Nicolas Derome, Département de biologie
The long-term objective of my research program is to predict and explain functional interactions between host and its associated microbial communities (host-microbiota interactions) and responses to selective pressures exerted by natural environmental changes.
Microbiota are substantially involved in a wide range of host functions, including immune defense, metabolism, and reproduction. This close interaction has been suggested to result from a highly coevolved symbiosis and commensalisms influenced by nutrition, physiology and immunological factors. Until recently, the endogenous microbiota of metazoan organisms has been inaccessible to taxonomic census in any reasonable detail. For example, in vitro cultivation, the stalwart of microbiology for the last 200 years frequently failed to detect even the most abundant members of microbial communities.
The health implications of the interaction between a host and its associated microbial species are now apparent. In the perspective of conservation and durable exploitation of aquatic species, it is thus crucial to also understand the implications of host-microbiota functional interactions and the influence of the environmental microbial communities in fish populations. With the advent of next generation DNA sequencing technologies, it is now possible to generate datasets of unprecedented size to simultaneously evaluate both the compositional and functional properties of microbial communities. Such technological developments shed new light on the intimate functional relationships between host and their endogenous microbial communities.
Our expertise on bacterial community profiling (taxonomy and functions) was applied to quantify the influence of both genetic (host QTLs) and environmental factors (surrounding water, physiological stress) that are at play to modulate the properties of host microbiota in salmonids. Our research team pioneered the development of endogenous probiotics for salmonid aquaculture, specifically selected to counteract opportunistic pathogens. In vivo trial on brook charr (Salvelinus fontinalis) revealed a decrease in mortality up to 85% in tanks treated with our probiotics. By monitoring the whole communities, we are also able to accurately identify where the probiotic counteracts the targeted pathogen, and to assess the innocuity of our probiotic strains on the microbiota homeostasis. Our research team is actually working in partnership with Lallemand Inc., an industrial company specialized in animal and human nutrition.
We are working on two animal models: fish (salmonids, perciforms, cichlids) and arthropods (honey bee, sea lice and more recently spruce budworm). In particular, by investigating how host microbiota provides the first immune barrier to its host, we decided to develop endogenous probiotic strains that proved to be very efficient in vivo.
An example of the integrated approach we use is identifying to what extent the host genotype is able to recruit specific bacterial strains, those will compose the host endogenous microflora, as exemplified in the Salvelinus and Atlantic salmon microbiota projects. We are currently using next generation sequencing, metagenomics and functional genomics to characterize our host-microbiota models. Applications of our research projects aim to develop sustainable practices in pathogen and pest control in aquaculture, forestry and apiculture.