Ultimate Guide to Gut Health
58 min read

The Ultimate Guide to Gut Health

Author_Cliff-Harvey Diet & Nutrition Digestive Support Protein Education healthy lifestyle Lifestyle Advice

By: Cliff Harvey PhD

When people talk about the gut, they’re referring to the gastrointestinal system, also known as the digestive system or digestive tract. This system includes the mouth, oesophagus, stomach, and the small and large intestine. It also includes the accessory organs which aid digestion by helping to break down larger particles of food into absorbable particles (i.e. the tongue, salivary glands, pancreas, liver, and gallbladder). Read on to learn all about gut health and some tips to have a healthy gut. 

Table of Contents

What is gut health?

Having a healthy digestive system, also known as having good gut health, allows us to absorb nutrients optimally and helps to reduce inflammation, support immunity, and even plays a role in helping us to feel better mentally. 

Why is gut health important?

Because it’s exposed to the external environment, the digestive system is an external organ by which we absorb the nutrients that make up the body’s structures, chemical messengers, and fuels. Because it’s exposed to the outside environment, it is also a potential site of infection from pathogens (disease-causing microbes) and pollutants in food and water and so, is part of our innate defences against disease and disorder that has an important relationship with the immune system of the body. 

Is gut health a fad?

Because the role of the gut is so important for both nourishment and immunity, gut health couldn’t be called a fad. Having a healthy gut is an essential component of wellbeing! However, there can be dubious claims made about supplements and diets for gut health that aren’t backed by strong evidence.  

What is the microbiome?

The microbiome is the community of microbes found in the body. Technically, microbiome refers to collective genomes of these microbes with microbiota used to describe the communities of microbes but in general use, these terms are used synonymously. Usually, the microbiome in common usage refers to the community of bacteria in the gut but it also includes other microbes like fungi, protozoa, and viruses and there is distinct microbiota of the skin, oral cavity, and other surfaces. 

What are probiotics?

Probiotics are microbes (usually bacteria) that can be taken as a supplement to help improve the balance of the microbiome. 

What are prebiotics?

Prebiotics are fuels that feed (beneficial) microbes in the gut. Usually, these are fibers and resistant starches that feed particular bacteria. 

Effects of the gut on health

Gut health and the microbiome play an important role in our overall health. Poor gut health caused by disturbances to the balance of good and bad microbes in the gut can affect both nourishment and growth and metabolic conditions like obesity and type 2 diabetes.1 

Nourishment and gut health

The key role of the gastrointestinal tract is to absorb nutrients from food. So, having a gut that functions correctly and absorb nutrients from food is essential to achieving optimal health. The microbiome also contains bacteria that produce nutrients, like short-chain fatty acids that feed cells of the digestive wall, other bacteria, and can be taken up into the body to use as fuel. These and other chemicals produced by bacteria in the gut also act as messengers that provide a metabolic interaction between the host (you) and the microbiota and digestive environment.2  

Inflammation and immunity and gut health

Far more than just being an organ to absorb nutrition, the gut is essential for the regulation of systemic inflammation, and plays a role in inflammatory conditions like psoriasis.3 Interestingly, in people with inflammatory conditions, there is typically a reduced diversity and abundance of bacteria in the gut,4-6 and reduced diversity and abundance of bacteria in the gut is also associated with increased inflammation.7

The gut-brain link and the effects of gut-health on mental health (and vice versa!)

The gut and brain are linked, and this has led some to call the gut the second brain. Mental health challenges were once considered to be structural problems or functional neurotransmitter imbalances within the brain, it is now known that overall health, inflammation, and gut-health play a role in the health of the brain, nervous system, and the psyche of an individual.8

Depression and gut health

Recent research indicates that depression is both an inflammatory disease and that there is communication between the gut and the brain and nervous system and that this is related to depression. Animal research has shown that when the faecal microbiome from animals showing depressive signs is transplanted into non-depressed subjects, they develop depressive symptoms, and most reported studies have shown a correlation between the gut microbiota and depression,9 although a 2020 meta-analysis showed no clear effect of either prebiotic or probiotic supplements.10  

Anxiety and gut health

Recent research suggests that the microbiome plays a role in regulating mood, anxiety, and stress.11 Anxiety and depression, and irritable bowel syndrome (IBS) are also common, and around 40-90% of those with anxiety share these conditions. Human and animal trials indicate that people with IBS and anxiety have a reduced diversity of bacteria and higher abundance of ProteobacteriaPrevotella/Prevotellaceae, Bacteroides and lower levels of Lachnospiraceae relative to healthy controls.12

Key points:

  • Gut and brain and nervous system health are linked.
  • Gut health is likely to play an important role in depression and anxiety.

Gut health and sleep

Poor sleep might also affect gut-health, contributing to an inflammatory state and metabolic diseases.13,14 Chemical messengers from the gut microbiome also help to influence circadian rhythms (day-night/sleep-wake cycles) and help to regulate sleep, metabolism, and body composition and both disturbed and short sleep are associated with gut dysbiosis. Additionally, the end products of bacterial species which grow in response to sleep loss can induce fatigue. Furthermore, probiotic supplementation has been found to improve sleep quality.15 

Disturbed sleep is known to worsen eating behaviors and may play a role in the disturbance to the microbiota seen with poor sleep. Animal and human research have shown that disturbed sleep increases food intake and changes the microbiota, leading to inflammation and insulin resistance.16 Antibiotics (which reduce bacteria number and diversity) have also been shown to reduce sleep in mice,17 while research in people with IBS also suggests that gut dysfunction affects sleep.18 However, in a study of young, active adults (18-35 years) no significant relationship between habitual sleep duration and microbiota diversity was observed.19

Key points:

  • Poor gut health affects sleep and poor sleep affects gut health.
  • Probiotics might help to improve sleep quality.

Gut health and skin health

The connection between gut and skin health has been known for some time. Many conditions of the skin such as psoriasis and eczema result from a combination of factors, which include allergy and inflammation and so, the barrier and immune functions of the gut are important for skin health. 

Gut health and acne

Acne is an inflammatory skin condition and for nearly a century the link between the gut, brain, and skin has been suggested.20 The gut microbiome is also important for this condition, as it affects immunity, inflammation and intestinal permeability, contributing to skin inflammation.21 Research shows that people with acne have different microbiota to those without acne.22 While changes in diet have typically been considered to have little effect on acne, clinical experience suggests otherwise. It is now suggested that diets that reduce inflammation and support a healthy microbiome, including those based on natural, unrefined foods and with plenty of gut-supporting fiber and resistant starch, be considered for acne.23

Gut health and eczema

Eczema is a common inflammatory condition of the skin affecting around 1 in 10 people at some point in their lives. Increasingly, studies are demonstrating a link between the gut microbiome and eczema.24 A significant proportion of children who develop food sensitivities go on to develop food allergies and eczema, and these anomalous immune responses are thought to be linked to the gut-immune axis of the body.25 Children with eczema also have lower bacterial diversity than those without,26-30 and different microbiome signatures.31-41

There is some debate about the role that probiotics might play in eczema. Overall, systematic reviews of the literature suggest a 26% reduction in risk for eczema with probiotic supplementation.42 Prebiotics can also be beneficial for correcting the microbiome, especially for formula-fed infants.43-45 

Gut health and psoriasis

The gut-skin axis is thought to be related to the immune-inflammatory cascade and there is an increased prevalence of psoriasis and psoriatic arthritis with inflammatory bowel disease.46 The gut microbiota of patients with psoriasis show reduced diversity,47 and a distinct signature compared to controls.48

Key points:

  • People with inflammatory skin conditions have different microbiota to those without these skin conditions.
  • The gut microbiome is important for regulating inflammation throughout the body.
  • Probiotics might help inflammatory skin conditions such as eczema.

Can gut health cause hair loss?

Hair loss can be due to genetic disposition (male pattern baldness), micronutrient deficiencies (such as a zinc deficiency) or to an autoimmune inflammatory disorder such as alopecia areata. In the case of alopecia, the gut biome is thought to play a similar role as it does in other inflammatory disorders,49 and people with alopecia are also likely to have different microbiome signatures than healthy controls.50

Can gut health affect blood pressure?

Blood pressure may also be partially mediated by the gut microbiome,51-54 along with gut health being associated with metabolic health which also causes high blood pressure. High intakes of fruit, vegetables, and fiber that are known to support the microbiome (by feeding beneficial bacteria) also result in short-chain fatty acids being produced by those bacteria. These short-chain fatty acids are linked to lower blood pressure.55-58 Chronic inflammation and “leaky gut” are also associated with blood pressure.59

Can gut health cause headaches?

The gut-brain axis is thought to play a role in the causation of migraines and headache.60 However, the reasons for this aren’t entirely clear. It is thought that a range of factors, from inflammation to pain signaling, blood pressure regulation, and other gut-related cell-signals could all be at play in the gut-headache relationship.61-63

While several randomized trials have shown reduced frequency and severity of migraine attacks with probiotic supplement use64, 65 (without changes in inflammation or intestinal permeability), a systematic review of the available trials published in 2020 found no significant effect of probiotic supplementation on migraines.66

How does gut health affect hormones?

The gut and microbiome play a role in the metabolism and clearance of various hormones such as oestrogen,67, 68 and oestrogen itself has an interrelationship with the gut-brain axis.69 This is important because oestrogen sensitive cancers are a significant risk, especially in postmenopausal women,70 and alterations to the gut microbiome that affect oestrogen regulation in the body could drive oestrogen-related illnesses.71Animal research also suggests a role for oestrogen inhibiting menopausal symptoms and preserving microbiome diversity.72,73

Testosterone function in males could also be affected by poor gut health. Overweight and obesity are associated with poorer gut health and endotoxin damage. In a study looking at the effects of these on testosterone, body fat was correlated with both endotoxins and inflammation and reduced testosterone.74 Animal research had previously demonstrated reduced testosterone production (and increased risk of obesity) resulting from the antibiotics doxycycline and ciprofloxacin,75, 76 that was improved by probiotics.75

Key points:

  • The microbiome helps process and eliminate steroid hormones.
  • Disturbances to the microbiome could worsen oestrogen-related illnesses and cancers in women.
  • The microbiome might affect optimal testosterone levels in men.

Does gut health affect weight loss?

The gut microbiome plays a role in hunger, satiety, and inflammation and there is a complex relationship with weight management. Emerging research suggests that there are distinct microbiome signatures associated with obesity,77 and with cardiometabolic states also associated with overweight and obesity, in particular, systemic inflammation.7 

Gut health, diabetes, and cardiometabolic health

The gut biome has a bidirectional relationship with hunger, satiety, inflammation and immunity, all of which interplay with the spectrum of acquired ‘diabesity’,78 and there is also likely to be involvement of the gut and microbiota with Type 1 (autoimmune) diabetes.79, 80

Reviews of the evidence suggest that supplementation with probiotics in diabetes and metabolic disorder benefits blood glucose control, lipids, insulin levels and sensitivity, and inflammation.81-89

Cardiovascular health

The microbiome and gut health Intestinal microbiota are linked to cardiovascular health and modifying the gut environment might help to prevent cardiovascular disease.7, 90

Use of probiotics is also linked to reductions in blood pressure,91 a marker of heart disease and reductions in inflammatory endotoxins92, 93 (toxins created within the body, usually by the breakdown of “bad” bacteria in the gut and the uptake of these into the body because of poor gut health), which also contribute to cardiometabolic diseases like heart disease, obesity, and diabetes.

Key points:

  • The microbiome affects inflammation, food intake, and various measures of cardiometabolic health.
  • The microbiome is likely affected by a poor diet and other lifestyle factors that contribute to metabolic disease and obesity.
  • The microbiome and gut health also cause conditions in the body related to metabolic health and obesity.
  • Probiotics may be beneficial for metabolic disease.

Are protein powders good for gut health?

Generally, the focus on nutrients for gut health falls on fibers, resistant starches, and fatty acids from fish oil, dairy, palm or coconut oils. Fermentation of excessive protein in the gut might contribute to dysbiosis and worsen gut health, but animal research suggests these effects are mitigated by increased fiber intake,94 (in other words, this isn’t likely to be an issue in a balanced diet) and few people over-consume protein in any event. In fact, the bigger issue for most people is not whether they consume too much protein, but that they don’t take in enough to thrive. Protein is critical to health, performance, and adherence to a good diet and so, taking supplementing your diet with a powder (like Clean Lean Protein) can help to support health, and by extension, gut health. 

Are probiotics good for gut health?

The research on probiotics is conflicting and there will be differences in results based on which species and strains of bacteria are used for which outcomes. Overall though, the accumulated evidence suggests that probiotic supplements can be useful for:

  • Dysbiosis95, 96
  • Dysbiosis in HIV97
  • Reducing inflammation and allergy98
  • Diarrhea, constipation, pain and bloating, symptoms of lactose intolerance, 99-102
  • Inflammatory bowel disease103  
  • Improved sleep15
  • Eczema42
  • Migraine64, 65
  • Possible improvement in both male and female hormone balance73, 75
  • Diabetes and metabolic syndrome81-89
  • Cardiovascular health91-93

There are different microbiome signatures associated with poor health and with different health conditions and so, specific strains may be more or less useful for particular conditions. If you require specific treatment for a health condition or disorder, see a qualified practitioner who is well-versed in gut-health. 

Other nutrients for a healthy gut

It is now known that the health of the gut has a big effect on the health of other organs and systems and particular focus has fallen on the interplay of gut-health with that of the brain and nervous system, and the skin. As with any other body system, the foundation of nutrition for gut health is a diet that is packed with essential nutrients, and that provides sufficient energy, protein, and essential fats. Specifically, the gut also benefits from sufficient amounts of prebiotic starches and fibers from foods like legumes, grains, and vegetables, that feed “good” bacteria in the gut,104 along with omega-3 fats,105 and short- and medium-chain fats that aid the balance of the microbiome (the community of microbes) in the gut.106, 107

Also, many nutrients have been shown to help support gut health, such as:

  • Plant phenols and antioxidants – Health-promoting compounds in plants that work together with probiotics to improve the balance of the microbiome. 108 Preclinical trials also provide evidence for the traditional use of the fruit Rosehip improved gastrointestinal health. 109, 110
  • Digestive and tonic herbs – Bitter greens (like dandelion) with anti-inflammatory and antioxidant actions. 111, 112 
  • Ginger – Known to reduce nausea (especially during pregnancy) 113-116
  • Adaptogenic herbs, especially Astragalus which offers protection against intestinal inflammation. 117
  • Soothing herbs such as slippery elm, considered to be soothing and anti-inflammatory and used as a digestive aid. 118, 119
  • Anti-inflammatory spices like turmeric 120, 121
  • Zinc – an important mineral for the gut because it helps to close ‘tight junctions’ in the gut wall, reducing the potential for allergens and pathogens to enter the body. 122, 123 Note: many people do not get enough zinc from diet alone.

Lifestyle and gut health

Exercise and gut health

Exercise is associated with greater diversity and health of the microbiome of the gut,124, 125 and benefits are likely to be greater with improved body composition.126, 127

Stress and gut health

Stress is a common, yet often overlooked factor in the health of the gut. Severe trauma (PTSD) is associated with an increased likelihood of developing IBS,128 as is stress overall, and other types of stressful life events.129 Additionally, mindfulness meditation reduces the severity of IBS.130

Other factors that can affect the health of the gut:

  • Poor sleep
  • Smoking
  • Excessive alcohol use

Interestingly, the combination of probiotics with plant phenols provides synergistic benefits, with greater survival, adhesion, and maintenance of beneficial bacteria and improved health benefits. 108

Do sweeteners harm the microbiome?

While some experimental animal studies have suggested the non-nutritive sweeteners can worsen blood glucose control, increase food consumption, and cause weight gain (possibly due to effects on the microbiome), the evidence from human studies suggests that have little if any effect. Meta-analyses (studies compiling data from many trials) have shown that non-nutritive sweeteners have little or no effect on blood glucose control in humans,131 or on gut health,132 and few negative functional effects on the human gut have been observed.132 Erythritol, in particular, does not appear to be fermentable by colonic bacteria and is unlikely to have any effect on the gut microbiome.133 

Relationship between gut health and overall health

The gut is intricately linked to the health of the entire body and every one of its systems. The relationship between gut health and the health of the body is bi-directional, meaning that one affects the other and vice versa. At this time much of the research is preliminary and especially with probiotic treatments, there are distinct differences between conditions, individuals, and their microbiota and therefore, the probiotic treatments that may be beneficial. But, on balance, broad-spectrum lactobacillus and bifidobacteria are beneficial to health, as are increased fiber intakes, along with other nutrients derived from a diet rich in vegetables, berries, and spices and herbs, and fermented foods. Exercise, mindfulness, sleep, and stress reduction also each play an interrelated role in the health of the gut and body. 



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