Probiotic means pro-bios, or for life. This is the opposite of antibiotic which means against life.

Breaking News

The world has turned upside down with regard to the use of probiotics. This information has come only recently and has been a challenge to all, including me, who have attempted to encourage people to be healthier by taking probiotics on a regular basis.

What you will learn here is that it is may no longer be considered useful to take probiotics on a regular basis and that taking probiotics following an antibiotic might actually slow down the recovery of the intestine.

We will start with an understanding of the role of beneficial bacteria and their helpers, the fungi, moulds and viruses. This community of organisms lives on the skin, in every body opening, in the nose, throat and sinuses, in the ears, respiratory passages, the lungs and throughout the digestive system and is collectively called the microbiome. We are host to some 30,000 different bacteria, some 100 thousand varieties of fungi and moulds, and millions of viruses.

This stunning number of organisms works in harmony in order to maintain our health. It produces the immune factors we require, produces amino acids as building blocks for our body, creates vitamins of many types within our intestine and has developed a communication system which allows it to communicate with our nervous system directly and with our external environment including other humans, plants and the diverse number of bacterial and fungal species.

Health from the time of our birth

During an normal birth the infant is exposed to the vaginal secretions of the mother for a considerable time. These secretions contain a wide variety of the mother's micro-biome which the child takes in through its mouth and which forms the basis of a healthy immune system.

Currently in North America somewhere around half of all births are surgical - that means the cesarean section where the child is delivered in a sterile fashion thus depriving them of an opportunity to ingest the healthy biome of the mother. This frequently leads to a series of infections early in life. The solution is for the vaginal secretions from the mother to be liberally applied to the mouth and nose of the newborn infant thus gifting them with the beginning of a healthy immune system.


How does taking regular probiotics make things worse? 

What these pills then create is a very limited microbiome so instead of having thousands of different species of bacteria working as a community to create nutrients and protect against foreign invaders we end up with a limited number of species thus reducing our immune capability and our general health.

Following taking an antibiotic the body undergoes a natural regeneration of the microbiome if we can provide it with a wide variety of different sources of bacteria, moulds and fungi through our exposure to the environment and raw and fermented foods.

It has been demonstrated that recovery of a healthy biome is slower in patients who take a probiotic following an antibiotic!

How can we create a healthy microbiome?

Dr Zach Bush has helped pioneer this new understanding of the microbiome through the many podcasts on YouTube. If you Google his name + microbiome, you will be lead to a number of excellent lectures - all heavily based on science - but done with a heart.

He teaches about avoiding an agricultural chemical (Glyphosate), being out in nature and in contact with the soil, plants and animals, and eating organic, naturally fermented foods like saurkraut, miso, natto, kimchee, olives and pickles. These foods need to be fermented without the use of "engineered" fermentation starters or acidified with commercial acids.

For a more rapid microbiome recovery I would add reducing ones intake of sugars, even from fruits and all but eliminating fruit juices.

Some foods contain a larger array of toxic compounds than others and if you chose to eat these foods, please make them organic - see the dirty dozen.

Some foods are safer - see the clean 15

Some ways we hurt our intestinal health.

THe health of our microbiome is injured when we eat too much food which converts to sugar which promotes the harmful growth of yeasts like Candida. 


Candida, and other harmrful fungi are made stronger when we eat certain foods including excess sweets (which includes fruit and fruit juices), certain grains like wheat, corn, and white rice, and yeasted foods like beer and wine.

We also hinder probiotic bacteria when we take non steroidal anti-inflammatories like, ibuprofen and ASA. These drugs thin the mucus layer and make it more difficult for the probiotics to survive.

The diagram to the right illustrates the probiotic layer (green) living on the surface of a layer of mucus (turquoise). The arrows indicate their ability to repel yeasts, bacteria and fungi.

We can 'poison' probiotics with chlorine in drinking water which reduces their numbers. Fast and certain probiotic death comes from a course of antibiotics. Slow death can come from low level antibiotics which may be found in some food products.

Low levels of antibiotics may be present in meats which come from animals, fowl or fish which have been raised using food laced with antibiotics. Poultry and pork raised in commercial units, when the creatures are packed together, are prone to bacterial illnesses. Farmers add antibiotics to promote rapid weight gain and reduce the chance of infection which can kill large numbers of animals when they are packed so closely together. In some cases, antibiotics are added to the ice water in which fish are transported to market in order to "preserve freshness". Food raised organically does not have these risks.

Acidophilus actually looks like this. Healthy IntestineThis friendly bacteria has many helpful functions and lives as the dominant species in the small intestine. Here, it creates an acidic microenvironment next to the absorption cells, promoting iron absorption. One of the causes of anemia can be damage to this acid layer as in celiac disease. Many people are anemic and correcting this lack by taking acidophilus daily can help promote iron absorption. A good acidophilus can be obtained directly from a reputable company. Click here for more information.

When acidophilus is in a healthy condition, one may observe projections from the tips of the bacteria - acidophilus buds. These are the beginning of new acidophilus cells which signifies the health of the bacteria.

The following drawing shows an illustration of the healthy intestinal villi. These finger-like projections are how we absorb our food. Probiotic bacteria stand on guard to protect us from potential bacterial, viral and yeast invaders. The probiotics are illustrated in green.

Probiotic benefits

The healthy large intestine has another dominant species, Bifido bacterium. This family of bacteria thrive on the soluble fibre in your diet - the type of fibre which comes from most fruits and grains. Bifido bacteria take this fibre and break it down, creating food (butyrate) for the large intestine. Butyrates are fatty acids which help promote healthy peristalsis in the colon and facilitate healthy easy bowel movements.

Probiotics as Immune Enhancers

It has been widely accepted in the medical community that probiotics have a beneficial effect on immunity. It was thought that this benefit was due to the effect of the live bacteria. A rather interesting recent study showed enhancement of immune function when lab animals were fed killed probiotics. It seems that there is something about probiotics that are protective even if they are not active.

Probiotics and Anemia

If you are one of the people who have been told they are anemic and who take iron without much benefit, the following explanation may make sense.

Iron is absorbed in the upper small intestine, the jejunum. The cells which take in iron can be partially blocked by a number of substances. Phytates from wheat and other grains as well as calcium are two important ones. Oxalates from rhubarb or spinach and phosphates from soft drinks can also have a negative impact on iron absorption.

In order to take iron into the cells, it must be in solution. It goes into solution in an acidic environment - rather like iron being rusted by acid rain. In the intestine, the pancreas pours a very alkaline fluid into the upper small intestine making the whole contents alkaline because the digestive enzymes work best in an alkaline state. This creates a problem for mineral absorption. That's where probiotics come in.

Acidophilus is the dominant probiotic in the small intestine. In health, it thrives on the mucus layer where it creates an acidic microenvironment which makes iron and other minerals more absorbable. I have seen many examples if people who, when they eliminate wheat, have an improvement in their iron levels.


Which Probiotic Works Best?

No one is absolutely sure of the answer. For years I had advised the use of L. Acidophilus DDS strain and have were pleased with the results. Recent medical trials have been done with L. acidophilus GG and L. acidophillus CL 1285 with marked benefits being shown. It may be that these strains are better. Certainly, both are heat sensitive and should be purchased either from the refrigerated section of a store or purchased from a company which keeps them fresh and ships them quickly to you.

Bifidobacterium bifidus, is the dominant strain in the lower intestine where it plays an important role. It feed primarily on dietary fibres which are soluble - those found in the husks of grains, fruit and vegetables. Bifidus takes this fibre, digests it and produces butyrates. These compounds, in turn, are absorbed by the cells of the colon which uses the butyrate to help with peristalsis - the natural rhythmic contraction of the bowel which when we are healthy makes for smooth, easy bowel movements.

Saccharomyces boulardii

This highly effective supplement is actually a live yeast. It differs from harmful yeasts in that it takes an active role in protecting the intestine without taking up permanent residence. In this role it is perfect for use when you take an antibiotic. Antibiotics kill bacteria but, because they are created from yeast like substances, they cannot kill Saccharomyces. So when you take Saccharomyces during the course of the antibiotic (and you can take them at the same time), you help to prevent the growth of harmful yeasts like Candida and harmful bacteria like C. dificile.

After you finish the antibiotic you should take probiotic bacteria like acidophilus and bifidus for a time to re-establish healthy bowel bacteria. This advice applies to people of all ages except those with severe inflammatory bowel disease or suppressed immune function when consultation with your physician is important. Saccharomyces is available in most health food stores, made by different companies, and in almost all pharmacies as Florastor™

Probiotics and Infants

I think that it is important to help the digestion and immune system of newborns with a strain of probiotic adapted for their intestine. Bifidobacterium infantis is the strain which is easily and safely taken by infants whether breast or bottle fed.

I generally advise mothers of newborns to keep a small amount of Bifidus powder in a saucer in the area where they generally feed the infant and at every feeding moisten their finger with a little milk or their own saliva and dip their finger in the powder and put it in the infant's mouth.

Infants who receive this blessing generally have fewer episodes of colic and fewer diaper rashes, usually related to Candida overgrowth.

Moms who give their infants Bifidobacteria infantis have, in my experience, the benefit of happier children and less of a chance of getting mastitis. This painful and dangerous condition is, in my experience, usually caused by infants getting Candida growing in their mouth and transmitting it to the nipple which then cracks, becomes inflamed, and allows bacteria to enter.

Generally it is best to transition infants from Bifidus to the adult strains of acidophilus and bifidus when they begin to eat adult foods - at about six months.

There have been recent reports of newborn infants who are either very premature or immunocompromised and who received probiotics and became ill. I believe these are special circumstances and that it is generally a good idea and quite safe to give newborns Bifidobacterium infantis however if you have concerns about this approach, please check with your physician.

Caesarian Section and Problems with Later Immunity

It turns out that infants delivered by section have a higher rate of allergies and asthma, celiac disease, obesity, and diabetes than infants delivered vaginally.

As part of a larger study, researchers in the Canadian Healthy Infant Longitudinal Development (CHILD) study examined the stools of children delivered by section and found that their gut bacteria were missing several beneficial bacteria ( Bacteroides and Escherichia-Shigella). Further, the gut of formula fed infants were more likely to contain harmful bacteria (Clostridium dificile), a leading cause of severe diarrhoea. Thus, attempting to increase the number of children born naturally and promoting breast feeding seems both health promoting and sensible.

Please see the section on Infant Colic for more information on this aspect of probiotics.

When to Take Probiotics?

Clinicians have differing opinions about when to take probiotics. I don't think it makes much difference. In general, probiotics can withstand the acid environment of the stomach so with meals is OK. Between meals the acid level is lower so perhaps there is an argument in favor of this timing. But it is better to take them than to forget.

Antibiotics and Probiotics

antibiotics kill good bacteriaAntibiotics (in greek = against life) generally kill all, or most of, the beneficial bacteria in the intestine.

This illustration demonstrates the situation in which antibiotics have largely killed off the probiotic bacteria (in green). The tips of the villi are exposed - a situation created by using NSAIDS which decrease mucus production. This leaves the intestine susceptible to invasion by yeasts and can lead to a condition called leaky gut.

During a course of antibiotics and for an extended period afterward it is important to protect the intestine by taking probiotics . Don't take the probiotics with the antibiotic - they just get killed. Take them in between.

An alternate approach which makes sense particularly if you have had a bad Candida overgrowth after having previously taken an antibiotic, is to take a protective supplement in the form of yeast - Saccharomyces boulardii. Because it is a yeast, it is not killed by the antibiotic. In the intestine, it displaces Candidaand other harmful bacteria. Saccharomyces has the benefit of not taking permanent root in the intestine. By contrast, we want probiotics like acidophilus and bifidus to be permanent residents.

Children who need antibiotics

Recent research has shown that, for children who take antibiotics, the rate of developing diarrhoea is significantly reduced by the addition of one of two types of probiotics - Lactobacillus rhamnosus GG which is a probiotic bacterium and Saccharomyces boulardii, a probiotic yeast.

Clostridium dificile is a bacterium which can be deadly in debilitated people and can otherwise be quite harmful. It can cause a fever, severe diarrhea, cramping and abdominal pain. It frequently occurs in hospitalized patients who receive antibiotics, Recent studies have demonstrated that pre treating patients with Saccharomyces reduces the likelihood of them getting C. Dificile. If they do contract C. dificile, taking Saccharomyces speeds the healing which is usually treated with oral metronidazole (a form of antibiotic). After several days, or up to one or two weeks, of taking Saccharomyces, you should return to taking acidophilus and bifidus, which need to be continued for weeks and perhaps longer.


These supplements are taken from food sources and are often found in products which include them with the claim that they will improve survival of the probiotic in the gut. These products are mostly taken from vegetable sources and are soluble fibre. Jerusalem artichoke fibre is often included as it is thought to promote survival of Bifidus in the colon. Certain harmful bacteria, Klebsiella sp. can also use these compounds for their own growth so some experts advise caution with their overuse.

Maintaining our intestinal probiotics may take a conscious effort. Cutting down in the refined sugars, alcohol and refined grains helps. Drinking non-chlorinated water is also of benefit. If you are in intestinal trouble, please turn to the Candida diet. Please also read the section on digestive immunity.