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Items: 35

1.

Re-evaluating the microbiology of the enhanced biological phosphorus removal process.

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

Curr Opin Biotechnol. 2019 Jun;57:111-118. doi: 10.1016/j.copbio.2019.03.008. Epub 2019 Apr 5. Review.

2.

Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman-FISH.

Fernando EY, McIlroy SJ, Nierychlo M, Herbst FA, Petriglieri F, Schmid MC, Wagner M, Nielsen JL, Nielsen PH.

ISME J. 2019 Aug;13(8):1933-1946. doi: 10.1038/s41396-019-0399-7. Epub 2019 Mar 20.

PMID:
30894691
3.

Proteogenomic Refinement of the Neomegalonema perideroedesT Genome Annotation.

Herbst FA, Gonçalves SCL, Behr T, McIlroy SJ, Nielsen PH.

Proteomics. 2019 May;19(9):e1800330. doi: 10.1002/pmic.201800330.

PMID:
30865376
4.

Genomic insights into the metabolism of 'Candidatus Defluviicoccus seviourii', a member of Defluviicoccus cluster III abundant in industrial activated sludge.

Onetto CA, Grbin PR, McIlroy SJ, Eales KL.

FEMS Microbiol Ecol. 2019 Feb 1;95(2). doi: 10.1093/femsec/fiy231.

PMID:
30476038
5.

The morphology and metabolic potential of the Chloroflexi in full-scale activated sludge wastewater treatment plants.

Nierychlo M, Milobedzka A, Petriglieri F, McIlroy B, Nielsen PH, McIlroy SJ.

FEMS Microbiol Ecol. 2019 Feb 1;95(2). doi: 10.1093/femsec/fiy228.

PMID:
30476032
6.

In situ visualisation of the abundant Chloroflexi populations in full-scale anaerobic digesters and the fate of immigrating species.

Petriglieri F, Nierychlo M, Nielsen PH, McIlroy SJ.

PLoS One. 2018 Nov 1;13(11):e0206255. doi: 10.1371/journal.pone.0206255. eCollection 2018.

7.

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. 2019 Jan;42(1):77-84. doi: 10.1016/j.syapm.2018.08.001. Epub 2018 Aug 16.

8.

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 Sep;12(9):2225-2237. doi: 10.1038/s41396-018-0187-9. Epub 2018 Jun 8.

9.

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.

10.

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.

PMID:
29478959
11.

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.

PMID:
29291348
12.

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.

13.

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.

14.

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.

15.

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.

16.

"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.

17.

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.

18.

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.

19.

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.

20.

Characterization of the In Situ Ecophysiology of Novel Phylotypes in Nutrient Removal Activated Sludge Treatment Plants.

McIlroy SJ, Awata T, Nierychlo M, Albertsen M, Kindaichi T, Nielsen PH.

PLoS One. 2015 Sep 4;10(9):e0136424. doi: 10.1371/journal.pone.0136424. eCollection 2015.

21.

High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov.

McIlroy SJ, Lapidus A, Thomsen TR, Han J, Haynes M, Lobos E, Huntemann M, Pati A, Ivanova NN, Markowitz V, Verbarg S, Woyke T, Klenk HP, Kyrpides N, Nielsen PH.

Stand Genomic Sci. 2015 Feb 27;10:23. doi: 10.1186/s40793-015-0013-1. eCollection 2015.

22.

MiDAS: the field guide to the microbes of activated sludge.

McIlroy SJ, Saunders AM, Albertsen M, Nierychlo M, McIlroy B, Hansen AA, Karst SM, Nielsen JL, Nielsen PH.

Database (Oxford). 2015 Jun 27;2015:bav062. doi: 10.1093/database/bav062. Print 2015.

23.

Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1.

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

Genome Announc. 2015 Jun 11;3(3). pii: e00624-15. doi: 10.1128/genomeA.00624-15.

24.

Isolation and characterization of two plasmids in a clinical Acinetobacter nosocomialis strain.

Gifford B, Tucci J, McIlroy SJ, Petrovski S.

BMC Res Notes. 2014 Oct 17;7:732. doi: 10.1186/1756-0500-7-732.

25.

Re-appraisal of the phylogeny and fluorescence in situ hybridization probes for the analysis of the Competibacteraceae in wastewater treatment systems.

McIlroy SJ, Nittami T, Kanai E, Fukuda J, Saunders AM, Nielsen PH.

Environ Microbiol Rep. 2015 Apr;7(2):166-74. doi: 10.1111/1758-2229.12215. Epub 2014 Dec 2.

PMID:
25224028
26.

Identification of active denitrifiers in full-scale nutrient removal wastewater treatment systems.

McIlroy SJ, Starnawska A, Starnawski P, Saunders AM, Nierychlo M, Nielsen PH, Nielsen JL.

Environ Microbiol. 2016 Jan;18(1):50-64. doi: 10.1111/1462-2920.12614. Epub 2014 Oct 22.

PMID:
25181571
27.

'Candidatus Competibacter'-lineage genomes retrieved from metagenomes reveal functional metabolic diversity.

McIlroy SJ, Albertsen M, Andresen EK, Saunders AM, Kristiansen R, Stokholm-Bjerregaard M, Nielsen KL, Nielsen PH.

ISME J. 2014 Mar;8(3):613-24. doi: 10.1038/ismej.2013.162. Epub 2013 Oct 31.

28.

Metabolic model for the filamentous 'Candidatus Microthrix parvicella' based on genomic and metagenomic analyses.

McIlroy SJ, Kristiansen R, Albertsen M, Karst SM, Rossetti S, Nielsen JL, Tandoi V, Seviour RJ, Nielsen PH.

ISME J. 2013 Jun;7(6):1161-72. doi: 10.1038/ismej.2013.6. Epub 2013 Feb 28.

29.

A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal.

Kristiansen R, Nguyen HT, Saunders AM, Nielsen JL, Wimmer R, Le VQ, McIlroy SJ, Petrovski S, Seviour RJ, Calteau A, Nielsen KL, Nielsen PH.

ISME J. 2013 Mar;7(3):543-54. doi: 10.1038/ismej.2012.136. Epub 2012 Nov 22.

30.

In situ profiling of microbial communities in full-scale aerobic sequencing batch reactors treating winery waste in australia.

McIlroy SJ, Speirs LB, Tucci J, Seviour RJ.

Environ Sci Technol. 2011 Oct 15;45(20):8794-803. doi: 10.1021/es2018576. Epub 2011 Sep 16.

PMID:
21875070
31.

The activated sludge bulking filament Eikelboom morphotype 0914 is a member of the Chloroflexi.

Speirs LB, McIlroy SJ, Petrovski S, Seviour RJ.

Environ Microbiol Rep. 2011 Apr;3(2):159-65. doi: 10.1111/j.1758-2229.2010.00201.x.

PMID:
23761247
32.

An examination of the mechanisms for stable foam formation in activated sludge systems.

Petrovski S, Dyson ZA, Quill ES, McIlroy SJ, Tillett D, Seviour RJ.

Water Res. 2011 Feb;45(5):2146-54. doi: 10.1016/j.watres.2010.12.026. Epub 2010 Dec 28.

PMID:
21239035
33.

Non-target sites with single nucleotide insertions or deletions are frequently found in 16S rRNA sequences and can lead to false positives in fluorescence in situ hybridization (FISH).

McIlroy SJ, Tillett D, Petrovski S, Seviour RJ.

Environ Microbiol. 2011 Jan;13(1):33-47. doi: 10.1111/j.1462-2920.2010.02306.x.

PMID:
20649647
34.

Filamentous members of cluster III Defluviicoccus have the in situ phenotype expected of a glycogen-accumulating organism in activated sludge.

McIlroy SJ, Nittami T, Seviour EM, Seviour RJ.

FEMS Microbiol Ecol. 2010 Oct;74(1):248-56. doi: 10.1111/j.1574-6941.2010.00934.x. Epub 2010 Jul 14.

35.

Extracting nucleic acids from activated sludge which reflect community population diversity.

McIlroy SJ, Porter K, Seviour RJ, Tillett D.

Antonie Van Leeuwenhoek. 2009 Nov;96(4):593-605. doi: 10.1007/s10482-009-9374-z.

PMID:
19768568

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