MoMIR-PPC: Monitoring the gut microbiota and immune response to predict, prevent and control zoonoses in humans and livestock in order to minimize the use of antimicrobials.

Start: 1 January 2018
Duration: 2 Years
Domain: Foodborne Zoonoses
Keywords: Gut microbiota, immune response, heterogeneity of infection, Salmonella, computational model
Contact: Philippe Velge (INRA)

The Project #MoMIR

MoMIR-PPC aims to develop new approaches to predict, identify and prevent the appearance of animal and human Super-shedders based on immune response and gut microbiota composition.

Many early studies on infectious disease epidemiology assumed that susceptible hosts within a population had equal  chances  of  becoming  infected.  Consequently, the  majority  of  control  measures  and  intervention strategies are based on this paradigm as well as the mathematical models of pathogen transmission. However, recent studies have uncovered the importance of host heterogeneity in infection and it has been shown that a minority  of  the  infected  individuals  are  responsible  for  the  majority  of  the  infections.  In  the  case  of pathogens transmitted via the faecal-oral route, these individuals are those that shed the highest numbers of bacteria and are known as Super-spreaders or Super-shedders. The most important zoonoses (salmonellosis, colibacillosis and campylobacteriosis) are no exception to this general rule (Marshall & French 2011 MAF; Bearson et al. Infect Genet Evol, 2013). To improve the microbial safety of food and to develop new preventive measures for controlling zoonosis, this heterogeneity of infection must be taken into account and the interventions to the super-shedders must be targeted.

MoMIR-PPC’s main objective is to improve EU industry sustainability and safe trade by providing information and tools leading to on-farm control of the bacteria. To maximise the feasibility of the project, the focus is put on Salmonella infection, which is a priority for Europe (The EFSA Journal, 2013 11(4)) . Salmonellosis will serve as a model for other zoonotic bacteria as Campylobacter and E. coli. The biomarkers, diagnostic tools and the control measures obtained in this project should be easily translated to these bacteria in a future project.

The main achievements will be the development of:

  1. Predictive markers based on that will sign the risk to become a super-shedder of Salmonella.
  2. Immune and microbiota biomarkers of excretion that will be useful to detect animal super- shedders and/ or human prolonged carriers.
  3. Preventive measures and /or control measures of this zoonotic problem by the characterisation of prebiotics, probiotics and nutraceutical products, which could be use in animals but also in human
  4. A pool of biosecurity measures at the farm levels, with a cost effectiveness, thanks to the mathematical models at  between-  and  within-host  scal  These  mathematical  models  will  provide  new  tools  to  risk managers for prevention and control of Salmonella infections but which should be easily adapted to other zoonotic pathogens.


Roche S. M., Holbert S., Le Vern Y., Rossignol C., Rossignol A., Velge P., Virlogeux-Payant I. (2021) A large panel of chicken cells are invaded in vivo by Salmonella Typhimurium even when depleted of all known invasion factors. Open Biology. 11, 210117 DOI:

Porras, N., Rebollada-Merino, A., Bárcena, C., Mayoral-Alegre, FJ., Lomillos, JM., Domínguez, L., Rodríguez-Bertos, A. (2021). Effect of Biscuit Flour and Fermented Defatted “Alperujo” Co-Administration on Intestinal Mucosa Morphology and Productive Performance in Laying Hens. Animals. 11, 1075. DOI:

van Wagenberg, CPA., van Horne, P.L.M., van Asseldonk, M.A.P.M. (2020). Cost-effectiveness analysis of using probiotics, prebiotics, or synbiotics to control Campylobacter in broilers. Poultry Science. 99 (8), pp. 4077-4084. DOI:

Labarthe, S., Laroche, B., Nguyen, T. N. T., Polizzi, B., Patout, F., Ribot, M., Stegmaier, T. (2020). A Multi-Scale Epidemic Model of Salmonella infection with Heterogeneous Shedding. ESAIM: Proceedings and Surveys, 67, p. 261-284. DOI:

Rebollada-Merino, A., Ugarte-Ruiz, M., Hernández, M., Miguela-Villoldo, P., Abad, D., Rodríguez-Lázaro, D., de Juan, L., Domínguez, L., Rodríguez-Bertos, A. (2020). Reduction of Salmonella Typhimurium cecal colonisation and improvement of intestinal health in broilers supplemented with fermented defatted ‘alperujo’, an olive oil by-product. Animals. 10(10), 1931. DOI:

Rebollada-Merino, A., Ugarte-Ruiz, M., Hernández, M., Miguela-Villoldo, P., Abad, D., Cuesta-Álvaro, P., Rodríguez-Lázaro, D., de Juan, L., Domínguez, L., Rodríguez-Bertos, A. (2020). Dietary supplementation with fermented defatted “alperujo” induces modifications of the intestinal mucosa and cecal microbiota of broiler chickens. Poultry Science. DOI:

Kempf, F., Menanteau, P., Rychlik, I., Kubasová, T., Trotereau, J., Virlogeux‐Payant, I., Schaeffer, S., Schouler, C., Drumo, R., Guitton, E., Velge, P. (2020) Gut microbiota composition before infection determines the Salmonella super‐ and low‐shedder phenotypes in chicken. Microbial Biotechnology. 13 (5), 1611– 1630. DOI:

Menanteau, P. Kempf, F., Trotereau, J., Virlogeux-Payant, I., Gitton, E., Dalifard, J., Gabriel, I., Rychlik, I., Velge, P. (2018). Role of systemic infection, cross contaminations and super-shedders in Salmonella carrier state in chicken. Environmental Microbiology. 20 (9), 3246–3260. DOI:

Moreno MA., Florez-Cuadrado D., Ugarte-Ruiz M. and Dominguez L Veterinarios y antibióticos: destinados a entenderse. Profesión Veterinaria. Asis, 2018 ISBN: 2253-7244. 2018.

Florez-Cuadrado D., Moreno MA., Ugarte-Ruiz M. and Dominguez L Antimicrobial Resistance in the Food Chain in the European Union. Advances in Food and Nutrition Research. Elsevier, 2018 DOI: 10.1016/bs.afnr.2018.04.004

Menanteau, P., Kempf, F., Trotereau, J., Virlogeux-Payant, I., Guitton, E., Dalifard, J., Gabriel, I., Rychlik, I., and Velge, P. (2018) Role of systemic infection, cross contaminations and super-shedders in Salmonella carrier state in chicken. Environmental Microbiology. DOI: 10.1111/1462-2920.14294

OpenAIRE Publications

Project Events

MoMIR Annual Meeting 8th February 2019

Project Deliverables

DMP of the MoMIR-PPC project

D0.1-Project initiation and management

D0.3- Minutes of project meetings (Kick off meeting)

D0.4- Minutes of project meetings (mid term meeting)

D1.1- Panel of immunological markers to assess in pig and chicken

D1.5- In vitro virulence levels of different Salmonella strains recovered from high and low shedders in animals and humans

D1.7- Definition of immunological markers associated to the high and low shedders in chickens and in pigs.

D1.9- Definition of microbiota markers associated with high and low-shedders in chickens and in pigs

D1.12- Antimicrobial susceptibility testing, serotyping and whole genome sequencing of all Salmonella isolates from participants submitted to the Norwegian Reference laboratory

D1.15- Understanding whether high and low shedder phenotypes are mainly related to Salmonella strain variation, immune status or microbiota composition

D2.1- In vitro effect of already characterised probiotics on Salmonella growth and cell invasion

D2.3- Characterisation of protective commensal bacteria able to inhibit Salmonella colonisation

D2.5- Impact of defined and undefined probiotics on Salmonella colonisation in pig and chicken

D2.8- Impact of prebiotics or feed on Salmonella colonisation in pig, chicken and human. Effect on the super-shedders and low-shedders.

D2.10- Evolution of the immune-signature in pig, chicken and/ or human according to the context (infection, treatment)

D3.3- Overview of measures against Salmonella at the poultry primary production level

D4.3- Creation of an animal experiment database



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