Bacteria are Neither Good nor Bad

Health experts call bacteria “good” and “bad”. Bad bacteria make us sick. Good bacteria help us digest food, and a few other things. Let me propose another view. Any bacteria (i.e., bacterial species) will make us sick if it becomes too numerous — so all bacteria are “bad”. All bacteria protect us against other bacteria — so all bacteria are “good”. The terms “good” and “bad” are misleading. It is like saying a person is inherently rich or poor. Anyone, given a lot of money, becomes rich. Anyone whose money is taken away becomes poor. Low bacterial diversity or reduction of diversity makes it more likely that one bacterial species can overwhelm its competitors, producing sickness. When this happens, to say that the species (e.g., H. pylori) that became numerous “caused” the sickness (e.g., ulcers) is to seriously misunderstand what happened and how to prevent it from happening. We are taught that our immune system protects us from infection. We should be taught that bacterial diversity does the same thing.

The following story, from a reader of this blog, suggested these ideas:

My wife had a lot of problems, visceral fat that wouldn’t go away being one of the most obvious symptoms. Every time I convinced her to try a ketogenic (= very low carb) diet, she would get sick. I went to NYC to see Paul Jaminet speak. He suggested that she likely had some type of gut infection or dysbiosis. Not a bad theory, as she’d undergone prophylactic antibiotic treatment to clear up an H. pylori infection. (Yes, I know, but at the time it seemed like the thing to do.)

She started putting on weight after that, which is typical.

Finally she gave VLC  [very low carb] one last try. She wound up getting inflamed lymph nodes in her thighs. Our doctor was wondering if she might have bovine tuberculosis or the bubonic plague, either of which would explain her symptoms. (The nodes were inflamed, black-and-blue, and sensitive. This is a typical symptom of bovine tuberculosis, and the disease spreads from the gut to the body through the bowel. As we consume raw milk, this wasn’t a crazy theory, but there have been no recorded outbreaks in Connecticut for years and years.) All the tests he did for an infection came back negative, but her symptoms clearly suggested she had one.

Finally she went to see a new OB-GYN. His nurse/dietician reaffirmed everything I’d been telling her, and she finally decided to go fully ketogenic. Once again, she got sick, but this time she decided to tough it out. Sure enough, after many weeks she started feeling better, and more importantly, the weight started coming off, and the visceral fat started reducing.

She did a stool test, and (I haven’t seen the results yet) we were told that she had the obesigenic gut biota. So she started an intensive probiotic regimen. This helped her one negative from the ketogenic diet: constipation.

She’s thrilled with the progress she’s seeing, and her few lingering issues after going primal 2.5 years ago seem to be resolving. The constant yeast infections have abated, and she’s planning a new wardrobe, heaven help me.

There are several interesting things here: 1. A very-low-carb diet made her sick. 2. This happened after antibiotic treatment. 3. Tests for infection were negative. 4. If she waited long enough, the low-carb-induced illness abated. 5. Probiotics helped. 6. Fermented foods didn’t help. At the time of Paul Jaminet’s diagnosis, says the reader, they were already eating plenty of fermented food: “Sauerkraut, yogurt, home-made kefir, the whole drill.  No effect.”

How can these observations be explained?

With some general ideas. Each bacterial species keeps similar species in check by competing for the same resources (food and location). No two species need exactly the same things but there is plenty of overlap. For example, Species 1 needs Resources A and B, Species 2 needs Resources A and C. They keep each other in check by reducing the supply of A. Suppose C = carbohydrate. By reducing C, a very-low-carb diet reduces the number of Species 2, making more A available. This allows Species 1 to greatly expand. Maybe this expansion kills off Species 2. Armed with vast amounts of A, Species 1 out-competes other competitors. Its numbers greatly increase, causing sickness.

The notion that some bacteria are good and others are bad is absurd because all are safe in small amounts and all will cause sickness in large amounts. If any one person was replicated in millions or billions of copies it would cause enormous damage, waste and disruption, no matter who it was. Suppose I was genetically replicated so that there were hundreds of millions of me. I only like a few singers, such as Michelle Shocked and Cat Power. There would be a huge undersupply of records by those singers and a huge oversupply of other music. The music industry would collapse. I am a certain size. There would be a huge shortage of clothes of my size and a huge oversupply of clothing of other sizes.

The bacterial ecosystem is not self-correcting. It is the opposite: disruptions tend to spread. Suppose you eat too little carbohydrate. This reduces Species 2 (which needs A and C = carbohydrate). This means there is more Resource A for Species 1 (which needs Resources A and B). Species 1 increases. By virtue of increased numbers, it pushes down its competitors for Resource B. These weakened competitors, which also need D, E, and F, begin to lose battles for those resources against other bacteria that need D, E, and F. They decline in number. No longer with substantial competition for what it needs (A and B), Species 1 multiplies unchecked and causes damage until A and B run out. (Which may be why the reader’s wife, after a long illness, got better.) Fever fights infection because bacteria that grow best at one temperature (normal body temperature) do less well against competitors at a higher temperature.

The tests for infection failed to come up positive because they looked for too few bacteria. According to this view, there are thousands of bacteria inside us that can run out of control. You can test for only a tiny fraction of them. Fermented foods failed to help because they did not provide enough diversity.

We have a huge preference for diversity in what we eat. We much prefer a meal with three foods than one food, for example. The usual view is that this preference evolved because we need many nutrients (e.g., many vitamins) to be healthy. Now I wonder. Maybe the protective effect of bacterial diversity was the main reason.  If so, taking a multi-vitamin pill is not going do much good, which is what research suggests.

These ideas are obviously supported by evidence that fermented foods improve health and antibiotics harm health, which I’ve covered many times. They are also supported by two recent studies with a different emphasis. One of them found that people with sinusitis had less bacterial diversity in their nose than people without sinusitis and that increasing diversity tended to prevent sinusitis. Someday the 2005 Nobel Prize for “showing” that ulcers are “caused” by H. pylori will seem as medieval as the 1949 Nobel Prize for prefrontal lobotomies.

The practical consequences of this view include: 1. Antibiotics should be a very last resort. When given, they should be followed by treatments that restore bacterial diversity.  The reader’s story suggests restoration of diversity may not be easy. Plainly diversity should be tracked after antibiotics. 2. Epidemiological studies should not just ask how did the germs spread? They should also ask why were they allowed to do harm?  Why didn’t natural defenses – the immune system and other bacteria – suppress them to harmless levels? To the epidemiological neglect of immune function we can add neglect of this line of defense. 3. There should be convenient ways to measure one’s bacterial diversity so each of us can learn where we are and what makes it go up and down.  4. Researchers should study what makes bacterial diversity go up and down. Here is a recent study about this: old people living in an old-age home, who ate a restricted diet, had less bacterial diversity than people the same age who lived independently and ate more varied foods.. 5. Researchers should learn the correlates of high and low diversity. Take a group of people, measure their bacterial diversity, track their health for six months.




15 Replies to “Bacteria are Neither Good nor Bad”

  1. Here are some articles and publications that support your arguments, includng the newly published work from PLOS Pathogens that found a mix of six specific bacteria was effective in suppressing C.difficile infection in mice.

    Pax on both houses (summarizes the PLOS publication below)

    Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

    Tending the Body’s Microbial Garden

    How Microbes Defend and Define Us

    I’m especially interested in this since I’m about to have major knee surgery and the docs will insist on hitting me with big jolts of antibiotics.

    Seth: Thanks for the links. I didn’t know knee surgery led to antibiotics. Can you refuse the antibiotics?

  2. Can’t remember now where I read an article/paper written by a leading gut flora doctor/researcher, but his recommendation was to eat a boring diet – the same few plants & animals on a regular basis. His theory is that a very diverse diet breeds too many “jack of all trades” bacteria – none of which are really good at their job. Where a simple/boring diet, breeds experts that are really good at their job.

    Of course a diet of junk/processed food will most likely breed a population of junk food junkie flora who are very good at their job – maybe, too good.


  3. As we learn more, we find that things are much more complicated than we thought, and much too complicated for the simplistic drug-everybody approach of doctors and their BigPharma friends.

    These things we do know, at least based on recent research:
    1. Fiber is good food for gut bacteria, so eat lots of fiber from things like beans, which also have lots of protein.
    2. Antibiotics disrupt the gut bacteria, so try to avoid antibiotics.
    3. Antacids and proton pump inhibitors disrupt the gut bacteria, so try to avoid antacids.

    And here’s the most important lesson: Doctors love antibiotics and antacids, so try to avoid doctors.

    Seth: Yeah. Antibiotics are said to be the most important medical advance of the last 100 years. Yet it is plausible they do more harm than good. What does that say about all the other “advances”?

  4. @ Jim,
    I wouldn’t be so fast to recommend beans, many types (especially soy, kidney and fava) have various components that are irritable/detrimental to many people.

    We should also draw a distinction between soluble and insoluble fibre. It is the soluble fibre we really want – which gut bacteria ferment into short chain fatty acids, among other things- and this can come from many sources other than beans.

    The focus on “healthy whole grains” has led to many people getting too much insoluble fibre, which causes problems of its own, in addition to gluten and other grain proteins.

    But your general point of more (soluble) fibre is in the mark, as are your points 2 & 3 (4). It is amazing how much we are prescribed things that do not cure our ills, but prolong them.

  5. There may be more to this story as my experience suggests. All bacteria are consumers of nutrients ie compete with human cells. Our bodies (the inside) are not perfectly sterile and so bacteria mass accumulates with age as the immune system has a capacity limit. Our cells receive incrementally ever smaller amounts of energy (nutrients) as they age ie become smaller with succeeding replications. I have been able to significantly reverse periodontal disease via measures to limit gut bacteria after decades of gradual decay.

  6. Seth: Thanks for the links. I didn’t know knee surgery led to antibiotics. Can you refuse the antibiotics?

    Probably not, and they are probably a good idea even though they will do a number on my internal flora. The concern with joint replacements is deep infections under or around the implants that can’t be effectively treated because of poor blood supply deep in the joint. So the docs want to avoid them at all costs.

    What’s more annoying is that after you have a joint replacement, you have to take antibiotics before dental work – for life, apparently. Supposedly nasty bacteria from your mouth can get into the bloodstream during the dental activities. They can supposedly get deposited around the implant and cause one of those hard-to-treat deep infections.

    I’ve had a hip replacement for 20 years. Four years ago when I moved, I didn’t find a new dentist and didn’t have my teeth cleaned or examined for all that time. I had fixed my acid reflux by adopting a low carb diet, and I didn’t want to undo that work by use of antibiotics.

    Finally I had to go to the dentist because I am required to get a dental clearance for the knee surgery. I had an exam and cleaning. Even though I have a lot of gum and bone recession extending back over more than 30 years, after those four years my teeth were fine and my gums were in better shape than four years earlier.

    What had changed? 1- low-carb diet. 2- stopped using toothpaste having a lot of glycerin (most of them … for a while I brushed my teeth with Ivory soap). 3- I stopped flossing and started to clean between my teeth with a little “proxy” brush instead – I had found that flossing would start infections in my gums, and that doesn’t happen when I use the proxy brush instead.

    So – no dentist, no flossing, no standard toothpaste but plenty of attention to cleaning my teeth safely, reduce carbs which cause lots of crud to build up on the teeth. Better results. Hurray!

  7. Well I can think of a few bacteria that are unequivocally “bad”. Bubonic plague. Typhus. I wouldn’t blame the Black Death depopulation of Europe on faulty immune systems.

    Or maybe you were only referring to gut bacteria, not to nasties directly injected into the bloodstream by insects or contaminated medical equipment.

    Seth: You mean “on faulty immune systems and too little microbial diversity”? Dosage also matters: Exposure to a large amount of Bacteria X may cause illness, exposure to a tiny amount may be safe. I am less convinced than you that exposure to tiny amounts of the bubonic plague bacteria would be dangerous if one had a well-working immune system and plenty of internal microbial diversity. At the time of the Black Death, people may have eaten narrow diets, low in some vital nutrients. Living conditions may have also caused first exposures to the bubonic plague bacteria to be large (dangerous) rather than small (safe). On the other hand, I think you’re right. We can be exposed to a large amounts of certain bacteria without harm (e.g., the bacteria in yogurt) yet exposure to a large amount of certain other bacteria is dangerous. In that sense some bacteria are more dangerous than other bacteria.

  8. Hi Seth,

    Great anecdote and very plausible theory. But I’m not sure the anecdote fits the theory, since the ketogenic diet on which she recovered is presumably more restrictive (less varied, even lower in carbs) than the diet on which she got sick.

    To me that suggests that what we need is a story of diet-microbe equilibria, in which there are multiple microbiomes that can be in equilibrium with any diet, and you can get stuck in a bad equilibrium. Dietary changes can depopulate an overgrown species, leading to a new equilibrium which may be more healthful. Then probiotics/fermented foods may enable a shift back to the original diet but with a different microbial equilibrium.

    So this view is not “good bacteria / bad bacteria” but “good microbiome / bad microbiome” as in your theory; but it is not a story simply of “diversity good / nondiversity bad” even though it is a story of overgrowth of a nondiverse flora causing problems. The ketogenic diet may be have created a nondiverse flora that is not abundant, so the symptoms disappeared.

    Best, Paul

  9. PS – It’s also a good example of why chronic infections are often very difficult to heal. Often steps toward healing lead to an initial aggravation of symptoms (usually ascribed to “die-off” releasing toxic cell wall components), causing people to reverse course, as she backed away from VLC/ketogenic diets several times.

    Seth: The die-off explanation is certainly different than what I am suggesting here (that a change in diet that eliminates a vital nutrient — vital to one or more bacteria — may thereby “unleash” other bacteria). I have never seen any evidence that the die-off explanation is correct but I will look around for such evidence.

  10. there was a recent article in the new yorker about bacteria and, as i recall, how H. pylori is good in childhood (and how the absence of it in childhood may account for increase in ?asthma?. as i recall it was one or two issues back.

    Seth: Thanks. Yeah, I saw it. After I read it again I may post about it.

  11. You may be interested to read René Dubos (one of the discoverers of antibiotics) , who wrote similar things in the 1950’s. From the May 1955 issue of Scientific American:

    “A new look at the biological formulation of the germ theory seems warranted. We need to account for the peculiar fact that pathogenic agents sometimes can persist in the tissues without causing disease and at other times can cause disease even in the presence of specific antibodies. During the first phase of the germ theory the property of virulence was regarded as lying solely within the microbes themselves. Now virulence is coming to be thought of as ecological. Whether man lives in equilibrium with microbes or becomes their victim depends upon the circumstances under which he encounters them. This ecological concept is not merely an intellectual game; it is essential to a proper formulation of the problem of microbial diseases and even to their control.”

  12. Here’s a fascinating article about a microorganism that can rapidly move in when its competitors die off: “Genetic Switch Underlies C. albicans Quick Change Act”

    “In most people, C. albicans is just another member of the body’s flora, harmlessly coexisting with other microorganisms in their host. Bacteria in particular are important competitors that keep its spread in check. However, if the environment suddenly changes, causing bacteria to die off, C. albicans quickly adapts and takes over. Usually the effects are minor. Elderly people who use dentures may experience a dry or burning mouth condition known as “thrush.” Women who suffer from irritating yeast infections and most babies fussing over diaper rash are the victims of an overaggressive population of C. albicans. However, if the patient’s white blood cells have been compromised, say because of chemotherapy or an aggressive steroid treatment, the effects can be devastating. Serious complications arise if the fungus enters the bloodstream, perhaps through a catheter, which C. albicans can only do while in the more benign yeast form. However, once in the bloodstream, the fungus can deposit throughout the body as invasive hyphae. At that point it becomes known as “hematogenously disseminated candidiasis,” which proves fatal in 40% of cases, even with the best modern treatments.”

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