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Commensal Escherichia coli Strains Can Promote Intestinal Inflammation via Differential Interleukin-6 Production.

Kittana H, Gomes-Neto JC, Heck K, Geis AL, Segura Muñoz RR, Cody LA, Schmaltz RJ, Bindels LB, Sinha R, Hostetter JM, Benson AK, Ramer-Tait AE.

Front Immunol. 2018 Oct 9;9:2318. doi: 10.3389/fimmu.2018.02318. eCollection 2018.


Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly.

Martínez I, Maldonado-Gomez MX, Gomes-Neto JC, Kittana H, Ding H, Schmaltz R, Joglekar P, Cardona RJ, Marsteller NL, Kembel SW, Benson AK, Peterson DA, Ramer-Tait AE, Walter J.

Elife. 2018 Sep 18;7. pii: e36521. doi: 10.7554/eLife.36521.


Effect of Mouthguard Use on Metabolic and Cardiorespiratory Responses to Aerobic Exercise in Males.

Green MS, Benson AK, Martin TD.

Res Q Exerc Sport. 2018 Jun;89(2):183-189. doi: 10.1080/02701367.2018.1451816. Epub 2018 Apr 25.


A gut pathobiont synergizes with the microbiota to instigate inflammatory disease marked by immunoreactivity against other symbionts but not itself.

Gomes-Neto JC, Kittana H, Mantz S, Segura Munoz RR, Schmaltz RJ, Bindels LB, Clarke J, Hostetter JM, Benson AK, Walter J, Ramer-Tait AE.

Sci Rep. 2017 Dec 18;7(1):17707. doi: 10.1038/s41598-017-18014-5.


The impact of the bovine faecal microbiome on Escherichia coli O157:H7 prevalence and enumeration in naturally infected cattle.

Kim M, Kuehn LA, Bono JL, Berry ED, Kalchayanand N, Freetly HC, Benson AK, Wells JE.

J Appl Microbiol. 2017 Oct;123(4):1027-1042. doi: 10.1111/jam.13545. Epub 2017 Sep 11.


A real-time PCR assay for accurate quantification of the individual members of the Altered Schaedler Flora microbiota in gnotobiotic mice.

Gomes-Neto JC, Mantz S, Held K, Sinha R, Segura Munoz RR, Schmaltz R, Benson AK, Walter J, Ramer-Tait AE.

J Microbiol Methods. 2017 Apr;135:52-62. doi: 10.1016/j.mimet.2017.02.003. Epub 2017 Feb 9.


Negative binomial mixed models for analyzing microbiome count data.

Zhang X, Mallick H, Tang Z, Zhang L, Cui X, Benson AK, Yi N.

BMC Bioinformatics. 2017 Jan 3;18(1):4. doi: 10.1186/s12859-016-1441-7.


The gut microbiome-an emerging complex trait.

Benson AK.

Nat Genet. 2016 Oct 27;48(11):1301-1302. doi: 10.1038/ng.3707.


Molecular characterization of the intestinal microbiota in patients with and without abdominal bloating.

Ringel-Kulka T, Benson AK, Carroll IM, Kim J, Legge RM, Ringel Y.

Am J Physiol Gastrointest Liver Physiol. 2016 Mar 15;310(6):G417-26. doi: 10.1152/ajpgi.00044.2015. Epub 2015 Dec 23.


Alignment behaviors of short peptides provide a roadmap for functional profiling of metagenomic data.

Sinha R, Clarke J, Benson AK.

BMC Genomics. 2015 Dec 21;16:1080. doi: 10.1186/s12864-015-2272-z.


Host genetic architecture and the landscape of microbiome composition: humans weigh in.

Benson AK.

Genome Biol. 2015 Sep 22;16:203. doi: 10.1186/s13059-015-0775-1. Review.


Host genetics and diet, but not immunoglobulin A expression, converge to shape compositional features of the gut microbiome in an advanced intercross population of mice.

Leamy LJ, Kelly SA, Nietfeldt J, Legge RM, Ma F, Hua K, Sinha R, Peterson DA, Walter J, Benson AK, Pomp D.

Genome Biol. 2014;15(12):552.


Microbial successions are associated with changes in chemical profiles of a model refrigerated fresh pork sausage during an 80-day shelf life study.

Benson AK, David JR, Gilbreth SE, Smith G, Nietfeldt J, Legge R, Kim J, Sinha R, Duncan CE, Ma J, Singh I.

Appl Environ Microbiol. 2014 Sep;80(17):5178-94. doi: 10.1128/AEM.00774-14. Epub 2014 Jun 13.


Molecular evolution of glycoside hydrolase genes in the Western corn rootworm (Diabrotica virgifera virgifera).

Eyun SI, Wang H, Pauchet Y, Ffrench-Constant RH, Benson AK, Valencia-Jiménez A, Moriyama EN, Siegfried BD.

PLoS One. 2014 Apr 9;9(4):e94052. doi: 10.1371/journal.pone.0094052. eCollection 2014. Erratum in: PLoS One. 2014;9(7):e102818.


Meat Science and Muscle Biology Symposium: Escherichia coli O157:H7, diet, and fecal microbiome in beef cattle.

Wells JE, Kim M, Bono JL, Kuehn LA, Benson AK.

J Anim Sci. 2014 Apr;92(4):1345-55. doi: 10.2527/jas.2013-7282. Epub 2014 Feb 3.


Molecular characterization of host-specific biofilm formation in a vertebrate gut symbiont.

Frese SA, Mackenzie DA, Peterson DA, Schmaltz R, Fangman T, Zhou Y, Zhang C, Benson AK, Cody LA, Mulholland F, Juge N, Walter J.

PLoS Genet. 2013;9(12):e1004057. doi: 10.1371/journal.pgen.1004057. Epub 2013 Dec 26.


Investigation of bacterial diversity in the feces of cattle fed different diets.

Kim M, Kim J, Kuehn LA, Bono JL, Berry ED, Kalchayanand N, Freetly HC, Benson AK, Wells JE.

J Anim Sci. 2014 Feb;92(2):683-94. doi: 10.2527/jas.2013-6841. Epub 2013 Dec 18.


Drosophila melanogaster Selection for Survival after Infection with Bacillus cereus Spores: Evolutionary Genetic and Phenotypic Investigations of Respiration and Movement.

Ma J, Benson AK, Kachman SD, Jacobsen DJ, Harshman LG.

Int J Evol Biol. 2013;2013:576452. doi: 10.1155/2013/576452. Epub 2013 Mar 21.


Drosophila melanogaster Selection for Survival of Bacillus cereus Infection: Life History Trait Indirect Responses.

Ma J, Benson AK, Kachman SD, Hu Z, Harshman LG.

Int J Evol Biol. 2012;2012:935970. doi: 10.1155/2012/935970. Epub 2012 Oct 9.


Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits.

McKnite AM, Perez-Munoz ME, Lu L, Williams EG, Brewer S, Andreux PA, Bastiaansen JW, Wang X, Kachman SD, Auwerx J, Williams RW, Benson AK, Peterson DA, Ciobanu DC.

PLoS One. 2012;7(6):e39191. doi: 10.1371/journal.pone.0039191. Epub 2012 Jun 18.


Next-generation sequencing reveals significant bacterial diversity of botrytized wine.

Bokulich NA, Joseph CM, Allen G, Benson AK, Mills DA.

PLoS One. 2012;7(5):e36357. doi: 10.1371/journal.pone.0036357. Epub 2012 May 1.


Dietary selenium affects host selenoproteome expression by influencing the gut microbiota.

Kasaikina MV, Kravtsova MA, Lee BC, Seravalli J, Peterson DA, Walter J, Legge R, Benson AK, Hatfield DL, Gladyshev VN.

FASEB J. 2011 Jul;25(7):2492-9. doi: 10.1096/fj.11-181990. Epub 2011 Apr 14.


The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri.

Frese SA, Benson AK, Tannock GW, Loach DM, Kim J, Zhang M, Oh PL, Heng NC, Patil PB, Juge N, Mackenzie DA, Pearson BM, Lapidus A, Dalin E, Tice H, Goltsman E, Land M, Hauser L, Ivanova N, Kyrpides NC, Walter J.

PLoS Genet. 2011 Feb;7(2):e1001314. doi: 10.1371/journal.pgen.1001314. Epub 2011 Feb 17.


A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences.

Russell DJ, Way SF, Benson AK, Sayood K.

BMC Bioinformatics. 2010 Dec 17;11:601. doi: 10.1186/1471-2105-11-601.


Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors.

Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, Zhang M, Oh PL, Nehrenberg D, Hua K, Kachman SD, Moriyama EN, Walter J, Peterson DA, Pomp D.

Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18933-8. doi: 10.1073/pnas.1007028107. Epub 2010 Oct 11.


Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution.

Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN, Roos S, Walter J.

ISME J. 2010 Mar;4(3):377-87. doi: 10.1038/ismej.2009.123. Epub 2009 Nov 19.


Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota.

Martínez I, Wallace G, Zhang C, Legge R, Benson AK, Carr TP, Moriyama EN, Walter J.

Appl Environ Microbiol. 2009 Jun;75(12):4175-84. doi: 10.1128/AEM.00380-09. Epub 2009 May 1.


Genomic instability in regions adjacent to a highly conserved pch prophage in Escherichia coli O157:H7 generates diversity in expression patterns of the LEE pathogenicity island.

Yang Z, Kim J, Zhang C, Zhang M, Nietfeldt J, Southward CM, Surette MG, Kachman SD, Benson AK.

J Bacteriol. 2009 Jun;191(11):3553-68. doi: 10.1128/JB.01738-08. Epub 2009 Mar 27.


Genomic deletion marking an emerging subclone of Francisella tularensis subsp. holarctica in France and the Iberian Peninsula.

Dempsey MP, Dobson M, Zhang C, Zhang M, Lion C, Gutiérrez-Martín CB, Iwen PC, Fey PD, Olson ME, Niemeyer D, Francesconi S, Crawford R, Stanley M, Rhodes J, Wagner DM, Vogler AJ, Birdsell D, Keim P, Johansson A, Hinrichs SH, Benson AK.

Appl Environ Microbiol. 2007 Nov;73(22):7465-70. Epub 2007 Sep 21.


Genome evolution in major Escherichia coli O157:H7 lineages.

Zhang Y, Laing C, Steele M, Ziebell K, Johnson R, Benson AK, Taboada E, Gannon VP.

BMC Genomics. 2007 May 16;8:121.


Identification of a putative operon involved in fructooligosaccharide utilization by Lactobacillus paracasei.

Goh YJ, Zhang C, Benson AK, Schlegel V, Lee JH, Hutkins RW.

Appl Environ Microbiol. 2006 Dec;72(12):7518-30. Epub 2006 Oct 6.


Identification of common subpopulations of non-sorbitol-fermenting, beta-glucuronidase-negative Escherichia coli O157:H7 from bovine production environments and human clinical samples.

Yang Z, Kovar J, Kim J, Nietfeldt J, Smith DR, Moxley RA, Olson ME, Fey PD, Benson AK.

Appl Environ Microbiol. 2004 Nov;70(11):6846-54.


Catabolite repression and virulence gene expression in Listeria monocytogenes.

Gilbreth SE, Benson AK, Hutkins RW.

Curr Microbiol. 2004 Aug;49(2):95-8.


DNA sequence analysis of regions surrounding blaCMY-2 from multiple Salmonella plasmid backbones.

Giles WP, Benson AK, Olson ME, Hutkins RW, Whichard JM, Winokur PL, Fey PD.

Antimicrob Agents Chemother. 2004 Aug;48(8):2845-52.


Genome diversity among regional populations of Francisella tularensis subspecies tularensis and Francisella tularensis subspecies holarctica isolated from the US.

Samrakandi MM, Zhang C, Zhang M, Nietfeldt J, Kim J, Iwen PC, Olson ME, Fey PD, Duhamel GE, Hinrichs SH, Cirillo JD, Benson AK.

FEMS Microbiol Lett. 2004 Aug 1;237(1):9-17.


Genome diversification in phylogenetic lineages I and II of Listeria monocytogenes: identification of segments unique to lineage II populations.

Zhang C, Zhang M, Ju J, Nietfeldt J, Wise J, Terry PM, Olson M, Kachman SD, Wiedmann M, Samadpour M, Benson AK.

J Bacteriol. 2003 Sep;185(18):5573-84.


Characterization of Escherichia coli O157:H7 from downer and healthy dairy cattle in the upper Midwest region of the United States.

Byrne CM, Erol I, Call JE, Kaspar CW, Buege DR, Hiemke CJ, Fedorka-Cray PJ, Benson AK, Wallace FM, Luchansky JB.

Appl Environ Microbiol. 2003 Aug;69(8):4683-8.


Role of sigma(B) in adaptation of Listeria monocytogenes to growth at low temperature.

Becker LA, Evans SN, Hutkins RW, Benson AK.

J Bacteriol. 2000 Dec;182(24):7083-7.


Octamer-based genome scanning distinguishes a unique subpopulation of Escherichia coli O157:H7 strains in cattle.

Kim J, Nietfeldt J, Benson AK.

Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13288-93.


Mutational analysis of the role of HPr in Listeria monocytogenes.

Christensen DP, Benson AK, Hutkins RW.

Appl Environ Microbiol. 1999 May;65(5):2112-5.


Purification, characterization, and reconstitution of DNA-dependent RNA polymerases from Caulobacter crescentus.

Wu J, Ohta N, Benson AK, Ninfa AJ, Newton A.

J Biol Chem. 1997 Aug 22;272(34):21558-64.


The role of FlbD in regulation of flagellar gene transcription in Caulobacter crescentus.

Benson AK, Wu J, Newton A.

Res Microbiol. 1994 Jun-Aug;145(5-6):420-30. Review.


The Caulobacter crescentus FlbD protein acts at ftr sequence elements both to activate and to repress transcription of cell cycle-regulated flagellar genes.

Benson AK, Ramakrishnan G, Ohta N, Feng J, Ninfa AJ, Newton A.

Proc Natl Acad Sci U S A. 1994 May 24;91(11):4989-93.

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