Characterization of Stool Virome in Children Newly Diagnosed With Moderate to Severe Ulcerative Colitis. Tokarz R, Hyams JS, Mack DR, Boyle B, Griffiths AM, LeLeiko NS, Sauer CG, Shah S, Markowitz J, Baker SS, Rosh J, Baldassano RN, Kugathasan S, Walters T, Tagliafierro T, Sameroff S, Lee B, Che X, Oleynik A, Denson LA, Lipkin WI. Inflamm Bowel Dis. 2019 Sep 18;25(10):1656-1662. doi: 10.1093/ibd/izz099. PMID: 31112614

Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids. Wang S, Martins R, Sullivan MC, Friedman ES, Misic AM, El-Fahmawi A, De Martinis ECP, O'Brien K, Chen Y, Bradley C, Zhang G, Berry ASF, Hunter CA, Baldassano RN, Rondeau MP, Beiting DP. Microbiome. 2019 Aug 31;7(1):126. doi: 10.1186/s40168-019-0740-4. PMID: 31472697

Gut microbiota features associated with Clostridioides difficile colonization in puppies. Berry ASF, Kelly BJ, Barnhart D, Kelly DJ, Beiting DP, Baldassano RN, Redding LE. PLoS One. 2019 Aug 30;14(8):e0215497. doi: 10.1371/journal.pone.0215497. eCollection 2019. PMID: 31469837

Role for diet in normal gut barrier function: developing guidance within the framework of food-labeling regulations. Camilleri M, Lyle BJ, Madsen KL, Sonnenburg J, Verbeke K, Wu GD. Am J Physiol Gastrointest Liver Physiol. 2019 Jul 1;317(1):G17-G39. Doi: 10.1152/ajpgi.00063.2019. Epub 2019 May 24.PMID: 31125257

Gut microbiota modulate dendritic cell antigen presentation and radiotherapy-induced antitumor immune response.
Uribe-Herranz M, Rafail S2, Beghi S, Gil-de-Gómez L, Verginadis I, Bittinger K, Pustylnikov S, Pierini S, Perales-Linares R, Blair IA, Mesaros CA, Snyder NW, Bushman F, Koumenis C, Facciabene A. J Clin Invest., Dec 9, 2019. DOI: 10.1172/JCI124332. PMID: 31815742. (Epub ahead of print).

Distinct cellular roles for PDCD10 define a gut-brain axis in cerebral cavernous malformation.
Tang AT, Sullivan KR, Hong CC, Goddard LM, Mahadevan A, Ren A, Pardo H, Peiper A,…Bittinger K, Lengner CJ, Schwaninger M, Velcich A, Augenlicht L, Abdelilah-Seyfried S, Min W, Marchuk DA, Awad IA, Kahn ML. Scientific Transl Med, Nov 27, 2019, 11(520). DOI: 10.1126/scitranslmed.aaw3521. PMID: 31776290.

Metabolic analysis of regionally distinct gut microbial communities using an in vitro platform.
Firrman J, Liu L, Tanes C, Friedman E, Bittinger K, Daniel S, van den Abbeele P, Evans BS. J Agric Food Chem, Nov 6, 2019. DOI: 10.1021/acs.jafc.9b05202. PMID: 31690071. (Epub ahead of print).

Childhood Adversity Impact on Gut Microbiota and Inflammatory Response to Stress during Pregnancy.
Hantsoo L, Jašarević E, Criniti S, McGeehan B, Tanes C, Sammel MD, Elovitz MA, Compher C, Wu G, Epperson CN. Brain Behav Immun, Jan 2019:240-250. doi:10.1016/j.bbi.2018.11.005. Epub 2018 Nov 3. PMID: 30399404.

Segmented filamentous bacteria prevent and cure rotavirus infection.
Shi Z, Zou J, Zhang Z, Zhao X, Noriega J, Zhang B, Zhao C, Ingle H, Bittinger K, Mattei LM, Pruijssers AJ, Plemper RK, Nice TJ, Baldridge M, Dermody TS, Chassaing B, Gewirtz AT. Cell, Oct 8, 2019. doi: 10.1016/j.cell.2019.09.028. PMID: 31607511. [Epub ahead of print]

Association of enterovirus D68 with acute flaccid myelitis, Philadelphia, Pennsylvania, USA, 2009-2018.
Graf EH, Elkan M, Fink JS, Zhao C, Bittinger K, Hopkins S, Ulloa ER, Rajagopalan R, Mitchell S, Darcy C.. Emerging Infectious Diseases. Sep 2019; 25(9). DOI: 10.3201/eid2509.190468. PMID: 31407660. Epub Sep 17, 2019.

Upper respiratory dysbiosis with facultative-dominated ecotype in advanced lung disease and dynamic change after lung transplant.
Simon-Soro A, Sohn M, McGinnis J, Imai I, Brown M, Knecht V, Bailey A, Clarke E, Cantu III E, Lee H, Bittinger K, Diamond J, Christie J, Bushman FD, Collman R. Annals of the American Thoracic Society. Aug 15, 2019. DOI: 10.1513/AnnalsATS.201904-299OC. PMID: 31415219. [Epub ahead of print].

Reproducible, interactive, scalable, and extensible microbiome data science using QIIME 2.
Bolyen E, Rideout JR, Dillion M, Bokulich N…Bittinger K, et al. Nature Biotechnology. Jul 24, 2019. DOI: 10.1038/s41587-019-0209-9. PMID: 31341288. [Epub ahead of print].

Host mitochondria influence gut microbiome diversity: A role for ROS.
Yardeni T, Tanes C, Bittinger K, Mattei LM, Schaefer P, Signh LN, Wu G, Murdock D, Wallace DC. Science Signaling. Jul 2, 2019; 12(588), pii:eaaw3159. DOI: 10.1126/scisignal.aaw3159. PMID: 31266851.

Metagenomic assessment of the Cebus apella gut microbiota.
Firrman J, LinShu L, Tanes C, Bittinger K, Mahalak K, Rinaldi W. American Journal of Primatology. Jun 26, 2019; e23023. DOI: 10.1002/ajp.23023. PMID: 31266851. [Epub ahead of print].

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments.
Clarke EL, Taylor LJ, Zhao C, Connell A, Lee JJ, Fett B, Bushman FD, Bittinger K. Microbiome, Mar 22, 2019;7(1):46. DOI: 10.1186/s40168-019-0658-x. PMID: 30902113

The gut microbiome regulates the increases in depressive-type behaviors and in inflammatory processes in the ventral hippocampus of stress vulnerable rats.
Bhatnagar S, Pearson-Leary J, Zhao C, Bittinger K, Eacret D, Luz S, Vigderman A., Dayanim G. Mol Psychiatry, Mar 4, 2019. doi: 10.1038/s41380-019-0380-x. [Epub ahead of print]. PMID: 30833676

Antigen presenting ILC3 regulate T cell-dependent IgA responses to colonic mucosal bacteria.
Melo-Gonzalez F, Kammoun H, Evren E, Dutton E, Papadopoulou M, Bradford B, Tanes C, Fardus-Reid F, Swann J, Bittinger K, Mabbott N, Vallance B, Willinger T, Withers D, Hepworth M. J Exp Med, Feb 27, 2019. pii: jem.20180871. doi: 10.1084/jem.20180871. [Epub ahead of print]. PMID: 30814299.

Applying advanced in vitro culturing technology to study the human gut microbiota.
Firrman J, Liu L, Van den Abbeele, P, Tanes C, Bittinger K, Tomasula P. JoVE (144), Feb 15, 2019. doi: 10.3791/59054. PMID: 30829328

Microbiota-dependent signals are required to sustain TLR-mediated immune responses.
Weaver LK, Minichino D, Biswas C, Chu N, Lee JJ, Bittinger K, Albeituni S, Nichols KE, Behrens EM. JCI Insight, 4(1), Jan 10, 2019. pii: 124370. doi: 10.1172/jci.insight 124370. [Epub ahead of print]. PMID 30626747.

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