The case against being a germaphobe
On bacteria & poop
Via (Wordpress):
Instead of introducing a specific article to y’all today, I’ve decided to present on a growing body of research on the human microbiome.
What is the human microbiome?
The human microbiome is defined as the conglomeration of microorganisms that resides in our body, including bacteria, fungi, and archaea. They reside on the surface and deeper layers of our skin, in our saliva, and gastrointestinal tract. The image below gives you an idea of where different types of bacteria can be found in our bodies.
In the human body, these microorganisms outnumber our human cells by a factor of ten. In other words, we are about 90% bacteria, 10% human. (How’s that for an identity crisis?) In the past decade or so, research on the human microbiome seems to have grown exponentially. The Human Microbiome Project was launched by the National Institutes of Health in 2007 to generate the resources and expertise needed to characterize the human microbiome and investigate its role in health and disease; approximately $170 million was allocated to this project for five years. Since then, advances in sequencing technologies coupled with new bioinformatic developments have allowed the scientific community to begin to investigate the human microbiome.
Researchers have discovered these microbes that live in our body aren’t just chillin’-out-maxin’-relaxin’-all-cool, but rather, provide functions that are vital to the maintenance of our health. The trillions of bacteria that live in our gut, for example, are thought to play important roles in the production of enzymes and vitamins in addition to the breakdown of food that our cells can’t do by themselves.
What is the contribution of the microbiota to human health?
Many of our beneficial bacteria are essential for the robust development of the immune system and maintenance of physiologic processes in multiple organs. However, numerous chronic infectious, inflammatory, and metabolic diseases in humans have been associated with alterations in the composition or localization of bacteria that result in dysregulated host-bacteria relationships. Interestingly, the cells of our immune system can communicate with bacteria to localize them in a particular region of our body. The microbiota, in turn, can also secrete certain proteins that affect immune cell function. In addition, studies have demonstrated that the microbiome we have at birth can influence fat-composition later on in life or that certain populations of bacteria can be correlated with the development & onset of Type-2 Diabetes.
How can our microbiomes be altered?
The human microbiome is particularly sensitive to perturbations. For example, changes in diet can alter the balance between certain types of bacteria, both short-term and long-term. In turn, some researchers have demonstrated links between microbiota composition and mood changes, giving ‘you are what you eat’ almost a literal meaning. You may have seen probiotics being sold in the organic section of some supermarkets — they are bacteria that help maintain the natural balance of microorganisms in the intestine. The normal human digestive tract contains about 400 types of probiotic bacteria that reduce the growth of harmful bacteria to promote a healthy digestive system. (The largest group of probiotic bacteria in the intestine is lactic acid bacteria, most commonly found in yogurt with live cultures.)
Since antibiotics do not discriminate against ‘good’ vs ‘bad’ bacteria, some strong antibiotic treatments can cause an overgrowth of ‘bad’ bacteria by concurrently eliminating the ‘good’/housekeeping bacteria populations. Clostridium difficile is a strain of bacteria that is best known for causing antibiotic-associated diarrhea. Normally, this population is present in minute amounts in healthy individuals. However, in some cases, antibiotic treatment can decrease the amount of good bacteria to a point at which C. difficile will essentially take over the gut, leading to diarrhea — and in more extreme cases — sepsis or even death. To treat such conditions, fecal transplants are performed and have been demonstrated to be quite successful, despite the huge yuck-factor. The transplantation involves first flushing the contents of the patients’ colon (to presumably eliminate as much of the C. difficile colonies as possible), and then taking feces (mixing it up with saline) from a healthy donor into the gastrointestinal tract of the ill recipient via enema, a process whereby liquids are introduced into the rectum and large intestine via the anus. These transplants have been done since the ’50s and ’60s to treat C. difficile. I can only envision the looks of disgust you all have on your faces right now, but here’s why it makes sense: roughly 60% of what is in your stool is bacteria, and by putting back normal, healthy microorganisms that had been wiped out by antibiotics, we can re-establish the patient’s resistance to colonization by C. difficile by introducing the colonies of healthy bacteria to restore balance to the local intestinal microbiota.
How should the growing body of knowledge involving the human microbiota inform my lifestyle choices?
Up to you! I love reading about how modifiable certain systems in our cells and bodies are (e.g., epigenetics) as I like the idea of having some sort of agency over how my lifestyle choices can affect my own health. At the same time, I also think it’s important to keep in mind that correlation does not imply causation. But of course, we can try to eat a healthy, low-fat diet and/or consume probiotics (As a tea-lover, I am a huge proponent of brewing my own kombucha, as it’s naturally fermented with a living colony of bacteria and yeast. Warning: you may gross out roommates and/or your significant other by doing this). Also, we can try to not overdose on antibiotics / put ourselves in situations where we’d have to get fecal transplants. Disclaimer: I do not have a medical degree, so take all this advice with a grain (or tub) of salt!
What are the challenges in this field?
While advances in DNA sequencing have made it feasible to analyze the entire human microbiome, it’s still extremely difficult to isolate the majority (>95%) of microorganisms and culture them, presumably because the separation and growth conditions have not necessarily been worked out. If this were possible, we could understand the role of specific species of bacteria in how they regulate metabolism or our immune system. (e.g., what proteins do they secrete? How do they communicate with neighboring human cells?) Additionally, there’s a great deal of interest in using the microbiome data to look for new kinds of probiotics. However, the most powerful of these probiotics are anaerobic (thus, cannot survive in the presence of oxygen) and produce by-products with foul odors, which could limit their use.
Further related non-technical (possibly even fun) reading:
[1] Michael Spector: Exploring the Human Microbiome. The New Yorker. Oct 22, 2012
[2] The right bacteria might help fight obesity. AP. Sept 5, 2013.
[3] Michael Pollan on the Links Between Biodiversity and Health. Yale Environment 360. May 28, 2013.
Sources:
[1] Gormon, Christine. “Explore the Human Microbiome [Interactive]“ Scientific American.May 15, 2012. <http://www.scientificamerican.com/article.cfm?id=microbiome-graphic-explore-human-microbiome >
[2] Arumugam et al. Enterotypes of the human gut microbiome. Nature. 2011. 473: 174-180.
[3] Sekirov et al. Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection. Infect Immun. 2008. 76: 4726-4736.
[4] Cho et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature. 2012. 488: 621-626.
[5] Qin et al. A metagenome-wide association of gut microbiota in Type 2 diabetes. Nature. 2012. 490: 55-60.
[6] Hildebrandt et al. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology. 2009. 137(5): 1716-1724.
