| Taxon ID | Genus △ | Species | Status | Body Site | Flag | Taxon Link | Genome Link | Genome Size |
| HMT-346 | Saccharibacteria (TM7) [G-1] | bacterium HMT 346 | Phylotype | Oral | | | | |
| HMT-347 | Saccharibacteria (TM7) [G-1] | bacterium HMT 347 | Phylotype | Oral | | | | |
| HMT-348 | Saccharibacteria (TM7) [G-1] | bacterium HMT 348 | Phylotype | Oral | | | | 0.11 - 0.47 Mbps |
| HMT-349 | Saccharibacteria (TM7) [G-1] | bacterium HMT 349 | Phylotype | Oral | | | | |
| HMT-352 | Saccharibacteria (TM7) [G-1] | bacterium HMT 352 | Phylotype | Oral | | | | |
| HMT-353 | Saccharibacteria (TM7) [G-1] | bacterium HMT 353 | Unnamed | Oral | | | | |
| HMT-488 | Saccharibacteria (TM7) [G-1] | bacterium HMT 488 | Unnamed | Oral | | | | 0.83 - 0.93 Mbps |
| HMT-869 | Saccharibacteria (TM7) [G-1] | bacterium HMT 869 | Phylotype | Oral | | | | |
| HMT-952 | Saccharibacteria (TM7) [G-1] | bacterium HMT 952 | Unnamed | Oral | | | | 0.71 - 0.71 Mbps |
| HMT-957 | Saccharibacteria (TM7) [G-1] | bacterium HMT 957 | Unnamed | Oral | | | | 0.78 Mbps |
| HMT-350 | Saccharibacteria (TM7) [G-2] | bacterium HMT 350 | Phylotype | Oral | | | | |
| HMT-351 | Saccharibacteria (TM7) [G-3] | bacterium HMT 351 | Phylotype | Oral | | | | |
| HMT-364 | Saccharibacteria (TM7) [G-3] | bacterium HMT 364 | Phylotype | Oral | | | | |
| HMT-367 | Saccharibacteria (TM7) [G-3] | bacterium HMT 367 | Phylotype | Oral | | | | |
| HMT-371 | Saccharibacteria (TM7) [G-3] | bacterium HMT 371 | Phylotype | Oral | | | | |
| HMT-355 | Saccharibacteria (TM7) [G-4] | bacterium HMT 355 | Phylotype | Oral | | | | |
| HMT-356 | Saccharibacteria (TM7) [G-5] | bacterium HMT 356 | Phylotype | Oral | | | | |
| HMT-870 | Saccharibacteria (TM7) [G-6] | bacterium HMT 870 | Phylotype | Oral | | | | |
| HMT-954 | Saccharibacteria (TM7) [G-7] | bacterium HMT 954 | Phylotype | Oral | | | | |
| HMT-986 | Saccharibacteria (TM7) [G-7] | bacterium HMT 986 | NonOralRef | NonOralRef | | | | 0.75 Mbps |
| HMT-987 | Saccharibacteria (TM7) [G-7] | bacterium HMT 987 | NonOralRef | NonOralRef | | | | 0.68 Mbps |
| HMT-989 | Saccharibacteria (TM7) [G-7] | bacterium HMT 989 | NonOralRef | NonOralRef | | | | 0.85 Mbps |
| HMT-955 | Saccharibacteria (TM7) [G-8] | bacterium HMT 955 | Unnamed | Oral | | | | 0.84 - 0.89 Mbps |
| HMT-856 | Sanguibacter | keddieii | Named | Unassigned | | | | 4.25 Mbps |
| HMT-642 | Scardovia | inopinata | Named | Unassigned | | | | 1.80 Mbps |
| HMT-195 | Scardovia | wiggsiae | Named | Oral | | | | 1.56 Mbps |
| HMT-850 | Schaalia | cardiffensis | Named | Oral | | | | 2.21 Mbps |
| HMT-617 | Schaalia | georgiae | Named | Oral | | | | 2.48 - 2.50 Mbps |
| HMT-181 | Schaalia | lingnae [Not Validly Published] | Named | Oral | | | | 1.90 Mbps |
| HMT-671 | Schaalia | meyeri | Named | Oral | | | | 2.05 Mbps |
| HMT-701 | Schaalia | odontolyticus | Named | Oral | | | | 2.34 - 2.43 Mbps |
| HMT-172 | Schaalia | sp. HMT 172 | Unnamed | Oral | | | | 2.47 Mbps |
| HMT-178 | Schaalia | sp. HMT 178 | Unnamed | Oral | | | | 2.82 Mbps |
| HMT-180 | Schaalia | sp. HMT 180 | Unnamed | Oral | | | | 2.37 Mbps |
| HMT-877 | Schaalia | sp. HMT 877 | Unnamed | Oral | | | | 2.71 Mbps |
| HMT-026 | Schlegelella | aquatica | Named | Unassigned | | | | |
| HMT-024 | Schlegelella | thermodepolymerans | Named | Unassigned | | | | 3.83 - 4.03 Mbps |
| HMT-261 | Segetibacter | aerophilus | Named | Unassigned | | | | 5.89 Mbps |
| HMT-124 | Selenomonas | artemidis | Named | Oral | | | | 2.21 - 2.35 Mbps |
| HMT-139 | Selenomonas | dianae | Named | Oral | | | | |
| HMT-125 | Selenomonas | flueggei | Named | Oral | | | | 2.17 Mbps |
| HMT-639 | Selenomonas | infelix | Named | Oral | | | | 2.41 Mbps |
| HMT-130 | Selenomonas | noxia | Named | Oral | | | | 2.05 - 2.11 Mbps |
| HMT-126 | Selenomonas | sp. HMT 126 | Unnamed | Oral | | | | 2.89 Mbps |
| HMT-133 | Selenomonas | sp. HMT 133 | Unnamed | Oral | | | | 2.07 Mbps |
| HMT-134 | Selenomonas | sp. HMT 134 | Phylotype | Oral | | | | |
| HMT-136 | Selenomonas | sp. HMT 136 | Unnamed | Oral | | | | 2.46 Mbps |
| HMT-137 | Selenomonas | sp. HMT 137 | Unnamed | Oral | | | | 2.48 Mbps |
| HMT-138 | Selenomonas | sp. HMT 138 | Unnamed | Oral | | | | 2.38 Mbps |
| HMT-146 | Selenomonas | sp. HMT 146 | Lost | Oral | | | | |
| HMT-149 | Selenomonas | sp. HMT 149 | Unnamed | Oral | | | | 2.47 Mbps |
| HMT-388 | Selenomonas | sp. HMT 388 | Phylotype | Unassigned | | | | |
| HMT-442 | Selenomonas | sp. HMT 442 | Phylotype | Oral | | | | |
| HMT-478 | Selenomonas | sp. HMT 478 | Unnamed | Oral | | | | 2.28 Mbps |
| HMT-479 | Selenomonas | sp. HMT 479 | Lost | Oral | | | | |
| HMT-481 | Selenomonas | sp. HMT 481 | Lost | Oral | | | | |
| HMT-501 | Selenomonas | sp. HMT 501 | Phylotype | Unassigned | | | | |
| HMT-892 | Selenomonas | sp. HMT 892 | Unnamed | Oral | | | | 2.31 Mbps |
| HMT-919 | Selenomonas | sp. HMT 919 | Unnamed | Oral | | | | |
| HMT-920 | Selenomonas | sp. HMT 920 | Unnamed | Oral | | | | 2.44 Mbps |
| HMT-936 | Selenomonas | sp. HMT 936 | Phylotype | Unassigned | | | | |
| HMT-937 | Selenomonas | sp. HMT 937 | Phylotype | Oral | | | | |
| HMT-151 | Selenomonas | sputigena | Named | Oral | | | | 2.56 Mbps |
| HMT-115 | Serratia | marcescens | Named | Unassigned | | | | 5.13 Mbps |
| HMT-095 | Shuttleworthia | satelles | Named | Oral | | | | 2.17 Mbps |
| HMT-683 | Simonsiella | muelleri | Named | Oral | | | | 2.37 Mbps |
| HMT-602 | Slackia | exigua | Named | Oral | | | | 2.10 Mbps |
| HMT-844 | Sneathia | amnii [Not Validly Published] | Named | Oral | | | | 1.33 Mbps |
| HMT-837 | Sneathia | sanguinegens | Named | Oral | | | | 1.29 Mbps |
| HMT-678 | Solobacterium | moorei | Named | Oral | | | | 2.01 - 2.34 Mbps |
| HMT-003 | Sphingomonas | echinoides | Named | Unassigned | | | | 4.26 Mbps |
| HMT-004 | Sphingomonas | sp. HMT 004 | Phylotype | Unassigned | | | | |
| HMT-006 | Sphingomonas | sp. HMT 006 | Phylotype | Unassigned | | | | |
| HMT-550 | Staphylococcus | aureus | Named | Nasal | | | | 2.72 - 2.97 Mbps |
| HMT-331 | Staphylococcus | auricularis | Named | Unassigned | | | | 2.20 Mbps |
| HMT-116 | Staphylococcus | capitis | Named | Unassigned | | | | 2.50 Mbps |
| HMT-567 | Staphylococcus | caprae | Named | Oral | | | | 2.47 Mbps |
| HMT-117 | Staphylococcus | cohnii | Named | Unassigned | | | | 2.63 Mbps |
| HMT-601 | Staphylococcus | epidermidis | Named | Oral | | | | 2.45 - 2.65 Mbps |
| HMT-120 | Staphylococcus | haemolyticus | Named | Unassigned | | | | 2.56 Mbps |
| HMT-127 | Staphylococcus | hominis | Named | Unassigned | | | | 1.98 Mbps |
| HMT-128 | Staphylococcus | lugdunensis | Named | Unassigned | | | | 2.61 Mbps |
| HMT-141 | Staphylococcus | pasteuri | Named | Unassigned | | | | 2.56 Mbps |
| HMT-142 | Staphylococcus | pettenkoferi | Named | Unassigned | | | | 2.50 Mbps |
| HMT-233 | Staphylococcus | schleiferi | Named | Unassigned | | | | 2.53 Mbps |
| HMT-076 | Staphylococcus | warneri | Named | Oral | | | | 2.43 - 2.56 Mbps |
| HMT-663 | Stenotrophomonas | maltophilia | Named | Unassigned | | | | 4.54 - 4.92 Mbps |
| HMT-037 | Stenotrophomonas | nitritireducens | Named | Unassigned | | | | 3.98 Mbps |
| HMT-419 | Stomatobaculum | longum | Named | Oral | | | | 2.31 Mbps |
| HMT-097 | Stomatobaculum | sp. HMT 097 | Unnamed | Oral | | | | |
| HMT-373 | Stomatobaculum | sp. HMT 373 | Phylotype | Oral | | | | |
| HMT-910 | Stomatobaculum | sp. HMT 910 | Phylotype | Oral | | | | |
| HMT-537 | Streptococcus | agalactiae | Named | Unassigned | | | | 2.02 - 2.46 Mbps |
| HMT-543 | Streptococcus | anginosus | Named | Oral | | | | 1.82 - 2.29 Mbps |
| HMT-073 | Streptococcus | australis | Named | Oral | | | | 2.13 Mbps |
| HMT-576 | Streptococcus | constellatus | Named | Oral | | | | 1.84 - 1.99 Mbps |
| HMT-578 | Streptococcus | cristatus clade 578 | Named | Oral | | | | 1.98 - 2.08 Mbps |
| HMT-886 | Streptococcus | cristatus clade 886 | Named | Oral | | | | 2.14 Mbps |
| HMT-594 | Streptococcus | downei | Named | Unassigned | | | | 2.24 Mbps |
| HMT-622 | Streptococcus | gordonii | Named | Oral | | | | 2.20 Mbps |
| HMT-431 | Streptococcus | infantis clade 431 | Named | Oral | | | | 2.18 Mbps |
| HMT-638 | Streptococcus | infantis clade 638 | Named | Oral | | | | 1.74 - 1.95 Mbps |
| HMT-644 | Streptococcus | intermedius | Named | Oral | | | | 1.91 - 2.00 Mbps |
| HMT-948 | Streptococcus | lactarius | Named | Oral | | | | |
| HMT-677 | Streptococcus | mitis | Named | Nasal, Oral | | | | 1.71 - 2.25 Mbps |
| HMT-686 | Streptococcus | mutans | Named | Oral | | | | 1.74 - 2.33 Mbps |
| HMT-058 | Streptococcus | oralis subsp. dentisani clade 058 | Named | Oral | | | | 1.85 Mbps |
| HMT-398 | Streptococcus | oralis subsp. dentisani clade 398 | Named | Oral | | | | 1.92 - 2.02 Mbps |
| HMT-707 | Streptococcus | oralis subsp. oralis | Named | Oral | | | | 1.85 - 2.02 Mbps |
| HMT-070 | Streptococcus | oralis subsp. tigurinus clade 070 | Unnamed | Oral | | | | 2.00 Mbps |
| HMT-071 | Streptococcus | oralis subsp. tigurinus clade 071 | Named | Oral | | | | 1.98 Mbps |
| HMT-411 | Streptococcus | parasanguinis clade 411 | Named | Oral | | | | 2.05 Mbps |
| HMT-721 | Streptococcus | parasanguinis clade 721 | Named | Oral | | | | 1.99 - 2.19 Mbps |
| HMT-728 | Streptococcus | peroris | Named | Oral | | | | 1.64 Mbps |
| HMT-734 | Streptococcus | pneumoniae | Named | Nasal | | | | 2.03 - 2.29 Mbps |
| HMT-745 | Streptococcus | pyogenes | Named | Oral | | | | 1.72 - 1.94 Mbps |
| HMT-755 | Streptococcus | salivarius | Named | Oral | | | | 2.05 - 2.43 Mbps |
| HMT-758 | Streptococcus | sanguinis | Named | Oral | | | | 2.07 - 2.43 Mbps |
| HMT-767 | Streptococcus | sinensis | Named | Oral | | | | 2.06 Mbps |
| HMT-768 | Streptococcus | sobrinus | Named | Oral | | | | 2.10 - 2.14 Mbps |
| HMT-056 | Streptococcus | sp. HMT 056 | Unnamed | Oral | | | | 1.94 Mbps |
| HMT-057 | Streptococcus | sp. HMT 057 | Lost | Oral | | | | |
| HMT-061 | Streptococcus | sp. HMT 061 | Lost | Oral | | | | 1.77 Mbps |
| HMT-064 | Streptococcus | sp. HMT 064 | Unnamed | Oral | | | | 2.01 Mbps |
| HMT-066 | Streptococcus | sp. HMT 066 | Unnamed | Oral | | | | 2.23 Mbps |
| HMT-074 | Streptococcus | sp. HMT 074 | Lost | Oral | | | | |
| HMT-423 | Streptococcus | sp. HMT 423 | Lost | Oral | | | | |
| HMT-152 | Streptococcus | thermophilus | Named | Unassigned | | | | 1.93 Mbps |
| HMT-021 | Streptococcus | vestibularis | Named | Oral | | | | 1.87 - 2.02 Mbps |
| HMT-435 | Syntrophomonadaceae [VIII][G-1] | bacterium HMT 435 | Phylotype | Unassigned | | | | |
