The human oral microbiome

Abstract

The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.

FIG. 1.

Neighbor-joining tree for human oral taxa in the phylum Tenericutes and the classes Bacilli and Erysipelotrichia of the phylum Firmicutes. The name of each taxon is followed by the oral taxon number, clone or strain number, GenBank accession number, the number of clones out of 34,879 that were identified as this taxon, and a symbol indicating that the taxon is a named species (•), an unnamed cultivated taxa (▪), or an uncultivated phylotype (□). The tree was constructed with MEGA 4.3 using the Jukes and Cantor correction neighbor-joining distance matrix. Comparisons with missing data were eliminated pairwise. The numbers to the left of the branches indicate the percentage of times the clade was recovered out of 1,000 bootstrap resamplings. Only bootstrap percentages greater than 50 are shown. Roman numerals in square brackets following a genus name indicate Collins' Clostridia cluster numbers (17). Major clades are marked as follows: encircled “1,” Bacilli; encircled “2,” Firmicutes; encircled “3,” Erysipelotrichia; and encircled “4,” Tenericutes (previously know as the class Mollicutes within Firmicutes).

FIG. 2.

Neighbor-joining tree for human oral taxa in the class Clostridia of the phylum Firmicutes. Labeling and methods used are as described in Fig. 1. Major clades are marked as follows: encircled “1,” Collins XI; encircled “2,” Peptostreptococcaceae; encircled “3,” Collins XIII; encircled “4,” unnamed family F1; encircled “5,” Collins XV, Eubacteriaceae; encircled “6,” Collins XIVa, Lachnospiraceae; encircled “7,” Peptococcaceae; encircled “8,” Collins XIII, Syntrophomonadaceae; and encircled “9,” unnamed family F2.

FIG. 3.

Neighbor-joining tree for human oral taxa in the Veillonellaceae (previously Acidaminococcaceae) family of the class Clostridia of the phylum Firmicutes. Labeling and methods used are as described in Fig. 1.

FIG. 4.

Neighbor-joining tree for human oral taxa in the phyla Actinobacteria and Fusobacteria. Labeling and methods used are as described in Fig. 1. Major clades are marked as follows: encircled “1,” phylum Actinobacteria; encircled “2,” order Actinomycetales; encircled “3,” order Bifidobacteriales; encircled “4,” order Coriobacteriales; and encircled “5,” phylum Fusobacteria.

FIG. 5.

Neighbor-joining tree for human oral taxa in the phylum Bacteroidetes. Labeling and methods used are as described in Fig. 1. Encircled “0” through “8” symbols refer to clades discussed in the text.

FIG. 6.

Neighbor-joining tree for human oral taxa in the phylum Proteobacteria. Labeling and methods used are as described in Fig. 1. The Proteobacteria classes are marked with the corresponding Greek letters.

FIG. 7.

Neighbor-joining tree for human oral taxa in the phyla Spirochaetes, Chlamydiae, Chloroflexi, Synergistetes, TM7, and SR1. Labeling and methods used are as described in Fig. 1. The phyla are labeled as follows: encircled “1,” Spirochaetes; encircled “2,” Chlamydiae; encircled “3,” Chloroflexi; encircled “4,” Synergistetes; encircled “5,” TM7; and encircled “6,” SR1.

FIG. 8.

Rank abundance graph for 34,753 16S rRNA clones obtained from oral samples in 1,179 taxa. Clones were placed in taxa on the basis of 98% BLASTN identities. The first ranked taxon was Veillonella parvula, with 2,304 clones. Ranks 769 to 1,179 were singletons.