H. Argüello, P. Rubio, A. Jaramillo, V. Barrios, M. García et al., Evaluation of cleaning and disinfection procedures against Salmonella enterica at swine farms, transport and lairage facilities, Proceedings of International Safepork Congress, Maastrich, pp.254-256, 2011.

S. M. Bearson, H. K. Allen, B. L. Bearson, T. Looft, B. W. Brunelle et al., Profiling the gastrointestinal microbiota in response to Salmonella: Low versus high Salmonella shedding in the natural porcine host, Infection, Genetics and Evolution, vol.16, pp.330-340, 2013.
DOI : 10.1016/j.meegid.2013.03.022

P. A. Beloeil, P. Fravalo, C. Fablet, J. P. Jolly, E. Eveno et al., Risk factors for Salmonella enterica subsp. enterica shedding by marketage pigs in French farrow-to-finish herds, Prev. Vet. Med, vol.63, 2004.

K. A. Borewicz, H. B. Kim, R. S. Singer, C. J. Gebhart, S. Sreevatsan et al., Changes in the Porcine Intestinal Microbiome in Response to Infection with Salmonella enterica and Lawsonia intracellularis, PLOS ONE, vol.8, issue.10, 2015.
DOI : 10.1371/journal.pone.0139106.s007

F. Boyen, F. Haesebrouck, D. Maes, F. Van-immerseel, R. Ducatelle et al., Non-typhoidal Salmonella infections in pigs: A closer look at epidemiology, pathogenesis and control, Veterinary Microbiology, vol.130, issue.1-2, pp.1-19, 2008.
DOI : 10.1016/j.vetmic.2007.12.017

M. Bratchikov and M. Mauricas, Development of a multiple-run highresolution melting assay for Salmonella spp. genotyping HRM application for Salmonella spp. subtyping, Diagn. Microbiol. Infect. Dis, vol.71, 2011.

J. G. Caporaso, C. L. Lauber, W. A. Walters, D. Berg-lyons, J. Huntley et al., Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms, The ISME Journal, vol.6, issue.8, pp.1621-1624, 2012.
DOI : 10.1038/ismej.2010.160

M. Castillo, S. M. Martin-orue, E. G. Manzanilla, I. Badiola, M. Martin et al., Quantification of total bacteria, enterobacteria and lactobacilli populations in pig digesta by real-time PCR, Veterinary Microbiology, vol.114, issue.1-2, pp.165-170, 2006.
DOI : 10.1016/j.vetmic.2005.11.055

M. C. Collado, E. Isolauri, K. Laitinen, and S. Salminen, Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women, The American Journal of Clinical Nutrition, vol.37, issue.12, pp.894-899, 2008.
DOI : 10.1111/j.1365-2222.2007.02849.x

D. Busser, E. V. Maes, D. Houf, K. Dewulf, J. et al., from Porcine Duodenal Content, Foodborne Pathogens and Disease, vol.10, issue.2, pp.182-188, 2013.
DOI : 10.1089/fpd.2012.1268

G. Den-besten, K. Van-eunen, A. K. Groen, K. Venema, D. Reijngoud et al., The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism, Journal of Lipid Research, vol.116, issue.9, pp.2325-2340, 2013.
DOI : 10.1080/089106002320644348

I. Dewaele, H. Van-meirhaeghe, G. Rasschaert, M. Vanrobaeys, E. De-graef et al., Persistent Salmonella Enteritidis environmental contamination on layer farms in the context of an implemented national control program with obligatory vaccination, Poultry Science, vol.91, issue.2, pp.282-291, 2012.
DOI : 10.3382/ps.2011-01673

D. B. Digiulio, B. J. Callahan, P. J. Mcmurdie, E. K. Costello, D. J. Lyell et al., Temporal and spatial variation of the human microbiota during pregnancy, Proceedings of the National Academy of Sciences, vol.88, issue.4, pp.11060-11065, 2010.
DOI : 10.1111/1467-9868.00293

A. Farzan, R. M. Friendship, C. E. Dewey, A. C. Muckle, J. T. Gray et al., Distribution of Salmonella serovars and phage types on 80 Ontario swine farms, Can. J. Vet. Res, vol.72, pp.1-6, 2004.

P. Fravalo, P. Lebel, J. Longpré, B. Laplante, É. Yergeau et al., Salmonella associated taxonomic and functional changes in the pig digestive tract during application of feed associated mitigation option in production, Proceedings of the 2013 International Symposium on Salmonella and Salmonellosis, 2013.

J. Funk and W. Gebreyes, Risk factors associated with Salmonella on swine farms, J. Swine Health Prod, vol.12, pp.247-251, 2004.

J. A. Funk, P. R. Davies, N. , and M. A. , in Swine Feces, Journal of Veterinary Diagnostic Investigation, vol.33, issue.5, pp.412-418, 1177.
DOI : 10.2307/1591981

J. A. Funk, P. R. Davies, N. , and M. A. , Longitudinal study of Salmonella enterica in growing pigs reared in multiple-site swine production systems, Veterinary Microbiology, vol.83, issue.1, pp.45-60, 2001.
DOI : 10.1016/S0378-1135(01)00404-7

I. Gantois, R. Ducatelle, F. Pasmans, F. Haesebrouck, I. Hautefort et al., Butyrate Specifically Down-Regulates Salmonella Pathogenicity Island 1 Gene Expression, Applied and Environmental Microbiology, vol.72, issue.1, pp.946-949, 2006.
DOI : 10.1128/AEM.72.1.946-949.2006

L. Gorski, Selective Enrichment Media Bias the Types of Salmonella enterica Strains Isolated from Mixed Strain Cultures and Complex Enrichment Broths, PLoS ONE, vol.21, issue.4, 2012.
DOI : 10.1371/journal.pone.0034722.t003

V. Gotter, G. Klein, S. Koesters, L. Kreienbrock, T. Blaha et al., Main risk factors for Salmonella-infections in pigs in north-western Germany, Preventive Veterinary Medicine, vol.106, issue.3-4, pp.301-307, 2012.
DOI : 10.1016/j.prevetmed.2012.03.016

A. A. Hill, R. R. Simons, L. Kelly, and E. L. Snary, A Farm Transmission Model for Salmonella in Pigs, Applicable to E.U. Member States, Risk Analysis, vol.75, issue.8, pp.461-481, 2015.
DOI : 10.2527/1997.7582129x

S. Hoffmann, M. B. Batz, M. , and J. G. Jr, Annual Cost of Illness and Quality-Adjusted Life Year Losses in the United States Due to 14 Foodborne Pathogens, Journal of Food Protection, vol.38, issue.2, pp.1292-1302, 2012.
DOI : 10.1086/381578

, 16S Metagenomic Sequencing Library Preparation [Online]. Illumina Available: https://www.illumina.com/content/dam/illumina-support/ documents/documentation/chemistry_documentation/16s/16s-metagenomic- library-prep-guide-15044223-b, Illumina, 2013.

H. B. Kim and R. E. Isaacson, in Swine: Microbiota Interactions, Annual Review of Animal Biosciences, vol.5, issue.1, pp.43-63, 2017.
DOI : 10.1146/annurev-animal-022516-022834

O. Koren, J. K. Goodrich, T. C. Cullender, A. Spor, K. Laitinen et al., Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy, Cell, vol.150, issue.3, pp.470-480, 2012.
DOI : 10.1016/j.cell.2012.07.008

J. J. Kozich, S. L. Westcott, N. T. Baxter, S. K. Highlander, and P. D. Schloss, ABSTRACT, Applied and Environmental Microbiology, vol.79, issue.17, pp.5112-5120, 1128.
DOI : 10.1128/AEM.01043-13

S. D. Lawhon, R. Maurer, M. Suyemoto, A. , and C. , Intestinal shortchain fatty acids alter Salmonella typhimurium invasion gene expression and virulence through BarA/SirA, Mol. Microbiol, vol.46, 2002.

P. Lebel, A. Letellier, J. Longpre, B. Laplante, E. Yergeau et al., shedding and specifically modulates the faecal microbiota, Journal of Applied Microbiology, vol.78, issue.Suppl 1, pp.30-39, 2016.
DOI : 10.1128/AEM.02036-12
URL : https://hal.archives-ouvertes.fr/pasteur-01534546

P. Legendre, L. F. Legendre, A. Letellier, G. Beauchamp, E. Guévremont et al., Numerical Ecology Risk factors at slaughter associated with presence of Salmonella on hog carcasses in Canada, J. Food Prot, vol.72, pp.2326-2331, 2009.

H. Lynch, F. C. Leonard, K. Walia, P. G. Lawlor, G. Duffy et al., Investigation of in-feed organic acids as a low cost strategy to combat Salmonella in grower pigs, Preventive Veterinary Medicine, vol.139, pp.50-57, 2017.
DOI : 10.1016/j.prevetmed.2017.02.008

C. F. Magistrali, N. Ciuti, F. Cucco, L. Maresca, C. Paniccià et al., Longitudinal study of fecal Salmonella shedding by sows Estudio longitudinal de excreción de Salmonella fecal en hembras Étude longitudinale sur l'excrétion fécale de Salmonella par des truies, J. Swine Health Prod, vol.19, pp.326-330, 2011.

T. Matsuki, K. Watanabe, J. Fujimoto, Y. Kado, T. Takada et al., Quantitative PCR with 16S rRNA-gene-targeted speciesspecific primers for analysis of human intestinal bifidobacteria, 2004.

, Appl. Environ. Microbiol, vol.70, pp.167-173, 2004.

X. C. Morgan, T. L. Tickle, H. Sokol, D. Gevers, K. L. Devaney et al., Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment, Genome Biology, vol.13, issue.9, 2012.
DOI : 10.1186/gb-2011-12-6-r60
URL : https://hal.archives-ouvertes.fr/hal-00736429

N. Nollet, K. Houf, J. Dewulf, L. Duchateau, L. De-zutter et al., Distribution of Salmonella Strains in Farrow-to-Finish Pig Herds: A Longitudinal Study, Journal of Food Protection, vol.53, issue.10, pp.2012-2021, 2005.
DOI : 10.1080/17843286.2000.11754316

N. Nollet, K. Houf, J. Dewulf, A. D. Kruif, L. D. Zutter et al., in sows: a longitudinal study in farrow-to-finish pig herds, Veterinary Research, vol.36, issue.4, pp.645-656, 2005.
DOI : 10.1051/vetres:2005022
URL : https://hal.archives-ouvertes.fr/hal-00902990

M. Nuriel-ohayon, H. Neuman, K. , and O. , Microbial Changes during Pregnancy, Birth, and Infancy, Frontiers in Microbiology, vol.2, issue.290, 2016.
DOI : 10.3389/fpubh.2014.00290

S. Park, M. Kim, and J. Bae, Blautia faecis sp. nov., isolated from human faeces, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.25, issue.24, pp.599-603, 2013.
DOI : 10.1093/nar/25.24.4876

S. E. Pryde, S. H. Duncan, G. L. Hold, C. S. Stewart, H. J. Flint et al., The microbiology of butyrate formation in the human colon, FEMS Microbiology Letters, vol.55, issue.Suppl. 216, pp.133-139, 2002.
DOI : 10.1016/0016-5085(93)91016-B

A. Rivière, M. Selak, D. Lantin, F. Leroy, D. Vuyst et al., Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut, Frontiers in Microbiology, vol.6, issue.1030, 2016.
DOI : 10.1038/ismej.2011.212

A. Thibodeau, P. Fravalo, É. Yergeau, J. Arsenault, L. Lahaye et al., Chicken Caecal Microbiome Modifications Induced by Campylobacter jejuni Colonization and by a Non-Antibiotic Feed Additive, PLOS ONE, vol.93, issue.6, 2015.
DOI : 10.1371/journal.pone.0131978.s005

P. Thiennimitr, S. E. Winter, and A. J. Bäumler, Salmonella, the host and its microbiota, Current Opinion in Microbiology, vol.15, issue.1, 2012.
DOI : 10.1016/j.mib.2011.10.002

M. K. Thomas, R. Murray, L. Flockhart, K. Pintar, F. Pollari et al., Estimates of the Burden of Foodborne Illness in Canada for 30 Specified Pathogens and Unspecified Agents, Circa 2006, Foodborne Pathogens and Disease, vol.10, issue.7, pp.639-648, 2006.
DOI : 10.1089/fpd.2012.1389

K. Walia, H. Argüello, H. Lynch, F. C. Leonard, J. Grant et al., Effect of feeding sodium butyrate in the late finishing period on Salmonella carriage, seroprevalence, and growth of finishing pigs, Preventive Veterinary Medicine, vol.131, pp.79-86, 2016.
DOI : 10.1016/j.prevetmed.2016.07.009

W. Wilkins, A. Raji´craji´c, C. Waldner, M. Mcfall, E. Chow et al., Distribution of Salmonella serovars in breeding, nursery, and grow-to-finish pigs, and risk factors for shedding in ten farrow-to-finish swine farms in Alberta and Saskatchewan, Can. J. Vet. Res, vol.74, pp.81-90, 2010.