Beginning as an Assistant Professor at Université de Sherbrooke and composing with COVID-19

If you are reading these lines I hope that you are doing well. The last few months have been quite strange and stressful for everyone. On my side, while I was opening my lab and getting started on projects, I had to put all activities on pause and manage the lab remotely. The upside is that I got to see my daughter learn to walk and to speak + lots of snuggles.

I have tried to vary activities during this COVID-19 situation and adapt to a different standard of productivity. I haven’t taken into baking though.

Here is a summary of what’s been going on for me:

Summary of the findings in the article Van Tilburg Bernardes et al. 2020 Nature Communications
  1. Publication of postdoctoral project in Nature Communications: Intestinal fungi are causally implicated in microbiome assembly and immune development in mice. Congratulations to Erik and Claire for leading this very important piece demonstrating that fungi are gut resident and that the human gut microbiota is fundamentally multi-kingdoms and multi-trophic.
  2. Co-organization of a special 14-articles issue in La Presse and (soon to be) republished in ACFAS: LA RELÈVE DU QUÉBEC PENSE L’APRÈS-COVID-19. Félix Mathieu, Catherine Girard and I organized this special issue and also made a collective contribution on Unir les générations (ACFAS link) in the hope that young researchers could contribute to the reflexion of a new society growing from the current challenge.
  3. Interview for Quebec Science 20%, a podcast on women in science.
  4. Interview for Radio-Canada Moteur de Recherche on the potential role of urban leaf bacterial communities in degrading atmospheric pollutants.
  5. Presented a live web-seminar for Microbiome Data Congress.
  6. Recorded a seminar for the remote ISAPP Annual Meeting.
  7. Submitted a preprint to biorxiv for the 1st time: Consumption of artificially sweetened beverages during pregnancy impacts infant gut microbiota and body mass index

Hopefully things can settle soon and if they are re-opening malls next week maybe I can hope to see our family and friends soon…

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Interview for Kristina Campbell in the Microbiome Times

“Why microbiome science needs to incorporate ecological perspectives – and five steps for making it happen”

 

Text from the article in the Microbiome Times

“Studies presented at leading microbiome conferences have grown in sophistication over the past several years and have uncovered important mechanistic links between the microbiome and aspects of host health. In fact, certain microorganisms (Akkermansia, Faecalibacterium prausnitzii) have become famous for their beneficial or detrimental effects. But across the field, is this limited approach going to enable scientists to grasp the full complexity of how human microbiomes influence health?

In a recent Nature Medicine Perspective article, Jack Gilbert and Susan Lynch emphasize just how complex human microbiomes are: not only are they highly variable from person to person, but they also exhibit spatial and temporal variation that is likely relevant to their effects on health. Gilbert and Lynch argue,

“…it has become imperative that we embrace a conceptual framework in which findings in the field can be interrogated and interpreted. Community ecology offers such a framework.”

Only a tiny fraction of the 40,000 microbiome studies in PubMed from the past few decades appear to have taken into account the microorganisms’ ecological community context. But this might be set to change.

One of the scientists at the forefront of microbial ecology frameworks in microbiome science is Dr. Isabelle Laforest-Lapointe, Canada Research Chair in Applied Microbial Ecology and Assistant Professor at the Université de Sherbrooke.

Laforest, a plant ecologist turned microbial ecologist with training in statistics and bioinformatics, says despite a history of microbiome studies that focused on different bugs and how they act as individuals, she never saw the microbiome as anything other than an ecosystem.

“I really think about how microbes interact together, how competition and facilitation happen,”

she said in an interview with Microbiome Times editors. Laforest and her fellow ecologists act on the premise that only by understanding the ecology of microbes will microbiome research ever lead to clinically robust interventions that can improve human health. Laforest has worked with immunologist Dr. Marie-Claire Arrieta, who focuses on microbiology and medicine, to explore how the infant human microbiome influences the later development of allergies and asthma. They examined the entire ecosystem of bacteria, fungi, and other microorganisms in early life to discover how they might shape the immune system and later-life disease.

Laforest is optimistic about where the field is going—microbiome scientists tackling the issue of ecology head-on. She says,

“Many things are promising because the researchers are starting to understand the bigger picture. And they’re doing a terrific job, because it’s hard to understand, at this level, how thousands of microorganisms are interacting. We’re not talking about a couple of zebras and lions, we’re talking about organisms that we’re unable to see. And they are really abundant.”

Nevertheless, she says, it’s going to take a significant amount of time and effort before researchers really understand these microbial ecologies and their two-way interactions with the host. Here, she outlines some of the tasks necessary for moving toward an ecological perspective in microbiome science:

1. Adapting definitions from macroecology to microecology

When microbiome scientists use words like ‘resilience’ and ‘resistance’, do they know precisely what they’re talking about? Laforest says more care should be taken to specify how the definitions used in macroecology can be applied to microbiology.

She observes,

“Microbiome researchers are starting to use the ‘buzzwords’ without really defining them and making the transition from macro to micro. This is the reflection they have to start thinking about more. If we use this vocabulary, we have to make sure we can apply them to the microscopic world.”

2. Looking beyond bacteria

The vast majority of microbiome studies to date have focused on bacteria, the most abundant microorganisms in human microbiomes like those of the skin and the gut. But Laforest points out that looking only at the bacterial members of an ecosystem leaves researchers with a major blind spot.

She takes the microbiome of the gut, for example:

“We have to think that bacteria are not the only actors in our gut. Other agents are there like fungi and phages,” she says. “But even if they’re less abundant than bacteria, they can have a huge impact on the ecosystem.”

3. Forming interdisciplinary collaborations

The ability to manipulate a microbiome with precision to have some effect on host health is something of a holy grail in this field of research. Perhaps drawing established ecologists into microbiome studies could help crack the code of how to manipulate microbial communities more effectively.

Says Laforest,

“I think you need people who are able to do interdisciplinary work and help microbiome scientists identify: what are these patterns that we see in bigger communities—which may or may not apply to what they see and can give them hints about how the community is interacting.”

4. Moving from simple to more complex models

Ecology is all about context, and Laforest emphasizes the importance of which model the microbiome researchers use to glean their insights.

“They’re experimenting with biochemistry, they’re experimenting with genes, with mutations. They’re really trying to make an effort in simple models to try to understand from them,” she says. “They eventually have to go into human models, which are way more complicated, to try to mimic the same results: what you see in mice or Drosophilaor C. elegans will probably not happen with humans, or will happen differently.”

5. Using appropriate bioinformatics analyses

Standing in between raw data and actionable insights are the all-important bioinformatics analyses. And since Laforest is trained in bioinformatics and statistics, she is no stranger to the many considerations that go into the choice of analysis.

“Bioinformatics is the most challenging part for anybody that wants to do microbial ecology,” she says. “At every turn you have ten decisions. So you have a couple of mainstream analyses that you can use. But you also have new pipelines that you can use that haven’t been proven but are supposed to be better.”

Each iteration of a study with careful bioinformatics analyses could thus lead to a better grasp of the ecological context.”

Thank you Kristina for the great interview.

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New Canada Research Chair in Applied Microbial Ecology

Article from the University News Website

I am very pleased to announce that I am the chairholder of a new Tier II Canada Research Chair in Applied Microbial Ecology. This means that I will receive 500 000$ over five years for my research on plant-microbe interactions.

These chairs are attributed to exceptional emerging scholars that show great promise for the advancement of their domain of research internationally. It is thus a great honour and privilege to be starting my professor position with such an investment.

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News for 2019

This year brings massive professional and personal changes for me as I am on maternity leave (big news #1) until January 2020 when I will start a new position of Assistant Professor at the Université de Sherbrooke (big news #2) in Quebec, which also means that we are moving from Calgary to Sherbrooke with a newborn baby girl this spring.

Université_de_Sherbrooke_(logo).svgAlthough I am navigating the joys and challenges of being a new mom, I still have many projects that I want to see through this year. I plan to attend the Canadian Society of Ecology and Evolution (CSEE) annual meeting in Fredericton in August, during which Dr. Carly Ziter (new prof. @ Concordia in Montreal) and I are organizing a symposium on “Integrating urban ecology across scales and trophic levels”. I am also hoping that I can complete some of the ongoing manuscripts from my postdoctoral fellowship and other collaborations.

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More recently, Dr. Briana Whitaker (postdoc at @ NCSU) and I have had the pleasure of collaborating on a perspective article in the Journal of American Botany: “Decrypting the phyllosphere microbiota: progress and challenges”. Hope you enjoy the read!

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Summer 2018 as a postdoc

Overview

I am writing this piece for my colleagues that are in their Ph.D. and wondering what it is like to be a postdoc bridging two disciplines (plant and human microbiomes). This post gives a synthesis of what I did this summer and why I chose to invest my time in these activities.

Writing a Banting Postdoctoral application

This year I have been invited by my University to apply to the Banting postdoctoral fellowship. This process is long and tedious, but the support to prepare my application at the University of Calgary has been outstanding. I was assigned a team of internal reviewers that commented my documents to make sure it was as well prepared as possible. I must say that this year I have spent a lot of time applying on a variety of awards and grants, of which I got very little. But even if I get only one, that can make a huge difference on a CV.

Mentoring a Ph.D. student on microbiome analyses

This summer I am collaborating with a Ph.D. student to help her in the analyses of her DNA sequencing data. I could have decided to do the analyses myself but I chose to teach her and help her through the process. This, for sure, takes more time then if I were to do the work myself, but as a future PI, you need to be able to mentor students and pass along your knowledge. So this was a great exercise of mentoring and positive leadership.

2-week Metagenomic Workshop in Calgary

As a postdoc, you need to continue to learn and improve your skillset. This is why I decided to take 2 weeks of my time to invest in learning metagenomics. I was very lucky because there was a metagenomic workshop in my hometown and it was great. I bet they will repeat it in the future so here’s a link to the description: Workshop

Poster at a conference on protists in Vancouver

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Organization of a symposium at ESA 2018 in New Orleans

This is one of the best things I decided to do this year. I reached out to a colleague in the US (Briana Whitaker) and together we proposed a session at the Ecological Society of America annual conference of 2018. These proposals have to be put in in September and we had to recruit 10 speakers for our session. We reached out to a variety of researchers working on plant leaf bacterial and fungal communities. The session was amazing, we got to spend the afternoon hearing about great projects that were of high interest for us. Big conference like ESA can feel a little scattered in terms of research quality and topic. So by organizing our own conference we got to hear only about the research we were interested in. Building a network as a postdoc is also essential, and this was a great exercise that extended the reach of my network.

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2-week crazy experiment end

Our lab completed at the end of August an experiment on germ-free and gnotobiotic mice. We worked hard and hopefully we will get great results out of this effort. When carrying out such big experiment, everyone participates in the lab.

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Invitation to give a seminar at Université Laval

My best moment of the summer was to give a seminar at the university where I did my undergraduate studies: Université Laval. By interacting on twitter with Dr. Christian Landry, I got an invitation to present my work at IBIS (Institut de Biologie Intégrative et des Systèmes). It was an amazing feeling to come back after all these years and be in front of a very full room to present my research to some of my former professors.

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Invitation to participate to a symposium on Microbial Ecology and Evolution in the Phyllosphere in Santa Barbara, California

Finally, I got an invitation to participate to a one-day symposium in Santa Barbara organized by two colleagues from UC Berkeley (Dr. Britt Koskella and Dr. Steven Lindow) and one colleague from U of Arizona (Dr. David Baltrus). Initially only the hotel was paid but one participant agreed to pay their own accommodations to I could have a $500 budget to pay for my travel. The symposium was amazing and I got to exchange ideas with many researchers I keep on citing in my papers, very humbling.

Left picture: Maria Brandl, me (four months pregnant), Carolyn Frank, and Johan Levau enjoying the sun during the break at the Santa Barbara Symposium. Right picture: The Santa Barbara beach and me (can I move there away from Quebec’s winter?).

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Anvi’o Workshop in Irvine, California

Where to find Anvi’o: http://merenlab.org/software/anvio/

What is Anvi’o: “Anvi’o is an open-source, community-driven analysis and visualization platform for ‘omics data.” (Definition taken directly from the software website)

On the 19th-20th of March 2018, I had the chance and privilege of attending a 2-days workshop on how to use Anvi’o as a tool to analyze my metagenomics data and produce cool figures. And Anvi’o is Open source! Open &*^$% Source! This is great that as a postdoc I get the chance to acquire new skills and I really appreciate the fact that my ACHRI and Cumming School of Medicine postdoctoral fellowship came with a 2K package to pay for workshops this year.

Here is the summary of my experience:

1. Meren is great but Anvi’o is greater.

I mean, the tutorial is smooth, well annotated in the website, and there is even a blog (with sassy humour all over it) written by users and managers alike.

Not only can you make amazing figures, and let’s be real, this helps to publish good papers, but you can also use Anvi’o to make sure your genome assembly is good. I haven’t had the time to explore yet all the possibilities Anvi’o offers, but it really seemed easy to explore and figure out. And the support community is real.

Only thing I would say, three days would be better. And I would liked to have a hands-on assignment on the third day where each participant would go through the whole process from the binning to the production of quality figures.

2. California, I miss you.

Coming from the Canadian winter… California smelled like summer, flowers, and earth. Wow. Can I go back?

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Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies

New paper in mSystems!

This is my first perpective/comment. It was really fun to get the chance to contribute to the special issue on Early-Career Systems Microbiology Scientists.

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Microbiome Keystone Symposia 2018

This week I am enjoying my first international conference on the human microbiome. This transition from plant microbiome to human microbiome has been challenging, I have to absorb an impressive amount of immunology and biochemistry knowledge, which was hidden deep in my previous undergraduate biology understanding.

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The conference (Keystone) is in Banff and we are staying at the Fairmont which, I must say, is incredible. My poster session was filled with interesting interactions with fellow researchers in the human microbiome field also working on interkingdom interactions.

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The University of Calgary is well represented at the meeting with all fantastic four PI of the microbiome core group present (Drs. Arrieta, Sycuro, McCoy, and Geuking), ass well as Dr. Hirota.

I think there is still a lot of improvement needed regarding the integration of real ecology in microbiome research. For what I see researchers use ecological buzz words but don’t investigate the concepts.

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Top 10 Découvertes 2017

Texte de Laurie Noreau pour Québec Science

Capsule vidéo de Benjamin Turquet pour Québec Science et le Canal Savoir

Un grand merci à mes directeurs Steven Kembel et Christian Messier, ainsi qu’à Alain Paquette pour la merveilleuse collaboration qui aura donné cette recherche dans Nature intitulée “Leaf bacterial diversity mediates plant diversity and ecosystem function relationships“.

Probiotiques forestiers

On en connaît de plus en plus sur les micro-organismes qui peuplent nos intestins. On en sait toutefois peu sur ceux qui colonisent les plantes. Ils sont pourtant aussi importants.

Quand Isabelle Laforest-Lapointe se promenait en forêt pour récolter ses échantillons, elle savait qu’elle n’était jamais seule : des milliards d’êtres vivants la dominaient du haut des arbres. Microscopiques, invisibles sur les feuilles, les microbes faisaient tranquillement leur travail.

Le microbiote humain – l’ensemble des bactéries qui fourmillent dans notre corps – a la cote en recherche. Toutefois, celui des plantes est peu connu. Encore moins celui des feuilles des arbres. « Pourtant tous les organismes macroscopiques, que ce soit les plantes ou les humains, ont des interactions avec les micro-organismes depuis la nuit des temps », rappelle la chercheuse de l’Université du Québec à Montréal (UQAM).

Les résultats de sa recherche, publiés dans Nature en juin dernier, sont venus redorer le blason de ces mal-aimés en révélant leur rôle important dans la productivité des plantes : plus un arbre a d’espèces microbiennes différentes sur ses feuilles, mieux il pousse.

Isabelle Laforest-Lapointe et son équipe ont fait un travail de moine en récoltant soigneusement 620 échantillons de feuilles d’arbre provenant de 19 essences différentes. En extrayant l’ADN de ces échantillons, ils ont pu découvrir quels champignons et bactéries se cachaient sur ces végétaux. Certains arbres, comme le sapin baumier, ont révélé une communauté de 2 000 espèces de micro-organismes différents !

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La jeune scientifique a pu bénéficier d’un environnement de recherche idéal grâce à l’expérience IDENT, une forêt expérimentale située à Sainte-Anne-de-Bellevue. Ici, l’évolution de la forêt est documentée chaque année. En comparant le diamètre et la taille des arbres depuis leur plantation en 2009, il était possible d’établir une corrélation entre la diversité des bactéries trouvées sur les feuilles et le développement de l’arbre.

Parmi tous les facteurs influençant la croissance, la biodiversité des bactéries pourrait expliquer 15 % de la variabilité observée. Un arbre hébergeant une grande variété de microbes peut donc avoir une croissance supérieure à celle d’un arbre de la même essence ayant peu d’espèces de microbes. Les micro-organismes, en recouvrant la totalité de la surface foliaire, empêcheraient les pathogènes de s’installer et d’endommager les feuilles. « C’est comme les probiotiques pour les humains : si on a une meilleure diversité de microbes dans l’intestin, on devrait avoir une meilleure digestion et une meilleure santé intestinale. »

Et les bactéries n’ont pas qu’un rôle de protection : elles produisent certaines vitamines, filtrent les polluants atmosphériques, facilitent la communication entre les arbres, etc.

Les chercheurs planchent aussi sur une autre hypothèse : et si la productivité des plantes était l’apanage de quelques bactéries clés ? « Des recherches antérieures nous laissent croire que certains taxons bactériens contribuent particulièrement à la croissance de l’arbre », avance Isabelle Laforest-Lapointe.

À quand l’ensemencement des pépinières par de « bonnes bactéries » ?

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The Tree Phyllosphere in Urban Environments

Last week the last paper of my phyllosphere project got published at mSystems. It is fair to say that my publishing journey at this journal was, by far, the best yet. Both reviewers gave us great comments and suggestions, which improved the quality of our final work. Trees in urban environments expose their leaves to both chemical contamination and biotic deposition that can come from many unusual sources (i.e. humans, exotic species). This project was aimed to enable comparisons with the more “natural” forest microbiome.

Here is the importance statement we wrote for this project: “In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.”

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Fig. 4. Nonmetric multidimensional scaling (NMDS) ordination of variation in bacterial community structure of tree phyllosphere along a gradient of urban intensity. Data represent ordination based on Bray-Curtis distances among 108 samples. Samples (points) are colored based on the urban gradient (blue for low intensity, orange for medium intensity, and red for high intensity). In panel a, shapes represent host species identity (squares for Acer platanoides; circles for Acer rubrum; triangles for Acer saccharum; diamonds for Celtis occidentalis; sun crosses for Fraxinus Americana; squares with cross for Fraxinus pennsylvanica; stars for Picea glauca); ellipses indicate 1 standard deviation confidence intervals around samples from urban gradient intensity. In panel b, arrows represent the significant (P < 0.001) correlations between NMDS axes versus the relative abundances of bacterial classes in communities.

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