World meat consumption patterns: an overview of the last fifty years, Meat Sci, vol.109, pp.106-111, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01281132
, United Kingdom poultry and poultry meat statistics-November and December, 2018.
Contact with adult hen affects development of caecal microbiota in newly hatched chicks, PLoS One, vol.14, 2019. ,
Microbiota of the chicken gastrointestinal tract: influence on health, productivity and disease, Appl Microbiol Biotechnol, vol.98, pp.4301-4310, 2014. ,
Incidence and tracking of Clostridium perfringens through an integrated broiler chicken operation, Avian Dis, vol.47, pp.707-711, 2003. ,
Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession, vol.8, p.821, 2019. ,
Factors affecting intestinal health in poultry, Poult Sci, vol.87, pp.2052-2063, 2008. ,
Bacterial enteritides of poultry, Poult Sci, vol.77, pp.1159-1165, 1998. ,
, FSA welcomes retailers' efforts to reduce Campylobacter on chickens, Vet Record, vol.176, pp.639-639, 2015.
Antibiotic growth promoters in agriculture: history and mode of action, Poult Sci, vol.84, pp.634-643, 2005. ,
History of the use of antibiotic as growth promoters in European poultry feeds, Poult Sci, vol.86, pp.2466-2471, 2007. ,
The chicken gastrointestinal microbiome, FEMS Microbiol Lett, vol.360, pp.100-112, 2014. ,
Development of the chick microbiome: how early exposure influences future microbial diversity, Front Vet Sci, vol.3, 2016. ,
Effect of in ovo administration of an adult-derived microbiota on establishment of the intestinal microbiome in chickens, Am J Vet Res, vol.77, pp.514-526, 2016. ,
Metagenomic bacterial community profiles of chicken embryo gastrointestinal tract by using T-RFLP analysis, Dokl Biochem Biophys, vol.466, pp.47-51, 2016. ,
Controlling contaminants in low-biomass 16S rRNA gene sequencing experiments, vol.4, pp.290-309, 2019. ,
The microflora of the alimentary tract and avian pathogens: translocation and vertical transmission, Microbiology of the avian egg, pp.117-138, 1994. ,
Absorption of methionine and 2-hydroxy-4-methylhiobutoanic acid in conventional and germ-free chickens, Poult Sci, vol.82, pp.1149-1153, 2003. ,
Evaluation of disinfectants and antiseptics to eliminate bacteria from the surface of turkey eggs and hatch gnotobiotic poults, Poult Sci, vol.96, pp.2412-2420, 2017. ,
Eggshell factors influencing eggshell penetration and whole egg contamination by different bacteria including Salmonella enteritidis, Int J Food Microbiol, vol.112, pp.253-260, 2006. ,
Prevention of the growth of Salmonella infantis in chicks by the flora of the alimentary tract of chickens, Br Poult Sci, vol.14, pp.627-630, 1973. ,
Sensitivity of young chickens to Salmonella typhimurium var copenhagen and S. infantis infection and the preventive effect of cultured intestinal microflora, Avian Dis, vol.23, pp.392-400, 1979. ,
Research note: in ovo administration of a competitive exclusion culture treatment to broiler embryos, Poult Sci, vol.71, pp.1781-1784, 1992. ,
In ovo injection of competitive exclusion culture in broiler hatching eggs, J Appl Poult Res, vol.6, pp.260-266, 1997. ,
In ovo inoculation of chicken embryos with probiotic bacteria and its effect on posthatch Salmonella susceptibility, Poult Sci, vol.93, pp.818-829, 2014. ,
Effect of immersion and inoculation in ovo of Lactobacillus spp. in embryonated chicken eggs in the prevention of Salmonella Enteritidis after hatch, Poult Sci, vol.92, pp.1560-1563, 2013. ,
Impact of egg disinfection of hatching eggs on the eggshell microbiome and bacterial load, Poult Sci, vol.91, pp.208-214, 2017. ,
The time-course of broiler intestinal microbiota development after administration of cecal contents to incubating eggs, PeerJ, vol.5, p.3587, 2017. ,
Balance trees reveal microbial niche differentiation, vol.2, pp.162-178, 2017. ,
Commensal clostridia: leading players in the maintenance of gut homeostasis, Gut Pathog, vol.5, p.23, 2013. ,
Steering endogenous butyrate production in the intestinal tract of broilers as a tool to improve gut health, Front Vet Sci, vol.2, p.75, 2015. ,
The structure of bacterial community in the intestines of newly hatched chicks, J Appl Poult Res, vol.14, pp.232-237, 2005. ,
Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures, BMC Genomics, vol.19, p.561, 2018. ,
Bifidobacteria are obligate inhabitants of the crop of adult laying hens, J Vet Med B Infect Dis Vet Public Health, vol.48, pp.227-233, 2001. ,
A consistent and predictable commercial broiler chicken bacterial microbiota in antibiotic-free production displays strong correlations with performance, Appl Environ Microbiol, vol.84, pp.362-380, 2018. ,
Bacterial census of poultry intestinal microbiome, Poult Sci, vol.92, pp.671-683, 2013. ,
Apathogenic intestinal segmented filamentous bacteria stimulate the mucosal immune system of mice, Infect Immun, vol.61, pp.303-306, 1993. ,
Differential roles of segmented filamentous bacteria and Clostridia in development of the intestinal immune system, Infect Immun, vol.67, pp.3504-3511, 1999. ,
Segmented filamentous bacteria take the stage, Mucosal Immunol, vol.3, pp.209-212, 2010. ,
Colonization and distribution of segmented filamentous bacteria (SFB) in chicken gastrointestinal tract and their relationship with host immunity, FEMS Microbiol Ecol, vol.81, pp.395-406, 2012. ,
Interrelations between the microbiotas in the litter and in the intestines of commercial broiler chickens, Appl Environ Microbiol, vol.76, pp.6572-6582, 2010. ,
A scanningelectron microscope study of the caecal tonsil: the identification of a bacterial attachment to the villi of the caecal tonsil and the possible presence of lymphatics in the caecal tonsil, Poult Sci, vol.57, pp.1408-1416, 1978. ,
Induction of intestinal Th17 cells by segmented filamentous bacteria, Cell, vol.139, pp.485-498, 2009. ,
Role of volatile fatty acids in development of the cecal microflora in broiler chickens during growth, Appl Environ Microbiol, vol.66, pp.2536-2540, 2000. ,
From the gut to the peripheral tissues: the multiple effects of butyrate, Nutr Res Rev, vol.23, pp.366-384, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-02668794
Regulation of immune cell function by short-chain fatty acids, Clin Transl Immunology, vol.5, 2016. ,
Butyrate and other short-chain fatty acids as modulators of immunity: what relevance for health?, Curr Opin Clin Nutr Metab Care, vol.13, pp.715-721, 2010. ,
Development of the caecal microbiota in three broiler breeds, Front Vet Sci, vol.6, 0201. ,
URL : https://hal.archives-ouvertes.fr/hal-02466825
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms, ISME J, vol.6, pp.1621-1624, 2012. ,
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample, Proc Natl Acad Sci U S A, vol.108, pp.4516-4522, 2011. ,
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling, BMC Genomics, vol.17, p.55, 2016. ,
Qiime 2: reproducible interactive scalable and extensible microbiome data science, PeerJ Preprints, vol.6, pp.27295-27297, 2018. ,
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis, ISME J, vol.11, pp.2639-2643, 2017. ,
The biological observation matrix (BIOM) format or: how I learned to stop worrying and love the ome, GigaScience, vol.1, 2012. ,
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-ASV-classifier plugin, vol.6, p.90, 2018. ,
The SILVA and "all-species Living Tree Project (LTP)" taxonomic frameworks, Nucleic Acids Res, vol.42, pp.643-648, 2014. ,
MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol, vol.30, pp.772-780, 2013. ,
FastTree 2: approximately maximumlikelihood trees for large alignments, PLoS One, vol.5, 2010. ,
UpSet: visualization of intersecting sets, IEEE Trans Vis Comput Graph, vol.20, 1983. ,
Hybrid Sankey diagrams: visual analysis of multidimensional data for understanding resource use, Resour Conserv Recycl, vol.124, pp.141-151, 2017. ,
Development of the intestinal villi associated with the increased epithelial cell mitosis in chickens, Poult Sci, vol.64, pp.340-350, 1993. ,
Review of a histological intestinal approach to assessing the intestinal function in chickens and pigs, Animal Sci J, vol.78, pp.356-370, 2007. ,
SciPy: open source scientific tools for Python, 2001. ,
Statsmodels: econometric and statistical modeling with Python, Proceedings of the 9th Python in Science Conference, pp.57-61, 2010. ,
Microflora ecology of the chicken intestine using 16S ribosomal DNA primers, Poult Sci, vol.83, pp.1093-1098, 2004. ,
Probiotics normalize the gut-brain-microbiota axis in immunodeficient mice, Am J Physiol Gastrointest Liver Physiol, vol.307, pp.793-802, 2014. ,
Molecular biological detection and characterization of Clostridium populations in municipal landfill sites, 2002. ,
, Appl Environ Microbiol, vol.68, pp.2049-2053, 2002.
Development of 16S rRNA-gene-targeted group-specific primers for the detections and identification of predominant bacteria in human feces, Appl Environ Microbiol, vol.68, pp.5445-5451, 2002. ,