You Are Only 50% You

Cell-for-cell, less than one half of our body is human. Consider this: while we have approximately thirty trillion tiny cells that make up a single adult body, we also have all of those good microbes — and often some nasties too — that are along for the ride. These good microbes colonize mainly the skin, the digestive system, and the vagina in a population of approximately thirty-fourty trillion strong — meaning for every human cell we also have around 1.3 bacterial cells! These microbes are not just hitchhikers; increasing evidence shows that they appear to be pivotal to normal human health, opening up the fascinating possibility of custom-engineered, personal disease fighting bugs.
In fact, our relationship with these microbes is deeply co-evolved, and lasts our entire life. Distinct and complex communities exist in every region of the body where microbes can grow, and seemingly everything we encounter in our environment has an impact on what our microbiota looks like.

An example skin microbiome composition, which is highly diverse in each punctate region of the body

While the bacteria are living commensally with us, at their level it appears more like full-blown warfare. Each bacterium competes for its place in the pecking order in order to persist within the population. With that comes a battle for resources. Everything you experience in your day-to-day world — from the food you eat to the country in which you live — affords a different set of resources for the microbiota face-off, and some are better than others. The balance is a constant tightrope walk — where disharmony between the body, the gut and the environment can manifest as illness.
Curing the incurable

This phenomenon has opened the floodgates for metagenomic research. By looking at the bacterial metagenome through next generation sequencing, the species living on different parts of our body can be compared.  Species composition can be analyzed across different populations in the hope of understanding how we should be caring for our microbiota, and how changes in lifestyle impact these specimens.
Professor George Weinstock of the Jackson Laboratory for Genomic Medicine spoke to the Festival of Genomics about how understanding this phenomenon has led to cures for bacteremias that had previously been difficult to treat. Clostridium difficile is a gut organism that usually exists harmlessly as part of the lower intestine microbiome. In a hospital environment, however, C. difficile often becomes a deadly disease. Patients who are already sick were at risk of extreme diarrhea and many have died as a result.

An electron micrograph closeup of Clostridium difficile.

This happens because C. difficile is resistant to antibiotics. When a sick patient takes antibiotics they decimate their microbiome (In fact, a course of antibiotics completely, and permanently changes a person’s microbiome structure). However C. difficile is not affected. A sick patient’s immune system can’t keep C. difficile at bay, and the organism becomes an opportunistic pathogen that cannot be treated with conventional medicine.
Surprisingly, the solution to this disease came out of a somewhat unpalatable ancient Chinese medicine called ‘yellow soup’. Yellow soup consists of warm water and the key ingredient: human feces. It was used to treat abdominal diseases in Chinese medical texts. If you went to your doctor now and were told your cure was to take a supplement of fecal matter, you would likely be hightailing it out of there looking for a new doctor while calling the FDA to report malpractice. However, when fecal matter was taken from a healthy patient, dried, put in pill form, and taken by patients with C. difficile, 60 of 60 cases had their C. difficile-related diarrhea cured within 72 hours. Transplantation of a healthy microbiome quashed the disease-causing bacteria.
Acne, Malnourishment and the Microbiome

In addition to the balance of gut bacteria, the microbiome plays a role in the normal working of many areas of your body including your skin, lungs and genitalia. This has left a fascinating door open for synthetic biology – which hoped to turn the microbiome into an even better disease-fighting force. For example, instead of having a strain of Propionibacterium acnes that causes acne, can we engineer a strain that works to quash the painful spot-causing strain while secreting beneficial molecules like antioxidants or molecules to promote the healing process? Alternatively, can we aid those who are malnourished by providing a low cost probiotic supplement that has been engineered to produce vitamins to improve health?

A teenager suffering from acne caused by certain subspecies of Propionibacterium acnes

While these ideas are somewhat utopian solutions, people are already working in this field. As mentioned in our previous blog post ‘Hive-Mind of iGEM’, many iGEMmers produce fascinating projects related to the microbiome. 2015’s iGEM saw 3D printed combs which allowed the application of bacteria engineered to fight the cause of male pattern baldness, long chain sugar-hungry bacteria that colonize the gut to help manage diabetes, and psychobiotics — microbiota members that can aid individuals with mental illnesses by tapping into the well-documented link between gut microbiota and mood.
A number of research pieces have also come out of this space, with a surprising interest being paid to yogurt. Yogurt is already an amazing vehicle to deliver probiotic organisms, with good lactobacilli commonly found in Greek yogurts on the market today. A paper from Mansour Mohamadzadeh at Northwestern University showed the deletion of a gene that causes inflammation from the genome of lactobacilli allowed the bacteria to only secrete the beneficial molecule Interleukin-10, bolstering the immune system without any negative effects.
Probiotic E. coli have also been hijacked to enhance our microbiome. Tal Danino’s team at MIT created a yogurt-delivered commensal that can scout for disease. As a proof of principle, they fed engineered probiotic E. coli to mice. If the mouse had liver cancer, the bacteria secreted a measurable signal which is passed in urine. The implications of this could be lifesaving. Dr. Danino described in his recent TED talk how liver tumor cells are difficult to diagnose visually because of their small size, so they are often discovered after it is too late.
CRISPR and the Microbiome

Notably, the CRISPR genome editing technology has been used in this field, making an engineered microbiome accessible. The brainchild of the Lu lab of MIT is a genome editing CRISPR toolbox , which allows the easy engineering of the common gut bacteria Bacteroides thetaiotaomicron. By using a non-cutting version of the CRISPR system in combination with a genetic circuit of binary-like gene expression switches, the team showed an important proof of principle – computer memory-like responses to different stimuli can be programmed into the bacteria under different disease states, all of which is tightly controlled and validated in the mouse model. If the B. thetaiotaomicron encounters a disease, CRISPR gets to work activating a small number of a consortium of genes to kill damaging organisms, or to repair damaged organic structures.
CRISPR can also be used to control the fine balance of the human microbiome and its impact on disease and mental health. If a particular bacteria is no longer needed (i.e. the disease state has passed, or it is found in a part of the body where it is not required), CRISPR can be activated to function like scissors, cutting up the bacteria’s genome and removing it from the population.

CRISPR-CAS9 gene editing complex from Streptococcus pyogenes. The Cas9 nuclease protein (teal/blue) uses a guide RNA (lime green) sequence to cut DNA (magenta) at a complementary site.

It will be fascinating to watch this relatively new space as it evolves. Synthetic biology is now far beyond just metabolic engineering. Microbiome engineering is a perfect example of this notion. To realize the possibility of microbiome engineering, we required both the genome engineering tools usually used by cell biologists or gene engineers in the form of CRISPR, as well as an understanding that our microbiota plays vital roles in human health afforded by metagenomics. With this converging of technologies, we are changing the way we think about the often forgotten 50% of the cells that make up the human body, and looking at new ways of diagnosing and treating complex diseases. Just think, in a few years’ time we could be eating our cancer cure as pots of probiotic-filled yogurt!