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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Arrieta Lab 2017

Wednesday 13th of July 2017

Lately I have been reflecting on where does my love of science stems from. So far I built this list:

  • Analyzing data
  • Coding (75% == debugging)
  • Reading the papers of others and appreciating the amount of work behind it
  • Spending way too much time making pretty figures
  • Communicating, teaching & sharing my knowledge
  • Lab DNA cuisine

But most of all, getting to meet and work with great human beings. Here is to my new lab in Calgary who have made the last few months a great beginning.

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The end of a beginning

Now this is not the end.
It is not even the beginning of the end.
But it is, perhaps, the end of the beginning.
Sir Winston Churchill, 1942

Yesterday, 24th of May 2017, the third chapter of my thesis got published in Nature: read it! It is so incredible that I didn’t believe it until I saw it on the website…

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Here’s a synthesis:

As recent researches have demonstrated that microbes are crucial actors of human health, microbial organisms could also play a similar role for plants, driving key functions such as productivity. The work of Laforest-Lapointe et al. provides the first evidence that the diversity of microbes on tree leaves influences positively tree community productivity, a finding that has critical implication for forestry and agriculture, as well as for future fundamental research on microbial ecology.

Plant diversity is known to play a crucial role in the functioning of terrestrial ecosystems. Plant ecosystem productivity (the biomass produced by a community of plants) is a key ecosystem function both in natural ecosystems as well as in agriculture and forestry. The productivity of an ecosystem increases when a higher diversity of plants is present in the community. Previously, this correlation between productivity and diversity was attributed to the fact that when more species with different ecological niches are present in a community, the resources available in an ecosystem will be more fully utilized, leading to increased overall productivity. Recent advances in DNA sequencing technology have revealed the incredible diversity of microorganisms living on and in plant tissues – the plant “microbiome” – the combined genetic material of microorganisms living on plants. These plant-associated microbes can have important effects on the growth and health of individual plants, but their importance for ecosystem function is not well understood. In this study, Dr. Isabelle Laforest-Lapointe and colleagues demonstrate that the bacteria living on tree leaves can also influence ecosystem productivity, even after accounting for the role of plant diversity. The research team, including Isabelle Laforest-Lapointe (UQAM), Alain Paquette (UQAM), Christian Messier (UQAM/UQO) and Steven Kembel (UQAM) measured and quantified the diversity of bacteria living on tree leaves in a biodiversity experiment with trees (IDENT) established near Montréal, Canada, where trees were planted in different combinations of species diversity and functional diversity and the productivity of these tree communities was measured after several years of growth. Through sequencing of bacterial barcode genes, the research team quantified the number of different bacterial taxa living on each tree. The principal finding of this study 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 extended 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. This study suggests that leaf microbiome diversity could play a key role for terrestrial ecosystem productivity, a discovery having multiple potential beneficial consequences 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.


Now I am not a Ph.D. student anymore. Today marks the day of my first pay as a Postdoctoral fellow at the University of Calgary, Cumming School of Medicine, Depts. of Physiology and Pharmacology & Pediatrics, under the supervision of the excellent Dr. Marie-Claire Arrieta.

From working on microbes inhabiting the leaves of trees, I will now be looking at samples of infant intestinal microbes or mice microbes! Poop it is!

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