Sub-pages:WelcomeReportsContactsLinksAsian hornet

The Honey Bee Microbiome – An adventure on the inside

A talk by Graham Kingham to East Devon Beekeepers, 5/10/23

‘You are what you eat’ or more correctly, what you digest. We will briefly look at human and honey bee digestion and the alimentary canal. The honey bee microbiome will be explained and the effects of disease, pathogens and chemicals mentioned.


The microbiome is the collection of all microbes, such as bacteria, fungi and viruses, and their genes, that naturally live on the outside and inside of bodies.

Microbes are very small but can contribute in a big way to the health and wellbeing of a human or a bee. They protect against pathogens, help the immune system develop, and enable digestion of food for energy production. Most microbes are harmless but nearly all life, including plants, cannot live without them. The human microbiome is composed of communities of bacteria, viruses, fungi, archaea and parasites that have greater complexity than the human genome itself.

Microbiome research is a relatively recent topic, with the human microbiome taking centre stage. Often-quoted numbers for human microbiome are 100 trillion microbes per person, 95% of all human microbiota is in the gut, the microbiome weighs 2kg, 90% of disease can be linked in some way to the gut and microbiome health. There are hundreds of different species of microbe in the human gut.

Every part of an animal has a microbiome e.g., skin, urogenital tract, mouth and digestive tract. All these sites, microbes and inter-relationships make the microbiome extremely complicated to research and understand.

The role of the human microbiome

The human microbiome has extensive functions such as the development of immunity, defence against pathogens, host nutrition including the production of short-chain fatty acids important in host energy metabolism, synthesis of vitamins and fat storage. It has an influence on human behaviour, making it an essential organ of the body without which we would not function correctly. The human microbiome tends to be dynamic and variable dependent on many factors, including food, environment and medication.

The honey bee gut and microbiome

Bees have a less variable diet compared to humans with only 5-9 species dominating the gut microbiome. The bee gut consists of a tube from the mouth to the anus with specialised regions along its length performing distinct tasks (see References).

Simplified diagram of honeybee gut

The crop

The crop or honey stomach receives the nectar/pollen mix during foraging. Also in the same region is the proventriculus or stomach mouth, a projection into the crop from the ventriculus or stomach. This valve prevents the collected honey from running into the stomach but allows the pollen to pass. Crop microbiome is mainly derived from the surrounding environment and tends to be variable with seasonally changing diets.


This is a long, wide tube lined with a membrane (the peritrophic membrane) which is continually in a state of proliferation. Muscle fibres force the gut contents towards the rear and the membrane is detached and mingles with the food. The membrane produces enzyme secretions which aid the digestion of the protein contained in the pollen grains. The microbiome at this stage can still be variable depending on the environment.

The peritrophic membrane was thought to protect the lining of the ventriculus from sharp, spiky pollen grains but is now considered to be important in concentrating a range of digestive enzymes where they are most needed.

Small intestine

This is a narrow tube which is surrounded with the outlets of the Malpighian tubules. These tubules act in a similar way to the human kidney. The tubules are followed by the pyloric valve which controls the flow of material along the intestine.


The small intestine opens into the rectum, which is capable of great distension to accommodate the waste material during long periods of confinement. The vast majority of the bacterial community live in this region as it is more stable.

The relative simplicity of the honey bee microbiome leads to a very consistent set of bacterial species known as core bacteria. These are present in all honey bee workers worldwide. Understanding how the microbiota interacts as a community helps predict how that community will react to change and how that change will affect the host.

Larvae and newly emerged bees have little bacterial colonisation. Cell cleaning provides a faecal origin for the initial inoculation. Thereafter, the microbiome will adapt to diet and environmental conditions. In a relatively constant colony, the core microbiota is maintained. Over time, as colonies split, some microbes may evolve to improve the survival of the colony, thus ensuring their own survival.

What effect does the beekeeper have on the microbiome?

  • Feeding liquid sugar syrup or fondant can lead to blistering in the ventriculus.
  • Food supplements such as pollen substitutes are not normally consumed by bees in their natural environment, so must have an effect on their microbiome.
  • Smoking bees and weekly inspections disturb and stress the colony, with loss of pheromones for possibly several days.
  • Varroa treatments and pesticides linger in wax for a long time. They have been shown to affect bee systems, such as the fertility of drones, but currently their effects on the bee microbiome have not been published.
  • Thymol additives to stop mould growth or treat Varroa can repel bees. The odour can mask the chemical cues that trigger the removal of diseased or dead brood thereby affecting hygienic behaviour. As a mould inhibitor, thymol must affect the microbiome.

Treating bees is a trade-off between starvation, disease and pest control.

What can we do?

We can be more proactive in helping bees. Bear in mind that they have survived for millions of years without our help!

  • Try to leave honey on the hive for winter feed. This is the best food for bees.
  • Consider the forage in your area, and whether you could move your colonies to an area with better forage. Can the forage in your area support the number of colonies in your apiary?
  • Practice good husbandry. Reduce stress of your bees wherever possible as stress adversely affects the microbiome.
  • Always practice good hygiene.
  • Consider your Varroa treatment. Is there a ‘kinder’ option?
  • Work towards becoming treatment-free.
  • Handle bees gently and use minimal smoke.


These references to honeybee anatomy are both available in the East Devon branch library.
H A DadeAnatomy and Dissection of the Honeybee. International Bee Research Association.
Celia F DavisThe Honeybee Inside Out. Bee Craft Ltd.

※ ※ ※ ※ ※


A Talk and Presentation at the December Social meeting 2022
Introduced by Val Bone, with Nick Silver and John Badley. 44 people attended the evening.

Introduction by Val Bone: Our Honey judge at Honiton Show said, ‘Show honey should sparkle’, hence the title. We aim to look at how you go that little bit further to produce honey for the Show table. Just as with livestock at the Show, the competitors spend time turning an everyday animal into a perfectly washed, groomed and polished specimen. It’s the same with honey. We have on show two perfectly good, wholesome jars of honey straight from stock, but how do you achieve that little extra to present it as ‘Show Honey’? Nick will now take you through those steps to produce the SPARKLE!

Nick. Processing Run Honey

The schematic below shows the steps necessary for processing run honey. Liquifying (if the honey is set), straining to remove debris, settling to remove bubbles and conditioning to produce the sparkle.

Scheme for processing run honey

How much heating?

Honey subjected to heating will produce a breakdown substance called hydroxymethylfurfuraldehyde (HMF) which has a legal limit in honey of 40mg/kg honey. The graph below shows the relationship between Time and Temperature. Following the blue dashed lines, a temperature of 40°C for c9days will reach the 40mg limit, whereas a temperature of 50°C will only take 2-3 days to reach the same amount. At 60°C the safe limit is well under 1 day!

Graph of Temperature vs Time for HMF production
HMF depends on temperature and time


This can be achieved by either heating in a warming cabinet (below left) or a bain marie (below right). Stirring occasionally will speed up the process. Hooper suggests 52°C for 2 days. Basterfield Honey Farm suggest ‘up to 50°C’


For the hobbyist beekeeper, straining immediately the honey is removed from the hive and spun from the frames is an easy option (below left). The honey is still warm so will flow through your straining system easily. Double stainless sieves recommended (coarse followed by fine) as they can be quickly washed and dried if blocking occurs.

Straining liquified honey can cause problems with sugar crystals blinding the mesh. The heated sieve (below right) is a useful piece of kit for speeding up the operation. The heated conical mesh is 350 micron, followed by a 200 micron straining cloth over the settling tank.


Settling allows any bubbles to rise to the top of the tank prior to bottling. Without settling your honey jars will look like the example on the left. Settling should produce sparkling honey shown on the right. Hooper suggests ’24 hours in a tall, narrow tank’.


Conditioning removes all the remaining tiny crystals and will ensure clear sparkling run honey for 3-6 months. Hooper recommends 62°C for 1 hour. Basterfield Honey Farm recommend 62°C for 30 mins.

See images below. In either case, add the water to just below the lid. Jars should not sit directly on a hot metal container. Cool rapidly after heating.

John. Hints and Tips for Award-winning Honey

Meet our Honey Judge

Jack Mummery

BBKA Senior Judge

Checking head space aroma

What is the Judge looking for?

Read the Schedule !

  • Class 1. Two matching 454g (1 lb) jars of Light English Honey.
  • Class 2. Two matching 454g (1 lb) jars of Medium English Honey.
  • Class 3. Two matching 454g (1 lb) jars of Dark English Honey.
  • Class 8. Six matching transparent jars of English Honey, minimum jar size 345g (12 oz), labelled as for sale…

There are also Novice Classes for honey. A novice is anyone who has NOT won a prize at any Honey Show.

  • Class 16. Two 454g (1 lb) jars Light English Honey.
  • Class 17. Two 454g (1 lb) jars Medium or Dark English Honey.
  • Class 18. Two 454g (1 lb) jars soft set English Honey.
  • Class 19. Three 454g (1 lb) matching jars of English Honey.

Honey should be:

  • Free from bubbles, crystals or debris.
  • All jars filled to the same level.
  • Once filled, keep jars upright.
  • Put lids on immediately to maximise head space aroma.

Do try this at home!

Checking for bubbles, crystals and debris.

Jars should be:

  • Matching i.e., from the same batch.
  • Must be spotlessly clean.
  • Free of chips or damage.
  • Polish the outside when on display.

Lids should be:

  • Matching i.e., from the same batch.
  • Must be spotlessly clean.
  • No rust or scratches.
  • Polish the outside when on display.

Lids must be spotlessly clean.

Some lids are manufactured with a powder on the polyurethane seal. This is what will happen if you do not wash your lids!!

The Joy of Winning!

East Devon branch win the Branch Cup (most points in the Show)

We look forward to seeing your honey and other exhibits at the Honiton Show on August 3rd 2023!

Sub-pages:WelcomeReportsContactsLinksAsian hornet

© 2024 East Devon Beekeepers

Queen marking colour for 2024 – GREEN

The International queen marking colour code:
Years ending 1 or 6 are White , 2 or 7 are Yellow, 3 or 8 are Red, 4 or 9 are Green, 5 or 0 are Blue
Remember with the mnemonic Why You Rear Good Bees.