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Gut Feeling: A Q&A with the American Gut Project's Jeff Leach
The American Gut Project is an open-source, community effort to better understand the diversity of our microbiomes.
Jeff Leach is an anthropologist with an unusual interest: the contents of your gut. After his daughter was diagnosed with Type 1 diabetes, he became very interested in how diet and lifestyle may influence disease states. And now, in partnership with the University of Colorado at Boulder's Rob Knight and a few dozen other collaborators across the U.S., Leach has founded the American Gut Project, an open-source, community effort to better understand the diversity of our microbiomes.
Q: So why take a closer look at our guts?
Leach: With a lot of acute and chronic diseases, we're learning that the problem may be an imbalance with the microbial world. It could be an imbalance on our skin, in our gut, in the genital area. But the question remains, "Well, what is normal? What is a healthy gut microbiology?" And the truth is, nobody knows. Because we're all compromised. We take antibiotics, we drink too much tequila, and we eat crap food. And so our gut bugs are basically incomplete, in total disarray. Maybe if we compare our guts to those of hunter-gatherers in Africa, who have never taken anti-biotics or seen a Coca-Cola, we can get at that question.
Q: Why is the microbiome so important?
Leach: You are more microbes than you are mammal. Everybody on Earth has two genomes. You have the one you got form your Mom and Dad which you inherited. Then you have your second genome which is all the genetic material that is packaged up in your gut and in your skin, all those microbes, and that is the genome you acquire. It's interesting that there are only 23,000 genes in your genome but over three million genes in your gut microbiome. So, in other words, those genes encode more instructions than your own genome. It begs the question, "Who is in charge?" We know that the microbiome may influence things like auto-immune disease, certain cancers, inflammatory bowel disease, colitis and rheumatoid arthritis. So it appears that a lot of disease may be related to a shift in your gut composition. We need to figure out whether the microbiology is causing the disease or the disease is making changes to the microbiology. But first we need to figure out what is normal. And that's what led us to the American Gut Project.
Q: So why a crowd-sourced project?
Leach: The Human Microbiome Project, which cost over $100 million, only looked at 250 people. The specific goal of that project was a detailed, deep analysis of those individuals. But we don't have any good idea of the variability across the United States--couch potatoes, athletes, vegans, seven-year-olds, high BMI, low BMI. We need a genometric landscape. So we asked ourselves how we could capture a large sample of the American public and do it quickly, while raising awareness of health and wellness and the role of microbiology? And there are so many interesting citizen science projects out there and we thought this is a project that everybody can wrap their head around. We all care about our health and well-being. So crowd-funding and sourcing gives us a platform to help meet all of our goals for the project.
Q: So what should participants in this project expect?
Leach: Let’s say you want to donate. This is not a commercial lab, this is not a fee for services. It is a straight up citizen science project we’re asking you to donate to. You donate $99 for the project between now and January 7, you’re signed up, and you’ll receive a kit at your home. The kit basically amounts to an eight inch long double-headed swab, just like something that you swab your ear with. It comes in a tube. What you’re going to do is, you’re going to wipe that across the toilet paper and you’re going to stick it back in the tube, and you’re going to mail it to us. We’re going to process the sample. It’s going to go through DNA sequencing. All the samples go to the University of Colorado at Boulder, to Rob Knight’s lab. All that data will be processed there. It will be given a number. When you receive your kit at home, you'll also get a questionnaire. You’ll also have a special ID number that nobody knows except you.
You’ll be able to input that number into a website to get your results. Results take anywhere from 30 to 90 days depending on how many people are on the project. Once your results are available you’ll be able to download, here’s a list of all your bacteria. Here’s the major groups, here’s the genus, here’s the species. And then, based on the metadata that you provide in the questionnaire, there could be anywhere from 3 to 20 graphs. Okay, let’s say you self-identified in the questionnaire as a vegetarian, and then you provide details. We’ll show you how you compare to the group of vegetarians--male and female, and age, and BMI, and macronutrient intake, and rural versus city, and antibiotics, and dogs, and kids. We show you how you fit into your group. We should also then show, are the vegetarians different, and how are they different, and what does it mean? So there will be little take home messages with everything. So you can see how you compare to your group, what you might think about doing differently, how your gut compares to extremes. There's a lot of interesting information in there. And you'll also help us better understand what's normal.
Want to participate in the American Gut Project? Head on over to the American Gut's IndieGoGo webpage. Sign up before January 7, 2013, to receive your sample kit and learn more about what's living in your gut.
Photo credit: Jeff Leach
Innovation in manufacturing has crawled since the 1950s. That's about to speed up.
Health officials in China reported that a man was infected with bubonic plague, the infectious disease that caused the Black Death.
- The case was reported in the city of Bayannur, which has issued a level-three plague prevention warning.
- Modern antibiotics can effectively treat bubonic plague, which spreads mainly by fleas.
- Chinese health officials are also monitoring a newly discovered type of swine flu that has the potential to develop into a pandemic virus.
Bacteria under microscope
needpix.com<p>Today, bubonic plague can be treated effectively with antibiotics.</p><p style="margin-left: 20px;">"Unlike in the 14th century, we now have an understanding of how this disease is transmitted," Dr. Shanthi Kappagoda, an infectious disease physician at Stanford Health Care, told <a href="https://www.healthline.com/health-news/seriously-dont-worry-about-the-plague#Heres-how-the-plague-spreads" target="_blank">Healthline</a>. "We know how to prevent it — avoid handling sick or dead animals in areas where there is transmission. We are also able to treat patients who are infected with effective antibiotics, and can give antibiotics to people who may have been exposed to the bacteria [and] prevent them [from] getting sick."</p>
This plague patient is displaying a swollen, ruptured inguinal lymph node, or buboe.
Centers for Disease Control and Prevention<p>Still, hundreds of people develop bubonic plague every year. In the U.S., a handful of cases occur annually, particularly in New Mexico, Arizona and Colorado, <a href="https://www.cdc.gov/plague/faq/index.html" target="_blank">where habitats allow the bacteria to spread more easily among wild rodent populations</a>. But these cases are very rare, mainly because you need to be in close contact with rodents in order to get infected. And though plague can spread from human to human, this <a href="https://www.healthline.com/health-news/seriously-dont-worry-about-the-plague#Heres-how-the-plague-spreads" target="_blank">only occurs with pneumonic plague</a>, and transmission is also rare.</p>
A new swine flu in China<p>Last week, researchers in China also reported another public health concern: a new virus that has "all the essential hallmarks" of a pandemic virus.<br></p><p>In a paper published in the <a href="https://www.pnas.org/content/early/2020/06/23/1921186117" target="_blank">Proceedings of the National Academy of Sciences</a>, researchers say the virus was discovered in pigs in China, and it descended from the H1N1 virus, commonly called "swine flu." That virus was able to transmit from human to human, and it killed an estimated 151,700 to 575,400 people worldwide from 2009 to 2010, according to the Centers for Disease Control and Prevention.</p>There's no evidence showing that the new virus can spread from person to person. But the researchers did find that 10 percent of swine workers had been infected by the virus, called G4 reassortant EA H1N1. This level of infectivity raises concerns, because it "greatly enhances the opportunity for virus adaptation in humans and raises concerns for the possible generation of pandemic viruses," the researchers wrote.
A new Harvard study finds that the language you use affects patient outcome.
- A study at Harvard's McLean Hospital claims that using the language of chemical imbalances worsens patient outcomes.
- Though psychiatry has largely abandoned DSM categories, professor Joseph E Davis writes that the field continues to strive for a "brain-based diagnostic system."
- Chemical explanations of mental health appear to benefit pharmaceutical companies far more than patients.
Challenging the Chemical Imbalance Theory of Mental Disorders: Robert Whitaker, Journalist<span style="display:block;position:relative;padding-top:56.25%;" class="rm-shortcode" data-rm-shortcode-id="41699c8c2cb2aee9271a36646e0bee7d"><iframe type="lazy-iframe" data-runner-src="https://www.youtube.com/embed/-8BDC7i8Yyw?rel=0" width="100%" height="auto" frameborder="0" scrolling="no" style="position:absolute;top:0;left:0;width:100%;height:100%;"></iframe></span><p>This is a far cry from Howard Rusk's 1947 NY Times editorial calling for mental healt</p><p>h disorders to be treated similarly to physical disease (such as diabetes and cancer). This mindset—not attributable to Rusk alone; he was merely relaying the psychiatric currency of the time—has dominated the field for decades: mental anguish is a genetic and/or chemical-deficiency disorder that must be treated pharmacologically.</p><p>Even as psychiatry untethered from DSM categories, the field still used chemistry to validate its existence. Psychotherapy, arguably the most efficient means for managing much of our anxiety and depression, is time- and labor-intensive. Counseling requires an empathetic and wizened ear to guide the patient to do the work. Ingesting a pill to do that work for you is more seductive, and easier. As Davis writes, even though the industry abandoned the DSM, it continues to strive for a "brain-based diagnostic system." </p><p>That language has infiltrated public consciousness. The team at McLean surveyed 279 patients seeking acute treatment for depression. As they note, the causes of psychological distress have constantly shifted over the millennia: humoral imbalance in the ancient world; spiritual possession in medieval times; early childhood experiences around the time of Freud; maladaptive thought patterns dominant in the latter half of last century. While the team found that psychosocial explanations remain popular, biogenetic explanations (such as the chemical imbalance theory) are becoming more prominent. </p><p>Interestingly, the 80 people Davis interviewed for his book predominantly relied on biogenetic explanations. Instead of doctors diagnosing patients, as you might expect, they increasingly serve to confirm what patients come in suspecting. Patients arrive at medical offices confident in their self-diagnoses. They believe a pill is the best course of treatment, largely because they saw an advertisement or listened to a friend. Doctors too often oblige without further curiosity as to the reasons for their distress. </p>
Image: Illustration Forest / Shutterstock<p>While medicalizing mental health softens the stigma of depression—if a disorder is inheritable, it was never really your fault—it also disempowers the patient. The team at McLean writes,</p><p style="margin-left: 20px;">"More recent studies indicate that participants who are told that their depression is caused by a chemical imbalance or genetic abnormality expect to have depression for a longer period, report more depressive symptoms, and feel they have less control over their negative emotions."</p><p>Davis points out the language used by direct-to-consumer advertising prevalent in America. Doctors, media, and advertising agencies converge around common messages, such as everyday blues is a "real medical condition," everyone is susceptible to clinical depression, and drugs correct underlying somatic conditions that you never consciously control. He continues,</p><p style="margin-left: 20px;">"Your inner life and evaluative stance are of marginal, if any, relevance; counseling or psychotherapy aimed at self-insight would serve little purpose." </p><p>The McLean team discovered a similar phenomenon: patients expect little from psychotherapy and a lot from pills. When depression is treated as the result of an internal and immutable essence instead of environmental conditions, behavioral changes are not expected to make much difference. Chemistry rules the popular imagination.</p>
Why Depression Isn't Just a Chemical Imbalance<span style="display:block;position:relative;padding-top:56.25%;" class="rm-shortcode" data-rm-shortcode-id="fbc027c9358dad4a6d9e2704fc9ddb04"><iframe type="lazy-iframe" data-runner-src="https://www.youtube.com/embed/GAC9ODvSxh0?rel=0" width="100%" height="auto" frameborder="0" scrolling="no" style="position:absolute;top:0;left:0;width:100%;height:100%;"></iframe></span><p>Many years ago, my best friend tried to quit smoking. He asked for help. While I'm no addiction expert, I offered what I knew from my fitness toolkit: breathing exercises and cardiovascular training, methods for strengthening his body and mind that could, I hoped, inspire him to take better care of himself in general. He replied, "No, I meant something like a pill."</p><p>A few years later, he quit for good. After failing the cold turkey method a number of times, it finally stuck. Maybe it was watching his children grow up—the reason my parents quit when I was young. This method is not easy, however. It challenges you; it forces you to confront your demons; it drastically affects your brain chemistry. Yet, in the long run, it sometimes works. </p><p>Sometimes pills work, too. But often they do not. The journalist Robert Whitaker, author of "Anatomy of an Epidemic," discussed the clinical trial process <a href="https://bigthink.com/mind-brain/antidepressants-dangers" target="_self">during our recent conversation</a>. While the FDA process appears thorough from the outside, pharmaceutical companies only need to prove that a drug works better than placebo, not that it works for the most amount of people. He continues, </p><p style="margin-left: 20px;">"Let's say you have a drug that provides a relief of symptoms in 20 percent of people. In placebo, it's 10 percent. How many people in that study do not benefit from the drug? Nine out of 10. How many people are exposed to the adverse effects of the drug? 100 percent."</p><p>Even though some pharmacological interventions show little efficacy, and even though Xanax, an addictive and destructive benzodiazepine that only showed <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5846112/" target="_blank">short-term (four weeks) efficacy</a> in clinical trials, is being prescribed for many months and years, doctors continue to use the language of clinical neuroscience to describe mental health issues. If chemistry is the problem, people will turn to chemistry for the solution. </p><p>Perhaps we should, as psychiatrist Dean Schuyler <a href="https://bigthink.com/surprising-science/antidepressant-effects" target="_self">writes</a> in a 1974 book, recognize that most depressive episodes "will run their course and terminate with virtually complete recovery without specific intervention." The problem is that idea isn't profitable. As long as the gatekeepers continue to use the language of chemical imbalances to describe what for many is just an episodic case of the "blahs," we'll continue creating more problems than we solve.</p><p>--</p><p><em>Stay in touch with Derek on <a href="http://www.twitter.com/derekberes" target="_blank">Twitter</a>, <a href="https://www.facebook.com/DerekBeresdotcom" target="_blank">Facebook</a> and <a href="https://derekberes.substack.com/" target="_blank">Substack</a>. His next book is</em> "<em>Hero's Dose: The Case For Psychedelics in Ritual and Therapy."</em></p>
SEAL training is the ultimate test of both mental and physical strength.
- The fact that U.S. Navy SEALs endure very rigorous training before entering the field is common knowledge, but just what happens at those facilities is less often discussed. In this video, former SEALs Brent Gleeson, David Goggins, and Eric Greitens (as well as authors Jesse Itzler and Jamie Wheal) talk about how the 18-month program is designed to build elite, disciplined operatives with immense mental toughness and resilience.
- Wheal dives into the cutting-edge technology and science that the navy uses to prepare these individuals. Itzler shares his experience meeting and briefly living with Goggins (who was also an Army Ranger) and the things he learned about pushing past perceived limits.
- Goggins dives into why you should leave your comfort zone, introduces the 40 percent rule, and explains why the biggest battle we all face is the one in our own minds. "Usually whatever's in front of you isn't as big as you make it out to be," says the SEAL turned motivational speaker. "We start to make these very small things enormous because we allow our minds to take control and go away from us. We have to regain control of our mind."