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In 1958, a surgeon in Denver, Colorado, used fecal enemas to save the lives of four patients.

The patients had fallen seriously ill after taking a course of antibiotics to treat a form of colitis, and Dr. Ben Eiseman concluded the drugs had disrupted their normal gut microbes, killing organisms that would normally keep them healthy. To restore the balance in their intestines, he infused the patients with stool from healthy women in a nearby maternity ward. They recovered within hours.

The procedure – with its remarkable results – was the first of its kind published in a Western medical journal.

Sixty-five years later, the microbiome revolution is roaring ahead. An enema-based therapy like the one administered in 1958, now known as fecal microbiota transplantation (FMT), was approved by the U.S. FDA in late 2022, and mounting research points to the potential of microbiome therapeutics to treat and protect against a range of intestinal illnesses, along with a host of other serious diseases, from autoimmune disorders to cancer.

Rapidly accumulating evidence shows associations between the microbiome and everything from aging and inflammation to infection protection to appetite and obesity. The link between the microbiome and health is clear – and microbiome therapeutics are advancing far beyond FMT.

“Our understanding of the microbiome has completely transformed. We are at the point now with the science where potential treatment options are generating strong data in clinical trials,” said Eric Shaff, president and CEO of Seres Therapeutics, a leading microbiome therapeutics company based in Cambridge, Massachusetts. “An entirely new class of medicines may be emerging.”

Leading biotherapeutic companies and researchers are identifying and isolating bacterial strains with the potential to treat various diseases by restoring the microbiome to a state of health.

There is ongoing research into investigational products to potentially modulate gut bacteria to make cancer treatments more effective and to protect medically compromised transplant patients from life-threatening infections and conditions like Graft-versus-Host Disease (GvHD). Microbiome therapeutics are also being studied for their potential to decolonize pathogens and modulate host function to reduce and prevent against antibiotic resistance, one of the world’s leading global public health threats.

“This novel type of technology has the potential to break the transmission cycle of antibiotic-resistant bacteria and prevent bloodstream infections,” said Matthew Henn, chief scientific officer for Seres, where he has led research and discovery for the past decade. “That could be transformative. It has the potential to fundamentally change public health.”

And new modalities are being explored – including orally through a pill – that are more familiar to patients, which could ignite a new wave of interest in microbiome therapeutics.

Extraordinary medical pursuits require continual innovation. As the science surrounding the microbiome continues to progress and lead to more breakthroughs, the industry is setting its sights on additional considerations, such as the need for safe, high-quality manufacturing and patient access. The rapid progress achieved over the past few years lends credibility to our commitment and perseverance to make discoveries and find solutions.

Microbiome research has come a long way since 1958.

Dr. Eiseman predicted that FMT would become a new standard treatment, but it was largely outcast to the medical fringes, and progress in microbiome-targeted therapies was sparse for decades. Then, in the early 2000s, new technology made it possible to quickly sequence the genetic material of bacterial strains that make up our microbiome, many of which cannot survive outside the human body and are all but impossible to study in a lab.

That kickstarted an explosion of research, including the Human Microbiome Project (HMP), an ambitious effort to take inventory of the microbiomes of 242 adults. The research boom enabled by the HMP’s foundational data and methods generated a new understanding of how microbes in and on the human body interact functionally with one another and human cells and tissues.

Researchers can now look with incredible resolution at the specific pathways impacted by the crosstalk between microbes and human cells. With their findings, they are designing drugs to potentially treat important diseases.

“This advancement in research is an excellent example of industry and academia identifying a promising path forward, and then collaborating to unlock the mysteries of the microbiome to get us where we are today,” said Shaff. “Tireless research and discovery efforts have brought the potential of the microbiome to support human health to the forefront.”

Today, the scientific and medical communities recognize the power of the microbiome as a complex ecosystem. It is incredibly abundant, diverse, and dynamic. Trillions of microorganisms swim inside people’s bodies and crawl on their skin, including thousands of species of bacteria, fungi, viruses, and other microbes that work together to aid digestion, synthesize vitamins and hormones, and protect against infection.

Shaped by genetics, age, diet, and environmental factors, the composition of each person’s microbiome is unique. And when the microbiome is thrown off balance or when its diversity dwindles, people become susceptible to serious diseases, including recurrent C. difficile, the bacteria that plagued Dr. Eiseman’s patients and continues to cause an estimated 156,000 cases in the U.S. annually.

In 2017, Dr. Eiseman reflected that the relatively simple procedure he had performed decades earlier made a “small splash.” Companies such as Seres and the entire scientific community now aspire to make that the biggest understatement in modern medicine.

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