AEROBIC BACTERIA - Bacteria that require oxygen to live and grow

ANAEROBIC BACTERIA - Bacteria that do not live or grow when oxygen is present

ANTIBIOTICS – a medicine that inhibits the growth of or destroys microorganisms

ANTIBODY – a protein produced by the body’s immune system in response to detecting a perceived threatening substance

ARCHAEA – single-celled prokaryotic microorganisms that are similar in size and structure to bacteria but radically different in molecular organisation

BACTERIA – single-celled prokaryotic microorganisms which have cell walls

BACTERIAL TAXONOMY – a classification system of different types of microorganisms. Microorganisms are first grouped into three domains (eukaryotes, bacteria and archaea), then into smaller specific ranks and hierarchy. There are eight major taxonomic ranks

BACTERIUM - a single organism of bacteria

BIFIDOBACTERIA – a genus of bacterial species naturally present in the gut, some fermented foods and probiotic drinks

COLON – Also known as the large intestine, and is the last part of the digestive tract. Most of our gut microbiota live here.

CLOSTRIDIUM DIFFICILE/C.DIFFICILE – A species of bacteria that live harmlessly in the gut, but can cause symptoms of diarrhoea to colon inflammation when present in overly large quantities

DYSBIOSIS – an imbalance of microbial colonies

EUKARYOTES – cells that have a nucleus

FAMILY – a category of bacteria that ranks above genus and species but below phylum

FEACAL - poo

FEACAL TRANSPLANT – faecal samples are transplanted from a healthy individual into a person with an unbalanced microbiota. It is effective in treating C.difficile infection but currently has not been authorised on a general basis

FUNGHI – funghi and in particular yeasts, are naturally present in the gut

FIBRE – Fibre is the indigestible parts of plant foods, such as vegetables, fruits, grains, beans and legumes. It is a carbohydrate that keeps our digestive systems healthy, and certain types feed the gut microbiome

GENUS – a category of bacteria that ranks above species and below family

GUT - Your intestines

GUT MUCOSA – A thin layer of tissue that lines the gut, separating substances we have digested from the rest of the body. Key absorptive functions take place on its surface

GUT MICROBIOME/FLORA - The community of microbes that is found in the gut, predominately in the colon or lower intestine

INTESTINAL PERMEABILITY – The inside of the gut is lined by a single layer of cells called the mucosa, which acts as a barrier between the inside of the gut and the rest of the body. This barrier absorbs nutrients while preventing most larger molecules and bacteria passing through from the gut into the bloodstream in the body. However, this permeability can be altered, with the gaps between the cells of the mucosa increase, letting other substances through. This may potentially cause knock on effects in the body such as inflammation

MICROBES – see microorganisms

MICROBIOTA - The entire population of bacterial population on or inside our bodies, present on the skin, our mouth, ears, vagina, or the intestines, amongst others. 

MICROORGANISM - a microscopic organism, especially a bacterium, virus or fungus

MUCOSA – See gut mucosa

PATHOGEN – a bacterium, virus, or other organism that can cause disease

PHYLUM – a category of bacteria that ranks below domain but above family, genus and species

POLYPHENOLS – a large group of phytochemicals found in plants that typically act as anti-oxidants

PREBIOTICS – Non-digestible food components (such as certain types of fibre) that promote the growth of beneficial gut microorganisms

PROBIOTICS – Live microorganisms that when taken in adequate amounts can have a health benefit. E.g. some fermented foods, probiotic drinks, yogurt

POSTBIOTIC – beneficial products or byproducts of probiotic organisms

PROKARYOTIC – cells that don’t have a nucleus

SPECIES – A category of bacteria that ranks below genus, family, phylum and domain

SYMBIOSIS – an interaction between two organisms that is beneficial for both parties

VIRUS – Viruses, like bacteria, can also be beneficial in human health and make up part of the microbiome


CELIAC DISEASE – a common digestive condition where the small intestine becomes inflamed and unable to absorb nutrients due to an adverse reaction to gluten, a type of protein found in wheat, barley and rye. This can cause symptoms of diarrhoea, stomach pain, bloating, constipation and indigestion amongst others. There is currently no cure of coeliac disease, but a gluten-free diet should help control symptoms and prevent the long-term consequences of the condition

CROHN'S DISEASE – an inflammatory bowel disease that can affect any part of the digestive tract from the mouth to the anus. Symptoms can include diarrhoea, stomach pains, diarrhoea (with blood), weight loss and fatigue. These symptoms can be constant, or can come and go every few weeks or months

DIVERTICULAR DISEASE – Diverticular disease and diverticulitis are related digestive conditions that affect the colon. Diverticula are small pockets or bulges that can form in the intestinal lining. Most people with diverticula don’t get any symptoms, however for some these pockets can cause symptoms such as stomach pain, bloating, constipation or diarrhoea or both (can be with mucus) – this is called diverticular disease. Diverticulitis is when these pockets or bulges become infected and inflamed, causing more severe symptoms such as severe stomach pain, feeling unwell, feeling sick or vomit, blood in your poo, and/or a high temperature

DIVERTICULITIS – see diverticular disease

GUT DYSBIOSIS – There are currently different definitions of this term, but it is generally associated with a change in composition of gut microorganisms. Sometimes this is described in association with illness, however currently there is not enough evidence to say whether this is the cause or consequence of a disease

GASTROENTERITIS – a common condition that causes inflammation of the stomach and intestines, typically with diarrhoea and vomiting. It is usually caused by a bacterial toxin or viral infection, e.g. food poisoning

GASTROPARESIS - Full or partial paralysis of the stomach. A condition in which the stomach cannot empty itself of food in a normal way, with food passing through the stomach slower than usual

INFLAMMATORY BOWEL DISEASE – a term mainly used to describe two conditions that cause inflammation of the gut, ulcerative colitis and crohn’s disease

IRRITABLE BOWEL SYNDROME (IBS) – IBS is a common condition that affects the digestive system, causing symptoms like stomach cramps, bloating, constipation and diarrhoea. These can come and go over time and can last from days to months. It’s usually a lifelong problem, and while there is no cure, dietary changes and medicine can help control the symptoms. While the exact cause is unknown, it is best to get a diagnosis from a doctor to first rule out more sinister conditions which have similar symptoms

LEAKY GUT SYNDROME – A relatively new proposed condition. While some conditions and medications can cause intestinal permeability, there is currently little evidence to support the theory that a porous bowel is the direct cause of any significant and wide-spread problems, with little evidence to support the treatments offered to ‘cure leaky gut syndrome’

SIBO (Small Intestinal Bacterial Overgrowth) – There is currently no consensus to the definition for SIBO. The most common definition currently describes SIBO as an overgrowth of bacteria in the small intestine above a certain level (105 CFU/mL). Some people with GI symptoms may have increased amounts of bacteria in the small intestine that is below this range. Currently, only if the overgrowth is from microorganisms that are commonly found in the colon is there a clear link to a disease state with GI symptoms. This overgrowth can be resolved with antibiotics. Some consequences of SIBO include weight loss, and deficiencies of fat soluble vitamins, vitamin B12, iron, amongst others. To read more click here

ULCERATIVE COLITIS - A disease that causes inflammation in the colon and rectum. Small ulcers can develop on the lining of the colon, which can bleed and produce pus. The main symptoms of ulcerative colitis are recurring diarrhoea (which may contain blood, mucus or pus), stomach pain, and needing to go to the bathroom frequently. The severity of the symptoms depends on how much of the rectum and colon is inflamed and how severe the inflammation is. Some people may go for weeks or months with very mild or no symptoms, followed by periods of flare-ups

For further information please visit the NHS website


BOOCH - Abbreviation for kombucha

BRINE - Salted water used as medium for pickling and preservation

BROTH - Technically this is any liquid that has meat cooked in it, but has more recently become a phrase for any flavoured liquid

CULTURE - A many layered word; in the context of fermentation, it generally refers to starters comprising either isolated organisms (pure cultures) or perpetuated communities of organisms (mixed cultures).  Live cultures contain living bacteria that remain alive and intact

FERMENTED NUT CHEESE -  Nuts are not easy to digest so by fermenting them we turn them into a highly digestible probiotic food. The bacteria comes from fermented vegetables or probiotic powder

FERMENT VINEGAR - Essentially the juice/brine of a ferment, left for a long time until it becomes a vinegar. This is what we call a drinking vinegar

GINGER BUG - Very simply grated ginger (or turmeric), with sugar and filtered water

JUN - This is a culture similar to kombucha made using raw sugar rather than sugar which gives a lovely, distinctive flavour.   Jun also seems to mature a little faster than Kombucha

KIMCHI - Kimchi, a staple in Korean cuisine.  A traditional side dish made from salted and fermented vegetables, most commonly napa cabbage and Korean radishes (Mooli), with a variety of seasonings including red pepper chili powder, spring onions, garlic and ginger

KOMBUCHA - A living tea.  A sugar-tea solution is fermented by a SKOBY similar to Kefir grains, but it looks more like a jellyfish.  It has tough translucent skin, and tastes a bit like a lychee. The booch mother floats at the top of the water in the fermentation vessel. You feed it with cooled green or black tea

KRAUT - Abbreviation for Saurkraut.  See below

KVASS - Traditionally a drink brewed with rye bread, but you can make kvass from any combination of fruit or vegetable. Choose your combination and just add a brine solution or a starter (e.g. kraut juice)

LABNEH - Strained yoghurt, that becomes like a soft cheese.  You can also make it from Milk Kefir

LEAVEN - Sourdough bread culture

MEAD - Ancient alcoholic brew made with fermented honey, water and yeast, and sometimes fruit

MILK KEFIR - Fermentation of milk kefir grains (SOBY), to create a probiotic-like yoghurt

MISO - A soybean paste, an ancient tradition from Japan.  Miso is made from fermenting soy beans, rice koji, salt, and usually a grain such as rice or barley, together. The fermentation process can be anything from a few weeks or as long as three years depending on the flavour desired. One ferment you are probably best to buy!

SAURKRAUT -  Finely cut cabbage that has been fermented by various lactic acid bacteria using a dry-salting method

SCOBY - Symbiotic community of bacteria and yeast; a starter culture that has taken on a physical form, which is transferred from batch to batch as a means of perpetuation

SHRUB - A shrub is essentially fermented fruit mixed with a drinking vinegar producing a vinegar-soured fruit drink.  By adding a starter as well, you can prevent the fermentation from turning alcoholic.   The starter adds the bacteria that will help the good lactic acid bacteria to take off before the alcohol producing yeast do. Whey or water kefir can act as a starter

STOCK - Animal bones simmered in water for a long time to extract gelatine, collagen, minerals and amino acids and flavour.  The thick, often gelatinous nature of stocks is only possible when bones are present

TEMPEH - Traditionally a fermentation of soybeans, rice vinegar and tempeh starter into a firm cake form. Like Tofu, it is seen as an alternative to meat

TEPACHE - Traditionally made in Mexico.  The bacteria and yeast that naturally live on pineapple skin will create a zingy fermented refreshing pineapple drink in only a few days

TIBICOS – The correct word for Water Kefir grains/SKOBY

VINEGAR MOTHER - Can be made with leftover wine add some raw vinegar and leave somewhere dark and allow If you leave a bottle of organic Apple Cider Vinegar long enough it will produce a vinegar mother

WATER KEFIR - Fermentation of water kefir grains (SCOBY) in sugar-water, to create an effervescent drink.   Traditionally flavoured with dried fruits, ginger and lemon.  Kefir grains are also called Tibicos.  They look like broken up translucent scrambled and sit at the bottom of a brew.

WHEY - Whey is the liquid remaining after milk has been curdled and strained. It is full of protein and nutrients.

gut health PROCESSES

ACTIVATION – A food that has been soaked in water for a period of time, which starts off the germination or sprouting process. Soaking has been suggested to break down some problematic compounds that can reduce the absorption of some nutrients in a food

BIOAVAILABILITY - The degree to which a nutrient or other substance is absorbed and utilised by your body

BIODYNAMICS - A holistic theory and method of organic agriculture

DRY-SALTING - Salting a solid food without the additional water

FERMENTATION - The chemical breakdown of a substance by bacteria, yeasts and other microorganisms, typically involving effervescence and the giving off of heat

LACTO-FERMENTATION -  Ant fermentation performed primarily by lactic acid bacteria

PICKLING - Preserving in an acidic medium

WILD FERMENTATION - Fermentation that relies on organisms spontaneously



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