The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

By Tsute Chen, Wen-Han Yu, Jacques Izard, Oxana V. Baranova, Abirami Lakshmanan, Floyd E. Dewhirst. Database J. Biol. Databases Curation, 2010

1,101 citations recorded by the source corpus.

The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity based on a curated 16S rRNA gene-based provisional naming scheme. Currently, two primary types of information are provided in HOMD—taxonomic and genomic. Named oral species and taxa identified from 16S rRNA gene sequence analysis of oral isolates and cloning studies were placed into defined 16S rRNA phylotypes and each given unique Human Oral Taxon (HOT) number. The HOT interlinks phenotypic, phylogenetic, genomic, clinical and bibliographic information for each taxon. A BLAST search tool is provided to match user 16S rRNA gene sequences to a curated, full length, 16S rRNA gene reference data set. For genomic analysis, HOMD provides comprehensive set of analysis tools and maintains frequently updated annotations for all the human oral microbial genomes that have been sequenced and publicly released. Oral bacterial genome sequences, determined as part of the Human Microbiome Project, are being added to the HOMD as they become available. We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites. Database URL: http://www.homd.org

Subfields: Molecular Biology, Periodontics

View Paper: https://www.semanticscholar.org/paper/5c86baa92ece7425ceb09232dddd9538c224ce5e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

MiDAS: the field guide to the microbes of activated sludge (2015, neutral): “A provisional solution has been to focus manual annotation on those organisms that are abundant in a particular habitat, i.e. the Human Oral Microbiome Database (HOMD) (15).”
Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study (2016, methodology): “…Adonis ’ function, vegan package, R) 28 of the UniFrac distance was used to test differences in overall oral microbiome composition according to pancreatic cancer status, controlling for potential confounders (age, sex, race, BMI, smoking status, alcohol consumption status and history of diabetes).”
Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences (2014, methodology): “When we limited our comparison to only the 329 most abundant MED nodes, numerically equal to the 329 OTUs found, the MED nodes still matched more HOMD taxa (138) than did the OTUs (112).”
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources (2020, methodology): “Single-omic repositories include MetaboLights [36] and Metabolomics Workbench [37] for metabolome data, the PRoteomics IDEntifications Database [38] for proteome data, Gene Expression Omnibus [39] and Sequence Read Archive [40] for genomic data, the Encyclopedia of DNA Elements [41] for functional e”
Mucosal microbiome dysbiosis in gastric carcinogenesis (2017, methodology): “21 The abundances of OTUs with 100% sequence identities with those found in the HOM database were compared among disease stages.”