The gut microbiome, a community of hundreds of bacterial species that inhabit the human digestive system, has been linked to changes in neurological development, the effectiveness of cancer immunotherapies, and other aspects of health, according to significant studies over the past ten years. But because of the complexity of these communities, it is difficult to identify the precise cells and substances that are connected to specific diseases.
The most intricate and well-defined synthetic microbiome has been created by Stanford University researchers, who have successfully transplanted over 100 different bacterial species into mice. The capacity to add, remove, and change specific species will help researchers better understand how the microbiome and health are related and, ultimately, create world-class microbiome therapeutics.
Fecal transplants, which transfer the entire natural microbiome from one organism to another, have been used in numerous important microbiome studies. There is no similar set of methods to remove or change one species out of the hundreds in a feces sample, but scientists often turn off a gene or get rid of a protein from a cell or even an animal.
Michael Fischbach, Institute Scholar at Sarafan ChEM-H and corresponding author on the study, which was published in Cell on September 6th, stated that “so much of what we know about biology we wouldn’t know if it weren’t for the ability to manipulate complex biological systems piecewise.”
Fischbach, an associate professor of bioengineering, microbiology, and immunology, and others came up with the idea of creating a microbiome from scratch by growing each of its component bacteria separately and then combining them.
Building the ark
Each microbiome cell fills a certain functional niche and performs chemical activities that disassemble and reassemble chemicals. The researchers had to make sure the final mixture was effective, carrying out all the functions of a full, natural microbiome, as well as stable, maintaining a balance without any one species dominating the others. Given the natural variety among individuals—two people chosen at random share less than half of their microbial genes—choosing the species to include in their synthetic community was equally challenging.
The Human Microbiome Project (HMP), a National Institutes of Health program to sequence the complete microbial genomes of more than 300 people, was consulted by the researchers when they decided to build their colony from the most common bacteria.
In the human gut, Fischbach explained, “We were looking for the Noah’s Ark of bacterial species, attempting to discover the ones that were nearly always there in any individual.”
Over 100 bacterial strains that were found in at least 20% of the HMP participants were chosen. They eventually had 104 species, which they cultivated in separate stocks before combining them into one combined culture to create what they refer to as human community one, or hCom1.
The ability of the strains to coexist in the lab was confirmed, but whether or not their new colony would establish itself in the gut remained to be seen. They administered hCom1 to mice that were specifically created to be bacterial-free. The relative abundance levels of each species remained consistent over a two-month period, and 98% of the constituent species of hCom1 colonized the stomachs of these germ-free mice.
Foreign invasion
The researchers intended to make sure that one or more species would carry out all essential microbiome tasks in order to make their colony more complete. They used a theory called “colonization resistance,” which says that a bacterium that is added to a colony that is already there will only stay if it can fill a niche that is not already filled.
They could create a more complete community by introducing a full microbiome—in the form of a human fecal sample—to their colony and keeping track of any new species that settled there.
Some questioned if this would succeed. According to Fischbach, the bacterial species in hCom1 had only coexisted for a brief period of time. “Here we were, introducing a neighborhood that had lived side by side for ten years. Some individuals believed they would completely destroy our colony. ”
Surprisingly, hCom1 made it, and only about 10% of the cells in the final community came from the fecal transplant.
In at least two of their three fecal transplant investigations, they discovered over 20 novel bacterial species. They created a new community of 119 strains, known as hCom2, by adding those to their original community and eliminating those that failed to establish themselves in mouse guts. This second version made mice much less likely to have problems with their poop than the first one. It was still made by growing each part separately and then putting them together.
Final challenge
The team confronted hCom2-colonized mice with a sample of E. coli to show the value of their synthetic microbiome. Similar to mice that had a natural microbiome colonized, these mice were resistant to infection.
A healthy natural microbiome has been linked to protection in previous studies, but Fischbach and colleagues might go one step further by systematically removing or altering particular strains to see which ones specifically offer protection. They found some important bacteria and plan to do more research to find out more about the most important ones.
Fischbach says that hCom2 or future versions will use the same kind of reductionist research to find the bacterial pathogens that cause other things, like immunotherapy responses.
“This consortium was created with the larger research community in mind. In order to have an impact on the field, we want to get this into as many hands as possible, “Fischbach added.
Additionally, he believes that this approach of creating a microbiome from scratch will one day allow for the development of engineered microbiome-based medicines. He wants to build engineered communities that could one day be transplanted into individuals to treat or prevent a variety of diseases as the director of the Stanford Microbiome Therapies Initiative (MITI), a project that was started in 2019 by Sarafan ChEM-H and the Department of Bioengineering.
This research was paid for by the National Institutes of Health, the Human Frontier Science Research Program, the Astellas Foundation for Research on Metabolic Disorders, the Stanford Microbiome Therapies Initiative, the National Science Foundation, the Helmsley Foundation, the Howard Hughes Medical Institute, the Leducq Foundation, the Stanford-Coulter Translational Research Grants Program, MAC3 Impact, and the Bill and Melinda Gates Foundation.
