McIlroy, S.J., Kirkegaard, R.H., McIlroy, B., Nierychlo, M., Kristensen, J.M., Karst, S.M., Albertsen, M., Nielsen, P.H., 2017. MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups. Database 2017. doi:10.1093/database/bax016

McIlroy, S.J., Saunders, A.M., Albertsen, M., Nierychlo, M., McIlroy, B., Hansen, A.A., Karst, S.M., Nielsen, J.L. and Nielsen, P.H. (2015) MiDAS: the field guide to the microbes of activated sludge. Database, Vol. 2015, Article ID bav062; doi:10.1093/database/bav062.

Read more about our conceptual model of the activated sludge ecosystem:

Saunders A. M., Albertsen M., Vollertsen J., Nielsen P.H. (2016) The activated sludge ecosystem contains a core community of abundant organisms. ISME Journal, 10: 11-20. doi: 10.1038/ismej.2015.117.

Albertsen M., Karst S.M., Ziegler A.S., Kirkegaard R.H., Nielsen P.H. (2015) Back to basics – the influence of DNA extraction and primer choice on phylogenetic analysis in activated sludge communities. PLOS ONE, doi: 10.1371/journal.pone.0132783.

Nielsen, P.H., Saunders, A.M., Hansen, A.A., Larsen, P., & Nielsen, J.L. (2012). Microbial communities involved in enhanced biological phosphorus removal from wastewater - a model system in environmental biotechnology. Current Opinion in Biotechnology, 23(3), 452–459.

Nielsen, P.H., Mielczarek, A.T., Kragelund, C., Nielsen, J.L., Saunders, A.M., Kong, Y., Hansen, A.A., Vollertsen J. (2010). A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants. Water Research, 44, 5070–5088.


Examples of articles citing and using MiDAS:


Bonk, F., Popp, D., Weinrich, S., Sträuber, H., Becker, D., Kleinsteuber, S., Harms, H., Centler, F. (2019) Determination of Microbial Maintenance in Acetogenesis and Methanogenesis by Experimental and Modeling Techniques. Front. Microbiol. 10.

Brand, V.R., Crosby, L.D., Criddle, C.S., 2019. Niche Differentiation among Three Closely Related Competibacteraceae Clades at a Full-Scale Activated Sludge Wastewater Treatment Plant and Putative Linkages to Process Performance. Appl. Environ. Microbiol. 85, e02301-18.

Bundgaard-Nielsen, C., Baandrup, U.T., Nielsen, L.P., Sørensen, S., 2019. The presence of bacteria varies between colorectal adenocarcinomas, precursor lesions and non-malignant tissue. BMC Cancer 19, 399.

Di Gregorio, L., R. Congestri, V. Tandoi, T. R. Neu, S. Rossetti, and F. Di Pippo (2019) Biofilm Diversity, Structure and Matrix Seasonality in a Full-Scale Cooling Tower. Biofouling, January 21, 2019, 1–17.

Global Water Microbiome Consortium, Wu, L., Ning, D., Zhang, B., Li, Y., Zhang, P., Shan, X., Zhang, Q., Brown, M., Li, Z., Van Nostrand, J.D., Ling, F., Xiao, N., Zhang, Y., Vierheilig, J., Wells, G.F., Yang, Y., Deng, Y., Tu, Q., Wang, A., Zhang, T., He, Z., Keller, J., Nielsen, P.H., Alvarez, P.J.J., Criddle, C.S., Wagner, M., Tiedje, J.M., He, Q., Curtis, T.P., Stahl, D.A., Alvarez-Cohen, L., Rittmann, B.E., Wen, X., Zhou, J., 2019. Global diversity and biogeography of bacterial communities in wastewater treatment plants. Nat Microbiol.

 Karačić, S., Wilén, B.-M., Suarez, C., Hagelia, P., Persson, F. (2019) Subsea tunnel reinforced sprayed concrete subjected to deterioration harbours distinct microbial communities. Biofouling 0, 1–14.

Kromann, S., A. Hvidtfeldt, M. Boye, D. Bratbo Sørensen, S. Jørgensen, J.P. Nielsen, R. Heidemann Olsen (2019) In Vitro Synergy of Sertraline and Tetracycline Cannot Be Reproduced in Pigs Orally Challenged with a Tetracycline Resistant Escherichia Coli. BMC Microbiology 19, no. 1 (January 11, 2019): 12.

Mandel, A., I. Zekker, M. Jaagura, and T. Tenno (2019) Enhancement of Anoxic Phosphorus Uptake of Denitrifying Phosphorus Removal Process by Biomass Adaption. International Journal of Environmental Science and Technology, January 8, 2019.

Nguyen, L.N., Mohammed, J.A.H., Commault, A., Bustamante, H., Aurisch, R., Lowrie, R., Nghiem, L.D., 2019. Impacts of mixing on foaming, methane production, stratification and microbial community in full-scale anaerobic co-digestion process. Bioresource Technology.

Nguyen, L.N., Nguyen, A.Q., Johir, M.A.H., Guo, W., Ngo, H.H., Chaves, A.V., Nghiem, L.D., 2019. Application of rumen and anaerobic sludge microbes for bio harvesting from lignocellulosic biomass. Chemosphere 228, 702–708.

Nierychlo, M., A. Miłobędzka, F. Petriglieri, B. McIlroy, P.H. Nielsen, S.J. McIlroy (2019) The Morphology and Metabolic Potential of the Chloroflexi in Full-Scale Activated Sludge Wastewater Treatment Plants. FEMS Microbiology Ecology 95, no. 2 (February 1, 2019).

Onetto, C.A., P.R. Grbin, S.J. McIlroy, K.L. Eales (2019) Genomic Insights into the Metabolism of ‘Candidatus Defluviicoccus Seviourii’, a Member of Defluviicoccus Cluster III Abundant in Industrial Activated Sludge. FEMS Microbiology Ecology 95, no. 2 (February 1, 2019).

Petrovich, M.L., A.F. Rosenthal, J.S. Griffin, G.F. Wells (2019) Spatially Resolved Abundances of Antibiotic Resistance Genes and IntI1 in Wastewater Treatment Biofilms. Biotechnology and Bioengineering,

Saheb-Alam, S., Persson, F., Wilén, B.-M., Hermansson, M., Modin, O., (2019) A variety of hydrogenotrophic enrichment cultures catalyse cathodic reactions. Scientific Reports 9, 2356.

White, J.K., Nielsen, J.L., Madsen, A.M., (2019) Microbial species and biodiversity in settling dust within and between pig farms. Environmental Research 171, 558–567.


Bonk, F., D. Popp, S. Weinrich, H. Sträuber, S. Kleinsteuber, H. Harms, F. Centler (2018): Ammonia Inhibition of Anaerobic Volatile Fatty Acid Degrading Microbial Communities. Front. Microbiol. 9 (November 30, 2018).

Bonk, F., D. Popp, H Harms, F Centler (2018): PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls. J Microbiol Methods, 153, 139-147.

Bonk, F., Popp, D., Weinrich, S., Sträuber, H., Kleinsteuber, S., Harms, H., Centler, F., (2018): Intermittent fasting for microbes: how discontinuous feeding increases functional stability in anaerobic digestion. Biotechnology for Biofuels 11, 274.

Fang, D., Zhao, G., Xu, X., Zhang, Q., Shen, Q., Fang, Z., Huang, L., Ji, F., (2018): Microbial community structures and functions of wastewater treatment systems in plateau and cold regions. Bioresource Technology 249, 684–693.

Gonzalez-Martinez, A., Sihvonen, M., Muñoz-Palazon, B., Rodriguez-Sanchez, A., Mikola, A., Vahala, R., (2018): Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea , Bacteria and Fungi. Scientific Reports 8, 2208.

Günther, S.,  D. Becker, T. Hübschmann, S. Reinert, S. Kleinsteuber, S. Müller, C. Wilhelm (2018): Long-Term Biogas Production from Glycolate by Diverse and Highly Dynamic Communities. Microorganisms, 6, 103; doi:10.3390/microorganisms6040103.

Jiang, X.-T., Ye, L., Ju, F., Li, B., Ma, L.-P., Zhang, T., (2018): Temporal dynamics of activated sludge bacterial communities in two diversity variant full-scale sewage treatment plants. Applied Microbiology and Biotechnology 102, 9379–9388.

Lukassen, M.B., Podduturi, R., Rohaan, B., Jørgensen, N.O.G., Nielsen J.L. (2018): Dynamics of geosmin-producing bacteria in a full-scale saltwater recirculated aquaculture system. Aquaculture 500, 170-177.

Qiu, G., R. Zuniga-Montanez, Y. Law, S. Swa Thi, T. Q. N. Nguyen, K. Eganathan, X. Liu, P. H. Nielsen, R. B. H. Williams, S. Wuertz (2018) Polyphosphate-Accumulating Organisms in Full-Scale Tropical Wastewater Treatment Plants Use Diverse Carbon Sources. Water Research 149: 496–510.

Tillmann, S., A. Abildgaard, G. Winther, G. Wegener (2018): Altered Fecal Microbiota Composition in the Flinders Sensitive Line Rat Model of Depression. Psychopharmacology, November 23, 2018.


Cokro, AA, Y Law, RBH Williams, Y Cao, PH Nielsen, S Wuertz (2017): Non-denitrifying polyphosphate accumulating organisms obviate requirement for anaerobic condition. Water Research 111, 393–403. doi:10.1016/j.watres.2017.01.006

Keene, N.A., Reusser, S.R., Scarborough, M.J., Grooms, A.L., Seib, M., Santo Domingo, J., Noguera, D.R., 2017. Pilot plant demonstration of stable and efficient high rate biological nutrient removal with low dissolved oxygen conditions. Water Research 121, 72–85.

Rubio-Rincón, F.J., Welles, L., Lopez-Vazquez, C.M., Nierychlo, M., Abbas, B., Geleijnse, M., Nielsen, P.H., van Loosdrecht, M.C.M., Brdjanovic, D., (2017): Long-term effects of sulphide on the enhanced biological removal of phosphorus: The symbiotic role of Thiothrix caldifontis. Water Research 116, 53–64.

Stokholm-Bjerregaard, M., McIlroy, S.J., Nierychlo, M., Karst, S.M., Albertsen, M., Nielsen, P.H., (2017): A Critical Assessment of the Microorganisms Proposed to be Important to Enhanced Biological Phosphorus Removal in Full-Scale Wastewater Treatment Systems. Front. Microbiol. 8.

Szabó, E., R Liébana, M Hermansson, O Modin, F Persson, and B-M Wilén (2017): Microbial Population Dynamics and Ecosystem Functions of Anoxic/Aerobic Granular Sludge in Sequencing Batch Reactors Operated at Different Organic Loading Rates. Frontiers in Microbiology 8. doi:10.3389/fmicb.2017.00770


Laureni, M., Falås, P., Robin, O., Wick, A., Weissbrodt, D.G., Nielsen, J.L., Ternes, T.A., Morgenroth, E., Joss, A., 2016. Mainstream partial nitritation and anammox: long-term process stability and effluent quality at low temperatures. Water Research 101, 628–639.

 Law, Y, RH Kirkegaard, AA Cokro, X Liu, K Arumugam, C Xie, M Stokholm-Bjerregaard, DI Drautz-Moses, PH Nielsen, S Wuertz, RBH Williams (2016): Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions. Scientific Rep. 6, 25719. doi:10.1038/srep25719.

Silva, A.F., Antunes, S., Saunders, A., Freitas, F., Vieira, A., Galinha, C.F., Nielsen, P.H., Crespo, M.T.B., Carvalho, G., 2016. Impact of sludge retention time on the fine composition of the microbial community and extracellular polymeric substances in a membrane bioreactor. Appl Microbiol Biotechnol 100, 8507–8521.

Ziegler, AS, SJ McIlroy, P Larsen, M Albertsen, AA Hansen, N Heinen, and PH Nielsen (2016): Dynamics of the fouling layer microbial community in a membrane bioreactor. PloSONE. DOI: 10.1371/journal.pone.0158811.


McIlroy, S.J., Awata, T., Nierychlo, M., Albertsen, M., Kindaichi, T., Nielsen, P.H., (2015): Characterization of the In Situ Ecophysiology of Novel Phylotypes in Nutrient Removal Activated Sludge Treatment Plants. PLOS ONE 10, e0136424.

to see full citation list, please click here (McIlroy et al., 2015) and here (McIlroy et al., 2017). 

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