Metagenomic Predictions: From Microbiome to Complex Health and Environmental Phenotypes in Humans and Cattle

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Ross, Elizabeth M ^a,b,c   Moate, Peter J ^d   Marett, Leah C ^d   Cocks, Ben G ^a,b,c   Hayes, Ben J ^a,b,c  

^a Biosciences Research Division   (Australia)

^b Department of Civil and Environmental Engineering   (Australia)

^c LA TROBE UNIVERSITY   (Australia)

^d Future Farming Systems Division   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

METHANE;

ACCURACY; ARTICLE; BODY MASS; DAIRY CATTLE; ENTERITIS; GENETIC PROCEDURES; GENETIC TRAIT; GREENHOUSE GAS; HUMAN GENOME; MASSIVELY PARALLEL SEQUENCING; METAGENOMICS; METHODOLOGY; MICROBIOME; PHENOTYPE; PREDICTION;

ANIMALS; CATTLE; ENVIRONMENT; HEALTH; HUMANS; INFLAMMATORY BOWEL DISEASES; METAGENOMICS; METHANE; MICROBIOTA; PHENOTYPE;

EID: 84883397143     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0073056     Document Type: Article

References (49)

1. Dethlefsen L, McFall-Ngai M, Relman DA, (2007) An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449: 811-818.
2. Cho I, Blaser MJ, (2012) The human microbiome: at the interface of health and disease. Nature Reviews Genetics 13: 260-270.
3. Savage DC, (1977) Microbial ecology of the gastrointestinal tract. Annual Review of Microbiology 31: 107-133.
4. Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, et al. (2012) Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biology 13: R42.
5. Li K, Bihan M, Yooseph S, Methe BA, (2012) Analyses of the Microbial Diversity across the Human Microbiome. PLoS One 7: e32118.
6. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, et al. (2007) The human microbiome project. Nature 449: 804-810.
7. Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, et al. (2012) Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy. Cell 150: 470-480.
8. 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.
9. Qin J, Li Y, Cai Z, Li S, Zhu J, et al. (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490: 55-60.
10. Lavery T, Be R, Seymour J, Mitchell J, Jeffries T (2012) High nutrient transport and cycling potential revealed in the microbial metagenome of Australian sea lion (Neophoca cinerea) Faeces.
11. Alcaide M, Messina E, Richter M, Bargiela R, Peplies J, et al. (2012) Gene Sets for Utilization of Primary and Secondary Nutrition Supplies in the Distal Gut of Endangered Iberian Lynx. PLoS One 7: e51521.
12. Barry KA, Middelbos IS, Vester Boler BM, Dowd SE, Suchodolski JS, et al. (2012) Effects of dietary fiber on the feline gastrointestinal metagenome. Journal of proteome research 11: 5924-5933.
13. Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, et al. (2011) Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. ISME Journal 5: 639-649.
14. Lamendella R, Santo Domingo JW, Ghosh S, Martinson J, Oerther DB, (2011) Comparative fecal metagenomics unveils unique functional capacity of the swine gut. BMC microbiology 11: 103.
15. Xu B, Xu W, Yang F, Li J, Yang Y, et al. (2013) Metagenomic Analysis of the Pygmy Loris Fecal Microbiome Reveals Unique Functional Capacity Related to Metabolism of Aromatic Compounds. PLoS One 8: e56565.
16. Durso LM, Harhay GP, Bono JL, Smith TPL, (2011) Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach. Journal of microbiological methods 84: 278-282.
17. Hildebrand F, Ebersbach T, Nielsen H, Li X, Sonne S, et al. (2012) A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens). BMC genomics 13: 514.
18. Dai X, Zhu Y, Luo Y, Song L, Liu D, et al. (2012) Metagenomic Insights into the Fibrolytic Microbiome in Yak Rumen. PLoS One 7: e40430.
19. Hess M, Sczyrba A, Egan R, Kim T-W, Chokhawala H, et al. (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331: 463-467.
20. Brulc JM, Antonopoulos DA, Berg Miller ME, Wilson MK, Yannarell AC, et al. (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proceedings of the National Academy of Sciences of the United States of America 106: 1948-1953.
21. Ross EM, Moate PJ, Bath CR, Davidson SE, Sawbridge TI, et al. (2012) High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing. BMC Genetics 13: 53.
22. Singh K, Ahir V, Tripathi A, Ramani U, Sajnani M, et al. (2012) Metagenomic analysis of Surti buffalo (Bubalus bubalis) rumen: a preliminary study. Molecular Biology Reports 39: 4841-4848.
23. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
24. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, et al. (2012) Human gut microbiome viewed across age and geography. Nature 486: 222-227.
25. Greenblum S, Turnbaugh PJ, Borenstein E, (2012) Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proceedings of the National Academy of Sciences 109: 594-599.
26. Papa E, Docktor M, Smillie C, Weber S, Preheim SP, et al. (2012) Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PLoS One 7: e39242.
27. Hirschhorn JN, Gajdos ZK, (2011) Genome-wide association studies: results from the first few years and potential implications for clinical medicine. Annual Review of Medicine 62: 11-24.
28. Yang J, Ferreira T, Morris AP, Medland SE, Genetic Investigation of ATC, et al. (2012) Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nature Genetics 44: 369-375, S361-363.
29. Pryce JE, Arias J, Bowman PJ, Davis SR, Macdonald KA, et al. (2012) Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers. Journal of Dairy Science 95: 2108-2119.
30. Meuwissen T, Hayes B, Goddard M, (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819.
31. Henderson CR (1984) Applications of linear models in animal breeding. Guelph, Canada: University of Guelph Press.
32. Sing T, Sander O, Beerenwinkel N, Lengauer T, (2005) ROCR: visualizing classifier performance in R. Bioinformatics. 21: 3940-3941.
33. Roccarina D, Lauritano EC, Gabrielli M, Franceschi F, Ojetti V, et al. (2010) The role of methane in intestinal diseases. American Journal of Gastroenterology 105: 1250-1256.
34. Ross EM, Moate PJ, Marett L, Cocks BG, Hayes BJ (2013) Investigating the effect of two methane mitigating diets on the rumen microbiome using massively parallel sequencing. Journal of dairy science: doi: 10.3168/jds.2013-6766.
35. Knights D, Costello EK, Knight R, (2011) Supervised classification of human microbiota. FEMS Microbiology Reviews 35: 343-359.
36. Liaw A, Wiener M, (2002) Classification and Regression by randomForest. R news 2: 18-22.
37. Belonsky GM, Kennedy BW, (1988) Selection on individual phenotype and best linear unbiased predictor of breeding value in a closed swine herd. Journal of Animal Science 66: 1124-1131.
38. Hayes B, Bowman P, Chamberlain A, Goddard M, (2009) Invited review: Genomic selection in dairy cattle: Progress and challenges. Journal of dairy science 92: 433-443.
39. Brito FV, Neto JB, Sargolzaei M, Cobuci JA, Schenkel FS, (2011) Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle. BMC genetics 12: 80.
40. Daetwyler HD, Swan AA, van der Werf JH, Hayes BJ, (2012) Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation. Genetics Selection Evolution 44: 1-11.
41. Jostins L, Barrett JC, (2011) Genetic risk prediction in complex disease. Human Molecular Genetics 20: R182-188.
42. Moate PJ, Williams SRO, Ribaux BE, Wales WJ (2012) Feeding grape marc to dairy cows suppresses methane emissions. The 5th Australasian Dairy Science Symposium. 454-455.
43. Johnson K, Huyler M, Westberg H, Lamb B, Zimmerman P, (1994) Measurement of methane emissions from ruminant livestock using a sulfur hexafluoride tracer technique. Environmental Science & Technology 28: 359-362.
44. Grainger C, Clarke T, McGinn SM, Auldist MJ, Beauchemin KA, et al. (2007) Methane Emissions from Dairy Cows Measured Using the Sulfur Hexafluoride (SF6) Tracer and Chamber Techniques. Journal of Dairy Science 90: 2755-2766.
45. Pryce J, Marett L, Wales W, Williams Y, Hayes B (2012) Calves selected for divergence in feed conversion efficiency for growth also exhibit divergence in feed conversion efficiency in lactation. Proceedings of the australiasian daiy science symposium: 45-46.
46. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
47. Gilmour AR, Gogel BJ, Cullis BR, Thompson R (2006) ASReml User Guide Release 2.0. VSN International Ltd, Hemel Hempstead, HP1 1ES, UK.
48. Endelman JB, (2011) Ridge regression and other kernels for genomic selection with R package rrBLUP. The Plant Genome 4: 250-255.
49. Marçais G, Kingsford C, (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27: 764-770.