Publications & Patents by Year

Last Updated in August of 2017.


  • Aura Ontiveros-Valencia; Chen Zhou, Ph.D.; Zehra  E Ilhan; Louis C de Saint Cyr; Rosa  Krajmalnik-Brown; Bruce E Rittmann. “Total electron acceptor loading and composition affect hexavalent uranium reduction and microbial community structure in a Membrane Biofilm Reactor.” Water Research, 2017, 125, 341 - 349.
  • YenJung S. L., Ontiveros-Valencia A., Ilhan Z.E., Zhou Y, Miranda E., Maldonado J., Krajmalnik-Brown R, and B. E Rittmann. 2017 “Enhancing biodegradation of C16-alkyl quaternary ammonium compounds using an oxygen-based Membrane Biofilm Reactor”. Water Research 123, 825-833.
  • Esquivel-Elizondo, S. V., Garcia-Pena, E. I., Ilhan, Z. E., Kang, D.-W., and Krajmalnik-Brown, R. “Insights into butyrate production in a controlled fermentation system via gene predictions” msystems, mSystems 2:e00051-17.
  • Sofia Esquivel-Elizondo, Anca G. Delgado, and Rosa Krajmalnik-Brown*. 2017 “Evolution of microbial communities growing with carbon monoxide, hydrogen and carbon dioxide”. FEMS Microbiology Ecology, 93 (6). doi: 10.1093/femsec/fix076
  • Ilhan ZE, DiBaise J.K, Isern N.G, Hoyt D.W, Marcus AK, Kang D-W, Crowell M.D, Rittmann B.E, and R Krajmalnik-Brown*. “Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding”. 2017 ISME Journal (Nature group), doi:10.1038/ismej.2017.71
  • Ilhan ZE, Marcus AK, Kang D-W, Rittmann BE, Krajmalnik-Brown* ”pH-mediated microbial and metabolic interactions in fecal enrichment cultures” msphere, 2:3 e00047-17
  • Chen, T., A. G. Delgado, B. M. Yavuz, J. Maldonado, Y. Zuo, R. Kamath, P. Westerhoff, R. Krajmalnik-Brown and B. E. Rittmann*. 2017. “Interpreting the interaction between ozone and residual petroleum hydrocarbons in soil”. Environmental Science & Technology, 51(1): 506-513 
  • Dae-Wook Kang, James B. Adams, Ann C. Gregory, Thomas Borody, Lauren Chittick, Alessio Fasano, Alexander Khoruts, Elizabeth Geis, Juan Maldonado, Sharon McDonough-Means, Elena L. Pollard, Simon Roux, Michael J. Sadowsky, Karen Schwarzberg Lipson, Matthew B. SullivanEmail author, J. Gregory CaporasoEmail author and Rosa Krajmalnik-Brown. MicrobiotaTransfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study.  Microbiome 2017 5:10 ​


  • Timothy R. Sampson, Justine W. Debelius, Taren Thron, Stefan Janssen, Gauri G. Shastri, Zehra Esra Ilhan, Collin Challis, Catherine E. Schretter, Sandra Rocha, Viviana Gradinaru, Marie-Francoise Chesselet, Ali Keshavarzian, Kathleen M. Shannon, Rosa Krajmalnik-Brown, Pernilla Wittung-Stafshede, Rob Knight, and Sarkis K. Mazmanian "Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease" Cell Volume 167 , Issue 6 , 1469 - 1480.e12
  • ​Sofia Esquivel-Elizondo, Prathap Parameswaran, Anga G. Delgado,  Juan Maldonado, Bruce E. Rittmann and Rosa Krajmalnik-Brown. 2016. "Archaea and Bacteria acclimate to high total ammonia in a methanogenic reactor treating swine waste". Archaea
  • Delgado AG, Fajardo-Williams D, Kegerreis KL, Parameswaran P, Krajmalnik-Brown R. 2016. Impact of ammonium on syntrophic organohalide-respiring and fermenting microbial communities. mSphere 10.1128/mSphere.00053-16.
  • Chen Zhou, Aura Ontiveros-Valencia, Zhao Cheng Wang,  Juan Maldonado, He-Ping Zhao, Rosa Krajmalnik-Brown, and Bruce E. Rittmann. 2016 “Palladium recovery in a H2-based membrane biofilm reactor:  formation of Pd(0) nanoparticles through enzymatic and autocatalytic reductions”. Environmental Science and Technology.
  • Aura Ontiveros-Valencia, Ryan Penton, Rosa Krajmalnik-Brown, Bruce E. Rittman. 2016 “Hydrogen-fed biofilm reactors reducing selenate and sulfate: community structure and location of elemental selenium within the biofilm” Biotechnology and Bioengineering. In press
  • Alexander S. Zevin, Bruce E. Rittmann, Rosa Krajmalnik-Brown. 2016 “The source of inoculum drives bacterial community structure in Synechocystis sp. PCC6803-based photobioreactors” Algal Research-Biomass Biofuels and Bioproducts13:109-115.


  • Richard E. Frye, John Slattery, Derrick F. MacFabe, Emma Allen-Vercoe, William Parker, John Rodakis, James B. Adams, Rosa Krajmalnik-Brown, Ellen Bolte, Stephen Kahler, Jana Jennings, Jill James, Carl E. Cerniglia, and Tore Midtvedt. 2015 “Approaches to studying and manipulating the enteric microbiome to improve autism symptoms” Microbial Ecology in Health and Disease26
  • Zevin, A.S., Nam, T.G., Rittmann, B.E., Krajmalnik-Brown, R.  2015. “Effects of phosphate limitation on soluble microbial products and microbial community structure in semi-continuous Synechocystis-based photobioreactors”Biotechnology and Bioengineering In Press
  • Krajmalnik-Brown R, Lozupone C, Kang D-W, Adams J.B. 2015. "Gut bacteria in children with Autism Spectrum Disorders: Challenges and promise of studying how complex community influences a complex disease. Microbial Ecology in Health and Disease 2015, 26: 26914
  • Badalamenti J, Torres CI, Krajmalnik-Brown R and Bond D. 2015 “Genomes of Geoalkalibacter ferrihydriticus Z-0531T and Geoalkalibacter subterraneus Red1T, two haloalkaliphilic metal-reducing Deltaproteobacteria" Genome Announcements, 3 (2).
  • Kang D-W, DiBaise JK, Ilhan ZE, Crowell MD, Rideout JR, Caporaso JR, Rittmann BE, Krajmalnik-Brown R. 2015. Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone, Anaerobe. 33: 33-41.


  • Kim, S., Krajmalnik-Brown, R. and Chung, J. 2014 “Remediation of Petroleum Hydrocarbon-Contaminated Sites by DNA Diagnosis-Based Bioslurping Technology” Science of the Total Environment. 497: 250-259
  • Zhou C,  Ontiveros-Valencia A, Cornette de Saint L,  Zevin AS,  Carey SA,  Krajmalnik-Brown R and Bruce E. Rittmann. 2014  “Uranium removal and microbial community in a H2-based membrane biofilm reactor:” Water Research. 64: 255-264        
  • Miceli JF III, Garcia-Peña I, Parameswaran P, Torres CI, Krajmalnik-Brown R. 2014. Combining microbial cultures for the efficient production of electricity from butyrate in a microbial electrochemical cell.  Bioresource Technology 169:169-174.
  • Delgado AG, Kang D-W, Nelson KG, Fajardo-Williams D, Miceli JF III, Done HY, Popat SC, Krajmalnik-Brown R. 2014. Selective enrichment yields robust ethene-producing dechlorinating cultures from microcosms stalled at cis-dichloroethene. PLoS ONE 9(6): e100654. doi:10.1371/journal.pone.0100654.
  • Ontiveros-Valencia A,Tang Y, Zhao, H-P,Friese D, Overstreet R, Smith J, Evans P, Rittmann BE, Krajmalnik-Brown R. in press. Pyrosequencing analysis yields comprehensive assessment of microbial communities in pilot-scale two-stage membrane biofilm reactors. Environmental Science & Technology. DOI: 10.1021/es5012466.
  • Ruiz V, Ilhan ZE, Kang D-W, Krajmalnik-Brown R, Buitrón G. 2014The source of inoculum plays a defining role in the development of MEC microbial consortia fed with acetic and propionic acid mixtures. Journal of Biotechnology 182-183:11-18.
  • Ontiveros-Valencia A, Tang Y, Krajmalnik-Brown R, Rittmann BE. in press. Managing the interactions between sulfate- and perchlorate-reducing bacteria when using hydrogen-fed biofilms to treat a groundwater with a high perchlorate concentration. Water Research.
  • Ekre, R., P.C. Johnson, B.E. Rittmann, and R. Krajmalnik-Brown. 2014. Method for Assessing Source Zone Natural Attenuation at Chlorinated Aliphatic Spill Sites. Groundwater Monitoring & Remediation 34(2):60-70.
  • Zhao H-P, Ontiveros-Valencia A, Tang Y, Kim B-O, VanGinkel S, Friese D, Overstreet R, Smith J, Evans PJ, Krajmalnik-Brown R, Rittmann BE. 2014. Removal of multiple electron acceptors by pilot-scale, two-stage membrane biofilm reactors. Water Research 54:115-122.
  • Delgado AG, Fajardo-Williams D, Popat SC, Torres CI, Krajmalnik-Brown R. 2014. Successful operation of continuous reactors at short retention times results in fast-rate, high-density Dehalococcoides dechlorinating cultures. Applied Microbiology and Biotechnology 98(6):2729-2737. pdf
  • Badalamenti JP, Torres CI and K

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