I Contain Multitudes

Chapter 9 brings up the concept of potentially administering bacteria as a medicine to cure a disease such as obesity or depression. As the chapter details, it isn’t that simple. That is also the case for probiotics that are sold on the market. A probiotic is a bacterium that imparts health benefits when consumed. Many scientists are looking for ways to use bacteria as probiotics to solve disease crises throughout the world. They are also looking at the opposite: eliminating single bacteria. Both routes are plausible, but both come with their own sets of challenges.

Chapter 9 opens by detailing a disease called elephantiasis, which is characterized by a swelling of lymph nodes to extreme sizes, particularly in the groin area. The disease is caused by a nematode that is passed through mosquito bites, which give the nematode larvae a route into the body and into the lymph tissue. A combination of the nematode and a familiar bacterium, Wolbachia, cause the disease. The nematodes need these bacteria to finish their life cycle, and when the worms die, they release the bacteria to trigger an immune response (213). The combination of the two immune responses, one towards the bacteria and one towards the nematode, causes the symptoms of the disease. In this case, killing the nematodes makes the disease worse because doing so releases more bacteria (213).

One organization is focusing on eliminating Wolbachia instead of the nematodes to cure the disease. This international team is called A.WOL—The Anti-Wolbachia Consortium—and its mission is to find drugs that target the bacteria specifically (214). By breaking this symbiosis, the team would be able to improve the lives of millions. However, it will take time to screen and identify compounds that are not only effective but more accessible to the populations that need them.

The landscape of medicine is fundamentally changing because of what we have learned studying the symbiosis of our microbes. Microbe-based prescriptions are becoming a reality with the development of cocktails of bacteria that will correct illnesses and ways of transplanting entire communities from one person to another (215). Things are not as simple as taking a pill of microbes, though: “To control a microbe is to sculpt an entire world—which is as hard as it sounds” (216), Yong says. It’s also difficult to predict the consequences of changing a community of bacteria. Removing or adding a microbe might mean dysbiosis of an entire community.

Control of amphibious diseases is an area of conservation in which bacteria are being considered as a solution for the spread of disease. Batrachochytrium dendrobatis (Bd) is a fatal fungus that is killing frogs at a rapid pace by thickening the amphibian’s skin and stopping them from absorbing salts (216). Bd was discovered in 1990 and has spread to six continents since, destroying populations in a matter of weeks (216). The spread can be attributed to our increased amount of travel via planes, cars, and boats. One scientist studying Bd found that one salamander was covered in antifungal chemicals that kept bacteria from growing (217-18). Bacteria, it turns out, produced those antifungals and might be the key to saving amphibians from Bd.

Spreading bacteria through entire populations isn’t easy, though, and it’s not clear how these bacteria are acting as antifungals. The few bacteria that seem to be good contenders worked to protect from Bd in the lab, but it is less clear if they will work in the wild. In one trial, frogs were dipped in the bacteria; 39% of those frogs survived, while their peers all died (219). Despite the minor success, it is not possible to dip every frog in bacteria. Seeding soils with these probiotics might be an option, but introducing an entire bacterium into an ecosystem can have larger consequences.

When we hear the term probiotic, we generally think of yogurts or capsules. Even the most heavy-duty probiotics only contain a few hundred billion bacteria, which is a small percentage of what our gut contains (222). The bacteria are also typically not found in our gut, so we are adding a small, rare number of bacteria to a larger pool. Most probiotic bacteria can’t even take hold in the gut for lack of room or necessary nutrients (222).

Many scientific studies showing a benefit to probiotics come with caveats that they used lab-grown strains or did not test them in humans. Findings from studies deemed reliable suggest there is evidence that probiotics can shorten bouts of diarrhea and reduce the risk for gut issues in patients taking antibiotics (223). There is no evidence the probiotics alleviate “allergies, asthma, eczema, obesity, diabetes, more common types of IBD, [or] autism” (223). For this reason, probiotics are typically classified not as medicine, but as food.

There is excessive hype in terms of probiotics, but the concept has potential (224). In theory, it should be possible to fix health issues by taking bacteria and changing our microbial community. We still aren’t using common microbes, or ones that take hold in our gut. It also isn’t clear what impact taking a probiotic can have or how introducing a foreign bacterium will impact the community. The details of those impacts matter.

Fecal microbiota transplants (FMT) are one example of how we can utilize bacteria to cure a dysbiotic microbiome, specifically one disrupted by C. diff. This bacterium causes diarrhea and gut issues and can be difficult to treat. It often rebounds after rounds of antibiotics and becomes resistant. A current treatment method is FMT, which introducing a new microbial community into the patient’s gut and keeps C. diff from taking hold. As Yong explains, “It’s an ecosystem transplant—and attempt to fix a faltering community by completely replacing it, like returfing a lawn that’s overrun by dandelions” (230). FMT cured 94% of patients who underwent the treatment in a clinical trial (231).

C. diff typically is contracted after a person takes antibiotics, and it is controlled by more antibiotics, so the combination of donor microbes and an already wiped out bacteria community might be what does the trick in this case, but the success gives hope to other methods using probiotics. To increase the effectiveness of these drugs, people are crafting personalized infusions intended to impart the maximum benefit and the least harm to the host. Doctors are also prescribing nutrients to help support the bacteria they are prescribing to their patients (236).

Yong closes the chapter inviting us to imagine a future in which microbiome medicine is common. You go to your doctor feeling anxious, and she gives you a bacterium. In fact, she gives you a bacterium for all your health conditions in a personalized cocktail that will best interact with your gut and immune system. These medicines could even offer designer bacteria that only carried the specific genes that were helpful to you.

Synthetic biology is a growing field that applies engineering to biological material and cells (239). Scientists in this field are looking to build a perfect bacterial genome piece by piece to craft a microbe that offers the benefits with none of the consequences and has less of a chance of not taking hold. Biology is complex and chaotic, so engineering these bacteria is not always easy. Scientists must make the bacteria work in the environment that they will eventually live in, and some are nervous at the idea of engineering bacteria that might be permanent inside our bodies (240). There are still plenty of skeptics in this type of medicine, but we aren’t even close to understanding the benefits or consequences of this kind of work. Yong says, “We have finally started to use everything we have learned since Leeuwenhoek first thought to study pond water to improve our lives” (249).