MIMISIPI - Metagenomics and metatranscriptomics of gut microbiota within the context of dysbiosis induced by Salmonella super shedding in pigs

The super shedding of Salmonella is a health problem in the pig industry. In a previous study (PMID:36629432), researchers showed that the holobiont disruption specific to high- and low-shedder pigs follows a complex scenario. First, the host animal presented an inflammatory peak; next, a disruption of the gut microbiota was observed, including functions linked to anaerobic respiration; finally, a peak in Salmonella shedding, exacerbated in super shedders, was observed.

Our theory is that changes in the gut microbiota at the functional level ultimately determine whether a pig becomes a low or high shedder. This is why we want to study this phenomenon with an approach that combines metagenomics (potential/predicted functions) and metatranscriptomics (expressed functions). For this study, we will reanalyse the samples already collected for the PMID:36629432 study to perform a metagenomic and metatranscriptomic characterization of the time points before and immediately after infection.

We will also perform an integrated data analysis to determine which of the metagenomic species expresses crucial functions, and specifically those linked to the inflammatory response and Salmonella colonization.
This project will provide a valuable addition to current knowledge of Salmonella super shedding and underpin work to modulate the gut microbiota to reduce the impact of Salmonella on this holobiont.

Goals

The objective of MiMiSiPi is to develop an approach involving the combined metagenomic and metatranscriptomic characterization of complex samples (e.g. gut microbiota).
We are proposing an interdisciplinary programme for bioinformaticians, mathematicians and microbiologists, based on three separate events:

A seminar for people from INRAE working on or interested in combined metatranscriptomic and metagenomic characterization to study complex samples, such as those from the gut microbiota;
A workshop focusing on the interest, tools and future applications of this approach, especially those related to the association between metagenomic species and the metatranscriptomic functions expressed, using biostatistics and mathematical modelling;
A second-year master’s internship with joint supervision focusing on the taxonomic reconstruction of metagenomic species and their association with expressed functions.

Contact - Coordination :

Florent KEMPF (ISP)

Project participants

INRAE structures

Division	Unit	Expertise
GA	GABI	Pig metagenomics; metatranscriptomics
MICA	ISP	Salmonella and salmonellosis; metagenomics
MATHNUM	MaIAGE	Mathematics; modelling; data analysis
MICA	MGP	Pig metagenomics; functional annotation

Non-INRAE partners

Partner	Expertise
ANSES (France)	Salmonella in pig production
University of Surrey (Royaume-Uni)	Salmonella in pig production; metagenomics

Name of the cookie	Purpose	Shelf life
CAS and PHP session cookies	Login credentials, session security	Session
Tarteaucitron	Saving your cookie consent choices	12 months

Name of the cookie	Purpose	Shelf life
atid	Trace the visitor's route in order to establish visit statistics.	13 months
atuserid	Store the anonymous ID of the visitor who starts the first time he visits the site	13 months
atidvisitor	Identify the numbers (unique identifiers of a site) seen by the visitor and store the visitor's identifiers.	13 months