Christian Furlan Freguia Ph.D. Director of Research Synthetic Biologics
Michael Kaleko M.D., Ph.D. Senior Vice President of Research and Development Synthetic Biologics

The Next Frontier for Novel Therapeutics

In the 17th century, the “Father of Microbiology,” Anton van Leeuwenhoek, used his newly invented microscope to describe “animalcules” in the plaque from his own teeth. We now know that the GI tract is teeming with bacteria, yeasts, protozoa, archaea, and viruses, collectively referred to as the microbiota. Their DNA content, the microbiome, has been estimated to contain up to 100-fold more genes than its human host.

The gut bacteria have long been known to aid in digestion, produce important nutrients such as vitamins, and protect from overgrowth of virulent pathogens. While studies of the gut microbiota have historically been limited by our inability to grow many of its fastidious organisms in a petri dish, the advent of rapid and inexpensive DNA sequencing has enabled the identification of gut bacteria en masse without the need to first culture them.

In the past decade, an explosion of research in this field has revealed a remarkable symbiotic relationship between the gut bacteria and its human host, and biotech companies are beginning to manipulate this relationship to improve human health. The most clear-cut example is for the treatment of the severe and sometimes fatal diarrheal illness caused by Clostridium difficile (C. diff). When patients are treated with antibiotics, these medications damage the microbiome, which enables the C. diff bacterium to set up shop. Unfortunately, when more antibiotics are used to treat the C. diff infection, they perpetuate this damage leading to frequent C. diff relapses. In contrast, transplantation of feces from a healthy donor, known as fecal microbiota transplantation (FMT), restores the microbiota and leads to a cure more than 90% of the time.

More amazingly, research in the last decade has revealed that the specific bacterial communities living in an individual’s gastrointestinal (GI) tract are closely associated with the person’s physiologic functions as they relate to both health and disease. Microbial profiles have been correlated with immune competence, metabolic activities, neurologic and cardiovascular functions, and cancer risk. Conversely, disruption of the indigenous microbiota is associated with many human conditions including obesity, diabetes, liver disease, inflammatory bowel disease, irritable bowel syndrome, celiac disease, asthma, autism, multiple sclerosis, HIV progression, and even aging. And the list continues to grow.

Thus far, in humans, the relationship between specific GI bacterial communities and health remains at the level of association, without evidence for causality. However, in mice, many published studies have demonstrated that manipulation of the microbiome can actually cause or treat certain diseases. Such studies are made possible through the use of gnotobiotic mice, which are born and raised without any intestinal microbiota. Providing gut bacteria to these animals enables tight control of their microbiomes. For example, mouse microbiomes can be manipulated to produce fat or thin animals, to treat asthma, and to render certain cancer treatments efficacious or not. In fact, a recent paper in the journal Science suggested that the reproducibility of some laboratory mouse studies could, in fact, be confounded simply by the bacteria living in the animals’ GI tracts—a new variable for scientists to worry about!

Whereas the concept of using fecal matter to treat human disease originated in ancient China, the potential to translate modern mouse data into human therapeutics has only recently opened the biotech doorway to the concept of “bugs as drugs.” So far, no indication has been as successful as the treatment of C. diff infection; but research is advancing quickly as exemplified by the two vignettes below.

Two disease areas that are increasing in frequency without obvious explanation and that may be exacerbated, at least in part, by alterations in gut flora are obesity and neurodevelopmental disorders. Obesity and associated diabetes were among the first correlations described with microbiome profiles. The agricultural industry has known for decades that providing antibiotics to farm animals increases their growth rate. And humans may be no exception. Recent data are beginning to suggest that repeated courses of antibiotics in early childhood may be associated with an increased risk of obesity later. Moreover, in mice, the microbial profiles in obese animals tend to be different from those of thin animals; and the same may be true for humans.

In a 2013 Science publication, feces were taken from monozygotic human twins, one of whom was thin and the other obese, and transplanted into mice. The feces from the thin twin yielded thin mice, and those from the obese donor yielded heavier mice. A subsequent paper in the journal Open Forum Infectious Diseases described an anecdotal story in which FMT, used to treat C. diff infection, was followed by obesity in a woman who had been thin all her life. While premature to conclude that microbial profiles can predispose to obesity, it seems reasonable to speculate that the GI microbiome and obesity may perpetuate each other in a vicious cycle. The microbiome may be shaped, in part, by obesity; but then it could contribute to further weight gain by increasing the efficiency of digestion or perhaps through appetite stimulation.

To date, there is no consensus on those specific microbiome characteristics that predispose to weight gain. Thus, the definitive role of the microbiome in the obesity epidemic will have to await further research. Not unexpectedly though, researchers are actively exploring FMT as a treatment for obesity and biotech companies are considering other microbiome-based treatments.

One minor note of caution—based on the gut flora’s integrated role in multiple aspects of human physiology, it will be interesting to learn if FMT or therapeutic microbiome manipulation could lead to unintended long-term consequences for human health and disease.

A second area attracting considerable attention is the unexpected relationship between the gut flora and central nervous system, the so called gut-brain-axis. Perhaps it is no coincidence that our most primal emotions are referred to as “gut feelings.” The intestines and brain have multiple channels for two-way communication that include a direct link via the vagus nerve and systemic signaling via cytokines, immune cells, hormones, and biologically active small molecules. Some gut bacteria can even make neurotransmitters such as GABA.

In animal models, germ-free, gnotobiotic mice tend to have altered behavior with social impairment and exaggerated responses to stress. Similarly, damaging the microbiome of normal mice with antibiotics can alter their behavior. And it is a two-way street. Changes to the microbiota can alter brain synaptic patterns and stresses on the mice can alter their gut microbial profiles. Moreover, FMT in mice can transmit the donors’ behavioral patterns. Most importantly, there are mounting data to suggest that humans with various neurological and psychiatric diseases can have distinct gut microbiome patterns. Researchers are actively characterizing the microbiomes of patients with depression, schizophrenia, autism spectrum disorders, addiction, multiple sclerosis, and others. While no microbiome-based therapeutics would seem to be on the near horizon for neurological disorders, there is real possibility of someday altering the gut flora to address mental illness.

One topic that is particularly fascinating is the role of the maternal microbiome in children with neurodevelopmental disorders. A review in Science in August of 2016 outlined how immune activation in pregnant mice can predispose the pups to lifelong behavioral changes. The paper discusses how maternal immune activation (MIA) may also be relevant to human susceptibility to schizophrenia, autism, and potentially a wide array of neurologic and psychiatric illnesses. MIA is generally attributed to infection, autoimmune disease, and genetic predisposition. However, microbiome-mediated leakage of bacterial toxins into the blood, known colloquially as “leaky gut,” is also an established cause of systemic inflammation. One may speculate that the maternal microbiome, in addition to that of the child, could play a role in neurodevelopmental disorders, thus providing a potentially tractable means of diminishing the risk for these disorders in the future.

Armed with ever improving DNA sequencing technologies and the newly recognized role of the microbiome in human health, biotech companies have already emerged to hunt for the magic bullet of beneficial bacteria to treat and prevent disease. While FMT for C. diff infection provided the initial spark, several key questions must be addressed to optimally apply this strategy more generally. Specifically: 1) what defines a healthy microbiome; 2) what factors shape the microbial communities and promote the durability of individual species; 3) how does the microbiome modulate human physiology; 4) what analytical analyses and preclinical studies will be most predictive for clinical success; and 5) what strategies can be envisioned to best utilize the microbiome to treat disease? These questions will be discussed in Part 2 of this article. Suffice it to say, the field is advancing rapidly and we can already predict that microbiome-based therapeutics will one day occupy a prominent niche in the medical armamentarium.

Christian Furlan Freguia, Ph.D. (, is director, research and Michael Kaleko, M.D., Ph.D. ( is senior vice president, research & development at Synthetic Biologics, Inc.


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