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A pilot study of fecal bile acid and microbiota profiles in inflammatory bowel disease and primary sclerosing cholangitis.

Vaughn BP, Kaiser T, Staley C, Hamilton MJ, Reich J, Graiziger C, Singroy S, Kabage AJ, Sadowsky MJ, Khoruts A.

Clin Exp Gastroenterol. 2019 Jan 10;12:9-19. doi: 10.2147/CEG.S186097. eCollection 2019.


Association between submerged aquatic vegetation and elevated levels of Escherichia coli and potential bacterial pathogens in freshwater lakes.

Mathai PP, Dunn HM, Magnone P, Zhang Q, Ishii S, Chun CL, Sadowsky MJ.

Sci Total Environ. 2018 Dec 2;657:319-324. doi: 10.1016/j.scitotenv.2018.11.484. [Epub ahead of print]


Putative Nitrogen-Fixing Bacteria Associated With the Rhizosphere and Root Endosphere of Wheat Plants Grown in an Andisol From Southern Chile.

Rilling JI, Acuña JJ, Sadowsky MJ, Jorquera MA.

Front Microbiol. 2018 Nov 20;9:2710. doi: 10.3389/fmicb.2018.02710. eCollection 2018.


Cultivar and phosphorus effects on switchgrass yield and rhizosphere microbial diversity.

Sawyer A, Staley C, Lamb J, Sheaffer C, Kaiser T, Gutknecht J, Sadowsky MJ, Rosen C.

Appl Microbiol Biotechnol. 2018 Dec 7. doi: 10.1007/s00253-018-9535-y. [Epub ahead of print]


Comparative decay of sewage-associated marker genes in beach water and sediment in a subtropical region.

Ahmed W, Zhang Q, Kozak S, Beale D, Gyawali P, Sadowsky MJ, Simpson S.

Water Res. 2018 Nov 2;149:511-521. doi: 10.1016/j.watres.2018.10.088. [Epub ahead of print]


Influence of Library Composition on SourceTracker Predictions for Community-Based Microbial Source Tracking.

Brown CM, Mathai PP, Loesekann T, Staley C, Sadowsky MJ.

Environ Sci Technol. 2018 Nov 26. doi: 10.1021/acs.est.8b04707. [Epub ahead of print]


Genome-Wide Association Analyses in the Model Rhizobium Ensifer meliloti.

Epstein B, Abou-Shanab RAI, Shamseldin A, Taylor MR, Guhlin J, Burghardt LT, Nelson M, Sadowsky MJ, Tiffin P.

mSphere. 2018 Oct 24;3(5). pii: e00386-18. doi: 10.1128/mSphere.00386-18.


Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies.

Staley C, Sadowsky MJ.

J Microbiol Methods. 2018 Nov;154:14-18. doi: 10.1016/j.mimet.2018.09.020. Epub 2018 Oct 1. Review.


Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation.

Staley C, Kaiser T, Vaughn BP, Graiziger CT, Hamilton MJ, Rehman TU, Song K, Khoruts A, Sadowsky MJ.

Microbiome. 2018 Sep 18;6(1):166. doi: 10.1186/s40168-018-0549-6.


Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF.

Dale JL, Beckman KB, Willett JLE, Nilson JL, Palani NP, Baller JA, Hauge A, Gohl DM, Erickson R, Manias DA, Sadowsky MJ, Dunny GM.

mSystems. 2018 Sep 11;3(5). pii: e00062-18. doi: 10.1128/mSystems.00062-18. eCollection 2018 Sep-Oct.


Spatial and temporal characterization of epiphytic microbial communities associated with Eurasian watermilfoil: a highly invasive macrophyte in North America.

Mathai PP, Dunn HM, Magnone P, Brown CM, Chun CL, Sadowsky MJ.

FEMS Microbiol Ecol. 2018 Nov 1;94(12). doi: 10.1093/femsec/fiy178.


CLOUD: a non-parametric detection test for microbiome outliers.

Montassier E, Al-Ghalith GA, Hillmann B, Viskocil K, Kabage AJ, McKinlay CE, Sadowsky MJ, Khoruts A, Knights D.

Microbiome. 2018 Aug 6;6(1):137. doi: 10.1186/s40168-018-0514-4.


Corrigendum to "Precipitation influences pathogenic bacteria and antibiotic resistance genes abundance in storm drain outfalls in coastal sub-tropical waters" [Environ. Int. 116 (2018) 308-318].

Ahmed W, Zhang Q, Lobos A, Senkbeil J, Sadowsky MJ, Harwood VJ, Saeidi N, Marinoni O, Ishii S.

Environ Int. 2018 Oct;119:239. doi: 10.1016/j.envint.2018.06.031. Epub 2018 Jul 4. No abstract available.


Decay of sewage-associated bacterial communities in fresh and marine environmental waters and sediment.

Ahmed W, Staley C, Kaiser T, Sadowsky MJ, Kozak S, Beale D, Simpson S.

Appl Microbiol Biotechnol. 2018 Aug;102(16):7159-7170. doi: 10.1007/s00253-018-9112-4. Epub 2018 Jun 5.


Fecal pollution: new trends and challenges in microbial source tracking using next-generation sequencing.

Unno T, Staley C, Brown CM, Han D, Sadowsky MJ, Hur HG.

Environ Microbiol. 2018 Sep;20(9):3132-3140. doi: 10.1111/1462-2920.14281. Epub 2018 Aug 5. Review.


Quantitative microbial risk assessment of microbial source tracking markers in recreational water contaminated with fresh untreated and secondary treated sewage.

Ahmed W, Hamilton KA, Lobos A, Hughes B, Staley C, Sadowsky MJ, Harwood VJ.

Environ Int. 2018 Aug;117:243-249. doi: 10.1016/j.envint.2018.05.012. Epub 2018 May 15.


Precipitation influences pathogenic bacteria and antibiotic resistance gene abundance in storm drain outfalls in coastal sub-tropical waters.

Ahmed W, Zhang Q, Lobos A, Senkbeil J, Sadowsky MJ, Harwood VJ, Saeidi N, Marinoni O, Ishii S.

Environ Int. 2018 Jul;116:308-318. doi: 10.1016/j.envint.2018.04.005. Epub 2018 May 10. Erratum in: Environ Int. 2018 Oct;119:239.


Seasonal metabolic analysis of marine sediments collected from Moreton Bay in South East Queensland, Australia, using a multi-omics-based approach.

Beale DJ, Crosswell J, Karpe AV, Metcalfe SS, Morrison PD, Staley C, Ahmed W, Sadowsky MJ, Palombo EA, Steven ADL.

Sci Total Environ. 2018 Aug 1;631-632:1328-1341. doi: 10.1016/j.scitotenv.2018.03.106. Epub 2018 Mar 28.


Complete Genome Sequence of Sinorhizobium meliloti Bacteriophage HMSP1-Susan.

Fleagle B, Imamovic A, Toledo S, Couves M, Jensen A, Vang M, Steevens A, Young ND, Sadowsky MJ, Martinez-Vaz BM.

Genome Announc. 2018 May 3;6(18). pii: e01450-17. doi: 10.1128/genomeA.01450-17.


Bacillus megaterium strains derived from water and soil exhibit differential responses to the herbicide mesotrione.

Dobrzanski T, Gravina F, Steckling B, Olchanheski LR, Sprenger RF, Espírito Santo BC, Galvão CW, Reche PM, Prestes RA, Pileggi SAV, Campos FR, Azevedo RA, Sadowsky MJ, Beltrame FL, Pileggi M.

PLoS One. 2018 Apr 25;13(4):e0196166. doi: 10.1371/journal.pone.0196166. eCollection 2018.


The complete replicons of 16 Ensifer meliloti strains offer insights into intra- and inter-replicon gene transfer, transposon-associated loci, and repeat elements.

Nelson M, Guhlin J, Epstein B, Tiffin P, Sadowsky MJ.

Microb Genom. 2018 Apr 19. doi: 10.1099/mgen.0.000174. [Epub ahead of print]


Urea Amendment Decreases Microbial Diversity and Selects for Specific Nitrifying Strains in Eight Contrasting Agricultural Soils.

Staley C, Breuillin-Sessoms F, Wang P, Kaiser T, Venterea RT, Sadowsky MJ.

Front Microbiol. 2018 Apr 4;9:634. doi: 10.3389/fmicb.2018.00634. eCollection 2018.


Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice.

Le Bastard Q, Ward T, Sidiropoulos D, Hillmann BM, Chun CL, Sadowsky MJ, Knights D, Montassier E.

Sci Rep. 2018 Apr 18;8(1):6219. doi: 10.1038/s41598-018-24342-x.


Comparisons of bacterial and archaeal communities in the rumen and a dual-flow continuous culture fermentation system using amplicon sequencing.

Salfer IJ, Staley C, Johnson HE, Sadowsky MJ, Stern MD.

J Anim Sci. 2018 Apr 3;96(3):1059-1072. doi: 10.1093/jas/skx056.


Antibiotic-induced Disruption of Intestinal Microbiota Contributes to Failure of Vertical Sleeve Gastrectomy.

Jahansouz C, Staley C, Kizy S, Xu H, Hertzel AV, Coryell J, Singroy S, Hamilton M, DuRand M, Bernlohr DA, Sadowsky MJ, Khoruts A, Ikramuddin S.

Ann Surg. 2018 Mar 8. doi: 10.1097/SLA.0000000000002729. [Epub ahead of print]


Application of SourceTracker for Accurate Identification of Fecal Pollution in Recreational Freshwater: A Double-Blinded Study.

Staley C, Kaiser T, Lobos A, Ahmed W, Harwood VJ, Brown CM, Sadowsky MJ.

Environ Sci Technol. 2018 Apr 3;52(7):4207-4217. doi: 10.1021/acs.est.7b05401. Epub 2018 Mar 13.


Current understanding of microbiota- and dietary-therapies for treating inflammatory bowel disease.

Eom T, Kim YS, Choi CH, Sadowsky MJ, Unno T.

J Microbiol. 2018 Mar;56(3):189-198. doi: 10.1007/s12275-018-8049-8. Epub 2018 Feb 28. Review.


Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments.

Burghardt LT, Epstein B, Guhlin J, Nelson MS, Taylor MR, Young ND, Sadowsky MJ, Tiffin P.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2425-2430. doi: 10.1073/pnas.1714246115. Epub 2018 Feb 16.


Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation.

Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, Sadowsky MJ, Allegretti JR, Smith MB, Xavier RJ, Alm EJ.

Cell Host Microbe. 2018 Feb 14;23(2):229-240.e5. doi: 10.1016/j.chom.2018.01.003.


Increased Denitrification Rates Associated with Shifts in Prokaryotic Community Composition Caused by Varying Hydrologic Connectivity.

Tomasek A, Staley C, Wang P, Kaiser T, Lurndahl N, Kozarek JL, Hondzo M, Sadowsky MJ.

Front Microbiol. 2017 Nov 22;8:2304. doi: 10.3389/fmicb.2017.02304. eCollection 2017.


Contemporary Applications of Fecal Microbiota Transplantation to Treat Intestinal Diseases in Humans.

Staley C, Khoruts A, Sadowsky MJ.

Arch Med Res. 2017 Nov;48(8):766-773. doi: 10.1016/j.arcmed.2017.11.006. Epub 2017 Nov 26. Review.


Genes and Gut Bacteria Involved in Luminal Butyrate Reduction Caused by Diet and Loperamide.

Hwang N, Eom T, Gupta SK, Jeong SY, Jeong DY, Kim YS, Lee JH, Sadowsky MJ, Unno T.

Genes (Basel). 2017 Nov 28;8(12). pii: E350. doi: 10.3390/genes8120350.


Effect of Different Treatment Technologies on the Fate of Antibiotic Resistance Genes and Class 1 Integrons when Residual Municipal Wastewater Solids are Applied to Soil.

Burch TR, Sadowsky MJ, LaPara TM.

Environ Sci Technol. 2017 Dec 19;51(24):14225-14232. doi: 10.1021/acs.est.7b04760. Epub 2017 Nov 28.


Phylogenetic Backgrounds and Virulence-Associated Traits of Escherichia coli Isolates from Surface Waters and Diverse Animals in Minnesota and Wisconsin.

Johnson JR, Johnston BD, Delavari P, Thuras P, Clabots C, Sadowsky MJ.

Appl Environ Microbiol. 2017 Dec 1;83(24). pii: e01329-17. doi: 10.1128/AEM.01329-17. Print 2017 Dec 15.


Optimization of conditions for decolorization of azo-based textile dyes by multiple fungal species.

Abd El-Rahim WM, Moawad H, Abdel Azeiz AZ, Sadowsky MJ.

J Biotechnol. 2017 Oct 20;260:11-17. doi: 10.1016/j.jbiotec.2017.08.022. Epub 2017 Aug 30.


Transcriptomic basis of genome by genome variation in a legume-rhizobia mutualism.

Burghardt LT, Guhlin J, Chun CL, Liu J, Sadowsky MJ, Stupar RM, Young ND, Tiffin P.

Mol Ecol. 2017 Nov;26(21):6122-6135. doi: 10.1111/mec.14285. Epub 2017 Sep 5.


Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula.

Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J.

BMC Genomics. 2017 Aug 4;18(1):578. doi: 10.1186/s12864-017-3971-4.


A multi-omics based ecological analysis of coastal marine sediments from Gladstone, in Australia's Central Queensland, and Heron Island, a nearby fringing platform reef.

Beale DJ, Crosswell J, Karpe AV, Ahmed W, Williams M, Morrison PD, Metcalfe S, Staley C, Sadowsky MJ, Palombo EA, Steven ADL.

Sci Total Environ. 2017 Dec 31;609:842-853. doi: 10.1016/j.scitotenv.2017.07.184. Epub 2017 Jul 30.


Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning.

Staley C, Kaiser T, Beura LK, Hamilton MJ, Weingarden AR, Bobr A, Kang J, Masopust D, Sadowsky MJ, Khoruts A.

Microbiome. 2017 Aug 1;5(1):87. doi: 10.1186/s40168-017-0306-2.


Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism.

Staley C, Ferrieri AP, Tfaily MM, Cui Y, Chu RK, Wang P, Shaw JB, Ansong CK, Brewer H, Norbeck AD, Markillie M, do Amaral F, Tuleski T, Pellizzaro T, Agtuca B, Ferrieri R, Tringe SG, Paša-Tolić L, Stacey G, Sadowsky MJ.

Microbiome. 2017 Jun 24;5(1):65. doi: 10.1186/s40168-017-0287-1.


A High-Throughput DNA-Sequencing Approach for Determining Sources of Fecal Bacteria in a Lake Superior Estuary.

Brown CM, Staley C, Wang P, Dalzell B, Chun CL, Sadowsky MJ.

Environ Sci Technol. 2017 Aug 1;51(15):8263-8271. doi: 10.1021/acs.est.7b01353. Epub 2017 Jul 10.


Novel Microbial Assemblages Dominate Weathered Sulfide-Bearing Rock from Copper-Nickel Deposits in the Duluth Complex, Minnesota, USA.

Jones DS, Lapakko KA, Wenz ZJ, Olson MC, Roepke EW, Sadowsky MJ, Novak PJ, Bailey JV.

Appl Environ Microbiol. 2017 Aug 1;83(16). pii: e00909-17. doi: 10.1128/AEM.00909-17. Print 2017 Aug 15.


Factors influencing the Salmonella internalization into seedpods and whole plants of Arachis hypogaea (L.).

Rossbach JD, Fink RC, Sadowsky MJ, Tong C, Diez-Gonzalez F.

Food Microbiol. 2017 Sep;66:184-189. doi: 10.1016/ Epub 2017 May 10.


Synthesis and Biological Evaluation of Bile Acid Analogues Inhibitory to Clostridium difficile Spore Germination.

Stoltz KL, Erickson R, Staley C, Weingarden AR, Romens E, Steer CJ, Khoruts A, Sadowsky MJ, Dosa PI.

J Med Chem. 2017 Apr 27;60(8):3451-3471. doi: 10.1021/acs.jmedchem.7b00295. Epub 2017 Apr 12.


Environmental Escherichia coli: ecology and public health implications-a review.

Jang J, Hur HG, Sadowsky MJ, Byappanahalli MN, Yan T, Ishii S.

J Appl Microbiol. 2017 Sep;123(3):570-581. doi: 10.1111/jam.13468. Epub 2017 Jul 3. Review.


Differential Impacts of Land-Based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs.

Staley C, Kaiser T, Gidley ML, Enochs IC, Jones PR, Goodwin KD, Sinigalliano CD, Sadowsky MJ, Chun CL.

Appl Environ Microbiol. 2017 May 1;83(10). pii: e03378-16. doi: 10.1128/AEM.03378-16. Print 2017 May 15.


A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System.

Beale DJ, Karpe AV, Ahmed W, Cook S, Morrison PD, Staley C, Sadowsky MJ, Palombo EA.

Int J Environ Res Public Health. 2017 Mar 14;14(3). pii: E303. doi: 10.3390/ijerph14030303.


Community dynamics drive punctuated engraftment of the fecal microbiome following transplantation using freeze-dried, encapsulated fecal microbiota.

Staley C, Vaughn BP, Graiziger CT, Singroy S, Hamilton MJ, Yao D, Chen C, Khoruts A, Sadowsky MJ.

Gut Microbes. 2017 May 4;8(3):276-288. doi: 10.1080/19490976.2017.1299310. Epub 2017 Feb 28.


Sleeve gastrectomy drives persistent shifts in the gut microbiome.

Jahansouz C, Staley C, Bernlohr DA, Sadowsky MJ, Khoruts A, Ikramuddin S.

Surg Obes Relat Dis. 2017 Jun;13(6):916-924. doi: 10.1016/j.soard.2017.01.003. Epub 2017 Jan 4.


Successful Resolution of Recurrent Clostridium difficile Infection using Freeze-Dried, Encapsulated Fecal Microbiota; Pragmatic Cohort Study.

Staley C, Hamilton MJ, Vaughn BP, Graiziger CT, Newman KM, Kabage AJ, Sadowsky MJ, Khoruts A.

Am J Gastroenterol. 2017 Jun;112(6):940-947. doi: 10.1038/ajg.2017.6. Epub 2017 Feb 14.

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