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Project Publications: Michigan State University: Research Support Core B: Environmental Molecular Analysis Core

Superfund Research Program

Research Support Core B: Environmental Molecular Analysis Core

Project Leader: James M. Tiedje
Grant Number: P42ES004911
Funding Period: 2006-2021

Project-Specific Links




  • Chai B, Tsoi TV, Sallach JB, Liu C, Landgraf J, Bezdek M, Zylstra GJ, Li H, Johnston CT, Teppen BJ, Cole JR, Boyd SA, Tiedje JM. 2020. Bioavailability of clay-adsorbed dioxin to Sphingomonas wittichii RW1 and its associated genome-wide shifts in gene expression. Sci Total Environ 712:135525. doi:10.1016/j.scitotenv.2019.135525 PMID:32050392



  • Stedtfeld RD, Guo X, Stedtfeld TM, Sheng H, Williams MR, Hauschild K, Gunturu S, Tift L, Wang F, Howe A, Chai B, Yin D, Cole JR, Tiedje JM, Hashsham SA. 2018. Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements. FEMS Microbiol Ecol 94(9):8. doi:10.1093/femsec/fiy130 PMID:52926
  • Zhang Y, Boyd SA, Teppen BJ, Tiedje JM, Zhang W, Zhu D, Li H. 2018. Bioavailability of tetracycline to antibiotic resistant Escherichia coli in water-clay systems. Environ Pollut 243(PtB):1078-1086. doi:10.1016/j.envpol.2018.09.059 PMID:30253298


  • Jagannathan L, Jose CC, Tanwar VS, Bhattacharya S, Cuddapah S. 2017. Identification of a unique gene expression signature in mercury and 2,3,7,8-tetrachlorodibenzo-p-dioxin co-exposed cells. Toxicol Res (Camb) 6(3):312-323. doi:10.1039/C6TX00432F PMID:29057067 PMCID:PMC5648359
  • Stedtfeld RD, Chai B, Crawford RB, Stedtfeld TM, Williams MR, Xiangwen S, Kuwahara T, Cole JR, Kaminski NE, Tiedje JM, Hashsham SA. 2017. Modulatory influence of segmented filamentous bacteria on transcriptomic response of gnotobiotic mice exposed to TCDD. Front Microbiol 8:12. doi:10.3389/fmicb.2017.01708 PMID:28936204 PMCID:PMC5594080
  • Stedtfeld RD, Sallach JB, Crawford RB, Stedtfeld TM, Williams MR, Waseem H, Johnston CT, Li H, Teppen BJ, Kaminski NE, Boyd SA, Tiedje JM, Hashsham SA. 2017. TCDD administered on activated carbon eliminates bioavailability and subsequent shifts to a key murine gut commensal. Appl Microbiol Biotechnol 101:7409-7415. doi:10.1007/s00253-017-8460-9 PMID:28812142
  • Stedtfeld RD, Stedtfeld TM, Fader KA, Williams MR, Bhaduri P, Quensen JF, Zacharewski TR, Tiedje JM, Hashsham SA. 2017. TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome. FEMS Microbiol Ecol 93:8. doi:10.1093/femsec/fix058 PMID:28475713 PMCID:PMC5458050
  • Stedtfeld RD, Stedtfeld TM, Waseem H, Fitschen-Brown M, Guo X, Chai B, Williams MR, Shook T, Logan A, Graham A, Chae J, Sul WJ, VanHouten J, Cole JR, Zylstra GJ, Tiedje JM, Upham BL, Hashsham SA. 2017. Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers. J Environ Manage 198:213-220. doi:10.1016/j.jenvman.2017.04.079 PMID:28460328
  • Waseem H, Williams MR, Stedtfeld TM, Chai B, Stedtfeld RD, Cole JR, Tiedje JM, Hashsham SA. 2017. Virulence factor activity relationships (VFARs): a bioinformatics perspective. Environ Sci Process Impacts 19(3):247-260. doi:10.1039/c6em00689b PMID:28261716 PMCID:PMC5897045
  • Williams MR, Stedtfeld RD, Stedtfeld TM, Tiedje JM, Hashsham SA. 2017. Quantification of microRNAs directly from body fluids using a base-stacking isothermal amplification method in a point-of-care device. Biomed Microdevices 19:45. doi:10.1007/s10544-017-0191-2 PMID:28536858
  • Williams MR, Stedtfeld RD, Tiedje JM, Hashsham SA. 2017. MicroRNAs-based inter-domain communication between the host and members of the gut microbiome. Front Microbiol 8:10. doi:10.3389/fmicb.2017.01896 PMID:29021788 PMCID:PMC5624305
  • Williams MR, Stedtfeld RD, Waseem H, Stedtfeld TM, Upham BL, Khalife WT, Etchebarne B, Hughes M, Tiedje JM, Hashsham SA. 2017. Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices. Analytical Methods 9:1229-1241. doi:10.1039/C6AY03405E PMID:29657581 PMCID:PMC5898395


  • Chai B, Tsoi TV, Iwai S, Liu C, Fish JA, Gu C, Johnson TA, Zylstra GJ, Teppen BJ, Li H, Hashsham SA, Boyd SA, Cole JR, Tiedje JM. 2016. Sphingomonas wittichii strain RW1 genome-wide gene expression shifts in response to dioxins and clay. PLoS One 11(6):e0157008. doi:10.1371/journal.pone.0157008 PMID:27309357 PMCID:PMC4911050
  • Stedtfeld RD, Williams M, Fakher U, Johnson TA, Stedtfeld TM, Wang F, Khalife WT, Hughes M, Etchebarne B, Tiedje JM, Hashsham SA. 2016. Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol Ecol 92(3):doi:10.1093/femsec/fiw020 PMID:26850162
  • Wang F, Stedtfeld RD, Kim O, Chai B, Yang L, Stedtfeld TM, Hong SG, Kim D, Lim HS, Hashsham SA, Tiedje JM, Sul WJ. 2016. Influence of soil characteristics and proximity to Antarctic research stations on abundance of antibiotic resistance genes in soils. Environ Sci Technol 50(23):12621-12629. doi:10.1021/acs.est.6b02863 PMID:27797533


  • Stedtfeld RD, Liu Y, Stedtfeld TM, Kostic T, Kronlein M, Srivannavit O, Khalife WT, Tiedje JM, Gulari E, Hughes M, Etchebarne B, Hashsham SA. 2015. Static self-directed sample dispensing into a series of reaction wells on a microfluidic card for parallel genetic detection of microbial pathogens. Biomed Microdevices 17(5):89. doi:10.1007/s10544-015-9994-1 PMID:26260693 PMCID:PMC4531140
  • Wang Q, Fish JA, Gilman M, Sun Y, Brown C, Tiedje JM, Cole JR. 2015. Xander: employing a novel method for efficient gene-targeted metagenomic assembly. Microbiome 3:32. doi:10.1186/s40168-015-0093-6 PMID:26246894 PMCID:PMC4526283





  • Yoo M, Zylstra GJ, Kim D, Kang BS, Kim E. 2011. Biphenyl hydroxylation enhanced by an engineered o-xylene dioxygenase from Rhodococcus sp strain DK17. Res Microbiol 162:724-728. doi:10.1016/j.resmic.2011.04.013 PMID:21575716


  • Chang H, Zylstra GJ. 2010. Xanthomonads. In: Handbook of Hydrocarbon and Lipid Microbiology. Springer Verlag GmbH, Heidelberg, Germany. pp.1805-1811.
  • Iwai S, Chai B, Sul WJ, Cole JR, Hashsham SA, Tiedje JM. 2010. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. ISME J 4(2):279-285. doi:10.1038/ismej.2009.104 PMID:19776767 PMCID:PMC2808446
  • Ni Chadhain SM, Zylstra GJ. 2010. Functional Gene Diversity, Biogeography, and Dynamics. In: Handbook of Hydrocarbon and Lipid Microbiology. Springer Verlag GmbH, Heidelberg, Germany. pp.2413-2422.
  • Parnell JJ, Denef VJ, Park J, Tsoi TV, Tiedje JM. 2010. Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400. Biodegradation 21(1):147-156. doi:10.1007/s10532-009-9289-4 PMID:19672561


  • Schuler L, Jouanneau Y, Ni Chadhain SM, Meyer C, Pouli M, Zylstra GJ, Hols P, Agathos SN. 2009. Characterization of a ring-hydroxylating dioxygenase from phenanthrene-degrading Sphingomonas sp strain LH128 able to oxidize benz[a]anthracene. Appl Microbiol Biotechnol 83(3):465-475. doi:10.1007/s00253-009-1858-2 PMID:19172265
  • Sul WJ, Park J, Quensen JF, Rodrigues JM, Seliger L, Tsoi TV, Zylstra GJ, Tiedje JM. 2009. DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Appl Environ Microbiol 75(17):5501-5506. doi:10.1128/AEM.00121-09 PMID:19648381 PMCID:PMC2737913


  • Schuler L, Ni Chadhain SM, Jouanneau Y, Meyer C, Zylstra GJ, Hols P, Agathos SN. 2008. Characterization of a novel angular dioxygenase from fluorene-degrading Sphingomonas sp strain LB126. Appl Environ Microbiol 74(4):1050-1057. doi:10.1128/AEM.01627-07 PMID:18156320 PMCID:PMC2258591
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