Supplementary Data McLean et al. 2018 Supplementary Data Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria a Department of Periodontics, University of Washington, Seattle, WA, 98195, USA b Department of Microbiology, University of Washington, Seattle, WA, 98195, USA c Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts 02142 dDepartment of Microbiology, The Ohio State University, Columbus, OH, USA This PDF contains: Supplementary Tables (separate file with tabs for each table) • Supplementary Table 1 | Genomic properties, sources and genome curation. • Supplementary Table 2 | Proposed names and taxonomic placement of genomes. • Supplementary Table 3 | Single copy ribosomal marker gene occurrence across genomes. • Supplementary Table 4 | Raw data for Figure 2a percentage of genome coverage from mapped metagenomics read sets to newly available genomes. • Supplementary Table 5 | Clusters of orthologous protein percentage distribution across genomes compared to mutualistic and parasitic bacteria indicating loss or gain of functional capacities. • Supplementary Table 6 | Core genes shared among full/ near complete genomes of Saccharibacteria • Supplementary Table 7 | Unique genes among each of the G5, G6, G3 and G1 genomes of Oral Saccharibacteria. Supplemental Data • Supplemental Figure 1 | Full matrix of AAI, orthologous genes and percent orthologous fraction provided for each genome pair in Figure 2. • Supplemental Data File 1 | Newick 16S RAXML tree. Supplementary Table 1| Genomic properties, sources and genome curation. Genome properties assessed for assemblies from this study and publically available/published genomes of Saccharibacteria. Some publically available genomes were manually curated to remove contaminating contigs from the submitted sequences delineated with columns for original (grey and red text) and curated properties (purple highlighting). CheckM assembly check results are presented. Completeness is normally based on 117 single core marker genes of bacterial genomes and not the recognized reduced genomes like the CPR with known marker genes that are missing therefore completeness are underestimated. Host, Habitat Curated Genome size (This study): # Curated Gene Count Curated Genome Size Change Group Designation Derived from Bioproject/IMG ID Derived from SRA/Accession New Genome Reference Uncultured Type Original Genome Size Original Gene Count Original Scaffold Count TM7_ EAM_G5_2_HOT_356 G5 PRJNA289925 SRP064209 This Study Population Enrichment Homo Sapiens, Oral Cavity NA NA NA 740987 681 TM7_ EAM_G5_1_HOT_356 G5 PRJNA289925 SRP064209 This Study Population Enrichment Homo Sapiens, Oral Cavity NA NA NA 730081 671 TM7_G3_2_Rum_HOT_351B G3 This Study Population Enrichment Moose , Rumen NA NA NA 726940 719 TM7_KMM_G3_1_HOT_351 G3 This Study Eniched Lab Culture Homo Sapiens, Oral Cavity NA NA NA 563755 535 TM7_CMJM_G6_1_HOT_870 G6 PRJNA48479 SRS013946 This Study Population Enrichment Homo Sapiens, Oral Cavity NA NA NA 625762 607 GWC2 G1 Brown et al.2015 Population Enrichment Environmental, groundwater 1038683 1038683 1092 0 RAAC3 G1 PRJNA217186 CP006915.1 Kantor et al. 2013 Population Enrichment Environmental, groundwater 845464 921 1 845464 921 0 S_aal G1 PRJNA201542 CP005957.1 Albertsen et al.2013 Population Enrichment Environmental, Slude reactor 1013781 1056 1 1013781 1056 0 TM7_S7_ G1 2236661026 IMG public release Single Cell Homo Sapiens, Oral Cavity 1306322 1465 176 889708 1007 416614 TM7_G1_3_12Alb G1 PRJNA289925 SRP064209 This Study Population Enrichment Homo Sapiens, Oral Cavity NA NA NA 462105 607 TM7_ANC_38.39_G1_1 G1 PRJNA216965 SRR957739,38 This Study Population Enrichment Homo Sapiens, Oral Cavity NA NA NA 756930 786 TM7_S1_ G1 2236661021 IMG public release Single Cell Homo Sapiens, Oral Cavity 456864 557 81 400460 473 56404 Type_Strain_TM7x HOT_952 G1 PRJNA241438 CP007496.1 He et al. Cultivated Strain Homo Sapiens, Oral Cavity 705138 711 1 705138 711 TM7_S2_ G1 2236661025 IMG public release Single Cell Homo Sapiens, Oral Cavity 781472 968 167 599808 711 181664 TM7c G1 PRJNA19085 Marcy et al 2007 Single Cell Homo Sapiens, Oral Cavity 474179 630 129 474179 587 0 * completeness is based on bacterial genomes and not reduced CPR genomes with known marker genes that are missing therefore completeness are underestimated. CheckM Results # scaffolds: Longest contig: GC: GC std Coding density: # contigs: # markers: Mean contig length: # marker sets: N50 (contigs): Completeness*: Contamination: # ambiguous bases: Longest scaffold: N50 (scaffolds): Mean scaffold length: Group Designation Metagenome bin TM7_ EAM_G5_2_HOT_356 G5 35 90811 0.51 0.01 0.90 35 171 21170 117 31148 57 0.00 36 90813 31148 21171 Yes TM7_ EAM_G5_1_HOT_356 G5 24 107046 0.50 0.01 0.90 24 171 30417 117 50725 57 1.71 73 107047 50725 30420 Yes TM7_G3_2_Rum_HOT_351B G3 6 232758 0.43 0.00 0.92 6 171 121157 117 ##### 63 0.00 0 232758 176314 121157 Yes TM7_KMM_G3_1_HOT_351 G3 29 66761 0.40 0.01 0.89 36 104 15580 58 23288 75 1.72 2888 107790 23288 19440 Yes TM7_CMJM_G6_1_HOT_870 G6 17 136145 0.32 0.02 0.90 17 171 36810 117 70435 65 0.00 0 136145 70435 36810 Yes GWC2 G1 1 1038683 0.46 0.00 0.90 1 171 ###### 117 ##### 65 0.00 0 1038683 1038683 1038683 Yes RAAC3 G1 1 845464 0.49 0.00 0.91 1 161 845464 108 ##### 66 0.00 0 845464 845464 845464 Yes S_aal G1 1 1013781 0.49 0.00 0.91 1 161 ###### 108 ##### 67 0.93 0 1013781 1013781 1013781 Yes TM7_S7_ G1 105 141643 0.48 0.03 0.89 106 161 8392 108 29598 54 7.41 105 141645 29598 8473 No TM7_G1_3_12Alb G1 189 22786 0.48 0.02 0.90 189 104 2431 58 4786 38 6.03 2631 23007 4863 2445 Yes TM7_ANC_38.39_G1_1 G1 71 40211 0.48 0.03 0.93 72 161 10501 108 13650 59 1.95 856 40214 13650 10661 Yes TM7_S1_ G1 73 49198 0.47 0.04 0.89 73 171 5485 117 17080 24 0.43 27 49198 17081 5486 No Type_Strain_TM7x HOT_952 G1 1 705126 0.44 0.00 0.93 1 171 705126 117 ##### 65 0.00 12 705138 705138 705138 No TM7_S2_ G1 102 37832 0.47 0.03 0.90 102 171 5880 117 13320 35 1.71 50 37832 13320 5880 No TM7c G1 129 61213 0.39 0.05 0.91 129 161 3676 108 8055 29 1.39 0 61213 8055 3676 No Supplementary Table 2| Proposed names and novel taxonomic levels based on phlyogenomic relationships of Saccharibacteria genomes using combined information from 16S rRNA phylogeny, concatenated marker gene trees (Figure 1 and Extended Data Figure 1) as well the average amino acid comparisons (Figure 3 and Supplemental Figure 1) between genomes. Strain_Name Alias GroupName Domain Phylum Class Order Family Genus Species Strain Full Species strain Type_Strain_TM7x HOT_952 TM7x G1_1_TM7x Bacteria Saccharibacteria Saccharimonia Nanosynbacterales Nanosynbacteraceae Nanosynbacter Lyticus Type_Strain_TM7x HOT_952 Nanosynbacter Lyticus Type_Strain_TM7x HOT_952 TM7_S2_ TM7_S2 G1_2_S2 Bacteria Saccharibacteria Saccharimonia Nanosynbacterales Nanosynbacteraceae Nanosynbacter sp. TM7_S2_ Nanosynbacter sp. TM7_S2_ TM7_G1_3_12Alb TM7_12A_lb G1_3_12Alb Bacteria Saccharibacteria Saccharimonia Nanosynbacterales Nanosynbacteraceae Nanosynbacter sp. TM7_G1_3_12Alb Nanosynbacter sp. TM7_G1_3_12Alb TM7c TM7_c G1_4_TM7c Bacteria Saccharibacteria Saccharimonia Nanosynbacterales Nanosynbacteraceae Nanosynbacter sp. TM7c Nanosynbacter sp. TM7c TM7_S7_ TM7_S7 G1_5_S7 Bacteria Saccharibacteria Saccharimonia Saccharimonales Sacchiramonaceaea Nanosynbacter sp. TM7_S7_ Nanosynbacter sp. TM7_S7_ TM7_S1_ TM7_S1 G1_6_S1 Bacteria Saccharibacteria Saccharimonia Saccharimonales Sacchiramonaceaea Nanosynbacter sp. TM7_S1_ Nanosynbacter sp. TM7_S1_ TM7_ANC_38.39_G1_1 ANC_38.39 Bacteria Saccharibacteria Saccharimonia Saccharimonales Sacchiramonaceaea Nanosynbacter sp. TM7_ANC_38.39_G1_1 Nanosynbacter sp. TM7_ANC_38.39_G1_1 TM7_ EAM_G5_1_HOT_356 TM7_9Asb G5_1_EAM Bacteria Saccharibacteria Nanoperiomorbia Nanoperiomorbales Nanoperiomorbaceae Nanoperiomorbus periodonticus TM7_ EAM_G5_1_HOT_356 Nanoperiomorbus periodonticus TM7_ EAM_G5_1_HOT_356 TM7_ EAM_G5_2_HOT_356 TM7_12Asb G5_2_EAM Bacteria Saccharibacteria Nanoperiomorbia Nanoperiomorbales Nanoperiomorbaceae Nanoperiomorbus periodonticus TM7_ EAM_G5_2_HOT_356 Nanoperiomorbus periodonticus TM7_ EAM_G5_2_HOT_356 TM7_CMJM_G6_1_HOT_870 TM7_G6 G6_1_CMJM Bacteria Saccharibacteria Nanosyncoccalia Nanogingivales Nanogingivalaceae Nanogingivalis gingivitcus TM7_CMJM_G6_1_HOT_870 Nanogingivalis gingivitcus TM7_CMJM_G6_1_HOT_870 TM7_KMM_G3_1_HOT_351 TM7_G3 G3_1_KMM Bacteria Saccharibacteria Nanosyncoccalia Nanosyncoccales Nanosyncoccacae Nanosyncoccus nanoralicus TM7_KMM_G3_1_HOT_351 Nanosyncoccus nanoralicus TM7_KMM_G3_1_HOT_351 TM7_G3_2_Rum_HOT_351B TM7_G32_Rum G3_2_Rum Bacteria Saccharibacteria Nanosyncoccalia Nanosyncoccales Nanosyncoccacae Nanosyncoccus alces TM7_G3_2_Rum_HOT_351B Nanosyncoccus alces TM7_G3_2_Rum_HOT_351B Strain_Name Name Derivation Genome Derived From %GC Notes Type_Strain_TM7x HOT_952 Syn=symbiosis Lyticus=lysis Cultured as Epibiont on Actinomyces 44.5 TM7_S2_ Single Cell MDA 46.8 TM7_G1_3_12Alb Metagenome (PRJNA289925; SRP064209) 48.2 TM7c Single Cell MDA 39.1 TM7_S7_ Single Cell MDA 48.2 TM7_S1_ Single Cell MDA 46.8 Ancient Calculus Sample TM7_ANC_38.39_G1_1 (SRASRR957738,SRR957739) 48.1 Dalheim B61 skeleton; label: B61 TM7_ EAM_G5_1_HOT_356 morbus = disease Metagenome (PRJNA289925; SRP064209) 50.8 TM7_ EAM_G5_2_HOT_356 Metagenome (PRJNA289925; SRP064209) 50.5 TM7_CMJM_G6_1_HOT_870 gingivalicus= found on gingiva HMP Sample (SRS013946) 32.3 TM7_KMM_G3_1_HOT_351 coccus = shape Lab Enrichment Culture