Missing Microbes Part II: The Plague of our Times

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This is Part II of my four-part series reviewing the key issues covered in Missing Microbes, How the Overuse of Antibiotics is Fueling our Modern Plagues, by Martin J. Blaser, MD. In Part I, I explained that the human body has co-evolved with slate of resident bacteria, collectively our microbiome, which performs a number of vital biological tasks for us. Our reliance on these bacteria can correctly be inferred from the noteworthy fact that approximately 99% of the DNA within our bodies is theirs, not ours. Over the past several decades, due to both an increasing number of babies delivered via C-section and a dramatic increase in the use of antibiotics, a growing number of people in the United States and around the world are now missing important species of bacteria, a condition I will refer to below as a low-diversity microbiome.

Before proceeding, I should make it clear that neither this column nor Dr. Blaser’s book are intended to reject the use of antibiotics, but rather to advise against their overuse. The invention of antibiotics is perhaps one of human kind’s greatest triumphs. It has been the key contributor to the dramatic reduction in the rate of deaths of children in the United States during their first year of life from one 1 in 4 in 1850 to 1 in 1,000 today.   However, since the assumption has long been that there are no downsides to the use of antibiotics, we have gone overboard and caused some very serious problems. I will review Dr. Blaser’s suggestions on how to better use antibiotics in Part III next week.

A low diversity microbiome can result in harm through two modes of action. First, when an expected species of bacteria is missing, your body is deprived of whatever biological services that species provides. In addition, eliminating species of bacteria from your body often allows space and resources to be available either for other resident species to expand their populations beyond what the body is expecting, and/or for pathogenic species to gain a foothold. Below is a discussion of some of the health issues which can arise from these imbalances.


The number of obese people – defined as having a body mass index (BMI) of greater than 30 – in the United States grew from 12% in 1990 to 30% in 2010! While an increase in calories in the average diet and a decrease in our average amount of exercise during this time period are contributing factors to this phenomenon, they are not sufficient to explain this dramatic rise in obesity on their own. A growing number of scientists, Dr. Blaser in particular, now believe that disrupted microbiomes are the missing link in explaining this obesity epidemic. While some details of the mechanism are still unclear, a key factor seems to be an over-representation of types of bacteria that can digest short-chain fatty acids, which otherwise would have left the body undigested. Therefore, people with this type of this microbiome will extract more calories and store more energy as fat from the same diet as someone with a high-diversity microbiome. Further, the fact that antibiotic use in humans results in weight gain should not be surprising to us. Farmers have long been “fattening up” their livestock by feeding them antibiotics.

Type I Diabetes

Type I Diabetes occurs in children when their immune systems attack the islet cells which produce insulin in their pancreases. The incidence of Type I Diabetes has been doubling every 20 years and the average age of diagnosis has dropped from 9 to 6 years old.   This is a very challenging, life-long condition for these children.

Before proceeding, we need a quick lesson on the role of two classes of white blood cells in your immune system, known has helper T-cells and suppressor T-cells. Helper T-cells circulate through the blood stream “looking” for unfamiliar proteins. These unfamiliar proteins, since they could be from a virus, pathogenic bacteria, or other toxin, are a potential health risk. Your helper T-cells “tag” these unfamiliar proteins, which signals the rest of the immune system to attack.   Suppressor T-cells moderate the actions of your immune system such that it does not go overboard and harm you while eliminating the suspected threat. Therefore, maintaining an appropriate balance of helper and suppressor T-cells is an important factor in maintaining good health.

The development of Type I Diabetes occurs in two steps. First, you must have a genetic predisposition such that proteins on the surface of your islet cells look “suspicious” to your helper T-cells. Second, your suppressor T-cells must fail in their job to moderate the response of your immune system after it has been summoned by your helper T-cells. In a person with a diverse microbiome, resident bacteria and suppressor T-cells exist in an equilibrium that has developed over the last couple hundred million years of evolution. When a person’s microbiome contains fewer species of bacteria, their body generates fewer suppressor T-cells. That is not the case with helper T-cells. People who generate fewer suppressor T-cells are unable to “calm” their immune systems and thus are far more susceptible to autoimmune diseases, type I diabetes and otherwise.

Food Allergies

Your likely impression that rates of food allergies in children have been rising dramatically is correct. In the United States, the rate of peanut allergies tripled from 1997 to 2008, and Celiac’s Disease, an allergy to wheat gluten, has quadrupled since 1950. The dynamics behind these increases are nearly identical to those described above for Type I diabetes. An allergic reaction occurs when the body considers a protein from things such as nuts, soy, eggs, milk, bee stings and the like, to be a potential threat and triggers the immune system to respond. Here again, if you have a less diverse microbiome and therefore have fewer suppressor T cells, you are vulnerable to being allergic to more things and more prone to having a an extreme, possibly life-threatening, reaction.


If I were to describe all of the medical issues covered in Missing Microbes that arise from having a low-diversity microbiome, this column would be far too long. I recommend reading Dr. Blaser’s book to learn more about the relationship between your microbiome and asthma, eczema, heartburn/reflux, ulcerative colitis, Crone’s Disease, and early-onset of puberty in girls.


Despite the complexity and thoroughness of Missing Microbes, the key conclusions are not difficult to grasp. In Part I we discussed that humans co-evolved with their resident bacteria and along the way outsourced key biological functions to them. With that background in mind, we’ve now explored how killing off some species of our bacterial partners can harm our health. Next week in Part III, I will review Dr. Blaser’s recommendations for what we can do about these problems. As a bit of foreshadowing, it appears that we can address these problems without giving up the benefits that antibiotics have brought us. See you next week.

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NC Scores Low on Public Health Report Card

According to the NC Prevention report card, North Carolina residents are struggling to meet public health goals for tobacco use, nutrition, obesity and physical activity.

Rachel Zuker is the research and evaluation coordinator for the Chapel Hill-based nonprofit Prevention Partners. She says the state’s grades are not looking good.

“Right now, we’re not doing great,” says Zuker. “We have a C in tobacco, a D in physical activity and Fs in both nutrition and obesity, so there’s definitely work to be done.”

The report measures state progress on national public health goals set for 2020.

Tobacco use continues to be the leading cause of preventable death in the US, and here in North Carolina, residents are smoking at a higher rate than elsewhere.

Zuker says this year North Carolina earned a C for tobacco use, down from a B grade last year.

“In tobacco policies, other states have continued to make progress, whereas we’ve kind of stayed the same, so I think we’re seeing ourselves slide a little bit in tobacco, which is too bad, because previously we’d been at a B and we were seeing that as a great area,” says Zucker.

The report points to policy changes at the state and local levels that could lower tobacco use, including designating more smoke-free places and increasing funding for cessation support services.

When it comes to nutrition and obesity, the report suggests economic challenges are hitting families hard. Seventeen percent of North Carolina households face hunger. At the same time, two out of every three adults and slightly more than a quarter of  high school students are overweight or obese, and the problem is more significant for those with lower levels of education and income.

Zuker says obesity and poor diet go hand in hand, as it costs more to eat well.

“You can be malnourished and obese. There’s a difference between malnourishment and obesity.”

Compounding the problem, the majority of North Carolina’s adults are not getting the recommended weekly minimum amount of physical activity.

Zuker says when it comes to changing the state’s health grade, workplace programs can have a big impact.

“People spend so much of their daily lives at work, and so if we see workplaces passing policies to promote cheaper, healthy foods, time for physical activities or access to those facilities, helping employees to quit [smoking], we really see that as key.”

Prevention Partners is launching an initiative with some of North Carolina’s largest employers to try to change the workplace culture to support healthy lifestyles. Zuker says the plan, called Healthy Together North Carolina, could reach up to 20 percent of the state’s workforce.

You can read the full interactive report card here.


Bacteria and Obesity, A Surprising Link

As a chemical engineer, I am naturally drawn to write columns about energy and manufacturing.  However, if you have been reading my columns for a while you will have noticed that I keep coming back to topics concerning the vital importance of maintaining a healthy population of beneficial bacteria within us, particularly within our gastrointestinal (GI) system.  I did not expect to return to this arena again so soon, but then I learned something new, something amazing.  So here we go again.

First, here are some relevant points of the past columns on this subject along with the associated links.

  • By a wide margin, most of the DNA in our bodies is not our own but rather belongs to our resident bacteria.  With this in mind, it is more accurate to consider our bodies as ecosystems rather than as isolated organisms.
  • When people are treated with antibiotics, their population of healthy GI system bacteria is temporarily reduced.  In some cases, the body is unable re-establish the former healthy bacterial equilibrium leading to debilitating diarrhea and, in extreme cases, death.  Recent studies have shown dramatic improvements for patients suffering from this condition by recolonizing their GI tract with bacteria from a healthy individual through a process known as a fecal transplant.
  • Prior to birth, babies have sterile GI tracts.  To ensure good health, and even survival, newborns must quickly populate their GI tracts with the proper bacteria.  Babies born vaginally ingest fluids from their mothers during birth which contain the necessary beneficial bacteria to colonize their intestines.  Babies born via C-section miss this opportunity and, due to this slow start on GI tract health, develop food allegories at a rate five times higher than babies born vaginally.

These previous columns on importance of bacteria in the GI tract had already piqued my curiosity and then I stumbled upon a new wrinkle to this story, an amazing wrinkle.   A recent study in the International Journal of Obesity (IJO) concluded that use of antibiotics in young children results in reduced diversity of GI tract bacteria for sustained periods of time.  This was not particularly surprising.  The noteworthy portion of the IJO study was that these children gained weight at increased rates and maintained higher body weights into adulthood. When I read the abstract for this study, I had the sensation of having the fog lifted from my brain and a whole series of ideas and concepts suddenly crystallized for me.  An “Aha!” moment, so to speak.

First it struck me that people are just like cows, pigs, and chickens.  For the past half century or so farmers have been feeding antibiotics to their livestock from the day they are born.  For reasons that have not been entirely clear, this practice results in dramatically increased rates of weight gain and much larger overall size.  The IJO study strongly suggests that same mechanism is operative in humans, feed them antibiotics, particularly at a very young age, and they gain weight faster and become larger.  This analogy between livestock and humans is not much of a reach.  However, in all of the discussions regarding increased rates of obesity in the United States I have not encountered any suggestion that increased antibiotic use was a possible root cause.

Next I thought about people who to seem to be able to eat a tremendous number of calories but don’t ever gain weight.  The popular view is that these people have a “fast metabolism”.   As an engineer, I have never been able to accept this explanation as the implied heat and energy balance doesn’t really work.   While there are some differences in people’s metabolic rates (calorie consumption at rest) they are not large enough to explain why my friend Chris 1 who, after a large meal at a Chinese Buffet often eats a large pizza for desert, has almost no body fat. (I’m not exaggerating, I promise.) If someone’s metabolic rate was high enough to expend this many calories, even while just sitting around, their skin would heat up and they would start to sweat.  Chris isn’t particularly sweaty. The fascinating implication of the IJO study is that Chris likely has a population of bacteria in his GI tract that limits his ability to gain weight even when he eats prodigious amounts of food.

So let’s take what we know about bacteria in the GI tract so far and extrapolate a little.  We already know from the fecal transplant experiments that we can colonize person A’s GI tract with bacteria from person B.   This suggests that if I can take bacteria from someone with a “high metabolism” like Chris and transplant it into the intestines of someone who seems to carry excess pounds no matter what, that he/she may become thin and stay that way.  Given the staggering amount of money currently expended on diet plans and weight loss pills, a simple bacterial transplant procedure which induces sustainable weight loss could be the invention of the century.

Have a comment or question?  Use the comment interface below or send me an email tocommonscience@chapelboro.com.

(1)    I have omitted Chris’ last name so people don’t start chasing him down the street demanding a bacterial sample.


Obesity Lawsuits Thwarted In Bill Going To McCrory

RALEIGH, N.C. (AP) – North Carolina companies that manufacture, advertise or distribute food could soon have additional legal protections from lawsuits by people claiming their products led to their obesity.

The House voted 99-16 Tuesday in favor of minor Senate changes to legislation barring civil actions on claims that long-term consumption of food or drinks led to excessive weight gain and health problems. Governor Pat McCrory next gets the legislation for his signature to become law.

The “Commonsense Consumption Act” makes clear local governments can’t pass ordinances like one passed in New York City prohibiting the sale of large soft drinks.

North Carolina is one of handful of states that follows the tort of contributory negligence, in which a plaintiff recovers nothing even if only slightly to blame for what happened.