Differences in CD8αα and cecal microbiome community during proliferation and late cytolytic phases of Marek's disease virus infection are associated with genetic resistance to Marek's disease

FEMS Microbiology Ecology

Volumn 92, Issue 12, 2016, Pages

  Perumbakkam, Sudeep ^a,b   Hunt, Henry D ^a   Cheng, Hans H ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b Michigan State University ^*  (United States)

Author keywords

16S rRNA; Chicken; CTL; Immune response; Marek's disease; Microbiome

Indexed keywords

AMINO ACID; BACTERIUM; CELLS AND CELL COMPONENTS; COLONIZATION; GENETIC ANALYSIS; IMMUNE RESPONSE; METABOLISM; MICROBIAL COMMUNITY; POULTRY; RNA; VIRAL DISEASE;

AVES; FAECALIBACTERIUM; GALLID HERPESVIRUS 2; GALLUS GALLUS; LACTOBACILLUS; STREPTOCOCCUS;

EID: 84995751591     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1093/femsec-fiw188     Document Type: Article

References (53)

1. Altermann E, Russell WM, Azcarate-Peril MA et al. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. P Natl Acad Sci USA 2005;102:3906-12.
2. Atarashi K, Tanoue T, Shima T et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 2011;331:337-41.
3. Baigent SJ, Davison TF. Development and composition of lymphoid lesions in the spleens ofMarek's disease virus-infected chickens: association with virus spread and the pathogenesis of Marek's disease. Avian Pathol 1999;28:287-300.
4. Beutler B. Inferences, questions and possibilities in Toll-like receptor signalling. Nature 2004;430:257-63.
5. Biddle AS, Black SJ, Blanchard JL. An in vitro model of the horse gut microbiome enables identification of lactate-utilizing bacteria that differentially respond to starch induction. PLoS One 2013;8:e77599.
6. Calnek BW, Schat KA, Ross LJ et al. Further characterization of Marek's disease virus-infected lymphocytes. I. In vivo infection. Int J Cancer 1984a;33:389-98.
7. Calnek BW, Schat KA, Ross LJ et al. Further characterization of Marek's disease virus-infected lymphocytes. II. In vitro infection. Int J Cancer 1984b;33:399-406.
8. Cannon JP, Lee TA, Bolanos JT et al. Pathogenic relevance of Lactobacillus: a retrospective review of over 200 cases. Eur J Clin Microbiol 2005;24:31-40.
9. Caporaso JG, Bittinger K, Bushman FD et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010a;26:266-7.
10. Caporaso JG, Kuczynski J, Stombaugh J et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010b;7:335-6.
11. Deng K, Pertea M, Rongvaux A et al. Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations. Nature 2015;517:381-5.
12. Desantis TZ, Hugenholtz P, Larsen N et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microb 2006;72:5069-72.
13. Edelmann KH, Richardson-Burns S, Alexopoulou L et al. Does Toll-like receptor 3 play a biological role in virus infections? Virology 2004;322:231-8.
14. Edgar RC. Search and clustering orders ofmagnitude faster than BLAST. Bioinformatics 2010;26:2460-1.
15. Erturk-Hasdemir D, Kasper DL. Resident commensals shaping immunity. Curr Opin Immunol 2013;25:450-5.
16. Frank DN, St Amand AL, Feldman RA et al. Molecularphylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. P Natl Acad Sci USA 2007;104:13780-5.
17. Gimeno IM, Cortes AL, Silva RF. Load of challenge Marek's disease virus DNA in blood as a criterion for early diagnosis of Marek's disease tumors. Avian Dis 2008;52:203-8.
18. Groscurth P, Filgueira L. Killing mechanisms of cytotoxic T lymphocytes. Physiology 1998;13:17-21.
19. Hamer HM, Jonkers DM, Bast A et al. Butyrate modulates oxidative stress in the colonicmucosa of healthy humans. Clin Nutr 2009;28:88-93.
20. Hill DA, Hoffmann C, Abt MC et al. Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunol 2010;3:148-58.
21. Institute for Laboratory Animal Research. Guide for the Care and Use of Laboratory Animals. 8th edn.Washington, DC: National Academies Press (US), 2011.
22. Ivanov II, Atarashi K, Manel N et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 2009;139: 485-98.
23. Johnson DC, Hill AB. Herpesvirus evasion of the immune system. Curr Top Microbiol Immunol 1998;232:149-77.
24. Kaiser P, Underwood G, Davison F. Differential cytokine responses following Marek's disease virus infection of chickens differing in resistance to Marek's disease. J Virol 2003;77: 762-8.
25. Khan MT, Duncan SH, Stams AJ et al. The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases. ISME J 2012;6:1578-85.
26. Kim HB, Borewicz K, White BA et al. Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin. P Natl Acad Sci USA 2012;109: 15485-90.
27. Langille MG, Zaneveld J, Caporaso JG et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 2013;31:814-21.
28. Liu C, Finegold SM, Song Y et al. Reclassification of Clostridium coccoides, Ruminococcus hansenii, Ruminococcus hydrogenotrophicus, Ruminococcus luti, Ruminococcus productus and Ruminococcus schinkii as Blautia coccoides gen. nov., comb. nov., Blautia hansenii comb. nov., Blautia hydrogenotrophica comb. nov., Blautia luti comb. nov., Blautia producta comb. nov., Blautia schinkii comb. nov. and description of Blautiawexlerae sp. nov., isolated fromhuman faeces. Int J Syst Evol Micr 2008;58:1896-902.
29. Mcmurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics ofmicrobiome census data. PLoS One 2013;8:e61217.
30. Mazmanian SK, Round JL, Kasper DL. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 2008;453:620-5.
31. Morimura T, Ohashi K, Kon Y et al. Apoptosis and CD8-downregulation in the thymus of chickens infected with Marek's disease virus. Arch Virol 1996;141:2243-9.
32. Morimura T, Ohashi K, Sugimoto C et al. Pathogenesis of Marek's disease (MD) and possible mechanisms of immunity induced by MD vaccine. J Vet Med Sci 1998;60:1-8.
33. Morrow C, Fehler F. Marek's disease: a worldwide problem. In: Davison F Nair V (eds) Marek's Disease, An Evolving Problem. Oxford, UK: Elsevier, 2004, 49-61.
34. Niikura M, Kim T, Hunt HD et al. Marek's disease virus upregulates major histocompatibility complex class II cell surface expression in infected cells. Virology 2007;359:212-9.
35. Oksanen J, Blanchet FG, Friendly M et al. vegan: Community Ecology Package. R Package Version 2.3-0. 2015. http://CRAN.R-project.org/package=vegan
36. Omar AR, Schat KA. Syngeneic Marek's disease virus (MDV)-specific cell-mediated immune responses against immediate early, late, and uniqueMDV proteins. Virology 1996;222:87-99.
37. Parks DH, Tyson GW, Hugenholtz P et al. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 2014;30:3123-4.
38. Parvizi P, Abdul-Careem MF, Mallick AI et al. The effects of administration of ligands for Toll-like receptor 4 and 21 against Marek's disease in chickens. Vaccine 2014;32:1932-8.
39. Peroval MY, Boyd AC, Young JR et al. A critical role for MAPK signalling pathways in the transcriptional regulation of toll like receptors. PLoS One 2013;8:e51243.
40. Perumbakkam S, Hunt HD, Cheng HH. Marek's disease virus influences the core gut microbiome of the chicken during the early and late phases of viral replication. FEMS Microbiol Ecol 2014;90:300-12.
41. Perumbakkam S, Muir WM, Black-Pyrkosz A et al. Comparison and contrast of genes and biological pathways responding to Marek's disease virus infection using allele-specific expression and differential expression in broiler and layer chickens. BMC Genomics 2013;14:64.
42. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009;26:1641-50.
43. Qu A, Brulc JM, Wilson MK et al. Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One 2008;3:e2945.
44. Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F et al. Recognition of commensalmicroflora by toll-like receptors is required for intestinal homeostasis. Cell 2004;118:229-41.
45. Round JL, Lee SM, Li J et al. The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science 2011;332:974-7.
46. Schat KA, Nair V. Marek's disease. In: Saif YM, Fadly AM, Glisson JR et al. (eds) Disease of Poultry. Ames, IA: Blackwell, 2008, 452-514.
47. Schloss PD, Westcott SL, Ryabin T et al. Introducingmothur: open source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microb 2009;75:7537-41.
48. Schnare M, Barton GM, Holt AC et al. Toll-like receptors control activation of adaptive immune responses. Nat Immunol 2001;2:947-50.
49. Sekirov I, Tam NM, Jogova M et al. Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection. Infect Immun 2008;76:4726-36.
50. Sergeant MJ, Constantinidou C, Cogan TA et al. Extensive microbial and functional diversity within the chicken cecal microbiome. PLoS One 2014;9:e91941.
51. Smith K, Mccoy KD, Macpherson AJ. Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin Immunol 2007;19:59-69.
52. Stone HA. Use of Highly Inbred Chickens in Research. Washington, DC: Agricultural Research Service, US Department of Agriculture, 1975.
53. Yu Z, Morrison M. Improved extraction of PCR-quality community DNA from digesta and fecal samples. BioTechniques 2004;36:808-13.