Megan Rodden
(BCS, DipNat, MedHerb, NMHNZ)
Margaux M. Tolley
MSc (Neuroscience), PgDipSci (Neuroscience), BSc (Neuroscience)
The gut is truly the foundation of health, a place where nutrients are absorbed, hormones are shaped, immunity is trained, and inflammation often begins. Understanding its importance is just the starting point.
In this article we’ll look more closely at how the gut, especially the microbiome, is linked to chronic disease and what the research shows about specific conditions regarding
- digestion
- immunity
- skin health
- mood
The gut’s influence reaches far beyond the stomach, with research now linking the gut microbiome to a number of chronic diseases.
What is the microbiome?
The gastrointestinal microbiome is a community of different microbes (bacteria, fungi, viruses) that live in our gut and play a role in our overall health and wellbeing.
This inner garden, when poorly cared for, can become disrupted with excess harmful bacteria (known as dysbiosis), setting the stage for disease.
Cardiovascular Disease
The gut microbiome is increasingly recognised as a key player in cardiovascular health. The most significant findings show differences in the composition of the microbiome between those with cardiovascular disease (CVD) and healthy controls as well as the influence of microbial byproducts on inflammation, metabolism and vascular function.[1]
Researchers have found that certain gut bacteria turn nutrients from foods like red meat and eggs into a compound called TMAO.
Elevated levels of TMAO have been associated with a higher risk of atherosclerosis and adverse cardiac events and it is produced through metabolism by gut microbes.
For example, a study of 4,007 people, in 2013, showed people with higher TMAO levels in their blood had a significantly greater risk of heart attack, stroke and death, independent of other factors.
Those in the highest quartile of blood TMAO levels had 2.5 times greater risk of having a major cardiovascular event compared to those in the lowest quartile.
TMAO was linked to 3.4-fold higher risk of death and 2.1-fold higher risk of heart attack or stroke.
These associations remained significant even after adjusting for traditional risk factors, showing that TMAO may be an independent predictor of cardiovascular risk.[2]
Research also suggests that supplementation of Vitamin D and Omega 3 fatty acids may help to reduce TMAO levels by modulating the gut microbiome.[3,4]
Cholesterol and blood pressure
Emerging research is revealing that the gut microbiome plays an important role in cholesterol and blood pressure regulation. Certain gut bacteria can influence how we absorb and process cholesterol by modifying bile acids, which act like chemical messengers that control whether cholesterol is stored, recycled or cleared.[5]
Several species have been shown to decrease cholesterol levels in humans and animal studies including, Akkermansia muciniphila, Bacteroides spp., Clostridium spp., Christensenella minuta, Eubacterium spp., and Faecalibacterium prausnitzii.[6]
Gut microbiome plays an important role in blood pressure regulation
Blood pressure is also impacted by fiber fermenting microbes that produce short-chain fatty acids (SFCA’s), which relax blood vessels, and regulate hormones involved in blood pressure control.
In a large, new analysis of 1,429 participants, researchers found that certain gut bacteria – especially Oscillibacter (genus) – were associated with lower blood cholesterol levels.
Findings also showed gut-microbiome impacted CVD risk markers, including blood pressure.[7] Oscillibacter can be increased by the consumption of foods rich in fiber, plant protein and polyphenols such as fruits, vegetables and coffee.
Metabolic disorders (Obesity, Insulin Resistance, Type 2 Diabetes)
An important connection has been identified between gut microbes and metabolic disorders. Research shows reduced microbial diversity and shifts in gut bacteria are linked to
- obesity
- insulin resistance
- type 2 diabetes
Obesity
When the balance of gut bacteria shifts to fewer “good” microbes and more “harmful” ones, this can lead to
- increased energy extraction from food
- excess fat storage
- inflammation
- insulin resistance[8]
Studies suggest that microbiome composition influences metabolism through short-chain fatty acid production, altering gut barrier integrity and appetite signalling.
Because of these links strategies to modulate the microbiome are under investigation as potential additional treatments alongside diet and exercise. Probiotic supplementation has been associated with reduced body weight, BMI, waist circumference and improved metabolic markers in some human trials.[9]
Insulin Resistance
Recent research shows that the gut microbiome plays a meaningful role in how the body responds to insulin, the hormone that helps move sugar from your blood into your cells.
Insulin resistance, a condition where cells stop responding well to insulin and blood sugar stays high, is a key early step in type 2 diabetes and other chronic diseases.
RELATED — Diabetes: Early Signs, Causes, Types and Treatment
Researchers have found that people with more diverse microbiomes and high levels of certain bacteria tend to have better insulin sensitivity, while some microbes are linked to insulin resistance.
Beneficial gut bacteria that have been identified in clinical trials are those that produce short-chain fatty acids (SFCA), such as, Akkermansia muciniphila, Faecalibacterium prausnitzii, Bifidobacterium species, and Alistipes indistinctus. These species have been found to regulate GLP-1, a hormone that improves insulin production.[10]
Diabetes
A 2025 study using genetic-level data found that some bacterial groups, such as, Actinomyces, Desulfovibrionaceae, Roseburia, Lachnoclostridium, Oscillospiraceae are associated with a higher risk of Type 2 diabetes, while others are protective, including, Bacilli Veillonella, and Bacteroides caccae.
Results showed some gut bacteria (Oscillospiraceae, Roseburia, Faecalibacterium, Eubacterium hallii, Bacteroidaceae, Actinomyces, Desulfovibrionaceae) were linked with a higher chance of Type 2 diabetes, 4-12% increased risk.
Other bacteria appeared to be protective with about a 5-6% lower risk (Bacilli, Veillonella, Bacteroides caccae, Lachnospiraceae and Eubacterium eligens) showing that some microbes can nudge your metabolism in the wrong direction and even small shifts may have a meaningful impact.[11,12]
Autoimmune and inflammatory conditions
A strong link has been identified between gut health and autoimmune diseases such as
- Inflammatory Bowel Disease (IBD)
- Psoriasis
- Lupus
- Type 1 diabetes
RELATED — Type 1 Diabetes: Autoimmune disease that is on the rise
Studies indicate that gut dysbiosis plays a role in the development of autoimmunity through complex interactions with bacteria and immune cells and increased inflammation.[12]
Physical trauma has the most significant effect on chromium depletion
While exact mechanisms vary between conditions, the pattern is consistent. When the gut is out of balance the immune system can become overactive and mistakenly attack the body.
Researchers have found that specific bacteria, Enterococcus gallinarum, are able to break through the gut lining and enter lymph nodes and organs driving autoimmunity in conditions such as,
- systemic lupus erythematosus (SLE)
- autoimmune hepatitis[13]
A 2025 multi-omics study of Crohn’s Disease (a type of IBD) identified a panel of 20 microbial species that could distinguish Crohn’s patients from healthy controls with very high accuracy – suggesting potential for microbiome based diagnosis.[14]
Neurological and mental health
The connection between the gut and the brain is often referred to as the “gut brain-axis” and an area of significant emerging research. The three main communication pathways between the gut and the brain are through the:
- Vagus nerve
- Endocrine system
- Immune system
We now know that gut bacteria help produce neurotransmitters, such as serotonin or gamma-aminobutyric acid (GABA), influence inflammation and send signals directly to the brain through the vagus nerve, which is our body’s main communication highway between the gut and brain.
RELATED — Serotonin 5-HT (for mood, sleep and digestion)
Studies have linked imbalances in the gut with symptoms of depression and anxiety, showing that certain microbial patterns can affect mood, stress responses and emotional regulation.
Lower levels of certain gut bacteria, such as Coprococcus and Faecalibacterium, has been shown in individuals with Major Depressive Disorder, while anxiety is associated with small intestinal bacterial overgrowth and a lack of specific Lactobacillus strains.[15,16,17,18]
These imbalances can trigger low-grade inflammation, alter production of the neurotransmitter, GABA, and alter production of short chain fatty acids like butyrate, which plays a major role in the integrity of the blood brain barrier.[19]
Altogether, this creates a pro-inflammatory storm and a reduction in neuroprotective mechanisms. Recent review has shown that probiotics are a promising potential treatment option, providing beneficial outcomes with low risk compared to other current treatment options.[20]
However, despite the lack of direct causative evidence, it is clear an unhealthy diet will not improve a depressive mood either. In fact, a poor diet can perpetuate depressive symptoms and further result in poor food choices (i.e., ‘comfort food’, high in sugar or carbohydrates), making a feed-back loop.
A 10-year longitudinal study demonstrated a correlation with poor diet and incidence of depression, while meta-analysis showed a healthy diet, with a variety of vegetables and fish, was associated with lower incidence of depression.[21,22]
RELATED — Introduction to: Depression
The association between the gut-brain axis and Alzheimer’s Disease is a very popular strain of research. Chen et al. (2021) experiment in mice suggests the vagal nerve may act as a direct ‘highway’ for amyloid and tau proteins, which are key players in Alzheimer’s, to travel from the gut directly to the brain.[23]
They had shown that after triggering gut inflammation in mice, amyloid and tau fibrils (potential seeds for amyloid plaques and tau tangles found in Alzheimer’s Disease) were found in the brain. They were able to significantly reduce the presence of such fibrils in the brain by severing the vagal nerve.
Recent review points to lifestyle factors, including diet and stress, can result dysbiosis, an imbalance of the gut microbiome, which alters the permeability of the intestinal tract allowing bacteria and inflammatory signals to enter the blood stream.[24]
Once in the bloodstream, the leakage can trigger inflammatory mechanisms, dysfunction to the blood-brain barrier, amyloid plaque accumulation and tau pathology.[25]
Research is also uncovering associations between gut changes and neurological conditions like Parkinson’s disease, where early alterations in the gut bacteria and gut function may appear years before motor symptoms develop.
For example, one recent study found a link between the gut microbes of people with Parkinson’s and Inflammatory Bowel Disease (IBD). Results showed reduced (SCFA)-producing bacteria, including Roseburia intestinalis, Faecalibacterium prausnitzii, Anaerostipes hadrus, and Eubacterium rectale in both conditions from 54 participants and analysis of larger published data.
Nurturing gut health may play an important role in supporting both mental wellbeing and long-term brain health. Gut and brain health are symbiotic, whereby if you take care of your gut you will in turn take care of your brain.
Megan helps her clients to rebalance their bodies through holistic nutrition, herbal medicine and a naturopathic lifestyle. Her personal health journey transitioned her from a communications consultant to a naturopath, sparked by struggles with chronic health issues, particularly after having children and finding vital support from natural therapies…
If you would like to learn more about Megan, see Expert: Megan Rodden.
Margaux is a neuroscientist with a strong academic background and hands-on experience in research, specializing in muscle physiology, electrophoresis, and protein analysis. Her Master’s research focused on identifying key protein…
If you would like to learn more about Margaux, see Expert: Margaux M. Tolley.
References
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