Much new research is now emerging on the importance of bacteria – intestinal bacteria, to be more exact. These are commonly referred to as probiotics, and are the antithesis to antibiotics, both of which I’ll discuss below.

These microscopic critters are also known as your microbiome.

Around 100 trillion of these beneficial bacterial cells populate your body, particularly your intestines and other parts of your digestive system. In fact, 90 percent of the genetic material in your body is not yours, but rather that of bacteria, fungi, viruses and other microorganisms that compose your microflora.

We’re now discovering that the composition of this microflora has a profoundimpact on your health. For example, we now know that your intestinal bacteria influence your:

  • Genetic expression
  • Immune system
  • Brain development, mental health, and memory
  • Weight, and
  • Risk of numerous chronic and acute diseases, from diabetes to cancer

Certain Gut Microbes Affect Absorption of Dietary Fats

Most recently, a research team that includes Carnegie’s Steve Farber and Juliana Carten has revealed that certain gut microbes increase the absorption of dietary fats.1 According to the authors:

“Diet-induced alterations in microbiota composition might influence fat absorption, providing mechanistic insight into how microbiota-diet interactions regulate host energy balance.”

Medical News Today2 recently reported on the findings, stating:

“Previous studies showed gut microbes aid in the breakdown of complex carbohydrates, but their role in dietary fat metabolism remained a mystery, until now… ‘This study is the first to demonstrate that microbes can promote the absorption of dietary fats in the intestine and their subsequent metabolism in the body,’ said senior study author John Rawls of the University of North Carolina. ‘The results underscore the complex relationship between microbes, diet and host physiology.'”

The bacteria identified as instrumental in increasing fat absorption are called Firmicutes, which, incidentally, have previously been linked to obesity, as they’re found in greater numbers in the guts of obese subjects. The researchers also found that the abundance of Firmicutes was influenced by diet. This adds weight to previous research postulating that gut bacteria can increase your body’s ability to absorb fat, and therefore extract more calories from your food compared to others who have a different composition of bacteria in their intestines – even when consuming the same amount of food.

New Research Suggests Bacteria are Social Microorganisms

Three years ago, I posted a TED video featuring Bonnie Bassler, in which she discusses how bacteria “talk” to each other using a chemical language that lets them coordinate defense and mount attacks.

Now, more recent research published in the journal Science3 reveals that bacteria may have “social structures similar to plants and animals.” According to the authors:

“In animals and plants, social structure can reduce conflict within populations and bias aggression toward competing populations; however, for bacteria in the wild it remains unknown whether such population-level organization exists. Here, we show that environmental bacteria are organized into socially cohesive units in which antagonism occurs between, rather than within, ecologically defined populations.

By screening approximately 35,000 possible mutual interactions among Vibrionaceae isolates from the ocean, we show that genotypic clusters known to have cohesive habitat association also act as units in terms of antibiotic production and resistance.

Genetic analyses show that within populations, broad-range antibiotics are produced by few genotypes, whereas all others are resistant, suggesting cooperation between conspecifics. Natural antibiotics may thus mediate competition between populations rather than solely increase the success of individuals.”

What this means is that certain bacteria have the ability to produce chemical compounds that inhibit the growth of other bacteria, while not harming their own kind or “close relatives.” These chemical compounds or natural antibiotics act as a type of chemical warfare, allowing the bacteria in question to gain a competitive edge by killing off the competition. Meanwhile, other “allies” are spared, as they are resistant to the antibiotic chemicals produced.

As reported by Medical News Today:4

“‘The research has the potential to bridge gaps in our understanding of the relationships between plants and humans and their non-disease- and disease-causing bacterial flora,’ said Robert Fleischmann, a program director in the Division of Biological Infrastructure for the National Science Foundation.

‘We use antibiotics to kill pathogenic microbes, which cause harm to humans and animals,’ said Polz. ‘As an unfortunate side effect, this has lead to the widespread buildup of resistance, particularly in hospitals where pathogens and humans encounter each other often.’

In addition, the results help scientists make sense of why closely related bacteria are so diverse in their gene content. Part of the answer, they say, is that the diversity allows the bacteria to play different social roles. Social differentiation, for example, could mitigate the negative effects of two species competing for the same limiting resource – food or habitat, for instance – and generate population level behavior that emerges from the interaction between close relatives.”

Beware of Fluoridated Antibiotics that Can Ruin Your Gut Flora and Your Health

Your lifestyle can and does influence your gut flora on a daily basis. All of these common exposures can wreak havoc on the makeup of bacteria in your gut, but researchers are now increasingly looking at the cascading ill effects of antibiotic drugs in particular. For example, your gut bacteria are extremely sensitive to:

  • Antibiotics
  • Chlorinated water
  • Antibacterial soap
  • Agricultural chemicals
  • Pollution

Antibiotics are severely overused – not just in medicine, but also in food production. In fact, about 80 percent of all the antibiotics produced are used in agriculture – not only to fight infection, but to promote unhealthy (though profitable) weight gain in the animals. Hence, if you want to avoid overexposure to antibiotics, it’s also crucial to avoid conventionally-raised meats.

That said, certain antibiotics prescribed in medicine are so harmful they probably shouldn’t be used at all. Medications such as Avelox, Cipro, and Levaquin have been named in over 2,000 drug injury lawsuits.5

These are all fluoroquinolones, a class of fluoridated antibiotics associated with a number of serious side effects, such as potentially blinding retinal detachment, kidney failure, and permanent tendon damage. Fluoroquinolones do carry a black box warning for tendonitis, ruptured tendons, and its potentially detrimental effect on neuromuscular activity, but many patients simply do not read the warning labels before taking the drug. Other serious injuries linked to fluoroquinolones include:


Learn More about the Dangers of Fluoroquinolone Antibiotics

Shockingly, despite all these risks, fluoroquinolones are one of the most commonly prescribed classes of antibiotics in the world. John Fratti, who was hired by the FDA in a part-time position as an FDA Patient Representative for drug safety, is on a quest to raise awareness on the dangers of fluoroguinolone toxicity. He filed a Freedom of Information (FOI) request with the FDA on two of the top fluoroquinolones, Levaquin and Cipro, and learned that they are associated with over 2,500 deaths.

A non-profit organization called Quinolone Vigilance Foundation, established by Mr. David Melvin, was created to spread awareness of the dangers associated with this class of drugs, and the Foundation’s website contains both information and support for those injured by these drugs. Fortunately, fluoroquinolones have started getting some well-deserved media attention as of late.

According to a recent article in The New York Times:6

“A half-dozen fluoroquinolones have been taken off the market because of unjustifiable risks of adverse effects. Those that remain are undeniably important drugs, when used appropriately. But doctors at the Centers for Disease Control and Prevention have expressed concern that too often fluoroquinolones are prescribed unnecessarily as a ‘one size fits all’ remedy without considering their suitability for different patients.

Experts caution against giving these drugs to certain patients who face higher than average risks of bad reactions – children under age 18, adults over 60, and pregnant and nursing women – unless there is no effective alternative. The risk of adverse effects is also higher among people with liver disease and those taking corticosteroids or nonsteroidal anti-inflammatory drugs.

When an antibiotic is prescribed, it is wise to ask what the drug is and whether it is necessary, what side effects to be alert for, whether there are effective alternatives, when to expect the diagnosed condition to resolve, and when to call if something unexpected happens or recovery seems delayed.”

Last year, PBS NewsHour7 aired a segment highlighting the dangers of fluoroquinolones. Fratti, who is himself a victim of fluoroquinolone toxicity, was interviewed. He was prescribed Levaquin a few years ago for a minor bacterial infection. The drug caused nerve damage, tendon damage and damage to his central nervous system.

Watch Certain Antibiotics Spur Widening Reports of Severe Side Effects on PBS. See more from PBS NewsHour.

How to Optimize Your Gut Flora

The good news is that positively influencing the bacteria growing in your body is relatively easy. Aside from reserving antibiotics for serious cases of infection only, one of the most important steps you can take is to stop consuming sugary foods. When you eat a healthy diet that is low in sugars and processed foods, one of the major benefits is that it causes the good bacteria in your gut to flourish and build up a major defense against the bad bacteria getting a foothold in your body in the first place.

This is one of the many reasons I highly recommend reducing, with the plan of eliminating, sugars and most grains from your diet. Following my recently updated nutrition plan will help you optimize your diet in a systematic step-by-step fashion. A healthy diet is the ideal way to maintain a healthy gut, and regularly consuming traditionally fermented or cultured foods is the easiest way to ensure optimal gut flora. Healthy options include:


Just make sure to steer clear of pasteurized versions, as pasteurization will destroy many of the naturally-occurring probiotics. For example, most of the “probiotic” yogurts you find in every grocery store these days are NOT recommended. Since they’re pasteurized, they will be associated with all of the problems of pasteurized milk products instead. They also typically contain added sugars, high fructose corn syrup, dyes, and/or artificial sweeteners; all of which are detrimental to your health.

Consuming traditionally fermented foods will also provide you with the following added benefits:

  • Important nutrients: Some fermented foods are excellent sources of essential nutrients such as vitamin K2, which is important for preventing arterial plaque buildup and heart disease. Cheese curd, for example, is an excellent source of both probiotics and vitamin K2. You can also obtain all the K2 you’ll need (about 200 micrograms) by eating 15 grams, or half an ounce, of natto daily. They are also a potent producer of many B vitamins
  • Optimizing your immune system: Probiotics have been shown to modulate immune responses via your gut’s mucosal immune system, and have anti-inflammatory potential. Eighty percent of your immune system is located in your digestive system, making a healthy gut a major focal point if you want to maintain optimal health, as a robust immune system is your number one defense system against ALL disease
  • Detoxification: Fermented foods are some of the best chelators available. The beneficial bacteria in these foods are very potent detoxifiers, capable of drawing out a wide range of toxins and heavy metals
  • Cost effective: Fermented foods can contain 100 times more probiotics than a supplement, so just adding a small amount of fermented foods to each meal will give you the biggest bang for your buck
  • Natural variety of microflora: As long as you vary the fermented and cultured foods you eat, you’ll get a much wider variety of beneficial bacteria than you could ever get from a supplement

When you first start out, you’ll want to start small, adding as little as half a tablespoon of fermented vegetables to each meal, and gradually work your way up to about a quarter to half a cup (2 to 4 oz) of fermented vegetables or other cultured food with one to three meals per day. Since cultured foods are efficient detoxifiers, you may experience detox symptoms, or a “healing crisis,” if you introduce too many at once.

Learn to Make Your Own Fermented Vegetables

Fermented vegetables are easy to make on your own. It’s also the most cost-effective way to get high amounts of healthful probiotics in your diet. To learn how, review the following interview with Caroline Barringer, a Nutritional Therapy Practitioner (NTP) and an expert in the preparation of the foods prescribed in Dr. Natasha Campbell-McBride’s Gut and Psychology Syndrome (GAPS) Nutritional Program. In addition to the wealth of information shared in this interview, I highly recommend getting the book Gut and Psychology Syndrome, which provides all the necessary details for Dr. McBride’s GAPS protocol.

Although you can use the native bacteria on cabbage and other vegetables, it is typically easier to get consistent results by using a starter culture. Caroline prepares hundreds of quarts of fermented vegetables a week and has found that she gets great results by using three to four high quality probiotic capsules to jump start the fermentation process.

Sources and References

1. Cell Host & Microbe 2012 Sep 13;12(3):277-88

2. Medical News Today September 14, 2012

3. Science 2012 Sep 7;337(6099):1228-31.

4. Medical News Today September 11, 2012

5. Drug Injury Lawyers blog September 13, 2012

6. New York Times September 10, 2012

7. PBS NewsHour June 16, 2011