Recent Microbiome Papers from Penn & CHOP

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes
Gary D. Wu, Jun Chen, Christian Hoffmann, Kyle Bittinger, Ying-Yu Chen, Sue A. Keilbaugh, Meenakshi Bewtra, Dan Knights, William A. Walters, Rob Knight, Rohini Sinha, Erin Gilroy, Kernika Gupta, Robert Baldassano, Lisa Nessel, Hongzhe Li, Frederic D. Bushman, James D. Lewis. Science. 2011 October 7; 334(6052): 105–108. Published online 2011 September 1. doi: 10.1126/science.1208344

The human gut virome: inter-individual variation and dynamic response to diet.
Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD. Genome Res. 2011 Oct;21(10):1616-25. doi: 10.1101/gr.122705.111. Epub 2011 Aug 31.

Bayesian community-wide culture-independent microbial source tracking.
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. Nat Methods. 2011 Jul 17;8(9):761-3. doi: 10.1038/nmeth.1650.

Topographical continuity of bacterial populations in the healthy human respiratory tract.
Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A,Bushman FD, Collman RG. Am J Respir Crit Care Med. 2011 Oct 15;184(8):957-63. doi: 10.1164/rccm.201104-0655OC. Epub 2011 Jun 16.

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags.
Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, Li H, Bushman FD. BMC Microbiol. 2010 Jul 30;10:206. doi: 10.1186/1471-2180-10-206.

Disordered microbial communities in the upper respiratory tract of cigarette smokers.
Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD, Collman RG. PLoS One. 2010 Dec 20;5(12):e15216. doi: 10.1371/journal.pone.0015216.