Gut Health Guide South Africa: Microbiome, Symptoms & Testing | Epicentre
Epicentre Gut Health Guide

Your Gut Has Trillions of Residents.
Do You Know Who They Are?

Your gut microbiome contains over 100 trillion microorganisms: bacteria, fungi, parasites, and viruses. When they're in balance, you feel well. When they're not, the effects reach far beyond your stomach.

70% of your immune system lives in your gut
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Medically reviewed by Dr. Samantha Naidoo, MB ChB, FCP (SA)
Medical Director, Epicentre Walk-In Labs. Last updated March 2026.
The basics

What Is Gut Health?

Gut health is how well your digestive system and the trillions of microbes living in it, your gut microbiome, work together to break down food, absorb nutrients, support your immune system and keep harmful organisms in check.

A healthy gut holds a diverse, balanced mix of beneficial bacteria. When that balance is disturbed, a state called dysbiosis, it can show up far beyond your stomach: low energy, skin flare-ups, frequent colds, mood changes and digestive discomfort. A large part of your immune system sits in and around the gut, which is why an unbalanced microbiome affects so much of how you feel.

In South Africa gut health varies widely, shaped by diet, water quality, a high burden of gut infections and the frequent use of prescription medication. Two people with the same symptoms can have very different things going on inside, which is why the only way to know what is in your gut is to test it.

Interactive tool

Is Your Gut Trying to Tell You Something?

Answer 8 quick questions about your symptoms. This is not a diagnosis, but it can help you decide whether gut testing is worth considering.

Gut Health Symptom Checker
8 questions. Takes 60 seconds.

Myth vs fact

What Most People Get Wrong About Gut Health

Tap any card to flip it and see the truth.


Warning signs

Symptoms of an Unbalanced Gut

Gut problems don't always feel like stomach problems. These are the signs your microbiome may be out of balance.

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Bloating and gas
Persistent fullness or distension after meals, even small ones
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Irregular bowel habits
Alternating between diarrhoea and constipation without clear cause
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Fatigue and brain fog
Your gut makes over 90% of your serotonin. Dysbiosis affects energy and focus.
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Skin flare-ups
Acne, eczema, and rosacea are often linked to gut inflammation
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Sugar cravings
Harmful bacteria thrive on sugar and can drive your cravings to feed themselves
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Frequent illness
70% of your immune system is gut-based. Dysbiosis weakens your defences.
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Unexplained weight changes
Imbalanced gut bacteria can disrupt how you absorb nutrients and store fat
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Anxiety or low mood
The gut-brain axis means bacterial imbalance can directly affect your mood
Many gut problems are silent. You can have significant dysbiosis with no obvious digestive symptoms. Subtle signs like fatigue, skin changes, or frequent colds can be your only clue. Regular testing catches problems before they escalate.

Meet your microbiome

The Organisms Living in Your Gut

Your gut hosts beneficial bacteria that keep you healthy, core species that can go either way, harmful pathogens, and parasites. Tap any organism to learn more.

ProbioticAkkermansia muciniphilaMaintains gut lining integrity. Linked to lower obesity and diabetes risk.Read full guide →ProbioticBifidobacterium bifidumBreaks down complex carbs. Supports immune function in infants and adults.Read full guide →ProbioticBifidobacterium breveFerments sugars, produces short-chain fatty acids. Supports infant gut health.Read full guide →ProbioticBifidobacterium lactisEnhances immune response. Reduces diarrhoea that can follow a prescribed course of treatment.Read full guide →ProbioticBifidobacterium longumProduces B vitamins, inhibits pathogens, reduces inflammation.Read full guide →ProbioticFaecalibacterium prausnitziiMajor butyrate producer. Anti-inflammatory. Low levels linked to Crohn's disease.Read full guide →ProbioticLactobacillus acidophilusProduces lactic acid, lowers gut pH, inhibits harmful bacteria.Read full guide →ProbioticLactobacillus gasseriSupports vaginal health, weight management, and immune function.Read full guide →ProbioticLactobacillus helveticusProduces bioactive peptides. Supports calcium absorption and gut barrier.Read full guide →ProbioticLactobacillus paracaseiModulates immune responses. Supports skin health and allergy management.Read full guide →ProbioticLactobacillus reuteriReduces colic in infants. Anti-inflammatory. Supports oral and gut health.Read full guide →ProbioticLactobacillus rhamnosusPrevents and treats diarrhoea. Supports vaginal and urinary tract health.Read full guide →ProbioticLactobacillus plantarumStrengthens the gut barrier. Produces antimicrobial compounds.Read full guide →ProbioticRoseburia hominisKey butyrate producer. Protects against colorectal cancer.Read full guide →ProbioticStreptococcus thermophilusUsed in yoghurt production. Helps digest lactose.Read full guide →

The basics

Probiotics vs Prebiotics: What Is the Difference?

Probiotics = the good bacteria

Live beneficial organisms like Lactobacillus and Bifidobacterium. Found in yoghurt, kefir, kimchi, sauerkraut, and supplements. They restore balance and support digestion, immunity, and mood.

Prebiotics = their food source

Non-digestible fibres that feed your good bacteria. Found in garlic, onions, bananas, oats, asparagus, and leeks. Think of them as fertiliser for your gut garden.

You need both. Probiotics introduce beneficial bacteria; prebiotics help them grow and thrive. A gut test can show you which probiotic species you're low on, so you can supplement with purpose rather than guessing.


Risk factors

Who Is Most at Risk for Gut Problems?

Processed food diet

Diets high in sugar, refined carbs, and seed oils starve beneficial bacteria and feed harmful ones.

Recent prescription treatment

A prescribed course that clears an infection reduces beneficial bacteria along with the harmful ones. Even one course can take months to recover from.

Chronic stress

Cortisol alters gut motility, increases inflammation, and shifts the balance of your microbiome.

Over 50

Microbial diversity naturally declines with age, increasing vulnerability to infections and inflammation.

IBS, IBD, or diabetes

Pre-existing conditions both cause and worsen dysbiosis, creating a cycle that is difficult to break without testing.

Travel to endemic areas

Traveller's diarrhoea, parasites like Giardia, and pathogenic E. coli strains are common in sub-Saharan Africa.


Gut health testing

Find Out What Is Actually in Your Gut

Epicentre uses PCR stool testing to identify specific organisms in your gut. No doctor's referral needed. Walk in or order a home collection kit.

H. Pylori Antigen Test

The standalone test. If you only want to know whether you have H. pylori, this is it. A stool antigen test that finds active infection rather than old antibodies.
1 target · stool sample
R269
No doctor's referral. Results in 5 to 7 working days.
See it on the test list Book on WhatsApp

Gut Essentials: Beneficial

A probiotic baseline snapshot of your most clinically relevant beneficial gut bacteria.
17 probiotic targets
R2,500
or ~R625/mo with Payflex (4x interest-free)
Learn more

Gut Essentials: Harmful

A 23-target screen for harmful gut microbes, H. pylori among them. Choose this if you want the wider picture; if H. pylori is the only question, the R269 standalone test above is the one you want.
23 harmful targets
R2,500
or ~R625/mo with Payflex (4x interest-free)
Learn more

Gut Deep Dive

Everything in the Complete Profile, plus disease association analysis linking your results to conditions like IBS, IBD, and metabolic disorders.
45 targets + disease associations
R5,950
or ~R1,488/mo with Payflex (4x interest-free)
Learn more
Home collection kits available. All gut tests can be done at home. We deliver a stool collection kit in discreet packaging with prepaid return. Results in 5 to 7 working days.

Prevention

How to Improve Your Gut Health

To improve your gut health, feed your beneficial bacteria with fibre and fermented foods, cut back on processed sugar, manage stress, stay hydrated and use prescription medication only when you need it. Small, consistent changes shift your microbiome within weeks. Our full guide to how to improve your gut health covers which food feeds which bacteria, and how a test tells you whether it worked.

Eat fibre-rich foods
Fruits, vegetables, whole grains, and legumes feed your beneficial bacteria.
Add fermented foods
Yoghurt, kefir, kimchi, sauerkraut, and kombucha introduce live probiotics.
Cut processed sugar
Sugar feeds harmful bacteria like Candida and displaces beneficial species.
Manage stress
Chronic stress alters gut motility and bacterial balance. Regular exercise helps.
Stay hydrated
Water supports the mucosal lining of the intestines and helps beneficial bacteria thrive.
Use prescription medication wisely
Take prescribed courses only as directed. Probiotics afterwards help restore the beneficial bacteria a course can deplete.


Plain English

Gut Health Terms Explained

Gut microbiome
The whole community of bacteria and other microbes living in your gut. Yours is different from everyone else's, and it shifts with diet, sleep, stress and medication.
Dysbiosis
An imbalance in that community, with too few beneficial microbes or too many harmful ones. It is linked to digestive symptoms, to inflammatory bowel disease and, through the gut-brain axis, to mood.
Probiotic
A live beneficial microbe, whether you take it as a supplement or eat it in yoghurt, kefir, kimchi or sauerkraut.
Prebiotic
Fibre you cannot digest that feeds your beneficial bacteria. Garlic, onions, bananas, oats, asparagus and leeks are all good sources.
Stool PCR test
A laboratory test that copies the genetic material of the organisms in a stool sample until they can be identified, so many organisms can be found from one sample.
Butyrate
A short-chain fatty acid your bacteria make from fibre. It feeds the cells lining your colon and lowers inflammation.
Common questions

Gut Health Testing FAQs


Ready to Find Out What Is in Your Gut?

45-target PCR stool test. No doctor's referral needed. Walk in or test at home. Results in 5 to 7 days.

Explore individual organisms
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