Probiotics, pathogens and superbugs and their effect on health

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There are times when the most difficult situations arise. They can act as a catalyst to heal important areas in life. They’re beneficial because they can be our greatest teachers.

To be forewarned, is to be forearmed. This article is a reminder that limiting beliefs, ignoring problematic situations, and risky or careless lifestyles must be addressed so that positive changes can take place.

In Victoria earlier this week, both Labor and the Liberals went to Frankston, wooing voters with competing promises on health. The Andrews government promised to spend $562 million on a major upgrade to Frankston Hospital if it is re-elected on November 24. Labor says it will transform the 77-year-old hospital into an 11-storey facility. Clearly there is a “booming demand” for attention to the health sector. Last week however, new research from Israel questioned an established approach to health care globally, which has far reaching consequences for how we look at health and growing immunity.

Our global food system contains many pathogens. Superbugs are no longer a rarity. When pathogens colonise the gut lining, they can create a leaky gut, and cause incredible damage to the gut lining, immunity and health. When the gut lining is packed with diverse-species beneficial microbes, and replenished often via the diet, the

probiotic residents in the gut lining offer protection against pathogens, food poisoning, chemical toxins and even the stomach virus. It is already clear that people need frequent access to more beneficial microbes to counter the bad ones, but where will we find them? Probiotic = pro life. At ARMM, we already know that research show probiotic pills and commercial yogurts are considered inferior probiotics by some scientists.

According to this article, almost 4 million adults in the U.S. consume probiotics in various forms, like yogurts,  supplements etc, but new research suggests that they may do nothing for some, and can even be detrimental. This is not good news for a growing, global probiotic market worth $45 billion in 2017. These probiotics may rake in the dollars for developers, manufacturers and shareholders, yet do not benefit all the consumers who tend to carry a belief in a one-size-fits all, quick fix approach. See the video below.


Two probiotic studies with 11 commonly found strains

Two studies were pusblished in the first week of September. They add to the growing body of research showing there isn't much benefit in taking over-the-counter probiotics to populate the human gut, or in how well they helped a person's gut recover after antibiotics.

Experiments in mice and people find that probiotic supplements don’t consistently change the composition of the gut microbiome, and may have adverse effects after antibiotics.

According to this article, the first study took two small groups of people, surveyed their gut bacteria with upper endoscopies and colonoscopies, and gave them either commercial probiotics or a placebo. The probiotic cocktail for both studies contained 11 of the most commonly found strains. Author Eran Elinav said the Israeli researchers from the Weizmann Institute of Science in Tel Aviv were surprised that in the group who took the commercial probiotics, the bacteria simply moved through the intestinal tract without attaching to the gut. "They were not doing anything to the human host. They were just failing to colonise," he said

The second study looked at the role of probiotics in helping people return to a normal gut microbiome after taking antibiotics. Eran, who was the co-author of both studies, explained that

there is a common conception that taking probiotics after antibiotics, would protect against pathogenic infection. In other words, it is commonly seen as one-size-fits-all solution. In the second study, three groups were given antibiotics, then... 

  1. One group was given commercial probiotics

  2. The second group was given transplants of their native gut bacteria, taken before the antibiotics were given,

  3. The third was not given further treatment.

According to the article: "Compared to the first study, the commercial probiotics were much better at colonizing the gut after people had taken antibiotics. But Elinav and his team also found that the probiotics were now preventing the original microbiome from returning to its original, healthy state."   

To the researchers' surprise, the supplement had the opposite effect: it took months for their microbiomes to return to its pre-antibiotic state, much longer than a group who took no probiotic and let their microbiome recover by itself.


According to this article, the first group, who took probiotics that colonised their gut, recovered more slowly. Their original gut microbes did not return. The volunteers were in a state that lasted for at least six months, which led to genetic changes, that if persisted long term, could predispose them to allergies and inflammation.

This goes against the idea that probiotics can help "repopulate" people's gut bacteria after antibiotics wipe them out. "Contrary to the current dogma that probiotics are harmless and benefit everyone, these results reveal a new potential adverse side effect of probiotic use with antibiotics that might even bring long term consequences. We need to be cautious about recommending this until further knowledge emerges," said Elinav. The side effects of antibiotic use is not a trivial matter. There can be significant changes in bowel habits, and in worse case scenario, a Clostridium difficile (C.diff) infection can develop. This affected half a million Americans in 2015 and was directly responsible for at least 15,000 deaths. According to the York Health Economics Consortium, 260,000 people in the UK develop sepsis every year. Around 46,000 people die from the fast-acting condition. In

Australia, sepsis is recognised as the silent killer that takes at least 5,000 lives each year. According to this article, it occurs when the body's immune system overreacts to infection, injuring tissues and organs. Sepsis is often misdiagnosed as gastro.

In stark contrast, the people who were given back samples of their own gut bacteria, from the second group, returned to a normal microbiome within days.

According to the CBC article, an Adelaide gastroenterologist, Daniel Worthley, said that the best way to support a healthy gut microbiome, was with a good diet. A good diet may be good advice, but Daniel too was concerned that probiotic use can delay the return of normal flora. He expressed concern about the vague descriptions of the health benefits that probiotic manufacturers often put on their products. "I think the use of the word 'may' on a lot of the packaging may confuse consumers. They probably associate greater health benefit than has been proven for probiotics," he said. Watch a Nine News video about the two studies here.


The second study also show that when the slate is wiped clean, with antibiotics, it may give the first colonisers a very good advantage to colonise, with an undesirable effect of a long recovery process. Over-the-counter probiotics often contain anything from 3 to 15 different microbial strains, depending on price and so-called quality. Science show a large diversity of species is key. Human breastmilk, for example, was found to contain more than 700 different kinds of microbial species.

A good diet alone may not be as helpful as believed, to see a permanent return of a set of healthy, diverse species microbes. It is possible that the commercial probiotics, as the first colonisers, may have created a significant disadvantage for the recipient. The nature of a microbe is to colonise the terrain by rapidly growing in number, so they can defend their turf against potential competition. There is another approach that is commonly taken in other countries. It may be more beneficial to bombard the early colonisers frequently with high doses of beneficial, diverse species microbes, via the diet, to see a satisfactory re-establishment of a healthy, diverse microbiome quicker. Keep reading... it gets very interesting…


A handful of microbe species vs a high-diversity in the terrain

Over-the-counter probiotics and commercial yogurts are excellent examples of how a few monoculture species in the terrain fail to deliver the most beneficial results.

Probiotic yogurts? A 2017 study showed that most probiotic yogurts don't contain enough 'good' bacteria for additional benefits. The researchers found that the probiotic levels in these yogurts were sometimes up to 25 times lower than what clinical trials have found to be effective. 

Probiotic pills? Experts also say that the lack of actual live microbes makes commercial yogurts and probiotic pills an inferior probiotic, read more here. Also, who is to be the judge on which beneficial microbes will have the most benefit when science show it is the diversity of species that is the key? Gut microbiome experts like British science tv presenter Dr. Michael Mosley, recommends that we culture our own microbes. He recommends culturing vegetables, making your own yogurt and your own kombucha.

In addition, there is also research by the Jena Experiment in Germany, and others, that show the way that plants acquire nutrients is a biological process. The Jena Experiment also shows why monoculture plant species will continue to degrade soil fertility and farm profit. Soil scientists, like Australian Dr Christine Jones and American Dr Elaine Ingham, say that soil microbes have different relationships with different plants. Soil microbes and plants work in a symbiotic relationship called nutrient-cycling, to extract various nutrients, minerals and trace elements from the soil. Certain plants, work with certain microbes to nutrient-cycle certain minerals, that’s why diversity is key. Christine says that only plants and their associated microbes can make fertile topsoil - and a diversity of plants and microbes make it even better. She says that about 85 - 90% of nutrient acquisition is microbially mediated, which means nutrients has to come via the microbes. Scientist Dr Kate Scow also say that you can’t sequester carbon without microbes.

“Building topsoil is a biological process.” - Dr Christine Jones, soil ecologist


Childhood cancer and probiotic microbes

Some of the UK's most eminent scientists say our modern germ-free life is the cause of the most common type of cancer in children. According to this article, acute lymphoblastic leukaemia affects one in 2,000 children. 

Professor Mel Greaves, from the Institute of Cancer Research, has amassed 30 years of evidence to show the immune system can become cancerous if it does not "see" enough bugs early in life. It means childhood leukaemia may be possible to prevent. This type of blood cancer is more prevalent in advanced, affluent societies where it is increasing in incidence at around 1% per year.

Professor Greaves, in collaboration with other researchers around the world, found there are three stages:

  1. The first is a seemingly unstoppable genetic mutation that happens inside the womb

  2. Then a lack of exposure to microbes in the first year of life fails to teach the immune system to deal with threats correctly

  3. This sets the stage for an infection to come along in childhood, cause an immune malfunction and leukaemia

He said: "The research strongly suggests that acute lymphoblastic leukaemia has a clear

biological cause and is triggered by a variety of infections in predisposed children whose immune systems have not been properly primed." According to the articlethere were other evidence that helped to build the case:

  • An outbreak of swine flu in Milan that led to seven children getting leukaemia

  • Studies showing children who went to nursery or had older siblings, which expose them to bacteria, had lower rates of leukaemia

  • Breastfeeding - which promotes good bacteria in the gut - protects against leukaemia

  • Lower rates in children born vaginally than by caesarean section, which transfers fewer microbes

  • Animals bred completely free of microbes developed leukaemia when exposed to an infection

The study found that there is a price to pay for those who live in modern society, because enjoying contact with beneficial bacteria, to help train the immune system, is very challenging.

“…it has always struck me that something big was missing, a gap in our knowledge – why or how otherwise healthy children develop leukaemia and whether this cancer is preventable.” - Prof Mel Greaves

Also see this article: ‘For 30 years I’ve been obsessed by why children get leukaemia. Now we have an answer’

In this video, Mark McAfee from the Raw Milk Institute explains that scientists now know that we need a lot of bacteria, a biodiversity of bacteria and the food to feed that bacteria. He says we are losing our biodiversity in the gut, which has a tremendous effect on stem cell differentiation and the function of our immune system. Our immune systems will be stronger when we are exposed to more diversity of bacteria. At the 27 minute time marker, Mark talks about Dr. Annett Jewett PHD at the UCLA Cancer center, who discovered that a large amount of bacteria is critical early in life to differentiation of stem cells, as well as control of inflammation in the body. Some of her early work has shown prevention and recovery from cancer. He says that Dr. Jewett found that stem cells misbehave, like become cancer cells, when they don’t have the load and biodiversity of bacteria. Mark also recommends Dr. Bonny Basler’s TEDx video about the human biome and genome and why we are literally '“bacteriosapiens”. Mark says the biome is what drives us genetically. “…They found out that there is 24,000 genes that make us human in terms of the framework, but that the deeper genetics was incredibly complex and it was made up of like 93% of the bacteria in our body, that actually share genomic information, genes, with our human cells, to complete our genome.” He says that Dr. Bassler’s diagrams show that the relationship of the cell count in our body of bacteria cells to human cells, are 10 to one. Mark says the bigger take-home is the relationship between the DNA contributed by that bacteria; it is 100 to one.


Superbugs and pathogenic microbes in Australia

and the beneficial microbes that crowd them out

Beneficial gut microbes in the gut perform a mind boggling amount of essential functions. 70 - 80% of human immunity is said to be in the gut. Almost 100 percent of the body's serotonin and about 75 percent of dopamine are produced in the gut with the help of microbes. Mother Nature gave us our own factory to produce these essentials. Beneficial bacteria also produce and release B vitamins into the bloodstream, as the body requires them. According to Dr. Natasha Campbell-McBride, this mechanism cannot be repeated with any supplement or food. She also says the beneficial microbes form a biofilm in the gut lining that prevents potentially harmful microbes from colonising. The only way a pathogen can get a foothold is if there isn’t enough beneficial bacteria in the gut. In this article however, there is information about how the human body is bombarded with a recipe for disease, that results in dysbiosis of the gut. Dr Natasha explains that microbes have the ability to neutralise and protect the body from cancer-causing chemicals or toxic metals.

“These microbes have an ability to neutralise these chemicals, in fact they are the best neutralisers and detoxifying substances on the planet known to us.” - Dr Natasha Campbell-McBride

Dr. Natasha also explains how harmful microbes, when they set up shop in the gut lining, release toxins and create what she calls 'drug addicts'. She recommends treatments like raw kefir, a fermented yogurt-like drink, for the rehabilitation of the gut. She is able to successfully pull children out of a cycle of addiction and stagnation, by changing their diets and introducing large amounts of beneficial bacteria to help crowd out pathogens.  

In many countries, like Victoria, Australia, citizens simply do not have access to a good source of diverse species, probiotic microbes.

There are laws and regulations that prevent people from accessing the beneficial microbial life found on farms that transfer to foods like raw dairy. In this recent Wise Traditions podcast, Mark McAfee from the Raw Milk Institute explained why he considers that raw dairy products were the ancient foods of wisdom, that was available for thousands of years. According to him, it was the 'medicine' that created a healthy immune system to survive. It contained the probiotics. It was ‘prevention through nutrition’. He says the biome was first discovered in 2003, and that medical schools have since been running around trying to figure out how to deal with it, because they have to rethink what is perceived as ‘medicine’. Mark says that it is wonderful for him to see some youngest paediatricians coming forward, and saying they will hold off on prescribing antibiotics for an ear infection, while reaching for the probiotic first. In California, where raw milk has never been illegal and is highly regulated for quality control, cultured raw milk kefir is sometimes recommended as a probiotic for a health recovery. Mark talks to Steve from Central Valley Business about raw dairy in the video below:


Australia is among the highest prescribers of antibiotics in the world according to this article. With 46% of Australia’s population being prescribed antimicrobials in 2014 alone, the average Australian's gut can't be in the best of shape, in terms of microbial diversity. Australians are among the sickest in the world according to this article. The government and health departments continue to heavily invest in building more hospitals for all the sick people, and for those they are expecting in the future.

In addition, many Australians now live with superbugs in their gut. Antibiotic-resistant microbes are created when some microbes survive, adapt and thrive, after an attempt on their lives. According to this Herald Sun article, two thirds of nursing-home residents are now carriers of antibiotic-resistant bacteria. The elderly are commonly overprescribed antibiotics. It is now understood that antibiotics create superbugs. The elderly may have a gut packed with potentially harmful microbes, and not enough good microbes, or a diversity of beneficial microbes via the diet to counter them. This article titled, Gut Microbiota and the Immune Compromised, explores how modern society came to be so immune depressed in the first place.

“Let food be your medicine and medicine be your food.”

”All diseases begins in the gut.”

”Do no harm.” - Hippocrates, the Father of Medicine

In this video, Mark explains how huge risks to the immune system are created with the abuse of antibiotics that create superbugs. He says high quality raw drinking milk is creating stronger immune systems, more resistance to bad bugs and less bad bugs.


How microbes colonise the virgin gut, the natural way

Kristin Lawless, the author of "Formerly Known as Food: How the Industrial Food System is Changing Our Minds, Bodies and Culture", recently wrote a brilliant article in the Opinion section for the New York Times. She wrote about the scientists at the University of California, Davis, who have found that a strain of bacteria called B. infantis that is thought to have been the dominant bacterium in the infant gut for all of human history, is now disappearing from the Western world.

According to the research, this was probably caused by the rise in cesarean births, the overuse of antibiotics and the use of infant formula in place of breast milk. Kristin wrote that nine out of 10 American babies don’t have this bacterium in their gut anymore, while researchers suspect that the majority of infants in less industrialised countries do.

Research by University California, Davis, Dr. Bruce German shows that human breast milk contains a carbohydrate called oligosaccharides. It is abundant in mother's milk, yet human babies cannot digest it. It seems to be there purely to feed microbes and encourage them to settle in the

gut lining. Dr. Bruce's study found that when B. infantis took over the entire lower intestine, it crowded out pathogenic bacteria, which can cause both acute illnesses and chronic inflammation that leads to disease. The studies show that change to the infant's gut may be at the root of rising prevalence of diseases and ailments, from allergies to certain cancers. Good bacteria already present in the gut lining, can prevent deadly infections in babies. Breast milk is raw milk. Remember that Spanish researchers found that human breastmilk can contain more than 700 different kinds of microbial species. Variety of microbial species is key.

Another article, illustrates how important it is to lay the right foundations in the gut microbiome as soon as possible. The first microbes that colonise it have a lasting effect on our health throughout our lives. Researchers at the University of Alberta found that individual differences in the microbiome probably depend on where the first microbes we acquired came from, and the order in which they arrive has a critical influence as well.


The protective function of components in raw milk from cows

Recently, Mark McAfee from the Raw Milk Institute spoke about the function of raw milk in this interview.  

Consider the following:

  1. This milk from healthy, grass- and hay fed animals is about the diverse microbes and the components that feed them.

  2. Raw milk straight from the udder also contains components like lactoferrin and lactoperoxidase that protects the live milk from potential pathogen contamination.

“Raw milk’s purpose is to transfer the immune system from the mother to the baby and build the gut of the baby.” - Mark McAfee

In simple terms, this means that raw milk can enable good microbes to flourish, because it naturally contains components that feed it. High-quality raw milk can also eliminate potentially harmful microbes, that may find its way to the milk before they can reproduce. Components like lactoferrin and lactoperoxidase can function in high-quality, carefully produced raw milk, and are not easily overwhelmed. Mark describes these systems as semi-protective and suppressed pathogen growth.

Oligosaccharides, or complex sugars as they are also known, function as the selective growth substrates for specific beneficial bacteria to grow in the gut. It has also been shown that oligosaccharides themselves, can bind pathogens and protect the infant from infection. 

The University of California, San Diego also published a study recently about the benefits of oligosaccharides, the complex sugars in human breast milk.

Like human breast milk, raw cow's milk is also abundant in oligosaccharides.

High-quality raw milk contains the probiotic microbes, the prebiotic food and the protective components to help the calf develop a rumen in the early stages. According to this Australian article, calves are born without any immunity. They acquire immunity as neonates from antibodies in colostrum (passive immunity) and then they develop immunity through exposure to different pathogens as they age. This is active immunity. The calf depends on its mother’s milk for nourishment, probiotics, prebiotics and the protective components needed while it is in a vulnerable stage. It is well known in the dairy industry that a calf's rumen does not develop quickly. It may take around 3 months for it to function properly. The microbes start to take hold in the rumen once the calf begins to eat fibre, because microbes require fibre from grass in the diet to establish themselves fully.


It seems that the mammal’s immune system rely on both early, successful colonisation of probiotic microbes in the gut lining, and exposure to some pathogens, to build a functioning immune system over time, more here. Research has also shown that human breastmilk can contain pathogens, and because of the baby’s exposure to them, can create stronger immunity.

Protective systems in raw milk from cows

Firstly, please remember there are two kinds of raw milk: one produced for human consumption, and the other is meant for pasteurisation. In this recent interview with the Wise Traditions podcast, Mark McAfee explained why raw milk should come from pastured animals: it increases the food safety of the raw milk.

Australian microbiologist Dr Ron Hull has given expert evidence about the safety of raw milk from  healthy grass- or hay fed animals. He describes raw milk as having “two systems of immunity to pathogens.” The first he calls “innate immunity.” This comprises a number of factors, such as a set of enzymes, white cells (as in human blood), antimicrobial fatty acids, as well as mineral apatite complexes, with antimicrobial activity. Ron says the existence and function of this innate immunity is well established in the scientific literature. Pasteurisation of milk also interferes with complex biological and chemical systems in the milk that begin to be destroyed by heat at 56°C. Pasteurisation destroys many of these anti-microbial and immune-enhancing components, read more here.  


Raw milk from cows can help breastfeading mothers

There is a lot of fear in modern, highly industrialised countries about giving raw milk from animals, to human babies who have not developed a functioning, healthy immune system yet. However, it may be beneficial when the mother drinks the carefully produced raw milk from cows, and then pass the benefits to the baby, via the human mother's breast milk.

Kaleigh Lutz is one of the owners from Organic Pastures Dairy in California. The dairy produce regulated raw milk under high quality controls, from a herd of 500 milking cows. OPD is the largest raw dairy in the U.S. Kaleigh was recently interviewed as part of the video series Farmers over Pharmacies, and gave a powerful and very personal testimony about how drinking the raw milk naturally increased her breast milk supply. Kaleigh came across this very common problem herself when she returned to work after maternity leave, and wasn't breastfeeding as often as before. With some quick thinking, she turned around her lactation and was back to a full supply. Watch and learn how she conquered this problem that working mothers face daily in this video.

Producing regulated raw milk in Australia

In Australia, we already know how to produce high-quality, pathogen-free, low risk raw drinking milk for human consumption, and what we don't know we can learn from organisations like the Raw Milk Institute. No food can be produced to be 100% safe, but we have identified that there can be a huge difference between raw milk produced to be pasteurised, and the kind of raw milk that can be regulated for human consumption. See the 11 categories of the Risk Identification and Risk Reduction Program if you'd like to learn more about these differences:

ARMM advocates for regulated raw drinking milk from cows and other animal species in Australia.

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