Nicolas Derome

Nicolas Derome
Laval University | ULAVAL · Department of Biology

PhD

About

149
Publications
43,184
Reads
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4,015
Citations
Citations since 2017
82 Research Items
2635 Citations
20172018201920202021202220230100200300400500
20172018201920202021202220230100200300400500
20172018201920202021202220230100200300400500
20172018201920202021202220230100200300400500
Additional affiliations
March 2007 - January 2016
Laval University
Position
  • Professor

Publications

Publications (149)
Article
Full-text available
Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian f...
Preprint
Full-text available
Amazonian blackwaters are extremely biodiverse systems containing some of the most naturally acidic, dissolved organic carbon-rich and ion-poor waters on Earth. Physiological adaptations of fish facing these ionoregulatory challenges are unresolved but could involve microbially-mediated processes. Here, we characterize the physiological response of...
Conference Paper
Full-text available
Wild Atlantic salmon populations in North America, essentially Canada, have faced a continuous declining process over the last 35 years. Current government programs to restore salmon stocks in rivers have not achieved the expected results, in terms of survival rates and fitness, of reintroduced individuals with respect to the wild born relatives. I...
Article
Full-text available
In recent years, the larval stage of Hermetia illucens, commonly known as the black soldier fly (BSFL), has been used to promote the circularity of the agri-food sector by bioconverting organic waste into larval biomass which has been used as a livestock feed. A secondary byproduct of this process is frass that can be used as an organic fertilizer....
Preprint
The study of the eukaryotic fraction of the microbiota using a metabarcoding approach is usually hindered by the high host to eukaryotic microbiota DNA ratio in samples. Indeed, the 18S rRNA gene is very similar for both the host and its eukaryotic communities, leading to a preferential amplification of the predominant host DNA when using universal...
Preprint
The study of the eukaryotic fraction of the microbiota using a metabarcoding approach is usually hindered by the high host to eukaryotic microbiota DNA ratio in samples. Indeed, the 18S rRNA gene is very similar for both the host and its eukaryotic communities, leading to a preferential amplification of the predominant host DNA when using universal...
Article
Associations between host genotype and host‐associated microbiomes have been shown in a variety of animal clades, but studies on teleosts mostly show weak associations. Our study aimed to explore these relationships in four sympatric Serrasalmidae (i.e. piranha) teleosts from an Amazonian lake, using datasets from the hosts genomes (SNPs from GBS),...
Article
Full-text available
Lowland central Amazonia is characterized by heterogeneous riverscapes dominated by two chemically divergent water types: black (ion-poor, rich in dissolved organic carbonate and acidic) and white (rich in nutrient and turbid) waters. Recent phylogeographic and genomic studies have associated the ecotone formed by these environments to an ecologica...
Preprint
Full-text available
Black soldier fly larvae (BSF, Hermetia illucens ) have gained much attention for their industrial use as biowaste recyclers and as a new source of animal proteins. The functional effect that microbiota has on insect health and growth performance remains largely unknown. This study clarifies the role of microbiota in BSF ontogeny by investigating t...
Preprint
Full-text available
Black soldier fly larvae (BSF, Hermetia illucens ) have gained much attention for their industrial use as biowaste recyclers and as a new source of animal proteins. The functional effect that microbiota has on insect health and growth performance remains largely unknown. This study clarifies the role of microbiota in BSF ontogeny by investigating t...
Article
Full-text available
Including probiotics in honeybee nutrition represents a promising solution for mitigating diseases, and recent evidence suggests that various microbes possess mechanisms that can bioremediate environmental pollutants. Thus, the use of probiotics capable of degrading pesticides used in modern agriculture would help to both reduce colony losses due t...
Conference Paper
Introduction and Objective: Recently, gut microbiota emerged as an important factor for success of immunity-based cancer treatments. However, its steady-state interaction and contribution to developing tumors is largely unexplored in non-intestinal cancers. Our objective was to investigate the connection between prostate tumor and the gut microbiot...
Article
Full-text available
Pesticides are increasing honeybee (Apis mellifera) death rates globally. Clothianidin neonicotinoid appears to impair the microbe-immunity axis. We conducted cage experiments on newly emerged bees that were 4-6 days old and used a 16S rRNA metataxonomic approach to measure the impact of three sublethal clothianidin concentrations (0.1, 1 and 10 pp...
Article
Full-text available
Aeromonas salmonicida subsp. salmonicida is a Gram-negative bacterium that causes furunculosis, a fish disease claiming substantial economic losses in the aquaculture industry. Major challenges exist in monitoring and controlling fish infections in aquaculture farms. Development of management practices to improve the sustainability of fish farming...
Preprint
Full-text available
Associations between host genotype and the microbiome of holobionts have been shown in a variety of animal clades, but studies on teleosts mostly show weak associations. Our study aimed to explore these relationships in four sympatric Serrasalmidae (i.e. piranha) teleosts from an Amazonian lake, using datasets from the hosts genomes (SNPs from GBS)...
Article
Full-text available
In supportive breeding programs for wild salmon populations, stocked parr experience higher mortality rates than wild ones. Among other aspects of phenotype, the gut microbiota of artificially raised parr differs from that of wild parr before stocking. Early steps of microbiota ontogeny are tightly dependent upon environmental conditions, both of w...
Preprint
Full-text available
The Amazon River basin sustains dramatic hydrochemical gradients defined by three water types: white, clear and black waters. Black waters contain important loads of allochthonous humic dissolved organic carbon (DOC), mostly coming from bacteria-mediated lignin degradation, a process that remains understudied. Here, we identified the main bacterial...
Article
Full-text available
Background One of the most charismatic, and yet not completely resolved example of mutualistic interaction is the partnership of clownfish and its symbiotic sea anemone. The mechanism explaining this tolerance currently relies on the molecular mimicry of clownfish epithelial mucus, which could serve as camouflage, preventing the anemone's nematocys...
Article
Full-text available
Shannon's entropy is a popular alpha diversity metric because it estimates both richness and evenness in a single equation. However, since its value is dependent on both those parameters, there is theoretically an infinite number of richness/evenness value combinations translating into the same index score. By decoupling both components measured by...
Preprint
Full-text available
Background One of the most charismatic, and yet not completely resolved example of mutualistic interaction is the partnership of clownfish and its symbiotic sea anemone. The mechanism explaining this tolerance currently relies on the molecular mimicry of clownfish epithelial mucus, which could serve as camouflage, preventing the anemone's nematocys...
Article
Full-text available
Background Disentangling the dynamics of microbial interactions within communities improves our comprehension of metacommunity assembly of microbiota during host development and under perturbations. To assess the impact of stochastic variation of neutral processes on microbiota structure and composition under disturbance, two types of microbial hab...
Preprint
Full-text available
Background Honeybees ( Apis mellifera ) are facing a number of interacting stress factors affecting their general health as well as their nervous and immune systems. Recent evidence proposed the clothianidin neonicotinoid as a potential disrupting factor for the microbiota-immunity axis. In this research, we conducted in vivo experiments to measure...
Article
Full-text available
Coral microbiomes are critical to holobiont health and functioning, but the stability of host-microbial interactions is fragile, easily shifting from eubiosis to dysbiosis. The heat-induced breakdown of the symbiosis between the host and its dinoflagellate algae (that is, "bleaching"), is one of the most devastating outcomes for reef ecosystems. Ye...
Preprint
Full-text available
Background One of the most charismatic, and yet not completely resolved example of mutualistic interaction is the partnership of clownfish and its symbiotic sea anemone. The mechanism explaining this tolerance currently relies on the molecular mimicry of clownfish epithelial mucus, which could serve as camouflage, preventing the anemone's nematocys...
Preprint
Full-text available
Shannon's diversity index is a popular alpha diversity metric because it estimates both richness and evenness in a single equation. However, since its value is dependent of both those parameters, there is theoretically an infinite number of richness / evenness value combinations translating into the same index score. By decoupling both components m...
Preprint
Full-text available
Background: Disentangling the dynamics of microbial interactions within communities improves our comprehension of metacommunity assembly of microbiota during host development and under perturbations. To assess the impact of stochastic variation of neutral processes on microbiota structure and composition under disturbance, two types of microbial ha...
Preprint
Full-text available
Background: Disentangling the dynamics of microbial interactions within communities improves our comprehension of metacommunity assembly of microbiota during host development and under perturbations. To assess the impact of stochastic variation of neutral processes on microbiota structure and composition under disturbance, two types of microbial ha...
Article
Full-text available
Microbial symbionts inhabiting the honeybee gut (i.e., gut microbiota) are essential for food digestion, immunity, and gut protection of their host. The taxonomic composition of the gut microbiota is dynamic throughout the honeybee life cycle and the foraging season. However, it remains unclear how drastic changes occurring in winter, such as food...
Article
Full-text available
Fast increase of fish aquaculture production to meet consumer demands is accompanied by important ecological concerns such as disease outbreaks. Meanwhile, food waste is an important concern with fish products since they are highly perishable. Recent aquaculture and fish product microbiology, and more recently, microbiota research, paved the way to...
Article
Whether host-associated microbiomes are mostly shaped by species-specific or environmental factors is still unresolved. In particular, it is unknown to what extent microbial communities from two different host tissues from the same host respond to these factors. Our study is one of the first to focus on the microbiome of teleost fish to shed a ligh...
Preprint
Full-text available
Background One of the most charismatic, and yet mostly unexplained example of mutualistic interaction is the partnership of clownfish and its symbiotic sea anemone. The mechanism explaining this tolerance currently relies on the molecular mimicry of clownfish epithelial mucus, which could serve as camouflage, preventing the anemone's nematocysts' d...
Preprint
Full-text available
Background One of the most charismatic, and yet not completely resolved example of mutualistic interaction is the partnership of clownfish and its symbiotic sea anemone. The mechanism explaining this tolerance currently relies on the molecular mimicry of clownfish epithelial mucus, which could serve as camouflage, preventing the anemone's nematocys...
Preprint
Full-text available
Background One of the most charismatic, and yet not completely resolved example of mutualistic interaction is the partnership of clownfish and its symbiotic sea anemone. The mechanism explaining this tolerance currently relies on the molecular mimicry of clownfish epithelial mucus, which could serve as camouflage, preventing the anemone's nematocys...
Preprint
Full-text available
Background One of the most charismatic, and yet not completely resolved example of mutualistic interaction is the partnership of clownfish and its symbiotic sea anemone. The mechanism explaining this tolerance currently relies on the molecular mimicry of clownfish epithelial mucus, which could serve as camouflage, preventing the anemone's nematocys...
Article
Full-text available
Background: The eco-evolutionary processes ruling post-disturbance microbial assembly remain poorly studied, particularly in host-microbiome systems. The community recovery depends not only on the type, duration, intensity, and gradient of disturbance, but also on the initial community structure, phylogenetic composition, legacy, and habitat (soil...
Poster
Full-text available
The microbiota’s impact on host’s development, metabolism and immunology has made microbial study integral to the biology of organisms. Microorganisms coevolve with their host and can be vital for development, to the point that some host cannot survive in their absence. Studies have explored Hermetia illucens (BSF) microbiome, an insect prized for...
Article
Full-text available
Investigating relationships between microbiota and their host is essential toward a full understanding of how animal adapt to their environment. Lake Whitefish offers a powerful system to investigate processes of adaptive divergence where the dwarf, limnetic species evolved repeatedly from the normal, benthic species. We compared the transient inte...
Article
The world's richest freshwater fish community thrives in gradients of contrasting environments in Amazonia, ranging from ion‐poor acidic black waters, to ion‐rich circumneutral white waters. These hydrochemical gradients structure Amazonian fish assemblages via ecological speciation events. Fish bacterial communities contain an important genetic he...
Article
Full-text available
Aeromonas salmonicida subsp. salmonicida is a Gram-negative bacterium causing furunculosis, an opportunistic infection of farmed salmonid fish. Current treatment methods against furunculosis rely heavily on antibiotherapy. However, strains of this opportunistic fish pathogen were found to possess genes that confer resistance to major antibiotics in...
Chapter
It is well known that antibiotics are playing leading roles in several areas such as human and animal health and farm production. Unfortunately, the use of antimicrobial compounds as a panacea is coming to an end. More and more antibiotic-resistant bacterial strains are listed in all spheres of activity where they were used. Aquaculture, which is a...
Chapter
Salmonids are second to carps as the most important group of farmed fish, with a total annual output of over 2 million tonnes. Intensive farming practices have been developed to maximize production but at the expense of exposing farmed fish to several simultaneous stressors including frequent handling procedures, overcrowding, and poor water qualit...
Article
Full-text available
It is easy for today's students and researchers to believe that modern bioinformatics emerged recently to assist next-generation sequencing data analysis. However, the very beginnings of bioinformatics occurred more than 50 years ago, when desktop computers were still a hypothesis and DNA could not yet be sequenced. The foundations of bioinformatic...
Article
Full-text available
Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between capti...
Article
Full-text available
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 being questioned, thus raising the...
Research
Full-text available
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...
Data
Classification of lake metacommunities based ORF approach at genus and phylum levels. (a) Distribution of ORF and annotated genus in the five metagenomes. This figure showed that not only the number of predicted ORFs (Supplementary File S2), comparable between metagenomes but also the genus count (Supplementary File S3). (b) Hierarchical clustering...
Data
Hierarchical clustering of taxon and function. (a) Hierarchical clustering of artificial replicates based on genus abundance using the subsampled reads approach. (b) Hierarchical clustering of samples based on abundance of subsystem level 1 using the ORF approach. (c, d) Hierarchical clustering of subsampled replicates based on subsystems level 1 a...
Data
Geographical localisation and metallic profiles of sampled lakes. (a) Geographical localisation of the sampling sites located in Ryoun-Noranda (West Quebec, Canada) visited in June 2011. Latitute and longitude coordinates of sampling sites are 48.25005489 and −79.40574646 in Opasatica lake (OPA-nc); 48.07601448 and −79.3082428 in Dasserat lake (DAS...
Data
Composition of metacommunities based on the ORFs approach. NMDS (with Bray-Curtis distance) of genera abundance for major abundant phyla fitted to trace metals for Proteobacteria (a), Actinobacteria (b), Cyanobacteria (c), the water pH, and trace metals which correlated significantly with NMDS axes were highlighted in red. Each small point in figur...
Data
Heatmap of subsystems in level 1. This heatmap represents metagenomes classification based on subsystems in level 1 (See Supplementary File S5). Dendrogram's topology identified two clusters. The first cluster grouped BAR-mc, LAR-hc and TUR-hc, and the second grouped DAS-lc and OPA-nc. The hierarchical clustering of relative abundance proportions o...
Data
Heatmap of subsystems in all levels. Subsystems relative abundance were clustered cross-metagenomes in different levels, level2 (981 modules), level3 (192 modules) and function level (6801 functions) (See Supplementary File S5). The same topology was observed in level 1 (See Supplementary Figure S5) and in all levels. The hierarchical clustering of...
Data
Gradual variation of functions cross-metagenomes. Two heatmaps represent gradual function abundance FP1 (106 functions) and FP2 (123 functions) along the contamination gradient. The hierarchical clustering of relative abundance proportions of functions was performed using Ward's method and Bray–Curtis dissimilarity distance. The ORF approach was us...
Data
This file resumed details of NMDS plots. NMDS loadings, abundance clusters and points labels of all genus (Table 1), Proteobacteria (Table 2), Actinobacteria (Table 3), Cyanobacteria (Table 4), then of all subsystems (Table 5) were reported for assuming a better understanding of NMDS figures and Supplementary Figures.
Data
Heatmap of multiple subsystems abundant in function level. This heatmap represents cross-metagenomes, the common and most abundant functions (>2%) in 22 subsystems (See Supplementary File S5). Functions of polymetallic resistance (Cation efflux system protein CusA and Cobalt–zinc–cadmium resistance protein CzcA) showed a profile of gradual abundanc...
Data
Subsystem of “Phages, prophages, plasmids, and transposable elements” cross-metagenomes. Under this subsystem multiple relevant functions (level 3) related to mobile elements and transfer vectors (Gene transfer agents, transposons, prophages, conjugative plasmids, integrons) were shared between DAS-lc, BAR-mc, LAR-hc, TUR-hc, and depleted in OPA-nc...
Data
Specific variation of functions cross-metagenomes. Two heatmaps represent specific function abundance FP3-OPA-nc (167 functions) and FP3 specific to pollution gradient (225 functions). The hierarchical clustering of relative abundance proportions of functions was performed using Ward's method and Bray–Curtis dissimilarity distance. The ORF approach...
Data
This file contains two tables. The first table resumed the geographical coordinates of sampled sites. The second table presented abiotic parameters measured for each sampled site 1 year before this study (Laplante and Derome, 2011).
Data
This file summarized in one table the relative abundance of major taxa at phylum, class, and genus levels.
Data
This file summarized statistics of reads, contigs, and ORFs MG-RAST annotations per lake metagenome.
Data
Metabolic abundance cross-metagenomes. This heatmap represents 1,842 annotated enzymes (See EC number in Supplementary File S7) in all samples. The hierarchical clustering of relative abundance proportions of enzymes, and of samples was performed using Ward's method and Bray–Curtis dissimilarity distance. The dendrogram shows dichotomy between OPA-...
Data
This file reported subsystems annotations and data analysis; All subsystems data (dataset output of STAMP software) in Table 1, subsystems level 1 relative abundance (RA) in Table 2, list of all annotated subsystems in Table 3, function profiles classification of RA proportions in Table 4, different function profiles (FP) (Tables 5, 6, 7, 8), resum...
Data
This file summarized details of NMDS correlation analysis with metadata. Each table resumed NMDS loadings (NMDS1, NMDS2), P-value of correlated trace metals of taxa (Table 1), subsystems level 1 (Table 2) and PMRGs.
Data
This file resumed diversity measures based relative abundance of taxa (genus) and function (subsystems) in Table 1 and all annotated enzymes by their EC-number in Table 2.
Article
Full-text available
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...
Preprint
Full-text available
It is becoming increasingly clear that wild animals have never existed without symbiotic interactions with microbiota. Therefore, investigating relationships between microbiota and their host is essential towards a full understanding of how animal evolve and adapt to their environment. The Lake Whitefish (Coregonus clupeaformis) is a well-documente...
Article
Full-text available
Background: It is well established that symbionts have considerable impact on their host, yet the investigation of the possible role of the holobiont in the host's speciation process is still in its infancy. In this study, we compared the intestinal microbiota among five sympatric pairs of dwarf (limnetic) and normal (benthic) lake whitefish Coreg...