HOMD Genomic Version History
2025-05-05 Genomic Reference Sequences Version 11.01 release notes
Genomic RefSeq V11.01 has a total of 8,488 genomes. This update is based on the search results of
1) Species names of the current version of HOMD Taxonomy (V4.0) and 2) Genbank assession IDs in the GENOME TAXONOMY DATABASE (GTDB).
2023-03-18 Genomic Reference Sequences Version 10.1 release notes
We now have a total of 8,622 genomes which is up from 2,123 before.
We started with 1,321,179 genomic sequences available in GenBank (as of July 5th, 2022) and identified those that belong to human oral microbial taxa based on taxonomy names and several other criteria.
Here is the detail report for this update: https://homd.org/ftp/genomes/V10.1/report.html
Here is the detail report for this update: https://homd.org/ftp/genomes/V10.1/report.html
2022-02-10 Genomic Reference Sequences Version 9.15 release notes
We have added 36 new genomes (taking the total to 2123):
SEQF3712 HMT-096 Lachnospiraceae_[G-2] bacterium_HMT_096 F0428
SEQF3708 HMT-194 Arachnia rubra DSMZ 100122
SEQF3703 HMT-218 Leptotrichia sp._HMT_218 F0707
SEQF3704 HMT-221 Pseudoleptotrichia sp._HMT_221 F0705
SEQF3680 HMT-275 Porphyromonas sp._HMT_275 W7780
SEQF3700 HMT-291 Prevotella denticola F0288
SEQF3701 HMT-291 Prevotella denticola F0119
SEQF3702 HMT-291 Prevotella denticola F0115
SEQF3711 HMT-291 Prevotella denticola F0105
SEQF3698 HMT-298 Prevotella histicola F0411
SEQF3696 HMT-313 Prevotella jejuni F0697
SEQF3697 HMT-313 Prevotella jejuni F0106
SEQF3705 HMT-374 Cellulosimicrobium cellulans ORNL-0100
SEQF3678 HMT-349 Saccharibacteria_(TM7)_[G-1] bacterium_HMT_349 PM007
SEQF3706 HMT-416 Fannyhessea sp._HMT_416 W9116
SEQF3687 HMT-469 Prevotella melaninogenica F0695
SEQF3688 HMT-469 Prevotella melaninogenica F0692
SEQF3689 HMT-469 Prevotella melaninogenica F0516
SEQF3690 HMT-469 Prevotella melaninogenica F0300
SEQF3691 HMT-469 Prevotella melaninogenica F0301
SEQF3693 HMT-469 Prevotella melaninogenica F0299
SEQF3694 HMT-469 Prevotella melaninogenica F0054
SEQF3695 HMT-469 Prevotella melaninogenica F0091
SEQF3683 HMT-475 Prevotella sp._HMT_475 F0059
SEQF3707 HMT-513 Aggregatibacter sp._HMT_513 W11186
SEQF3681 HMT-572 Prevotella veroralis F0319
SEQF3692 HMT-685 Prevotella multiformis F0096
SEQF3684 HMT-693 Prevotella nigrescens F0109
SEQF3685 HMT-693 Prevotella nigrescens F0630
SEQF3686 HMT-693 Prevotella nigrescens F0103
SEQF3709 HMT-739 Arachnia propionica F0231
SEQF3710 HMT-739 Arachnia propionica F0714
SEQF3699 HMT-782 Prevotella fusca W1435
SEQF3682 HMT-885 Prevotella scopos W2052
SEQF3679 HMT-948 Streptococcus lactarius CCUG 66490
SEQF3677 HMT-998 Victivallales_[G-1] bacterium_HMT_998 CCUG 44730
2020-11-13 Genomic Reference Sequences Version 9.14 release notes
We have removed 45 Porphyromonas gingivalis, 28 Prevotolla intermedia, 45 Aggregatibacter actinomycetemcomitans, 245 Streptococcus mutans, 123 Streptococcus mitis, 1 Treponema Denticola and 1 Fusobacterium massiliense which takes current version of the Genomic Refseq to 9.14 and contains total of 2087 genomic DNA sequences.
2020-08-28 Genomic Reference Sequences Version 9.13 release notes
We have removed 14 survey genomes and 3 genomes of ncbi GenBank is deleted which takes current version of the Genomic Refseq to 9.13 and contains total of 1599 genomic DNA sequences.
2020-08-28 Genomic Reference Sequences Version 9.12 release notes
We have removed 5 duplicate genomes which takes current version of the Genomic Refseq to 9.12 and contains total of 1616 genomic DNA sequences.
2020-08-07 Genomic Reference Sequences Version 9.11 release notes
We have added 11 new genomes which takes current version of the Genomic Refseq to 9.11 and contains total of 1621 genomic DNA sequences
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 HB001
HMT-042 Mogibacterium timidum W9173
HMT-340 Brevibacterium paucivorans UMB1301
HMT-061 Streptococcussp. HMT 061 F0704
HMT-902 Capnocytophaga sp. HMT 902 W10638
HMT-102 Oribacteriumsp. HMT 102 W9097
HMT-903 Capnocytophagasp. HMT 903 W10654
HMT-223 Leptotrichiasp. HMT 223 F0708
HMT-417 Leptotrichiasp. HMT 417 F0703
HMT-081 Peptostreptococcaceae [XI][G-7] bacterium HMT 081 W5028
HMT-169 Actinomycessp. oral taxon 169 F0496
HMT-042 Mogibacterium timidum W9173
HMT-340 Brevibacterium paucivorans UMB1301
HMT-061 Streptococcussp. HMT 061 F0704
HMT-902 Capnocytophaga sp. HMT 902 W10638
HMT-102 Oribacteriumsp. HMT 102 W9097
HMT-903 Capnocytophagasp. HMT 903 W10654
HMT-223 Leptotrichiasp. HMT 223 F0708
HMT-417 Leptotrichiasp. HMT 417 F0703
HMT-081 Peptostreptococcaceae [XI][G-7] bacterium HMT 081 W5028
HMT-169 Actinomycessp. oral taxon 169 F0496
2020-06-16 Genomic Reference Sequences Version 9.10 release notes
We have added prokka annotation for SEQF2736 which was missing any annotation. And we added 40 new genomes. This takes current version of the Genomic Refseq to 9.10 and contains a total of 1610 genomic DNA sequences. The 1610 sequences include both oral, nasal and non-oral/non-nasal reference genomes.
Following 40 Genomes were added:
HMT-677 Streptococcus mitis NCTC 12261
HMT-725 Treponema pectinovorum Marseille-1-CSURP6641
HMT-725 Treponema pectinovorum Marseille-3-CSURP7641
HMT-725 Treponema pectinovorum Marseille-4-CSURP7639
HMT-725 Treponema pectinovorum Marseille-2-CSURP6642
HMT-689 Fusobacterium naviforme NCTC13121
HMT-689 Fusobacterium naviforme CCUG 50052
HMT-050 Corynebacterium macginleyi NML 080212
HMT-050 Corynebacterium macginleyi NML 120205
HMT-024 Schlegelella thermodepolymerans DSM 15344
HMT-213 Leptotrichia hongkongensis JMUB5056
HMT-725 Treponema pectinovorum ATCC 700769
HMT-261 Segetibacter aerophilus NBRC 106135
HMT-024 Schlegelella thermodepolymerans DSM 15264
HMT-024 Schlegelella thermodepolymerans DSM 15344
HMT-548 Peptoniphilus asaccharolyticus DSM 20463
HMT-101 Neisseria perflava UMB0023
HMT-689 Fusobacterium naviforme ATCC 25832
HMT-747 Erythromicrobiumr amosum JCM 10282
HMT-835 Corynebacterium mucifaciens ATCC 700355
HMT-050 Corynebacterium macginleyi CCUG 32361
HMT-636 Bosea vestrisii 3192
HMT-017 Anaerococcus octavius NCTC9810
HMT-017 Anaerococcus octavius UMB0119
HMT-708 Actinomyces oricola R5292
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 FS03P
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 CM010
HMT-955 Saccharibacteria (TM7) [G-8] bacterium HMT 955 CM009
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 CM006
HMT-955 Saccharibacteria (TM7) [G-8] bacterium HMT 955 CM003
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 CM002
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 CM001
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 AC002
HMT-955 Saccharibacteria (TM7) [G-8] bacterium HMT 955 FS17P
HMT-955 Saccharibacteria (TM7) [G-8] bacterium HMT 955 FS14P
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 FS15P
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 FS13P
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 FS07P-B
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 FS05P-B
HMT-991 Absconditabacteria (SR1) [G-3] bacterium HMT 991 RAAC1_SR1_1
HMT-725 Treponema pectinovorum Marseille-1-CSURP6641
HMT-725 Treponema pectinovorum Marseille-3-CSURP7641
HMT-725 Treponema pectinovorum Marseille-4-CSURP7639
HMT-725 Treponema pectinovorum Marseille-2-CSURP6642
HMT-689 Fusobacterium naviforme NCTC13121
HMT-689 Fusobacterium naviforme CCUG 50052
HMT-050 Corynebacterium macginleyi NML 080212
HMT-050 Corynebacterium macginleyi NML 120205
HMT-024 Schlegelella thermodepolymerans DSM 15344
HMT-213 Leptotrichia hongkongensis JMUB5056
HMT-725 Treponema pectinovorum ATCC 700769
HMT-261 Segetibacter aerophilus NBRC 106135
HMT-024 Schlegelella thermodepolymerans DSM 15264
HMT-024 Schlegelella thermodepolymerans DSM 15344
HMT-548 Peptoniphilus asaccharolyticus DSM 20463
HMT-101 Neisseria perflava UMB0023
HMT-689 Fusobacterium naviforme ATCC 25832
HMT-747 Erythromicrobiumr amosum JCM 10282
HMT-835 Corynebacterium mucifaciens ATCC 700355
HMT-050 Corynebacterium macginleyi CCUG 32361
HMT-636 Bosea vestrisii 3192
HMT-017 Anaerococcus octavius NCTC9810
HMT-017 Anaerococcus octavius UMB0119
HMT-708 Actinomyces oricola R5292
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 FS03P
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 CM010
HMT-955 Saccharibacteria (TM7) [G-8] bacterium HMT 955 CM009
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 CM006
HMT-955 Saccharibacteria (TM7) [G-8] bacterium HMT 955 CM003
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 CM002
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 CM001
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 AC002
HMT-955 Saccharibacteria (TM7) [G-8] bacterium HMT 955 FS17P
HMT-955 Saccharibacteria (TM7) [G-8] bacterium HMT 955 FS14P
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 FS15P
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 FS13P
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 FS07P-B
HMT-488 Saccharibacteria (TM7) [G-1] bacterium HMT 488 FS05P-B
HMT-991 Absconditabacteria (SR1) [G-3] bacterium HMT 991 RAAC1_SR1_1
2019-09-02 Genomic Reference Sequences Version 9.03 release notes
The genomic sequences provided by the eHOMD are referred to as "Genomic Reference Sequences" or in short "Genomic Refseq". The current version of the Genomic RefSeq is V9.02 and contains a total of 1,570 genomic DNA sequences representing the eHOMD taxa. The 1,570 sequences include both oral, nasal and non-oral/non-nasal reference genomes.
