Resistance to bacterial infections and raw milk Part 1

Both animals and people need a good diet to build strong resistance to disease and bacterial infections. For ruminants it is a nutrient-dense forage, and for humans it is a diet of diverse living foods. These foods support beneficial microbes in the microbiome and rumen. An appropriate diet becomes food for mutualistic microbes that protect their hosts. Protection is the function of these microbes. Neither animals or people can really thrive on a diet high in grains and industrial, sterilised food. This is not about who is right, but what is right.

There are many good reasons to return to pasture-based feed for livestock, and install national policies to teach farmers how to grow a large mass of nutrient-dense forage in a biological farming or regenerative farming setting.

Farmers need more incentives and support from government and the community to return to sustainable farming. Industrial agriculture has created more problems for us as a nation than people realise. It has taken away the resilience of our pastures during drought. It has resulted in an attitude of profit over care. It has resulted in plants, animals and humans more susceptible to disease. Cattle and humans need nutrients, minerals, and trace elements from their food for increased resistance to bacterial infections. This can be achieved when the conditions are right in healthy soil for nutrient-cycling between soil microbes and plants, resulting in remineralised plants, that deliver these benefits to cattle and humans, more here.

The microbiome function in maintaining health in humans

Researchers think the human microbiome is growing more susceptible to dangerous infections. Now researchers find that the weakened gut biome is directly related to Clostridium difficile death rates. C.diff can cause diarrhea and a life-threatening infection of the intestines. The bug was associated with nearly 30,000 deaths in 2011 in the USA. The class of bacteria known as Clostridia are abundant in nature and most strains are harmless, but tetanus, botulism and gangrene are caused by clostridial species. C. diff is problematic for the human microbiota in particular.

According to this article, scientists have long suspected that antibiotics trigger the infection. The reason appears to be simple ecology. In healthy intestines, the sheer diversity of bacteria meant that C. diff couldn't establish a foothold for out-of-control growth. But once a round of antibiotics had purged the normal flora, C. diff could take over. It is the antibiotics that initially disrupts the intestinal microbiome.

Traditional risk factors like antibiotics and hospitalisation, however, can no longer explain the many infections seen. Researchers are finding that infections may be community-acquired, even without antibiotic exposure. It can also be

due to popular heartburn drugs that lower stomach acid, common food additives and other seemingly innocent antimicrobials.

When microbes in a terrain are killed, beneficials are the first to reduce in diversity and die, allowing bad ones to take over. Superbugs are also born.

According to this Herald Sun article, more than a third of ­nursing-home residents are carriers of antibiotic-resistant bacteria (also called superbugs). These mutant microbes are the result of an attempt on their lives, often due to antibiotics being over-prescribed.

Infections are becoming more commonplace because people don’t have a source of diverse species beneficial microbes to counter and crowd out the pathogens, as part of a regular diet. Remember that the role of the beneficials is to protect. If they are not there, there is no protection in the gut lining.

Up to 80% of the human immune system lies in the gut. It is an area where beneficial microbes like to colonise.

Healthy rumen function in maintaining health in cattle

Pasture-based = increased immune function

Ruminant animals also rely on a healthy rumen micro-organism balance for health, and pasture-based systems can assure this. When animals enjoy re-mineralised pasture over a long period of time, resistance to bacterial infections and immune function increase significantly. Experts like Dr Elaine Ingham says that the need for a veterinarian decreases on this kind of pasture, because the dairy cows are healthier, produce higher quality milk and more milk. Regenerative farmer from North Dakota, USA, Gabe Brown, says that his beef cattle calf unassisted in the paddocks and enjoy extreme good health after a decade on his re-mineralised paddocks. He has several scientists on the farm studying the remarkable results of increasing soil health, which influences animal health as well. Pasture grown without use of agrochemicals have remarkable health benefits for animals, because it creates a nutrient-dense forage. This has a knock-on effect on the health of humans who consume the meat and dairy products.

Growing a high plant diversity pasture builds robust grassland that keeps a protective ‘skin’ on the soil, preventing topsoil from being removed by dust storms or rain.

Many farmers don’t have resilient pasture anymore. In the colonial days, Victorian grasslands had 300 - 400 different native plant species and in February during 37’C weather conditions, the grasslands were described as lush and “hydrated”. Today in the dairy industry, some farmers still grow monocultures of ryegrass, and in February the paddocks are often dry and grazed to the ground. In good times, both beef and dairy cattle often overgraze the pasture, and if an intense rotational grazing system is not in place, cattle can destroy their favourite plants, decreasing plant diversity, and with it soil health. Farmers have been herded away from sustainable farming, with the ‘get big or get out’ mantra, to everyone’s detriment. Many grasslands today cannot cope with the harmful modern farming practices that can rob the soil of its biology, and it is affecting animal health, more here.

When grasslands are healthy, with a high diversity of plants and soil microbiology, this ecosystem enjoys an ability to sanitise and regenerate itself after animals leave a paddock. The soil may contain both beneficial and harmful micro-organisms, but a homeostasis is maintainable, because the terrain is a functioning ecosystem where beneficial microbes dominate and protect. This is the function and nature of beneficial microbes, in various terrains. In addition, when cattle enjoy a 100% pasture-based diet, they are unlikely to have pathogens in their rumen, nor can they shed in their manure.


“A Regenerative Secret” is a powerful mini-documentary that breaks the thinking that cows are the problem. Contrasting the catastrophe of the current cattle industry with the hopeful and inspiring paradigm of Regenerative Ranching. This emerging form of ranching is not only restoring ecosystems but also reversing global warming and helping ranchers across the world become more prosperous. Click to watch it here.

Grain based = decreased immune function in cattle

In times of drought farmers run into many problems. Farmers sometimes have too much livestock, and not enough forage. In these times, some farmers rely more on grain and other supplements that may not necessarily benefit the health of the animals. Some of these grain-based mixed feeds can decrease the immune function of the animals, because they can alter the beneficial microbe balance in the rumen, cause pathogens to grow or even outcompete the beneficials, block mineral and trace element absorption, pose toxicity risks or they can even pass microbial dangers to raw milk. Only a few of these will be described briefly. Detailed information and resources can be found in the 11 categories of the Risk Identification and Risk Reduction program.


Seeds like cottonseed are given to both beef and dairy cattle in industrial systems as a supplement in mixed feed during dry times. Cottonseed, however, has a natural toxin called gossypol. It is a natural toxin present in the cotton plant that protects it from insect damage. According to this article cattle cannot be allowed to eat too much of it, or for extended periods of time, due to toxicity that can cause heart failure and death. Toxicity has also been reported in young calves, because they do not have well-developed rumen microorganisms yet to protect them. Seeds and grain contain a wide variety of anti-nutrients that can have a negative impact on cattle health.


Grains are often high in phytic acid, which is the protective layer preventing seeds and grains from germinating until the conditions are right. Healthy adult cows, with a balanced rumen, can eat small amounts of grain without problem. Rumen microorganisms produce an enzyme called phytase. Phytase neutralise phytic acid and liberates the phosphorus. This system, however, can be overwhelmed when large amounts of grain are fed. Phytic acid can combine with calcium, magnesium, copper, iron and especially zinc in the intestinal tract and block their absorption. Minerals are essential for animal health and growing resistance to bacterial infections. When cattle eat a lot of grain it can also alter the rumen microorganisms, which they depend on for health, in ways that cannot be briefly described here. Mineral deficiencies can also make cows susceptible to common diseases or bacterial infections, prone to infertility problems or prone to premature births, weak calves or prenatal deaths etc. It is a very serious problem, that is commonly swept under the carpet. Attempting to fix these deficiencies artificially can have other negative consequences, like toxicity.

Food waste, like spent brewer’s grain

Studies show that distillers grain can change the cow’s gut microbial balance. If fed to cattle, their gut begins to favour and encourage e.coli pathogens, when pasture or dry forage based diets does not. Cows are mammals just like humans, who also depend on a balanced set of rumen micro-organisms to digest their food and protect them from pathogens.

Mixed Feed

Mixed, grain-based feed is vulnerable to microbial contamination, as explored in the Feed category. Bacteria, moulds, yeasts and toxins may be introduced through feed ingredients sourced from various places. Contamination can also occur during production, handling, storage and transportation. There are many intervention strategies, chemical treatment strategies, heat treatment (sterilisation) and additives to reduce the risk that mixed feed may pose to rumen function. Scientists attempt to make these feeds pathogen-free and toxin-free but it is not risk-free. Animals in large industrial systems are now also given prebiotics and probiotics to prevent dysbiosis, because it can be a result of being supplied commercial grain-based feeds. Mixed feed is a potential minefield of risk for animal health, and ultimately for human health.


Cattle are meant to eat pasture for good health. They are not biologically designed to live on large amounts of anything else, for extended periods of time or their health, immunity and resistance to disease will suffer. Grain crops are often grown in de-generative farming systems and then shipped thousands of kilometres to feedlots, as described in this video. When cattle become prone to disease, antibiotics are usually given. It is a cycle that can only end in long term dysfunction…

In this video, Dr. Zach Bush talks about how modern farming robs the soil and the plants of the ability to make essential, medicinal qualities. The nutrients and medicinal quality in food can be diminished when people move away from the established systems in nature. Part of learning how to grow nutrient-dense forage, is learning how to wean soil from their addiction to inorganic fertilisers and other chemicals like herbicides, because they can harm the micro-organisms in the soil which are involved in increasing soil health.

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The prevalence of beneficial and potentially harmful microbes in the environment

According to Peter Pollard, an Australian microbial ecologist in this TEDx video, 99% of all microbes on this planet are "essential for our very existence. We would not be here if it weren't for these microbes." He says only a few of the disease causing bacteria and viruses gives microbes a bad name. "Microbes ensure that both carbon, nitrogen, hydrogen, phosphorus and oxygen are all recycled on our planet".

Harmful bacterial species make up a tiny minority in the environment but they have become problematic because of our modern farming methods. Chemicals with antimicrobial properties eliminate probiotic microbes, grow antibiotic-resistant microbes and increase pathogenic ones via unsustainable industrial agriculture practices. Harmful bacteria has also increased in many terrains because of the kinds of foods and eating habits of both people and cattle.

Recently the oldest solid cheese ever identified, dating back 3,200 years, was found in the tomb of Ptahmes, a mayor of the Egyptian city Memphis in the 13th century BC. Techniques revealed it was made from a mixture of cow milk and goat/sheep milk. The cheese was also contaminated by zoonotic Brucella melitensis bacteria. According to Wikipedia, this bacterium can infect sheep, cattle and can sometimes transfer to humans. If this bacterium has been around for ages, how did ancient civilisations live with it?

It is possible that these societies had more resistance to bacterial infections, because they consumed more nutrient-dense and live foods.

Dr. Elaine Ingham's research - discussed in-depth in the Farm and Land category - describes how ancient civilisations in Babylon in Mesopotamia, and also in ancient Rome, made their own compost tea, which they used to fertilise the soil and increase nutrient cycling, which lead to healthier crops and pastures.

Increasing beneficial microbes to protect against, and block potentially harmful microbes

Image:   beneficial microbes are like generals that are always on guard. We just have to ensure that they remain in charge…

Image: beneficial microbes are like generals that are always on guard. We just have to ensure that they remain in charge…

In this video, Cornell University professor Rodney Dietert, describes how the microbiota of healthy people can effectively inhibit colonisation and overgrowth by invading pathogens. It was first observed in 1954 and termed colonisation resistance. It is associated with a stable gut microbiota that do not trigger inflammation. It’s homeostasis. It involves specific interaction between the immune system and the microbiota.

He also explains how beneficial bacteria actively protect against infections and pathogens, and why we need proper therapies to recolonise the microbiota after antibiotic use.

Prof Dietert explains the multiple layers of ways in which using commensal, mutualistic microbes can block pathogens:

  • These microbes outcompete pathogens for the same nutrient source.

  • They can stimulate signalling that can block production of the pathogen’s nutrient source.

  • They stimulate mucin production to protect the mucus layer and inhibit pathogen access.

  • They directly produce bacteriocin (anti-microbial) effective against some pathogens.

  • They stimulate intestinal cells to make REG3-gamma (anti-microbial).

  • They produce short chain fatty acids to block pathogens and change host defence.

  • They metabolise primary bile acids to block pathogens.

  • There are signalling molecules, that they can produce, that can block quorum sensing capabilities in some pathogens.


Prof Dietert says that there are multiple layers of ways in which mutualistic microbes in the gut, in the airways, on the skin or in the genital tract naturally block pathogens from getting a foothold.

He says we need to be using this as a first line of defence, and using it as a strategy, rather than just making assumptions that everything will be fine or problems can be fixed by prescribing antibiotics. The immune system and the microbiome need to co-mature to avoid persistent immune dysfunction, and to reduce the risk of infections. For more information, see the work of senior microbiologist and risk analyst Peg Coleman here.

Video: Professor Dietert presents a seminar introducing recently published research on microbiome completeness, immunology, and more holistic ecological approaches for neonatal health. This research fills gaps in knowledge for minimising health risks for neonates. Video by Al Pagan 5 Nov 2018

Farmers who want to produce raw milk for human consumption, often have a desire beyond making money. They often desire to connect directly with the consumer and to provide the live product that consumers are asking for, to heal their gut. Remember there are two kinds of raw milk: one intended to be pasteurised and another intended for human consumption.

Proceed to part 2 of this article