1 |
Sogin, M. L., H. G. Morrison, J. A. Huber, D. Mark Welch, S. M. Huse, P. R. Neal, J. M. Arrieta, and G. J. Herndl. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc. Natl. Acad. Sci. USA 103:12115-12120
DOI
ScienceOn
|
2 |
Stanley, D., R. J. Hughes, and R. J. Moore. 2014. Microbiota of the chicken gastrointestinal tract: Influence on health, productivity and disease. Appl. Microbiol. Biotechnol. 98:4301-4310.
DOI
ScienceOn
|
3 |
Stedtfeld, R. D., S. W. Baushke, D. M. Tourlousse, S. M. Miller, T. M. Stedtfeld, E. Gulari, J. M. Tiedje, and S. A. Hashsham. 2008. Development and experimental validation of a predictive threshold cycle equation for quantification of virulence and marker genes by high-throughput nanoliter-volume PCR on the OpenArray platform. Appl. Environ. Microbiol. 74:3831-3838.
DOI
ScienceOn
|
4 |
Sul, W. J., J. R. Cole, E. D. Jesus, Q. Wang, R. J. Farris, J. A. Fish, and J. M. Tiedje. 2011. Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering. Proc. Natl. Acad. Sci. USA 108:14637-14642.
DOI
ScienceOn
|
5 |
Tang, Y., A. Underwood, A. Gielbert, M. J. Woodward, and L. Petrovska. 2014. Metaproteomics analysis reveals the adaptation process for the chicken gut microbiota. Appl. Environ. Microbiol. 80:478-485.
DOI
ScienceOn
|
6 |
Thomas, T., J. Gilbert, and F. Meyer. 2012. Metagenomics - A guide from sampling to data analysis. Microb. Inform. Exp. 2:3.
DOI
ScienceOn
|
7 |
Turnbaugh, P. J., M. Hamady, T. Yatsunenko, B. L. Cantarel, A. Duncan, R. E. Ley, M. L. Sogin, W. J. Jones, B. A. Roe, J. P. Affourtit, M. Egholm, B. Henrissat, A. C. Heath, R. Knight, and J. I. Gordon. 2008. A core gut microbiome in obese and lean twins. Nature 457:480-484.
|
8 |
Videnska, P., F. Sisak, H. Havlickova, M. Faldynova, and I. Rychlik. 2013. Influence of Salmonella enterica serovar Enteritidis infection on the composition of chicken cecal microbiota. BMC Vet. Res. 9:140.
DOI
ScienceOn
|
9 |
Wang, Q., J. F. Quensen, J. A. Fish, T. K. Lee, Y. Sun, J. M. Tiedje, and J. R. Cole. 2013. Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. mBio. 4:e00592-13.
|
10 |
Xin, H., R. S. Gates, A. R. Green, F. M. Mitloehner, P. A. Moore Jr., and C. M. Wathes. 2011. Environmental impacts and sustainability of egg production systems. Poult. Sci. 90:263-277.
DOI
ScienceOn
|
11 |
Xu, Z. R., C. H. Hu, M. S. Xia, X. A. Zhan, and M. Q. Wang. 2003. Effects of dietary fructooligosaccharide on digestive enzyme activities, intestinal microflora and morphology of male broilers. Poult. Sci. 82:1030-1036.
DOI
|
12 |
Yeoman, C. J., N. Chia, P. Jeraldo, M. Sipos, N. D. Goldenfeld, and B. A. White. 2012. The microbiome of the chicken gastrointestinal tract. Anim. Health Res. Rev. 13:89-99.
DOI
ScienceOn
|
13 |
Zhou, H., J. Gong, J. T. Brisbin, H. Yu, B. Sanei, P. Sabour, and S. Sharif. 2007. Appropriate chicken sample size for identifying the composition of broiler intestinal microbiota affected by dietary antibiotics, using the polymerase chain reactiondenaturing gradient gel electrophoresis technique. Poult. Sci. 86:2541-2549.
DOI
ScienceOn
|
14 |
Beckmann, L., O. Simon, and W. Vahjen. 2006. Isolation and identification of mixed linked beta -glucan degrading bacteria in the intestine of broiler chickens and partial characterization of respective 1,3-1,4-beta-glucanase activities. J. Basic Microbiol. 46:175-185.
DOI
ScienceOn
|
15 |
Andersson, A. F., M. Lindberg, H. Jakobsson, F. Backhed, P. Nyren, and L. Engstrand. 2008. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One. 3(7):e2836.
DOI
ScienceOn
|
16 |
Aydin, R., M. W. Pariza, and M. E. Cook. 2001. Olive oil prevents the adverse effects of dietary conjugated linoleic acid on chick hatchability and egg quality. J. Nutr. 131:800-806.
|
17 |
Baurhoo, B., L. Phillip, and C. A. Ruiz-Feria. 2007. Effects of purified lignin and mannan oligosaccharides on intestinal integrity and microbial populations in the ceca and litter of broiler chickens. Poult. Sci. 86:1070-1078.
DOI
|
18 |
Brisbin, J. T., J. Gong, S. Sharif. 2008. Interactions between commensal bacteria and the gut-associated immune system of the chicken. Anim. Health Res. Rev. 9:101-110.
DOI
ScienceOn
|
19 |
Caporaso, J. G., J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K. Costello, N. Fierer, A. G. Pena, J. K. Goodrich, and J. I. Gordon et al. 2010. QIIME allows analysis of highthroughput community sequencing data. Nat. Methods 7:335-336.
DOI
ScienceOn
|
20 |
Case, R. J., Y. Boucher, I. Dahllof, C. Holmstrom, W. F. Doolittle, and S. Kjelleberg. 2007. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl. Environ. Microbiol. 73:278-288.
DOI
ScienceOn
|
21 |
Chichlowski, M., W. J. Croom, F. W. Edens, B. W. McBride, R. Qiu, C. C. Chiang, L. R. Daniel, G. B. Havenstein, and M. D. Koci. 2007. Microarchitecture and spatial relationship between bacteria and ileal, cecal, and colonic epithelium in chicks fed a direct-fed microbial, PrimaLac, and salinomycin. Poult. Sci. 86:1121-1132.
DOI
|
22 |
Claesson, M. J., Q. Wang, O. O'Sullivan, R. Greene-Diniz, J. R. Cole, R. P. Ross, and P. W. O'Toole. 2010. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucl. Acids Res. 38:e200.
DOI
|
23 |
Clemente, J. C., L. K. Ursell, L. W. Parfrey, and R. Knight. 2012. The impact of the gut microbiota on human health: An integrative view. Cell 148:1258-1270.
DOI
ScienceOn
|
24 |
Cole, J. R., Q. Wang, J. A. Fish, B. Chai, D. M. McGarrell, Y. Sun, C. T. Brown, A. Porras-Alfaro, C. R. Kuske, and J. M. Tiedje. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucl. Acids Res. 42:D633-642.
DOI
ScienceOn
|
25 |
Colwell, R. K. 2009. Biodiversity: concepts, patterns, and measurement. In: The Princeton Guide to Ecology (Ed. S. A. Levin). Princeton University Press, Princeton, NJ, USA. PP. 257-263.
|
26 |
Cruaud, R., A. Vigneron, C. Lucchetti-Miganeh, P. E. Ciron, A. Godfroy, and M. A. Cambon-Bonavita. 2014. Influence of DNA extraction method, 16S rRNA targeted hypervariable regions, and sample origin on microbial diversity detected by 454 pyrosequencing in marine chemosynthetic ecosystems. Appl. Environ. Microbiol. 80:4626-4639.
DOI
ScienceOn
|
27 |
Dunkley, K. D., C. S. Dunkley, N. L. Njongmeta, T. R. Callaway, M. E. Hume, L. F. Kubena, D. J. Nisbet, and S. C. Ricke. 2007. Comparison of in vitro fermentation and molecular microbial profiles of high-fiber feed substrates incubated with chicken cecal inocula. Poult. Sci. 86:801-810.
DOI
|
28 |
Darling, A. E., G. Jospin, E. Lowe, F. A. Matsen 4th, H. M. Bik, and J. A. Eisen. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2:e243.
DOI
ScienceOn
|
29 |
DeSantis, T. Z., P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G. L. Andersen. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:5069-5072.
DOI
ScienceOn
|
30 |
Dethlefsen, L., S. Huse, M. L. Sogin, and D. A. Relman. 2008. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6(11):e280.
DOI
ScienceOn
|
31 |
Edgar, R. C., B. J. Haas, J. C. Clemente, C. Quince, and R. Knight. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194-2200.
DOI
ScienceOn
|
32 |
Elnifro, E. M., A. M. Ashshi, R. J. Cooper, and P. E. Klapper. 2000. Multiplex PCR: optimization and application in diagnostic virology. Clin. Microbiol. Rev. 13:559-570.
DOI
|
33 |
Eren, A. M., L. Maignien, W. J. Sul, L. G. Murphy, S. L. Grim, H. G. Morrison, and M. L. Sogin. 2014. Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol. Evol. 4:1111-1119.
|
34 |
Fernandez, F., M. Hinton, and B. Van Gils. 2002. Dietary mannanoligosaccharides and their effect on chicken caecal microflora in relation to Salmonella Enteritidis colonization. Avian Pathol. 31:49-58.
DOI
ScienceOn
|
35 |
Gilles, A., E. Meglecz, N. Pech, S. Ferreira, T. Malausa, and J. F. Martin. 2011. Accuracy and quality assessment of 454 GSFLX Titanium pyrosequencing. BMC Genomics 12:245.
DOI
ScienceOn
|
36 |
Fish, J. A., B. Chai, Q. Wang, Y. Sun, C. T. Brown, J. M. Tiedje, and J. R. Cole. 2013. FunGene: the functional gene pipeline and repository. Front Microbiol. 4:291.
|
37 |
Finn, R. D., J. Clements, and S. R. Eddy. 2011. HMMER web server: interactive sequence similarity searching. Nucl. Acids Res. 39:W29-37
DOI
|
38 |
Ganner, A. and G. Schatzmayr. 2012. Capability of yeast derivatives to adhere enteropathogenic bacteria and to modulate cells of the innate immune system. Appl. Microbiol. Biotechnol. 95:289-297.
DOI
ScienceOn
|
39 |
Haas, B. J., D. Gevers, A. M. Earl, M. Feldgarden, D. V. Ward, G. Giannoukos, D. Ciulla, D. Tabbaa, S. K. Highlander, E. Sodergren, B. Methe, T. Z. DeSantis; Human Microbiome Consortium, J. F. Petrosino, R. Knight, and B. W. Birren. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21:494-504.
DOI
ScienceOn
|
40 |
Hang J., V. Desai, N. Zavajevski, Y. Yang, X. Lin, R. V. Satya, L. J. Martinez, J. M. Blaylock, R. G. Jarman, S. J. Thomas, and R. A. Kuschner. 2014. 16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles. Microbiome 2:31
DOI
ScienceOn
|
41 |
He, Z., T. J. Gentry, C. W. Schadt, L. Wu, J. Liebich, S. C. Chong, Z. Huang, W. Wu, B. Gu, P. Jardine, C. Criddle, and J. Zhou. 2007. GeoChip: A comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J. 1:67-77.
DOI
ScienceOn
|
42 |
Jin, L. Z., Y. W. Ho, N. Abdullah, and S. Jalaludin. 1998. Growth performance, intestinal microbial populations, and serum cholesterol of broilers fed diets containing Lactobacillus cultures. Poult. Sci. 77:1259-1265.
DOI
|
43 |
Howe, A. C., J. K. Jansson, S. A. Malfatti, S. G. Tringe, J. M. Tiedje, and C. T. Brown. 2014. Tackling soil diversity with the assembly of large, complex metagenomes. Proc. Natl. Acad. Sci. USA 111:4904-4909.
DOI
ScienceOn
|
44 |
Hughes, J. B., J. J. Hellmann, T. H. Ricketts, and B. J. Bohannan. 2011. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:4399-4406.
|
45 |
Huse, S. M., J. A. Huber, H. G. Morrison, M. L. Sogin, and D. M. Welch. 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8:R143.
DOI
|
46 |
Johnson, D. R., T. K. Lee, J. Park, K. Fenner, and D. E. Helbling. 2014. The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability. Environ. Microbiol. doi: 10.1111/1462-2920.12429.
DOI
ScienceOn
|
47 |
Jumpertz, R., D. S. Le, P. J. Turnbaugh, C. Trinidad, C. Bogardus, J. I. Gordon, and J. Krakoff. 2011. Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am. J. Clin. Nutr. 94:58-65.
DOI
|
48 |
Kaakoush, N. O., N. Sodhi, J. W. Chenu, J. M. Cox, S. M. Riordan, and H. M. Mitchell. 2014. The interplay between Campylobacter and Helicobacter species and other gastrointestinal microbiota of commercial broiler chickens. Gut Pathog. 6:18.
DOI
ScienceOn
|
49 |
Latshaw, J. D. and L. Zhao. 2011. Dietary protein effects on hen performance and nitrogen excretion. Poult. Sci. 90:99-106.
DOI
ScienceOn
|
50 |
Kunin, V., A. Engelbrektson, H. Ochman, and P. Hugenholtz. 2010. Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 12:118-123.
DOI
ScienceOn
|
51 |
Lei, F., Y. Yin, Y. Wang, B. Deng, H. D. Yu, L. Li, C. Xiang, S. Wang, B. Zhu, and X. Wang. 2012. Higher-level production of volatile fatty acids in vitro by chicken gut microbiotas than by human gut microbiotas as determined by functional analyses. Appl. Environ. Microbiol. 78:5763-5772.
DOI
|
52 |
Lauber, C. L., N. Zhou, J. I. Gordon, R. Knight, and N. Fierer. 2010. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol. Lett. 307(1):80-86.
DOI
ScienceOn
|
53 |
Lei, F., Y. Yin, Y. Wang, B. Deng, H. D. Yu, L. Li, C. Xiang, S. Wang, B. Zhu, and X. Wang. 2012. Higher-level production of volatile fatty acids in vitro by chicken gut microbiotas than by human gut microbiotas as determined by functional analyses. Appl. Environ. Microbiol. 78:5763-5772.
DOI
|
54 |
Looft, T., T. A. Johnson, H. K. Allen, D. O. Bayles, D. P. Alt, R. D. Stedtfeld, W. J. Sul, T. M. Stedtfeld, B. Chai, J. R. Cole, S. A. Hashsham, J. M. Tiedje, and T. B. Stanton. 2012. In-feed antibiotic effects on the swine intestinal microbiome. Proc. Natl. Acad. Sci. USA 109:1691-1696.
DOI
|
55 |
Lozupone, C. A. and R. Knight. 2005. UniFrac: A new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235.
DOI
ScienceOn
|
56 |
Lozupone, C. A. and R. Knight. 2007. Global patterns in bacterial diversity. Proc. Natl. Acad. Sci. USA 104:11436-11440.
DOI
ScienceOn
|
57 |
McCubbin, D. R., B. J. Apelberg, S. Roe, and F. Divita. 2002. Livestock ammonia management and particulate-related health benefits. Environ. Sci. Technol. 36:1141-1146.
DOI
ScienceOn
|
58 |
Lozupone, C. A., J. I. Stombaugh, J. I. Gordon, J. K. Jansson, and R. Knight. 2012. Diversity, stability and resilience of the human gut microbiota. Nature 489:220-230.
DOI
ScienceOn
|
59 |
Luo, C., D. Tsementzi, N. Kyrpides, T. Read, and K. T. Konstantinidis. 2012. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One. 7(2):e30087.
|
60 |
Martiny, J. B. H., J. A. Eisen, K. Penn, S. D. Allison, and M. C. Horner-Devine. 2011. Drivers of bacterial beta-diversity depend on spatial scale. Proc. Natl. Acad. Sci. USA 108:7850-7854.
DOI
ScienceOn
|
61 |
Medinger, R., V. Nolte, R. V. Pandey, S. Jost, B. Ottenwalder, C. Schlotterer, and J. Boenigk. 2010. Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol. Ecol. 1:32-40.
|
62 |
Mende, D. R., A. S. Waller, S. Sunagawa, A. I. Jarvelin, M. M. Chan, M. Arumugam, J. Raes, and P. Bork. 2012. Assessment of metagenomic assembly using simulated next generation sequencing data. PLoS One. 7(2):e31386.
DOI
ScienceOn
|
63 |
Metzker, M. L. 2010. Sequencing technologies - the next generation. Nat. Rev. Genet. 11:31-46.
DOI
ScienceOn
|
64 |
Morris, S. C. 2003. Life's Solution: Inevitable Humans in a Lonely Universe. Cambridge University Press, Cambridge, UK.
|
65 |
Pedroso, A. A., A. L. Hurley-Bacon, A. S. Zedek, T. W. Kwan, A. P. O. Jordan, G. Avellaneda, C. L. Hofacre, B. B. Oakley, S. R. Collett, J. J. Maurer, and M. D. Lee. 2013. Can probiotics improve the environmental microbiome and resistome of commercial poultry production? Int. J. Environ. Res. Public Health 10:4534-4559.
DOI
|
66 |
Newell, D. G., K. T. Elvers, D. Dopfer, I. Hansson, P. Jones, S. James, J. Gittins, N. J. Stern, R. Davies, I. Connerton, D. Pearson, G. Salvat, and V. M. Allen. 2011. Biosecurity-based interventions and strategies to reduce Campylobacter spp. on poultry farms. Appl. Environ. Microbiol. 77:8605-8614.
DOI
ScienceOn
|
67 |
Nielsen, H. B., M. Almeida, A. S. Juncker, S. Rasmussen, J. Li, S. Sunagawa, D. R. Plichta, L. Gautier, A. G. Pedersen, and E. Le Chatelier et al. 2014. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat. Biotechnol. 32:822-828.
DOI
ScienceOn
|
68 |
Oakley, B. B., H. S. Lillehoj, M. H. Kogut, W. K. Kim, J. J. Maurer, A. Pedroso, M. D. Lee, S. R. Collett, T. J. Johnson, and N. A. Cox. 2014. The chicken gastrointestinal microbiome. FEMS Microbiol. Lett. 360:100-112.
DOI
ScienceOn
|
69 |
Pereyra, L. P., S. R. Hiibel, M. V. Prieto Riquelme, K. F. Reardon, and A. Pruden. 2010. Detection and quantification of functional genes of cellulose- degrading, fermentative, and sulfate-reducing bacteria and methanogenic archaea. Appl. Environ. Microbiol. 76:2192-2202.
DOI
ScienceOn
|
70 |
Powell, S., K. Forslund, D. Szklarczyk, K. Trachana, A. Roth, J. Huerta-Cepas, T. Gabaldon, T. Rattei, C. Creevey, M. Kuhn, L. J. Jensen, C. von Mering and P. Bork. 2014. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucl. Acids Res. 42:D231-239.
DOI
ScienceOn
|
71 |
Schloss, P. D., S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann, E. B. Hollister, R. A. Lesniewski, B. B. Oakley, D. H. Parks, C. J. Robinson, J. W. Sahl, B. Stres, G. G. Thallinger, D. J. Van Horn, and C. F. Weber. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541.
DOI
ScienceOn
|
72 |
Pruesse, E., C. Quast, K. Knittel, B. M. Fuchs, W. Ludwig, J. Peplies, and F. O. Glockner. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35:7188-7196.
DOI
ScienceOn
|
73 |
Purschke, O., B. C. Schmid, M. T. Sykes, P. Poschlod, S. G. Michalski, W. Durka, I. Kuhn, M. Winter, and H. C. Prentice. 2013. Contrasting changes in taxonomic, phylogenetic and functional diversity during a long-term succession: Insights into assembly processes. J. Ecol. 101:857-866.
DOI
ScienceOn
|
74 |
Qu, A., J. M. Brulc, M. K. Wilson, B. F. Law, J. R. Theoret, L. A. Joens, M. E. Konkel, F. Angly, E. A. Dinsdale, R. A. Edwards, K. E. Nelson, and B. A. White. 2008. Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One 3(8):e2945.
DOI
ScienceOn
|
75 |
Sergeant, M. J., C. Constantinidou, T. A. Cogan, M. R. Bedford, C. W. Penn, and M. J. Pallen. 2014. Extensive microbial and functional diversity within the chicken cecal microbiome. PLoS ONE 9(3):e91941.
DOI
ScienceOn
|
76 |
Skraban, J., S. Dzeroski, B. Zenko, L. Tusar, and M. Rupnik. 2013. Changes of poultry faecal microbiota associated with Clostridium difficile colonisation. Vet. Microbiol. 165:416-424.
DOI
ScienceOn
|
77 |
Smith, C. J. and A. M. Osborn. 2009. Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS. Microbiol. Ecol. 67:6-20.
DOI
ScienceOn
|