Ssshhh… don’t speak it, don’t even think it… Antibiotics might actually cause you harm!!!

Like that other elephant in the room… dare I say it… vaccines… (aarrgghh!!) there are many healthcare practitioners that simply won’t utter a word counter to the long established dogma that effective medicine = pharmaceutical drugs, for fear of being publicly flogged and labelled a quack.

NH21 Weekly thus honours Martin Llewelyn, professor in infectious diseases at Brighton and Sussex medical school, for his brave efforts in questioning whether finishing course of antibiotics, even after the infection is clear and you feel well, might not be a little overzealous and counter to our health.

Reporting in the British Medical Journal, Llewelyn and his team note that;

“The idea that stopping antibiotic treatment early encourages antibiotic resistance is not supported by evidence, while taking antibiotics for longer than necessary increases the risk of resistance.”

As with all old wives’ tales people tend to assume things are true simply because they have heard them enough times, often without stopping to question the logic of their entrenched beliefs. We’re led to believe that even though the drugs do work, and the offending bacteria has been banished from the body, we should finish the entire prescription just in case; chasing the enemy not just out the door but a good long way down the road for good measure.

The conspiracy theorist in me might suggest it to be a simple ploy by Big Pharma to sell more pills (perish the notion); but others think it to be good medical science, including the Royal College of GPs chair, Prof Helen Stokes-Lampard who cautions;

“We are concerned about the concept of patients stopping taking their medication midway through a course once they ‘feel better’, because improvement in symptoms does not necessarily mean the infection has been completely eradicated. It’s important that patients have clear messages and the mantra to always take the full course of antibiotics is well known. Changing this will simply confuse people.”

Mantras and Confusion

NH21 isn’t concerned with mantra’s in healthcare, and feels that the public are already quite confused; yet might be less so if given an opportunity to hear the science, weigh up the pro’s and con’s (risk vs reward) of their prescribed care, and make an informed decision about how best to safeguard their own health.

In that spirit, the following overview of bacteria in general, and also those specific to the human gut; may help the individual to discern for themselves whether destroying the entire ecosystem each time we get sick is truly in our best interests.

Bacteria are microorganisms that lack a distinct nuclear membrane and so are considered more primitive than animal and plant cells. Most bacteria are unicellular i.e. individuals that do not tend to form tissues. Mammals evolved on earth roughly 200 million years ago; the modern human is thought to be just 200,000 years old. Bacteria have existed on the earth for over 3 billion years.

Bacteria reproduce asexually by simple division, giving rise to vast colonies that are widely distributed in the air, water, and soil; plus, in plants and animals including humans. Some bacteria cause disease by producing toxic poisons; but many do not harm their host, and some in fact protect them.

The human body can be described as a superorganism. For every one cell that makes up the body, there are nine bacterial cells that have co-evolved to reside upon and within it. There are more bacteria in the large intestine, for example, than there are cells that make-up the entire physical body; some 100 trillion from around 4000 different species.

These commensal organisms, living upon and within us, are essential to physicality and inseparable from the sum of being human. Bacteria in the gut (‘microbiota’ or ‘gut flora’) are vital for proper digestion, and perform other important functions such as preventing the overgrowth of yeast and other pathogens, plus synthesizing vitamin’s K and B12.

There are numerous different strains (types) of gut bacteria, and each individual contains colonies as unique as their fingerprints; yet there are two major bacterial groups that reside in most people; Lactobacillus and Bifidobacterium.

  1. Lactobacillus is a type of ‘friendly’ bacteria that assists the digestion of proteins. It has antifungal properties, helps reduce blood cholesterol and enhances the absorption of nutrients.
  2. Bifidobacterium aids the synthesis of B-vitamins; plus, improves bowel function by aiding peristalsis, resulting in the production of a softer, well-formed stool.

The gut is a complex ecosystem of myriad ‘good’ and ‘bad’ bacteria, and a short-term disruption of the guts microbes can have long lasting effects on the bodies overall composition. In the words of evolutionary biologist Allana Collen, PhD;

“Imagine a virgin rainforest dense with life. Insects rule the undergrowth and primates the canopy. Now see loggers move in, chainsawing the forests leafy infrastructure and bulldozing the rest. Imagine too, a weed invading, perhaps bought in on the wheels of the diggers, and crowding out the natives as it takes hold. The forest may regrow, given time, but it will not be the same as before; diversity will drop, sensitive species will die out and invaders flourish.”

An unhealthy balance of microbiota is termed dysbiosis; which describes reduced numbers of ‘good’ bacteria and an increase in the ‘bad’. Factors that can destroy beneficial bacteria include use of antibiotics, and diets high in meat and sugar whilst low in fruits and vegetables. The afflicted digestive tract is prone to becoming leaky, inflamed, constipated and infected. 

Dysbiosis sits at the heart of 21st century illnesses because it unravels the immune process that occurs in the intestines; contributing to problems in distant parts of the body, including infections, autoimmune diseases and chronic inflammation.


The cecum is a pouch-like area that marks the start of the large intestine (colon). Food residue in the cecum flows upward on the right side of the body in the ascending colon. Attached to the base of the cecum is the vermiform appendix; an organ with a reputation as an evolutionary relic. So little does medical science know of the appendix that the Oxford Medical Dictionary describes it as, “having no known function in humans and liable to become infected and inflamed.”

(NB: utter nonsense at best, medical ignorance worse).

From the mid-late 20th century, removing the appendix was among the most common surgical procedures carried out in the developed world. This occurs less in recent times, due in part to new scientific understanding that the appendix; which averages about 8cm in length and forms a tube protected from the flow of digested foods passing by; acts as a safe-house for the body’s gut microbes.

After an episode of food poisoning or gastrointestinal infection (historically), or a course of antibiotics (more recently), the gut can be repopulated with its normal quota of bacteria from the stockpile residing in the appendix.


Dietary fiber, or roughage, is the carbohydrate portion of plants that is resistant to digestive enzymes and cannot be fully digested and absorbed to produce energy. Instead, most of it moves through the gastrointestinal tract and ends up in the stool.

We tend to think that the stool contains remnants of the foods we consume; yet on its passage through the gut most the food we eat is digested and absorbed by the body’s cells and gut microbes, leaving only a small amount to come out the other end. Around 75% of the weight of feces is bacteria, some dead, some alive, with plant fiber making up about 17%; the remainder is mostly water. Fiber can be split into two groups:

Soluble fiber: 

  • Soluble in water, forms a gel when mixed with liquid.
  • Binds to fatty acids, lowers total cholesterol levels.
  • Regulates blood sugar.
  • Prologues stomach emptying so that sugar is absorbed more slowly into the bloodstream.

Insoluble fiber:

  • Not soluble in water.
  • Helps to move bulk through the digestive system.
  • Helps to balance intestinal pH.
  • Promotes regular bowel movements.


The idea that carbohydrates as an entire food group play a role in obesity and insulin resistance does not mean that people should switch a Low-Carb-High-Fat (Banting) diet. Most types of dietary fiber are carbohydrates; including ‘non-starch polysaccharides’ such as cellulose and pectin (from apples), and ‘resistant starches’ found in bananas, whole grains, seeds, rice and peas.

Gut bacteria have genes that code for enzymes allowing them to break down plant cellulose, the otherwise indigestible compounds that form the structure of plant cell walls; known nutritionally as insoluble fiber. With healthy levels of gut bacteria, we are able to extract nutrition from the grains, legumes, beans and vegetables that many people consider should comprise much of the normal diet; but which cause bloating and gas in people who believe themselves to be intolerant.

The banner ‘carbohydrate’ incorporates a huge spectrum of foods. Low-carb diets give the impression that a spoonful of jam and a carrot are the same thing. Often people who increase the amount of fat in the diet cause their fiber intake to go down.

Proponents of LCHF claim that all carbs are bad; yet consider that whilst sugar is a carbohydrate, so are lentils. A piece of cake can be 60% carbohydrate thanks to refined sugar and flour, all of which are rapidly absorbed in the small intestine; but broccoli contains even more, at around 70% carbohydrate, nearly half of which is fiber, the remainder vitally important micronutrients and other trace elements.

Studies on mice show that feeding them a high fat diet the levels of Bifidobacterium decline. It has also been recorded in human studies that the higher a person’s BMI (body fat), the fewer Bifidobacterium they have.

Eating a high fat diet is not bad, providing there’s enough fiber in the diet to protect the gut lining from its inflammatory effects. Fiber bolsters microbe’s communities that strengthen the gut walls defences; toxins thus cannot get into the blood, the immune system can keep calm and fat cells will become more numerous rather than filling up; storing energy in a physiologically appropriate way.

A high-fiber diet reduces the risk of colon cancer by speeding up the rate at which stools pass through the intestine, and by keeping the digestive tract clean. In addition, fiber binds to substances that would otherwise result in the production of cholesterol, and eliminates them from the body. In this way fiber helps to lower cholesterol levels resulting in decreased risk of heart disease.

Refined foods contain little or no fiber. Foods with a high fiber content include fruits and vegetables; whole grains and cereals; beans, pulses and legumes; seeds and nuts.

Complex carbohydrates digest slowly and release glucose into the bloodstream at a steady rate, requiring less work on behalf of the pancreas and ensuring a constant supply of usable energy; promoting physiological function and long term health. The addition of dietary fiber slows the absorption of natural food sugars further, maximizing the efficacy of the digestive system and enabling the individual to extract the most fuel out of their food.


Probiotics are live, beneficial microorganisms that can be taken as a dietary supplement or in food. Yogurt products that state ‘live and active cultures’ on the label contain probiotics. Other sources include naturally fermented foods like unpasteurized sauerkraut and kimchi, and traditionally cultured dairy products like kefir.

Commercial probiotics typically provide Lactobacilli or Bifidobacteria. Strong scientific evidence exists for their use as a supplement to antibiotic therapy to prevent acute diarrhea and adverse effects in the GIT, and to prevent atopic dermatitis (eczema) in infants. Yet their effects are fleeting because these bacteria colonize the gut only temporarily, making regular consumption necessary to sustain their population in the gut.

As such, supplemental use of probiotics can be beneficial for acute (short-term) health conditions, or for general maintenance of the gastrointestinal health in the longer-term, provided they are administered every day. Yet even then, they are at best only equal, if not less beneficial, than eating an abundance of dark green vegetables; our gut microbes preferred food source.

Prebiotics are food for gut microbes. A prebiotic cannot be broken down by human digestive enzymes but can be fermented by gut bacteria. These non-digestible substrates stimulate the growth of beneficial bacteria in the colon. Food products with prebiotic effects are usually non-digestible carbohydrates.

The two compounds most extensively tested and with confirmed prebiotic effects are inulin-type fructans (ITFs) and galacto-oligosaccharides (GOS). ITFs occur naturally in a variety of foods such as leeks, asparagus, artichokes, garlic, onions, chicory, wheat, bananas, and soybeans. Other sources include honey, oatmeal, red wine, and legumes. As with probiotics, the influence of a prebiotic on the gut microbiota is momentary. Changes in microbial composition respond rapidly, normally within 24 hours of exposure, and disappear equally fast upon withdrawal.

Ultimately, whatever the strains or products used, probiotics are a remedy only, a salve, a band-aid. They pass through us but don’t hang around for very long. To obtain their benefits you must keep taking them, which can become extremely expensive; often over R1000 per month. And, even if you do take them daily, adding probiotics alone is, in the words of Allana Collen once more, “like sending a foot soldier to war without a box of ammunition.”

Remembering that the gut houses around 100 trillion microbes; more than 5-billion colony-forming-units (CFUs) are normally recommended per day for children, and more than 10-billion colony-forming units per day for adults; which even then is comparatively few.

For a long-term therapeutic effect, it is important to provide an internal bodily environment where beneficial microbes can thrive, day after day, without needing outside intervention to replenish their numbers. This is best achieved by eating a variety of fresh, seasonal, whole foods, in their natural state with the bare minimum of processing. Providing the body with adequate dietary fiber is essential to good gut health because it brings the number of beneficial bacteria back up to healthy levels.