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Microbial Communities Associated With Passive Acidic Abandoned Coal Mine Remediation.

Ly T, Wright JR, Weit N, McLimans CJ, Ulrich N, Tokarev V, Valkanas MM, Trun N, Rummel S, Grant CJ, Lamendella R.

Front Microbiol. 2019 Aug 23;10:1955. doi: 10.3389/fmicb.2019.01955. eCollection 2019.


Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection.

Stewart DB Sr, Wright JR, Fowler M, McLimans CJ, Tokarev V, Amaniera I, Baker O, Wong HT, Brabec J, Drucker R, Lamendella R.

mSphere. 2019 Aug 28;4(4). pii: e00454-19. doi: 10.1128/mSphere.00454-19.


Surface water microbial community response to the biocide 2-2-dibromo-3-nitrilopropionamide used in unconventional oil and gas extraction.

Campa MF, Techtmann SM, Ladd MP, Yan J, Patterson M, Garcia de Matos Amaral A, Carter KE, Ulrich N, Grant C, Hettich RL, Lamendella R, Hazen T.

Appl Environ Microbiol. 2019 Aug 23. pii: AEM.01336-19. doi: 10.1128/AEM.01336-19. [Epub ahead of print]


The role of fungi in C. difficile infection: An underappreciated transkingdom interaction.

Stewart D, Romo JA, Lamendella R, Kumamoto CA.

Fungal Genet Biol. 2019 Aug;129:1-6. doi: 10.1016/j.fgb.2019.04.007. Epub 2019 Apr 10. Review.


Using Bacterial Transcriptomics to Investigate Targets of Host-Bacterial Interactions in Caenorhabditis elegans.

Chan JP, Wright JR, Wong HT, Ardasheva A, Brumbaugh J, McLimans C, Lamendella R.

Sci Rep. 2019 Apr 3;9(1):5545. doi: 10.1038/s41598-019-41452-2.


Draft Genome Sequences of Violacein-Producing Duganella sp. Isolates from a Waterway in Eastern Pennsylvania.

Lamendella R, Jude BA.

Microbiol Resour Announc. 2018 Sep 27;7(12). pii: e01196-18. doi: 10.1128/MRA.01196-18. eCollection 2018 Sep.


Excess Dietary Zinc Intake in Neonatal Mice Causes Oxidative Stress and Alters Intestinal Host-Microbe Interactions.

Podany A, Rauchut J, Wu T, Kawasawa YI, Wright J, Lamendella R, Soybel DI, Kelleher SL.

Mol Nutr Food Res. 2019 Feb;63(3):e1800947. doi: 10.1002/mnfr.201800947. Epub 2018 Dec 12.


Tree Nut Consumption and Adipose Tissue Mass: Mechanisms of Action.

Tindall AM, Petersen KS, Lamendella R, Shearer GC, Murray-Kolb LE, Proctor DN, Kris-Etherton PM.

Curr Dev Nutr. 2018 Aug 3;2(11):nzy069. doi: 10.1093/cdn/nzy069. eCollection 2018 Nov. Review.


Host Developmental Toxicity of BPA and BPA Alternatives Is Inversely Related to Microbiota Disruption in Zebrafish.

Catron TR, Keely SP, Brinkman NE, Zurlinden TJ, Wood CE, Wright JR, Phelps D, Wheaton E, Kvasnicka A, Gaballah S, Lamendella R, Tal T.

Toxicol Sci. 2019 Feb 1;167(2):468-483. doi: 10.1093/toxsci/kfy261.


High-Resolution Identification of Multiple Salmonella Serovars in a Single Sample by Using CRISPR-SeroSeq.

Thompson CP, Doak AN, Amirani N, Schroeder EA, Wright J, Kariyawasam S, Lamendella R, Shariat NW.

Appl Environ Microbiol. 2018 Oct 17;84(21). pii: e01859-18. doi: 10.1128/AEM.01859-18. Print 2018 Nov 1.


Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States.

Mackelprang R, Grube AM, Lamendella R, Jesus EDC, Copeland A, Liang C, Jackson RD, Rice CW, Kapucija S, Parsa B, Tringe SG, Tiedje JM, Jansson JK.

Front Microbiol. 2018 Aug 15;9:1775. doi: 10.3389/fmicb.2018.01775. eCollection 2018.


Bacterial Biomarkers of Marcellus Shale Activity in Pennsylvania.

Chen See JR, Ulrich N, Nwanosike H, McLimans CJ, Tokarev V, Wright JR, Campa MF, Grant CJ, Hazen TC, Niles JM, Ressler D, Lamendella R.

Front Microbiol. 2018 Aug 2;9:1697. doi: 10.3389/fmicb.2018.01697. eCollection 2018.


Exposure to Arsenic Alters the Microbiome of Larval Zebrafish.

Dahan D, Jude BA, Lamendella R, Keesing F, Perron GG.

Front Microbiol. 2018 Jun 21;9:1323. doi: 10.3389/fmicb.2018.01323. eCollection 2018.


Comment on "Mucus Microbiome of Anastomotic Tissue During Surgery Has Predictive Value for Colorectal Anastomotic Leakage".

Lamendella R, Stewart DB.

Ann Surg. 2019 May;269(5):e68-e69. doi: 10.1097/SLA.0000000000002856. No abstract available.


Impacts of Glutaraldehyde on Microbial Community Structure and Degradation Potential in Streams Impacted by Hydraulic Fracturing.

Campa MF, Techtmann SM, Gibson CM, Zhu X, Patterson M, Garcia de Matos Amaral A, Ulrich N, Campagna SR, Grant CJ, Lamendella R, Hazen TC.

Environ Sci Technol. 2018 May 15;52(10):5989-5999. doi: 10.1021/acs.est.8b00239. Epub 2018 Apr 30.


Response of Aquatic Bacterial Communities to Hydraulic Fracturing in Northwestern Pennsylvania: A Five-Year Study.

Ulrich N, Kirchner V, Drucker R, Wright JR, McLimans CJ, Hazen TC, Campa MF, Grant CJ, Lamendella R.

Sci Rep. 2018 Apr 9;8(1):5683. doi: 10.1038/s41598-018-23679-7.


Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures.

Lamendella R, Wright JR, Hackman J, McLimans C, Toole DR, Bernard Rubio W, Drucker R, Wong HT, Sabey K, Hegarty JP, Stewart DB Sr.

mSphere. 2018 Jan 10;3(1). pii: e00572-17. doi: 10.1128/mSphere.00572-17. eCollection 2018 Jan-Feb.


HFE Genotype Restricts the Response to Paraquat in a Mouse Model of Neurotoxicity.

Nixon AM, Meadowcroft MD, Neely EB, Snyder AM, Purnell CJ, Wright J, Lamendella R, Nandar W, Huang X, Connor JR.

J Neurochem. 2018 May;145(4):299-311. doi: 10.1111/jnc.14299. Epub 2018 Apr 1.


Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation.

Wright J, Kirchner V, Bernard W, Ulrich N, McLimans C, Campa MF, Hazen T, Macbeth T, Marabello D, McDermott J, Mackelprang R, Roth K, Lamendella R.

Front Microbiol. 2017 Nov 22;8:2300. doi: 10.3389/fmicb.2017.02300. eCollection 2017.


Natural Attenuation of Nonionic Surfactants Used in Hydraulic Fracturing Fluids: Degradation Rates, Pathways, and Mechanisms.

Heyob KM, Blotevogel J, Brooker M, Evans MV, Lenhart JJ, Wright J, Lamendella R, Borch T, Mouser PJ.

Environ Sci Technol. 2017 Dec 5;51(23):13985-13994. doi: 10.1021/acs.est.7b01539. Epub 2017 Nov 13.


Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome.

Maier TV, Lucio M, Lee LH, VerBerkmoes NC, Brislawn CJ, Bernhardt J, Lamendella R, McDermott JE, Bergeron N, Heinzmann SS, Morton JT, González A, Ackermann G, Knight R, Riedel K, Krauss RM, Schmitt-Kopplin P, Jansson JK.

MBio. 2017 Oct 17;8(5). pii: e01343-17. doi: 10.1128/mBio.01343-17.


The Microbial Ecosystem Distinguishes Chronically Diseased Tissue from Adjacent Tissue in the Sigmoid Colon of Chronic, Recurrent Diverticulitis Patients.

Schieffer KM, Sabey K, Wright JR, Toole DR, Drucker R, Tokarev V, Harris LR, Deiling S, Eshelman MA, Hegarty JP, Yochum GS, Koltun WA, Lamendella R, Stewart DB Sr.

Sci Rep. 2017 Aug 16;7(1):8467. doi: 10.1038/s41598-017-06787-8.


NOD2 Genetic Variants Predispose One of Two Familial Adenomatous Polyposis Siblings to Pouchitis Through Microbiome Dysbiosis.

Schieffer KM, Wright JR, Harris LR, Deiling S, Yang Z, Lamendella R, Yochum GS, Koltun WA.

J Crohns Colitis. 2017 Oct 27;11(11):1393-1397. doi: 10.1093/ecco-jcc/jjx083.


Draft Genome Sequence of Mycobacterium chimaera Type Strain Fl-0169.

Pfaller S, Tokarev V, Kessler C, McLimans C, Gomez-Alvarez V, Wright J, King D, Lamendella R.

Genome Announc. 2017 Feb 23;5(8). pii: e01620-16. doi: 10.1128/genomeA.01620-16.


Dynamics of the human gut microbiome in inflammatory bowel disease.

Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D'Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK.

Nat Microbiol. 2017 Feb 13;2:17004. doi: 10.1038/nmicrobiol.2017.4.


ZnT2-Mediated Zinc Import Into Paneth Cell Granules Is Necessary for Coordinated Secretion and Paneth Cell Function in Mice.

Podany AB, Wright J, Lamendella R, Soybel DI, Kelleher SL.

Cell Mol Gastroenterol Hepatol. 2016 Jan 8;2(3):369-383. doi: 10.1016/j.jcmgh.2015.12.006. eCollection 2016 May.


Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk.

Bergeron N, Williams PT, Lamendella R, Faghihnia N, Grube A, Li X, Wang Z, Knight R, Jansson JK, Hazen SL, Krauss RM.

Br J Nutr. 2016 Dec;116(12):2020-2029. doi: 10.1017/S0007114516004165. Epub 2016 Dec 20.


Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor.

Bagchi S, Lamendella R, Strutt S, Van Loosdrecht MC, Saikaly PE.

Sci Rep. 2016 Jun 20;6:28327. doi: 10.1038/srep28327.


Bacterial and Fungal Microbiota Changes Distinguish C. difficile Infection from Other Forms of Diarrhea: Results of a Prospective Inpatient Study.

Sangster W, Hegarty JP, Schieffer KM, Wright JR, Hackman J, Toole DR, Lamendella R, Stewart DB Sr.

Front Microbiol. 2016 May 25;7:789. doi: 10.3389/fmicb.2016.00789. eCollection 2016.


Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy.

Ulrich N, Rosenberger A, Brislawn C, Wright J, Kessler C, Toole D, Solomon C, Strutt S, McClure E, Lamendella R.

Appl Environ Microbiol. 2016 May 31;82(12):3525-3536. doi: 10.1128/AEM.00520-16. Print 2016 Jun 15.


Marcellus and mercury: Assessing potential impacts of unconventional natural gas extraction on aquatic ecosystems in northwestern Pennsylvania.

Grant CJ, Weimer AB, Marks NK, Perow ES, Oster JM, Brubaker KM, Trexler RV, Solomon CM, Lamendella R.

J Environ Sci Health A Tox Hazard Subst Environ Eng. 2015;50(5):482-500. doi: 10.1080/10934529.2015.992670.


Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania.

Trexler R, Solomon C, Brislawn CJ, Wright JR, Rosenberger A, McClure EE, Grube AM, Peterson MP, Keddache M, Mason OU, Hazen TC, Grant CJ, Lamendella R.

Front Microbiol. 2014 Nov 4;5:522. doi: 10.3389/fmicb.2014.00522. eCollection 2014.


Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time.

Bagchi S, Tellez BG, Rao HA, Lamendella R, Saikaly PE.

Appl Microbiol Biotechnol. 2015 Mar;99(5):2361-70. doi: 10.1007/s00253-014-6134-4. Epub 2014 Oct 19.


FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus.

Prestat E, David MM, Hultman J, Taş N, Lamendella R, Dvornik J, Mackelprang R, Myrold DD, Jumpponen A, Tringe SG, Holman E, Mavromatis K, Jansson JK.

Nucleic Acids Res. 2014 Oct 29;42(19):e145. doi: 10.1093/nar/gku702. Epub 2014 Sep 26.


Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities.

Lamendella R, Strutt S, Borglin S, Chakraborty R, Tas N, Mason OU, Hultman J, Prestat E, Hazen TC, Jansson JK.

Front Microbiol. 2014 Apr 3;5:130. doi: 10.3389/fmicb.2014.00130. eCollection 2014.


Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease.

Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK.

PLoS One. 2012;7(11):e49138. doi: 10.1371/journal.pone.0049138. Epub 2012 Nov 28.


Molecular diversity of Bacteroidales in fecal and environmental samples and swine-associated subpopulations.

Lamendella R, Li KC, Oerther D, Santo Domingo JW.

Appl Environ Microbiol. 2013 Feb;79(3):816-24. doi: 10.1128/AEM.02535-12. Epub 2012 Nov 16.


Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill.

Mason OU, Hazen TC, Borglin S, Chain PS, Dubinsky EA, Fortney JL, Han J, Holman HY, Hultman J, Lamendella R, Mackelprang R, Malfatti S, Tom LM, Tringe SG, Woyke T, Zhou J, Rubin EM, Jansson JK.

ISME J. 2012 Sep;6(9):1715-27. doi: 10.1038/ismej.2012.59. Epub 2012 Jun 21.


'Omics' of the mammalian gut--new insights into function.

Lamendella R, VerBerkmoes N, Jansson JK.

Curr Opin Biotechnol. 2012 Jun;23(3):491-500. doi: 10.1016/j.copbio.2012.01.016. Epub 2012 May 23. Review.


Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill.

Baelum J, Borglin S, Chakraborty R, Fortney JL, Lamendella R, Mason OU, Auer M, Zemla M, Bill M, Conrad ME, Malfatti SA, Tringe SG, Holman HY, Hazen TC, Jansson JK.

Environ Microbiol. 2012 Sep;14(9):2405-16. doi: 10.1111/j.1462-2920.2012.02780.x. Epub 2012 May 23.


Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume.

Lu Z, Deng Y, Van Nostrand JD, He Z, Voordeckers J, Zhou A, Lee YJ, Mason OU, Dubinsky EA, Chavarria KL, Tom LM, Fortney JL, Lamendella R, Jansson JK, D'haeseleer P, Hazen TC, Zhou J.

ISME J. 2012 Feb;6(2):451-60. doi: 10.1038/ismej.2011.91. Epub 2011 Aug 4.


Comparative fecal metagenomics unveils unique functional capacity of the swine gut.

Lamendella R, Domingo JW, Ghosh S, Martinson J, Oerther DB.

BMC Microbiol. 2011 May 15;11:103. doi: 10.1186/1471-2180-11-103.


Deep-sea oil plume enriches indigenous oil-degrading bacteria.

Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'haeseleer P, Holman HY, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU.

Science. 2010 Oct 8;330(6001):204-8. doi: 10.1126/science.1195979. Epub 2010 Aug 24.


Microbial community structure during nitrate and perchlorate reduction in ion-exchange brine using the hydrogen-based membrane biofilm reactor (MBfR).

Van Ginkel SW, Lamendella R, Kovacik WP Jr, Santo Domingo JW, Rittmann BE.

Bioresour Technol. 2010 May;101(10):3747-50. doi: 10.1016/j.biortech.2009.12.028. Epub 2010 Jan 25.


Identification of Naegleria fowleri in warm ground water aquifers.

Laseke I, Korte J, Lamendella R, Kaneshiro ES, Marciano-Cabral F, Oerther DB.

J Environ Qual. 2009 Dec 30;39(1):147-53. doi: 10.2134/jeq2009.0062. Print 2010 Jan-Feb.


Identification of bacterial populations in drinking water using 16S rRNA-based sequence analyses.

Revetta RP, Pemberton A, Lamendella R, Iker B, Santo Domingo JW.

Water Res. 2010 Mar;44(5):1353-60. doi: 10.1016/j.watres.2009.11.008. Epub 2009 Nov 14.


Evaluation of swine-specific PCR assays used for fecal source tracking and analysis of molecular diversity of swine-specific "bacteroidales" populations.

Lamendella R, Santo Domingo JW, Yannarell AC, Ghosh S, Di Giovanni G, Mackie RI, Oerther DB.

Appl Environ Microbiol. 2009 Sep;75(18):5787-96. doi: 10.1128/AEM.00448-09. Epub 2009 Jul 24.


Phylogenetic diversity and molecular detection of bacteria in gull feces.

Lu J, Santo Domingo JW, Lamendella R, Edge T, Hill S.

Appl Environ Microbiol. 2008 Jul;74(13):3969-76. doi: 10.1128/AEM.00019-08. Epub 2008 May 9.


Bifidobacteria in feces and environmental waters.

Lamendella R, Santo Domingo JW, Kelty C, Oerther DB.

Appl Environ Microbiol. 2008 Feb;74(3):575-84. Epub 2007 Nov 9.


Identifying fecal sources in a selected catchment reach using multiple source-tracking tools.

Vogel JR, Stoeckel DM, Lamendella R, Zelt RB, Santo Domingo JW, Walker SR, Oerther DB.

J Environ Qual. 2007 Apr 5;36(3):718-29. Print 2007 May-Jun.


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