We Are Human-Microbe Superorganisms

The microbiome revolution in medicine is beginning to uncover the underappreciated role our healthy gut bacteria play in nutrition and health.

Recently, it has become apparent that our DNA “does not tell the whole story of our individuality and other factors, environmental factors, play an important role in human health and disease,” researchers concluded. We can thank two revolutions in biology for this revelation. First, there was epigenetics, where diet and lifestyle changes have been shown to turn genes on and off. Second was our unfolding understanding of our microbiome—that is, how changes in our gut flora “appear to impact greatly on human biology.”

“Until relatively recently, the colon was viewed as a retention tank for waste,” and water absorption was its big biological function. The problem was it was hard to get in there, and we weren’t able to grow most of the bugs in a lab. As many as 99% of all microbes fail to grow under standard laboratory conditions. How do you study something you can’t study? Well, now we have fancy genetic techniques.

It took 13 years to sequence the DNA of the first bacteria ever. These days, the same feat might only take two hours. What we’ve learned is that we can each be thought of as a super-organism, a kind of “human-

microbe hybrid,” as one researcher called it. We have trillions of bacteria living inside us. One commentator went as far as to say, “We are all bacteria,” which is a provocative way of acknowledging there are more bacterial cells and genes in our own body than there are human cells and genes, and most of those bacteria live in our gut.

All animals and plants appear to establish symbiotic relationships with microorganisms and, in us, our gut flora can be considered like a “forgotten organ.” Studies indicate that the health-promoting effects of our good bacteria include boosting our immune system, improving digestion and absorption, making vitamins, inhibiting the growth of potential pathogens, and keeping us from feeling bloated. But, should bad bacteria take roost, they can release carcinogens, putrefy protein in our gut, produce toxins, mess up our bowel function, and cause infections.

Researchers are still in the process of figuring out which bacteria are which. There are more than a thousand different types of bacteria that take up residence in the human colon. In my video, Microbiome: The Inside Story, I include a diagram from a typical study of gut flora that gives a sense of the complexity. It comes from what happens to be the largest such study done on the elderly and shows that the frailest tend to harbor similar bugs. The study goes on to suggest that it may be the lousy diet in nursing homes that’s causing this shift, which may play a role in ill health as we grow older.

Based on studying what comes out of fraternal versus identical twins, those who eat different habitual diets, and stools from around the world, “[i]t has become evident that diet has a dominant role on the [bacteria in our colon] and that diet-driven changes in it occur within days to weeks,” the research found. Change your diet, change your gut flora.

“The hope of impacting health through diet may be one of the oldest concepts in medicine; however, only in recent years has our understanding of human physiology grown to the point where we can begin to understand how individual dietary components affect specific illnesses,” researchers explain, through our gut bacteria. Milk fat on that piece of pizza, for example, may feed the bacteria that produces the rotten egg gas hydrogen sulfide, and has experimentally been associated with colitis (inflammatory bowel disease). Fiber, on the other hand, feeds our good bacteria and decreases inflammation in the colon. Both choline, which is found in eggs, seafood, and poultry, and carnitine, which is found in red meat, can be turned into trimethylamine oxide and contribute to heart disease and perhaps fatty liver disease. Excess iron may also muck with our good bacteria and contribute to inflammation, as well.


The good news, researchers found, is that “[s]pecific dietary interventions offer exciting potential for nontoxic, physiologic ways to alter [gut microbiology] and metabolism to benefit the natural history of many intestinal and systemic disorders.”

 If you’re interested in more information about friendly flora, I suggest watching the following:

In health,

Michael Greger, M.D.

PS: If you haven’t yet, you can subscribe to my free videos here and watch my live, year-in-review presentations:

Which Vegetables Have the Most Nitrates?

What is the optimal timing and dose of nitrate-containing vegetables? In terms of timing for improving athletic performance, since every person is different, two to three hours before a competition is about as specific as we can get.

What about the best dose? How much borscht do we have to have for breakfast? To date, most studies have used a narrow range of doses so it’s not clear if it’s a matter of more is better or if there’s a ceiling, or threshold amount. A group of researchers decided to find out. They set up folks on an exercise bike and had them cycle furiously until they dropped. The subjects made it about eight minutes after drinking a placebo. After one shot of beetroot juice, which is about a quarter of a cup, they may or may not have gained a few seconds. However, drinking a half-cup gave them about a full extra minute. Drinking even more didn’t seem to offer any additional benefit.

That half-cup or so of beet juice corresponds to 8 “units” of nitrate. So, 4 units didn’t significantly work, and 16 did no better than 8. Thus, 8 units appear to be the sweet spot for improving athletic performance. What about for lowering blood pressure? Again, we see the same thing. Blood pressure may have been helped a little by 4 units, but 8 worked better and about equally well as 16. A 10-point drop in blood pressure, which may not sound like a lot, but that may translate into dropping heart attack risk by 25% and stroke risk by 35%.

But, beet juice is perishable and hard to find. What about V8 juice, which has both beet and spinach juice? It must not have much, though, because you’d have to drink 19 quarts a day to hit the target. That why I have a cooking video on making my own!

Straight beet juice is nitrate-packed, but it’s a processed food. How many actual beets or green leafy vegetables would one have to eat to reach the target of eight units? Well, the British Heart Foundation did the work for you and produced a useful chart that you can see in my “Veg-Table” Dietary Nitrate Scoring Method video at the 2:10 minute mark. They took into account both nitrate concentration and serving size for a range of foods, and arranged all of the foods into three groups: a high nitrate group that’s worth two nitrate units per serving, a medium group that’s worth about a half unit per serving, and a low nitrate group that’s worth one-tenth of a unit per serving. The serving sizes they analyzed are pretty small, though, less than three ounces. (Remember, we’re trying to get up to eight units a day.) So, a typical 15-ounce can of beets would nail the daily eight-unit target, as would a really big salad of greens, both of which are in the high nitrate group. Most people only get about a unit a day, and even vegetarians need to double their vegetable intake, and those eating organic may have to eat even more.

Organic produce may have more vitamin C, iron, magnesium, and phosphorus, but it tends to have fewer nitrates since synthetic nitrogen fertilizers are banned by law from organic agriculture. Eating 15% more organic veggies to get the same nitrate intake is easy, but, for beets, the spread can be larger. On the other hand, organic beets may have more of certain phytonutrients, like the red pigment for which beets are known, which may explain why the organic beet extracts had significantly higher anti-cancer effects in vitro compared to conventional beets.


For more information on why one would want to boost their nitrate consumption, check out these videos: Whole Beets vs. Juice for Improving Athletic Performance, Oxygenating Blood with Nitrate-Rich Vegetables, and Slowing Our Metabolism with Nitrate-Rich Vegetables.

If you really want to take a really deep dive into the background of this fascinating area, see my original 16-part series:

  1. Doping with Beet Juice
  2. Priming the Proton Pump
  3. Don’t Use Antiseptic Mouthwash
  4. Out of the Lab & Onto the Track
  5. Asparagus Pee
  6. Pretty in Pee-nk
  7. Vegetables Rate by Nitrate
  8. Is Bacon Good or Is Spinach Bad?
  9. When Nitrites Go Bad
  10. Hearts Shouldn’t Skip a Beet
  11. Bacon and Botulism
  12. Are Nitrates Pollutants or Nutrients?
  13. Prevention Is Better Than Cured Meat
  14. Carcinogens in the Smell of Frying Bacon
  15. Vitamin C-Enriched Bacon
  16. So Should We Drink Beet Juice or Not?

In health,

Michael Greger, M.D.

PS: If you haven’t yet, you can subscribe to my free videos here and watch my live, year-in-review presentations:

The Risks of Fish Oil Supplements

It’s been a bad few years for fish oil, as I discuss in my video, Omega 3s, Prostate Cancer, and Atrial Fibrillation. Claims were crushed that the long-chain omega 3s in fish oil—EPA/DHA—would stop the progression of heart disease. Then, DHA was associated with increased risk of prostate cancer and “monumentally” failed to treat macular degeneration. This over-the-top rhetoric sounded a little suspicious, and, indeed, the paper was retracted because the author sells some rival supplement he failed to disclose, but he does have a point.

I covered the fish oil failure for heart disease in my Is Fish Oil Just Snake Oil? video. But, what about the increased cancer risk? Men with the highest circulating levels in their blood of the long-chain omega 3 fat DHA were found to be at higher risk for prostate cancer, though a subsequent compilation of all such studies suggested EPA, the other major long-chain omega 3 in fish and fish oil, may be more closely associated with increased cancer risk. Either way, these long-chain omega 3s have been promoted for prevention of heart disease and cancer. We now know, however, that not only does there appear to be no benefit for death, heart attack, or stroke, there may be an elevation in cancer risk. The general recommendations to increase the intake of these fats should consider its potential risks.

How could eating more fish or fish oil increase cancer risk? Well, there are some industrial pollutants, like PCBs, linked to increased prostate cancer risk, and the “primary source of exposure in the general population is believed to be through diet from fish, meat, and dairy products.” If you do a supermarket survey, the PCBs are highest in freshwater fish and lowest in plant-based foods. Vegans have been tested, and they were found to be significantly less polluted than omnivores of the PCB linked to prostate cancer.

However, the prostate cancer study was done in North America where people don’t eat a lot of fish, and indeed, even the group with the highest DHA levels weren’t that high. So, maybe the confounding factor was meat consumption in general, not just fish. Lower meat consumption may be a reason for the lower rates of prostate cancer in the lower DHA group, as the consumption of well-done meat is associated with an increased risk of prostate cancer, and intake should therefore be restricted.

We also used to think omega 3s could protect us from arrhythmias—abnormal heart rhythms, like atrial fibrillation. Millions suffer from the condition, which causes an irregular heartbeat and a higher risk of stroke and death, but fish and fish oil consumption does not appear effective for preventing it or treating it.

Other arrhythmias can be life-threatening and can cause sudden death. Despite initial encouraging results, more recent studies have not only failed to reduce sudden cardiac death with omega 3s, but have actually increased mortality in cardiac patients. For example, men with heart disease advised to eat more oily fish or supplied with fish oil capsules were found to have a higher risk of cardiac death, possibly because of the contaminants in fish, such as mercury. In either case, given the inconsistent benefits and the potential adverse effects, omega 3s must be prescribed with caution and generalized recommendations to increase fish intake or to take fish oil capsules need to be reconsidered.


I was as surprised as you to learn that fish oil doesn’t help with heart disease. Learn why in my Is Fish Oil Just Snake Oil? video.

In terms of PCB contamination, see Food Sources of PCB Chemical Pollutants and PCBs in Children’s Fish Oil Supplements. Our oceans and waterways have become humanity’s sewer—everything eventually flows into the sea. For discussion of all the other industrial contaminants that build up in the aquatic food chain, see:

For ways to decrease the risk of prostate cancer and slow its progression, see:

In health,

Michael Greger, M.D.

PS: If you haven’t yet, you can subscribe to my free videos here and watch my live, year-in-review presentations: