Aerobic Digestion

An industrial or domestic process which uses microorganisms to breakdown biological materials in the presence of oxygen. Examples of aerobic digestion include composting and waste water treatments.

Anaerobic Digestion

A process whereby bacteria and other microorganisms hydrolyse (break down) biodegradable material in an environment without oxygen. The process commonly generates gas that can be used as an energy source.

Bacillus cereus

Infection with Bacillus cereus is characterised by an exceptionally rapid incubation period that can be as small as 30 minutes after ingestion.  B. cereus manufactures two types of enterotoxin; one that causes vomiting and one that causes diarrhoea.  B. cereus infections begin and end rapidly, a typical infection can be cleared within 24-48 hours.


A biofilm is a collection of microorganisms, frequently of different species, growing on top of a surface in a tightly bonded film. Biofilms are resistant to a variety of environmental stresses such as drying out,  cleaning and sanitation chemicals.


A borehole is a type of well. Typically, it is composed of a narrow shaft, 5-10cm in diameter, and a pump is used to extract water from the well.


Brucella is the bacterial causative agent of brucellosis; an illness characterised by abdominal pain, diarrhoea, vomiting, rapid weight loss and impaired liver function. Brucellosis is a zoonosis transmitted by ingesting contaminated food, direct contact with infected wildlife or domesticated animals or the inhalation of contaminated aerosol.


Calciviruses are a class of viruses that include a range of individual organisms.  The most common caliciviruses that causes human illness are the Noroviruses. Infection tends to be by oral ingestion.  Calciviruses multiply in the small intestine where their increasing numbers cause cellular lysis and the formation lesions in the wall of the intestinal mucosa.  Calciviruses are shed in faeces and the most common source of infections is other humans with poor hygienic practices when using a lavatory.  Foodborne infections tend to be caused by infected food handlers or harvesting staff.


The genus Campylobacter causes the most bacterial foodborne illness in the UK.  Exact numbers of people made ill by campylobacters is hard to determine, because not everyone who has gastroenteritis visits a doctor.  However, an informed estimate is that around 280,000 people in the UK become infected from Campylobacter-contaminated food each year.  The principal source is contaminated chicken meat, but manure from other livestock and animals can also contain campylobacters.  The manure from wild birds especially commonly contains Campylobacter. Therefore, fresh fruit and vegetables soiled with bird manure can cause illness in humans.


The movement of an organism in response to a chemical stimulus. For example a bacterium that detects a diffusing nutrient may swim towards the source by following an increasing concentration of nutrient.


Citrobacter are a subgroup of the Enterobacteriaceae. The majority of strains are not pathogenic, and they rarely cause human illness. Citrobacter are widely dispersed in soils, waters and the waste from mammalian gastrointestinal tracts. The Enterobacteriaceae are indicators of the general hygiene of the environment used to grow and process crops.


A specific type of virus that infects E. coli bacteria.


The process that a microorganism undertakes to establish a population inside a new host.


The first leaves to appear from a germinating seed.


Cowpox is a zoonotic disease spread from animals to humans. The causative agent is the cowpox virus. Human cases are very rare, although the UK has a higher incidence than continental Europe. Domestic cats and cattle udders are common sources of human infections. Cowpox is generally self-limiting, but can be fatal in immunocompromised patients.

Cryptosporidium parvum

A protozoa that can cause gastroenteritis, diarrhoea and severe cramping of the gastrointestinal tract in humans. A common route of infection for C. parvum is via contaminated drinking water. C. parvum is largely unaffected by common water treatments such as chlorination which is normally used to render water potable and consequently, outbreaks can be quite large. Ruminants such as cattle and sheep are common sources for the contamination of surface waters.

Cyclospora cayatenansis and Cyclospora

Pathogenic strains of Cyclospora cayatenansis and Cyclospora can cause gastroenteritis of the small intestine in humans.  The key vectors of infection are consumption of contaminated food or water.  Cyclospora infections are rare in the temperate climate of the UK, and more commonly associated with the tropics, or foods sourced from tropical and sub-tropical regions. Cyclospora infections tend to have a moderate duration from a few days to around one month and are characterised by bloating, stomach and muscle cramps and flatulence.  In some cases, the infection causes a loss of appetite and rapid weight loss.

E. coli

E. coli (Escherichia coli) are a group of bacteria which are commonly found in the  gastrointestinal tracts of a wide variety of human, mammalian, reptile and avian hosts. The majority of E. coli strains are harmless, however  a small number can cause serious illness in people. 

E. coli O157 & E. coli O157:H7

Although the majority of E. coli are harmless, some acquire virulence genes then enable attachment to intestine walls and the manufacture of toxins that allow them to cause illness in humans. Infection with E. coli O157 can result in severe illness


Enterobacter are a subgroup of the Enterobacteriaceae. There are some strains that are pathogenic, although food is rarely a vector of infection. Commonly the Enterobacter cause infections of respiratory equipment, human airways and human urinary tracts. The Enterobacter are a member of the indicator group of bacteria known as coliforms, but tend not to grow at the elevated incubation temperatures required for faecal coliforms. The Enterobacter are also a member of the Enterobacteriaceae, a general hygiene indicator of the environment used to grow and process crops.


The Enterobacteriaceae are a large and diverse collection of more than 30 different species of bacteria. Despite the name (entero = meaning associated with the gut), some members of the Enterobacteriaceae group can be isolated from surface waters and soil, although the majority are composed of bacteria associated with human and animal digestive tracts. The numbers of Enterobacteriaceae present in a test sample can be thought of as a general indicator of the degree of contamination acquired by fresh produce from contaminated water, insects, faecal material, wildlife, soil and other plants (including some plant pathogens). 


A word used to describe a microorganism that is capable of causing disease and cellular damage to the gastrointestinal tract of a human or other animal.


A weak solution of nutrients that has been secreted or otherwise leaked from an organ or plant root.

Faecal coliforms

Coliforms are a subgroup of the Enterobacteriaceae. They comprise mostly of the Escherichia, Klebsiella, Citrobacter, Enterobacter, and Serratia species. Some members of the coliform group can also be isolated from the environment although they are more closely correlated with faecal material than the true Enterobacteriaceae. Faecal coliforms are a sub-group of the coliforms. It is worth noting that a very high percentage (more than 80%) of a faecal coliform count is typically made up of generic E. coli.

Faecal Oral Route

Many of the microorganisms that cause human illness are enteric pathogens, which means they colonise the gut of animals and humans. When they are colonised, animals shed pathogens into their faeces. The pathogens can then spread from the manure to other hosts. The faecal oral route is a common vector whereby the pathogens in faeces somehow finds its way from waste into the mouth of a new host. Common routes are infected people not washing their hands and touching doors and similar, leaving infectious agents behind, which are then picked up by other people.

Farmyard Manure

A mixture of livestock faecal material and spent bedding. Typically, farmyard manure (FYM) has a dry matter content of greater than 13% (w/w). Unless it is properly composed or otherwise treated, FYM can be a source of microorganisms capable of causing human illness.


Fermentation is a metabolic process that converts nutrients into acid, combustible gas, alcohol or other beneficial product such as ketones.


A fomite is an inanimate substance or object that is contaminated with an infectious agent. Fomites facilitate the transfer of contamination from one person to another. Examples of fomites include door handles, clothing or processing equipment.

Heavy metal salts

Heavy metal salts are a class of compounds that are composed of a heavy metal such as lead, mercury, arsenic or cadmium and a salt such as chloride, nitrite or phosphate. Heavy metal salts can pose a health risk to humans.

Hepatitis A

A pathogenic virus that causes illness and liver damage in humans. Like most viruses, the Hepatitis virus family has a very narrow range of hosts they can infect. Hepatitis A is only transmitted by the faeces of infected humans. The Hepatitis A virus and Hepatitis A infection of workers are specific indicators of quite fresh human faecal wastes.


A method of cultivating crops in mineral nutrient solutions without the use of soil.


A molecule composed of chlorine and oxygen that is also the active agent in bleach.


The stem of a plant located between the cotyledons and the root.


Inoculation is the process of introducing microorganisms such as bacteria onto a surface such as a growth medium for the purpose of increasing the numbers of microorganism.


Leptospirosis is a zoonosis, spread to humans from animals. Infection is commonly by touching soil or water contaminated with the urine of wild animals infected with the Leptospira bacteria. Typically, leptospirosis causes flu-like symptoms, including headaches and muscle pain. More severe forms of the infection are called Weil's disease, which is characterised by liver damage, bleeding and meningitis. Animals known to be carriers of Leptospira include cattle, pigs, dogs and rodents, particularly rats.


Listeria is the genus name for a range of closely-related bacteria that are widely dispersed in soils and on vegetation. 

Listeria ivanovii

Listeria ivanovii is a type of Listeria that can cause infection in humans. However, L. ivanovii infection in humans is quite rare and the bacteria more commonly infects ovine hosts such as sheep. Infection with L. ivanovii can lead to sepsis (colonisation and multiplication of L. ivanovii in blood and an immune response that is damaging to the human) with enteritis (infection and inflammation of the small intestine) and the spontaneous abortion of lambs.

Listeria monocytogenes

Listeria monocytogenes is a bacteria that can be pathogenic to vulnerable groups of humans. The vulnerable groups include pregnant women, elderly people and the immunocompromised. 

Metabolic Heat

The process of breaking down food and nutrients into energy causes heat to be released. The heat released from metabolic processes is called metabolic heat.

Mycobacterium bovis

The Mycobacterium are a class of bacteria that are particularly robust. Their ability to survive outside a suitable host for extended periods is due to a particularly thick cell wall that is composed of waxy lipids and strongly hydrophobic. Common food vectors include the consumption of unpasteurised milk from an infected animal and the inhalation of air containing Mycobacterium aerosols.

Newcastle Disease

Newcastle disease is a zoonotic illness that is typically spread from avian (bird) sources. The symptoms are mild conjunctivitis (inflammation of the eye) and flu-like symptoms, such as headache and muscle pain. The Newcastle disease virus is not considered to be very dangerous to human health.

Nitrate pollution

Animal manures contain high concentrations of nitrogenous compounds including nitrates. If faecal wastes are disposed of by spreading to agricultural land close before rainfall or if too much waste material is applied to land, some of the nitrate can be washed into watercourses such as rivers and lakes. Nitrate pollution of surface water can cause rapid algal growth, which removes oxygen from the water, reduces fish numbers and has other negative impacts on aquatic populations.


Norovirus is a highly-infectious virus, which causes the majority of cases of human gastroenteritis in the UK.  The illness caused is commonly called the winter vomiting bug.  In contrast to most foodborne illness, the main source of norovirus is other humans infected with the virus.  The infection is typically spread by the faecal-oral route, whereby poor hygiene when using a lavatory by an infected person spreads the infection to other people.  Each year, there are around 100,000 confirmed cases of norovirus in the UK.  Infected food preparation and harvesting staff are commonly implicated in the spread of norovirus.


A hardy body designed to enable protozoan parasites such as Cryptosporidium to survive for extended periods of several months in water, faeces and other environments such as soil without a host organism. 


Osmosis is a process that allows the movement of water across a natural or synthetic semi-permeable membrane. The process is driven by different salt or sugar concentrations on either side of the membrane. Generally, water will move from a low solute concentration to a high one in an attempt to equalise the solute concentrations on either side of the membrane.


An organism that is capable of causing disease in another organism.


The phyllosphere is the above ground external surfaces of plants. Phyllospheres include leaf surfaces (called phylloplanes) and the surfaces of flowers (anthoplane), seed bodies (carpoplane) and stems (cauloplane).


Protozoa are single celled eukaryotic organisms. In many ways they are considered to be an evolutionary stepping stone between bacteria and other prokaryotic organisms and simple multicellular life forms such as pond algae.


The rhizosphere is a narrow band of soil surrounding the roots of a plant. Rhizospheres benefit from nutrient exudates that leak from the plant roots. These exudates can support the growth of microorganisms some of which are beneficial to the plant. 


The salmonellae are a complex genera of bacteria that are widely dispersed in mammalian, avian and reptile wildlife. Some strains of Salmonella have the ability to infect humans and cause illness, although the majority of strains do not appear to significantly distress the wildlife they colonise. Thus Salmonella are classed as zoonotic agents. Typical symptoms of human infections include fever, such as typhoid fever; gastroenteritis including vomiting and diarrhoea; and sepsis.

Salmonella Bovismorbificans

Salmonella Bovismorbificans is one of the serovars of the Salmonella enterica species of human pathogens. Typical symptoms of human infections include fever, gastroenteritis including vomiting and diarrhoea; and sepsis. It has been linked in recent times with infections from chickpeas, sesame seeds and products such as hummus and tahini made from these.

Salmonella enterica

Salmonella enterica is a species of Salmonella that contains many serious human pathogens, including Salmonella enterica Enteritidis and S. enterica Typhi and S. enterica Typhimurium. S. enterica infections are commonly traced back to contaminated foods. Typical symptoms of human infections include fever, such as typhoid fever; gastroenteritis including vomiting and diarrhoea; and sepsis.

Salmonella Typhimurium

Salmonella Typhimurium is one of the serovars of the Salmonella enterica species of human pathogens. S. Typhimurium is particularly problematic because it can infect a wide range of hosts including humans, cattle, pigs, sheep, foxes, cats and dogs, horses, rodents and chickens, geese and ducks. S. Typhimurium is an example of an invasive infection (the infection leaves the gut and travels in the bloodstream to other parts of the body such as the cerebrospinal fluids). Typical symptoms of human infections include fever, gastroenteritis including vomiting and diarrhoea; and sepsis.


A chemical that removes (i.e. destroys) bacteria and other microorganisms from surfaces.


Serratia are a subgroup of the Enterobacteriaceae. There are some strains that are pathogenic, although food is rarely a vector of infection. It is more common for Serratia to cause nosocomial (hospital-acquired) infections. A common member of the genus is S. marcescens, which is readily isolated from area that are constantly wet. The Enterobacteriaceae are a general hygiene indicator of the environment used to grow and process crops.

Shigella sonnei, Shigella flexneri and Shigella spp.

Infection with a pathogenic strain of Shigella is called shigellosis.  Unusually for a bacterium, the host range that can be infected is narrow and restricted only to primates.  Mild stomach cramps and bloody diarrhoea are the main symptoms of shigellosis. Shigella sonnei and S. flexneri can be transmitted by contaminated food or by drinking in contaminated water.  However, it is most common for the bacteria to be transmitted via the faecal-oral route. Infections in young children are most common and not washing hands effectively after changing diapers can cause infection. Foodborne infections tend to be caused by infected food handlers or harvesting staff.


Slurry is a type of livestock waste which is commonly generated by cattle being fed a specific diet. Slurry has quite a watery consistency and has a dry matter content of between 4% and 9% (w/v). Some farmers favour waste generated as slurry because it can be collected in pits beneath slatted flooring in livestock sheds and readily pumped away. 


A small, reproductive body that is highly resistant to environmental stresses such as desiccation, heat and the action of sanitisers and other chemicals. Fungi and some bacteria create spores as a survival mechanism in response to unfavourable, stressful environmental conditions or a shortage of nutrients. Some spores may remain viable for decades.

Streptococcus & Enterococcus 

Streptococcus and Enterococcus are closely related bacteria that have been used as alternative indicators for faecal pollution of water. The isolation of different species of faecal Streptococcus, have been used with some success to enable differentiation between animal and human faecal pollution as a way of providing clues to the sources of water contamination. Human-derived faecal material contains a large percentage of Enterococci as the dominant cocci whereas animal-derived material contains high numbers of streptococcus. Although attempting to use the ratios of Enterococci to other Streptococci may have a potential for use as pollution source indicators, although the strategy has at least one pitfall. The main drawback is that Enterococci and Streptococci populations decline in the environment at different rates. Enterococci, which are present at low levels in animal manures are more hardy than generic Streptococci. In addition, the ratio of faecal coliforms to faecal Streptococci (FC:FS) also has a potential for differentiating pollution sources. For fresh pollution, FC:FS ratios of >4 correlate well with human faeces, and <0.7 is more representative of animal faeces. However, as for the cocci discussed above, these ratios are subject to change with time because individual members of the coliform group, coliforms collectively and Enterococci decline in the environment at different rates

Tannery wash

Tannery wash is the waste product generated by the leather industry. Skins are tanned to make leather, which is less likely to decompose compared with untreated skin. Tannery wash is typically composed of preservatives such as dithiocarbamates, fungicides, the solutions used to de-hair and degrease the skins, and alkali.


Trihalomethanes are a class of chemical compounds in which three of the four hydrogen atoms of methane (CH4) are replaced by a halogen atom. The halogens include fluorine, chlorine, iodine and bromine. Trihalomethanes are environmental pollutants that spontaneously form when sanitisers such a chlorine are applied to water or surfaces with a high organic content. Many trihalomethanes are considered carcinogenic (can cause cancer).

Vibrio cholera

Some strains of Vibrio cholera can cause cholera, which is potentially fatal if not treated.  The classic symptoms of V. cholera infection are same as many gastrointestinal infections and includes diarrhoea, vomiting and stomach and muscle cramping.  The use of water contaminated with faecal material from an infected person is a common source for illness.  The genus Vibrio, which also contains non-pathogenic strains, can be commonly found in saltwater or in estuaries where fresh and salt water mix (brackish waters).


Yersinia are a subgroup of the Enterobacteriaceae. The majority of strains are not pathogenic, although some members of the genera can cause illness such as bubonic plague and have been linked with inflammatory bowel disease. The Enterobacteriaceae are an indicator of general hygiene of the environment used to grow and process crops.


A transmittable disease of humans that is transmitted from an animal source. Zoonotic infections are characterised by no apparent disease symptoms in animals, but illness upon colonisation of humans.

Zoonotic Agent

A zoonotic agent is an infectious microorganism that causes illness in humans but does not cause any apparent upset when it colonises livestock or wildlife.