Blog Posts - DEROME LABORATORY

New Publication

8/7/2018

A brief history of bioinformatics
Jeff Gauthier, Antony T. Vincent, Steve J Charette and Nicolas Derome

Briefings in Bioinformatics | https://doi.org/10.1093/bib/bby063

To access the article, click here.
(for personal use only, do not redistribute this link)

Here we present an integrative timeline of key events in bioinformatics and related fields during the past half-century, as well as some background on parallel advances in molecular biology and computer science, and some reflections on the future of bioinformatics.

Team Highlights - Sentinel North Scholarship

5/14/2018

Congratulations to Amine Chaabane, who was awarded a Sentinel North scholarship for international graduate students.

Through this program, Sentinel North seeks to attract new talent, foster the development of young international scientists able to tackle and help resolve complex northern issues, and encourage the sharing of knowledge and experience across borders.

Amine's project aims to study two populations of Arctic char (Salvelinus alpinus) from the North region of Canada and trying to observe the impact of climate change and physiological parameters differences on this microbiota.
For more information about the Sentinel North international scholarship program, click here.

New Publication

5/12/2018

Deleterious interaction between honeybees (Apis mellifera) and its microsporidian intracellular parasite Nosema ceranae was mitigated by administrating either endogenous or allochthonous gut microbiota strains.

Sarah El Khoury, Nicolas Derome, Pierre Giovenazzo, Andrée Rousseau, Alexandre Lecoeur, Pierre-Luc Mercier, Bachar Cheaib, Sidki Bouslama, Vanessa Demey and Mathieu Castex

Frontiers in Ecology and Evolution | doi: 10.3389/fevo.2018.00058
(Full-text will be available on Frontiers soon)

ABSTRACT: Honey bees (Apis mellifera) are facing multiple stressors affecting their lifespan, health and productivity. Among them, Nosema ceranae is an intracellular microsporidian parasite, which plays a major impact on honey bees colonies. However, both efficiency and innocuity of current treatment against N. ceranae are observed, thus raising the urgent need to develop alternative prophylactic and curative strategies. Endogenous microbial...

New Publication in Frontiers

5/9/2018

Source: USGS // Public Domain.

Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient
Bachar Cheaib, Malo Le Boulch, Pierre-Luc Mercier et Nicolas Derome
Frontiers in Microbiology // 03 May 2018

Abstract: Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon—function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.

New Publication in Front. Microbiol.

12/20/2017

Image: Northwest Fisheries Science Center

Strong Genomic and Phenotypic Heterogeneity in the Aeromonas sobria Species Complex
Jeff Gauthier, Antony T. Vincent, Steve J. Charette and Nicolas Derome
Front. Microbiol., 08 December 2017

Aeromonas sobria is a mesophilic motile aeromonad for which, despite increasing evidence of mutualistic interactions in salmonid fish, the determinants of its host-microbe associations remain poorly understood. The ongoing confusion between A. sobria (sensu stricto) and A. veronii bv. sobria further increases this knowledge gap.

In this new publication, we assessed the genomic and phenotypic heterogeneity among five A. sobria strains. Two clinical isolates recovered from infected fish (JF2635 and CECT 4245), one from an infected amphibian (08005) and two recently isolated brook charr probionts (TM12 and TM18) which inhibit in vitro growth of A. salmonicida subsp. salmonicida (a salmonid fish pathogen).

[To read the article click here]

New Publication in Frontiers

7/18/2017

Image: NOAA // CC BY-SA

Walleye Autochthonous Bacteria as Promising Probiotic Candidates against Flavobacterium columnare
Hamza Seghouani, Carlos Enrique Garcia Rangel, Jérémie Füller, Jeff Gauthier and Nicolas Derome
Frontiers in Microbiology / Aquatic Microbiology, 18 July 2017

In this publication, we report two novel Pseudomonas fluorescens strains isolated from the walleye gut microbiota. Those two strains improved by 54% the survival of walleye juveniles infected by Flavobacterium columnare, a major opportunistic pathogen of walleye and salmonid fish.

(To view this article, click on the title above.)

New Publication in Scientific Reports

7/17/2017

Image: Magnus Manske // CC-BY 2.0 (2008)

Vertically and horizontally transmitted microbial symbionts shape the gut microbiota ontogenesis of a skin-mucus feeding discus fish progeny
Scientific Reports 7:5263 (2017)

This new publication, authored by François-Étienne Sylvain and Nicolas Derome, discusses the gut microbiota acquisition patterns in the Discus fish, which display a unique parenting behaviour by feeding their fry off their own skin mucus in the early life stages.

To read this article, click the link below:
https://www.nature.com/articles/s41598-017-05662-w

Omega-3, Microbiota and Cancer - New MSc Position

5/23/2017

SUBMISSION DEADLINE : June 30th, 2017 -- The is a new opening for a MSc (Master's) position in our research group. The candidate will study the impact of anti-Inflammatory Omega-3 supplementation on gut microbiota in healthy and prostate cancer patients.

Relevant background in molecular biology (with related laboratory experience) and bioinformatics are required.

For more information, please click the link below :

MSc : Omega-3 & Gut Microbiota

This MSc project is part of a Prostate Cancer Canada research project (Movember Discovery Grants 2016 D2016-1336) leaded by Dr Vincent Fradet (CHUQ).

New PhD Opportunities @ Derome Lab

2/20/2017

NEW SUBMISSION DEADLINE: May 31st, 2017 -- The Derome Laboratory has an exceptional opportunity available for two PhD students to join our research team, in the context of the Sentinel North program (https://www.ulaval.ca/en/sentinel-north.html). Sentinel North aims to help us monitor and prepare for changes in northern environments using state-of-the-art technologies and intervention strategies in the pursuit of sustainable health and development.

PhD #1 Arctic Char Microbiota Project

PhD #2 Zebrafish-Microbiota Model

To apply, please forward a current CV, a cover letter and two support letters via e-mail to Nicolas DEROME (nicolas.derome@bio.ulaval.ca) by May 31, 2017.

-- Learn more about the Sentinel North Research Strategy below --

Northern ecosystems are facing unprecedented assaults resulting from direct (e.g. industrial activities, such as mining and hydroelectricity) and indirect (global warming) anthropogenic activities, thus amplifying the risk of disturbing essential ecosystem services mediated by microbial communities (nitrogen cycle, primary production) and contaminate the whole food web. Because gut microbiota is critically implicated in modulating the host response to contaminants and toxins, such bio-accumulated contaminants (e.g. iron, mercury, arsenic, lead, cadmium, arsenic and manganese) are expected to have serious consequences on major host functions such as immune response, energetic performance and development. Furthermore, there are enough results suggesting that climate change could alter stages and rates of development of endemic pathogens, modify host resistance, and result in changes in the physiology of host-pathogen interactions. Because microbiota constitutes the first immune barrier by both producing specific antimicrobial compounds and outcompete invasive microbes for host resources, it is crucial to develop a sentinel model for studying skin and gut microbiota resilience when facing allochthonous pathogens in controlled conditions.

Come see us @ RAQ Quebec 2016

11/17/2016

We will give talks and poster presentations at the 2016 General Meeting of Ressources Aquatiques Quebec, the largest group of Quebec researchers in fisheries and aquaculture. The meeting will be held on Nov. 22nd and 23rd at Hotel Quartier, Quebec City.

Bachar Cheaib Experimental evolution of the yellow perch microbiome under sublethal exposure to heavy metals. (Poster)
Hamza Seghouani Endogenous bacteria from walleye (Sander vitreus), with probiotic potential against Flavobacterium columnare. (Poster)
François-Étienne Sylvain You are what you eat : get mature faster by foraging on your parents, the discus fish example. (Poster)
Jeff Gauthier Probiotic-based therapeutic tools against Aeromonas salmonicida, a major salmonid pathogen. (Talk; Nov. 23rd @ 2h30 PM).