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HOMD specifications


Unique identifier OMICS_29834
Alternative name Human Oral Microbiome Database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • person_outline homd-info
  • person_outline Tsute Chen

Additional information


Publication for Human Oral Microbiome Database

HOMD citations


Research on oral microbiota of monozygotic twins with discordant caries experience in vitro and in vivo study

Sci Rep
PMCID: 5940813
PMID: 29740156
DOI: 10.1038/s41598-018-25636-w
call_split See protocol

[…] stered with 98.5% similarity cutoff using UPARSE (version 7.1). The taxonomy of each 16S rRNA gene sequence was analyzed by Ribosomal Database Project Classifier (http://rdp.cme.msu.edu/) against the Human Oral Microbiome Database with confidence threshold of 70%. Alpha diversity indices (Shannon index, Simpson index) and richness estimators (ACE index and Chao 1 index) calculations were performed […]


Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging

Front Microbiol
PMCID: 5943489
PMID: 29774014
DOI: 10.3389/fmicb.2018.00862
call_split See protocol

[…] ysis. The operational taxonomic units (OTUs) were clustered at 97% sequence similarity using USEARCH and then assessed using BLASTN 2.6.0+ against four sets of 16S rRNA reference sequences, including HOMD RefSeq V14.5, HOMD RefSeq Extended V1.1, modified GreenGeneGold, and the NCBI's Microbial 16S set (Al-Hebshi et al., , ). Taxonomy classification was also assigned according to the Greengenes dat […]


Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults

PMCID: 5914044
PMID: 29685174
DOI: 10.1186/s40168-018-0448-x

[…] 9] sequences per sample), with similar number of reads in all cohorts []. Filtered sequence reads were clustered into operational taxonomic units (OTUs) and subsequently assigned to taxa by using the Human Oral Microbiome Database (HOMD) pre-defined taxonomy map of reference sequences with ≥ 97% identity []. Summary of sequence reads per sample which were assigned to HOMD reference is shown in Add […]


Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis

PMCID: 5904416
PMID: 29666288
DOI: 10.1128/mBio.00575-18

[…] ipeline QIIME (). Paired-end reads were assembled and then quality filtered using the QIIME Python scripts multiple_join_paired_ends.py and multiple_split_libraries_fastq.py. Reads were mapped to the Human Oral Microbiome Database (HOMD) 16S rRNA reference (v14.51) to determine the number of reads mapping to each distinct OTU using the QIIME Python script pick_closed_reference_otus.py. Relative ab […]


Species Level Description of the Human Ileal Bacterial Microbiota

Sci Rep
PMCID: 5856834
PMID: 29549283
DOI: 10.1038/s41598-018-23198-5
call_split See protocol

[…] group-level identification) whereas OTU’s with a similarity of 97–99.2% was assigned to the genus level. When appropriate, the provisional taxonomy developed by the Human oral microbiome project (www.homd.org) was used for hitherto unnamed species. Chimeras and any species/OTU found in the negative controls were rejected. A comparison between results obtained by QIIME, the software package typical […]


Ancient pathogen DNA in human teeth and petrous bones

Ecol Evol
PMCID: 5869295
PMID: 29607044
DOI: 10.1002/ece3.3924

[…] of tooth, many such as Clostridium and Citrobacter have both pathogenic species and ones commonly found in soil. Also, genera associated with human natural and pathogenic oral microbiome (http://www.homd.org/) such as Actinomyces, Methanobrevibacter, and Streptococcus were also much more abundant in the tooth‐derived dataset than in the petrous bone data. Among the eight genera being skewed in fa […]

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HOMD institution(s)
The Forsyth Institute, Boston, MA, USA; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
HOMD funding source(s)
Supported by National Institute of Dental and Craniofacial Research (contract U01 DE016937 and grant DE017106, partial); American Recovery and Reinvestment Act of 2009 (DE016937, supplement).

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