Extensive microbial and functional diversity within the chicken cecal microbiome, PLoS ONE, vol.9, p.91941, 2014. ,
Characteristics of the gastrointestinal microbial communities, with special reference to the chicken. World's, Poult Sci J, vol.60, pp.223-255, 2004. ,
The chicken gastrointestinal microbiome, FEMS Microbiol Lett, vol.10, pp.100-112, 2014. ,
Carbohydrate fermentation in the avian ceca: a review, Anim Feed Sci Technol, vol.133, pp.1-15, 2004. ,
Immune response of chicken gut to natural colonization by gut microflora and to Salmonella enterica serovar Enteritidis infection, Infect Immun, vol.79, pp.2755-63, 2011. ,
Uric acid decomposition in the lower gastrointestinal tract, J Exp Zool, vol.252, pp.70-74, 1989. ,
The structure of bacterial community in the intestines of newly hatched chicks, J Appl Poult Res, vol.14, pp.232-239, 2005. ,
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 adultderived microbiota on establishment of the intestinal microbiome in chickens, Am J Vet Res, vol.77, pp.514-540, 2016. ,
Spatial and temporal variation of the intestinal bacterial community in commercially raised broiler chickens during growth, Appl Environ Microbiol, vol.69, pp.286-93, 2002. ,
Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives, BMC Vet Res, vol.360, p.282, 2014. ,
Quantitative analysis of the intestinal bacterial community in one-to three-week-old commercially reared broiler chickens fed conventional or antibiotic-free vegetable-based diets, J Appl Microbiol, vol.102, pp.1138-1187, 2007. ,
Composition of microbiota in content and mucus from caeca of broiler chickens as measured by fluorescent in situ hybridization with group-specific, 16S rRNA-targeted oligonucleotide probes, Poult Sci, vol.82, pp.1242-1251, 2003. ,
Early life microbial colonization of the gut and intestinal development differ between genetically divergent broiler lines, BMC Genomics, vol.16, p.418, 2015. ,
Evaluation of the bacterial community and intestinal development of different genetic lines of chickens, Poult Sci, vol.89, pp.1614-1635, 2010. ,
Quantitative genetic background of the host influences gut microbiomes in chickens, Sci Rep, vol.3, p.1163, 2013. ,
Interrelations between the microbiotas in the litter and in the intestines of commercial broiler chickens, Appl Environ Microbiol, vol.76, pp.6572-82, 2010. ,
Microbial populations in naked neck chicken ceca raised on pasture flock fed with commercial yeast cell wall prebiotics via an Illumina MiSeq platform, PLoS ONE, vol.11, 2016. ,
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample, Proc Natl Acad Sci, vol.108, pp.4516-4538, 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 Prepr, vol.6, pp.27295-27297, 2018. ,
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis, ISME J, vol.11, pp.2639-2682, 2017. ,
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome, GigaScience, vol.1, p.7, 2012. ,
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin, Microbiome, vol.6, p.90, 2018. ,
The SILVA and 'all-species Living Tree Project (LTP)' taxonomic frameworks, Nucleic Acids Res, vol.42, pp.643-651, 2014. ,
MAFFT multiple sequence alignment software version 7 : improvements in performance and stability, Mol Biol Evol, vol.30, pp.772-80, 2013. ,
FastTree 2 approximately maximumlikelihood trees for large alignments, PLoS ONE, vol.5, p.9490, 2010. ,
Balance trees reveal microbial niche differentiation. mSystems, vol.2, pp.162-178, 2017. ,
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms, ISME J, vol.6, pp.1621-1625, 2012. ,
Vancomycin-sensitive bacteria trigger development of colitis-associated colon cancer by attracting neutrophils, Sci Rep, vol.6, p.23920, 2016. ,
Spatial organization of intestinal microbiota in the mouse ascending colon, ISME J, vol.5, pp.627-665, 2011. ,
Use of 16S rRNA genetargeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces, Appl Environ Microbiol, vol.70, pp.7220-7228, 2004. ,
Molecular biological detection and characterization of Clostridium populations in municipal landfill sites, Appl Environ Microbiol, vol.68, pp.2049-53, 2002. ,
Development of 16S rRNA-gene-targeted groupspecific primers for the detections and identification of predominant bacteria in human feces, Appl Environ Microbiol, vol.68, pp.5445-51, 2002. ,
Bacteroides fragilis metabolises exopolysaccharides produced by Bifidobacteria, BMC Microbiol, vol.16, p.150, 2016. ,
Exopolysaccharides produced by intestinal Bifidobacterium strains act as fermentable substrates for human intestinal bacteria, Appl Environ Microbiol, vol.74, pp.4737-4782, 2008. ,
Chapter 2 -targeting the microbiota: considerations for developing probiotics as functional foods, The Gut-Brain Axis, pp.17-30, 2016. ,
Protective effects of Bifidobacterium on intestinal barrier function in LPS-induced enterocyte barrier injury of Caco-2 monolayers and in a rat NEC model, PLoS ONE, vol.11, 2016. ,
Effect of a probiotic mixture on intestinal microflora, morphology, and barrier integrity of broilers subjected to heat stress, Poult Sci, vol.93, pp.581-589, 2014. ,
Acetate-producing Bifidobacteria protect the host from enteropathogenic infection via carbohydrate transporters, Gut Microbes, vol.3, pp.449-54, 2012. ,
Immune response to Bifidobacterium bifidum strains support Treg/Th17 plasticity, PLoS ONE, vol.6, p.24776, 2011. ,
The role of intestinal Bifidobacteria on immune system development in young rats, Early Hum Dev, vol.86, pp.51-59, 2010. ,
Identification of chicken intestinal microbiota correlated with the efficiency of energy extraction from feed, Vet Microbiol, vol.164, pp.85-92, 2013. ,
High through put 16S rRNA gene-based pyrosequencing analysis of the fecal microbiota of high FCR and low FCR broiler growers, Mol Biol Rep, vol.39, pp.10595-602, 2012. ,
Human gut microbes associated with obesity, Nature, vol.444, pp.1022-1025, 2006. ,
Untangling the genetic basis of fibrolytic specialization by Lachnospiraceae and Ruminococcaceae in diverse gut communities, Diversity, vol.5, pp.627-667, 2013. ,
Butyrate production in phylogenetically diverse Firmicutes isolated from the chicken caecum, Microb Biotechnol, vol.4, pp.503-515, 2011. ,
Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques, Poult Sci, vol.85, pp.1151-64, 2006. ,
Identification and characterization of potential performance-related gut microbiotas in broiler chickens across various feeding trials, Appl Environ Microbiol, vol.77, pp.5868-78, 2011. ,
Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patient, Proc Natl Acad Sci, vol.105, pp.16731-16737, 2008. ,
Low counts of Faecalibacterium prausnitzii in colitis microbiota, Inflammatory Bowel Dis, vol.15, pp.1183-1192, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00657435
Faecalibacterium prausnitzii supernatant improves intestinal barrier function in mice DSS colitis, Scand J Gastroenterol, vol.48, pp.1136-1180, 2013. ,
Butyric acid-producing anaerobic bacteria as a novel probiotic treatment approach for inflammatory bowel disease, J Med Microbiol, vol.59, pp.141-144, 2010. ,
Human genetics shape the gut microbiome, Cell, vol.159, pp.789-99, 2014. ,
Shifts on gut microbiota associated to mediterranean diet adherence and specific dietary intakes on general adult population, Front Microbiol, vol.9, p.890, 2018. ,
Types and prevalence of extended spectrum beta lactamase producing Enterobacteriaceae in poultry, Anim Health Res Rev, vol.18, pp.46-57, 2017. ,
Succession and replacement of bacterial populations in the caecum of egg laying hens over their whole life, PLoS ONE, vol.9, p.115142, 2014. ,
Role of volatile fatty acids in development of the cecal microflora in broiler chickens during growth, Appl Environ Microbiol, vol.66, pp.2536-2576, 2000. ,
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota, Nat Rev Microbiol, vol.11, pp.497-504, 2013. ,
Utilisation of mucin glycans TEST by the human gut symbiont Ruminococcus gnavus is strain-dependent, PLoS ONE, vol.8, p.76341, 2013. ,
Complete genome sequence of Coriobacteriaceae Strain 68-1-3, a novel mucus-degrading isolate from the swine intestinal tract, Genome Announce, vol.3, pp.2014-2029, 2015. ,
Mucin glycan foraging in the human gut microbiome, vol.6, p.81, 2015. ,
Adhesion of Bifidobacterium spp. to human intestinal mucus, Microbiol Immunol, vol.45, pp.259-62, 2001. ,
The mucus binding of Bifidobacterium lactis Bb12 is enhanced in the presence of Lactobacillus GG and Lact. delbrueckii subsp. bulgaricus, Appl Microbiol, vol.30, pp.10-13, 2000. ,
Adhesion of selected Bifidobacterium strains to human intestinal mucus and the role of adhesion in enteropathogen exclusion, J Food Prot, vol.68, pp.2672-2680, 2005. ,
Important metabolic pathways and biological processes expressed by chicken cecal microbiota, Appl Environ Microbiol, vol.82, pp.1569-76, 2016. ,
Effects of the dietary protein and carbohydrate ratio on gut microbiomes in dogs of different body conditions, vol.8, pp.1703-1719, 2017. ,
Live probiotic Lactobacillus johnsonii BS15 promotes growth performance and lowers fat deposition by improving lipid metabolism, intestinal development, and gut microflora in broilers, Front Microbiol, vol.8, p.1073, 2017. ,
Effects of Lactobacillus cultures on growth performance, abdominal fat deposition, serum lipids and weight of organs of broiler chickens, Brit Poult Sci, vol.44, pp.139-183, 2003. ,