Category: fermented food

Fecal Transplant Roundup

Seth Roberts12 Comments

A new study has found that fecal transplants work better than antibiotics for clearing up a common and dangerous infection:

Such transplants cured 15 of 16 people who had recurring [= difficult-to-get-rid-of] infections with Clostridium difficile bacteria, whereas antibiotics cured only 3 of 13 and 4 of 13 patients in two comparison groups.

Clostridium difficile infections often result from antibiotic treatment. It is a big step forward for modern medicine to manage to grasp that the bacteria in our bodies protect us from infection. Here is a blog about the value of fecal transplants; here is another blog.

The comments contain many interesting details:

I spent Thanksgiving of 2012 in ICU and almost died from C-Diff. It was a harrowing experience for both me and my family. It required two months of care, recuperation and doses of vancomycin. My hospital bills are outrageous. [Fecal transplants are much cheaper — Seth] I am praying it doesn’t return, having just finished my last dose of vancomycin. I had a dental implant and was on clyndamycin for two weeks and that was the culprit. Dentists should be required to inform patients that C-Diff could be a reaction to that specific antibiotic. I was not warned about this being a possible side effect.

Our mother was hospitalized at a major university hospital and came down with C. diff. The antibiotics they gave her to fight the infection finally destroyed her kidneys and hearing and she decided that life was not worth living in that condition.

We have using this “treatment” for years and years in horses with difficult intestinal issues which didn’t respond to other medications. We pass a slurry of fecal material from a heathy horse ( often mixed with electrolytes and baking soda) directly into the stomach of the sick horse. It works in almost all cases.

After my gut microflora was destroyed by 9 months of antibiotics for Lyme disease, I got C. diff this past June. Was flabbergasted that NONE of my doctors, ALL of whom prescribe antibiotics, ( & hopefully read the NYT or the INTERNET) [knew] about fecal transplants! I ditched my Lyme doctor (who said along with my GI & GP): “Take Flagyll” (which didn’t work) and then Vancomycin. No thanks. Wasn’t going to wait around for the C. diff to corrode my guts or till I was almost dead, so I went right to Dr. Brandt for a transplant and in ONE day the symptoms were gone.

I had recurring c diff for 12 months.Tried a myriad of antibiotics and a colon cleanse.Nothing worked. I was getting sicker and weaker by the day, not to mention very depressed. I was “beyond” desperate. My husband (an internist) performed a fecal transplant (using my brothers stool–close DNA donor) at home (hanging the saline/stool bag from the ceiling fan!) 3+ years ago. I have been healthy ever since.

[A doctor:] This important study . . . is a big step in the right direction, however the study is quite small. [A doctor who doesn’t understand statistics even after it is explained in plain English. The evidence from this “small” study is very strong. In case you didn’t understand the numbers, the article says it in words: “the antibiotic groups were faring so poorly compared with the transplant patients that it was considered unethical to continue”. — Seth] A larger RCT is needed before this becomes standard of care [implying that his or her lack of understanding of statistics is the norm — Seth]. Since no one is currently in position to reap monopoly profits from this treatment, I predict the study will be a long time coming. [Which, if true, implies that doctors’ lack of understanding of statistics will kill a lot of people.–Seth]

The majority of cases of C. difficile infection occur in the hospital where they were usually brought on by use of broad-spectrum antibiotics destroying the natural balance of intestinal flora in the gut. A great many people outside the hospital setting walk around healthy colonized by C. difficile without becoming infected. Others become colonized while in the hospital, a virtual surety if you stay long enough. Broad-spectrum antibiotics wipe out bacteria that normally out-compete C. difficile at different niches within the intestinal ecosystem. [In other words, gross overuse of antibiotics has created a new ecosystem — modern hospitals — where C. difficile thrives. — Seth]

After a reaction to an antibiotic caused C Diff which lasted almost a year, was treated with multiple antibiotics of which Vancomycin was the only one that kept it at bay, having had a number of courses without success, meanwhile weight was down 25 lbs and health was deteriorating as in my opinion Vancomycin also presented some problems of its own, teeth browning, lethargy etc. C Diff ruins body and soul. After a lot of research was lucky to have found a doctor who checked out the fecal transplant history/procedure and performed the transplant. The feces donor was my brother having first had blood & feces testing. The transplant was a success, after suffering C Diff for almost a year my quality of life is great – normal.

The [squeamish] tone of this article is enraging. [It begins “The treatment may sound appalling”. The headline calls it “This, er, Option”. — Seth] I contracted ulcerative colitis when I was fifteen, and the squeamishness of my parents and doctors in my small town prevented me from accessing real care. More concerned with being grossed out than dealing with the problem at hand, I was allowed to go a year without receiving proper care. As a result, I ended up with such extreme internal bleeding that I was sent unconscious to the intensive care unit at Swedish Hospital in Seattle, three hours away from home, where a surgeon removed my entire colon. He chided my parents and local doctors for not seeking help from a specialist sooner; had they done so, I would not have been in such dire condition. I spent the next year of my childhood in the hospital. All this is to say: get over feeling grossed out by the human body and consider any possible treatments that might work. If this one does, great. Ditch the whole “ew” reaction because it stands in the way of saving lives.

I was plagued for decades with room-clearing gas and stomach cramps. Yogurt and probiotics didn’t stand a chance against the established bad bugs. Then I went for my first colonoscopy (which gave me a whistle-clean gut.) I was told I could have anything I wanted. First thing, I drank a full quart of organic kefir. I haven’t had a problem since. [Very interesting. Before a colonoscopy, you take something special to clean out your gut.–Seth]

Thanks to Alex Blackwood and Karen Goeders.

Assorted Links

Seth Roberts8 Comments

 

Assorted Links

Seth Roberts5 Comments
  • Unusual fermented foods, such as shio koji (fermented salt, sort of)
  • David Healy talk about problems with evidence-based medicine. Example of Simpson’s paradox in suicide rates.
  • The ten worst mistakes of DSM-5. This is miserably argued. The author has two sorts of criticisms: 1. Narrow a diagnosis (e.g., autism): People who need treatment won’t get it! 2. Widen a diagnosis (e.g., depression) or add a new one (many examples): This will cause fads and over-medication! It isn’t clear how to balance the two goals (helping people get treatment, avoiding fads and over-medication) nor why the various changes being criticized will produce more bad than good. Allen Frances, the author, was chair of the committee in charge of DSM-4. He could have written: “When we wrote DSM-4, we made several mistakes . . . . The committee behind DSM-5 has not learned from our mistakes. . . .” That would have been more convincing. That the chair of the committee behind DSM-4, in spite of feeling strongly about it, cannot persuasively criticize DSM-5 speaks volumes.
  • The Lying Dutchman. “Very few social psychologists make stuff up, but he was working in a discipline where cavalier use of data was common. This is perhaps the main finding of the three Dutch academic committees which investigated his fraud. The committees found many bad practices: researchers who keep rerunning an experiment until they get the right result, who omit inconvenient data, misunderstand statistics, don’t share their data, and so on.”

One Reason for French Longevity: Molded Cheese

Seth Roberts9 Comments

A new article emphasizes the benefits of cheese, especially “molded” cheese, such as Roquefort and Gorganzola. Fermentation, if that is the right word, is essential:

The advantageous properties of cheese appear dynamically during the ripening process. Cheese which has been ripened for longer has been shown to be more effective in restoration of glucose tolerance, prevention of steatosis [fat deposition inside a cell] and adipose tissue oxidative stress than short-ripened specimens. This data suggests that organic substances responsible for the health benefits of cheese emerge not merely due to mixing the ingredients required for cheese production, but rather as a result of a complex time-dependent enzymatic transformation of the cheese core controlled by probiota, temperature, humidity and possibly other factors.

Only in South Korea and Japan do people have less heart disease than in France, says the article. Readers of this blog will quickly see what South Korea, Japan, and France have in common. All of them eat much more fermented food than most people in rich countries. South Korea: kimchi. Japan: miso and pickles. France: cheese and wine.

Thanks to Peter MacLeod.

Assorted Links

Seth Roberts10 Comments
  • “Light” Ph.D. — a less expensive research degree
  • Umami Burger expands
  • A diuretic reduces autism symptoms. Does water balance influence brain function in people without autism?
  • This Amazon reviewer is almost always disappointed and his one-star reviews are fun to read. I suggest that ratings (book ratings, product ratings, etc.) compare the rating to other ratings given by the rater. A 5-star rating is more impressive if a rater’s average rating is 2 than if it is 5. I suggest percentiles. For example, rating = 5 (90%ile) is more impressive than rating = 5 (50%ile). I’d also like to know the average percentile across raters.
  • Lack of variation in heart rate predicts infection in neonates. The writer (Mike Loukides) is too surprised (“astonishing connection”). Many studies have found associations between too-little variation in heart rate and serious health problems.

Thanks to Adam Clemens and Patrick Vlaskovits.

Why Do Fermented Foods Improve Health? A New Idea

Seth Roberts11 Comments

I became interested in the health value of fermented foods after I noticed a curious coincidence. Humans have three mysterious food preferences: for (a) sour food, (b) food with umami flavor, and (c) food with complex flavor. I realized that all three preferences made bacteria-laden food more attractive. Bacteria change sugars to acids, increasing sourness. They break down proteins, creating glutamate, which produces umami flavor. And the many chemicals they introduce into a food make its flavor more complex. After I noticed this, I came across many studies that supported the idea that fermented foods are good for health. I also found studies that suggest the bacteria in our digestive system are crucial to health.

This raised the question: What fermented foods to eat? How many? How often? To begin to answer these questions, it would help to know how bacteria in our food help us be healthy. There were two obvious answers:

1. Stimulate the immune system. The bacteria in fermented food are inherently safe: they are specialized to reproduce on/in food, which is so different than inside the human body. But the immune system doesn’t know this. If this was one benefit of fermented food, you could study which ones to eat by measuring immune system activation. Unfortunately, that is nearly impossible.

2. Improve digestion. Many people have digestive problems and some of them are helped by fermented foods. Obviously they contain bacteria that digest food. I don’t have digestive problems so I can’t study this by figuring out which fermented foods help.

Recently, I have begun to think there is a third reason:

3. Place competition. To make us sick, outside bacteria need to stick inside us. To digest our food, the surfaces of our digestive system, such as the inside of our intestines, is much more porous than other surfaces, such as our skin. It is our digestive system, therefore, that is most vulnerable to dangerous microbes. The totally-safe microbes in fermented foods compete for sticky spots with other, more dangerous microbes. If there are plenty of safe bacteria — say, billions in a serving of yogurt — they may do a lot to protect us against the dozen or so similar dangerous bacteria we might get from touching the same surface as a sick person. I think of a wooden floor where the lumber is not quite well-fitted. If you want to protect what’s below that floor from black sand (dangerous), an excellent method would be to pour an enormous amount of white sand (safe) on the floor.

If Effect #3 (place competition) is the main reason fermented food protects us from disease, it implies that dead bacteria work as well as live bacteria (in contrast, live bacteria do not digest food, Effect #2). This might explain the potency of alcoholic beverges such as wine, where most of the bacteria are dead. It also suggests that what matters is diversity of where bacteria stick and how much they stick. It might someday be possible to feed people (non-radioactive) bacteria and learn where in the body they end up.

 

 

Bacteria are Neither Good nor Bad

Seth Roberts15 Comments

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 teenagers who had more biodiversity near home had more bacterial diversity on their skin. (Maybe there are other important drivers of diversity besides fermented foods.) The other 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.

 

 

 

Assorted Links

Seth Roberts6 Comments
  • You can major in Fermentation Science. No joke. When I was eight, I learned the concept of college major. I asked my mom, “What did you major in?” “Extracurricular activities,” she said. I failed to get the joke. She later explained she had spent more time working on the school paper than on her classes.
  • In a famous paper, the statistician Ronald Fisher accused Mendel of faking his data. Fisher wrote: “the data of most, if not all, of the experiments have been falsified so as to agree closely with Mendel’s expectations.” This is not terribly consistent with the fact that Mendel’s highly improbable conclusions were correct. It’s as if Fisher had said “Person X used false info to claim he is worth $10 billion” and (b) in fact Person X is worth $10 billion. You can see that (a) and (b) may both be literally correct but that the term “false info” (Fisher’s “falsified”) probably conveys the wrong impression. This paper (“A Statistical Model to Explain the Mendel–Fisher Controversy”) has a more plausible explanation of the pattern in the data that Fisher noticed.
  • Conflict of interest in the Nobel Prize in Literature. The conflicts of interest underlying the Nobel Prize in Physiology and Medicine — which are given out for “pure” science, thus justifying more funding — remain unnoticed by journalists.

Thanks to Bryan Castañeda.

More Fermented Foods, Less Runny Nose?

Seth Roberts5 Comments

As recently as four or five years ago,and for many years before that, I often had a runny nose. I went through boxes and boxes of Kleenex. I carried a handkerchief everywhere and often used it. Not because I had a cold–I almost never got colds. It was different than that. You might say I was mildly allergic to something in the air.

Because of reading an article I will discuss in a moment, I have just noticed that my runny nose has vanished, both in Berkeley (clean air) and Beijing (dirty air). So I don’t think it’s due to the dirty air in Beijing. There was no sharp change but as best I can remember it went away during the period when I started eating lots of fermented foods. Most days I eat about three types — yogurt and two other things, such as kimchi or kombucha. It is plausible that more exposure to bacteria caused my immune system to stop overreacting.

The article, from The Scientist, describes research suggesting that not enough bacteria can cause disease — specifically, sinusitis. Sinusitis, just like ulcers, has been associated with a particular bacterium, but the researcher involved, Susan Lynch of UCSF, has a more sophisticated understanding of causality than those two bacteria-causes-ulcers scientists and the committee that gave them a Nobel Prize. Lynch points out, quite reasonably, that the bacteria associated with sinusitis “have also been detected in the sinuses of healthy individuals . . . “Just because you find these organisms, it does not mean they are driving disease.” (The bacterium that supposedly caused ulcers, C. pylori, turned out to be very common. Almost everyone infected did not have ulcers.)

Lynch and her colleagues discovered

Samples from [sinusitis] patients tended to have less diversity of bacterial species than those of healthy controls. Furthermore the relative abundance of certain species differed between patients and controls. Sinusitis patients’s noses were enriched with a skin bacteria called Corynebacterium tuberculostearicum, for example, while samples from healthy controls were enriched with Lactobacillus bacteria, including L. sakei.

Which you could obviously get from fermented food. Following up this observation, the researchers did a mouse study that found that giving mice the bad bacteria caused sinusitis-like symptoms but giving mice both bad bacteria and good bacteria did not cause the symptoms. The good bacteria were protective.