Protecting the human gut microbiome with synthetic biology

April 11, 2022

(News from Nanowerk) Many of us have seen our gut go out of balance as a result of unavoidable antibiotic therapy. Not only do antibiotics kill the pathogenic bacteria causing an infection, but they also wreak indiscriminate havoc on the trillions of “good” bacteria that make up the human microbiota.

Known as ‘dysbiosis’, this alteration in the microbial composition of our gut triggers bothersome diarrhea in up to 35% of short-term patients, and can take months to resolve, often with the help of corrections and dietary supplements. In some patients, the microbiota can even be permanently disrupted, which becomes a serious risk factor for many autoimmune, metabolic and neurological diseases.

Indeed, we have developed a mutually highly symbiotic relationship with the microbes of our gut microbiome and have in fact formed with them a “superorganism” in which we, as “hosts”, shape the composition of our microbiome with our environment. intestinal, as well as our diet and other habits.

In turn, our microbial “guests” produce various compounds that profoundly affect how we digest food, use energy, and support our immunity, among many other functions. Despite the importance of our microbiome to our health, until now there has been no silver bullet to prevent antibiotic-induced dysbiosis.

Human patients treated with antibiotics experience damage to their gut microbiota (lower branch) resulting in an imbalance in its normal composition. Known as “dysbiosis, this imbalance is a risk factor for a host of autoimmune, metabolic, and neurological diseases. As a solution, treating patients who receive an antibiotic simultaneously with a modified living biotherapeutic product (eLBP, upper limb) developed at the Wyss Institute and MIT, which degrades antibiotics in the gut, prevents the destructive effects of antibiotics on the gut microbiome. Since eLBP does not change the concentration of antibiotics in the blood, they still reach infections everywhere else in the body. (Image: Harvard University’s Wyss Institute)

Now, a research team from the Wyss Institute for Biologically Inspired Engineering at Harvard University and the Massachusetts Institute of Technology (MIT), using a synthetic biology approach, has developed a modified living biotherapeutic product (eLBP) that, when it is administered with commonly used antibiotics known as β-lactam antibiotics (which includes the famous antibiotic penicillin), protects the gut microbiome from dysbiosis.

The study is published in Nature Biomedical Engineering (“A living biotherapeutic designed for the prevention of antibiotic-induced dysbiosis”).

“When designing the eLBP, we tapped into the synthetic biology kit we’ve developed over the past two decades and enabled Lactococcus lactis, a safe-to-use microbe, to secrete a b-lactamase enzyme that altruistically degrades β-lactams in the bacteria’s environment,” said James Collins, Ph.D., Wyss Core faculty member and lead of the Institute’s Living Cellular Device platform. , who led the study. “The enzyme essentially becomes a ‘commons’ that cannot confer a selective advantage to the producing bacterium or be easily transferred to other bacteria, minimizing the risk and maximizing the clinical benefits of our approach.”

Collins is also the Termeer Professor of Medical Engineering and Science at MIT. In 2018, his team used L. lactis to develop a probiotic intervention designed to detect and treat cholera infections.

Antibiotic protection is in place

Usually, β-lactamase enzymes are encoded by a single gene that can be passed between bacteria via a process called horizontal gene transfer, and the enzymes themselves reside in the cell wall or membrane enclosures of the bacteria. This not only makes the producing bacterial strain resistant to certain antibiotics attacking these outer enclosures, but also allows their resistance to spread to other bacteria in the gut microbial population.

“To guard against the development and spread of antibiotic resistance, we engineered various control units in the b-lactamase expression system. Essentially, we split a specific gene encoding β-lactamase, distributed the two genetically unrelated halves to different parts of the bacteria’s DNA, and then engineered them to be secreted away from the producing cell and bind to each other with high affinity. to reassemble a functional enzyme in its external environment,” said first author Andrés Cubillos-Ruiz, Ph.D., who led the project in Collins’ group.

Cubillos-Ruiz and colleagues on Collins’ team then showed that when they gave their eLBP intervention to mice that received the antibiotic ampicillin as an oral treatment, it indeed minimized dysbiosis in each animal’s gut. By sequencing a portion of the bacterial genome known as 16S rDNA, which provides a genetic zip code for all bacterial species and families, they found that eLBP significantly mitigated the collapse of microbial populations and allowed them to regain their original diversity and composition fully three days after antibiotic treatment.

The mice treated with ampicillin which were not protected by the eLPB, underwent a much greater loss of their microbial diversity which they could not recover during the entire course of the experiment.

“Importantly, during its transient stay in the digestive tract, eLBP protected the microbiome without altering the concentration of ampicillin circulating in the blood, which is important because the antibiotic has yet to reach infections anywhere else in the body to do its job,” says Cubillos-Ruiz. “eLBP also reduced the enrichment of various antibiotic resistance genes within the microbial community, which typically occurs under antibiotic selection pressure.”

The gut microbiome contains a natural pool of bacteria with genes, including β-lactamase genes, that induce antibiotic resistance through different mechanisms – including resistance even to unrelated antibiotics. With each antibiotic treatment, their number skyrockets and also contributes to the spread of antibiotic resistance through horizontal gene transfer.

Finally, the team looked at a common consequence of dysbiosis: the hostile takeover of liberated gut territory by problematic bacteria such as Clostridioides difficile. These “opportunistic bacteria” live in the intestines of many people in smaller numbers and, when given the opportunity to multiply out of control, trigger inflammation, diarrhea and can contribute to the development of inflammatory bowel disease. intestine.

The team modeled a full-fledged human being It’s hard infection by infecting ampicillin-treated mice with spores of It’s hard. eLBP successfully prevented intestinal colonization with It’s hardunlike an unmodified normal L. lactis strain not producing the split β-lactamase enzyme.

“This is one of the strongest examples of a live cell therapy designed to tackle a pressing clinical problem emanating from academia to date,” Collins said.

“We are now focused on bringing these live therapies to patients and are finalizing the design of an effective, short and inexpensive clinical trial,” said Cubillos-Ruiz, adding that, “We also believe that our general eLBP approach can be extended to a therapeutic platform that could be applied not only to other antibiotics, but also to treat diseases where gut dysbiosis is central.

“This elegantly designed and highly effective living cell therapeutic device could be a game-changer in the treatment of infectious diseases both in helping to maintain a healthy microbiome in patients treated with antibiotics and, perhaps equally important in the longer term. , by preventing the growing problem of antibiotic resistance which is a growing problem worldwide,” said Wyss founding director Donald Ingber, MD, Ph.D., who is also the Judah Folkman Professor of Vascular Biology at the HMS and Boston Children’s Hospital, and Hansjörg Professor of Bioinspired Engineering at Harvard John A. Paulson School of Engineering and Applied Sciences.

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