Microbiome Insights is proud to be the sponsor of season 3 of Ruairi Robertson's Biomes Podcast.

In this fifth episode, Ruairi speaks with Dr. Carlotta Ronda about her groundbreaking research in genome engineering of microbiomes. Dr. Ronda is a researcher at the Innovative Genomics Institute in Berkeley, working alongside Nobel laureate Jennifer Doudna. Their conversation explores the revolutionary potential of CRISPR technology in transforming both human health and environmental sustainability.

Transformative Insights from Dr. Carlotta Ronda

Dr. Carlotta Ronda’s passion for bacteria and genetic engineering has driven her academic journey from Padua University in Italy to DTU in Denmark and finally to Columbia University in New York. Currently, she focuses on using CRISPR technology to understand and manipulate bacterial communities, aiming to unlock their complex roles in health and disease.

CRISPR: A Game-Changer in Genetic Engineering

CRISPR, particularly the Cas9 protein, allows precise cutting and pasting of DNA sequences, revolutionizing genetic engineering. While using Cas9 in bacteria often results in the bacteria's death due to their inability to repair DNA cuts, newer systems like CRISPR transposase can insert genetic material without causing cell death, making them ideal for microbiome engineering.

Addressing Challenges and Ethical Considerations

Dr. Ronda’s team is tackling the rapid mutation rates of bacteria, which can lead to antimicrobial resistance, by co-engineering beneficial traits that provide a fitness advantage. They also emphasize the ethical use of CRISPR technology, ensuring responsible advancements in this powerful field.

Current Applications in Health and Environment

Human Health

Dr. Ronda is exploring treatments for diseases like phenylketonuria (PKU) by engineering the microbiome to metabolize phenylalanine, offering a novel approach to genetic therapy without altering human DNA.

Environmental Sustainability

Her research also focuses on reducing methane emissions from cows by targeting methane-producing bacteria in the cow rumen, presenting a promising solution to a significant environmental challenge.

Conclusion

Dr. Carlotta Ronda’s great work shows the immense potential of CRISPR technology in microbiome engineering. Her efforts promise to transform human health and address global environmental issues, highlighting the critical intersection of genetic engineering and microbiome science.

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Links to Apple, Spotify, and Podbean

Full Transcript 

Ruairi: Thanks very much, Carlotta Ronda, for agreeing to have a chat today and talking all about your research in genome engineering of microbiomes. Before we start, do you want to just give a little introduction to who you are, what's your background, and how you got into the field of genetic engineering of microbiomes?

Carlotta: Thank you for having me here, Dr. Robertson. It's my pleasure. I've been fascinated with bacteria since I can remember. I was born and raised in Italy. I did my undergrad at Padua University, where I majored in molecular biology. Then I did my master's and PhD at DTU in Denmark, where I specialized in genetic engineering and systems biology. I always had this fascination with bacteria, viruses, and how they were so smart to manipulate the host and make the host do things for them. Especially pathogens—they evade and use host mechanisms and reprogram them in a certain way. From Denmark, I flew to New York at Columbia University, where I did my postdoc in Harris Wang's lab. There, I decided to focus my entire career on the microbiome. I was always interested in genetic engineering and worked on CRISPR and novel genetic engineering mechanisms in a systems biology context during my PhD. I wanted to apply this knowledge to understand bacterial communities because, at the time, we couldn't look into communities beyond genetic content. The microbiome revolution happened once 16S sequencing and metagenome sequencing occurred, and we realized that bacterial communities play a major role in our physiology. They are not just there to help us digest food but have myriad functions, affecting the brain, organs, and overall health.

When I started my postdoc, we could only get snapshots of communities, looking at distribution and phylogeny without understanding their functions at the molecular level. I focused on increasing the resolution at which we can understand these communities by genetically modifying them. By altering genetic content and shifting the communities, we can understand and decouple their functions. Now, my research continues to develop technologies to understand bacterial communities and to ask fundamental questions about the molecular mechanisms mediating phenotypes or disease effects. We use different models, from mice to organoids and in situ communities, to model how bacterial communities can change human physiology and lives.

Ruairi: That's great. You've summarized it perfectly—you are working at the forefront of two of the most exciting areas in science, merging genetic engineering with the microbiome. You’re now at the Innovative Genomics Institute in Berkeley, working in collaboration with Jennifer Doudna, who won the Nobel Prize for CRISPR technologies. Before we delve into genetic engineering and microbiomes, can you give a brief introduction to CRISPR and its applications in both human genetic engineering and microbiome engineering?

Carlotta: CRISPR technology has revolutionized science. In the early 2000s, the Human Genome Project opened new doors, but we realized that sequencing alone wasn't enough. We needed to modify genes to understand their functions. CRISPR, especially the Cas9 protein, acts as a programmable scissor, allowing us to cut and paste DNA sequences. Before CRISPR, other technologies like TALENs existed but were less efficient and more cumbersome.

CRISPR changed everything because it made genome engineering accessible. By using a small RNA guide, we can target specific DNA sequences and modify them, providing insights into gene functions. CRISPR is more efficient and cost-effective compared to previous methods. It has led to FDA-approved therapies, such as for sickle cell anemia, where the mutated gene is replaced with a healthy one.

In microbiomes, CRISPR is used differently. Bacteria don’t repair DNA as efficiently as human cells, so using Cas9 in bacteria often results in killing the cells, acting as a targeted antibiotic. However, other CRISPR systems, like CRISPR transposase, can insert genetic material without killing the bacteria. This system is more suitable for microbiome engineering because it doesn’t rely on the bacteria’s ability to repair DNA.

Ruairi: You mentioned that bacteria mutate rapidly, which can lead to antimicrobial resistance. What are the risks of introducing genetic changes to microbiomes, and how can we mitigate them?

Carlotta: Biocontainment is crucial in microbiome engineering. Bacteria can indeed mutate and change the introduced genetic material. To mitigate this, we can co-engineer beneficial traits that give bacteria a fitness advantage. If the modification helps the bacteria thrive, they are less likely to mutate. For example, we can link a beneficial metabolic function to the genetic modification, ensuring that the engineered bacteria outcompete wild-type bacteria.

We also consider the ethical and safety implications of CRISPR. At IGI, we discuss these aspects regularly and aim to use CRISPR responsibly. Editing microbiomes offers a safer alternative to editing human genomes, as it avoids direct modification of human DNA and leverages the symbiotic relationship between humans and their microbiomes.

Ruairi: That's a great point. Using microbiomes as a therapeutic avenue seems promising. What are some specific examples of ongoing research in this field, both for human health and environmental applications?

Carlotta: In human health, we’re looking at treating diseases like phenylketonuria, where the body can’t break down phenylalanine. Instead of modifying the human genome, we can engineer the microbiome to metabolize phenylalanine, providing a form of trans-kingdom metabolic replacement therapy. This approach avoids the ethical and practical challenges of directly editing human DNA.

For environmental applications, we’re focusing on reducing methane emissions from cows, a significant contributor to greenhouse gases. We aim to engineer the cow rumen microbiome to reduce methane production. This involves sequencing and analyzing cow microbiomes and developing genetic tools to target methane-producing bacteria.

And then now we are working into analyzing, modeling this community dynamics and trying to pinpoint the key metabolic functions that then eventually we're going to specifically edit using our genetic editors and genetic engineering tools. But that's, I think, are the major challenges we are taking on accessibility to material and then these difficult strains that they're very tough.

Ruairi: Oh, well, great. Well, from the human microbiome project to the cow microbiome project, I'm sure there'll be a lot of potential there for not only human health, but also environmental health as well. I think we'll leave it there. So thanks a million, Carlotta, for a fascinating discussion.