Table S1. Summary of datasets used in this study

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1 Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is The Royal Society of Chemistry 206 Table S. Summary of datasets used in this study No DOI number for paper Publication year Disinfectant residual type Country of sampling Sampling points Sequencing instrument Hypervariable region amplified Reference number Number of treatment plants Average % of matches in SILVA database 0.06/j.watres Chlorinated UK POU Illumina Miseq V % ± 3.79% 2 doi: 0.06/j.watres Chlorinated UK DWDS Roche 454 FLX V-V /j.watres Chlorinated/Chloraminated USA POU Roche 454 FLX Titanium V-V % ± 6.22% 79.69% ± 2.42% /j.ecoenv Chlorinated China DWTP outlet, POU Roche 454 FLX Titanium V3-V4 37 * 6.6% ± 2.48% /AEM Chlorinated/Chloraminated USA DWDS Roche 454 FLX Titanium V4-V % ± 3.88% /journal.pone Chlorinated/Chloraminated USA DWTP outlet, POU Illimina Miseq V /acs.est.5b Chlorinated China DWTP outlet, POU Roche 454 FLX Titanium V-V * 67.2% ± 8.08% 85.28% ± 8.29% /j.watres Chlorinated China DWTP outlet Roche 454 FLX V-V % /es No disinfectant residual Netherlands POU Roche 454 FLX Titanium V4-V6 26 ** 63.6% ± 4.24% /mBio Chloraminated USA DWTP outlet, POU Roche 454 GS-FLX V4-V5 7 0./ No disinfectant residual Netherlands DWDS Illumina MiSeq/Roche 454 GS-FLX /es502646d 204 Chlorinated/Chloraminated USA DWDS V4 and V5- V6 Illumina MiSeq V ** 69.98% ± 2.3% 45.22% ± 6.65% 68.93% ± 2.65% /s Chloraminated China DWTP outlet, POU Roche 454 GS-FLX V3-V % ± 0.64% /AEM Chloraminated Australia DWTP outlet, DWDS Ion Torrent V % ± 6.82% *Both studies sampled at the same treatment plant **Plant from study No.9 may have been sampled in study No.

2 Figure S: The number of samples retained (primary Y-axes, blue squares) with increasing subsampling depths and their corresponding Good s coverage (secondary Y-axes, red squares) is shown. A subsampling depth of 500 sequences per sample was chosen as this allowed for an average Good s coverage 0.8 while retaining maximum number of samples (42 out of 45) in the analyses. Number'of'samples' Average'Good's'coverage' Number of samples Average Good's coverage Subsampling depth!

Figure S2: Workflow illustrating data collection, data processing and data analysis steps. Data$collec)on$ Data$processing$ Data$analysis$ 6S,rRNA,gene:based, studies.

3 Figure S2: Workflow illustrating data collection, data processing and data analysis steps. Data$collec)on$ Data$processing$ Data$analysis$ 6S,rRNA,gene:based, studies.,, Samples,from,full,scale, drinking,water,systems,, Sampling,points:,DWTP outlet,, DWDS,,Point,of,use., Microbial,regrowth, control,strategies:, Chlorinated, Chloraminated, Disinfectant, residual,free, Single,end, Fastq,files, sickle,v..33,,,(min,quality, score=28;,min, length=50bp),, Paired,end, Fastq,files, pear,v , (min,quality, score=28;,min, length=50bp),,, Fastq,to,FASTA,format,using, the,fastq_to_fasta,command, from,fastx:toolkit,v ,, In,mothur,,unique.seqs., blastn,against,the,silva,9,ssuref_nr, database,(iden\ty,,97%,,e: value< ),, Extrac\on,of,full,length,sequences,from, SILVA,database., Data,colla\on, In,mothur:, Best:match,sequences,were,aligned,against,the, SILVA,seed,alignment.,, screen.seqs,command,(ver\cal,=t,and,trump,=.),, OTU,clustering,(cutoff,97%),, Taxonomic,classifica\on,(command,classify.seq), using,silva,taxonomy., Subsampled, OTU,table, (a), Full,dataset, (b), Taxonomic, classifica\on, Fasta,file, (OTUs), (3), Alpha,diversity,es\mates,(observed, OTUs,,Inverse,Simpson,index,, Shannon,index,,Pielou s,evenness), Beta,diversity,(Bray,Cur\s,distances), PERMANOVA,(func\on,Adonis),, Mean,rela\ve,abundance,of,taxonomic, groups,,otus,,poten\al,opportunis\c, pathogens,,target,groups,(nitrifiers,and, predatory,bacteria), Phylogene\c,tree,construc\on,in, RaxML, Es\ma\on,of,poten\al, contamina\on, Tax4Fun,,metabolic,profile, predic\on, Explanatory, variables, (4), (a), (4), (b), (3), (b), (a),

Figure S3: Heatmap of OTU abundance (OTUs with relative abundance >0.0% in the subsampled OTU table). Abundances were scaled with a Z-score transformation to improve visualization.

4 Figure S3: Heatmap of OTU abundance (OTUs with relative abundance >0.0% in the subsampled OTU table). Abundances were scaled with a Z-score transformation to improve visualization. The sampling location dendrogram was generated with Bray Curtis distances and UPGMA clustering method. Grouping information is indicated by the color legend (Chl: chlorinated, Chm: chloraminated, Drf: disinfectant residual-free). Sampling)loca,ons)

5 Figure S4: Dendrogram of sampling locations generated with Bray Curtis distances and UPGMA clustering method. Color legends indicate type of source water (SW: surface water; GW: groundwater; Mix: mixed source water including surface water, groundwater and desalinated seawater), and disinfection group (Chl: chlorinated, Chm: chloraminated, Drf: disinfectant residual-free). Reference numbers of each dataset are at the bottom of the plot.

Nature Biotechnology: doi: /nbt Supplementary Figure 1. Detailed overview of the primer-free full-length SSU rrna library preparation.

Nature Biotechnology: doi: /nbt Supplementary Figure 1. Detailed overview of the primer-free full-length SSU rrna library preparation. Supplementary Figure 1 Detailed overview of the primer-free full-length SSU rrna library preparation. Detailed overview of the primer-free full-length SSU rrna library preparation. Supplementary Figure