Poultry meat is the most common protein source of animal origin for humans. However, intensive breeding of animals in confined spaces has led to poultry colonisation by microbiota with a zoonotic potential or encoding antibiotic resistances. In this study we were therefore interested in the prevalence of selected antibiotic resistance genes and microbiota composition in feces of egg laying hens and broilers originating from 4 different Central European countries determined by real-time PCR and 16S rRNA gene pyrosequencing, respectively. strA gene was present in 1 out of 10,000 bacteria. The prevalence of sul1, sul2 and tet(B) in poultry microbiota was approx. 6 times lower than that of the strA gene. tet(A) and cat were the least prevalent being present in around 3 out of 10,000,000 bacteria forming fecal microbiome. The core chicken fecal microbiota was formed by 26 different families. Rather unexpectedly, representatives of Desulfovibrionaceae and Campylobacteraceae, both capable of hydrogen utilisation in complex microbial communities, belonged among core microbiota families. Understanding the roles of individual population members in the total metabolism of the complex community may allow for interventions which might result in the replacement of Campylobacteraceae with Desulfovibrionaceae and a reduction of Campylobacter colonisation in broilers, carcasses, and consequently poultry meat products.

Biotechnical Faculty University of Ljubljana Ljubljana Slovenia

Department of Biomedical Engineering Brno University of Technology Brno Czech Republic

Faculty of Veterinary Medicine University of Zagreb Zagreb Croatia

Institute for Veterinary Medical Research Hungarian Academy of Sciences Budapest Hungary

Veterinary Research Institute Brno Czech Republic

Zobrazit více v PubMed

Lillehoj HS (1993) Avian gut-associated immune system: implication in coccidial vaccine development. Poult Sci 72: 1306–11. PubMed

Gaboriau-Routhiau V, Rakotobe S, Lecuyer E, Mulder I, Lan A, et al. (2009) The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 31: 677–89. PubMed

Ismail AS, Behrendt CL, Hooper LV (2009) Reciprocal interactions between commensal bacteria and gamma delta intraepithelial lymphocytes during mucosal injury. J Immunol 182: 3047–54. PubMed PMC

Hill DA, Hoffmann C, Abt MC, Du Y, Kobuley D, et al. (2010) Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunol 3: 148–58. PubMed PMC

Lu J, Idris U, Harmon B, Hofacre C, Maurer JJ, et al. (2003) Diversity and succession of the intestinal bacterial community of the maturing broiler chicken. Appl Environ Microbiol 69: 6816–24. PubMed PMC

Stanley D, Keyburn AL, Denman SE, Moore RJ (2012) Changes in the caecal microflora of chickens following Clostridium perfringens challenge to induce necrotic enteritis. Vet Microbiol 159: 155–62. PubMed

Videnska P, Sisak F, Havlickova H, Faldynova M, Rychlik I (2013) Influence of Salmonella enterica serovar Enteritidis infection on the composition of chicken cecal microbiota. BMC Vet Res 9: 140. PubMed PMC

Videnska P, Faldynova M, Juricova H, Babak V, Sisak F, et al. (2013) Chicken faecal microbiota and disturbances induced by single or repeated therapy with tetracycline and streptomycin. BMC Vet Res 9: 30. PubMed PMC

Callaway TR, Dowd SE, Wolcott RD, Sun Y, McReynolds JL, et al. (2009) Evaluation of the bacterial diversity in cecal contents of laying hens fed various molting diets by using bacterial tag-encoded FLX amplicon pyrosequencing. Poult Sci 88: 298–302. PubMed

Qu A, Brulc JM, Wilson MK, Law BF, Theoret JR, et al. (2008) Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One 3: e2945. PubMed PMC

Nordentoft S, Molbak L, Bjerrum L, De Vylder J, Van Immerseel F, et al. (2011) The influence of the cage system and colonisation of Salmonella Enteritidis on the microbial gut flora of laying hens studied by T-RFLP and 454 pyrosequencing. BMC Microbiol 11: 187. PubMed PMC

Gerzova L, Videnska P, Faldynova M, Sedlar K, Provaznik I, et al. (2014) Characterization of microbiota composition and presence of selected antibiotic resistance genes in carriage water of ornamental fish. PLoS One 9: e103865. PubMed PMC

Faldynova M, Videnska P, Havlickova H, Sisak F, Juricova H, et al. (2013) Prevalence of antibiotic resistance genes in faecal samples from cattle, pigs and poultry. Vet Med Czech 58: 298–304.

Czekalski N, Berthold T, Caucci S, Egli A, Bürgmann H (2012) Increased levels of multiresistant bacteria and resistance genes after wastewater treatment and their dissemination into lake Geneva, Switzerland. Front Microbiol 3: 106. PubMed PMC

Walsh F, Ingenfeld A, Zampicolli M, Hilber-Bodmer M, Frey JE, et al. (2011) Real-time PCR methods for quantitative monitoring of streptomycin and tetracycline resistance genes in agricultural ecosystems. J Microbiol Methods 86: 150–155. PubMed

Cheng W, Chen H, Su C, Yan S (2013) Abundance and persistence of antibiotic resistance genes in livestock farms: a comprehensive investigation in eastern China. Environ Int 61: 1–7. PubMed

Kembel SW, Wu M, Eisen JA, Green JL (2012) Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol 8: e1002743. PubMed PMC

Rastogi R, Wu M, Dasgupta I, Fox GE (2009) Visualization of ribosomal RNA operon copy number distribution. BMC Microbiol 9: 208. PubMed PMC

Cressman MD, Yu Z, Nelson MC, Moeller SJ, Lilburn MS, et al. (2010) Interrelations between the microbiotas in the litter and in the intestines of commercial broiler chickens. Appl Environ Microbiol 76: 6572–82. PubMed PMC

Sekelja M, Rud I, Knutsen SH, Denstadli V, Westereng B, et al. (2012) Abrupt temporal fluctuations in the chicken fecal microbiota are explained by its gastrointestinal origin. Appl Environ Microbiol 78: 2941–8. PubMed PMC

Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59–65. PubMed PMC

Vignais PM, Billoud B (2007) Occurrence, classification, and biological function of hydrogenases: an overview. Chem Rev 107: 4206–72. PubMed

Kim T, Mundt E (2011) Metagenomic analysis of intestinal microbiomes in chickens. Methods Mol Biol 733: 185–94. PubMed

Sergeant MJ, Constantinidou C, Cogan TA, Bedford MR, Penn CW, et al. (2014) Extensive microbial and functional diversity within the chicken cecal microbiome. PLoS One 9: e91941. PubMed PMC

Benjdia A, Martens EC, Gordon JI, Berteau O (2011) Sulfatases and a radical S-adenosyl-L-methionine (AdoMet) enzyme are key for mucosal foraging and fitness of the prominent human gut symbiont, Bacteroides thetaiotaomicron . J Biol Chem 286: 25973–82. PubMed PMC

Rey FE, Gonzalez MD, Cheng J, Wu M, Ahern PP, et al. (2013) Metabolic niche of a prominent sulfate-reducing human gut bacterium. Proc Natl Acad Sci U S A 110: 13582–7. PubMed PMC

Szmolka A, Anjum MF, La Ragione RM, Kaszanyitzky EJ, Nagy B (2012) Microarray based comparative genotyping of gentamicin resistant Escherichia coli strains from food animals and humans. Vet Microbiol 156: 110–8. PubMed

Levesque C, Piche L, Larose C, Roy PH (1995) PCR mapping of integrons reveals several novel combinations of resistance genes. Antimicrob Agents Chemother 39: 185–91. PubMed PMC

Tseng CP, Cheng JC, Tseng CC, Wang C, Chen YL, et al. (2003) Broad-range ribosomal RNA real-time PCR after removal of DNA from reagents: melting profiles for clinically important bacteria. Clin Chem 49: 306–9. PubMed

Nossa CW, Oberdorf WE, Yang L, Aas JA, Paster BJ, et al. (2010) Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. World J Gastroenterol 16: 4135–44. PubMed PMC

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335–6. PubMed PMC

Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228–35. PubMed PMC

Eggshell and Feed Microbiota Do Not Represent Major Sources of Gut Anaerobes for Chickens in Commercial Production

Gut Anaerobes Capable of Chicken Caecum Colonisation

Bipartite Graphs for Visualization Analysis of Microbiome Data

Characterization of Antibiotic Resistance Gene Abundance and Microbiota Composition in Feces of Organic and Conventional Pigs from Four EU Countries

Succession and replacement of bacterial populations in the caecum of egg laying hens over their whole life