Posts Tagged microbiome

Everything you always wanted to know about fermented foods 

Delicious homemade Kimchi (fermented cabbage). It's alive!

Delicious homemade Kimchi (fermented cabbage). It’s alive! Click for a closer look.

Fermented foods, such as sauerkraut and kombucha, have become popular for health reasons. I have made my own sauerkraut in the past and have recently made the tasty, fermented Korean side dish, kimchi. I did it not only for the taste but also for the hope that the bacteria responsible for the fermentation of the cabbage — lactic acid bacteria (LAB) — would contribute to the diversity of my gut microbiota.

As a research scientist in the field of bacterial pathogenesis, this made sense to me. Now that I have started blogging about health and fitness and have been writing more in depth articles about health related topics, I started wondering what research has been done on the health benefits of fermented foods. Can the bacteria in fermented foods even survive the harsh conditions of the human gastrointestinal (GI) tract, particularly the stomach?

I was amazed to learn that the fermentation of food has been used by humans for thousands of years as a way to preserve foods, and that the health benefits go beyond their microorganisms (don’t worry, citations are provided below). The fermentation process enhances the nutritional quality of food by contributing beneficial compounds such as vitamins, and by increasing the bioavailability of minerals. Probiotics, including those found in kimchi, have a range of positive effects on health, including the improvement of various intestinal inflammatory conditions, positive impacts on the immune system and even weight loss, and can alter the composition of the gut microbiome.

However, these effects mostly depend on whether the bacteria actually make it in sufficient numbers to the colon. And let me tell you, the journey to the colon is one harsh and dangerous ride!


Posted in: Herbs & Supplements, Nutrition, Science and Medicine

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Gut Check

Lactobacillus acidophilus

Some apparently rather useless Lactobacillus acidophilus

I always cringe when I see an acupuncture headline with ‘needle’ or ‘point’ in the title. Can’t the writer avoid the clichéd pun? I had an editor who commented that the titles of my essays are often obtuse. Probably true. In going back over my essays on SBM I often can’t tell from the title what I have written about until I read the article. It is a fine line between (what I think) is a clever title and obscurity. So gut check it is.

Time flies when you are having fun. I wrote about probiotics back in 2009.

My conclusion at the time:

Probiotics are useful for the prevention of antibiotic-associated diarrhea. Probiotics may be helpful in preventing other overgrowth syndromes or diseases associated, and perhaps with perturbations of the gut microbial flora such as IBS and colic.

Probiotics are foreign bacteria that are not a normal part of your GI tract; they do not enhance your immune system and, in normal people do not promote the nebulous bowel health.

If you are a normal human, with a normal diet, save your money. Probiotics have nothing to offer but an increased cost.

Medicine is not static and there have been interesting advances in the understanding of the human microbiome in health and disease since 2009, so for SBM and my own medical understanding, I thought it would be a good opportunity to review the topic. Although with over 12,000 references on the PubMeds, I will only touch on a smattering of the papers. My ID attending in medical school always referred to reading the medical literature as drinking from a fire hose. Indeed. (more…)

Posted in: Herbs & Supplements

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Meet Your Microbes: uBiome Offers New Service

We are not alone. Walt Whitman didn’t know how right he was when he said, “I contain multitudes.” The microbes on and in our bodies outnumber our own cells 10:1.  Perhaps that creeps you out. Perhaps that makes you curious to know just who all these billions of creatures are that are using your body for a home and a transportation device.

For just $89 you can learn what’s in your gut, nose, mouth, skin, genitals…or sample anything!

The offer comes from uBiome, a “citizen science startup” that has scientific goals somewhere down the line, but for the moment is happy to just provide a personal service, to sequence your microbiome and tell you how you compare to others. The current utility of this offering is questionable. It’s just not ready for prime time. (more…)

Posted in: Diagnostic tests & procedures, Medical Ethics

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Remember this picture when I start talking about your wife.

Remember this picture when I start talking about your spouse.

The Wall Street Journal has an assessment of probiotics in the Jan 13, 2009 issue entitled “Bug Crazy: Assessing the Benefits of Probiotics.” For some reason when I wander around the hospital on rounds people show me articles such as this and ask, so whatcha think about this? Probiotics are interesting. They are live bacteria given to treat and prevent diseases. It is one of those overlap areas for scientific medicine and so called alternative medicine. There are good clinical trials to suggest areas where these agents are of benefit, but other aspects of their use are blown out of proportion for the real or imagined benefit probiotics may provide. Much of alternative medicine where it overlaps with real medicine is the art of making therapeutic mountains out of clinical molehills. The Wall Street Journal article is the kind of reporting that drives. Me. Nuts. It drives me nuts because the reporting acts as if the underlying assumptions of the therapies are true. (more…)

Posted in: Basic Science, Science and Medicine, Science and the Media

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