Quantitative molecular assays for evaluating changes in broiler gut microbiota linked with diet and performance
V. A. Torok A B C , C. Dyson A , A. McKay A and K. Ophel-Keller A
+ Author Affiliations
- Author Affiliations
A South Australian Research and Development Institute, Urrbrae, SA 5064, Australia.
B Australian Poultry CRC, University of New England, Armidale, NSW 2351, Australia.
C Corresponding author. Email: valeria.torok@sa.gov.au
Animal Production Science 53(12) 1260-1268 https://doi.org/10.1071/AN12272
Submitted: 3 August 2012 Accepted: 13 March 2013 Published: 21 May 2013
Journal Compilation © CSIRO Publishing 2013 Open Access CC BY-NC-ND
Abstract
Changes in the levels of specific gut bacteria have been linked to improved broiler feed efficiency. Quantitative polymerase chain reaction (qPCR) assays were developed to five potential performance-related bacteria (Lactobacillus salivarius, L. crispatus, L. aviarius, Gallibacterium anatis and Escherichia coli) and generic eubacteria. These were used to screen broiler gut samples from four geographically diverse Australian feeding trials showing significant treatment-related differences in feed efficiency. It was our aim to validate the association of particular bacteria with broiler feed efficiency across a broad range of environmental and dietary conditions, and hence to evaluate their predictive potential for monitoring broiler performance. Across trials L. salivarius, L. crispatus, L. aviarius, E. coli and total eubacterial numbers were significantly altered by diet, environment (litter), and/or sex of birds. Furthermore, changes in the numbers of these gut bacteria were significantly linked to broiler performance. Lactobacilli and total eubacteria were significantly decreased in birds that were more feed efficient. E. coli was not consistently linked with either improved or decreased performance and these discrepancies may be due to differences at the strain level which were not detectable using our assays. G. anatis was detected only in two of the four trials and found not to be significantly linked with broiler performance. These qPCR assays have been useful in either validating or disproving previous reported findings for the association of specific gut bacteria with broiler feed efficiency. This qPCR format can be easily expanded to include other organisms and used as a quantitative screening tool in evaluating dietary additives for improved broiler production.
Additional keywords: feed conversion efficiency, microbial diversity, poultry, poultry nutrition.
References
Amend AS, Seifert KA, Bruns TD (2010) Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Molecular Ecology 19, 5555–5565.| Quantifying microbial communities with 454 pyrosequencing: does read abundance count?Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhtlagsb0%3D&md5=d7587fefc4f59d2077510f353d001a8fCAS | 21050295PubMed |
Barth S, Duncker S, Hempe J, Breves G, Baljer G, Bauerfeind R (2009) Escherichia coli Nissle 1917 for probiotic use in piglets: evidence for intestinal colonization. Journal of Applied Microbiology 107, 1697–1710.
| Escherichia coli Nissle 1917 for probiotic use in piglets: evidence for intestinal colonization.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXhsVKhu7nE&md5=24c9756d7c9925755bf32c610c050275CAS | 19457029PubMed |
Bjerrum L, Engberg RM, Leser TD, Jensen BB, Finster K, Pedersen K (2006) Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and cellular-based techniques. Poultry Science 85, 1151–1164.
Bojesen AM, Nielsen SS, Bisgaard M (2003a) Prevalence and transmission of haemolytic Gallibacterium species in chicken production systems with different biosecurity levels. Avian Pathology 32, 503–510.
| Prevalence and transmission of haemolytic Gallibacterium species in chicken production systems with different biosecurity levels.Crossref | GoogleScholarGoogle Scholar | 14522706PubMed |
Bojesen AM, Torpdahl M, Christensen H, Olsen JE, Bisgaard M (2003b) Genetic diversity of Gallibacterium anatis isolates from different chicken flocks. Journal of Clinical Microbiology 41, 2737–2740.
| Genetic diversity of Gallibacterium anatis isolates from different chicken flocks.Crossref | GoogleScholarGoogle Scholar | 12791918PubMed |
Burkholder KM, Thompson KL, Einstein ME, Applegate TJ, Patterson JA (2008) Influence of stressors on normal intestinal microbiota, intestinal morphology, and susceptibility to Salmonella enteritidis colonization in broilers. Poultry Science 87, 1734–1741.
| Influence of stressors on normal intestinal microbiota, intestinal morphology, and susceptibility to Salmonella enteritidis colonization in broilers.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXhtFWqu7nE&md5=3f5c7e6fe40cbf60d56c6374e7dca69bCAS | 18753440PubMed |
Callaway TR, Dowd SE, Wolcott RD, Sun Y, McReynolds JL, Edrington TS, Byrd JA, Anderson RC, Krueger N, Nisbet DJ (2009) Evaluation of the bacterial diversity in cecal contents of laying hens fed various molting diets by using bacterial tag-encoded FLX amplicon pyrosequencing. Poultry Science 88, 298–302.
| Evaluation of the bacterial diversity in cecal contents of laying hens fed various molting diets by using bacterial tag-encoded FLX amplicon pyrosequencing.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD1M%2FotFWrtA%3D%3D&md5=4cd409a8691519962f7182b88670782bCAS | 19151343PubMed |
Choct M, Hughes RJ, Bedford MR (1999) Effects of a xylanase on individual bird variation, starch digestion throughout the intestine, and ileal and caecal volatile fatty acid production in chickens fed wheat. British Poultry Science 40, 419–422.
| Effects of a xylanase on individual bird variation, starch digestion throughout the intestine, and ileal and caecal volatile fatty acid production in chickens fed wheat.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1MXlvVaisLk%3D&md5=d5f89cabddb963c0de39807e40c67390CAS | 10475642PubMed |
Claesson MJ, O’Sullivan O, Wang Q, Nikkila J, Marchesi JR, Hauke S, De Vos WM, Ross RP, O’Toole PW (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 4, e6669
| Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine.Crossref | GoogleScholarGoogle Scholar | 19693277PubMed |
Fraher MH, O’Toole PW, Quigley EMM (2012) Techniques used to characterize the gut microbiota: a guide for the clinician. Nature Reviews in Gastroenterology and Hepatology. 9, 312–322.
| Techniques used to characterize the gut microbiota: a guide for the clinician.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XotVOhsbY%3D&md5=2ae37a4c3558dd4636483100cb4feb20CAS |
Geier MS, Torok VA, Allison GE, Ophel-Keller K, Hughes RJ (2009) Indigestible carbohydrates alter the intestinal microbiota but do not influence the performance of broiler chickens. Journal of Applied Microbiology 106, 1540–1548.
| Indigestible carbohydrates alter the intestinal microbiota but do not influence the performance of broiler chickens.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXmtVOisrg%3D&md5=5b506823098028ec9714315f2a5b3519CAS | 19187131PubMed |
Gordon HA, Pesti L (1971) The gnotobiotic animal as a tool in the study of host–microbial relationships. Bacteriological Reviews 35, 390–429.
Gunal M, Yayli G, Kaya O, Karahan N, Sulak O (2006) The effects of antibiotic growth promoter, probiotic or organic acid supplementation on performance, intestinal microflora and tissue of broilers. International Journal of Poultry Science 5, 149–155.
| The effects of antibiotic growth promoter, probiotic or organic acid supplementation on performance, intestinal microflora and tissue of broilers.Crossref | GoogleScholarGoogle Scholar |
Hammons S, Oh PL, Martinez I, Clark K, Schlegel VL, Sitorius E, Scheideler SE, Walter J (2010) A small variation in diet influences the Lactobacillus strain composition in the crop of broiler chickens. Systematic and Applied Microbiology 33, 275–281.
| A small variation in diet influences the Lactobacillus strain composition in the crop of broiler chickens.Crossref | GoogleScholarGoogle Scholar | 20554146PubMed |
Harrow S, Ravindran V, Butler R, Marshall J, Tannock G (2007) Real-time quantitative PCR measurement of ileal Lactobacillus salivarius populations from broiler chickens to determine the influence of farming practices. Applied and Environmental Microbiology 73, 7123–7127.
| Real-time quantitative PCR measurement of ileal Lactobacillus salivarius populations from broiler chickens to determine the influence of farming practices.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXnsFOqtA%3D%3D&md5=43f997ba39c4f2b55f63748773034799CAS | 17890342PubMed |
Hubener K, Jahjen W, Simon O (2002) Bacterial responses to differrent dietary cereal types and xylanase supplementation in the intestine of broiler chicken. Archives of Animal Nutrition 56, 167–187.
Hume ME, Barbosa NA, Dowd SE, Sakomura NK, Nalian AG, Martynova-Van Kley A, Oviedo-Rondon EO (2011) Use of pyrosequencing and denaturing gradient gel electrophoresis to examine the effects of probiotics and essential oil blends on digestive microflora in broilers under mixed Eimeria infection. Foodborne Pathogens and Disease 8, 1159–1167.
| Use of pyrosequencing and denaturing gradient gel electrophoresis to examine the effects of probiotics and essential oil blends on digestive microflora in broilers under mixed Eimeria infection.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhtlKkt7jF&md5=be74c9b39292d43b1b8c1210f86b567cCAS | 21793655PubMed |
Knarreborg A, Engberg RM, Jensen SK, Jensen BB (2002) Quantitative determination of bile salt hydrolase activity in bacteria isolated from the small intestine of chickens. Applied and Environmental Microbiology 68, 6425–6428.
| Quantitative determination of bile salt hydrolase activity in bacteria isolated from the small intestine of chickens.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD38Xptlaru7g%3D&md5=7610d3dbe70c4d4c408323f63819d347CAS | 12450872PubMed |
Lu J, Idris U, Harmon B, Hofacre C, Maurer JJ, Lee MD (2003) Diversity and succession of the intestinal bacterial communities of the maturing boiler chicken. Applied and Environmental Microbiology 69, 6816–6824.
| Diversity and succession of the intestinal bacterial communities of the maturing boiler chicken.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXptVyktbs%3D&md5=edc0ffc8175725ab2f8de8ca3c81c055CAS | 14602645PubMed |
Lumpkins BS, Batal AB, Lee M (2008) The effect of gender on the bacterial community in the gastrointestinal tract of broilers. Poultry Science 87, 964–967.
| The effect of gender on the bacterial community in the gastrointestinal tract of broilers.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD1c3mtVWitA%3D%3D&md5=cb2550d07e33044829cc4e42ad7a8851CAS | 18420988PubMed |
Lumpkins BS, Batal AB, Lee MD (2010) Evaluation of the bacterial community and intestinal development of different genetic lines of chickens. Poultry Science 89, 1614–1621.
| Evaluation of the bacterial community and intestinal development of different genetic lines of chickens.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXhtVOntr%2FN&md5=3b68945de1a9e65684489ec72a9d64daCAS | 20634515PubMed |
Majidzadeh Heravi R, Kermanshahi H, Sankian M, Nassiri MR, Heravi Moussavi A, Roozbeh Nasiraii L, Varasteh AR (2011) Screening of lactobacilli bacteria isolated from gastrointestinal tract of broiler chickens for their use as probiotic. African Journal of Microbiology Research 5, 1858–1868.
| Screening of lactobacilli bacteria isolated from gastrointestinal tract of broiler chickens for their use as probiotic.Crossref | GoogleScholarGoogle Scholar |
Pedroso AA, Menten FFM, Lambais MR, Racanicci AMC, Longo FA, Sorbara JOB (2006) Intestinal bacterial community and growth performance of chickens fed diets containing antibiotics. Poultry Science 85, 747–752.
Perez-Maldonado RA, Rodrigues HD (2009) Nutritional characteristics of sorghums from Queensland and New South Wales for chicken meat production. RIRDC Publication No. 09/170. Rural Industries Research and Development Corporation, Kingston, ACT.
Stanley D, Denman SE, Hughes RJ, Geier MS, Crowley TM, Chen H, Haring VR, Moore RJ (2012) Intestinal microbiota associated with differential feed conversion efficiency in chickens. Applied Microbiology and Biotechnology 96, 1361–1369.
| Intestinal microbiota associated with differential feed conversion efficiency in chickens.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38Xhs1ektL7P&md5=7922fe153cb425bb8500d4e3eb85ed82CAS | 22249719PubMed |
Teirlynck E, Gussem MD, Dewulf J, Haesebrouck F, Ducatelle R, Van Immerseel F (2011) Morphometric evaluation of ‘dysbacteriosis’ in broilers. Avian Pathology 40, 139–144.
| Morphometric evaluation of ‘dysbacteriosis’ in broilers.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC3MvktlWisA%3D%3D&md5=fb1cbef814211568c96428df01a7955cCAS | 21500033PubMed |
Torok VA, Ophel-Keller K, Loo M, Hughes RJ (2008) Application of methods for identifying broiler chicken gut bacterial species linked with increased energy metabolism. Applied and Environmental Microbiology 74, 783–791.
| Application of methods for identifying broiler chicken gut bacterial species linked with increased energy metabolism.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXhvVWjsr0%3D&md5=9ad23b085c83cf2927e07355256cfe35CAS | 18065621PubMed |
Torok VA, Hughes RJ, Ophel-Keller K, Ali M, MacAlpine R (2009) Influence of different litter materials on cecal microbiota colonization in broiler chickens. Poultry Science 88, 2474–2481.
| Influence of different litter materials on cecal microbiota colonization in broiler chickens.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD1Mjltlaktw%3D%3D&md5=2b95d796f8bf1eb2e3f749d17389e48cCAS | 19903943PubMed |
Torok VA, Allison GE, Percy NJ, Ophel-Keller K, Hughes RJ (2011a) Influence of antimicrobial feed additives on broiler commensal posthatch gut microbiota development and performance. Applied and Environmental Microbiology 77, 3380–3390.
| Influence of antimicrobial feed additives on broiler commensal posthatch gut microbiota development and performance.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXns1SltL0%3D&md5=f8c425001776b8e1834224072df097e8CAS | 21441326PubMed |
Torok VA, Hughes RJ, Mikkelsen LL, Perez-Maldonado R, Balding K, MacAlpine R, Percy NJ, Ophel-Keller K (2011b) Identification and characterization of potential performance-related gut microbiotas in broiler chickens across various feeding trials. Applied and Environmental Microbiology 77, 5868–5878.
| Identification and characterization of potential performance-related gut microbiotas in broiler chickens across various feeding trials.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXht1OjurvO&md5=897de70efec2698e2aa15b171ed9b1f6CAS | 21742925PubMed |
Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JAM (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Research 35, W71–W74.
| Primer3Plus, an enhanced web interface to Primer3.Crossref | GoogleScholarGoogle Scholar | 17485472PubMed |
Waidmann M, Bechtold O, Frick JS, Lehr HA, Schubert S, Dobrindt U, Loffler J, Bohn E, Autenrieth IB (2003) Bacteroides vulgatus protects against Escherichia coli-induced colitis in gnotobiotic interleukin-2-deficient mice. Gastroenterology 125, 162–177.
| Bacteroides vulgatus protects against Escherichia coli-induced colitis in gnotobiotic interleukin-2-deficient mice.Crossref | GoogleScholarGoogle Scholar | 12851881PubMed |
Yin Y, Lei F, Zhu L, Li S, Wu Z, Zhang R, Gao GF, Zhu B, Wang X (2010) Exposure of different bacterial inocula to newborn chicken affects gut microbiota development and ileum gene expression. The ISME Journal 4, 367–376.
| Exposure of different bacterial inocula to newborn chicken affects gut microbiota development and ileum gene expression.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXitVWgtb8%3D&md5=b08c2d61c5fa5ae9d713f2d86453e13fCAS | 19956274PubMed |
Zhou Z, Wu L, Deng Y, Zhi X, Jiang YH, Tu Q, Xie J, van Nostrand JD, He Z, Yang Y (2011) Reproducibility and quantitation of amplicon sequencing-based detection. The ISME Journal 5, 1303–1313.
| Reproducibility and quantitation of amplicon sequencing-based detection.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXptVynuro%3D&md5=49a13e355a819744f4954f16552c0ddfCAS |
Zhu XY, Zhong TZ, Pandya Y, Joerger RD (2002) 16S rRNA-based analysis of microbiota from the cecum of boiler chickens. Applied and Environmental Microbiology 68, 124–137.
| 16S rRNA-based analysis of microbiota from the cecum of boiler chickens.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD38Xjt1WgsQ%3D%3D&md5=de30cbe182ee3c160f9384e034b719f0CAS | 11772618PubMed |
Zozaya-Hinchliffe M, Lillis R, Martin DH, Ferris MJ (2010) Quantitative PCR assessments of bacterial species in women with and without bacterial vaginosis. Journal of Clinical Microbiology 48, 1812–1819.
| Quantitative PCR assessments of bacterial species in women with and without bacterial vaginosis.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXnt1Cnsrw%3D&md5=f1b1253e14737b3383d1c84ab75c63d0CAS | 20305015PubMed |
