Probiotic Microbes, Colonisation Resistance and the protective benefits in different terrains

Beneficial microbes improve health in many terrains.

Colonisation resistance is a completely different way of thinking.

When the information is applied, it is both pioneering and revolutionary. Fortunately there is a lot of evidence to support it. The use of good bacteria to decrease risks to health, however, may require a dramatic change in perception for some bacteria phobic scientists and regulators. It is crucial that dairy farmers who want to produce for the raw dairy market, learn to grow a large amount of the right set of microbes in various terrains on the farm. It is also vital to learn how to avoid the use of antibiotics and other chemicals with antimicrobial properties, that may kill beneficial, commensal microbes. Disrupting the balance often leads to potentially harmful ones taking over.

The colonisation resistance reality has been discussed from many different points of view on this website over the years. Here is a recap and some new information.

The human gastrointestinal tract

This article follows from the information presented in previous articles about colonisation resistance in the human gut:

  1. Resistance to bacterial infections and raw milk Part 2

  2. The contributions of Peg Coleman to the raw milk movement

Colonisation resistance explains the power of beneficial microbes: they colonise terrains like the gut lining that prevent pathogens from doing the same or causing harm. It was first observed in 1954 and later termed colonisation resistance. It is associated with a dense, diverse gut microbiota that does not trigger inflammation, but promotes homeostasis. It also involves specific interaction between the immune system and the microbiota. The microbiota of healthy people can effectively inhibit colonisation and overgrowth by invading pathogens.

However, when the normally diverse protective microbiota is disturbed by antibiotics, drugs, or stresses in various environments, susceptibility to pathogens greatly increases. The human microbiota is our gatekeepers to health. Immunocompromised patients are at a higher risk than the average population due to abnormal or depleted microbiota, loss of colonisation resistance, and higher susceptibility to low pathogen loads or doses often present in hospital environments. Having a low diversity of species in the gut, low abundance of Lactobacillus (the microbes common in yogurt) and altered microbial-network structures are actually dangerous for human beings. Mark McAfee from the Raw Milk Institute refers to the human race as “bacteriosapiens” because we need the right set of bacteria to prime our immune system and improve our health, and so do other mammals like cows.

The paddocks

In two previous articles we’ve explored how cultivating the right set of beneficial microbes (like mycorrhizal fungi, nematodes, protozoa, micro-arthropods etc.) grown with the use of compost tea, chemical-free farming and other regenerative farming strategies, can make the soil very fertile and increase the food safety of raw dairy. A mob grazed paddock has the ability to ‘sanitise’ itself when the animals are moved around frequently.

  1. Growing nutrient-dense food for dairy cows and humans

  2. Nutrient-dense food in Australia

A large amount of the right set of microbes in the soil nutrient-cycle with plants, and result in a large biomass of nutrient-dense food for animals. The healthy chemical-free grasslands are also an environment where good microbes dominate.

Antimicrobials, like some herbicides, pesticides and even inorganic nitrogen fertiliser can kill these essential microbes, disable a plant’s innate protective symbiotic relationship with microbes, and allow pathogens to overgrow in the terrain.

The rumen of the cows

Another previous article, Resistance to bacterial infections and raw milk Part 1, briefly described why it is important that healthy rumen function in cattle are maintained with the feeding of a nutrient-dense, pasture-based diet, not a high-grain diet. The cow’s rumen is a microbial digester and when the microbial balance is disturbed, increased susceptibility to bacterial infections and disease follows.

Increasing beneficial bacteria in different terrains to outcompete potentially harmful microbes, have already been described in many different forms on this website. This strategy will now be presented from yet another very interesting perspective

Utilising beneficial microbes in other terrains on the farm:

These risk mitigation strategies to improve health can be applied to water pipelines, water troughs, animal bedding, calving pens, and buckets commonly used to feed calves. These strategies improves the calve’s chances of survival, increases the health of straw bedding, increases the health and immune function of cows, cleans the cow’s udders post-milking, reduce mastitis, lameness and other bacterial and fungal infections.

In this video, Aled Davies from a Welsh company called Pruex offers a rather unique and enjoyable perspective on how soil microbes can be utilised in terrains where lots of pathogens live. The soil microbes function in a beneficial way to increase the health of animals.

Pruex is a company that aims to help with constructive ways to limit anti-microbial resistance (AMR).

Pruex work with farmers, regardless of species of animal farmed, to develop evidence based strategies on their farms that enable them to show their prudent, as opposed to excessive use, of antibiotics. In the video, Aled demonstrates how good soil microbes can be added to various terrains, with credible evidence of increased colonisation resistance. He visits all types of farms, including intensively farmed operations where animals are often surrounded with large amounts of infective bacteria, putrid water and where the air they breathe is contaminated. Unsustainable farming practices in industrial farming systems, often produce unsustainably produced microbes in the terrain, that have to be sterilised.

Aled found that the use of disinfectants is maintaining sick animals, as opposed to reducing disease.

At the 8 minute time marker, Aled displays a slide showing how natural microflora consists of dominant beneficial microbes, and how disinfection with biocides changes that microflora to a predominantly bad ratio of microbes. This is why we need to explore different forms of “cleaning” and sanitation. See the image below.

Image: A snapshot from Aled’s video presentation, showing the typical nature of a terrain before and then after a terrain has been disinfected with a biocide. The green dots represent the good, and the red the bad microbes. He says the result is often the quick return of bad microflora because of biofilm in the terrain. Click to enlarge.


Aled also explains how biofilm build-up in terrains can be a strong source of contamination. He shows how he uses soil bacteria to clean biofilm that can be a re-occurring source of infection, and also to correct the microbial ratio in terrains. The good bugs that he introduces have a pleasant and sweet smell. The disease-causing bugs have a putrid smell. Aled says that we can rely on our noses to identify the health of terrains, and the effect bad microbes have on them. This includes harmful E.coli, Enterococcus, Staph Aureus and Streptococcus. He shows how his approach operates in water pipelines, cow’s water troughs, animal bedding, calving pens, buckets commonly used to feed calves, and cleaning cow’s udders post-milking. These strategies are reducing mastitis, dermatitis, lameness and are also helping with bacterial and fungal infections in the hooves. Certain bacteria in the environment can cause a cow to have a high Somatic Cell Count and mastitis, and dairy farmers now have an alternative strategy to antibiotic use.

In the UK it is very important to improve dairy cow housing conditions due to the winter climate for all dairy systems large and small. In this article, Aled explains why having an environment that is non-infective during this crucial period is vital for cow recovery and calf health post calving. In the article is a testimony from Cornishman Andrew Brewer, who milks around 700 cows on a low cost, once a day system. Andrew discusses how he has worked with Pruex to help solve some of the issues he was facing that were a drain on financial resources and increased his costs significantly. By concentrating on improving the environment his cows are housed in during the winter, he has seen bedding and animal health costs reduce. He has achieved in excess of a 70% reduction in antibiotic use for mastitis since focusing on his animals' environment. Teat condition has dramatically improved. He has also not had a single case of scours or pneumonia all year in the calves.

“We’re using nature to benefit agriculture and animal health” - Aled Davies on S4C

Image: Another snapshot from Aled’s video presentation, showing how a large ratio of good microbes in the terrain is achieved as a “cleaning” solution. Click to enlarge.


Aled demonstrates decontamination of different terrains by introducing soil bacteria.

The terrains Aled treats become totally dominated by non-infective bacteria.

In the video, Aled describes why the goal is to maintain a ratio of more than 60% beneficial bacteria. When bacteria get up to 60% of a resource, they stop “doubling”, which is also call quorum sensing. When the bacteria is no longer doubling anymore, they go into what he calls “hibernation” and the bad bacteria can no longer produce toxins or enzymes that make a terrain putrid. With his methods, Aled says he is converting indoor areas, where animals spend some of their time, into terrains with the same microbial safety as out in pasture.

At the 8 minute time marker, Aled shows how Pruex works to provide clean water for cows. Aled explains how biofilm in terrains (like pipes) can be a strong source of contamination. This biofilm can contain putrid bacteria releasing enzymes into the cow’s drinking water, creating immune problems and other infections. At the 11 minute time marker, Aled shows how he uses soil bacteria with a pump to clean pipelines. He says this significant increases the health of the cows, and also the amount of milk they produce by two

litres a day, see this example. Clean water can reduce immune burden and help fertility and production. Water troughs for cows can be a serious infective place of disease for cows unless cleaned properly.

Aled says his methods are making it easier for the animals to maintain health and to properly fight off any infections.

It is also reducing the need for antibiotics in the UK dairy sector, see this example. In this video, veterinarian Rob Drysdale discusses how he and his team have benefited from a determined approach to reduce toxins in their animals' environments.

Aled’s solutions work miracles in large, intensively farmed operations where there is great need for them, but the principles are also working for some UK raw milk cheese producers. This is valuable information in understanding the microbial nature of terrains and how farming practices influences the microbial ratio.

Image: Healthy, chemical-free pasture-based terrains are often home to a large ratio of beneficial soil microbes.

Image: Industrial agriculture - with feedlots as worst case scenario - tend to create terrains where lots of potentially harmful microbes dominate, because of high grain feeding that influence the rumen microbiology of cows and pathogens that then shed into the environment. Click to enlarge.


The idea behind exploring these examples, is to show how important a good ratio of good bugs are in different terrains. This is another concept that some food regulators, legislators, health department officials and food safety experts don’t seem to understand. Live foods have a different risk profile and a different set of protective benefits because of the microbial nature. When these live foods are produced in healthy, pasture-based systems with good hygiene and husbandry protocol, this can be done very safely. Raw dairy is often produced from small, boutique dairies who can take a great deal of care. Pasteurised, sterilised foods have no innate protection because the different protective components were wiped out after heat treatment. Dairy farmers producing for the raw dairy market have to implement many strategies to increase animal health and avoid the need for antibiotics.

We need to redefine definitions around food safety of live foods produced in healthy farming systems, and develop a holistic view of how raw dairy production can be done very safely when farmers mind-their-microbes.

In addition, academics spend a lot of time viewing objects in isolation, sometimes under a microscope. They also spend a lot of time isolating themselves from the whole. Academics and researchers must reorient themselves. They need to quit looking at individual things and ignore a gushing wound in society. Many Australians lack good gut health because they don’t have access to a source of good gut bugs. Academics need to stop addressing only symptoms, instead of the root cause. The real problems need to be solved and looked at holistically.

“An object seen in isolation from the whole is not the real thing.” - Masanubo Fukuoka

The Ethical Dairy

The cow/calf friendly dairy that produce raw milk cheese

Audio: Listen to this interview on BBC Radio Scotland. Euan McIlwraith talks to The Ethical Dairy about Bacillus Subtilis (also known as hay or grass bacillus), a beneficial microbe utilised in the water to significantly increase the health of the water, the calves and the cows. B. subtilis is found in soil and the gastrointestinal tract of ruminants and humans. Date 29 April 2019.