Table 1.
Overview of the studies included that investigated the root canal microbiota by means of 16S rRNA gene next-generation sequencing.
| Study | Santos et al. [76] | Siqueira et al. [77] | Hsiao et al. [52] | Özok et al. [78] | Hong et al. [71] |
|---|---|---|---|---|---|
| I | |||||
| Microbial outcome | Asymptomatic PIs (roots) vs. symptomatic AA (pus) | PIs' microbiota | Oral swabs vs. AA-associated roots and pus | Coronal vs. apical root segments in PI's | PIs vs. SPI |
| 16S variable regions | V4 | V1–V3 | V1–V2 | V5–V6 | V1–V3 |
| Taxa id. (OTUs) | 916 | 187 | 325 | 606 | 803 |
| Sampling method. | In vivo: paper points and abscess aspiration | Ex vivo: cryo-pulverized roots | In vivo: paper points and abscess aspiration | Ex vivo: cryo-pulverized roots | In vivo: paper points |
| Main findings | 13 phyla subdivided into 67 genera. 20 genera exclusively in pus from AAs and 18 in PIs. 18% of the 165 OTUs detected in both pus and PI-associated root canal. | 84 genera belonging to 10 phyla detected. Majority were low-abundant OTUs. Important interindividual variation in the composition of the apical microbiota. | 11 Phyla detected. Lower bacterial diversity in AAs root canals and pus than in oral swabs. Streptococcus spp. most abundant in oral swabs, Prevotella and Fusobacterium most abundant in AAs root canals and pus. | 24 bacterial phyla detected, Proteobacteria more abundant in apical segments and Actinobacteria more abundant coronal. Apical segments displayed higher diversity than the coronal segments. | 10 phyla subdivide into 148 genera. No significant differences in bacterial composition between PIs and SPI. |
| Main phyla (max. top 6) | In PIs: Firmicutes (59%), Bacteroidetes (14%), Actinobacteria (10%), Fusobacteria, Proteobacteria, Spirochetes. | Proteobacteria (43%), Firmicutes (25%), Fusobacteria (16%), Bacteriodetes (9%), Actinobacteria (5%), Synergistetes. | Firmicutes (21.6%), Bacteroidetes, Fusobacteria, Proteobacteria, Actinobacteria, Synergistetes. TM7, Tenericutes, Deinococcus-Thermus, SR1, Euryarchaeota, and Cyanobacteria. |
Firmicutes (48%), Actinobacteria (30%), Bacteroidetes (12%), Acidobacteria, BRC1, Chlamydiae. | In both infection types: Bacteriodetes (29.6%), Firmicutes (23.2%), Actinobacteria (10.5%), Fusobacteria (13.1%), Protobacteria (8.8%), Synergistetes (6.3%). |
| Main genera/species (max. top 12) | In PIs: Phocaeicola (12.5%), Eubacterium (12%) and Pseudoramibacter (10%). Most abundant genera from pus sampling: Fusobacterium (19%), Parvimonas (11%) and Peptostreptococcus (10%). | Fusobacterium (15%), Pseudoramibacter (8%), Novosphingobium (8%), Ralstonia (6%), Bacterioides (5%). | Fusobacterium, Prevotella, Granulicatella, Eubacterium, Streptococcus, Porphyromonas, Afipia, Phocaeicola, Veillonela, Parvirmonas, Gemella, Pyramidobacter. | Lactobacillus (14.3%), Actinomyces (11.9%), Streptococcus (0.4%), unclass. Actinobacteria (6.9), Prevotella (6.1%), Parvimonas (3.4%), Pseudoramibacter (3%), Order Bacteroidales (2.7%), Fam. Veillonellaceae (2.5%), Fusobacterium (2%), Peptostreptococcus (2%), Porphyromonas (1.8%). | In PIs: Prevotella, Propionibacterium and Pyramidobacter. In SPI: Fusobacterium, Porphyromonas and Prevotella. |
| II | |||||
| Microbial outcome measured | Symptomatic vs. asymptomatic SPIs | PIs vs. SPIs vs. AAs | PIs vs. SPIs. | PIs vs. periodontal pockets in cases of endo-perio lesions | Apical segments of SPIs |
| 16S variable regions | V1–V2 | V6 | V1–V2 | V3–V4 | V4 |
| Total taxa id. (OTUs) | 741 | PIs: 36; SPIs: 43; AAs: 45 | 339 | 289 | 538 |
| Sampling method. | In vivo: paper points | In vivo: paper points | In vivo: paper points | In vivo: paper points | Ex vivo: cryo-pulverized roots |
| Main findings | Symptomatic SPIs had more Firmicutes and Fusobacteria than asymptomatic ones. In turn, asymptomatic SPIs exhibited more Proteobacteria and Actinobacteria. | Highly diverse microbiota in all infection types. E. faecalis identified only in SPIs. One AA sample displayed a significantly high proportion (47%) of Proteobacteria (Janthinobacterium lividum). | Bacteroidetes most abundant phylum in both infection types. Different bacterial compositions in symptomatic and asymptomatic infections. SPIs significantly enriched with Proteobacteria and Tenericutes as compared to PIs. 14 genera differentially abundant between PIs and SPIs. | Firmicutes most abundant in all sampling sites. Desulfobulbus sp. oral taxon 041 was associated w/periapical lesions ≤ 2 mm. | 11 phyla subdivided into 103 genera. Fusobacterium and Pseudomonas dominated. Enterococcus spp. found in 4 cases, relatively low-abundant. |
| Main phyla (max. top 6) | Firmicutes (29.9%), Proteobacteria (26.1%), Actinobacteria (22.72%), Bacteroidetes (13.31%) and Fusobacteria (4.55%). | In all infection types: Firmicutes, Actinobacteria, Bacteriodetes, Fusobacteria, Proteobacteria, Synergistetes. | In all infection types: Bacteroidetes (36.2%), Firmicutes (32.9%), Actinobacteria (8.1%), Synergistetes (7.4%), Fusobacteria (7.4%), Proteobacteria (5.2%). | In PIs: Firmicutes (75.09%), Proteobacteria (7.85%), Actinobacteria (7.01%), Bacteroidetes (6.77%) | Proteobacteria (46%), Firmicutes (18%), Fusobacteria (15%) and Actinobacteria (8%) |
| Main genera/species (max. top 12) | Streptococcus (10.9%), Prevotella (8.21%), Lactobacillus (8.06%), Kocuria (5.17%), Neisseria (3.38%), Enterococcus (2.59%), Acinetobacter, Atopobium, Rothia, Pseudomonas, Propionibacterium, Schlegelella. | No relative abundances were reported for any of the genera detected. | PIs enriched with: Bacteroidaceae_unclassified, Pyramidobacter, Parvimonas. SPIs enriched with: Fusobacterium, Bacteroidaceae_unclassified, and Prevotella. | In PIs: Enterococcus faecalis, Parvimonas micra, Bacteroidaceae [G-1] sp. oral taxon 272, Peptostreptococcaceae [G-1] sp. oral taxon 113, Mogibacterium timidum, Peptostreptococcus stomatis, Filifactor alocis, and Fretibacterium fastidiosum. | Fusobacterium and Pseudomonas (15%), Klebsiella, Stenotrophomonas, Pseudoramibacter, Pyramidobacter, Enterococcus. |
| III | |||||
| Microbial outcome | In PIs: microbiota vs. mycobiome and coronal vs. apical root segments | PIs vs. SPIs | SPIs | PIs vs. aSPIs | |
| 16S variable regions | V3–V4 | V4 | V3–V5 | V3–V4 | |
| Total taxa id. (OTUs) | 338 | Not specified | 152 | 347 | |
| Sampling method. | Ex vivo: cryo-pulverized roots | Ex vivo: cryo-pulverized roots | In vivo: paper points | Ex vivo: intraradicular content collected with endodontic files | |
| Main findings | Coronal and apical root segments had similar microbiome and mycobiome. No correlations between microbiota and mycobiomes. | 160 genera belonging to 15 phyla were detected. PIs and SPIs displayed no significant differences in microbiota composition. | 125 bacterial species belonging to 68 genera and 9 phyla were detected. | 18 phyla subdivided into 177 genera. Microbiotas were differentially abundant in each infection type. Co-occurrence analysis demonstrated microbial interactions specific to each infection type. | |
| Main phyla (max. top 6) | No phylum level assessment | Proteobacteria (33.4%), Firmicutes (32.3%), Bacteroidetes (26.3%), Fusobacteria (4.2%), and Actinobacteria (2.9%) | Prior to disinfection: Firmicutes (47%), Fusobacteria (14%), Bacteroidetes (12%), Proteobacteria (12%), Actinobacteria (9%), Synergistetes (4%) | Firmicute (PI 36/SPI 48.4%), Bacteroidetes (PI 23.8/SPI 9.5%), Actinobacteria (PI 6.4/SPI 23.4%), Fusobacteria (PI 16/SPI 5.6%), Synergistetes (PI 9.9/SPI 4.5%), Proteobacteria (PI 2.4/SPI 4.8%) | |
| Main genera/species (max. top 12) | PIs-microbiota: Prevotella (12.7%), Lactobacillus (11.2%), Actinomyces (7.5%), Fusobacterium (7.2%), Atopobium (6.9%), Streptococcus (4.4%), Leptotrichia (4.3%), Phocaeicola (3.5%), Pyramidobacter (2.9%), Porphyromonas (2.7%) | Prevotella (PI 23.5%/SPI 15.7%), Porphyromonas (16.5% mean PI-SPI), Neisseria (13.2% mean PI-SPI), Lactobacillus (11.7% mean PI-SPI), Parvimonas (11.1% mean PI-SPI), Streptococcus (PI 9.4%/SPI 12%), Enterococcus (PI 2%/SPI 5%), Camplyobacter (PI 2%/SPI 0.1%), and Granulicatella (1% mean PI-SPI) | Prior to disinfection: Enterococcus (13.9%), Fusobacterium (12.7%), Streptococcus (9.8%), Actinomyces (8.2%), Desulfobulbus (5.2%), Fretibacterium (3.6%), Treponema (2.3%), Prevotella (2%), Alloprevotella (0.01%) | Fusobacterium nucleatum (PI 16/SPI 5.3%), Enterococcus faecalis (PI 0.01/SPI 18.9%), Parvimonas micra (PI 8/SPI 2.6%), Porphyromonas endodontalis (PI 5.7/SPI 2%), Streptococcus constellatus (PI 0.6/SPI 3.5%), Slackia exigua (PI 0.7/SPI 1.3%), Schwatzia AF287291 (PI 1/SPI 3.5%), Dialister pneumosintes (PI 3.4/SPI 1.2%), Prevotella oris (PI 5.7/SPI 1.5%) |
AA, apical abscess; OTU, operational taxonomic unit; PI, primary infection; SPI, secondary/persistent infection.