Glossary

Absorption

In biology, absorption is the process of in which substances pass into a cell, tissue, or organ. It is done through diffusion or active transport. An example of biological absorption is the passage of digested food through the wall of the intestine into our blood vessels. An another example is the passage of substances which reach the colon into members of our microbiota.

Acetyl CoA

A complicated molecule derived from the metabolism of macronutrients and acts as the main fuel used by all human cells

Adsorption

The accumulation of a substance on the surface of another.  Adsorption of water from the air is often visible, for example, on a bedroom window on a cold morning

Amino acid

An amino acid is a fundamental  building block of a protein.  Each of our proteins consists of one or more chains of amino acids.  There are 20 different amino acids.  Some can be synthesized in our body, but others (essential amino acids) cannot and must be obtained from our diet.

Amino acid - aromatic

Aromatic amino acids are part of the group of amino acids considered essential for humans. One of their important functions is to capture UV light in the human skin.

Amino acid - branched chain

The term branched chain amino acid is often abbreviated to BCAA. The term branched chain refers to the chemical structure of BCAA. Nine of the EAA are BCAA, namely leucine, isoleucine, and valine which are present in protein-rich foods such as eggs, meat, and dairy products

Amino acid - essential

The term essential amino acid is abbreviated to EAA. Our bodies need all 20 amino acids to grow and function properly. However, we cannot synthesize nine of those 20 and those are the EAA. They are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. The best sources of EAA are animal proteins such as meats and eggs. Some made from soy such as edamame and tofu also contain all nine EAAs

Antioxidant

In biology antioxidants are compounds that inhibit potential damage caused by the by-products of normal metabolism. The most common and effective antioxidant present in most life forms is melatonin. Known dietary antioxidants are vitamins A, C, and E.

Outside of biology, antioxidants are frequently added to industrially processed food ingredients and other industrial products to slow spoilage, for example.

Atherosclerosis

Atherosclerosis is a process of damage leading to plaque formation that can occur in the cell membranes of our arteries. Arteries throughout our body can be affected although they tend to be associated with the arteries supplying blood to our heart and to our brain.

Autonomic nervous system (ANS)

The autonomic nervous system for most of us acts unconsciously and controls things like heart rate and strength of contraction, digestion, respiratory rate, urination, etc. It is divided into two parts, namely the sympathetic nervous system, the parasympathetic nervous system. The sympathetic nervous system is often considered the “fight or flight” system, while the parasympathetic nervous system is often considered the “rest and digest” or “feed and breed”.

Autophagy

Simply put, autophagy is our body’s machinery for getting rid of faulty components. It occurs regularly in our cells and is responsible for ridding us of unnecessary or broken components such as pathogens, and faulty proteins and other sub-cellular elements. Some of the recycled components are subsequently used by our body to make new cells and their inner machinery. By ridding us of faulty components and promoting efficient metabolism, autophagy makes us healthier and less likely to suffer from so-called chronic diseases such as heart disease, cancer, type 2 diabetes, etc.

Blood clot

Blood that has changed from liquid to partially solid in our veins or arteries. Clotting is a normal reaction to damage that stops our body from bleeding too much from an injury. The clot may stay where it forms or move through the body in our blood system and lodge elsewhere. Clots that move may be especially dangerous.

Blood plasma

A light amber-colored liquid component of blood in which blood cells are absent, but which contains all other components of whole blood. It is blood serum plus clotting factors

Blood serum

The clear, yellowish liquid left after cells and clotting factors have been removed from whole blood. Serum contains non-clotting proteins, electrolytes, antibodies, antigens, hormones, human metabolites, macro- and micro-nutrients, microbiome metabolites, pharmaceutical and recreational drugs, alcohol, etc. It is frequently used for diagnostic testing

Carbohydrate

One of three important human nutritional macro-nutrients (the others being protein and fat).  Carbohydrates are also sometimes called glycans and saccharides.  Carbohydrates may be simple in structure (e.g., glucose) or more complex (e.g., starch).  Carbohydrates are often also attached to proteins and fats to form very complex substances in our bodies (see glycan)

Cerebrospinal fluid (CSF)

CSF is a clear, colorless liquid surrounding the brain and spinal cord of all vertebrates (e.g., mammals and fish). It is produced by the brain constantly and resembles blood albeit without red blood cells, most protein, and some electrolytes.

CSF provides buoyancy for the brain (it essentially floats in CSF), protection from jolt or hitting injury, homeostatic regulation (prevents wide fluctuations of substances critical to brain function), and helps to clear waste.

Cholesterol

A type of essential fat (see below) that we mostly produce ourselves but also get from what we eat.  It is not soluble in our blood so is transported by lipoproteins (HDL and LDL).  When we get a cholesterol blood concentration from the doctor, we are actually getting an lipoprotein (HDL or LDL) measure since cholesterol does not exist on its own in the blood

Chronic disease

A chronic disease is any condition not passed from person to person and that persists for long periods of time. Examples of chronic diseases are obesity, type-2 diabetes, poly-cystic ovarian syndrome, hypertension, dementia, cancer, and non-alcoholic fatty liver disease.   It is estimated that at least 80 percent of premature heart disease, stroke and type 2 diabetes and 40 percent of cancer diagnoses could be prevented through healthy nutrition and lifestyle.  It has been shown that some such as type-2 diabetes and poly-cystic ovarian syndrome are reversible with proper nutrition and lifestyle whilst the progression of others such as heart disease may be halted

Electromagnetic radiation (EMR)

EMR can be thought of as energy (radiation) that constantly radiates from sources in space and reaches earth where it affects all living things. EMR consists of a spectrum of different wavelengths and energy, where shorter wavelengths are more energetic.

Some forms of EMR such as ultra-violet, visible light, and infrared are considered essential for human health when we receive it from the sun. This type of EMR is considered non-ionizing. Other types of EMR (e.g., X-rays, gamma rays) are harmful because they contain so much energy that they can damage our cells. This is known as ionizing radiation. It is ionizing radiation that has given rise to the fear of the word “radiation”.

Endorphin

Endorphins are peptides (chains of amino acids smaller than proteins) produced and stored in the brain during exercise and orgasm. They block the perception of pain, inhibit muscle cramps, relieve stress, and increase feelings of wellbeing.

Enzyme

A protein produced by a living organism, capable of producing a chemical reaction. Most processes in living organisms require an enzyme to allow reactions to proceed at a rate sufficient to support life. There are many enzymes, each specifically involved in a different chemical reaction.  These enable most of the physiological changes observed in life

Fat

One of three important human nutritional macro-nutrients (the others being carbohydrate and protein).  Fats are sometimes referred to as lipids.  There are many different kinds of fats that are described according to their chemical structure, their origin in nature (e.g., pastured animal fats and wild-caught fish oils), their industrially harvested source (e.g., farmed fish, feed-lot cattle, and battery fowl), and their industrial manufacture (e.g., seed oils). 

Fatty acid

Fatty acids are the building blocks of fats and as such are analogous to the role played by amino acids for proteins.  Some fatty acids are not made by our bodies and must be obtained from our food. There are three main classes of fatty acid, namely saturated (SFA), mono-unsaturated (MUFA), and poly-unsaturated (PUFA).

Fibre

A general term for those carbohydrates which are not digested and absorbed by the human body and make their way into the lower reaches of the gut.  Once there digestible fibres may be digested by our microbiota (microbiota-accessible carbohydrates) or pass through in our stool undigested.  Fibre may be soluble or insoluble (in water)

Foam Cell

Foam cells are macrophages which were unable to stop accumulating oxidised LDL, cholesterol and other fats. Foam cells can accumulate in arterial plaque formations where they can breakdown and leave their oxidised fatty cargo

FODMAP

FODMAPs are types of plant fibre found in foods such as wheat and beans. The acronym literally stands for fermentable oligosaccharides, disaccharides, monosaccharides and polyols. These carbohydrates resist digestion, and pass onto the colon where they are fermented by members of the gut microbiota

Some people are sensitive to the presence of certain FODMAPs and may suffer from irritable bowel syndrome (IBS) with symptoms such as gas, bloating, stomach pain, diarrhea, and constipation. Elimination of certain FODMAP fibres from their diet can provide relief from IBS.

Food matrix

The natural complex state within which dietary nutrients exist.  The natural food matrix exhibits properties  which are different from those exhibited by the nutritional components on their own

Fructose

A simple carbohydrate that makes up 50% of table sugar (with glucose), is present in most fruits, and is industrially manufactured from corn syrup and present in soft drinks.  Fructose is very sweet and may be addictive

Glucose

The simplest and most common carbohydrate used as a starting material for human metabolism and energy production

Glycan 

Glycan is another word for carbohydrate or saccharide. Whereas carbohydrates and saccharides tend to be written of as reasonably well understood nutritional components, the literature on glycan (carbohydrate) biology is still so poorly understood that it is referred to as the biological equivalent of dark matter in the study of our universe.  These natural carbohydrates are integral to the enormous biological complexities inherent in the development, growth, and functioning of diverse animal and plant holobionts

Glycogen

A complex carbohydrate (highly branched polymer of glucose) that serves as a storage for excess glucose.  Glycogen is stored in the liver and in muscles.  We typically store only 2,000 calories worth of energy (500 in the liver and 1,500 in our muscles) so it’s only for short-term use.  Our fat reserves contain much more energy and are used for longer-term storage.

HDL - C

high density lipoprotein concentration. When we hear the term good cholesterol, it actually means a measure of this lipoprotein, not cholesterol at all

Heart disease

Heart disease is a common term which may refer to a number of ailments.  The one that kills most people and which affects the author of this blog is otherwise know as atherosclerosis.  Technically it is a disease of the arteries which supply blood to the heart and certain other organs, such as the brain.  The disease involves the creation of plaques which progress over time from fatty streaks on artery walls and get bigger and harder until they eventually cause the artery wall to calcify and stiffen.  In its middle stages of growth a plaque resembles a cyst full of fatty material.  This stage is considered unstable, may burst and create a blood clot which may cause surrounding tissue (e.g., heart) to die

Holobiont

The term applies to plants, animals and humans to define a host and its associated microbiota.  The symbiotic associations between host and microbiota are so integral and important that plants and animals are no longer described in biology as autonomous entities.  Instead, every plant and animal is considered to be an organized biological unit, or holobiont

Hormesis

The characteristic of stressors such as metals, chemicals, pharmaceuticals, radiation, exercise and food deprivation which can be beneficial in small amounts but harmful above a certain level

Inflammatory bowel disease (IBD)

IBD is a disorder involving long-standing (chronic) inflammation of the digestive tract. IBD may cause diarrhea, bleeding, pain, fatigue, and weight loss. In some, IBD is only a mild illness but for others it can be debilitating and result in loss of life.

There are two type of IBD:

• Crohn's disease - most commonly affects the small intestine but can affect the large intestine. Symptoms include inflammation of the intestinal lining

• Ulcerative colitis - inflammation and sores (ulcers) along the lining of the large intestine and rectum

Insulin

The most important hormone controlling the major events in metabolism—storing fat and carbohydrate as glycogen, encouraging protein synthesis.  Levels of insulin in our blood are controlled by glucose in our blood

Insulin resistance

Reduced response of our cells to insulin which causes our body to produce even more insulin to keep blood glucose at a safe level.  This can occur when we eat large amounts of carbohydrate over long periods of time.  When our cells become insulin resistant, we need to have high levels of insulin in our blood at all times to make our metabolism work.  Those high levels of insulin can lead to things like heart disease, obesity, type-2 diabetes, poly-cystic ovarian syndrome, hypertension, dementia, cancer, and non-alcoholic fatty liver disease, amongst others

Irritable bowel syndrome (IBS)

The symptoms of IBS can include cramping, abdominal pain, bloating and gas, constipation, and diarrhea. IBS occurs quite differently for individuals. Some people have ongoing symptoms whilst others aren’t always persistent but may decline, only to recur.

Some people respond to the elimination of certain FODMAP plant fibres in their diet.

Ketogenic diet

The ketogenic (keto) diet is one designed to create ketones for energy in the human body. This diet typically restricts absorbable carbohydrates to between 25 and 50 grams per day. The keto diet has been used treat epilepsy and mental health issues

Ketone

Ketones are also called ketone bodies.   They are created in the liver from the breakdown of fats and used for energy in the human body.   The liver makes ketones when there is insufficient access to glucose from the food we eat or from the glycogen stores in our liver and muscles.

Ketosis

Ketosis is the metabolic state in which the liver creates ketones to be used as energy in the body

LDL - C

Low density lipoprotein concentration.  When we hear the term bad cholesterol, it actually means a measure of this lipoprotein, not cholesterol at all

Leucine

Leucine is an amino acid that is important in the creation of protein and in particular muscle. It is one of three branched chain amino acids (BCAA) and, therefore, an essential amino acid (EAA) that must be obtained from our food. The best sources of dietary leucine include most meats, some nuts, and soy products

Linoleic acid (LA)

LA is an essential omega-6 PUFA which is present in very small amounts in most natural sources of fat. However, LA is present in very large amounts in unnatural, industrially manufactured seed oils. If we cook with or consume seed oils, we are exposing ourselves to unhealthy levels of LA which have been shown to cause widespread damage to our bodies and are specifically thought to be involved in the development of heart disease (atherosclerosis).

Lipid

Scientific word for fat and fat-like substances

Lipoprotein

lipoproteins are small spheres made of fats (lipids) and proteins.  Lipoproteins are needed to transport cholesterol around our bodies because cholesterol itself is not soluble in the blood.  The two most heard of lipoproteins are low density lipoprotein (LDL) and high density lipoprotein (HDL)

Liver

The most important chemical reaction centre in the human body and an important glycogen store for quick release to maintain blood glucose levels.  The place where proteins and fats are converted for use in metabolism at times when carbohydrates from food are low

Lumen

In biology, the lumen is the inner open space of a tubular organ such as a blood vessel or an intestine. When we think of the gut microbiome, we tend to divide it between outer mucus layers and the lumen. The composition and functions of the two are quite different

Macronutrient

The major dietary nutrients involved in healthy human metabolism.  There are three macronutrients, namely carbohydrates, proteins and fats.

Macrophage

A macrophage is a type of white blood cell in our immune system. They are found in all parts of our body where they patrol for potential harm-causing agents. They will engulf and digest anything that does not have surface proteins showing that they belong there. This includes infective agents, cancer cells, cell breakdown products, damaged cells and damaged cell components.

Melanin

Melanin is the main determinant of skin colour in humans. It acts to protect human skin from the harmful effects of prolonged exposure to certain types of ultraviolet radiation from natural sunlight.

Because of the decreased exposure to sunlight from the equator to the northern and southern poles, humans evolved (lighter) skin with less melanin as they migrated away from their equatorial origins.

As exposure to sunlight increases in the summer months, human skin receives more ultraviolet radiation. This stimulates production of more protective melanin by human skin, and the suntan we often value.

Melatonin

Melatonin is a hormone produced by living organisms, including plants, animals, algae, fungi, bacteria, and archaea. It primarily functions as a powerful anti-oxidant and acts to prevent damage caused by reactive (oxidative) by-products of normal metabolism.

In humans, melatonin can be produced by exposure to natural sunlight, by symbiotic microbiota (especially on the skin), and by the pineal gland at night.

Melatonin has evolved a secondary purpose in humans in which, stimulated by an absence of blue spectrum sunlight, it is produced by the pineal gland and signals that it is time for the body to go to sleep. In such a role it may be referred to the “Hormone of Darkness”.

Metabolic flexibility

The ability to switch between using carbohydrates, fats, and proteins for energy

Metabolic syndrome

A constellation of disorders caused by insulin resistance.  These may include heart disease, obesity, type-2 diabetes, poly-cystic ovarian syndrome, hypertension, dementia, and non-alcoholic fatty liver disease

Metabolism

The way our cells use and expend energy.  Can be modified by many factors including sex, age, exercise, illness, body weight, and nutrition

Metabolite

Substances produced by various enzymes during metabolism, that occur naturally within cells

Microbe

Used interchangeably with microorganism.  A form of life too small to be seen by the naked eye.  Applies to bacteria, fungi, protozoa, yeasts, archaea, and similar organisms.  Microorganisms work synergistically with each other and their larger animal and plant hosts to produce a healthy holobiont.  Microorganisms also work synergistically with each other in the environment (e.g., soil, ocean, lake, etc.) to produce a healthy environment.  A small number of microorganisms (pathogens) may cause ill-health when the healthy microorganisms are disturbed by things like antibioticsItem description

Microbial

Adjective - of, relating to, or caused by microbes or microorganisms

Microbiota

All living microorganisms that form a microbiome, and may include bacteria, archaea, fungi, algae and small protists.  Viruses, phages, plasmids, prions, viroids, and free DNA are not living organisms, and are not part of the microbiota

Microbiota-accessible carbohydrates

Carbohydrates which are fermented by our microbiota.  May come from dietary plants, dietary animal meat, breast milk, mucus secreted by our bodies, and from members of our microbiota themselves

Microbiome

The community of microorganisms (microbiota) and the structural elements, cell transformation products (metabolites), signaling molecules, and surrounding environmental conditions that have evolved within every environment (e.g., soil, lake, ocean), plant, and animal on earth

Micronutrient

A substance, such as a vitamin or mineral (e.g., sodium, calcium, magnesium, iron, zinc) , that is essential in minute amounts for the proper growth and metabolism of a living organism

Microorganism

Used interchangeably with microbe.  A form of life too small to be seen by the naked eye.  Applies to bacteria, fungi, protozoa, yeasts, archaea, and similar organisms.  Microorganisms work synergistically with each other and their larger animal and plant hosts to produce a healthy holobiont.  Microorganisms also work synergistically with each other in the environment (e.g., soil, ocean, lake, etc.) to produce a healthy environment.  A small number of microorganisms (pathogens) may cause ill-health when the healthy microorganisms are disturbed by things like antibiotics

Mitochondria (singular is mitochondrion)

Mitochondria are small components of all higher-order (plants, animals, algae, fungi) cells. They are originally derived from a bacterium invading another cell. Over time the bacterium evolved into a component of the other cell. Now all higher order cells require mitochondria to survive, and vice versa. Mitochondria are enormously important and despite their tiny size they constitute about 10% of our total weight. They are involved in energy production, neurotransmitter production, hormone production, gene expression, cell growth and differentiation, cell maintenance, disposal of old and damaged cells, and regulation of metabolism, immune system, and stress response. Mitochondria can multiply, change shape and move around a cell depending on the needs of their host cell at any point in time.

Monounsaturated fatty acid (MUFA)

MUFA is found in nature in things like meat, dairy and in products such as olive oil. As its name suggests, a MUFA is chemically composed with one double bond in its structure, as opposed to multiple in a PUFA. MUFAs in our diet are considered largely safe, as with SA, but unlike PUFA.

Mucin

Substance forming mucous on our gut walls and other surfaces potentially exposed to the outside world.  Mucin is made of  carbohydrate-rich substances which combine carbohydrates and proteins (glycoproteins)

Neurotransmitter

A neurotransmitter is a signaling molecule released by a nerve cell. Once released they may affect other nerve cells, muscle cells or glands. Examples of neurotransmitters include nitric oxide, serotonin, and glycine.

Nitric oxide

May be the single most important molecule in our body when it comes to heart health.  Nitric oxide acts as a powerful ant-clotting agent, it helps keep arteries of the heart open, lowers blood pressure, and stimulates new blood vessel wall cells

Nixtamalisation

A process to prepare maize and other grains, in which the grain is soaked and cooked in an alkaline (pH>7) solution, washed, and then hulled. Nixtamalised grain is more easily ground, its nutritional value, flavor and aroma are improved, and mold toxins can be reduced by up to 97%–100%.

Nutrient synergy

Certain nutrients in real food may work together to produce a health benefit that's greater than the sum of the individual parts. This may happen because they improve each other's bioavailability or because they have greater effects on health when present together

Oxalate

Otherwise known as oxalic acid, oxalate is found in many plants, such as leafy greens, vegetables, fruits, cocoa, nuts, and seeds. It binds to micronutrients like calcium and iron and may cause deficiencies in those over time. Deficiencies rarely occur in those of us consuming a micronutrient-dense diet

Pathogen

A microorganism which causes disease

Peptide

Similar to proteins but smaller.  Peptides are short strings of amino acids, typically comprising 2–50 amino acids. Amino acids are also the building blocks of proteins, but proteins contain more

Phytate

Otherwise known as phytic acid, phytate is found in plant seeds, nuts, legumes and some roots and tubers.  It impairs our body’s absorption of iron, zinc, and calcium. Over time this may result in deficiencies of those micronutrients, but this is rarely a problem for those consuming a nutrient dense diet

Pineal gland

The pineal gland is sometimes also called the pineal body. It is a small gland located in the brain of most vertebrates (e.g., mammals and fish). It produces the hormone melatonin (Hormone of Darkness) which induces sleepiness in the absence of blue spectrum sunlight at the end of the day.

Plaque

A thickened area that forms in blood system artery walls.  Plaque is composed of oxidized LDL cholesterol, immune system cells, calcium, and smooth muscle tissue

Polyphenol

Exist in many and varied forms and released by gut microbiota fermentation.  Many polyphenols are anti-inflammatory and beneficial.  They are found in foodstuffs such as vegetables, pasture-fed ruminant meats, fruits, nuts, coffee, chocolate, beer, wine.  Examples include resveratrol, quercetin and berberine

Polyunsaturated fatty acid (PUFA)

Fat that is derived in small amounts from natural sources and and in large amounts from unnatural, industrial sources (e.g., margarine and seed oils).  PUFAs are come in two forms, namely omega-3 PUFA and omega-6 PUFA. Both types of PUFA contain double bonds in their chemical structure. Those double bonds render PUFA very susceptible to chemical degradation by oxidation. The most common PUFA in seed oils is an omega-6 PUFA called linoleic acid (LA). LA is very harmful if our body contains too much because it damages the membranes of things like our cells and mitochondria. When the cells lining our arteries are damaged by oxidised LA, hear disease (atherosclerosis) can follow.

Prebiotic

Food component which encourages healthy microbiota.  Found in breast milk, , plants and other complex (glycan) meat products

Postbiotic

Chemical products (metabolites) of microorganisms that have beneficial effects for the holobiont (host or other microbiota).  These include short chain fatty acids

Probiotic

Food or supplement containing live microorganisms considered beneficial for holobiont health.  Examples include, kefir, yoghurt, sauerkraut, kimchi, and kombucha. Best consumed in foods daily as opposed to supplements

Saccharide

Used interchangeably with carbohydrate and glycan.  The unitstructure of carbohydrates (as amino acid is to peptide and protein).  Can be simple sugars or polymers such as starch and cellulose

Sarcopenia

Sarcopenia is a type of age- or mobility-related muscle degradation that may include loss of skeletal muscle mass, quality, and strength. The rate of degradation depends on nutrition (especially bioavailable protein), appropriate exercise, diseases, and other lifestyle factors such as substance abuse 

Saturated fatty acid (SFA)

Fat that is naturally produced by our bodies and is present in many things in our diets, including meats, dairy, coconut oil, olive oil, and mothers milk. SFA are not prone to oxidation and are not a cause of heart disease as previously believed.

Seed oil

Also called vegetable oil.  Fat which is liquid at room temperature.  Derived through an industrial chemistry process from certain plant seeds.  These oils oxidise readily when used in cooking and produce inflammation in the human body.  Examples include corn, rapeseed, soy

Serotonin

Serotonin is a signaling molecule secreted by nerve cells (neurotransmitter) which affects mood, cognition, learning, and memory. It is produced mostly in the human gut but also in the brain, skin, and tongue.

Short-chain fatty acid

May be referred to as SCFA.  Postbiotics produced by our gut microbiota as a byproduct of MAC fermentation. SCFA differ in the number of carbon atoms they contain. The most well studied are acetate (2C), propionate (3C), butyrate (4C), and pentanoate (5C). SCFAs are considered and butyrate, for example, helps maintain a healthy intestinal barrier which in turn reduces inflammation and helps immune system function