Concordance of HOMIM and HOMINGStechnologies in the microbiome analysis of clinical samples

Abstract

BackgroundOver 700 bacterial species reside in human oral cavity, many of which are associated with local or distant site infections. Extensive characterization of the oral microbiome depends on the technologies used to determine the presence and proportions of specific bacterial species in various oral sites.ObjectiveThe objective of this study was to compare the microbial composition of dental plaque at baseline using Human Oral Microbe Identification Microarray (HOMIM) and Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technologies, which are based on 16S rRNA.MethodsDental plaque samples were collected from 96 patients at baseline prior to a dental procedure involving manipulation of gingival tissues. The samples were surveyed for 293 and 597 oral bacterial species via HOMIM and HOMINGS, respectively, based on 16S rRNA gene sequences. We determined the concordance between the two technologies for common species. Genus level analysis was performed using HOMINGS-specific genus identification capabilities.ResultsHOMINGS detected twice the number of species in the same dental plaque samples compared to HOMIM. For the species detected by both HOMIM and HOMINGS, there was no difference in relative proportions of overall bacterial composition at the species, genus or phylum levels. Additionally, there was no difference in relative proportion for total species per patient between the two technologies.ConclusionHOMINGS significantly expanded oral bacterial species identification compared to HOMIM. The genus and species probes, combined in HOMINGS, provided a more comprehensive representation of oral bacterial community, critical for future characterization of oral microbes in distant site infections.

A practical guide to the oral microbiome and its relation to health and disease

“…The advantages of HOMINGS are that it is computationally efficient, rapid, and reproducible and can identify the majority of the oral microbiome at the species level. There is good correlation between HOMINGS and HOMIM (Mougeot et al, 2016). HOM-INGS has been used in several recent studies demonstrating bacterial associations with endodontic lesions (Gomes et al, 2015), salivary microbiomes in caries and periodontitis (Belstrom et al, 2016b), temporal differences in salivary microbiomes (Belstrom et al, 2016a), and in biofilm models in response to sucrose-induced dysbiosis (Rudney et al, 2015).…”

The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health

“…As characterizations of oral microbiomes move from strictly culture-based methods to using the Human Oral Microbiome Identification Microarray (HOMIM)[122] and, lately, whole community profiling using high throughput 16S rRNA sequencing and shotgun metagenomics, the concepts of the “ecological plaque hypothesis”[71] and a super complex oral ecosystem have become more relevant. This complexity, however, has also pointed out that understanding microecosystem functioning requires a multi level view that includes taxonomic assessment (composition), potential (metagenome -transcriptome), and encoded functions (proteome and metabolome) [123, 124].…”

“…Along these lines, we are already making efforts to identify oral microbial markers at increased taxonomic depth and diversity coverage, a particularly relevant issue in oral disease. For instance, the improved Human Oral Microbiome using next generation sequencing (HOMIN GS ), from the Forsyth institute (http://forsyth.org) [122], harbors a well-curated collection of sequences from oral bacteria at the species level, allowing researchers to accurately expand marker identification in the highly diverse oral ecosystem. Likewise, more rigorous studies on infant twin cohorts and using genome-wide analyses, host gene expression levels and deep sequencing in the oral cavity could provide clues on the extent to which oral disease in children is explained by heritable or environmentally-acquired taxa.…”

Analysis of oral bacterial communities: comparison of HOMINGS with a tree-based approach implemented in QIIME

“…HOMINGS has been shown to support and expand results of HOMIM [17], but direct comparison of HOMINGS with the more generally accepted treebased methods is lacking even though the initiatory MiSeq library lends itself to parallel analysis. In the present study, 10 mock-community mixtures of 16S rRNA gene amplicons, together with 119 MiSeq libraries prepared from supragingival plaque samples acquired from primary Sjögren's Syndrome (pSS) patients and from subjects with normal salivary flow, are analyzed in parallel using HOMINGS and a tree-based approach implemented in the QIIME pipeline.…”