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Additional reading: Chapter 17

Additional Reading:

Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE. Conducting a Microbiome Study. Cell. 2014 Jul 17;158(2):250-262. doi: 10.1016/j.cell.2014.06.037.

Handelsman, J., J. Tiedje, L. Alvarez-Cohen, M. Ashburner, I. K. O. Cann, E. F. Delong, W. Ford Doolittle et al. "The new science of metagenomics: revealing the secrets of our microbial planet." Nat Res Council Report 13 (2007): 47-84.

Lively, C. M., de Roode, J. C., Duffy, M. A., Graham, A. L., & Koskella, B. (2014). Interesting open questions in disease ecology and evolution. The American Naturalist, 184(S1), S1-S8.

Mandal RS, Saha S, Das S. Metagenomic Surveys of Gut Microbiota. Genomics, Proteomics & Bioinformatics 2015; 13(3): 148-158.

Pacheco et al (2015) The Impact of the Milk Glycobiome on the Neonate Gut Microbiota. Annu Rev Anim Biosci. 2015 Feb 16; 3: 419–445.

Taupp M, Mewis K, Hallam SJ. The art and design of functional metagenomics screens. Curr Opin Biotechnol. 2011 Jun;22(3):465-72. doi:10.1016/j.copbio.2011.02.010.

Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol. 2010;6(2):e1000667.

Xochitl C. Morgan1, Nicola Segata1, and Curtis Huttenhower. Biodiversity and Functional Genomics in the Human Microbiome. Trends Genet. 2013. 29(1): 51–58.

Additional Reading for Boxes:

Tool Box 17.1

Jordana’s BOE – All the BOEs are missing from the HC website even though they are an HHMi spotlighted resource.  Please can we retrieve this one from HC archives and place it in the ORC?  Any chance we can see a full list to determine whether others are relevant to EGG.  Finally, if we can dig up Jordana’s, I’d appreciate having Nina, Faith’s and Amy’s (Amy’s in particular) for my own record.

Box 17.1

Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP. The bacterial species challenge: making sense of genetic and ecological diversity. Science. 2009 Feb 6;323(5915):741-6. doi: 10.1126/science.1159388.

Box 17.2

Blanton LV, Barratt MJ, Charbonneau MR, Ahmed T, Gordon JI. Childhood undernutrition, the gut microbiota, and microbiota-directed therapeutics. Science. 2016 Jun 24;352(6293):1533. doi: 10.1126/science.aad9359.

Box 17.3

Tito RY, Knights D, Metcalf J, Obregon-Tito AJ, Cleeland L, Najar F, Roe B, Reinhard K, Sobolik K, Belknap S, Foster M, Spicer P, Knight R, Lewis CM Jr. Insights from characterizing extinct human gut microbiomes. PLoS One. 2012;7(12):e51146. doi: 10.1371/journal.pone.0051146.