Category: umami hypothesis

A Brief History of Antibiotics

Seth Roberts7 Comments

This excellent article by Carl Zimmer gives a brief history of the development of antibiotics. It makes the usual points that the microbes within us improve our health and killing them (with antibiotics) can have bad effects. One study found that children given antibiotics had a higher risk of developing inflammatory bowel disease (IBD) later in life. Giving antibiotics to a child younger than one year was especially dangerous — the risk of IBD increased by a factor of 6.

The article makes the minor mistake of taking seriously what researchers say about number of species:

Each of us is home to several thousand [bacterial] species. . . . My own belly button, I’ve been reliably informed, contains at least 53 species.

Counting the number of species inside us is like measuring the length of the coast of England. The more closely you look (in the case of coastlines, the shorter the ruler you use), the larger the number you will arrive at. I’d be surprised if the researchers who count bacterial species adjust for this.

What I found most interesting about the article is it says nothing about fermented foods. Apparently the connection is not so obvious.

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.

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.

 

 

 

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.

 

 

 

 

 

 

 

New Product: Cascal Fermented Soda

Seth Roberts3 Comments

This low-calorie soda (60 to 80 calories in a 12-ounce can) falls somewhere between kombucha and less-sweet sodas such as the aptly named GUS (Grown Up Soda). Its hook is the use of fermented juices as its base, resulting in a more complex flavor than sodas and sparkling waters based on plain juice.

$1.25 at Whole Foods. I’m in.

My interest in fermented foods partly derives from learning about a similar product. At a Fancy Food Show a few years ago, I learned about someone who wanted to develop a high-end non-alcoholic alternative to wine. He found he couldn’t get enough complexity without fermentation. That emphasized to me how our food preferences — in this case, a desire for complexity — push us to eat fermented foods.

The Complex Flavor of Fermented Foods

Seth Roberts5 Comments

One of the main reasons I think we need to eat fermented foods to be healthy is that their flavors correspond neatly to the flavors we like. Fermentation of fruits and other sweet foods changes sugars to acids, making the food taste sour — and we like sour food. Fermentation of proteins produces glutamate, which produces an umami flavor — and we like umami-flavored food. With many foods, their fermentation produces many microbial byproducts, giving the food a complex flavor — and we like complex flavors.

The connection between fermentation and complex flavor is well-put in a Saveur article about fermented foods:

[As a child] I only knew Claussen and other vinegar-cured pickles, the kind you buy in jars off the supermarket shelf, and I liked them just fine. But when I finally tasted a real pickle—the kind made the old-fashioned way, fermented with nothing more than salt, water, and time—I realized what I had been missing. A vinegary pickle plows through your palate with its tartness (often in a most pleasing way), but a live-cultured, salt-cured, fermented one tells a more multifaceted story. It is sour, to be sure, but it tastes of something more, something elusive: It’s the flavor of Middle Europe captured in one bite. When I started cooking for a living, I realized that the complexity I’d tasted in that pickle is the hallmark of well-made fermented foods, which include some of my very favorite things to eat and drink: not just pickles, but aged cheeses, tangy sourdough breads, blistering kimchis, tart yogurts, winy salamis, and of course, wine itself.

 

Assorted Links

Seth Roberts7 Comments

Thanks to Adam Clemens.

Double Interview on the Benefits of Probiotics

Seth Roberts2 Comments

This curious 2006 article has an interview with one researcher in one column and an interview with another researcher in another column. Their results differed.

Pro probiotic. “Children with [infectious acute diarrhea] who took Lactobacillus [various strains and species, in nutritional supplement form, not in yogurt form] had a shorter duration of diarrhea (on average 0.7 days shorter) than those who took placebo. Also, they had fewer episodes of diarrhea, i.e. fewer stools, on the second day of treatment than those in the placebo group. Interestingly, the children who took higher doses of Lactobacillus had shorter duration of diarrhea, and it seems that a daily dose of at least 10 billion viable bacteria is necessary to have a beneficial effect.”

Anti probiotic. “I published a big study looking at Lactobacillus GG in kids with Crohn’s disease who were already doing fairly well on medication. We put them on the probiotic or a placebo for two years. We followed them for two years and looked for whether the probiotic group had a lower rate of relapse and whether there were any differences between the two groups. We didn’t find any differences.”

Assorted Links

Seth Roberts7 Comments
  • New study shows that a Yakult probiotic drink helps people with lactose intolerance and the benefits persist 3 months after one month of drinking it. Yakult is common in Chinese and Japanese supermarkets but rare in American ones. Until I read this article, I didn’t realize that people drink it because of lactose intolerance, which is much more common in Asia than America. Via Cooling Inflammation.
  • news from the Human Microbiome Project. “To the scientists’ surprise, they also found genetic signatures of disease-causing bacteria lurking in everyone’s microbiome. But instead of making people ill, or even infectious, these disease-causing microbes simply live peacefully among their neighbors.” You may recall that a Nobel Prize was given for the discovery that ulcers are caused by a certain species of bacteria. However, almost everyone with the “disease-causing” bacteria does not get ulcers. Apparently the “surprise[d]” scientists studying the human microbiome did not know that. If it were better known that you don’t need to kill bacteria to make them harmless, antibiotic usage would be less attractive.
  • Air pollution epidemiologist fired from UCLA after his research contradicts claims about the danger of air pollution.
  • How to conduct a personal experiment: biphasic sleeping

Thanks to Melissa McEwen, Peter Spero, Tim Beneke, Dave Lull and Bryan Castañeda.