Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples

Figures & data

Table 1. Demographic and clinical characteristics of study cohort

Characteristics^a	All subjects (n=96)
Mean age in years (SD)	39.8 (12.4)
Male sex	55 [57%]
Ethnicity
White	26 [27%]
African American	65 [68%]
Hispanic	4 [4%]
Other	1 [1%]
Pocket depth^b
Mean (SD)	3.37 (0.97)
Range	1.83–7.89
Calculus index^c
Mean (SD)	1.18 (0.72)
Range	0–2.89
Gingival index^d
Mean (SD)	1.84 (0.68)
Range	0.17–3.00
Plaque index^e
Mean (SD)	1.53 (0.68)
Range	0.07–3.00

^aContinuous values are mean (SD), discrete values are number [percentage].

^bPocket depth: mean periodontal pocket depth for all remaining teeth.

^cCalculus index: mean score for all tooth scores based on scale: 0=no calculus; 1=supra-gingival (not more than 1 mm); 2=moderate supra-gingival and/or sub-gingival calculus; and 3=abundance of supra-gingival and sub-gingival calculus.

^dGingival index: mean score of all tooth scores based on scale: 0=normal gingiva; 1=mild inflammation, a slight change in color and edema, and no bleeding on probing; 2=moderate inflammation, redness, edema, and bleeding on probing; and 3=severe inflammation, marked redness and edema, ulcerations, and a tendency toward spontaneous bleeding.

^ePlaque index: mean score of all tooth areas scores (mesial, distal, facial, and lingual) based on scale: 0=no plaque in the gingival area; 1=no plaque visible to the unaided eye, but plaque is visible on the probe after being moved across the gingival crevice; 2=gingival area covered with a thin to moderately thick layer of plaque visible to the naked eye; and 3=heavy plaque accumulation and soft debris in the interdental area (8).

Table 2. HOMINGS and HOMIM capacities based on Human Oral Taxonomy (HOT) designation.

Capacity criteria	HOMIM	HOMINGS
Species probes^a (genera)	379 (92)	672 (158)
Identifiable species^b (genera)	293 (91)	597 (158)
Genus probes^c (genera)	N/A	93 (83)
Species + Genus probes^d (genera)	N/A	765 (159)

^aSpecies probes provide three categories of species identification: a unique species that is recognized by a single probe (vast majority), a unique species that is recognized by 2–3 probes, and groups of 2–3 species that are recognized by a single probe.

^bThe number of single species that can be identified by each technology, after processing of multiple recognition occurrences, is presented.

^cThis principle also applies to genus probes.

^dIn HOMINGS, species probes hits may be summed with genus probes hits to account for total genera hits. The combination of species and genus probes can identify 159 genera, as a few species or genus probes do not have matching genus or species probes, respectively.

(genera): Number of corresponding genera.

Table 3. Dental plaque microbiome composition by HOMIM and HOMINGS

a. Comparative analysis of the taxa detected by both HOMIM and HOMINGS
				Common identification comparison
Taxonomic group	Identifiable species	Identified taxa	Common identification	Raw p-value	FDR
HOMIM species	293	244	198	0.093	0.139
HOMINGS species	597	489
HOMIM genera	91	84	74	0.034	0.102
HOMINGS genera	158	129
HOMIM phyla	10	10	10	0.695	0.695
HOMINGS phyla	12	12
b. HOMINGS versus HOMIM added taxa identification capacity
	HOMINGS (% hits)				HOMIM (% intensity)
Taxonomic group^a	Species probes	Genus probes	All probes		Species probes
Species	100	N/A	100		100
Porphyromonas gingivalis	5.6	N/A	5.6^b		1.2^b
Diaiister invisus	3.0	N/A	3^b		21^b
Filifactor afocis	2.8	N/A	2.8		1.3
Prevotella melaninogenica	2.7	N/A	2.7		0.1
Rothia dentocariosa	2.6	N/A	2.6		0.6
Remainder species	83.3	N/A	83.3		94.7
Genus	61.3	38.7^c	100		100
Fusobacterium	2.1	21.3	23.4^d		2.8^d
Streptococcus	6.2	7.9	14.1^d		16.4^d
Prevotella	7.7	0.7	8.4		4.0
Leptotrichia	4.3	1.1	5.4		0.2
Porphyromonas	4.9	0.2	5.1		2.8
Remainder genera	36.1	7.5	43.6		73.8
Phylum	61.3	38.7	100		100
Firmicutes	22.1	10.5	32.6		64.4
Fusobacteria	6.9	22.5	29.4^e		3.8^e
Bacteroidetes	15.8	1.2	17		11.8
Actinobacteria	8.8	2.1	10.9		3.5
Spirochaetes	2.1	1.3	3.4		1.6
Remainder phyla	5.6	1.1	6.7		14.9

The data from patient cohort (n=96) are presented. Gray shaded areas show notable results. (a) The number of taxa (species, genera, and phyla) were determined based on the designation of species and/or genus probes. For the species identified in common by both HOMIM and HOMINGS (based on species probes only), there was no overall difference at species, genus, or phylum level, as determined by Wilcoxon signed-rank test with FDR procedure (FDR > 0.05). (b) Additional HOMINGS species and genus probes capacities are taken into account for comparison. Relative proportions are shown in percentage.

^aFor each taxonomic group, the five taxa with the highest relative proportion are shown.

^bAt species level, relative proportions for Porphyromonas gingivalis and Dialister invisus show inverse trend between HOMIM and HOMINGS.

^cAt genus level, genus probes account for 38.7% of total hits corresponding to all the genera identified. The largest contributors were Fusobacterium and Streptococcus. Compared to Streptococcus, Fusobacterium demonstrated the largest contribution by HOMINGS genus probes for genera undetected by HOMIM.

^dRelative proportions for Fusobacterium and Streptococcus show inverse trend between HOMIM and HOMINGS, due to genus probes.

^eAt the phylum level, Firmicutes and Fusobacteria were the largest contributors by HOMINGS, with the latter benefiting most from genus probes hits.

Fig. 1.  HOMINGS versus HOMIM comparison of total taxa relative proportion per patient. Total taxa (i.e. species common to both technologies) relative proportion for a patient was calculated by dividing the sum of the intensity scores (HOMIM) or hits (HOMINGS) of all bacterial taxa of the patient by the total number of these values for all 96 patients. (a) Differences in relative taxa proportions are illustrated by patient to patient line chart (HOMINGS [blue]; HOMIM [red]). These differences were not statistically significant overall (p=0.617, Wilcoxon signed-rank test). (b) Grubbs test identified six patients as outliers, with patient 26 (Pt26) representing the most prominent outlier. Removing Pt26 from the analysis also showed that differences in taxa relative proportions were overall not statistically significant (p=0.805).

Fig. 2.  Dental plaque bacterial genera composition by HOMINGS with added taxa identification capacity compared to HOMIM. *HOMINGS microbiome profiling of dental plaque samples from a patient cohort (n=96) shows a large increase (>100%) in the detection of Actinomyces, Fusobacterium, Leptotrichia, and Prevotella genera compared to HOMIM, likely due to additional genera probes. Relative proportions per genus were calculated based on total hits by HOMINGS or total intensity scores by HOMIM per 96 patients. Genera accounting for 96% of total hits by HOMINGS are represented.

Fig. 3.  Dental plaque bacterial phyla composition by HOMINGS with added taxa identification capacity compared to HOMIM. *HOMINGS microbiome profiling of dental plaque samples from a 96 patients cohort shows a large shift in relative proportions for Fusobacteria (3.8% HOMIM vs. 29.4% HOMINGS) and Firmicutes (64.4% HOMIM vs. 32.6% HOMINGS). Relative proportions per phylum were calculated based on total hits by HOMINGS or total intensity score by HOMIM per 96 patients. Chloroflexi, GN02 and SR1 were omitted due to negligible representation.

Lockhart PB, Brennan MT, Sasser HC, Fox PC, Paster BJ, Bahrani-Mougeot FK. Bacteremia associated with toothbrushing and dental extraction. Circulation. 2008; 117: 3118–25.

 Google Scholar