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Microbiome – Be a Good Host

Updated: Nov 16, 2021

LifeHakx – Be a Good Host

By Eva Wisenbeck 14/03/2021

Listen to the podcast here.

See the video interview here.

There has been an explosion in our understanding of the human microbiome, the genome of all our microbes, in the recent years. Advances in genome sequencing and metagenomic analysis (genetic study of genomes taken directly from environmental samples) have enabled scientists to study these microbes and their function and to research microbiome–host interactions both in health and disease.

Where does my gut microbes come from? Do I just pick them up from my surroundings? Partly. But it is more complicated than that. As we are being born, through the birth canal, we get this handover bacteria. That bacteria are really important for starting the whole process, which is then added to by breast milk, and after that our whole life, food, environment, encounters and much much more.

During pregnancy a mother’s microbiome shifts to an optimum mix for offspring. If you are not born by vaginal delivery, but by caesarean section, studies suggest this can be one of the reasons why c-section babies have a higher risk of conditions including asthma and type 1 diabetes.

Our gut microbiome changes quickly over our first year or two, shaped by breast milk, the environment and other factors, and stabilises by the time we are about three years old. But our environment, our long-term diet, stress and the drugs we take, such as antibiotics, continue to play a role as we age, meaning our microbiome, can and does, change hugely throughout our life.

Are microbes the same in my gut as on my skin?

No, different parts of the body – the skin, vagina, gut – all have very different, distinct communities of microbes. While gut microbes have gained a lot of attention, microbes elsewhere are also important, in recent studies, scientists have found that for example bacteria commonly found on the skin might help protect against skin cancer.

Microbiomes also differ from person to person. “When you look at the overall active microbiomes between two healthy people, even if they are living in the same city, you see a tremendous amount of disagreement in their microbiome,” said Rob Knight, professor of paediatrics, computer science and engineering at the University of California San Diego and an expert on the human microbiome.

Variability in the gut microbiome, Knight notes, helps to explain why people respond differently to the same foods. “Whether tomatoes are good or bad for you, whether rice is good for you or worse for you than ice cream and so on is explained by your microbiome,” he said.

Does any of this actually practically affect medical treatments?

In mainstream current conventional medicine, yes, up to a point. The field has already led to advances in the treatment of C difficile – an infection that causes serious diarrhoea and can prove deadly. Patients can now receive faecal transplants (FMT) from a donor with a healthy microbiome to “reset” their inner ecosystem – a procedure that has been shown to rapidly cure the condition.

According to a study published in the journal of Gastroenterology Hepatology, fecal transplants, also known as microbiota transplants, have a 91 percent cure rate in treating clostridium difficile (C-Diff) and may also help treat IBS, colitis and many autoimmune disease. There are several instances where someone with a life-threatening infection had fecal transplant actually save their life.

A fecal transplant is a procedure in which fecal matter, or stool, is collected from a pre-qualified healthy donor, mixed with a saline or another solution, strained and then placed into the colon of another patient using a colonoscopy, endoscopy or an enema.

Why do such a thing? Well, the intent is to repopulate the receiver’s gut with normal, healthy bacteria and microbes that are living in the donor’s gut. You can repopulate the gut with good microbes by consuming probiotics-rich foods and taking quality probiotic supplements, but this can take much longer to repopulate the gut. Your average probiotic food or supplement may contain between 1–30 strains of probiotics at billions of units while healthy poop contains 1,000+ strains of microbes (bacteria, yeast, bacteriophages, etc.) at hundreds of trillions of units.

Before you judge and dismiss this procedure, please realise that Fecal Microbiota Transplants (FMTs) are actually backed up by some very compelling early clinical research. While FMTs haven’t exactly become “mainstream” medicine just yet, fecal transplants are providing huge relief to people with a range of painful, even deadly, digestive disorders and symptoms. Recently, findings from new studies have even suggested that fecal transplants may be able to play a role in treatment of cancer and Parkinson’s disease.

The gut microbiome has also been linked to how individuals respond to certain drugs, including how cancer patients respond to chemotherapy, and it has even, tentatively, been linked to things like how well we sleep.

There is also a new field coined ‘psychobiotics’ researching, and already treating, various mental health issues. What does the gut have to do with the brain you ask?

The nervous system and the gastrointestinal tract are communicating through a bidirectional network of signalling pathways called the Gut-Brain axis, which consists of multiple connections, including the vagus nerve, the immune system, and bacterial metabolites and products. During dysbiosis, these pathways are dysregulated and associated with altered permeability of the blood-brain barrier (BBB) and neuroinflammation.

However, numerous mechanisms behind the impact of the gut microbiota in neuro-development and -pathogenesis remain poorly understood. There are several immune pathways involved in CNS homeostasis and inflammation. Among those, the inflammasome pathway has been linked to neuroinflammatory conditions such as multiple sclerosis, Alzheimer’s and Parkinson’s diseases, but also anxiety and depressive-like disorders.

The inflammasome complex assembles upon cell activation due to exposure to microbes, danger signals, or stress and lead to the production of pro-inflammatory cytokines (interleukin-1β and interleukin-18) and to pyroptosis. Evidences suggest that there is a reciprocal influence of microbiota and inflammasome activation in the brain.

However, how this influence is precisely working is yet to be discovered. Herein, we discuss the status of the knowledge and the open questions in the field focusing on the function of intestinal microbial metabolites or products on CNS cells during healthy and inflammatory conditions, such as multiple sclerosis, Alzheimer’s and Parkinson’s diseases, and also neuropsychiatric disorders. In particular, we focus on the innate inflammasome pathway as immune mechanism that can be involved in several of these conditions, upon exposure to certain microbes.

I appreciate that might sound like a lot of gobbledegook – in summary, it’s complicated and yes there is an awful lot of communication going in both directions, to and from, the brain and the gut, using various pathways and carriers. And researchers know very little – yet!

A problem of our own making - Warfare! Many of the disease phenomena making news headlines these days underscore the deficiencies of the current pharmaceutical model and reveal challenges that are the direct result of our take-no-prisoners assault and warfare on germs.

Our ancestors were exposed to billions of microbes in their homes and in their foods. Most of my food comes from a supermarket. By inhibiting microbial growth in these foods to extend shelf life, or sterilising them for safety, most of my food is devoid of microbial diversity. By sanitizing my home and living space, furnished with unnatural and chemically produced materials, and eating these relatively sterile foods, my microbiome has become less diverse than my ancestor’s microbiomes were for hundreds of thousands of years. Even nowadays, populations living more traditional lifestyles have greater gut diversity than those of us in the industrialised world. We now know that industrialised gut microbiomes are less diverse than the microbiomes of more traditional lifestyles.

However before we all panic and go live in a forest somewhere, there are lots of things we can do to help our ‘ecosystem’. And as the wonderful Sarah Ballantyne says “It’s only effort before it’s habit”. By shopping and eating locally and seasonally, using gentler cleaning products, not being afraid of getting our hands dirty in soil we can have a massive impact on our ‘ecosystem’. By eating a diverse diet with as many types of plant foods as we can, remembering to eat the rainbow as each colour has different functions, focussing on the “How not the What” so how was the vegetable/animal reared, grown, handled is much more important.

We need to feed our guests prebiotics, invite more friendly guests by eating probiotics and encourage the right postbiotics. For more details read the Pre- and Probiotic blog.

And as we discussed one of the easiest and quickest way to become A Good Host is to avoid ultra-processed foods – so anything with 5 or more ingredients on the label – put it back!

Even better buy foods with no labels as Dr Mark Hyman says.

Right now back to our warfare, dangerous superbugs are emerging, largely due to overuse of “anti-everything” drugs such as antibiotics and antifungals, and are ushering in a potential return “to a world in which infectious diseases drastically shorten lives.” Some have estimated that drug-resistant pathogens will become a bigger killer than cancer by 2050. Now that is something worth considering for sure!

Functional Medicine already utilise the makeup of a patients’ microbiomes for personalised and precision medicine as well as using phages and other microorganisms as treatments. It is a fascinating field of medicine, one which is moving very rapidly so stay curious and ask questions.

If you are curious and would like more information about the Microbiome here are some great resources.

BMJ “What is the microbiome?”

“The Gut-Brain Axis: How Microbiota and Host Inflammasome Influence Brain Physiology and Pathology”

“The Simplified Guide to the Gut-Brain Axis – How the Gut and The Brain Talk to Each Other”


Meet The Team


Eva Wisenbeck

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Eva Wisenbeck is a Co-Presenter of LifeHakx & a Wellness Coach

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Mary Collins

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Mary Collins is the Creator and Presenter of LifeHakx Media.

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