Meet a microbiome researcher: Q&A with Dr. Isabelle Laforest-Lapointe


As a part of our Microbiome research interview series, we spoke with Dr. Isabelle Laforest-Lapointe, a Postdoctoral Research Fellow in the Arrieta lab, departments of Physiology & Pharmacology, and Pediatrics at the University of Calgary, Canada. Dr. Laforest-Lapointe received her Ph.D. from Université du Québec à Montréal (UQAM), Montreal, Canada. Her research interests include microbial ecology, from host-microbe interactions to ecosystem dynamics. She is a recipient of the Alberta Children’s Hospital Research Institute Postdoctoral Fellowship Excellence Award and Cumming School of Medicine Postdoctoral Scholarship. We interviewed Dr. Laforest-Lapointe, to discuss her research, her typical day in the lab and her hobbies.

What is your background and how did you become interested in science?

As a child, I was always interested in camping and outdoor venturing and was looking at every possible opportunity to make it happen. I was a girl scout and then a scout counsellor from 11 to 20 years-old. It got me to love nature, forests [and] animals, thus, I started to want to understand more about general biology. During my biology undergraduate studies, I had a tremendous professor of community ecology who fostered my love for this field of research and started my path towards microbial ecology.

Can you provide a summary of your project?

My Ph.D. focused on the interactions between microbes and plants, mainly focused on the bacterial communities that inhabit temperate tree leaves. My project started by answering questions such as: Does every tree species have their own leaf microbiome or does it change at different geographical locations and in time? How much does the tree leaf microbiome vary between conspecific individuals and between different leaves of the same tree? And then we looked at the relation[ship] between leaf bacterial diversity and tree community productivity, reporting a positive correlation between both. Finally, my last chapter focused on the urban tree microbiome at different urban density levels and degree of tree isolation. So, to summarize I have worked on plant-microbe interactions and microbial ecology in natural forest, experimental settings and in the urban environment for the last five years now.

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Figure 1. Dr. Laforest-Lapointe collecting samples during her field trip.

Are you working on any other new projects in the field of microbiome research? If so can you tell us a little about these?

Yes, so to extend my field of research and challenge myself to increase my knowledge, I am now working in the laboratory of Dr. Marie-Claire Arrieta at the University of Calgary. She works on the influence of the early-life human gut microbiome on the development of the immune system, mostly in relation to future development of asthma and atopy. A big jump for me, but also a challenge that pushes me to learn a lot while bringing community ecology concepts to a field (human microbiome) that overlooked ecological concepts in the past.

Can you describe a typical day for you in the lab?

We are a small team (but mighty!), so I get involved in pretty much everything, from striking anaerobic bugs to handling our mice experiment[s], DNA extraction from baby poop and qPCR on lung tissues, but my favorite time is spent in front of my computer coding, analyzing data and writing papers. Also, the Cumming School of Medicine and Snyder Institute for Chronic Diseases have weekly seminars which present ground-breaking research led by the great research team at the University of Calgary. They just launched the International Microbiome Centre which hosts the biggest germfree facility in the world directed by Dr. Kathy McCoy. I am looking forward to using these new facilities too! 

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What do you find most interesting about your project? What is the most interesting or surprising result you have found?

Since I just started working on the human microbiome, I feel that more surprising results are definitely coming soon from that field. In my previous work, we showed a potential link between the leaf diversity and the productivity of the tree community and it completely surprised me. Considering that we were implementing in our model plant-related variables that are known to have a very strong influence on tree community productivity I wasn’t expecting that leaf bacterial diversity would significantly contribute. Now, future work is needed to understand the mechanisms behind this trend. For example, is it a niche complementarity mechanism where a diverse bacterial community protects leaves from pathogen colonization? Or is it a selection effect where the presence of key bacterial taxa is responsible for this higher productivity through the production of phytohormones?

What are the important benefits of your research to science/human or animal health?

As I mention above, one of our principal finding[s] was that tree communities whose leaves host a more diverse set of bacterial taxa were more productive, producing more biomass even after accounting for the importance of plant diversity. This discovery suggests that the plant microbiome could play a key role in terrestrial ecosystem productivity, and that models of the relationship between plant diversity and ecosystem productivity could be improved by adding information on the microbial communities associated with plants. The study also demonstrated that plant diversity influences microbial diversity on leaves, with each tree species possessing a distinctive bacterial community, and with trees growing amongst a diverse set of neighbour trees tending to have a higher diversity of bacteria on their leaves than trees growing among trees from the same species. Our results suggest that leaf microbiome diversity could play a key role for terrestrial ecosystem productivity, a discovery having multiple potential beneficial applications in agriculture and forestry, as well as for fundamental research on the roles of multitrophic networks in terrestrial ecosystems and the theories that attempt to explain relationships between biodiversity and ecosystem function.

What are your hobbies?

I am a sports person so I love to play any team sport, but I must confess that for the last 3 years I have dedicated most of my free time to crossfit. I believe it got me through my Ph.D. with a healthy mind in a healthy body. And, I am a board game geek. I love to play board games, especially those that ask for optimization. I love hiking, so this is why I am sharing a picture of mine in the beautiful Rockies.

What are the major challenges you face in your research with regards to sample collection, nucleic acid isolation and data analysis?

In my opinion, one of the greatest challenges now for microbial ecologists is to tackle the missing taxonomical information that we get from genomics data. Also, we definitely need more microbiology-oriented understanding of what is happening in these microbial communities, but cross-discipline collaboration between bioinformatics-statistics-ecology-microbiology are needed to ensure that our research is robust and informative. Finally, the recent push toward a true open science and open access to articles or even to reviews is also promising. I hope that more established scientists, acting as mentor to the future generation, using public funding to do research, will see the importance of making their research open. And by making the research open, I mean going further than giving access to your sequences but not to any relevant metadata or code.

Which MO BIO or QIAGEN products do you use/have you used in the past and what did you like about the products?

I have been using QIAGEN products since my grad days and [I am] extremely satisfied with them in terms of [their] high quality and the ease of use. I have used PowerSoil kits (DNeasy PowerSoil Kit & RNeasy PowerSoil Total RNA Kit), Microbial DNA qPCR Arrays, QIAquick Gel Extraction Kit, and QIAquick PCR Purification Kit.

Find out more about how QIAGEN is advancing microbiome research with its microbiome solutions.



Vishwadeepak Tripathi

Vishwadeepak Tripathi, PhD is a Global Market Manager at QIAGEN. He received his PhD in biochemistry at the Faculty of Medicine from Ruhr-University Bochum, Germany. Dr. Tripathi studied the role of chaperones and co-chaperones in protein folding and quality control and authored a number of scientific publications. He was also at RIKEN Institute in Japan where he studied the pathogenesis of Huntington's disease in cellular and mice models. He is currently interested in biomarker research, NGS and neurodegeneration.

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