Counselling and the Gut Microbiome: An Overview

If you’ve been at the game of counselling for a while, you know the ropes – and the rules. The client comes and you listen to their presenting issues; often those are anxiety and/or depression or unbearable angst at some aspect of life. You work out if it is within your sphere of competence to work with the person, and outline a treatment plan – or at least a suggestion of a modality that would work well for them – and the client hopefully agrees. Most of the time the treatment plan of mental health practitioners involves some version of a “talking cure”: that is, a psychological healing effort for what appears to be psychological distress: equivalent and thus logical, right? But this way of thinking about what is “wrong” and thus what is needed to put things “right” may be about to change.

Recent microbiome research: A complete game-changer

For most Westerners, including many practitioners of allopathic medicine in various sub-disciplines, the prevailing paradigm has been that the body displays its level of wellness through various physical symptoms, and the mind displays its wellness (or not) mostly through various psychological and emotional symptoms. Holistic practitioners have gone further, trying to inculcate awareness that how we think and feel – the thoughts and emotions issuing from our mind/brain – affect our body, and particularly affect our intestinal health.

But research findings in the last decade have now added evidence from numerous studies to show that the converse is also true: that is, the state of the gut has a huge effect on how we are feeling and thinking: our mental health. The gut, increasingly referred to as “the second brain” (Abbott Nutrition News, 2018), has been shown to be involved in problems from depression, anxiety, P.T.S.D., and obsessive-compulsive disorder to autism, Alzheimer’s, sleep disorders, and obesity: all conditions which fall within the sphere of influence of mental health professionals. Dear counsellor, psychologist, psychotherapist, or social worker, we need to tell you, these findings are a true game-changer.

There are about 100 trillion bacteria living in our body (Perlmutter, 2015). These microbial residents of our gut, skin, eyes, and nasal passages – most of which reside in the gut – are collectively called the microbiome, and to be able to work effectively as mental health professionals in the new paradigm, we need to understand how they work in interaction with the client’s body-mind.

First we need to define what we are talking about when we say “microbiome”. Then, with a shared understanding of what that means, we can respond to the “So what?” question of why we should be concerned about it.

Some definitions

The microbiome refers specifically to the vast ecosystem of microorganisms, or microbes, that live in or on our bodies (or those of any host animal), including bacteria, yeasts, fungi, viruses, and protozoans. Their collective genome interacts with our host genes; it does this peacefully with healthy hosts. The microbiota used to be called “microflora” and there are more of them than human cells in the body, with some claiming that our microbial friends outnumber our own cells by a factor of ten to one (Robertson, 2017; Foroutan, 2015; Fleming, 2017).

The gut microbiome: The gastrointestinal tract, where most of the microbes live, hosts the gut microbiome, which contains more than 1000 species of bacteria, each playing a different role in the human body. Most of these are integral to health, although some of them cause disease. The microbiota collectively weigh up to two kilograms: that is, heavier than the average brain. Increasingly, scientists are treating the gut microbiome as an organ in its own right (Mercola, 2015; Fleming, 2017; Robertson, 2017).

Why the gut microbiome is crucial for health

Most people think negatively about bacteria: a foe whose presence is to be defeated in order to continue our sanitised modern lifestyle and – we hope – enhance our health. As we will see in this two-article series, however, recent findings show us that the opposite is true: our too-clean lives have resulted in not enough of our microbial friends, and our collective health is the worse for it. Gut bacteria help us digest food by breaking down otherwise indigestible plant fibres into short-chain fatty acids that intestinal cells can access for energy. The bacteria break down toxins and make B-complex and fat-soluble vitamins, vitamin K, and hormones; in fact, the key enzymes needed to form vitamin B12 are only found in bacteria, not in plants and animals (HSPH, circa 2015). Our microbial residents train our immune systems to distinguish friend from foe. They also crowd out pathogens, help our bodies absorb nutrients such as calcium and iron, keep our pH balanced, maintain the integrity of the gut lining, metabolise drugs, modulate genes, neutralise cancer-causing compounds, and produce digestive enzymes (Chutkan, 2015; Mercola, 2015; Fleming, 2017; Foroutan, 2015).

When the gut bacteria get out of balance, the result is gastrointestinal conditions such as IBD (inflammatory bowel disease), IBS (inflammatory bowel syndrome), and manifestations in the wider system such as Type 2 diabetes, obesity, and other problems. In fact, the microbiome is now seen as so important that the U.S. National Institute of Mental Health spent more than one million dollars on a new research program targeting the microbiome-brain connection. And a symposium at the annual Society for Neuroscience meeting in 2014 presented evidence for the link; the meeting was called “Gut microbes and the brain: Paradigm shift in neuroscience.”

Dr. Joseph Mercola notes that, fewer than 20 years ago, it was anticipated that the Human Genome Project (HGP) would usher in a new era of ground-breaking gene-based therapies for virtually every disease known to man. Experts were certain that health and disease were governed by genetic predisposition. But surprise, surprise: the HGP discovered that genetics are only responsible for about ten percent of human disease. The remaining 90 percent is induced by environmental factors: that is, nutrients, toxins, thoughts, emotions, and other influences. In more recent years, science has come to realise that the microbiome is one of the factors that drive genetic expression, turning genes on and off, depending on which microbes are present (Mercola, 2015). Let’s look at what science is saying about how these tiny microbes affect our mental/emotional state.

The importance of probiotics and pre-biotics

Both human and animal studies are now showing how the microbiome may be affecting our health, on both physical and mental-emotional levels. The research, in its infancy at this stage, often attempts to improve gut conditions for some subjects by adding substances such as pre-biotics, probiotics, and faecal transplants. Note that pre-biotics are defined as the non-digestible food parts that nourish the probiotics in your digestive tract. Fruit, grains, and legumes have pre-biotic components. Probiotics are the good bacteria or live cultures that are like those found naturally in the gut. Some dairy foods, fermented foods, and grains such as sourdough bread contain probiotics. Faecal transplants are an attempt to re-colonise the microbiome of people with gut dysbiosis in order to assist them in attaining a healthier gut. Here are summaries of some of the studies now illuminating the landscape of the microbiome-health connection.

What the studies show

Anorexia nervosa

Evidence is growing that the gut microbiome interacts with the central nervous system and the immune system, influencing weight regulation and psychopathology, such as anxiety and depression. A “leaky gut”, characterised by antigens going through the intestinal wall, was demonstrated in an animal model of anorexia nervosa, and could underlie the low-grade inflammation and increased risk of autoimmune disease found in that condition. Beyond that, starvation has a significant impact on the gut microbiome, and diets used for re-nutrition based on animal products may support the growth of bacteria capable of triggering inflammation (Herpetz-dahlmann, Seitz, & Baines, 2017).

Obsessive-compulsive disorder

The aetiology of OCD is complex and involves multiple pathways, with imbalances in central serotonin, glutamate, and dopamine neurotransmitter systems thought to play a causative role. The gut bacteria may be able to alter levels of neurotransmitters, as they produce them. One study revealed that two and four weeks of pre-treatment with a probiotic (Lactobacillus rahmnosus GG) attenuated OCD symptoms to the same degree as fluoxetine in mouse models of OCD. Another study showed that, in healthy people, 30 days of daily intake of a probiotic formulation containing Lactobacillus helveticus and Bifidobacterium longum was shown to reduce a variety of subscores on the Hopkins Symptom checklist, including “obsessive-compulsive” and global Hospital Anxiety and Depression Scale score, compared to placebo (Turna, Patterson, & Van Ameringen, 2017).

Obesity, Type 2 diabetes, and metabolic syndrome

In a study of the microbiome of identical twins where one was obese and one was healthy, the gut microbiome differed completely. When the microbiome of the obese twin was transferred to mice, they gained more weight than those that had received the microbiome of the lean twin, despite both groups of mice eating the same diet (Robertson, 2017).

Studies of people with Type 2 diabetes have consistently shown gut dysbiosis. Healthy control subjects tend to have more of the helpful bacteria that produce the SCFA butyrate, whereas people with type 2 diabetes tend to have higher levels of pathogenic bacteria, such as the Clostridium species. Moreover, when pathogen-free microbiota from lean, healthy donors are transferred to individuals with metabolic disease, insulin sensitivity improves (Foroutan, 2015).

Helping control blood sugar/lowering risk of diabetes

In one study, 33 infants with a genetically high risk of developing Type 1 diabetes were examined. The findings were that the diversity of the microbiome dropped suddenly before the onset of Type 1 diabetes, and also that the levels of a number of unhealthy bacterial species increased just before the onset of Type 1 diabetes. Another study found that, even when people ate the exact same foods, their blood sugar could vary greatly; this was thought to be due to the types of bacteria in their guts (Robertson, 2017).

Alcohol dependency and leaky gut

One investigation examined the gut microbiome in a group of alcohol-dependent subjects admitted to hospital for withdrawal treatment. A major subgroup presented with increased intestinal permeability (that is, leaky gut) and strong alterations of specific gut microbiota composition, whereas the remainder showed gut permeability and microbiota similar to those of healthy controls. The dysbiosis was characterised by decreased levels in the anti-inflammatory bacteria Faecalibacterium prausnitzii and Bifidobacterium and increased scores of depression, anxiety, and alcohol craving (Leclercq et al, 2016).

Cognitive function (in healthy adults)

43 community-dwelling older adults (ages 50-85) completed a brief cognitive test battery and provided stool samples for gut microbiome sequencing. Participants performing more than one standard deviation below normative performance on two or more tests were compared to persons with one or fewer impaired scores. Results showed different distributions of Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia between intact and impaired groups. These species were significantly correlated with cognitive test performances, particularly Verrucomicrobia and attention/executive function measures (Manderino, Carroll, Azcarate-Peril, Rochette, Heinberg, et al, 2017).

Depression, probiotics, and the gut: summary of a systematic review

The last decade of neurogastroenterology investigation has revealed extensive and direct biochemical signalling between the gastrointestinal tract and the central nervous system (the “gut-brain axis”). The health research community has known for many decades that stress and other psychological factors affect the health of the physical body, particularly the gut. But, thanks to recent studies, we now have evidence that the communication network is bidirectional: that is, central nervous system psychiatric disorders such as major depressive disorder are linked to changes in the gut microbiome.

These findings are further corroborated by the high rate of comorbidity between psychiatric disorders and those of the gut. Preclinical studies showed that consumption of probiotics increased expression of brain-derived neurotrophic factor (BDNF), a growth factor for brain plasticity, memory, and neuronal health that is abnormally reduced in individuals with depression. Other pre-clinical studies noted that consumption of probiotics increased levels of a precursor (tryptophan) to the “feel-good” neurotransmitter serotonin. Thus, looking at the relationship between consumption of probiotic and depression could be fruitful.

A systematic review by Wallace and Milev (2017) did just that, analysing the current body of research assessing the effects of probiotics on symptoms of depression in humans such as mood, anxiety, and cognition. Ten studies met the inclusion criteria.

Mood. Five of the ten studies assessed mood symptoms and all but two reported improvements after treatment with a probiotic.
Anxiety and stress. In the seven of ten studies assessing anxiety and stress, all but two reported improvements after treatment with a probiotic.
Cognition. Three of the studies evaluated some aspect of cognition, and two of them reported positive effects when a probiotic was consumed.


While the body of research showing how gut health affects the whole person is still small, it is steadily growing and already has amply demonstrated that we need to update our traditional views on what is needed for a healthy, happy life. The good news is that the microbiome, unlike our DNA, is utterly modifiable. The bad news is that we can no longer assume that a client’s anxiety, depression, OCD symptoms, or many other aspects of psychological distress are “all in their head”. We now need to collectively get our heads around the idea that the angst may actually begin in the gut. In our next blog, we examine what a counsellor can do to help an individual improve the health of that all-important “second brain”.

This article was adapted from Mental Health Academy’s upcoming “The Client and the Microbiome” professional development course.


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