Recent Microbiome Papers from Penn & CHOP

Endothelial TLR4 and the microbiome drive cerebral cavernous malformations
Tang A, Choi J, Kotzin J, Yang Y, Hong C, Hobson N, Girard R, Zeineddine H, Lightle R, Moore T, Cao Y, Shenkar R, Chen M, Mericko P, Yang J, Li L, Tanes C, Kobuley D, Vosa U, Whitehead K, Li D, Franke L, Hart B, Schwaninger M, Heano-Mejia, et al. Nature. 2017 May 10; doi:10.1038/nature22075.

A Summary of the First HIV Microbiome Workshop 2015.
Williams B, Mirmonsef P, Boucher CA, Bushman F, Carrington-Lawrence S, Collman RG, Dandekar S, Dang Q, Malaspina A, Paredes R, Stone A, Landay A. AIDS Res Hum Retroviruses. 2016 Jul 14.  PMID: 27267576.

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota.
Lauder AP, Roche AM, Sherrill-Mix S, Bailey A, Laughlin AL, Bittinger K, Leite R, Elovitz MA, Parry S, Bushman FD. Microbiome. 2016 Jun 23;4(1):29. doi: 10.1186/s40168-016-0172-3. PMID: 27338728.

Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium.
Shen TC, Chehoud C, Ni J, Hsu E, Chen YY, Bailey A, Laughlin A, Bittinger K, Bushman FD, Wu GD. PLoS One. 2016 May 13;11(5):e0155620. doi: 10.1371/journal.pone.0155620. eCollection 2016. PMID: 27176607

Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation.
Chehoud C, Dryga A, Hwang Y, Nagy-Szakal D, Hollister EB, Luna RA, Versalovic J, Kellermayer R, Bushman FD. MBio. 2016 Mar 29;7(2):e00322. doi: 10.1128/mBio.00322-16. PMID: 27025251.

Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria.
Sundararaman SA, Plenderleith LJ, Liu W, Loy DE, Learn GH, Li Y, Shaw KS, Ayouba A, Peeters M, Speede S, Shaw GM, Bushman FD, Brisson D, Rayner JC, Sharp PM, Hahn BH. Nat Commun. 2016 Mar 22;7:11078. doi: 10.1038/ncomms11078. PMID: 27002652.

Peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis.
Hergott CB, Roche AM, Tamashiro E, Clarke TB, Bailey AG, Laughlin A, Bushman FD, Weiser JN. Blood. 2016 May 19;127(20):2460-71. doi: 10.1182/blood-2015-10-675173. Epub 2016 Mar 17. PMID: 26989200.

Composition and dynamics of the respiratory tract microbiome in intubated patients.
Kelly BJ, Imai I, Bittinger K, Laughlin A, Fuchs BD, Bushman FD, Collman RG. Microbiome. 2016 Feb 11;4:7. doi: 10.1186/s40168-016-0151-8. PMID: 26865050.

Bidirectional interactions between indomethacin and the murine intestinal microbiota.
Liang X, Bittinger K, Li X, Abernethy DR, Bushman FD, FitzGerald GA. Elife. 2015 Dec 23;4:e08973. doi: 10.7554/eLife.08973. PMID: 26701907.

Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees.
Barbian HJ, Li Y, Ramirez M, Klase Z, Lipende I, Mjungu D, Moeller AH, Wilson ML, Pusey AE, Lonsdorf EV, Bushman FD, Hahn BH. Am J Primatol. 2015 Dec 16. doi: 10.1002/ajp.22515. PMID: 26676710.

Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.
Beck JM, Schloss PD, Venkataraman A, Twigg H 3rd, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, Frank I, Ghedin E, Huang L, Lynch SV, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB; Lung HIV Microbiome Project. Am J Respir Crit Care Med. 2015 Dec 1;192(11):1335-44. doi: 10.1164/rccm.201501-0128OC. PMID: 26247840.

Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts.
Kelsen J, Bittinger K, Pauly-Hubbard H, Posivak L, Grunberg S, Baldassano R, Lewis JD, Wu GD, Bushman FD. Inflamm Bowel Dis. 2015 Dec;21(12):2797-805. doi: 10.1097/MIB.0000000000000557. PMID: 26288001.

Microbiota-Dependent Priming of Antiviral Intestinal Immunity in Drosophila.
Sansone CL, Cohen J, Yasunaga A, Xu J, Osborn G, Subramanian H, Gold B, Buchon N, Cherry S. Cell Host Microbe. 2015 Nov 11;18(5):571-81. doi: 10.1016/j.chom.2015.10.010.
PMID: 26567510

The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome.
Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA. MBio. 2015 Oct 20;6(5):e01578-15. doi: 10.1128/mBio.01578-15. PMID: 26489866.

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. 
Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD.  Cell Host Microbe. 2015 Oct 14;18(4):489-500. doi: 10.1016/j.chom.2015.09.008. PubMed PMID: 26468751.

Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) Study. Sarcoidosis Protocol.
Moller DR, Koth LL, Maier LA, Morris A, Drake W, Rossman M, Leader JK, Collman RG, Hamzeh N, Sweiss NJ, Zhang Y, O'Neal S, Senior RM, Becich M, Hochheiser HS, Kaminski N, Wisniewski SR, Gibson KF; GRADS Sarcoidosis Study Group. Ann Am Thorac Soc. 2015 Oct;12(10):1561-71. doi: 10.1513/AnnalsATS.201503-172OT.  PMID: 26193069.

Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts.
Kelsen J, Bittinger K, Pauly-Hubbard H, Posivak L, Grunberg S, Baldassano R, Lewis JD, Wu GD, Bushman FD. . Inflamm Bowel Dis. 2015 Aug 17. [Epub ahead of print] PubMed PMID: 26288001.

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock.
Liang X, Bushman FD, FitzGerald GA. Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10479-84. doi: 10.1073/pnas.1501305112. Epub 2015 Aug 3. PMID: 26240359.

Engineering the gut microbiota to treat hyperammonemia.
Shen TD, Albenberg L, Bittinger K, Chehoud C, Chen YY, Judge CA, Chau L, Ni J, Sheng M, Lin A, Wilkins BJ, Buza EL, Lewis JD, Daikhin Y, Nissim I, Yudkoff M, Bushman FD, Wu GD.J Clin Invest. 2015 Jun 22. pii: 79214. doi: 10.1172/JCI79214.

Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease.
Chehoud C, Albenberg LG, Judge C, Hoffmann C, Grunberg S, Bittinger K, Baldassano RN, Lewis JD, Bushman FD, Wu GD. Des. 2015 Jun 16.

Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9.
Bryson AL, Hwang Y, Sherrill-Mix S, Wu GD, Lewis JD, Black L, Clark TA, Bushman FD. MBio. 2015 Jun 16;6(3). pii: e00648-15. doi: 10.1128/mBio.00648-15

Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease.
Lee D, Baldassano RN, Otley AR, Albenberg L, Griffiths AM, Compher C, Chen EZ, Li H, Gilroy E, Nessel L, Grant A, Chehoud C, Bushman FD, Wu GD, Lewis JD. Inflamm Bowel Dis. 2015 May 12. [Epub ahead of print]

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.
Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD, Li H. Bioinformatics. 2015 Mar 29. pii: btv183.

Complement deficiency promotes cutaneous wound healing in mice.
Rafail S, Kourtzelis I, Foukas PG, Markiewski MM, DeAngelis RA, Guariento M, Ricklin D, Grice EA, Lambris JD. J Immunol. 2015 Feb 1;194(3):1285-91. doi:0.4049/jimmunol.1402354. Epub 2014 Dec 29.

The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites.
Misic AM, Davis MF, Tyldsley AS, Hodkinson BP, Tolomeo P, Hu B, Nachamkin I, Lautenbach E, Morris DO, Grice EA. Microbiome. 2015 Jan 23;3:2. doi: 10.1186/s40168-014-0052-7. eCollection 2015.

Current Concepts and Ongoing Research in the Prevention and Treatment of Open Fracture Infections.
Hannigan GD, Pulos N, Grice EA, Mehta S. Adv Wound Care (New Rochelle). 2015 Jan 1;4(1):59-74. Review.

Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research.
Hodkinson BP, Grice EA. Adv Wound Care (New Rochelle). 2015 Jan 1;4(1):50-58. Review.

Interactions between host factors and the skin microbiome.
SanMiguel A, Grice EA. Cell Mol Life Sci. 2015 Apr;72(8):1499-515. doi: 10.1007/s00018-014-1812-z. Epub 2014 Dec 30. Review.

Ethnic/racial and genetic influences on cerumen odorant profiles.
Prokop-Prigge KA, Mansfield CJ, Parker MR, Thaler E, Grice EA, Wysocki CJ, Preti G. J Chem Ecol. 2015 Jan;41(1):67-74. doi: 10.1007/s10886-014-0533-y. Epub 2014 Dec 13.

Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing.
Bittinger K, Charlson ES, Loy E, Shirley DJ, Haas AR, Laughlin A, Yi Y, Wu GD, Lewis JD, Frank I, Cantu E, Diamond JM, Christie JD, Collman RG, Bushman FD. Genome Biol. 2014;15(10):487.

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production.
Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, Chehoud C, Albenberg LG, Nessel L, Gilroy E, Star J, Weljie AM, Flint HJ, Metz DC, Bennett MJ, Li H, Bushman FD, Lewis JD. Gut. 2014 Nov 26. pii: gutjnl-2014-308209. doi: 10.1136/gutjnl-2014-308209. 

Membrane-based, sedimentation-assisted plasma separator for point-of-care applications.
Liu C, Mauk M, Gross R, Bushman FD, Edelstein PH, Collman RG, Bau HH. Anal Chem. 2013 Nov 5;85(21):10463-70. doi: 10.1021/ac402459h. Epub 2013 Oct 25.

Widespread colonization of the lung by Tropheryma whipplei in HIV infection.
Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TB, Flores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SV, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP; Lung HIV Microbiome Project. Am J Respir Crit Care Med. 2013 May 15;187(10):1110-7. doi: 10.1164/rccm.201211-2145OC.

Antiviral effects of autologous CD4 T cells genetically modified with a conditionally replicating lentiviral vector expressing long antisense to HIV.
Tebas P, Stein D, Binder-Scholl G, Mukherjee R, Brady T, Rebello T, Humeau L, Kalos M, Papasavvas E, Montaner LJ, Schullery D, Shaheen F, Brennan AL, Zheng Z, Cotte J, Slepushkin V, Veloso E, Mackley A, Hwang WT, Aberra F, Zhan J, Boyer J, Collman RG,Bushman FD, Levine BL, June CH. Blood. 2013 Feb 28;121(9):1524-33. doi: 10.1182/blood-2012-07-447250. Epub 2012 Dec 20. Erratum in: Blood. 2014 Jul 24;124(4):663.

Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota.
Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A, Grunberg S, Baldassano RN, Lewis JD, Li H, Thom SR, Bushman FD, Vinogradov SA, Wu GD. Gastroenterology. 2014 Nov;147(5):1055-63.e8. doi: 10.1053/j.gastro.2014.07.020. Epub 2014 Jul 18.

Diet, gut enterotypes and health: is there a link?
Bushman FD, Lewis JD, Wu GD. Nestle Nutr Inst Workshop Ser. 2013;77:65-73. doi: 10.1159/000351385. Epub 2013 Aug 29. Review.

Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment.
Dollive S, Chen YY, Grunberg S, Bittinger K, Hoffmann C, Vandivier L, Cuff C, Lewis JD, Wu GD, Bushman FD. PLoS One. 2013 Aug 19;8(8):e71806. doi: 10.1371/journal.pone.0071806. 

Rapid evolution of the human gut virome.
Minot S, Bryson A, Chehoud C, Wu GD, Lewis JD, Bushman FD. Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12450-5. doi: 10.1073/pnas.1300833110. Epub 2013 Jul 8.

Dendritic cell expression of the signaling molecule TRAF6 is critical for gut microbiota-dependent immune tolerance.
Han D, Walsh MC, Cejas PJ, Dang NN, Kim YF, Kim J, Charrier-Hisamuddin L, Chau L, Zhang Q, Bittinger K, Bushman FD, Turka LA, Shen H, Reizis B, Defranco AL, Wu GD, Choi Y. Immunity. 2013 Jun 27;38(6):1211-22. doi: 10.1016/j.immuni.2013.05.012. Epub 2013 Jun 20.

Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.
Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD. PLoS One. 2013 Jun 17;8(6):e66019. doi: 10.1371/journal.pone.0066019. Print 2013.

Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis.
Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, Fu X, Wu Y, Li L, Smith JD, DiDonato JA, Chen J, Li H, Wu GD, Lewis JD, Warrier M, Brown JM, Krauss RM, Tang WH, Bushman FD, Lusis AJ, Hazen SL. Nat Med. 2013 May;19(5):576-85. doi: 10.1038/nm.3145. Epub 2013 Apr 7.

Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis.
Chen J, Bushman FD, Lewis JD, Wu GD, Li H. Biostatistics. 2013 Apr;14(2):244-58. doi: 10.1093/biostatistics/kxs038. Epub 2012 Oct 15.

Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts.
Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG,Bushman FD. PLoS One. 2012;7(9):e42786. doi: 10.1371/journal.pone.0042786. Epub 2012 Sep 6.

Conservation of gene cassettes among diverse viruses of the human gut.
Minot S, Wu GD, Lewis JD, Bushman FD. PLoS One. 2012;7(8):e42342. doi: 10.1371/journal.pone.0042342. Epub 2012 Aug 10.

Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant.
Charlson ES, Diamond JM, Bittinger K, Fitzgerald AS, Yadav A, Haas AR, Bushman FD, Collman RG. Am J Respir Crit Care Med. 2012 Sep 15;186(6):536-45. doi: 10.1164/rccm.201204-0693OC. Epub 2012 Jul 12.

Associating microbiome composition with environmental covariates using generalized UniFrac distances.
Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H. Bioinformatics. 2012 Aug 15;28(16):2106-13. doi: 10.1093/bioinformatics/bts342. Epub 2012 Jun 17.

Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria.
Sonnenberg GF, Monticelli LA, Alenghat T, Fung TC, Hutnick NA, Kunisawa J, Shibata N, Grunberg S, Sinha R, Zahm AM, Tardif MR, Sathaliyawala T, Kubota M, Farber DL, Collman RG, Shaked A, Fouser LA, Weiner DB, Tessier PA, Friedman JR, Kiyono H,Bushman FD, Chang KM, Artis D. Science. 2012 Jun 8;336(6086):1321-5. doi: 10.1126/science.1222551. Epub 2012 Jun 6.

Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis.
Kong HH, Oh J, Deming C, Conlan S, Grice EA, Beatson MA, Nomicos E, Polley EC, Komarow HD; NISC Comparative Sequence Program, Murray PR, Turner ML, Segre JA. Genome Res. 2012 May;22(5):850-9. doi: 10.1101/gr.131029.111. Epub 2012 Feb 6.

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.

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.

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.

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.

 

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