Gut Flora And Antibiotics:

The Missing Nutrition Link

If you want health, you'd best learn to let your gut flora thrive, which is no easy thing in a society that often thinks of bacteria as microscopic pests which should be wiped out with whatever weapons we can bring to bear.

Human health is not just the product of eating right and exercising the body because the proper function of our own flesh is not the only element in play.

We live in symbiosis with what has been deemed a kind of forgotten organ (1) - the 100 trillion microorganisms living in our intestines. This group, a diverse mix of an estimated 1,000 different species of bacteria, (along with a number of fungi and protozoa which researchers have barely begun to understand), carry out a number of metabolic function which our bodies cannot manage on their own, or carry out only at a greatly reduced capacity.

Although this "organ" may be unknown to the general population, nutritional and medical research in recent decades has continued to point out its staggering contributions to our health.

In this article we'll be examining why gut flora matters, how modern medicine, infrastructure, and sterile living have left many of us with damaged colonies of bacteria no longer capable of producing the full range of benefits we need to thrive, and what we can do to get our gut flora back on track.


The Power Of Mutualistic Symbiosis


Gut Flora Long


Our relationship with our gut flora is best described as mutualistic symbiosis, or just mutualism for short (2).

We do not have a parasitic relationship (with the parasite damaging the host), nor a commensal one (where we merely coexist).

We are partners, with each group thriving at a higher level because of the other. To the bacteria we give our waste products and a home, and in return they do a lot of unglamorous tasks which allow us to live.

While it appears that humans will not die without gut flora (3), our health will certainly degrade without them.

Our bacteria have a hand in everything from nutrient production and energy absorption to our likelihood of becoming obese or developing diabetes.

This leaves us in a precarious position because many of our medical treatments and hygiene safeguards revolve around what amounts of carpet bombing the bacteria that live inside and around us with broad-spectrum antibiotics, other medications, and a host of chemicals. In many cases, these measures end up culling beneficial bacteria and allowing harmful antibiotic-resistant strains to become dominant. In such situations, the bacteria inside of us becomes a danger.

These imbalances are not something that can be repaired overnight, and the long-term consequences may leave us stripped of essential nutrients, regardless of how great our diet is.

Remember that with 100 trillion microorganisms inside of us but only 10 trillion cells making up our body, we are literally more bacteria than we are human. Doing anything that drastically affects our bacteria is likely to come back to haunt us.


Humans Vs Antibiotics


Gut Flora CandidiaIt doesn't take much to mess up our gut flora and open the path for colonization by damaging bacteria.

After a single treatment of antibiotics, large-scale changes begin to show up in the bacteria present in our stools, and the pathogen Clostridium difficile, which leads to diarrhea and colitis, starts showing up (6).

The diversity of species in our gut flora is widely reduced by a single dose of antibiotics, with roughly a third of the species affected. Although many of the affected types eventually return on their own, six months after one study several species had yet to reappear, which may indicate that some of these changes are permanent without outside intervention (7).


Absorbing Energy And Obesity

Our bodies are best at absorbing the simple sugars found in fruit, but quite a bit of potential fuel would be discarded if we had to rely on our own resources alone. Luckily, our gut flora produces a range of enzymes capable of breaking down long-chain carbohydrates such as starchy polysaccharides, fiber, oligosaccharides, and some of the sugars which did not get absorbed by the body during the initial digestion phase (2).

In one fascinating study, rats who had been kept in a sterilized environment with disabled gut flora had to eat 30 percent more calories than the control group just to maintain the same body weight (2), which would seem to indicate that much of our energy comes from the work of our gut flora.

Occasionally you'll meet a very sick person who loses weight despite taking in far more calories than they should require. Others are not in such dire straights, but struggle to eat the required amounts to not be scrawny.

Although metabolic rates differ and some people have problems with their physical digestive system, it's likely that many of these people have damaged colonies of gut flora living inside of them.

However, it also works the other way. When we eat poorly, not only do we generally take in more calories and gain fat that way, but we promote the establishment of several types of bacteria which extract more calories from our food than we otherwise would.

Several studies on mice have shown that you can get mice to start putting on body fat just by switching their gut flora from, "thin" bacteria to "fat" bacteria (10).

So how do you establish the "thin" gut flora? Well a group of Austrian researchers found that vegetarians seem to have the thin gut flora in place, while meat eaters do not. What does the difference amount to? The researchers estimate the gut flora in the meat eaters was extracting 2 percent more calories from their food than the vegetarians, which isn't a lot, but over the course of a year that might add up to 3-7 pounds of extra body fat, depending on intake (11).


The "Missing" Vegan Nutrients


One of the claims you'll periodically hear about the nutrients available on a raw food vegan diet is that humans cannot get critical vitamins usually sourced from animal foods.

Most commonly we'll hear about the vitamins B12 and K2.

Gut Flora PearAfter someone has failed to thrive as a vegan or raw foodists you'll often see successful foodists poo poo their complaints about nutrient deficiency, saying that the real issue was a failure to follow, "the program," closely enough.

While this may be a valid complaint in some situations, the knee-jerk defensiveness and blame the failed dieters face is not going to help anyone. If you've got teeth degradation, for instance, the most common cause is poor eating and dental hygiene habits, which have hurt a lot of raw foodists. But nutritional deficiency can certainly play a roll, and it's an issue we should not ignore.

If we cannot get critical nutrients from our food nor produce them internally our health is probably going to suffer sooner or later, and to take no steps nor monitor the situation is a recipe for disaster.

Because of this, and despite the fact that nutrient supplements have a well-established history of damaging health, B12 and K2 are the only two vitamins I consider recommending to my coaching clients if they're having certain types of problems, and my reasoning has nothing to do with the lack of animal foods in their diet.


The Bacteria Disconnect


Saying that a healthy raw food diet and good lifestyle cannot supply us with the nutrients we need is odd, because there are long-term raw foodists and vegans apparently thriving at high levels with no signs of deficiency.

I've been a (non supplementing) vegan since 2004, on a primarily low fat raw food vegan diet since 2005, and on a 100 percent raw food diet since 2007. So far, I haven't seen the slightest indication that I may be deficient in anything. Quite the opposite; I continue to thrive at a much higher level than I ever achieved while eating animal foods.

My blood tests show healthy levels of B12, and although there is no reliable test for K2 levels, my teeth and bones (which require K2 for the body to maintain them) are in excellent shape.

How can this be? Why do some vegans thrive while others experience deficiency? And more interestingly, why do some meat eaters who theoretically take in plenty of B12 and K2 in their diets also have deficiency?

A likely answer is that whether or not our diets are critical for bringing in these nutrients, if we don't have thriving colonies of gut bacteria we're not going to be able to utilize them properly, or produce what we need to make up for any dietary lack.


Primate B12 Vs Antibiotics


Some of the most interesting and telling vitamin B12 studies I've seen have been done on chimps and baboons. These species share a similar ancestral diet and digestive system with us, and there's a fair chance that our nutrient requirements are similar.

Researchers have been unable to induce B12 deficiency in these primates by feeding them a purified diet that contains absolutely no B12. This is fascinating, because we are commonly urged to get our B12 from food or oral supplements. Yet all that's needed to lower primate B12 levels dramatically is to inject them with ampicillin and other antibiotics, which, it would be assumed, destroy the gut flora which cranks out their B12 supply (4, 5).

Some active forms of B12 are produced by members of the bacteria genera Klebsiella and Pseudomonas, however it's likely that there are others as well (20).

Doing a similar study on humans outside of a controlled lab environment wouldn't be easy, but I think it's likely that the average person's history of antibiotic use has affected their ability to absorb or utilize B12.


Vitamin K2 And Antibiotics


We do not need to eat animal products to get sufficient Vitamin K2.

The bacteria we host in our intestines produce it (22, 23), and we can absorb that K2 for use in the body (24).

Unfortunatley, that's only the case if we have healthy intestinal flora, and since antibiotics reduce vitamin K2 production by as much as 74 percent (21), it's fair to say that many of us are no longer capable of meeting our own requirements.


Protecting Your Gut Flora


It's far easier to maintain healthy gut flora than to rebuild from scratch. Here are some steps you can take to keeps yours functioning properly.


Eat a Low Fat Diet.

Putting mice on a high-fat diet lowers the amount of bifidobacteria group bacteria -a dominant member of healthy intestinal communities which are associated with good health - inside of them (12).

Sticking with a low fat, high carb raw food diet will ensure that the bacteria inside of you are properly fueled and supported.

These Books Will Help You Get Started:

Raw Food Weight Loss And Vitality 3D Cover

Lose weight, regain the energy that is your birthright, and feel fantastic when you start eating the raw fruits and vegetables that are our natural diet.

The book explains what to eat, why, and answers the many questions you'll likely have when you're starting off

Check Out Raw Food Weight Loss And Vitality!

Index Savory Raw Dressings Cover
Sinfully delicious raw dressings can spice up your salad every night of the week. Don't worry, they're also low fat and incredibly healthy.

Find out how to create amazing salad dressings and sauces from scratch.

Check out Savory Raw Dressings and Sauces!


Stay Away From Processed Foods


Human intestinal bacteria goes through a major flora shift after having the diet feeding them go downhill.

After originally being fed low-fat plant-based diets, half the mice in one study whose intestines were colonized with human gut flora were switched to a junk food diet that was high in processed fats and sugars. Within less than a day their flora had shifted significantly to favor obesity-promoting microbes (19).


Don't Drink Treated Tap Water

Many municipalities treat their tap water with chlorine and other disinfectants because they can kill a wide variety of bacteria effectively (13).

Although the matter has not been thoroughly studied, it's assumed that chlorine-treated water goes on killing bacteria as it moves through our bodies, including the beneficial bacteria of our gut flora.

If you get your drinking water from a well, stream, or rain-water collector this isn't an issue.

If you get treated tap water, than distilling it is a good idea. There are numerous models on the market in all price ranges. I've found this cheap one to be quite effective, and it's still running after four years of regular use.


Avoid Antibiotics And Other Drugs Like The Plague

As pointed out in this article, just a single dose of antibiotics can have a tremendous impact on your gut flora, and without outside intervention things may never entirely return to normal.

There are some situations in which I'd consider taking antibiotics and other drugs known to effect bacteria- just not many of them.

Gut Flora BacteriaOther than some Novocaine (procaine) injected when I was getting my wisdom teeth removed, I haven't taken any drugs for about a decade. In my youth, my parents were not big on taking us to the doctor unless we were in serious pain or trouble, which wasn't common.

I think my avoidance of drugs has done me a lot of good, but it isn't an easy thing to do if you go to doctors regularly. Most practitioners will tell you to take antibiotics in far more situations than actually require them because they'd rather err on the side of caution. Unfortunately, their caution can do serious damage to your intestinal bacteria.

I'm a physically active guy prone to doing risky things, and have gotten my fair share of injuries. In the last two years I've gotten large gashes on my chin and foot that required stitches, and in both cases I was told to take antibiotics because the risk of infection was high. I refused and and my wounds healed just fine.

I can do this confidently because I live a healthy lifestyle and eat a good raw diet.

Sick, run-down people are more likely to have immune systems which can be overrun by bacteria.

It comes down how you want to live; I'd rather thrive at a high enough level that I don't require help to carry out basic bodily functions like fighting off infections.


Avoid Foods And Drinks Which Kill Bacteria

There are a wide variety of foods and beverages which either contain antibiotics themselves or which simply have an antibiotic effect.


  • Alcoholic beverages (remember that alcohol is a frequently used topically as an antiseptic ) kill bacteria.


  • The vast majority of animal products available in supermarkets contain second-hand antibiotics because the animals they're sourced from were injected with them. This is sometimes not the case with animals raised on small farms using organic methods.


  • Both raw garlic and onions are considered to have antibiotic properties, and can kill a wide variety of living organisms.


Avoid Cesarean Births, and Breast feed Newborns

If you wanted to give your child the worst possible start in life when it comes to gut health, you'd give birth to them via cesarean section and then bottle feed them with formula.

One of the last formative gifts a mother gives to her child prior to birth is the bacteria inside of her. A baby's intestines are mostly sterile in the womb, and primary colonization actually occur's during vaginal birth.

Children born via cesarean section don't get colonized by their mother's bacteria, and even six months later they haven't caught up to children born via vaginal births (14). It's unknown if infants will ever achieve a more balanced colonization without outside intervention.

In recent decades cesarean births have been used not out of medical necessity, but preference, which just isn't a good idea.

Breast feeding can help recolonization, but this may not be enough to make up for a cesarean delivery (15).


Rebuilding Your Gut Flora


If you have reason to believe you have a significantly reduced diversity of beneficial bacterial species or a profusion of harmful ones, I suggest you have a stool profile test done. When you know what's in you, you'll have a better idea about if and how you should act.

Probiotics Aren't Enough

Gut Flora Pills

The standard recommendation after antibiotic use is to to take probiotic pills, which are generally loaded with Lactobacillus or Bifidobacterium species. These will help you digest milk and fight off diarrhea and many food-borne infections, and are probably a good place to start for people having minor problems. They will not, however, go far enough for people who are in serious trouble.

A survey of the bacterial species in an average gut shows that Lactobacillus and Bifidobacterium do not even appear among the 57 most abundant species (16).

Since people with IBS, colitis, and Crohn's have 25 percent less bacteria diversity than healthy people (because a few pathogenic species are running rampant), even if the probiotics could get the eight-or-so species these usually contain established, you'd still be about 242 species short of average (16).

The Icky Option

Faced with patients who could not get healthy colonies of flora established or shake harmful ones, doctors have discovered a fascinating, if somewhat disgusting method of establishing healthy species in our guts.

In one case (17), a gastroenterologist was treating a patient with an infection of Clostridium difficile. The patient was crippled by constant diarrhea and wearing diapers. A variety of antibiotics failed to kill off the harmful bacteria, and the patient was wasting away.

The doctor collected a stool sample full of her husband's healthy bacteria and gave it to the patient. Amazingly, two weeks later the patient was recovered, and healthy bacteria had completely taken over her gut.

Unfortunately, this technique is still on the medical fringe, and you're not going to find it prescribed by your average doctor.

I am not experienced in this procedure by any means, and there are possible dangers, but this technique could theoretically be reproduced on your own if you swallow a tiny stool sample from someone with healthy gut flora and then drink tons of water to help wash the bacteria through the stomach and its acid barrier. Others have suggested inserting it into the rectum.

As always, ask your doctor if this is a good idea for you.

The Rotting Food Option

I do not suggest healthy people consume fermented food. Fresh food is simply superior. However, one benefit of a food rotting is that it's being dismantled by bacteria, some of which has the potential to recolonize a damaged gut environment with beneficial species.

Take Kimchi (fermented cabbage). In the early stages of pickling you start seeing Leuconostoc mesenteroides and Lactobacillus plantarum show up. As the kimchi ages, the bacterial environment diversifies (18).

If I felt I had damaged my gut flora, I might consider eating some fermented food and seeing if there was a benefit.


Gut Flora: Keeping Your Head On Straight


A number of benefits can be gained by having healthy gut flora, but it's important to not lose sight of the forest for the trees.

Yes, some people have had success fighting intestinal disorders and other health problems by introducing beneficial bacteria, but it's something of a chicken and egg scenario.

I cured my colitis by improving my diet, not by doing anything with my gut flora situation. However, my gut flora has likely changed significantly as a result. Losing weight is, at the end of the day, about what we eat and how we move, not what's in our intestines.

Before you worry yourself to death over gut flora, start eating in a way that promotes good health, a low fat raw vegan diet.

Get off to the right start with Raw Food Weight Loss And Vitality, a diet that will get your gut flora on the right track.


Gut Flora And Antibiotics: Sources

You can find the sources for this article here.

Receive the free Raw Food Health Journal

Keep up to date with new articles from this site.

Search Raw-Food-Health.net

Copyright © raw-food-health.net | All rights reserved.
Click here for the mandatory privacy policy and terms of use, which you agree to by using this site.

Raw Food Health Site Build It