My staph infection!

After spending a couple of hours in the hot sun pruning a large shrub (wearing gloves), I noticed something on the inside of my ring finger that looked like a pink blister. After a week or so, a tiny open wound appeared, which, over the days, continued to expand. I sort of freaked out and went to the doctor who seemed unconcerned but prescribed an antibiotic ointment (more about that next week).

Infection at four weeks

The bacteria that likely caused my staph infection is Staphyloccus epidermidis—normal members of everyone’s skin flora. That is, they’re always hanging around our skin and mucous membranes, and comprise about 5% of the 1000 bacteria species that live on our skin. They’re generally not harmful and can even be beneficial by preventing pathogenic organisms from colonizing on your skin. But they are considered “opportunists” and sometimes cause infections if they are able gain a foothold. (They’re also the most common cause of infections that occur on knee and hip replacements.)

The reason that we’re not permanently covered in staph and other infections is that our immune systems produce cells (neutrophils) that kill bacteria that penetrate the skin barrier. But our immune systems may have evolved not to over-react to bacteria, otherwise we’d be in a constant state of inflammation. At the same time, the bacteria have evolved defense mechanisms to protect themselves from being ingested by our immune cells. It’s a very tricky balancing act.

What I have not been able to find out is why otherwise benign bacteria became pathogenic. One friend got a staph infection from a bee sting (common); another has become infected a few times from cat bites. I have concluded that the bacteria must gain their foothold when a very small object—maybe a sticker, in my case—pierces the skin in a certain way under certain conditions. That’s the best I can come up with.

Because all my other wounds have always healed quickly, I always thought my immune system could handle anything that came its way. “Pride goeth before a fall.”

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Psychedelic therapy

Therapists and researchers are increasingly interested in testing psychedelic drugs to help people struggling with psychological problems, such as depression, for which the pharmacological toolbox has little to offer. In addition to depression, institutions, such as Johns Hopkins, New York University, and UCLA are conducting trials to test the efficacy of psychedelic drugs for people who are dying and who are addicted to alcohol and/or nicotine.  

Dying: For those who are dying, the purpose of using psychedelic drugs is to alleviate anxiety and depression. It seems to work. Almost uniformly, patients come to view death as a transition into another type of existence and rather than the absolute end of everything. They also—even the atheists—have the feeling of being bathed in God’s love. Most also felt powerful feelings of connection to loved ones. Weeks after his session, one man even felt the happiest in his life.

Addiction: Most of the people treated found the experience to be helpful, mostly because they gain a radical new perspective on their lives. They are able let go of a pattern of thinking in which their selves and their addiction are the center of their lives. Apparently, the sense of awe experienced during a psychedelic “trip”—a sense of the small self in the presence of something greater—also enables patients to recognize the harm they’re doing not only to themselves but to loved ones.

Depression: As with electroconvulsive therapy, treatment with psychedelic drugs performs a kind of brain "re-boot." Most of the people treated with psychedelic drugs found their depression had lifted. As one patient said, “it was like a holiday away from the prison of my brain. I felt free, carefree, re-energized…I feel like I used to before the depression.” Unfortunately, more than half of the people treated saw the clouds of their depression eventually return. Nevertheless, they feel they have gained a new perspective on life and been given new hope.

Note: These experimental treatment sessions were conducted with a trained guide in a tightly controlled environment. Don’t try this at home!

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Your brain off the leash

I recently finished Michael Pollan’s new book, How to Change Your Mind (with long subtitle). It’s about the resurgence in studies of psychedelic substances, such as LSD and psilocybin, and how they affect the brain (including his). It’s also about how they might be useful therapeutically.

For me, the most interesting bit was learning about the default mode network—brain structures first described in 2001. I’d never heard of this network (DMN). It links parts of the cerebral cortex with older (evolutionarily speaking) parts of the brain and acts as a sort of orchestra conductor, keeping order in a system that might otherwise “descend into the anarchy of mental illness.” It acts as a kind of filter, admitting only the information required for us to get through the day. Otherwise, the torrent of information coming at our senses at any given moment would be difficult to process. It also plays a role in the creation of various mental constructs, the most important of which is our sense of self (our egos). It’s most active when we are involved in higher-level cognitive processes such as self- reflection, mental time travel, and trying to imagine what it is like to be someone else. By the way, the DMN isn’t operational until late in a child’s development.

When the default mode network goes quiet—the effect of psychedelics—our other centers of mental activity are “let off the leash,” allowing material otherwise unavailable to us to float to the surface. In this state, people feel a loss of ego and that they are a part of nature. Here’s a graphic image comparing the brain activity when the DMN is in charge (left) and when it is not (under the effect of psilocybin).

Kind of exciting, don't you think? (I'll discuss therapeutic uses next week.)

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Getting to know your gut bacteria

The ability to sequence DNA has made it possible for scientists to learn about our microbiome—all the organisms that live on and within us. At the moment, there’s a big push to learn about the bacteria in our guts, which harbor about 1000 different species of bacteria. Researchers have found that bacteria affect most of our physiologic functions, including our immune systems. One of the ways scientists are learning about gut bacteria is to study the variations in bacteria among diverse populations all over the world.

To determine the relationships between gut bacteria and health, they’re also comparing the bacteria of healthy individuals to those of diseased people and have found some connections. So far, it appears that gut bacteria play a role in the development of arthritis, colorectal cancer, colitis, obesity, diabetes, and even heart diseases. They have also found that most of these diseases are more prevalent in the US than in many other populations. A key reason for the link between our microbiome and these diseases has to do with our fiber-poor diets—a paltry 15 grams of fiber daily. As hunter-gatherers, we were likely eating close to ten times the amount of fiber than we do today. (In last week’s post, I explained how fiber keeps our gut bacteria in good working order.) Our use of antibiotics, which negatively affect gut bacteria, also contribute to the problem.

Unfortunately, there’s not a lot you can do to change the makeup of your gut bacteria other than increase dietary fiber and, maybe, probiotic food, such as yogurt. These foods can alter the relative abundance of the various species. But to dramatically change the population of bacteria you’d need a fecal transplant, which the FDA approves only if you are harboring Clostridium difficile (c. diff). Of course, you can always do it yourself.

In the interests of science, I signed up for one of the studies: the American Gut Project. (This requires a stool sample, of course.) I got a lengthy report complete with colorful graphs that show the relative abundance of the various phyla and families of bacteria in my gut. Unfortunately, the report doesn’t rate the quality of my bacteria—whether good or bad. Elsewhere, however, I learned that a ratio of more Bacteroidetes to fewer Firmicutes (these are phyla)—is correlated with lower body mass index. Unfortunately, my ratio is the opposite, but not by much. I’m a little fat. I think that means I need to eat more fiber. On a happier note, I did learn that my most abundant microbe (family Prevotella) is inversely correlated with Parkinson’s disease. So that’s something.

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Fiber: it’s not just for “roughage”

I think most of us thought that the value of eating fiber-rich foods was for the roughage it provides—undigestable bulk that keeps food moving through your digestive tract. It turns out that eating fiber is way more important than that. It feeds billions of bacteria in our guts, keeping them happy and, in turn, keeping our intestines and immune systems in good working order.

Here’s how it works: enzymes in our bodies break down food molecules, enabling us to digest the food. But our bodies make a limited range of enzymes, so we can’t break down many of the tough compounds in plants. That’s where the bacteria come in. Hundreds of species of bacteria live atop a layer of mucus that line our intestines. Some of them have the enzymes needed to break down various kinds of fibers—the kind present in vegetables, fruits, and nuts. After they’ve used the fiber for their own purposes, they cast off the leftovers in the form of short-chain fatty acids, which are absorbed by the intestinal cells that use it as fuel. Some of the short-chain fatty acids pass into the bloodstream and travel to other organs, where they act as signals to quiet down the immune system. Intestinal cells also rely on chemical signals from the bacteria to work properly: to make a healthy supply of mucus and to release bacteria-killing molecules when needed.

Scientists have found that diets low in the fiber result in a variety of negative effects. For one thing, certain populations of bacteria crash; many common species become rare and rare species become common. Without a steady stream of chemical signals from bacteria, the intestinal cells slow their production of mucus as well as bacteria-killing poisons, which are needed to wipe out the bacteria that get too close to the gut wall—a condition that kicks the immune system into high gear. In the words of one of the scientists, “The gut is always precariously balanced between trying to contain these organisms and not to overreact.  It could be a tipping point between health and disease.”

I hate to be tiresome, but I'm afraid it's important to eat those fruits and vegetables.

For an introduction to this blog, see I Just Say No; for a list of blog topics, click the Topics tab.