Microbiome Resilience: 5 Ways To Achieve It

Microbiome Resilience

Welcome to my blog on microbiome resilience. I am going to briefly discuss what a resilient microbiome is, and then highlight 10 ways to build one.

What Is Microbiome Resilience?

Microbiome resilience is “the amount of stress or perturbation that can be tolerated before a system’s trajectory changes towards a different equilibrium state.”

Perturbations can include: acute infectious diarrhoea, dietary life events (for example, phases of malnutrition) and treatment with antibiotics.

A slightly more technical definition microbiome resilience is: “the capacity of a system to absorb disturbance and reorganise while undergoing change so as to still retain essentially the same function, structure, identity, and feedbacks”.

Why is microbiome resilience important?

A healthy microbiome, one characterised by diversity and resilience, may enable one person at a dinner party to escape food poisoning while their companions fall ill.

However there is a ‘dark side’ to microbiome resilience. And that is that someone can develop a dysbiotic resilient microbiome. Some clients reach a ‘tipping point’ whereby their ecosystem seems to collapse – potentially due to a loss of key stone species.

This is discussed in the research as a ‘catastrophic regime shift’. This occurs when there is a sufficient degree of environmental change to “degrade the landscape, cause a threshold effect, and tip a community into a new alternative basin of attraction.”

Several papers use this term ‘basin of attraction’ to refer to the set point or make up of the ecosystem. Ultimately it is where there has been a change in the function, structure, identity, and feedbacks of the microbiome.

Measuring Microbiome Resilience

There are some key concepts discussed in the literature including elasticity, amplitude and resistance.

Elasticity: the rate at which the system returns to its pre-disturbance equilibrium, or the time it takes to return.

Amplitude: the magnitude of the maximum displacement the system can absorb and still recover.

Resistance: a measure that describes the property of a community to remain unchanged during a perturbation, sometimes described as a part of resilience. Resistance is an important first layer of resilience. It describes how easily a system can shift away from its stable state.

We obviously can’t test this in clinical practice. They are more theoretical principles, or characteristics of a resilient ecosystem.

But we can evaluate one marker which will shed insight in how resilient our microbiome is, and that is microbial diversity.

“We identify measurable metrics of the gut microbiome that could be used to infer the degree to which the host is experiencing chronic stress, including microbial diversity, flexibility, and gene richness.”

What’s Critical For Microbiome Resilience?

  1. Microbial diversity.
  2. Functional redundancy.
  3. Metabolic flexibility.
  4. Microbe–microbe interactions.
  5. Host–microbe interactions.
  6. Growth rates of community members.
  7. Nutrient availability

I go in to these in detail in the webinar ‘Microbiome Resilience‘ which is part of The Resiliency Program.

Recovery After Antibiotics

The most common example of a perturbation impacting our microbiome is the use of antibiotics. Research has found four key factors that influence our microbial recovery after antibiotics:

  1. Microbiota composition prior to treatment.
  2. Functional redundancy.
  3. Level of opportunistic pathogens.
  4. Level of antibiotic resistance genes.

Our Gut-Microbiome Supports Resilience

Research over the last couple of years has also started to demonstrate that our gut microbiome actually supports our overall resilience. So a resilient microbiome helps us become more resilient too. Check out these three quotes from the research:

  1. Gut microbiome and gut-brain axis (GBA) play a significant role in developing resilience or susceptibility to stress.
  2. Studies revealed that the homeostasis of gut microbiota is intimately involved in the regulation of the host’s psychology, emotions, and cognition in response to stressful events.
  3. Numerous studies in animal models of chronic stress have demonstrated the association between gut microbial composition and susceptibility or resilience to stress.
  4. A growing body of research indicates the influence of the microbiota on brain structural and functional connectivity as well.

We can also consider the research demonstrating that our level of inflammation before a traumatic experience may increase our risk of PTSD onset. One reason way a resilient microbiome is so improtant is that it can help modify our immune system and ‘manage’ our inflammatory state.

The Blood Brain Barrier – An increasingly Important Area Of Resilience Research

The blood brain barrier is being increasingly discussed in the research as a key element of resiliency.

Researchers have started to realise that stress and imbalances in the gut microbiota can result in blood brain barrier disruption. You’ve likely heard of leaky gut, well we can have leaky brain too.

In animal studies learned helplessness-induced mice show increased permeability of the blood brain barrier.  Additionally, the impaired blood brain barrier could be repaired by TNF-alpha inhibitor treatment.

In another animal study it was shown that the clearance of the microbiome by antibiotics may also lead to the down-regulation of tight-junction proteins and an increase in blood brain barrier permeability. To strenghten this connection further, fecal microbiota transplantation could rescue the disruption of blood brain barrier.

As such, gut microbiota-induced or stressful events-induced blood brain barrier impairments may be considered another therapeutic target for resilience research.

5 Ways To Build A Resilient Microbiome

Diversify Your Diet

Dietary diversity has been positively associated with α diversity of the gut microbiota.

Eat Fermented Foods

Research has clearly shown that fermented foods can affect the gut microbiome in both the short and long term, and should be considered an important element of the human diet.


Research has demonstrated that exercise of moderate to high-intensity for 30–90 min ≥3 times per week (or between 150–270 min per week) for ≥8 weeks is likely to produce changes in the gut microbiota. This is true for both clinical and healthy populations.


People with larger social networks tend to have a more diverse microbiome, suggesting that social interactions may shape the microbial community of the human gut. In contrast, anxiety and stress are linked to reduced diversity and an altered microbiome composition.

Photobiomodulation (light therapy)

Light therapy was shown to increase the abundance of certain beneficial bacteria, such as Akkermansia, Faecalibacterium, and Roseburia and decrease the number of potentially pathogenic genera. Furthermore, PBMT was shown to reduce inflammation in the gut, which may contribute to its positive effects on gut microbiota.

You can read more about red light therapy here.

Microbiome Resilience Webinar

You can learn more about how to build a resilient microbiome by purchasing my ‘How To Build A Resilient Microbiome‘ webinar which forms part of The Resiliency Program.


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Alex is a certified Functional Medicine Practitioner (IFMCP) and has a MSc in Personalised Nutrition. He is also a breathwork facilitator with a background in personal training and massage therapy. He also runs The Resiliency Program - a 24 week program aimed at building physical, mental, emotional, and spiritual resilience.

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