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  1. Zehra Esra Ilhan*, John K. DiBaise, Sydney E. Dautel, Nancy G. Isern, Young-Mo Kim, David W. Hoyt, Athena A. Schepmoes, Heather M. Brewer, Karl K. Weitz, Thomas O. Metz, Michael D. Crowell, Dae-Wook Kangx, Bruce E. Rittmann & Rosa Krajmalnik-Brown* 2020 “Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery” npj biofilms and microbiomes 6:12.

  2. Jordan R Yaron, Sriram Ambadapadi, Liqiang Zhang, Ramani N Chavan, Scott A Tibbetts, Shahar Keinan, Arvind Varsani, Juan MaldonadoX, Simona Kraberger, Amanda M Tafoya, Whitney L Bullard, Jacquelyn Kilbourne, Alison Stern-Harbutte, Rosa Krajmalnik-Brown, Barbara H Munk, Erling O Koppang, Efrem S Lim, Alexandra R Lucas. 2020. “Immune protection is dependent on the gut microbiome in a lethal mouse gammaherpesviral infection” Scientific Reports, 2371 (2020).

  3. Yuqiang Bi, Andrew K Marcus, Hervé Robert, Rosa Krajmalnik-Brown, Bruce E Rittmann, Paul Westerhoff, Marie-Hélène Ropers, Muriel Mercier-Bonin. 2020. “The complex puzzle of dietary silver nanoparticles, mucus and microbiota in the gut” Journal of Toxicology and Environmental Health, Part B. (1)1-21. Jan 2020.

  4. Daniel Gutierrez, Anthony Weinstock, Vijay C Antharam, Haiwei Gu, Paniz Jasbi, Xiaojian Shi, Blake Dirks, Rosa Krajmalnik-Brown, Juan Maldonadox, Jack Guinan, Shankar Thangamani. 2020. “Antibiotic-induced gut metabolome and microbiome alterations increase the susceptibility to Candida albicans colonization in the gastrointestinal tract”. FEMS microbiology ecology. Jan 1;96(1)

  5. Boya Wang, Rosa Krajmalnik-Brown, Chen Zhou, Yihao Luo, Bruce E. Rittmann, Youneng Tang. 2020. “Modeling Trichloroethene Reduction, Methanogenesis, and Homoacetogenesis in a H2-based Biofilm”. Journal of Environmental Engineering. 146:2


  1. Jim Adams, Thomas Borody, Daewook Kangx, Alexander Khoruts, Rosa Krajmalnik-Brown, Michael Sadowsky. 2019. “Microbiota Transplant Therapy and Autism: Lessons for the Clinic”. Expert Review of Gastroenterology & Hepatology. 13:11, 1033-1037.

  2. James B Adams, Troy Vargason, Dae-Wook Kangx, Rosa Krajmalnik-Brown, Juergen Hahn. 2019. “Multivariate Analysis of Plasma Metabolites in Children with Autism Spectrum Disorder and Gastrointestinal Symptoms Before and After MicrobiotaTransfer Therapy”. Processes.  7:11, 806.

  3. Tengfei Chen, Burcu M. Yavuz, Anca G. Delgadox, Brielle Januszewski, Yi Zuo, Paul Westerhoff, Rosa Krajmalnik-Brown, and Bruce E. Rittmann. 2019. “Multi-cycle Ozonation + Bioremediation for Soils Containing Residual Petroleum”. Environmental Engineering and Science, 36 (12), 1443-1451.

  4. Voth-Gaeddert, L.E.*; Torres, O.; Maldonadox, J.; Krajmalnik-Brown, R.; Rittmann, B.E.; Oerther, D.B. 2019. “Aflatoxin Exposure, Child Stunting, and Dysbiosis in the Intestinal Microbiome Among Children in Guatemala”. Environmental Engineering Science. ttps://

  5. Gil Sharon, Nikki Jamie Cruz, Dae-Wook Kangx, Michael J Gandal, Bo Wang, Young-Mo Kim, Erika M Zink, Cameron P Casey, Bryn C Taylor, Christianne J Lane, Lisa M Bramer, Nancy G Isern, David W Hoyt, Cecilia Noecker, Michael J Sweredoski, Annie Moradian, Elhanan Borenstein, Janet K Jansson, Rob Knight, Thomas O Metz, Carlos Lois, Daniel H Geschwind, Rosa Krajmalnik-Brown, Sarkis K Mazmanian. 2019 “Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice”. Cell, 177:6, 1600-1618.

  6. Dae-Wook Kangx, James B. Adams, Devon Coleman, Elena L. Pollard, Juan Maldonado,
    Sharon McDonough-Means, J. Gregory Caporaso, and Rosa Krajmalnik-Brown. 2019 "Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota" Scientific Reports, 9,5821 (2019).

  7. Krajmalnik-Brown. 2019 “A Fruitful Discovery: Can Gut Bacteria Control Hyperactive Behavior?”. Molecular Cell, 7-2-2019. DOI: 10.1016/j.molcel.2019.01.031

  8. Tomasz Kalinowski, Kristin McClellan, Thomas A Bruton; Rosa Krajmalnik-Brown, Erin M Driver, Rolf U Halden, 2019 “Autonomous Screening of Groundwater Remediation Technologies in the Subsurface Using the In Situ Microcosm Array (ISMA). Hazardous Materials. 367, 668-675.

  9. Levi Straka, Brendan Cahill, Juan MaldonadoX, Bruce Rittmann, Rosa Krajmalnik-Brown. 2019 “Effects of Light Intensity on Soluble Microbial Products Produced by Synechocystis sp. PCC 6803 and Associated Heterotrophic Communities” Algal Research. 38: 101409

  10. Chen Zhou, Aura Ontiveros-Valencia, Robert Nerenberg, Youneng Tang, David Friese, Rosa Krajmalnik-Brown, Bruce E Rittmann. 2019. “Hydrogenotrophic Microbial Reduction of Oxyanions with the Membrane Biofilm Reactor”.  Frontiers in Microbiology, 9:3268 doi:10.3389/fmicb.2018.03268


  1. Corrie M Whisner, Brandon Dente, Juan MaldonadoX, Rosa Krajmalnik-Brown, Meg Bruening. 2018. “Diet, physical activity and screen time but not body mass index are associated to the gut microbiome of a diverse cohort of college students living in university housing: A cross-sectional study”.  BMC Microbiology 2018 18:210.

  2. Yue Deng, Nai-Yuan Liu, Francis Tsow, Xiaojun Xian, Rosa Krajmalnik-Brown, Nongjian Tao *, Erica Forzani. 2018. “Tracking personal health-environment interaction with novel mobile sensing devices”. Sensors. 18 (8), 2670.

  3. Ontiveros-Valencia A, Zhou C, Zhao H-PX, Krajmalnik-Brown R, Tang Y, Rittmann BE. 2018. “Managing microbial communities in membrane biofilm reactors”. Applied Microbiology and Biotechnology, 1-12.

  4. Sofia Esquivel-Elizondo, Juan MaldonadoX, and Rosa Krajmalnik-Brown*. 2018. “Anaerobic carbon monoxide metabolism by Pleomorphomonas carboxyditropha sp. nov., a new mesophilic hydrogenogenic carboxydotroph”. FEMS Microbiology Ecology, 94, 2018. doi: 10.1093/femsec/fiy056.

  5. Tengfei Chen, Burcu M Yavuz, Anca G DelgadoX, Garrett Montoya, Delaney Van Winkle, Yi Zuo, Roopa Kamath, Paul Westerhoff, Rosa Krajmalnik-Brown, Bruce E Rittmann.  2018. “Impacts of Moisture Content during Ozonation of Soils Containing Residual Petroleum”. Journal of Hazardous Materials. 344: 1101–1108

  6. Esquivel-Elizondo, Sofia, Joseph Miceli III, Cesar I. Torres, and Krajmalnik-Brown, Rosa*. 2018. “Impact of carbon monoxide partial pressures on methanogenesis and medium chain fatty acids production during ethanol fermentation”. Biotechnology and Bioengineering.  115:341–350 DOI: 10.1002/bit.26471

  7. Dae-Wook KangX.; Zehra E Ilhan, Nancy G Isern; David W Hoyt, Ph.D.; Daniel P Howsmon; Michael Shaffer; Catherine A Lozupone, Ph.D.; Juergen Hahn, Ph.D.; James B Adams, Ph.D.; Rosa Krajmalnik-Brown*. 2018. “Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders”. Anaerobe. 49:121-131.


  1. Esquivel-Elizondo, Sofia, Delgado AncaX, Bruce E Rittmann, and Krajmalnik-Brown, Rosa*. 2017. “The effects of CO2 and H2 on CO metabolism by pure and mixed microbial cultures”.  Biotechnology for Biofuels, 10:220,

  2. Anca G. Delgado, Devyn Fajardo-Williams, Emily Bondank#, Sofia Esquivel-Elizondo, and Rosa Krajmalnik-Brown*. 2017. “Coupling bioflocculation of Dehalococcoides mccartyi to high-rate reductive dehalogenation of chlorinated ethenes”. Environmental Science and Technology, 51 (19), 11297-11307.

  3. Aura Ontiveros-Valencia; Chen Zhou, Ph.D.; Zehra  E Ilhan; Louis C de Saint Cyr; Rosa  Krajmalnik-Brown; Bruce E Rittmann. 2017, “Total electron acceptor loading and composition affect hexavalent uranium reduction and microbial community structure in a Membrane Biofilm Reactor.” Water Research, 125, 341-349.

  4. YenJung S. L., Ontiveros-Valencia A., Ilhan Z.E., Zhou Y, Miranda E., Maldonado JX., 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.

  5. Esquivel-Elizondo, S. V., E. I., Ilhan, Z. E., Garcia-Pena, and Krajmalnik-Brown, R*.  2017. “Insights into butyrate production in a controlled fermentation system via gene predictions” msystems, 2(4): e00051-17. DOI: 10.1128/mSystems.00051-17. 

  6. Sofia Esquivel-Elizondo, Anca G. DelgadoX, 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

  7. Ilhan ZE, DiBaise J.K, Isern N.G, Hoyt D.W, Marcus AK, Kang D-WX, Crowell M.D, Rittmann B.E, and R Krajmalnik-Brown*. 2017. “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

  8. Ilhan ZE, Marcus AK, Kang D-WX, Rittmann BE, Krajmalnik-Brown* 2017 ”pH-mediated microbial and metabolic interactions in fecal enrichment cultures” msphere, 2:3 e00047-17

  9. Kang, D. WX., J. B. Adams, A. C. Gregory, T. Borody, L. Chittick, A. Fasano, A. Khoruts, E. Geis, J. Maldonado, S. McDonough-Means, E. L. Pollard, S. Roux, M. J. Sadowsky, K. S. Lipson, M. B. Sullivan*, J. G. Caporaso* and R. Krajmalnik-Brown*. 2017. “Microbiota transfer alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study”. Microbiome 5:10. DOI: 10.1186/s40168-016-0225-7. 

  10. Chen, T., A. G. DelgadoX, B. M. Yavuz, J. MaldonadoX, 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 


  1. Sampson*, T. R., J. W. Debelius, T. Thron, S. Janssen, G. G. Shastri, Z. E. Ilhan, C. Challis, C. E. Schretter, S. Rocha, V. Gradinaru, M. F. Chesselet, A. Keshavarzian, K. M. Shannon, R. Krajmalnik-Brown, P. Wittung-Stafshede, R. Knight and S. K. Mazmanian*. 2016, “Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease”. Cell 167, 1469–1480

  2. Miceli J, Torres C.I. and R. Krajmalnik-Brown*. 2016 “Shifting the balance of fermentation products between hydrogen and volatile fatty acids: microbial community structure and function” FEMS Microbiology Ecology, 92(12): fiw195. DOI: 10.1093/femsec/fiw195.

  3. Esquivel-Elizondo S, Parameswaran P, Delgado AG, Maldonado JX, Rittmann BE, Krajmalnik-Brown R*.  2016.  Archaea and Bacteria acclimate to high total ammonia in a methanogenic reactor treating swine waste.  Archaea Special Issues on “To Cooperate or Compete? Archaea in Symbiosis”.

  4. Chen T, Delgado AGX, Yavuz BM Proctor A, Maldonado Ortiz JX, Zuo Y, Westerhoff P, Krajmalnik-Brown R, Rittmann BE*. 2016  “Ozone enhances the biodegradability of heavy hydrocarbons in soil” Journal of Environmental Engineering and Science.  11(1):7-17.

  5. Delgado AGX, Fajardo-Williams D, Kegerreis KL, Parameswaran P, Krajmalnik-Brown R*.  2016.  Impact of ammonium on syntrophic organohalide-respiring and fermenting microbial communities. mSphere 1(2):e00053-16.doi:10.1128/mSphere.00053-1.

  6. Zhou, C*., A. Ontiveros-Valencia, Z. Wang, J. MaldonadoX, H. P. Zhao, R. Krajmalnik-Brown and B. E. Rittmann. 2016 “Palladium recovery in a H2-based membrane biofilm reactor:  formation of Pd(0) nanoparticles through enzymatic and autocatalytic reductions” Environmental Science & Technology, 50(5): 2546-2555.

  7. Ontiveros-Valencia, A., C. R. Penton, R. Krajmalnik-Brown and B. E. Rittmann*, 2016. “Hydrogen-fed biofilm reactors reducing selenate and sulfate: community structure and location of elemental selenium within the biofilm” Biotechnology and Bioengineering. 113(8): 1736-1744.

  8. Zevin, A.S., Nam, T.G., Rittmann, B.E., Krajmalnik-Brown, R*.  2016 “The source of inoculum drives bacterial community structure in Synechocystis sp. PCC6803-based photobioreactors” Algal Research-Biomass Biofuels and Bioproducts, 13:109-115.


  1. Frye, R. E., J. Slattery, D. F. MacFabe, E. Allen-Vercoe, W. Parker, J. Rodakis, J. B. Adams, R. Krajmalnik-Brown, E. Bolte, S. Kahler, J. Jennings, J. James, C. E. Cerniglia and T. Midtvedt. 2015 “Approaches to studying and manipulating the enteric microbiome to improve autism symptoms” Microbial Ecology in Health and Disease. 26

  2. 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 112:9 1761-1769.

  3. Krajmalnik-Brown*, R., Louzopone C., Kang DWX, and J. Adams. 2015 “Gut bacteria in children with Autism Spectrum Disorders: Challenges and promise of studying how a complex community influences a complex disease” Microbial Ecology in health and Disease. 26 

  4. Badalamenti, J. P., R. Krajmalnik-Brown, C. I. Torres and D. R. Bond*. 2015 “Genomes of Geoalkalibacter ferrihydriticus Z-0531T and Geoalkalibacter subterraneus Red1T, two haloalkaliphilic metal-reducing Deltaproteobacteria" Genome Announcements, 3 (2).

  5. Kang, D. WX., J. K. DiBaise, Z. E. Ilhan, M. D. Crowell, J. R. Rideout, J. G. Caporaso, B. E. Rittmann and R. Krajmalnik-Brown. 2015* “Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone”  Anaerobe. 33:33-41.


  1. 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.

  2. Zhou, C., A. Ontiveros-Valencia, L. Cornette de Saint Cyr, A. S. Zevin, S. E. Carey, R. Krajmalnik-Brown and B. E. Rittmann*. 2014  “Uranium removal and microbial community in a H2-based membrane biofilm reactor:” Water Research. 64: 255-264.

  3. Ontiveros-Valencia, Aura; Tang, Youneng; Zhao, He-PingX; Friese, David; Overstreet, Ryan; Smith, Jennifer; Evans, Patrick; Rittmann, Bruce; Krajmalnik-Brown, Rosa*. 2014. "Pyrosequencing analysis yields comprehensive assessment of microbial communities in pilot two-stage Membrane Biofilm Reactors" Environmental Science & Technology, 48(13): 7511-7518. DOI: 10.1021/es5012466.

  4. Miceli, J. Garcia-Pena, E. I, Torres C.I., and Rosa Krajmalnik-Brown.* 2014 ”Combining Microbial Cultures for Efficient Production of Electricity from Butyrate in a Microbial Electrochemical Cell”  Bioresource Technology, Vol 169, page 169-174. DOI: 10.1016/j.biortech.2014.06.090.

  5. Delgado, Anca; Kang, Dae-WookX; Nelson, Katherine; Fajardo-Williams, Devyn; Miceli, Joseph; Done, Hansa#; Popat, Sudeep; Krajmalnik-Brown, Rosa*. 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.

  6. Vianey Ruiz, Zehra Esra Ilhan, Dae-Wook KangX, Rosa Krajmalnik-Brown, Germán Buitrón*. The source of inoculum plays a defining role in the development of MEC microbial consortia fed with acetic and propionic acid mixtures. 2014. Journal of Biotechnology. Volume 182, page 11-18.

  7. 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”.  Ground Water Monitoring and Remediation. 34(2):60-70.

  8. Ontiveros-Valencia A., Tang Y., Krajmalnik-Brown R., Rittmann BE*. 2014. Managing the interactions between sulfate- and perchlorate-reducing bacteria when treating highly perchlorate-contaminated groundwater with hydrogen-fed biofilms. Water Research. Volume 55, pages 215-224.

  9. He-Ping ZhaoX, Aura Ontiveros-Valencia, Youneng Tang, Bi-O  Kim, Steven  VanGinkel, David  Friese, Ryan  Overstreet, Jennifer  Smith, Patrick  Evans, Rosa  Krajmalnik-Brown, Bruce  E Rittmann. 2014. Removal of multiple electron acceptors by pilot-scale, two-stage membrane biofilm reactors. Water Research. Volume 54, page 115–122.

  10. Anca G. Delgado, Devyn Fajardo-Williams, Sudeep C. Popat, César I. Torres, Rosa Krajmalnik-Brown*, 2014. “Successful operation of continuous reactors at short retention times results in high-density, fast-rate Dehalococcoides dechlorinating cultures”. Applied Microbiology and Biotechnology , Volume 98, Issue 6 (2014), Page 2729-2737. DOI 10.1007/s00253-013-5263-5.

  11. Ziv-El, M., T. Kalinowski,  R. Krajmalnik-Brown and R.U. Halden*, 2014. Simultaneous determination of chlorinated ethenes and ethene in groundwater using automated headspace solid phase microextraction. Journal of Chromatographic Science. 52 (2): 137-142 doi:10.1093/chromsci/bms258.

  12. Badalamenti JP, Torres CI and Krajmalnik-Brown R*, 2014. Coupling dark metabolism to electricity generation using photosynthetic cocultures. Biotechnology and Bioengineering, 111(2), 223-231.


  1. Gilbert JA, Krajmalnik-Brown R,  Porazinska DL, Weiss SJ, Knight R. 2013. Toward effective probiotics for autism and other neurodevelopmental disorders. Cell 155(7):1446-1448.

  2. Ontiveros-Valencia A, Tang Y, Krajmalnik-Brown R, Rittmann BE, 2013. Perchlorate reduction from a highly contaminated groundwater in the presence of sulfate-reducing bacteria in a hydrogen-fed biofilm. Biotechnology and Bioengineering 110(12):3139-3147.

  3. Zhao H-P, Ontiveros-Valencia A, Tang Y, Kim B-O, Ilhan ZE, Krajmalnik-Brown R, Rittrnann BE. 2013. Using a two-stage hydrogen-based membrane biofilm reactor (MBfR) to achieve complete perchlorate reduction in the presence of nitrate and sulfate. Environmental Science & Technology 47(3):1565-1572.

  4. Zhao H-P, Ilhan ZE, Ontiveros-Valencia A, Tang Y, Rittmann BE, Krajmalnik-Brown R. 2013. Effects of multiple electron acceptors on microbial interactions in a hydrogen-based biofilm. Environmental Science & Technology 47(13):7396-7403.

  5. Badalamenti JP, Krajmalnik-Brown R, Torres CI. 2013. Generation of high current densities by pure cultures of anode-respiring Geoalkalibacter spp. under alkaline and saline conditions in microbial electrochemical cells. Mbio 4(3).

  6. Badalamenti JP, Torres CI, Krajmalnik-Brown R. 2013. Light-responsive current generation by phototrophically enriched anode biofilms dominated by green sulfur bacteria. Biotechnology and Bioengineering 110(4):1020-1027.

  7. Kang D-W, Park JG, Ilhan ZE, Wallstrom G, LaBaer J, Adams JB, Krajmalnik-Brown R. 2013. Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children. PLoS ONE 8(7).

  8. Tang Y, Krajmalnik-Brown R, Rittmann BE. 2013. Modeling trichloroethene reduction in a hydrogen-based biofilm. Water Science and Technology 68(5):1158-1163.

  9. Tang Y, Ontiveros-Valencia A, Feng L, Zhou C, Krajmalnik-Brown R, Rittmann BE. 2013. A biofilm model to understand the onset of sulfate reduction in denitrifying membrane biofilm reactors. Biotechnology and Bioengineering 110(3):763-772.

  10. Ontiveros-Valencia A, Ilhan ZE, Kang D-W, Rittmann B, Krajmalnik-Brown R. 2013. Phylogenetic analysis of nitrate- and sulfate-reducing bacteria in a hydrogen-fed biofilm. FEMS Microbiology Ecology 85(1):158-167.

  11. Young MN, Krajmalnik-Brown R, Liu W, Doyle ML, Rittmann BE. 2013. The role of anaerobic sludge recycle in improving anaerobic digester performance. Bioresource Technology 128:731-737.


  1. Ziv-El M, Delgado AG, Yao Y, Kang DW, Nelson KG, Halden RU, Krajmalnik-Brown R. 2012. Erratum to: Development and characterization of DehaloR^2, a novel anaerobic microbial consortium performing rapid dechlorination of TCE to ethene (vol 92, pg 1063, 2011). Applied Microbiology and Biotechnology 95(1):273-274.

  2. Ziv-El M, Popat SC, Cai K, Halden RU, Krajmalnik-Brown R, Rittmann BE. 2012. Managing methanogens and homoacetogens to promote reductive dechlorination of trichloroethene with direct delivery of H2 in a membrane biofilm reactor. Biotechnology and Bioengineering 109(9):2200-2210.

  3. Ziv-El M, Popat SC, Parameswaran P, Kang DW, Polasko A, Halden RU, Rittmann BE, Krajmalnik-Brown R. 2012. Using electron balances and molecular techniques to assess trichoroethene-induced shifts to a dechlorinating microbial community. Biotechnology and Bioengineering 109(9):2230-2239.

  4. Hartmann EM, Badalamenti JP, Krajmalnik-Brown R, Halden RU. 2012. Quantitative PCR for tracking the megaplasmid-borne biodegradation potential of a model sphingomonad. Applied and Environmental Microbiology 78(12):4493-4496.

  5. Ontiveros-Valencia A, Ziv-El M, Zhao H-P, Feng L, Rittmann BE, Krajmalnik-Brown R. 2012. Interactions between nitrate-reducing and sulfate-reducing bacteria coexisting in a hydrogen-fed biofilm. Environmental Science & Technology 46(20):11289-11298.

  6. Delgado AG, Parameswaran P, Fajardo-Williams D, Halden RU, Krajmalnik-Brown R. 2012. Role of bicarbonate as a pH buffer and electron sink in microbial dechlorination of chloroethenes. Microbial Cell Factories 11(128).

  7. Miceli JF, Parameswaran P, Kang DW, Krajmalnik-Brown R, Torres CI. 2012. Enrichment and analysis of anode-respiring bacteria from diverse anaerobic inocula. Environmental Science & Technology 46(18):10349-10355.

  8. Parameswaran P, Torres CI, Kang DW, Rittmann BE, Krajmalnik-Brown R. 2012. The role of homoacetogenic bacteria as efficient hydrogen scavengers in microbial electrochemical cells (MXCs). Water Science and Technology 65(1):1-6.

  9. Krajmalnik-Brown R, Ilhan Z-E, Kang D-W, DiBaise JK. 2012. Effects of gut microbes on nutrient absorption and energy regulation. Nutrition in Clinical Practice 27(2):201-214.

  10. Tang Y, Zhao H, Marcus AK, Krajmalnik-Brown R, Bruce ER. 2012. A steady-state biofilm model for simultaneous reduction of nitrate and perchlorate, part 1: Model development and numerical solution. Environmental Science & Technology 46(3):1598-1607.

  11. Tang Y, Zhao H, Marcus AK, Krajmalnik-Brown R, Bruce ER. 2012. A steady-state biofilm model for simultaneous reduction of nitrate and perchlorate, part 2: Parameter optimization and results and discussion. Environmental Science & Technology 46(3):1608-1615.


  1. Zhao H-P, Van Ginkel S, Tang Y, Kang D-W, Rittmann B, Krajmalnik-Brown R. 2011. Interactions between perchlorate and nitrate reductions in the biofilm of a hydrogen-based membrane biofilm reactor. Environmental Science & Technology 45(23):10155-10162.

  2. Ziv-El M, Delgado AG, Yao Y, Kang DW, Nelson KG, Halden RU, Krajmalnik-Brown R. 2011. Development and characterization of DehaloR^2, a novel anaerobic microbial consortium performing rapid dechlorination of TCE to ethene. Applied Microbiology and Biotechnology 92(5):1063-1071.

  3. Parameswaran P, Torres CI, Lee HS, Rittmann BE, Krajmalnik-Brown R. 2011. Hydrogen consumption in microbial electrochemical systems (MXCs): The role of homo-acetogenic bacteria. Bioresource Technology 102(1):263-271.

  4. Garcia-Pena EI, Parameswaran P, Kang DW, Canul-Chan M, Krajmalnik-Brown R. 2011. Anaerobic digestion and co-digestion processes of vegetable and fruit residues: Process and microbial ecology. Bioresource Technology 102(20):9447-9455.

  5. Sheng J, Kim HW, Badalamenti JP, Zhou C, Sridharakrishnan S, Krajmalnik-Brown R, Rittmann BE, Vannela R. 2011. Effects of temperature shifts on growth rate and lipid characteristics of Synechocystis sp PCC6803 in a bench-top photobioreactor. Bioresource Technology 102(24):11218-11225.

  6. Torres CI, Ramakrishna S, Chiu C-A, Nelson KG, Westerhoff P, Krajmalnik-Brown R. 2011. Fate of sucralose during wastewater treatment. Environmental Engineering Science 28(5):325-331.


  1. Zhang HS, Ziv-El M, Rittmann BE, Krajmalnik-Brown R. 2010. Effect of dechlorination and sulfate reduction on the microbial community structure in denitrifying membrane-biofilm reactors. Environmental Science & Technology 44(13):5159-5164.

  2. Parameswaran P, Zhang HS, Torres CI, Rittmann BE, Krajmalnik-Brown R. 2010. Microbial community structure in a biofilm anode fed with a fermentable substrate: The significance of hydrogen scavengers. Biotechnology and Bioengineering 105(1):69-78.

  3. Torres CI, Marcus AK, Lee H-S, Parameswaran P, Krajmalnik-Brown R, Rittmann BE. 2010. A kinetic perspective on extracellular electron transfer by anode-respiring bacteria. FEMS Microbiology Reviews 34(1):3-17.


  1. Zhang H, Banaszak JE, Parameswaran P, Alder J, Krajmalnik-Brown R, Rittmann BE. 2009. Focused-Pulsed sludge pre-treatment increases the bacterial diversity and relative abundance of acetoclastic methanogens in a full-scale anaerobic digester. Water Research 43(18):4517-4526.

  2. Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, Yu Y, Parameswaran P, Crowell MD, Wing R, Rittmann BE and others. 2009. Human gut microbiota in obesity and after gastric bypass. Proceedings of the National Academy of Sciences of the United States of America 106(7):2365-2370.

  3. Lee H-S, Krajmalnik-Brown R, Zhang H, Rittmann BE. 2009. An electron-flow model can predict complex redox reactions in mixed-culture fermentative BioH2: Microbial ecology evidence. Biotechnology and Bioengineering 104(4):687-697.

  4. Parameswaran P, Torres CI, Lee HS, Krajmalnik-Brown R, Rittmann BE. 2009. Syntrophic interactions among anode respiring bacteria (ARB) and Non-ARB in a biofilm anode: Electron balances. Biotechnology and Bioengineering 103(3):513-523.

  5. Torres CI, Krajmalnik-Brown R, Parameswaran P, Marcus AK, Wanger G, Gorby YA, Rittmann BE. 2009. Selecting anode-respiring bacteria based on anode potential: Phylogenetic, electrochemical, and microscopic characterization. Environmental Science & Technology 43(24):9519-9524.


  1. Chung J, Krajmalnik-Brown R, Rittmann BE. 2008. Bioreduction of trichloroethene using a hydrogen-based membrane biofilm reactor. Environmental Science & Technology 42(2):477-483.

  2. Rittmann BE, Krajmalnik-Brown R, Halden RU. 2008. Pre-genomic, genomic and postgenomic study of microbial communities involved in bioenergy. Nature Reviews Microbiology 6(8):604-612.

  3. DiBaise JK, Zhang H, Crowell MD, Krajmalnik-Brown R, Decker GA, Rittmann BE. 2008. Gut microbiota and its possible relationship with obesity. Mayo Clinic Proceedings 83(4):460-469.


  1. Krajmalnik-Brown R, Sung Y, Ritalahti KM, Saunders FM, Löffler FE. 2007. Environmental distribution of the trichloroethene reductive dehalogenase gene (tceA) suggests lateral gene transfer among Dehalococcoides. FEMS Microbiology Ecology 59(1):206-214.


  1. He J, Sung Y, Krajmalnik-Brown R, Ritalahti KM, Löffler FE. 2005. Isolation and characterization of Dehalococcoides sp strain FL2, a trichloroethene (TCE)- and 1,2-dichloroethene-respiring anaerobe. Environmental Microbiology 7(9):1442-1450.

  2. Waller AS, Krajmalnik-Brown R, Löffler FE, Edwards EA. 2005. Multiple reductive-dehalogenase-homologous genes are simultaneously transcribed during dechlorination by Dehalococcoides-containing cultures. Applied and Environmental Microbiology 71(12):8257-8264.


  1. Hölscher T, Krajmalnik-Brown R, Ritalahti KM, von Wintzingerode F, Gorisch H, Löffler FE, Adrian L. 2004. Multiple nonidentical reductive-dehalogenase-homologous genes are common in Dehalococcoides. Applied and Environmental Microbiology 70(9):5290-5297.

  2. Krajmalnik-Brown R, Hölscher T, Thomson IN, Saunders FM, Ritalahti KM, Löffler FE. 2004. Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp strain BAV1. Applied and Environmental Microbiology 70(10):6347-6351.


  1. Lendvay JM, Löffler FE, Dollhopf M, Aiello MR, Daniels G, Fathepure BZ, Gebhard M, Heine R, Helton R, Shi J and others. 2003. Bioreactive barriers: A comparison of bioaugmentation and biostimulation for chlorinated solvent remediation. Environmental Science & Technology 37(7):1422-1431.

Book Chapters

Zhang H, Parameswaran P, Badalamenti JP, Rittmann BE, Krajmalnik-Brown R. Integrating high-throughput pyrosequencing and quantitative real-time PCR to analyze microbial communities. 2011. In High-Throughput Next Generation Sequencing, Methods in Molecular Biology 733:107-128.