Chickens in commercial production are subjected to constant interaction with their environment, including the exchange of microbiota. In this review, we therefore focused on microbiota composition in different niches along the whole line of chicken production. We included a comparison of microbiota of intact eggshells, eggshell waste from hatcheries, bedding, drinking water, feed, litter, poultry house air and chicken skin, trachea, crop, small intestine, and cecum. Such a comparison showed the most frequent interactions and allowed for the identification of microbiota members that are the most characteristic for each type of sample as well as those that are the most widespread in chicken production. Not surprisingly, Escherichia coli was the most widely distributed species in chicken production, although its dominance was in the external aerobic environment and not in the intestinal tract. Other broadly distributed species included Ruminococcus torque, Clostridium disporicum, and different Lactobacillus species. The consequence and meaning of these and other observations are evaluated and discussed.

Estudio recapitulativo- Microbiota de pollos y su entorno en producción comercial. Los pollos en producción comercial están sujetos a una interacción constante con su entorno, incluido el intercambio de microbiota. Esta revisión, por lo tanto, se enfoca en la composición de la microbiota en diferentes nichos a lo largo de toda la línea de producción de pollos. Se incluye una comparación de microbiota de cascarones de huevo intactos, desechos de cascarones de huevos de plantas de incubación, cama, agua potable, alimento, cama, aire de gallinero y piel de pollo, tráquea, buche, intestino delgado y ciego. Tal comparación mostró las interacciones más frecuentes y permitió identificar los miembros de la microbiota más característicos para cada tipo de muestra, así como los más extendidos en la producción de pollos. No en vano, Escherichia. coli fue la especie más ampliamente distribuida en la producción de pollos, aunque su dominio fue en el ambiente aeróbico externo y no en el tracto intestinal. Otras especies ampliamente distribuidas incluyeron Ruminococcus torque, Clostridium disporicum y diferentes especies de Lactobacillus. Se evalúan y discuten la consecuencia y el significado de estas y otras observaciones.

Veterinary Research Institute Brno 621 00 Czech Republic

Zobrazit více v PubMed

Haberecht S, Bajagai YS, Moore RJ, Van TTH, Stanley D. Poultry feeds carry diverse microbial communities that influence chicken intestinal microbiota colonisation and maturation.

Torok VA, Hughes RJ, Ophel-Keller K, Ali M, Macalpine R. Influence of different litter materials on cecal microbiota colonization in broiler chickens.

Johnson TJ, Youmans BP, Noll S, Cardona C, Evans NP, Karnezos TP, Ngunjiri JM, Abundo MC, Lee CW. A Consistent and predictable commercial broiler chicken bacterial microbiota in antibiotic-free production displays strong correlations with performance.

Oakley BB, Morales CA, Line J, Berrang ME, Meinersmann RJ, Tillman GE, Wise MG, Siragusa GR, Hiett KL, Seal BS. The poultry-associated microbiome: network analysis and farm-to-fork characterizations.

Volf J, Crhanova M, Karasova D, Faldynova M, Kubasova T, Seidlerova Z, Sebkova A, Zeman M, Juricova H, Matiasovicova J, et al. Eggshell and feed microbiota do not represent major sources of gut anaerobes for chickens in commercial production.

Karasova D, Faldynova M, Matiasovicova J, Sebkova A, Crhanova M, Kubasova T, Seidlerova Z, Prikrylova H, Volf J, Zeman M, et al. Host species adaptation of obligate gut anaerobes is dependent on their environmental survival.

Videnska P, Faldynova M, Juricova H, Babak V, Sisak F, Havlickova H, Rychlik I. Chicken faecal microbiota and disturbances induced by single or repeated therapy with tetracycline and streptomycin.

Kubasova T, Kollarcikova M, Crhanova M, Karasova D, Cejkova D, Sebkova A, Matiasovicova J, Faldynova M, Pokorna A, Cizek A, et al. Contact with adult hen affects development of caecal microbiota in newly hatched chicks.

Seidlerova Z, Kubasova T, Faldynova M, Crhanova M, Karasova D, Babak V, Rychlik I. Environmental impact on differential composition of gut microbiota in indoor chickens in commercial production and outdoor, backyard chickens.

Kollarcikova M, Kubasova T, Karasova D, Crhanova M, Cejkova D, Sisak F, Rychlik I. Use of 16S rRNA gene sequencing for prediction of new opportunistic pathogens in chicken ileal and cecal microbiota.

Trudeau S, Thibodeau A, Cote JC, Gaucher ML, Fravalo P. Contribution of the broiler breeders' fecal microbiota to the establishment of the eggshell microbiota.

Olsen R, Kudirkiene E, Thofner I, Pors S, Karlskov-Mortensen P, Li L, Papasolomontos S, Angastiniotou C, Christensen J. Impact of egg disinfection of hatching eggs on the eggshell microbiome and bacterial load.

Maki JJ, Bobeck EA, Sylte MJ, Looft T. Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens.

Shterzer N, Rothschild N, Sbehat Y, Stern E, Nazarov A, Mills E. Large overlap between the intestinal and reproductive tract microbiomes of chickens.

Videnska P, Sedlar K, Lukac M, Faldynova M, Gerzova L, Cejkova D, Sisak F, Rychlik I. Succession and replacement of bacterial populations in the caecum of egg laying hens over their whole life.

Rychlik I. Composition and function of chicken gut microbiota.

De Cesare A, Caselli E, Lucchi A, Sala C, Parisi A, Manfreda G, Mazzacane S. Impact of a probiotic-based cleaning product on the microbiological profile of broiler litters and chicken caeca microbiota.

De Cesare A, Sala C, Castellani G, Astolfi A, Indio V, Giardini A, Manfreda G. Effect of Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in drinking water on chicken crop and caeca microbiome.

Clavijo V, Morales T, Vives-Flores MJ, Reyes Munoz A. The gut microbiota of chickens in a commercial farm treated with a

Crhanova M, Karasova D, Juricova H, Matiasovicova J, Jahodarova E, Kubasova T, Seidlerova Z, Cizek A, Rychlik I. Systematic culturomics shows that half of chicken caecal microbiota members can be grown in vitro except for two lineages of Clostridiales and a single lineage of Bacteroidetes.

Kingsbury JM, Thom K, Erskine H, Olsen L, Soboleva T. Prevalence and genetic analysis of

Voss-Rech D, Kramer B, Silva VS, Rebelatto R, Abreu PG, Coldebella A, Vaz CSL. Longitudinal study reveals persistent environmental

Shang K, Wei B, Kang M. Distribution and dissemination of antimicrobial-resistant

Beauchemin J, Frechette A, Theriault W, Dufour S, Fravalo P, Thibodeau A. Comparison of microbiota of recycled manure solids and straw bedding used in dairy farms in eastern Canada.

Cressman MD, Yu Z, Nelson MC, Moeller SJ, Lilburn MS, Zerby HN. Interrelations between the microbiotas in the litter and in the intestines of commercial broiler chickens.

Lu J, Sanchez S, Hofacre C, Maurer JJ, Harmon BG, Lee MD. Evaluation of broiler litter with reference to the microbial composition as assessed by using 16S rRNA and functional gene markers.

Bucher MG, Zwirzitz B, Oladeinde A, Cook K, Plymel C, Zock G, Lakin S, Aggrey SE, Ritz C, Looft T, et al. Reused poultry litter microbiome with competitive exclusion potential against

Wang L, Lilburn M, Yu Z. Intestinal microbiota of broiler chickens as affected by litter management regimens.

Hinton A, Jr., Ingram KD. Use of oleic acid to reduce the population of the bacterial flora of poultry skin.

Oppliger A, Charriere N, Droz PO, Rinsoz T. Exposure to bioaerosols in poultry houses at different stages of fattening; use of real-time PCR for airborne bacterial quantification.

Martin E, Fallschissel K, Kampfer P, Jackel U. Detection of

Oakley BB, Lillehoj HS, Kogut MH, Kim WK, Maurer JJ, Pedroso A, Lee MD, Collett SR, Johnson TJ, Cox NA. The chicken gastrointestinal microbiome.

Grice EA, Segre JA. The skin microbiome.

Flowers L, Grice EA. The skin microbiota: balancing risk and reward.

Zhou Y, Zhang M, Liu Q, Feng J. The alterations of tracheal microbiota and inflammation caused by different levels of ammonia exposure in broiler chickens.

Sohail MU, Hume ME, Byrd JA, Nisbet DJ, Shabbir MZ, Ijaz A, Rehman H. Molecular analysis of the caecal and tracheal microbiome of heat-stressed broilers supplemented with prebiotic and probiotic.

Taylor KJM, Ngunjiri JM, Abundo MC, Jang H, Elaish M, Ghorbani A, Kc M, Weber BP, Johnson TJ, Lee CW. Respiratory and gut microbiota in commercial turkey flocks with disparate weight gain trajectories display differential compositional dynamics.

Wang J, Ishfaq M, Fan Q, Chen C, Li J. A respiratory commensal bacterium acts as a risk factor for

Shabbir MZ, Malys T, Ivanov YV, Park J, Shabbir MA, Rabbani M, Yaqub T, Harvill ET. Microbial communities present in the lower respiratory tract of clinically healthy birds in Pakistan.

Varmuzova K, Kubasova T, Davidova-Gerzova L, Sisak F, Havlickova H, Sebkova A, Faldynova M, Rychlik I. Composition of gut microbiota influences resistance of newly hatched chickens to

Wang S, Huang A, Gu Y, Li J, Huang L, Wang X, Tao Y, Liu Z, Wu C, Yuan Z, et al. Rational use of danofloxacin for treatment of

Van Goor A, Redweik GAJ, Stromberg ZR, Treadwell CG, Xin H, Mellata M. Microbiome and biological blood marker changes in hens at different laying stages in conventional and cage free housings.

Trela J, Kieronczyk B, Hautekiet V, Jozefiak D. Combination of

Ranjitkar S, Lawley B, Tannock G, Engberg RM. Bacterial succession in the broiler gastrointestinal tract.

Krieg J, Borda-Molina D, Siegert W, Sommerfeld V, Chi YP, Taheri HR, Feuerstein D, Camarinha-Silva A, Rodehutscord M. Effects of calcium level and source, formic acid, and phytase on phytate degradation and the microbiota in the digestive tract of broiler chickens.

Ren H, Vahjen W, Dadi T, Saliu EM, Boroojeni FG, Zentek J. Synergistic effects of probiotics and phytobiotics on the intestinal microbiota in young broiler chicken.

Witzig M, Carminha-Silva A, Green-Engert R, Hoelzle K, Zeller E, Seifert J, Hoelzle LE, Rodehutscord M. Spatial Variation of the gut microbiota in broiler chickens as affected by dietary available phosphorus and assessed by T-RFLP analysis and 454 pyrosequencing.

Park SH, Dowd SE, McReynolds JL, Byrd JA, Nisbet DJ, Ricke SC. Evaluation of feed grade sodium bisulfate impact on gastrointestinal tract microbiota ecology in broilers via a pyrosequencing platform.

Kubasova T, Kollarcikova M, Crhanova M, Karasova D, Cejkova D, Sebkova A, Matiasovicova J, Faldynova M, Sisak F, Babak V, et al. Gut anaerobes capable of chicken caecum colonisation.

Wen C, Yan W, Sun C, Ji C, Zhou Q, Zhang D, Zheng J, Yang N. The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens.

Glendinning L, Watson KA, Watson M. Development of the duodenal, ileal, jejunal and caecal microbiota in chickens.

Azcarate-Peril MA, Butz N, Cadenas MB, Koci M, Ballou A, Mendoza M, Ali R, Hassan H. An attenuated

Xiao Y, Xiang Y, Zhou W, Chen J, Li K, Yang H. Microbial community mapping in intestinal tract of broiler chicken.

Bindari YR, Moore RJ, Van TTH, Hilliar M, Wu SB, Walkden-Brown SW, Gerber PF. Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum.

Nurmi E, Rantala M. New aspects of

Rantala M, Nurmi E. Prevention of the growth of

Medvecky M, Cejkova D, Polansky O, Karasova D, Kubasova T, Cizek A, Rychlik I. Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures.

Kubasova T, Seidlerova Z, Rychlik I. Ecological adaptations of gut microbiota members and their consequences for use as a new generation of probiotics.

Herp S, Brugiroux S, Garzetti D, Ring D, Jochum LM, Beutler M, Eberl C, Hussain S, Walter S, Gerlach RG, et al.

Liu D, Mariman R, Gerlofs-Nijland ME, Boere JF, Folkerts G, Cassee FR, Pinelli E. Microbiome composition of airborne particulate matter from livestock farms and their effect on innate immune receptors and cells.

Bindari YR, Moore RJ, Van TTH, Walkden-Brown SW, Gerber PF. Microbial taxa in dust and excreta associated with the productive performance of commercial meat chicken flocks.

Luiken REC, Van Gompel L, Bossers A, Munk P, Joosten P, Hansen RB, Knudsen BE, Garcia-Cobos S, Dewulf J, Aarestrup FM, et al. Farm dust resistomes and bacterial microbiomes in European poultry and pig farms.

Cheng S, Chen M, Gao M, Qiu T, Tian S, Li S, Wang X. Effects of

Pan D, Yu Z. Intestinal microbiome of poultry and its interaction with host and diet.

Jeong JS, Kim IH. Effect of

Menconi A, Morgan MJ, Pumford NR, Hargis BM, Tellez G. Physiological properties and

Contact with adult hens affects the composition of skin and respiratory tract microbiota in newly hatched chicks