In the late 1970s and early 1980s, besides new wave music and computers, genetic engineering sounded very cool. It was a new technology, exciting and mysterious, just like in one of those Sci-Fi movies. It was certainly one of the main reasons for me and for many of my colleagues, why we decided to study molecular biology.

More than thirty years later, advancement in technologies of genetic manipulations gave us power to selectively modify, repair or kill an organism. Only few months ago, Nobel Prize for discovery of CRISPR-Cas system and its use as a novel technology for precise genome editing, has been awarded.

It´s important to remind that genetic manipulations were initially developed using bacteria and bacterial viruses (bacteriophages). Techniques of genetic engineering were later applied in higher organisms like plants. Thanks to these advances and our understanding of cellular processes, during last twenty years a whole new branch of biology named “Synthetic Biology” evolved. Only recently, we began considering applications of these technologies not only on single cells but on the level of microbial populations – namely for microbiomes.

Microbiome Engineering is the trend of the 2020s and probably of the next decades to come.

COVID-19 pandemic taught us how important is the immediate availability of new biotechologies in the health sector. We should not wait for the next crisis to re-consider possible applications of our knowledge about microbiomes!

Anyway, emergence of Microbiome Engineering is not very surprising. During last 10-15 years we have seen unprecedented and almost simultaneous development of new technologies for analysis of microbial populations (e.g. next-generations-sequencing) as well as more efficient and more precise opportunities for genetic manipulations, such as the above mentioned CRISPR-Cas.

So, which possibilities for Microbiome Engineering are actually out there?

As a microbiologist and someone who believes that awareness about power of microbiomes is, and will be of tremendous importance I am extremely curious to answer the above question.

Bacteria are certainly those microorganisms which have attracted most attention so far. However, important is NOT to forget that in each microbial community there are many other members such as viruses, protozoans and fungi. All of them can be genetically manipulated and their importance in future microbiome-based therapeutics is yet to be established.

Methods of addition of new features to an existing microbiome, either by living, non-engineered or by engineered strains of probiotic bacteria or yeasts, are referred to as Additive Therapies. On the other side, if only one kind of target-microorganism is eliminated, these are called Subtractive Therapies. Finally, if we change either structure or function (activity) of a microbiome by adding non-living components (e.g. genes, proteins), we talk about Modulatory Therapies1,2.

Additive Therapies include:

a) Supplementing microbiomes with native, non-engineered strains of the probiotic bacteria such as (already sold over-the counter) Escherichia coli, Lactobacilli, Bifidobacteria, yeast strains and others, as well as Fecal Microbiome Transplant Therapy – FMT (for details see section about human gut microbiomes on our website…).
b) Production of specific therapeutic molecules (e.g. missing enzyme) by bacteria with engineered genetic circuits. Experiments in rats and mice already have shown the efficacy of this “synthetic biology“ approach for diabetes and hyperammonemia, a disease of abnormally high and toxic ammonia production in the gut2. CRISPR-Cas is currently the most promising technology for engineering of the synthetic bacterial genetic circuits.
c) Engineering of the whole microbial population (so-called “microbial consortia”) is based on the comparison between a healthy and a diseased person. This means actual “re-programming” of the damaged microbiome.

Subtractive Therapies include our traditional antimicrobial antibiotic treatments – unfortunately known for having a side effect of killing many beneficial bacteria as a “collateral damage”. Another big trouble with over-use of antibiotics is creation of antibiotic resistance, which already poses a global threat. Alternative antimicrobials attracting researcher´s focus include bacteriophages, peptides and other chemicals and metabolites. Bacteriophages are bacterial viruses, present in all microbiomes. Since more than hundred years, bacteriophages are known to selectively kill certain bacterial species. However, generation of phage-resistance, their stability and possible transfer of unwanted genes to other bacteria are among the main concerns which need to be thoroughly studied before possible approval of massive use of bacteriophages as antibacterial therapeutics, or so-called “phage therapy3. An alternative to the natural phages are modified or synthetic ones (so-called “superphages”). A great example in this area is Canadian company Cytophage, currently developing superphage-based solutions for humans, animals and plants. 

A recent innovative example of the application of Microbiome Engineering are “Sequence-Specific Antimicrobials (SSAM)”, developed by the company Eligo Bioscience (Paris, France). They use bacteriophages as delivery vehicle for the modified CRISPR-Cas systems which than either selectively kill bacteria by introducing double-stranded DNA breaks (Subtractive Therapy), or they can introduce additional functions (e.g. therapeutic protein production), so-called “Functional Addition to MicrobiomE (FAME)” – an example of Modulatory Therapy.

Another great application of Subtractive Therapies are Guided Biotics of the British company Folium Science. Guided Biotics are also using CRISPR-Cas technology to eliminate unwanted bacteria. Primary target group of the company is massive animal breeding, such as poultry and fisheries. They are also developing similar new products for protection of fruits, vegetables and crops by engineered plant microbiomes.

We are looking forward to see more examples like these…

So, what else do we need to consider to accelerate development of new products and therapies based on microbiome engineering?

I will repeat: Microbiome Engineering started very recently and it is happening right in front of our eyes!

We still have general unknowns about: a) rare microbial species not detectable by our current methods (which might be very important for the proper functioning of the microbiomes as a whole!); b) possible diversity of certain microbial species and, in between different species in a microbiome; c) about functions of the microbiomes in general.

Concerning use of engineered microbiomes, before adding or deleting single microbial species, we need to understand better their importance for the whole community and to check how robust our engineered strains and genetic circuits are to mutations and other perturbations?

Due to the individual difference in microbiomes, future therapies will likely develop in the direction of personalized solutions.

Microbiome-based biosensors, as a tool for detection of biomarkers linked with a particular disease or condition, are another interesting field of research, which we will address in one of our next blog posts.

Finally, an important step is to simplify regulatory procedures regarding engineered microbiomes, thus accelerating their entry to the markets worldwide3,4.

1. Ramachandran G, Bikard D. Editing the microbiome the CRISPR way. Phil. Trans. R. Soc. B. 2019, 374: 20180103.
2. Lu TK, Mimee M, Citorik RJ, and Pepper K. The Chemistry of Microbiomes: Proceedings of a Seminar Series. National Academies of Sciences, Engineering, and Medicine (in Chapter 10: Engineering the Microbiome for Human Health Applications, 2017, p. 65-76); Division on Earth and Life Studies; Board on Chemical Sciences and Technology; Chemical Sciences Roundtable. Washington (DC): National Academies Press (US).
3. Principi N, Silvestri E and Esposito E. 2019. Advantages and Limitations of Bacteriophages for the Treatment of Bacterial Infections. Front. Pharmacol., 08 May 2019.
4. Thomas AM and Segata N. Multiple levels of the unknown in microbiome research. BMC Biology 2019, 17:48.