Meet your microbes

Dr Hayley

Posted on January 16 2019

Meet your microbes

Meet your microbes - they do more than you think

Microbes, or microrganisms are microscopic organisms such as bacteria, viruses and fungi. We play host to so many microbes that for every 1 human cell there are 10 microbes on and in our body. The community of microbes that inhabit our body is referred to as our microbiome.

Over the past 100 years or so, we have dramatically changed the way we live. We’ve introduced antimicrobial treatments, vaccinations, disinfecting and cleaning products, on top of making profound changes to our diet. These have all had a significant and lasting effect on our microbiome. Changes in the gut microbiome, in particular, have been implicated in a number of chronic diseases.

Chronic diseases affect 1 in 2 Australians (according to self-reported data in the 2014-15 National Health Survey), including anxiety, depression, metabolic syndrome, non-alcoholic fatty liver disease, Type 2 diabetes, cardiovascular disease and autoimmune diseases.

It is suggested that inflammation and a lack of microbial diversity could be the root cause of these diseases. It is therefore suggested that if we reduce inflammation and repopulate our microbiome, we will improve our health.

In order to support the microbes that we play host to we need to provide them with nutrition. But do we really want to feed and encourage microbes in our bodies? After so many years of being told bacteria are bad and advertising campaigns that claim to kill 99.9% of germs and bacteria, it is understandable that many of us are confused. Let’s be clear: microbes are our friends. They are essential to our health. Without them, we are unable to keep ourselves well. Symbiotic bacteria assist with our immune tolerance, keep our intestinal tract intact and functioning, and even synthesise amino acids and vitamins for us. They are essential to a healthy metabolism. There are bacteria that can cause disease, referred to as pathogenic bacteria. Our greatest defense against pathogenic bacteria, is a strong population of commensal and symbiotic bacteria.

Where do our microbes come from and what are they doing?

Our microbiome is first seeded by our mothers, passed to us through the placenta and amniotic fluid within the womb. When we are born we receive even more microbes, and our mode of delivery impacts the bacteria that populate our gut. Over the first week of life our microbiome is highly dynamic. Over 1000 distinct, non-digestible molecules are found in breast milk. These molecules provide the ideal nutritional source for bacterial fermentation – the process by which bacteria get their energy so that they can survive and reproduce.

We establish our ‘adult’ microbiome when we transition to eating solid foods. The specific species of microbes that populate our gut change during this time, reflecting the different types of foods that are coming in via diet. The development of the gastrointestinal tract and the microbes that populate it can have a profound effect on health, and in particular the development of our immune system.

Our microbiome can change throughout our life, with alterations in our diet having an effect on our gut microbiome in as little as 24 hours. Changes can be temporary if we resume our regular diet, or long term if we make more permanent changes. Evidence is emerging for benefits to our health by manipulation of our microbiome.

How does the gut affect my brain?

You may have heard of the gut-brain connection, which refers to a series of neuronal pathways, hormones, microbial molecules and metabolites that allow communication between the gut and the brain. Recent studies show that microbes in our gut produce molecules that activate immune cells in the brain, signaling to other brain cells to regulate inflammation in our central nervous system. Therefore, it can be said that, depending on the microbes that are in our gut, and depending on the food we provide those microbes, different messages might be sent to our brain with different effects on our cells.

Bacteria in our gut produce different nutrients and neurotransmitters including serotonin and dopamine. Our lifestyle choices, such as diet, stress and drugs/medications, change the diversity of gut microbes.

Generally speaking, if we are stressed, have a poor diet, or take drugs or medications, we will have different microbes in our gut than people who are calm, eat a quality diet and are not reliant on medications. Evidence suggests that a poor lifestyle favours species of bacteria that produce molecules that are inflammatory and negatively influence the health of our entire body system.

Most of the research available on relationships between the microbiome and depression or anxiety come from animal models. Collectively, these studies show that administration of particular bacterial species can induce anxiety and depression-like behaviours. Conversely, other bacterial species – administered as probiotics – can reverse symptoms of depression and anxiety, reduce stress and regulate the immune system. Limited research in humans shows similar benefits when taking specific probiotics.

How do I get the right microbes in my gut and keep them happy?

To meaningfully support our gut microbes, we need to eat foods that contain microbes. We should also eat foods that provide nutrition for the microbes we have in our body (prebiotics). The message about what to eat to support your microbes is the same as the ancestral diet message: remove processed foods and artificial food products from your diet. Instead, eat whole foods: vegetables (and root vegetables), fruits, pasture-fed meats, wild fish, eggs, nuts and seeds, fats such as olive oil, coconut oil. It is also advised to consume fermented foods and drinks such as pickles, kimchi and kefir. Wherever possible, avoid medication and toxins as the diversity of our microbiome can change under the influence of these. And be sure to spend lots of time outside, in amongst the dirt where the microbes live.


  • Clapp M, et al (2017) Gut Microbiota’s effect on mental health: The gut-brain axis. Clinics and Practice. 7(987):131-136
  • Evrensel A, Ceylan ME (2015) The Gut-Brain Axis: The Missing Link in Depression. Clinical Psychopharmacology and Neuroscience. 13(3): 239-244
  • Rothhammer V, et al (2018) Microglial control of astrocytes in response to microbial metabolites. Nature. 557:724-728


Dr Hayley Dickinson is a research scientist with a PhD in women’s reproductive health, who does not claim to be a medical practitioner. We seek to offer insights into the health of women experiencing the reproductive, menstrual and hormonal characteristics of female biology. In addition, we offer scientific insight into wellness and lifestyle choices relevant to all. Neither endota nor Dr Hayley Dickinson accept any liability for the information or advice (or use of such information or advice) which is provided in this blog or incorporated into it by reference. We provide this information on the understanding that all persons accessing it take responsibility for evaluating its relevance and accuracy. Women are encouraged to discuss their health needs with a health practitioner. If you have concerns about your health, you should seek advice from your health care provider or if you require urgent care you should go to the nearest hospital Emergency Department. © endota, 2018-2019

More Posts