Bacteria in your body

The result of taking antibiotics

Helicobacter pylori - our dominant microbe now near-extinct

Sources of good probiotic bacteria

List of good probiotic bacteria and yeasts


Bacteria in your body

Up to 2.5% of your body's weight consists of bacteria. Bacteria have lived in and on all animals since life evolved. About 1000 different strains of bacteria, yeasts, protozoa and other microorganisms weighing up to 2 kg live in your body (7). Most of them are in your digestive tract, but they are also in your nose, throat, ears, eyes, skin, genitals, urethra and throughout your body. It is essential to have good bacteria on your throat, urethra, nasal passages, vaginal walls etc. (9) They play an critical part in your immune system, and protect you from invading pathogenic bacteria, fungi and viruses. Bacteria are resident on all your membranes, protecting you against infection. Bacteria play an essential role in your digestion - without them, you cannot break down many foods and absorb the nutrients. Bacteria also assist in the production of some vitamins(B12, K, etc). The bacteria, fungi, protozoa and other microflora making up your microbiome are essential for life and good health, and a healthy balance (symbiosis) is built up over your lifetime (7).

Babies get their founding bacterial population from their mothers while passing through the vagina at birth. Babies born by caesarean section miss out on this important dose of bacteria. Mothers milk from breast feeding contains a wide variety of bacteria that the infant will not get when fed pasteurised formula milk. Breast feeding builds up a wide range of healthy gut bacteria in the infant. Research (10) shows that breast fed infants have a significantly different intestinal microbial biome from those which are bottle fed, and that these bacteria lock in a strengthened immune system for their whole life. (10)
In the first few years of their life, infants add to this bacterial population by crawling around and putting all sorts of things in their mouths. The presence of animals (pets or farm animals) and siblings is also important. This is a once-only opportunity to build up these bacteria, before the stomach acid gets too strong and the immune system becomes a powerful bacterial barrier. New research (8) confirms that dirty kids are healthy kids.

The result of taking antibiotics

By the time the average child in the USA and other developed countries is 18 years old, he or she has received 10-20 courses of antibiotics (1). In a few cases, the use of these antibiotics has been life-saving or has stopped a serious infection. However, the assumption that antibiotics are generally safe has:

  • Encouraged the overuse of antibiotics. They are routinely prescribed for a wide variety of ailments, regardless of whether they are necessary and effective. They are added to stockfeeds, and given to agricultural animals to encourage growth.
  • Led to widespread bacterial resistance to commonly used antibiotics.
  • Permanently destroyed the protective microflora of most people in the USA and other developed countries (2). Each generation is starting life with a smaller endowment of ancient microbes than the last.
  • Replaced the dominant natural bacteria in our bodies with new antibiotic-resistant or partially resistant organisms.

When you take an antibiotic, you indiscriminately destroy most of the friendly microflora in your body in addition to the target bacteria. There is evidence that the friendly flora that take a lifetime to build up never fully recover. After taking an antibiotic, you are vulnerable to invasion by bacteria, fungi and viruses.

Here are some of the problems that can arise from bacterial imbalance. The level of these diseases have more than doubled in many populations in line with the increased use of antibiotics (2). This list is not complete - I suspect that many more degenerative diseases have a lack of beneficial bacteria, or a bacteria imbalance as their root cause.

Helicobacter pylori - our dominant microbe now near-extinct

A century ago, Helicobacter pylori was the dominant microbe in the stomachs of almost all people (it is one of few bacteria that can actually live in the acidity of the stomach). By the year 2000, fewer than 6% of children in the USA, Sweden and Germany were carrying it. This is almost certainly because of antibiotics - for example, a single course of amoxicillin or a macrolide (used to treat ear infections in children) eradicates h. pylori in up to half of all cases.

H. pylori is associated with gastritis, gastric ulcers, duodenal ulcers and stomach cancer. However, most people who harbour this bacterium have no symptoms. It is more likely that such problems have developed because of a bacterial imbalance allowing the h. pylori to get out of control.

Having some of the benign strains of h. pylori in your stomach and colon is likely to be highly beneficial (7). Several significant benefits have already been identified from having h. pylori in your stomach. It affects the regulation of two hormones, ghrelin and leptin produced in the stomach and involved in hunger, sateity (feeling full) and energy balance. With the disappearance of h. pylori from most people's digestive tracts, there has been an increase in gastroesophageal reflux and related diseases such as Barrett's oesophagus and oesophageal cancer.

Several large studies have found that people without h. pylori are more likely to develop asthma, hay fever, and skin allergies in childhood (4,7). Another study showed that infecting the stomachs of mice with h. pylori protected them against asthma (5). Bacterial imbalance may cause the overproduction of fat cells, in preference to the production of muscle and bone cells.

Eventually, some sub-species of h. pylori will be made available as a probiotic supplement. But right now, there is only one way that I can think of, that you can get a dose of this essential but much maligned bacteria: by means of a fecal transplant.

Bacteroides fragilis is another example of a beneficial bacteria that is being wiped out. B. fragilis moderates the immune system and prevents excessive inflammation. The absence of this bacteria is likely responsible for a significant increase in many autoimmune disorders such as Crohn's disease, type I diabetes and multiple sclerosis.

Sources of good probiotic bacteria

My recipe book The Grow Youthful Recipe Book includes the recipes for many live-bacteria probiotic foods. It includes several live-culture foods and drinks, and lots practical advice.

  • Sauerkraut is a rich source of lactic acid and other probiotic bacteria.
  • Milk kefir is by far the best dairy source of a range of bacteria, usually containing at least thirty strains (yogurt usually contains only 1 - 3 strains).
  • Water kefir is a miracle probiotic source, particularly rich in lactobacillus bacteria.
  • Rejuvelac a living drink rich in a variety of bacteria and enzymes.
  • EM (essential microorganisms) discussed in detail in Grow Youthful.
  • Fecal transplant.
  • Fresh-picked fruits and vegetables with their natural blooms. Unsprayed, organic foods fresh from your back garden or an organic farm.
  • Probiotic supplements. Supplements that you buy as powders or capsules are beneficial, but most probiotics only contain two or three different bacteria so they are not usually very effective in re-establishing the full range of micro-organisms in your digestive system. Your gut needs hundreds of different beneficial bacteria to function normally.

NOTE: Store-bought cultured foods are usually pasteurised, which means that all the living bacteria they used to contain have been killed. If you buy any cultured food, it is essential that it is alive. This is why it is much better to make these foods yourself, or buy them direct from someone who has made them with integrity.

List of good probiotic bacteria and yeasts

This list of bacteria and yeasts is only a short example of what can be found in living foods, as opposed to the strictly-bred bacteria in probiotic supplements. Bacteria are not like other living organisms that breed true according to the genetic program that is passed down through successive generations. Instead, bacteria are actually able to morph from one species to another, horizontally transferring their genes through a variety of wonderful biological mechanisms. This means that the this list of bacterial species is just a starting point. The microorganisms can morph and change in response to the environment in which they are living. It is quite possible for one species of Lactobacillus to morph into another, and I would assume it is also possible for lactobacillus to morph into other bacilli. With bacteria it is more or less that case that whatever the environment dictates will spontaneously appear. So whilst probiotics provide a starting point to regaining good health, the condition of your body,(particularly) the food you eat, and the environment that you live in will also have a large affect.

  • bifidobacterium animalis
  • bifidobacterium bifidum
  • bifidobacterium breve ss. breve
  • bifidobacterium infantis ss. infantis
  • bifidobacterium lactis
  • bifidobacterium longum
  • enterococcus faecalis TH 10
  • lactobacillus acidophilus
  • lactobacillus brevis
  • lactobacillus bulgaricus
  • lactobacillus casei ss. casei
  • lactobacillus casei shirota
  • lactobacillus fermentum
  • lactobacillus helveticus ss. jugurti
  • lactobacillus paracasei
  • lactobacillus plantarum
  • lactobacillus rhamnosus
  • lactobacillus salivarius
  • saccharomyes boulardii
  • saccharomyes cerevisae
  • saccharomyes fermentate
  • streptococcus thermophilus


1. Sharland, M. J. Antimicrob. Chemoth. 60 (suppl. 1), i15-i26 (2007).

2. Martin Blaser. Antibiotic overuse: Stop the killing of beneficial bacteria. Nature, 24 August 2011. 476,393-394.

3. Blaser, M. J. & Falkow, S. Nature Rev. Microbiol. 7, 887-894 (2009).

4. Chen. Y. & Blaser, M. J. Arch. Intern. Med. 167, 821-827 (2007).

5. Arnold, I. C. et al. J. Clin. Invest. 121, 3088-3093 (2011).

6. Dominguez-Bello, M. G. et al. Proc. Natl Acad. Sci. USA 107, 11971-11975 (2010).

7. Blaser, Martin J. Who are we? Indigenous microbes and the ecology of human diseases EMBO reports 7 (10): 956-60. doi:10.1038/sj.embor.7400812. PMC 1618379. PMID 17016449.

8. Torsten Olszak, Dingding An, Sebastian Zeissig, Miguel Pinilla Vera, Julia Richter, Andre Franke, Jonathan N. Glickman, Reiner Siebert, Rebecca M. Baron, Dennis L. Kasper, and Richard S. Blumberg. Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function. Science Published online 22 March 2012; DOI:10.1126/science.1219328

9. Shruti Naik, et al. Compartmentalized Control of Skin Immunity by Resident Commensals. Published Online July 26 2012, Science DOI: 10.1126/science.1225152

10. Dennis J. Hartigan-O'Connor, Amir Ardeshir, Nicole R. Narayan, Gema Mendez-Lagares, Ding Lu, Marcus Rauch, Yong Huang, Koen K. A. Van Rompay, Susan V. Lynch. Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems. Science Translational Medicine, 3 September 2014: Vol. 6, Issue 252, p. 252. ra120. DOI: 10.1126/scitranslmed.3008791.

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