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Living technologies: Current prospects in microbe engineering

Updated: Jun 6, 2019

Microbes don’t have the best reputation. People usually strive to prevent any potential contact with microorganisms that might be considered harmful. While some microscopic organisms, such as bacteria, virus, fungi and algae may indeed be the agents of several diseases, most work as a crucial component of ecosystems. Microorganisms are essential for maintaining balance in the environment by fixating gases and breaking down organic matter. Some microorganisms are able to form communities known as microbiomes, which allows them to interact and communicate among themselves. There are even microbiomes that exist in association with other organisms, forming synergistic relationships that are vital for the survival of both microorganisms as well as their hosts. This is the case of microbiomes found in many plants and also the gastrointestinal system of animals, including the human gut.

Recently, microbes have become the target of much research aimed at harnessing their natural properties for health and agricultural applications. While many of these studies are at early stages, others are well advanced and demonstrate that living microbial technologies may become available for use sooner than we might have expected. Here are some examples of revolutionary developments in microbiome research.

Engineering probiotic therapies

Over the past few years, microorganisms have become central in the development of living therapies. Several studies have focused on engineering microbes as a new way to treat human diseases. In a paper recently published in Science Translational Medicine, researchers presented how they developed microbial therapeutics to modulate metabolites, a by-product of diet and cell metabolism. Some metabolites may become toxic at high concentrations, which happens when they are not properly processed in the body. Ammonia is a metabolite generated in the gut as a by-product from breaking down proteins and certain amino acids by epithelial cells and associated microbiome. Typically, ammonia is processed in the liver by enzymes, rendering them non-toxic. However, hepatic disorders, such as cirrhosis, and defects of ammonia-detoxifying enzymes in the liver impair ammonia metabolism. This may lead to a condition called hyperammonemia, in which the excess of non-processed ammonia in blood may result in brain injury and even death. Current treatment options include antibiotics that decrease ammonia production by microbes and laxatives that limit ammonia absorption in the gut. However, drugs for hyperammonemia have severe side effects for patients, such as diarrhea, abdominal pain and headache, limiting adherence to treatment.

Synlogic has developed probiotics that act in the gut to regulate toxic levels of ammonia in the human body.

Source: Synlogic

To tackle this challenge, the biotechnology company Synlogic (Cambridge, MA) specializing in living medicines has developed a probiotic therapy to treat hyperammonemia and restore proper ammonia metabolism in the gut. Using the bacterium Escherichia coli Nissle as a model organism, researchers at Synlogic developed a strain that is capable of converting ammonia into the non-toxic arginine in vitro under oxygen-limited conditions, such as those found in the gut. They named this strain SYNB1020. The next step was to test how SYNB1020 would perform in live organisms fed with the probiotics. Among the challenges of developing microbial therapies is ensuring that (1) the probiotics reach only the targeted region in the body, (2) are capable of replicating and (3) retain their therapeutic properties as they transit in the gastrointestinal tract. Mice models of hyperammonemia that were fed SYNB1020 showed lower levels of ammonia in their blood compared to a control group, which were fed dead probiotics. In addition, biopsy indicated that the engineered bacteria were only found in the gut of treated animals and completely eliminated after one week of treatment completion. The remarkable results found in animal models pushed testing of SYNB1020 probiotics in clinical settings. In a phase I randomized clinical trial, the probiotics were found to be safe, viable and produce a metabolically active microbiome in the gut of human participants. More recently, SYNB1020 probiotic is being studied in a phase II trial in patients with cirrhosis. This engineered, ammonia-converting probiotic shows great promise for treating diseases associated with toxic levels of ammonia in blood and highlights the next generation of microbial therapies.

Enhancing natural fertilizers for plant crops

Nitrogen is a great source of nutrients for plants. However, most nitrogen is present in the atmosphere in the form of gas. To become accessible for plant use, nitrogen must be converted into less volatile forms through the process of nitrogen fixation. In nature, this process is performed by a select group of microorganisms. This is the case of bacteria called Rhizobium that form symbiotic associations within the roots of legumes, providing great levels of fixed nitrogen to the plant. Other cereal crops, such as rice, wheat and corn, may also interact with other nitrogen-fixing bacteria in the soil to acquire nutrients. Currently, the amount of fixed nitrogen represents a bottleneck for obtaining more crops for cultivation.

Nitrogen-fixing bacteria are becoming the target of genetic enhancement for economically viable and sustainable agriculture.

Source: Genetic Literacy Project

To increase nitrogen levels in soil, chemical fertilizers have been developed and used to cultivate crops at very large scales. But those synthetic fertilizers have devastating consequences for the environment. Nitrogen-rich chemicals leach from the soil and reach water streams. The increase of nitrogen levels results in proliferation of bacteria that consume nearly all oxygen in water. As a result, 500 dead zones appeared in the last century, comprising regions where oxygen levels are so low that most organisms can’t survive. On top of contaminating water, chemical fertilizers can also decompose into toxic greenhouse gases that are 300 times more polluting than carbon.

To prevent the catastrophic effects of chemical fertilizers and promote sustainable agriculture, biotech companies are modifying microorganisms found in nature to fixate more nitrogen in soil. Pivot Bio (Berkeley, CA) is among those companies. They developed an assay that allowed them to identify nitrogen-fixing bacteria from soil microbiomes. Among those was a nitrogen-fixing bacterium that associates with the roots of corn plants. Scientists at Pivot Bio used genome engineering to modify these bacteria for increased nitrogen fixation. In 2018, their engineered bacteria, named Pivot Bio PROVEN™, were used to colonize agricultural soils across 13 states in the US. These microorganisms supported crop growth by constantly providing fixed nitrogen to corn plants until harvest, significantly outperforming chemical fertilizers. The use of engineered microorganisms in agriculture is likely to have great economic impact for producers. This is because Pivot Bio PROVEN™ doesn’t leach from soil like chemical fertilizers, preventing loss. From an environmental perspective, switching to enhanced nitrogen-fixing organisms has also several advantages. According to Pivot Bio’s projections, the use of Pivot Bio PROVEN™ may help prevent 20,000 metric tons of toxic gases from chemical fertilizers from being released into the atmosphere and 500,000 metric tons of toxic compounds from contaminating water streams. Technologies like this have the potential for taking us one step closer to agricultural practices that are both sustainable and economically viable.


Kurtz CB, Millet YA, Puurunen MK, Perreault M, Charbonneau MR, Isabella VM, Kotula JW, Antipov E, Dagon Y, Denney WS, Wagner DA, West KA, Degar AJ, Brennan AM, Miller PF. An engineered E. coliNissle improves hyperammonemia and survival in mice and shows dose-dependent exposure in healthy humans. Sci Transl Med. 2019;11:eaau7975.

Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu M-H, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ané J-M, Petersa JW. Symbiotic nitrogen fixation and the challenges to its extension to nonlegumes. Appli Environ Microbiol. 2016; 82(13):3698-3710.

Pivot Bio. Nitrogen-producing microbes. Accessed June 4, 2019.

Pivot Bio. 2018 performance report. Accessed June 4, 2019.

About the author:

Eduardo Gutierrez is an evolutionary biologist with a passion for research and science writing. He believes good communication can make science accessible and interesting for everyone. With a background in molecular biology and evolution, he also likes to keep up with the latest development in biotechnology and health sciences.



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