Reviewed by the BioHackers Lab Team | Last updated: May 25, 2020

In today’s interview I get to speak with microbiologist, Amy Proal PhD.

We talk about what the microbiome and virome are and why keeping these systems in balance is important for our health.

Amy is very passionate about the latest research on the microbiome and the various ways it impacts on our health.

The presence of the gut microbiome in humans is not a novel idea, but new research has uncovered that microbiome populations exist throughout our body in many tissues previously thought to be sterile.

Microbiomes have been uncovered in the blood, the brain and the bladder for example.

We get a chance to talk about what the microbiome is and how these new discoveries have implicated the microbiome imbalance in diseases such as cancer, Alzheimer’s and even autoimmune disease.

If you know someone who is interested in learning more about:

  • What is the microbiome & virome)
  • What they role is in keeping us healthy
  • How these ecosystems in our bodies are also involved in a multitude of diseases including Alzheimer’s, cancer and autoimmune disorders such as Crohn’s

Then this interview is for them.

I enjoyed this interview with Amy as she sheds some light on new research and what it means for the way we think about disease and treatment.

She believes that a paradigm shift is necessary to get at the root cause of illnesses and working with our immune system and keeping the microbiome in check should be the focus.

Special thanks to Amy for joining me on the show.

Enjoy the episode!

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Speaker Links

Dr Amy Proal
Amy Proal PhD: Microbiologist

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Show Notes with Timestamp Links

Find summarised highlights of what we talk about during the interview.

Use the clickable timestamp links to jump direct to those points in the audio file below:

[00:19] – Introducing, Amy Proal PhD. Amy has a degree in biology from Georgetown University and a PhD in microbiology from Murdoch University. She is a member of the research team at Autoimmunity Research Foundation, has authored papers that examine the role of the human microbiome and human virome in chronic inflammatory disease and has also written book chapters for organizations like the J.Craig Venter Institute and lectured on the subject at the NIH and other conferences.

[01:13] – Amy explains that the microbiome, in simple terms, is the ecosystem of microbes (bacteria, viruses, fungi, and archaea) that inhabit the entire human body. The metabolites and proteins they create interact with our own and our own biology.

[02:46] – We often hear about our gut microbiome (this is also the best studied microbiome) but there are many other microbiomes. Amy explains how around the year 2000 there was a change in the way that research teams went about studying the microbes in the human body, due to the new technology that became available.

BioHackers Lab Tip: To hear more about the mouth microbiome listen to our interview with Dr Steven Lin.

[05:35] – In the last five years or so there has been an explosion of research on microbiome ecosystems in other parts of the body long taught to be sterile; changing the way we look at health and disease. We now know there is a bladder microbiome, the placental microbiome, breast milk microbiome. This indicates that microbes are inherited and raises questions about breastfeeding vs formula.

[09:40] – Amy explains how the Brain Microbiome Project, which studies Alzheimer’s, has had some interesting preliminary results showing evidence of a brain microbiome. Their early findings also indicate that in disease such as Alzheimer’s there is a shift in the microbiome community. We know there is a lot of neuro-inflammation in Alzheimer’s disease. Amy explains how this could be in response to infectious agents.

[13:34] – The same research team also found that the plaque we see created in Alzheimer’s is actually antimicrobial peptides that are created by the immune system as a response to different bacteria, viruses etc.

[15:39] – Amy explains that in response to these findings we should be changing the way we think about autoimmune disease. Autoimmune suppressant drugs are top-selling drugs but incidence is on the rise and patients often relapse, so we are not treating the root cause of the problem. Amy believes it is more likely that the immune system is reacting to the imbalance of the microbes, generating the autoimmune response, rather than to its own tissue.

[21:11] – Identifying the area that is out of balance can be challenging and often depends on the condition. Gut conditions such as Crohn’s are easier to identify and result from an imbalance of microbes in the gut. Amy explains some people may still need to take immunosuppressants, but the goal with trying to improve the composition of the microbiome is a long-term solution. For lupus and arthritis, we need to explore more.

[24:42] – Amy explains how there is a whole aspect of research related to the microbiome that has to do with the gut-brain access. Because there are neurological pathways and nerves connecting the brain to the gut, microbes can signal from the gut in the way that affects the immune response and the brain. Research show that patients with inflammatory conditions have an imbalance in the gut microbiome and the microbes in the gut can impact symptoms outside of the gut due to the gut-brain access impaired signalling.

[26:24] – Amy believes we need to take a closer look at microbes other than just those found in tissues and blood. Microbes that can persist inside the cells of the immune system, for example, are huge drivers of human disease. Intracellular pathogens will disrupt a cells gene expression and metabolic pathways.

[27:25] – With what we know now, what can you do today to improve your microbiome? Amy believes trying to improve the gut microbiome is a good start. While at this stage she has no firm opinion on what is beneficial some trends she recommends looking at are probiotics such as the VCL3, fermented food that contains microbes and lower carb/lower sugar diets. Having a healthy gut microbiome can have flow-on effects by improving gut brain access and so on.

[28:51] – Amy explains why she believes there should be more focus on antiviral medication and supplements such as those that break up biofilm. Microbes form biofilm to protect themselves from the immune system and can form in a lot of conditions. Medicine should explore developing preventative treatments that keep the microbiome in check and support our own natural immune systems so that we can defend ourselves.

[30:38] – Recently the Nobel prize was awarded to cancer immunotherapy researchers which has shown promise in early trials. She explains that while these types of therapies can trigger the Herxheimer response, once past that stage, patients have had more success than with chemotherapy. Research on tumour microbiome is also exploding and it has been demonstrated that infection and pathogens are directly involved in the pathogenesis of cancer. Amy believes we need a paradigm shift of looking at the immune system as something that can help us.

[35:55] – Previously, research has always focused on looking at single pathogens. We now have a new understanding that there are communities of organisms interacting with each other.

[37:41] – The virome refers to the viral ecosystems in the human body. Bacteriophages are viruses that affect bacteria and modulate how they act. Amy explains that the viral ecosystems are something that we have recently started paying more attention too. To date we have only sequenced about 1% of the viruses that live in the human body.

[40:41] – Intestinal permeability causing autoimmune disease is a big topic. Could an imbalance in gut microbiomes be part of the problem? Amy explains that microbes can probably move in and out of tissues more easily than we taught. In addition, we are exposed to many more pathogens in today’s modern society with international travel and the way our food is sourced.

BioHackers Lab Tip: For more on intestinal permeability listen to our interview with Dr Zsófia Clemens.

[46:01] – At this point in time the gut is the easiest point where we can intervene in a way that can result in an outcome and diet is an important part of that.

[48:25] – A multitude of diets can work for a multitude of people. Amy is hesitant to recommend one particular diet type as she has seen patients improve on ketogenic diet as well as vegan diet. But generally, she noticed that a trend with people deciding to take action and change their diet is an improvement in the quality of ingredients eg. meat without antibiotics, hormone free eggs, veg from a local farmers market. That could be the big consideration.

[51:16] – Are stool tests worthwhile or just confusing? Amy doesn’t prioritise these highly as we know so little about the microbiome at this point in time. We don’t know what the results mean yet or how to interpret them in an actionable way. What’s more, a lot of things will impact the microbiome and your results e.g. location, time of day, what you just ate, time of month for women.

[54:13] – When it comes to her microbiome, Amy tends to focus on symptoms. She charts how she feels when taking a probiotic, for example.  When choosing a probiotic, she recommends you do some research as not all brands will be effective. Make sure you take a probiotic that is well made with surviving live cultures.

[56:26] – For other ways to keep in touch, visit Amy’s blog, Microbe Minded, where she posts important studies and will narrate some of her writings in podcast form and video form. She is also very active on Twitter.