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Genomic insights into Candidatus Amarolinea aalborgensis gen. nov., sp. nov., associated with settleability problems in wastewater treatment plants.

Andersen MH, McIlroy SJ, Nierychlo M, Nielsen PH, Albertsen M.

Syst Appl Microbiol. 2018 Aug 16. pii: S0723-2020(18)30235-2. doi: 10.1016/j.syapm.2018.08.001. [Epub ahead of print]


Plasma Concentrations of Long Chain N-3 Fatty Acids in Early and Mid-Pregnancy and Risk of Early Preterm Birth.

Olsen SF, Halldorsson TI, Thorne-Lyman AL, Strøm M, Gørtz S, Granstrøm C, Nielsen PH, Wohlfahrt J, Lykke JA, Langhoff-Roos J, Cohen AS, Furtado JD, Giovannucci EL, Zhou W.

EBioMedicine. 2018 Sep;35:325-333. doi: 10.1016/j.ebiom.2018.07.009. Epub 2018 Aug 3.


Characterization of the First "Candidatus Nitrotoga" Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria.

Kitzinger K, Koch H, Lücker S, Sedlacek CJ, Herbold C, Schwarz J, Daebeler A, Mueller AJ, Lukumbuzya M, Romano S, Leisch N, Karst SM, Kirkegaard R, Albertsen M, Nielsen PH, Wagner M, Daims H.

MBio. 2018 Jul 10;9(4). pii: e01186-18. doi: 10.1128/mBio.01186-18.


Toward Better Understanding of EBPR Systems via Linking Raman-Based Phenotypic Profiling with Phylogenetic Diversity.

Li Y, Cope HA, Rahman SM, Li G, Nielsen PH, Elfick A, Gu AZ.

Environ Sci Technol. 2018 Aug 7;52(15):8596-8606. doi: 10.1021/acs.est.8b01388. Epub 2018 Jul 24.


Novel prosthecate bacteria from the candidate phylum Acetothermia.

Hao L, McIlroy SJ, Kirkegaard RH, Karst SM, Fernando WEY, Aslan H, Meyer RL, Albertsen M, Nielsen PH, Dueholm MS.

ISME J. 2018 Jun 8. doi: 10.1038/s41396-018-0187-9. [Epub ahead of print]


Genomic and in Situ Analyses Reveal the Micropruina spp. as Abundant Fermentative Glycogen Accumulating Organisms in Enhanced Biological Phosphorus Removal Systems.

McIlroy SJ, Onetto CA, McIlroy B, Herbst FA, Dueholm MS, Kirkegaard RH, Fernando E, Karst SM, Nierychlo M, Kristensen JM, Eales KL, Grbin PR, Wimmer R, Nielsen PH.

Front Microbiol. 2018 May 23;9:1004. doi: 10.3389/fmicb.2018.01004. eCollection 2018.


Monitoring foaming potential in anaerobic digesters.

Jiang C, Qi R, Hao L, McIlroy SJ, Nielsen PH.

Waste Manag. 2018 May;75:280-288. doi: 10.1016/j.wasman.2018.02.021. Epub 2018 Mar 2.


Peatland Acidobacteria with a dissimilatory sulfur metabolism.

Hausmann B, Pelikan C, Herbold CW, Köstlbacher S, Albertsen M, Eichorst SA, Glavina Del Rio T, Huemer M, Nielsen PH, Rattei T, Stingl U, Tringe SG, Trojan D, Wentrup C, Woebken D, Pester M, Loy A.

ISME J. 2018 Jun;12(7):1729-1742. doi: 10.1038/s41396-018-0077-1. Epub 2018 Feb 23.


Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias.

Karst SM, Dueholm MS, McIlroy SJ, Kirkegaard RH, Nielsen PH, Albertsen M.

Nat Biotechnol. 2018 Feb;36(2):190-195. doi: 10.1038/nbt.4045. Epub 2018 Jan 1.


Structural valve deterioration in the Mitroflow biological heart valve prosthesis.

Issa IF, Poulsen SH, Waziri F, Torp Pedersen C, Nielsen PH, Riber L, Dahl JS, Søgaard P, Nørgaard MA, Møller JE.

Eur J Cardiothorac Surg. 2018 Jan 1;53(1):136-142. doi: 10.1093/ejcts/ezx321.


Quality assurance of the Western Denmark Heart Registry, a population-based healthcare register.

Rasmussen LA, Bøtker HE, Jensen LO, Ravkilde J, Riber L, Nielsen PH, Andreasen JJ, Jakobsen CJ.

Dan Med J. 2017 Oct;64(10). pii: A5414.


The impact of immigration on microbial community composition in full-scale anaerobic digesters.

Kirkegaard RH, McIlroy SJ, Kristensen JM, Nierychlo M, Karst SM, Dueholm MS, Albertsen M, Nielsen PH.

Sci Rep. 2017 Aug 24;7(1):9343. doi: 10.1038/s41598-017-09303-0.


Functional redundancy ensures performance robustness in 3-stage PHA-producing mixed cultures under variable feed operation.

Carvalho G, Pedras I, Karst SM, Oliveira CSS, Duque AF, Nielsen PH, Reis MAM.

N Biotechnol. 2018 Jan 25;40(Pt B):207-217. doi: 10.1016/j.nbt.2017.08.007. Epub 2017 Aug 22.


Microbial biotechnology and circular economy in wastewater treatment.

Nielsen PH.

Microb Biotechnol. 2017 Sep;10(5):1102-1105. doi: 10.1111/1751-7915.12821. Epub 2017 Aug 22.


A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis.

Rouse SL, Hawthorne WJ, Berry JL, Chorev DS, Ionescu SA, Lambert S, Stylianou F, Ewert W, Mackie U, Morgan RML, Otzen D, Herbst FA, Nielsen PH, Dueholm M, Bayley H, Robinson CV, Hare S, Matthews S.

Nat Commun. 2017 Aug 15;8(1):263. doi: 10.1038/s41467-017-00361-6.


Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition.

Marshall IPG, Karst SM, Nielsen PH, Jørgensen BB.

Mar Genomics. 2018 Feb;37:58-68. doi: 10.1016/j.margen.2017.08.004. Epub 2017 Aug 12.


Direct Identification of Functional Amyloid Proteins by Label-Free Quantitative Mass Spectrometry.

Danielsen HN, Hansen SH, Herbst FA, Kjeldal H, Stensballe A, Nielsen PH, Dueholm MS.

Biomolecules. 2017 Aug 4;7(3). pii: E58. doi: 10.3390/biom7030058.


Membrane filtration device for studying compression of fouling layers in membrane bioreactors.

Jørgensen MK, Bugge TV, Larsen P, Nielsen PH, Christensen ML.

PLoS One. 2017 Jul 27;12(7):e0181652. doi: 10.1371/journal.pone.0181652. eCollection 2017.


Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge.

McIlroy SJ, Kirkegaard RH, Dueholm MS, Fernando E, Karst SM, Albertsen M, Nielsen PH.

Front Microbiol. 2017 Jun 23;8:1134. doi: 10.3389/fmicb.2017.01134. eCollection 2017.


Diversity of microbial carbohydrate-active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge.

Wilkens C, Busk PK, Pilgaard B, Zhang WJ, Nielsen KL, Nielsen PH, Lange L.

Biotechnol Biofuels. 2017 Jun 21;10:158. doi: 10.1186/s13068-017-0840-y. eCollection 2017.


Metabolism and ecological niche of Tetrasphaera and Ca. Accumulibacter in enhanced biological phosphorus removal.

Marques R, Santos J, Nguyen H, Carvalho G, Noronha JP, Nielsen PH, Reis MAM, Oehmen A.

Water Res. 2017 Oct 1;122:159-171. doi: 10.1016/j.watres.2017.04.072. Epub 2017 Apr 29.


Thirty-Year Mortality After Coronary Artery Bypass Graft Surgery: A Danish Nationwide Population-Based Cohort Study.

Adelborg K, Horváth-Puhó E, Schmidt M, Munch T, Pedersen L, Nielsen PH, Bøtker HE, Toft Sørensen H.

Circ Cardiovasc Qual Outcomes. 2017 May;10(5):e002708. doi: 10.1161/CIRCOUTCOMES.116.002708.


A Critical Assessment of the Microorganisms Proposed to be Important to Enhanced Biological Phosphorus Removal in Full-Scale Wastewater Treatment Systems.

Stokholm-Bjerregaard M, McIlroy SJ, Nierychlo M, Karst SM, Albertsen M, Nielsen PH.

Front Microbiol. 2017 Apr 27;8:718. doi: 10.3389/fmicb.2017.00718. eCollection 2017.


Unified understanding of physico-chemical properties of activated sludge and fouling propensity.

Jørgensen MK, Nierychlo M, Nielsen AH, Larsen P, Christensen ML, Nielsen PH.

Water Res. 2017 Sep 1;120:117-132. doi: 10.1016/j.watres.2017.04.056. Epub 2017 Apr 26.


MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups.

McIlroy SJ, Kirkegaard RH, McIlroy B, Nierychlo M, Kristensen JM, Karst SM, Albertsen M, Nielsen PH.

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax016.


Long-term effects of sulphide on the enhanced biological removal of phosphorus: The symbiotic role of Thiothrix caldifontis.

Rubio-Rincón FJ, Welles L, Lopez-Vazquez CM, Nierychlo M, Abbas B, Geleijnse M, Nielsen PH, van Loosdrecht MCM, Brdjanovic D.

Water Res. 2017 Jun 1;116:53-64. doi: 10.1016/j.watres.2017.03.017. Epub 2017 Mar 7.


The role of inoculum and reactor configuration for microbial community composition and dynamics in mainstream partial nitritation anammox reactors.

Agrawal S, Karst SM, Gilbert EM, Horn H, Nielsen PH, Lackner S.

Microbiologyopen. 2017 Aug;6(4). doi: 10.1002/mbo3.456. Epub 2017 Mar 10.


Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system.

Sauder LA, Albertsen M, Engel K, Schwarz J, Nielsen PH, Wagner M, Neufeld JD.

ISME J. 2017 May;11(5):1142-1157. doi: 10.1038/ismej.2016.192. Epub 2017 Feb 14.


Deep Sternal Wound Infection after Open-Heart Surgery: A 13-Year Single Institution Analysis.

Juhl AA, Hody S, Videbaek TS, Damsgaard TE, Nielsen PH.

Ann Thorac Cardiovasc Surg. 2017 Apr 20;23(2):76-82. doi: 10.5761/atcs.oa.16-00196. Epub 2017 Feb 3.


Non-denitrifying polyphosphate accumulating organisms obviate requirement for anaerobic condition.

Cokro AA, Law Y, Williams RBH, Cao Y, Nielsen PH, Wuertz S.

Water Res. 2017 Mar 15;111:393-403. doi: 10.1016/j.watres.2017.01.006. Epub 2017 Jan 3.


Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections.

Rudkjøbing VB, Thomsen TR, Xu Y, Melton-Kreft R, Ahmed A, Eickhardt S, Bjarnsholt T, Poulsen SS, Nielsen PH, Earl JP, Ehrlich GD, Moser C.

BMC Infect Dis. 2016 Nov 8;16(1):652.


Percutaneous coronary angioplasty versus coronary artery bypass grafting in treatment of unprotected left main stenosis (NOBLE): a prospective, randomised, open-label, non-inferiority trial.

Mäkikallio T, Holm NR, Lindsay M, Spence MS, Erglis A, Menown IB, Trovik T, Eskola M, Romppanen H, Kellerth T, Ravkilde J, Jensen LO, Kalinauskas G, Linder RB, Pentikainen M, Hervold A, Banning A, Zaman A, Cotton J, Eriksen E, Margus S, Sørensen HT, Nielsen PH, Niemelä M, Kervinen K, Lassen JF, Maeng M, Oldroyd K, Berg G, Walsh SJ, Hanratty CG, Kumsars I, Stradins P, Steigen TK, Fröbert O, Graham AN, Endresen PC, Corbascio M, Kajander O, Trivedi U, Hartikainen J, Anttila V, Hildick-Smith D, Thuesen L, Christiansen EH; NOBLE study investigators.

Lancet. 2016 Dec 3;388(10061):2743-2752. doi: 10.1016/S0140-6736(16)32052-9. Epub 2016 Oct 31. Erratum in: Lancet. 2016 Dec 3;388(10061):2742.


Epigallocatechin Gallate Remodels Overexpressed Functional Amyloids in Pseudomonas aeruginosa and Increases Biofilm Susceptibility to Antibiotic Treatment.

Stenvang M, Dueholm MS, Vad BS, Seviour T, Zeng G, Geifman-Shochat S, Søndergaard MT, Christiansen G, Meyer RL, Kjelleberg S, Nielsen PH, Otzen DE.

J Biol Chem. 2016 Dec 16;291(51):26540-26553. Epub 2016 Oct 26.


"Candidatus Propionivibrio aalborgensis": A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants.

Albertsen M, McIlroy SJ, Stokholm-Bjerregaard M, Karst SM, Nielsen PH.

Front Microbiol. 2016 Jul 4;7:1033. doi: 10.3389/fmicb.2016.01033. eCollection 2016.


Dynamics of the Fouling Layer Microbial Community in a Membrane Bioreactor.

Ziegler AS, McIlroy SJ, Larsen P, Albertsen M, Hansen AA, Heinen N, Nielsen PH.

PLoS One. 2016 Jul 11;11(7):e0158811. doi: 10.1371/journal.pone.0158811. eCollection 2016.


Impact of sludge retention time on the fine composition of the microbial community and extracellular polymeric substances in a membrane bioreactor.

Silva AF, Antunes S, Saunders A, Freitas F, Vieira A, Galinha CF, Nielsen PH, Barreto Crespo MT, Carvalho G.

Appl Microbiol Biotechnol. 2016 Oct;100(19):8507-21. doi: 10.1007/s00253-016-7617-2. Epub 2016 Jun 6.


Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions.

Law Y, Kirkegaard RH, Cokro AA, Liu X, Arumugam K, Xie C, Stokholm-Bjerregaard M, Drautz-Moses DI, Nielsen PH, Wuertz S, Williams RB.

Sci Rep. 2016 May 19;6:25719. doi: 10.1038/srep25719.


In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study.

Xu Y, Maltesen RG, Larsen LH, Schønheyder HC, Le VQ, Nielsen JL, Nielsen PH, Thomsen TR, Nielsen KL.

BMC Microbiol. 2016 May 5;16:80. doi: 10.1186/s12866-016-0695-6.


Phylogenetic diversity and ecophysiology of Candidate phylum Saccharibacteria in activated sludge.

Kindaichi T, Yamaoka S, Uehara R, Ozaki N, Ohashi A, Albertsen M, Nielsen PH, Nielsen JL.

FEMS Microbiol Ecol. 2016 Jun;92(6):fiw078. doi: 10.1093/femsec/fiw078. Epub 2016 Apr 17.


Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters.

Kirkegaard RH, Dueholm MS, McIlroy SJ, Nierychlo M, Karst SM, Albertsen M, Nielsen PH.

ISME J. 2016 Oct;10(10):2352-64. doi: 10.1038/ismej.2016.43. Epub 2016 Apr 8.


Durability after aortic valve replacement with the Mitroflow versus the Perimount pericardial bioprosthesis: a single-centre experience in 2393 patients.

Nielsen PH, Hjortdal V, Modrau IS, Jensen H, Kimose HH, Terp K, Poulsen SH, Smerup M, Nielsen SL.

Eur J Cardiothorac Surg. 2016 Jun;49(6):1705-10. doi: 10.1093/ejcts/ezv432. Epub 2016 Mar 16.


Proteomic dataset of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor.

Schiffmann CL, Otto W, Hansen R, Nielsen PH, Adrian L, Seifert J, von Bergen M, Jehmlich N.

Data Brief. 2016 Feb 22;7:253-6. doi: 10.1016/j.dib.2016.02.037. eCollection 2016 Jun.


Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge.

McIlroy SJ, Karst SM, Nierychlo M, Dueholm MS, Albertsen M, Kirkegaard RH, Seviour RJ, Nielsen PH.

ISME J. 2016 Sep;10(9):2223-34. doi: 10.1038/ismej.2016.14. Epub 2016 Feb 23.


Detection of Pathogenic Biofilms with Bacterial Amyloid Targeting Fluorescent Probe, CDy11.

Kim JY, Sahu S, Yau YH, Wang X, Shochat SG, Nielsen PH, Dueholm MS, Otzen DE, Lee J, Delos Santos MM, Yam JK, Kang NY, Park SJ, Kwon H, Seviour T, Yang L, Givskov M, Chang YT.

J Am Chem Soc. 2016 Jan 13;138(1):402-7. doi: 10.1021/jacs.5b11357. Epub 2016 Jan 4.


Enhancing metaproteomics--The value of models and defined environmental microbial systems.

Herbst FA, Lünsmann V, Kjeldal H, Jehmlich N, Tholey A, von Bergen M, Nielsen JL, Hettich RL, Seifert J, Nielsen PH.

Proteomics. 2016 Mar;16(5):783-98. doi: 10.1002/pmic.201500305. Epub 2016 Jan 21. Review.


Complete nitrification by a single microorganism.

van Kessel MA, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJ, Kartal B, Jetten MS, Lücker S.

Nature. 2015 Dec 24;528(7583):555-9. doi: 10.1038/nature16459. Epub 2015 Nov 26.


Complete nitrification by Nitrospira bacteria.

Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M.

Nature. 2015 Dec 24;528(7583):504-9. doi: 10.1038/nature16461. Epub 2015 Nov 26.


Functional bacterial amyloid increases Pseudomonas biofilm hydrophobicity and stiffness.

Zeng G, Vad BS, Dueholm MS, Christiansen G, Nilsson M, Tolker-Nielsen T, Nielsen PH, Meyer RL, Otzen DE.

Front Microbiol. 2015 Oct 7;6:1099. doi: 10.3389/fmicb.2015.01099. eCollection 2015.


One-year clinical and angiographic results of hybrid coronary revascularization.

Modrau IS, Holm NR, Mæng M, Bøtker HE, Christiansen EH, Kristensen SD, Lassen JF, Thuesen L, Nielsen PH; Hybrid Coronary Revascularization Study Group.

J Thorac Cardiovasc Surg. 2015 Nov;150(5):1181-6. doi: 10.1016/j.jtcvs.2015.08.072. Epub 2015 Aug 28.


Limited dissemination of the wastewater treatment plant core resistome.

Munck C, Albertsen M, Telke A, Ellabaan M, Nielsen PH, Sommer MO.

Nat Commun. 2015 Sep 30;6:8452. doi: 10.1038/ncomms9452.

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