiome Elements of the gut microbiome that influence mood, cognition,
and mental health.
Pyruvate Chemical compound used for energy as a result of glucose
being broken down.
Regulatory T cell The process by which cells become specialized T cells. T cells
differentiation secrete anti-inflammatory substances to regulate immune
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function.
Relative Abundance (RA) The percent composition of an organism of a particular kind
relative to the total number of organisms in the area.
Relative Abundance IQR When using the cohort of healthy samples, rather than looking
Range (%) / Healthy RA IQR% at the mean or median abundance for a particular microbe,
which often does not represent the range that most samples fall
into for that given organism, the interquartile range (IQR),
represents the middle 50% of the abundance. It incorporates the
abundance range for most of the healthy samples and ignores
those more likely to be outliers.
Resistant starch Starch that is resistant to digestion and functions like soluble
fiber, passing through the stomach and small intestine
undigested, eventually reaching the colon and feeding friendly
gut bacteria, and producing helpful by-products. Found in foods
like raw potatoes, cooked and then cooled potatoes, green
bananas, various legumes, cashews, and raw oats.
Saccharolytic Fermentation Fermentation of carbohydrate fibers by gut bacteria. Bacteria
utilize non-digestible carbohydrates in the human diet to ferment
and produce by-products like short-chain fatty acids.
Serotonin Neurotransmitter that enables brain cells and other nervous
system cells to communicate with each other. Modulates mood,
cognition, reward, learning, memory and plays a role in
sleeping, eating, and digestion.
Short-chain fatty acids (SCFA) Fatty acids produced by gut bacteria during the fermentation of
non-digestible carbohydrates (fiber). SCFA are beneficial to our
health, acting as the preferred fuel for epithelial cells of the
colon. Three short-chain fatty acids are acetate, propionate, and
butyrate. SCFA help to reduce inflammation and oxidative
stress, and improve insulin sensitivity, energy expenditure,
intestinal motility, and immune regulation. Butyrate also
increases mucin production by up regulating the muc2 gene.
Synapse The site of transmission of electric nerve impulses between two
nerve cells (neurons).
Synaptic cleft A space that separates two neurons (cells within then nervous
system), allowing nerve impulses pass from one neuron to the
other.
Taurine An amino acid found in meat, fish, dairy products, and human
milk.
Trimethylamine (TMA) An amine with a fishy odor. It is synthesized from choline (found
in eggs, beans, peanuts, soy products, and more), L-carnitine,
betaine, and lecithin by microbial enzymes.
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Tryptophan An essential amino acid, meaning your body cannot produce it
and it must be obtained from diet. Found in foods like milk,
turkey and chicken, oats, cheese, nuts, and seeds.
Tyrosine Nonessential amino acid the body makes from another amino
acid called phenylalanine. It is an essential component for the
production of several important brain chemicals called
neurotransmitters, including epinephrine, norepinephrine, and
dopamine.
Virulence Factors Virulence is the measure of the pathogenicity of an organism, or
its ability cause disease. Factors that increase an organism’s
virulence include toxins, enzymes, adherence factors, and
protective capsules, among others. BiomeFx measures toxin
virulence factors.
Vitamin Biosynthesis The process by which vitamins are synthesized by bacteria.
Water-soluble vitamins Vitamins that dissolve in water and are readily absorbed into
tissues for immediate use. Water-soluble vitamins are not stored
in the body and include B vitamins and vitamin C.
Xenobiotic-metabolizing Xenobiotic is a chemical substance found within an organism
enzymes like cytochrome that is not naturally produced or expected to be present within
P450 an organism. Metabolizing means to be processed. Enzymes
are proteins that accelerate chemical reactions. Cytochrome
P450 is a hemeprotein that plays a key role in the metabolism of
drugs and other xenobiotics.
XOS (xylooligosaccharides) Non-digestible carbohydrates considered a prebiotic and found
in corn cob, milk, honey, bamboo shoots, and more.
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