Positive leadership

In academia, becoming a good leader or an apt mentor is a skill most often acquired through work and life experiences. Few professors/researchers receive real training on how to manage human resources, how to resolve conflicts, how to rally a community around shared values and vision, or how to create a healthy work environment. Instead, we are trained and selected for research excellence and teaching/communication skills (to a varying degree) but land in a job where we will mostly manage a SME, spending way more time doing administration and human resource management than research. Yet, professors frequently have to write lengthy documents on why and how they will act as champions in Equity/Diversity/Inclusion, mental health and excellence for their trainees, as if we had all the extra resources in the world or could clone ourselves three times. Most of us can’t afford to hire multiple research associates / lab managers to help us create the perfect unbiased benevolent lab team and culture, but there are small/short-time actions that we can do to support our trainees’ development.

In our labs, trainees are young (and not so young) adults working together. In the 20’s-30’s life gets busy with them: moves, relationships, identity definition, health and family issues, financial precariousness, etc. Topping these situations, in the lab, they often develop friendships and antagonisms, face challenges and envy, have different culture, personalities or work strategies, which can result in tensions. As a PI, it is easy to turn a blind eye and not get involved, you know, we are already so busy with our committees, form filling, grants’ writing, emails (!!!). But we can, and probably must, for our own sake, contribute to give our trainees the skills to become positive leaders in order to maintain a healthy work environment.

As a young prof managing a young lab, this train of thoughts occupied my mind lately. I proposed to my lab to do an atelier on leadership (inspired by https://www.sessionlab.com/methods/leadership-envelopes) to work towards improving ourselves as mentors and leaders. Five strengths were chosen because they are believed to be important for positive leadership and mentorship.

Here is a summary of the discussion on the topic that ensued:

#1 Emotional intelligence

This one is mitigated. To manage a group of human requires to be able to sense the individual and collective mood: is it tense? is it collaborative? does someone need help? do I need to act to modify a behaviour? when should I be the good cop or the bad cop? Having a strong emotional intelligence is very helpful yet, it is very costly, personally. I have to remind myself to draw the line and limit the impact of my work on my personal life. This is a constant struggle, a balance to be found.

#2 Active listening

How many times are we not really listening but preparing an answer? Human communication is plagued by perception mistakes, loss in translation, and silent / body language cues. An active listener does not need to talk a lot, to dominate the discussion, but is able to identify the key messages and modulate a response accordingly.

#3 Model the way

Most of us don’t see ourselves as leaders. Impostor syndrome is rampant in academia and contributes to undermine the self-confidence to take initiatives and assume novel ideas. Leadership is not limited to specific job positions or to our work environment, it comes with all our actions. Self-deprecation is probably the more common negative leadership action that we all take part in and probably one of the easiest to fix.

#4 The three sieves

This one is fairly famous and broad in application, especially important in Homo sapiens‘ interactions. Is the comment or fact you are saying true? (as in did you witness it personally?) Is it positive? And is it useful? If you can’t answer positively to all these questions, you should keep it to yourself.

#5 Inspire a shared vision

From my long two years and almost seven months in this position (^^), I have the feeling that the next generation of researchers needs to see their values align with their research subject and work environment. Amidst the great many challenges of the 2020s, accelerating global change, disruption of democracies by war and far-right movements, loss of important rights for women (just to name a few), the youth are thirsty to spend their time and energy to make a difference in a safe and fertile work environment. When we as professors successfully align our research vision of excellence and ethics with our trainees’, we give our group an extra layer of determination and intention.

So, in summary, it was a nice experiment that we will repeat and try with different topics. And in your opinion, what are the skills of a positive leader?

Celebrating the 2-year anniversary

No, I am not talking of two years of pandemic, but two years of holding the position of Assistant professor at the Université de Sherbrooke (UDS).

As I struggle with making sure to eat during some days (time flies it’s maddening), I have also struggled to find time for writing blog posts. Balance in this job is easy to forget and difficult to achieve especially before tenure. I do have given myself the goal to take at least half an hour of break per day to move or relax, take five deep breaths, and remember to have fun. Here, I would like to share some of my thoughts on the challenges of the last two years of starting my own lab.

In the lab, I now have 10+ amazing humans from diverse backgrounds and of varied interests. The first wave of recruitment of lab members came with a higher demand of time for me. It felt like I wanted to set the tone quickly: what type of PI am I? what are my priorities? how do I support adequately my group to perform well accounting for their individual aspirations, capacities, needs, and challenges? Having no senior members in the lab meant all queries and initiatives came directly to and from me. It felt like a forced brain expansion, and each time the lab has grown or more funding came in, I felt another push for more brain capacity. My multitasking skills, as well as strategy of prioritizing and time management have been put to the test. Learning to say no is another skill I am working on. But email management takes the gold medal of challenges. Somebody told me I needed to use the five Ds to succeed in managing my emails:

  • Deny: junk mail, not interested, no important information.
  • Deflect: if someone asks you to do something, asks for more info or a first draft.
  • Delegate: it doesn’t have to be all you doing all the work.
  • Delay: no need to answer right now.
  • Do: do it now, and keep answer short and clear. 5-line email rules.

After two years, I am starting to have senior members (e.g., finishing students, a postdoc, a lab professional) so that some of the burden is off my shoulders. But, I do have more to do in terms of supporting projects that are at multiple different stages.

In addition, I have been confronted with situations that tested my ability to communicate, my patience, my diplomacy, my gros bon sens as we would say in French. Sometimes I have been frustrated by the status quo or lack of organization of the system. But most of the time, the experience has been incredibly exciting, motivating, and amazing. Especially teaching undergraduates, what a pleasure but I can’t believe how many times I have to repeat things, things that I say in the recorded classes, things that are in the Plan de cours, things that are on the forum and sent by emails. Drives me crazy… Another good piece of advice to be a good prof was the four Cs:

  • Clarity: say what you mean clearly.
  • Concision: say what you mean simply/shortly.
  • Coherence: be prepared and be coherent in your design and actions.
  • Confidence: show confidence even and especially when it is lacking.

Sometimes I struggle to put my limit, where is it enough for me to give to my job, which is also my passion. As in most experiences of my not-so-long life, the most mesmerizing and my favorite part is definitely the humans I meet and see evolve. None has left the lab yet and I look to this moment with both pride and dread.

Anyway, to whomever is reading this post, I wholeheartedly recommend the experience, especially when surrounded by wonderful colleagues and collaborators.

Here is the lab in 2022 and cheers to many more years.

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…

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.

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.

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?).

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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