Many bacteriome studies employing next-generation sequencing (NGS) have focused on the partial sequencing of the 16S rRNA gene (rDNA). This limits both species-level resolution and quantitative interpretation of bacterial abundance, which have been addressed in this study.
Methods
Nanopore sequencing was used to analyze nearly the entire 16S rDNA sequence for species-level classification, and quantitative PCR for bacterial quantification. This approach was applied in a small-cohort feasibility study to investigate oral bacterial changes in orthodontic patients. Saliva samples were collected from 10 patients before and 1, 3, and 6 months after the initiation of orthodontic treatment.
Results
Dental caries was not detected during the study, and periodontal pockets ≥4 mm were rarely observed. However, all patients exhibited changes in bleeding on probing (BOP), which is indicative of early stage gingivitis. Although the compositional analysis did not reveal any significant association between specific bacterial species and BOP changes, the quantitative analysis showed a positive correlation between BOP changes and two bacterial species in the phyla Candidatus Saccharibacteria: Candidatus Saccharimonas aalborgensis and Candidatus Saccharibacteria bacterium oral taxon TM7x. No correlation was observed with representative periodontal disease-associated bacteria.
Conclusions
These findings support the feasibility of species-level and quantitative bacteriome analysis in a small cohort and highlight the bacterial species potentially linked to early stage gingivitis.
{"title":"Broad-range 16S rDNA sequencing and quantitative bacteriome profiling: a small-cohort feasibility study in orthodontic patients with early gingivitis","authors":"Tadaharu Yokogawa , Keiji Nagano , Hiroshi Miyakawa , Mari Fujita , Chen-Hsuan Chiu , Masahiro Iijima","doi":"10.1016/j.job.2025.100732","DOIUrl":"10.1016/j.job.2025.100732","url":null,"abstract":"<div><h3>Objectives</h3><div>Many bacteriome studies employing next-generation sequencing (NGS) have focused on the partial sequencing of the 16S rRNA gene (rDNA). This limits both species-level resolution and quantitative interpretation of bacterial abundance, which have been addressed in this study.</div></div><div><h3>Methods</h3><div>Nanopore sequencing was used to analyze nearly the entire 16S rDNA sequence for species-level classification, and quantitative PCR for bacterial quantification. This approach was applied in a small-cohort feasibility study to investigate oral bacterial changes in orthodontic patients. Saliva samples were collected from 10 patients before and 1, 3, and 6 months after the initiation of orthodontic treatment.</div></div><div><h3>Results</h3><div>Dental caries was not detected during the study, and periodontal pockets ≥4 mm were rarely observed. However, all patients exhibited changes in bleeding on probing (BOP), which is indicative of early stage gingivitis. Although the compositional analysis did not reveal any significant association between specific bacterial species and BOP changes, the quantitative analysis showed a positive correlation between BOP changes and two bacterial species in the phyla Candidatus <em>Saccharibacteria</em>: Candidatus <em>Saccharimonas aalborgensis</em> and Candidatus <em>Saccharibacteria</em> bacterium oral taxon TM7x. No correlation was observed with representative periodontal disease-associated bacteria.</div></div><div><h3>Conclusions</h3><div>These findings support the feasibility of species-level and quantitative bacteriome analysis in a small cohort and highlight the bacterial species potentially linked to early stage gingivitis.</div></div>","PeriodicalId":45851,"journal":{"name":"Journal of Oral Biosciences","volume":"68 1","pages":"Article 100732"},"PeriodicalIF":2.3,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145883337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
It is widely accepted that Taste bud cells originate from the epithelium; however, evidence indicates that these cells are also derived from the mesenchyme beneath the epithelium. In this study, the cell lineage expressing Twist2, a transcription factor that is specifically expressed in the mesenchyme within taste buds, were examined to gain a deeper understanding of its biological characteristics.
Methods
Immunohistochemical analyses and taste organoid cultures were performed using Twist2 lineage-tracing reporter mice (Twist2-Cre mice crossed with tdTomato mice) to identify Twist2-derived cells in taste buds. The transgenic mice were harvested at 7, 14, and 21 days, post-administration of 5-ethynyl-2′-deoxyuridine (EdU), to assess the label retention of Twist2-derived cells.
Results
tdTomato-positive cells expressed Type III taste cell markers in the taste papillae and soft palate. tdTomato-positive organoids derived from the circumvallate papilla contained numerous taste bud cells. EdU analysis revealed that tdTomato-positive cells expressing a Type III taste cell marker persisted for longer than tdTomato-negative cells that expressed the same marker. In addition, almost all the long-term cultured tdTomato-positive organoids contained cells expressing a Type II taste cell marker.
Conclusions
The findings support the hypothesis that mesenchymal cells contribute to the taste bud cell population.
{"title":"Lineage tracing of Twist2-expressing cells in mouse taste buds","authors":"Namiki Takaku-Tanoue , Kae Matsuyama , Takashi Toyono , Shinji Kataoka , Mitsushiro Nakatomi , Shingo Takai , Noriatsu Shigemura , Tatsuo Kawamoto , Yuji Seta","doi":"10.1016/j.job.2025.100729","DOIUrl":"10.1016/j.job.2025.100729","url":null,"abstract":"<div><h3>Objectives</h3><div>It is widely accepted that Taste bud cells originate from the epithelium; however, evidence indicates that these cells are also derived from the mesenchyme beneath the epithelium. In this study, the cell lineage expressing <em>Twist2</em>, a transcription factor that is specifically expressed in the mesenchyme within taste buds, were examined to gain a deeper understanding of its biological characteristics.</div></div><div><h3>Methods</h3><div>Immunohistochemical analyses and taste organoid cultures were performed using <em>Twist2</em> lineage-tracing reporter mice (<em>Twist2-Cre</em> mice crossed with <em>tdTomato</em> mice) to identify <em>Twist2</em>-derived cells in taste buds. The transgenic mice were harvested at 7, 14, and 21 days, post-administration of 5-ethynyl-2′-deoxyuridine (EdU), to assess the label retention of <em>Twist2</em>-derived cells.</div></div><div><h3>Results</h3><div>tdTomato-positive cells expressed Type III taste cell markers in the taste papillae and soft palate. tdTomato-positive organoids derived from the circumvallate papilla contained numerous taste bud cells. EdU analysis revealed that tdTomato-positive cells expressing a Type III taste cell marker persisted for longer than tdTomato-negative cells that expressed the same marker. In addition, almost all the long-term cultured tdTomato-positive organoids contained cells expressing a Type II taste cell marker.</div></div><div><h3>Conclusions</h3><div>The findings support the hypothesis that mesenchymal cells contribute to the taste bud cell population.</div></div>","PeriodicalId":45851,"journal":{"name":"Journal of Oral Biosciences","volume":"68 1","pages":"Article 100729"},"PeriodicalIF":2.3,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145883339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that plays an essential role in skeletal homeostasis. Increasing evidence indicates that AhR critically regulates osteoclast differentiation and activity, thereby influencing bone mass, bone resorption, and susceptibility to skeletal diseases. Although AhR has also been implicated in osteoblast-lineage cells, its regulatory roles in osteoclasts and immune cells are less well understood but are increasingly recognized as central to bone remodeling. In particular, AhR signaling modulates immune cell subsets relevant to bone metabolism and governs the differentiation of bone marrow-derived macrophages into osteoclasts.
Highlight
This review summarizes the recent findings regarding the regulation of osteoclast differentiation by AhR and its ligands under both physiological and pathological conditions. Special emphasis is placed on the interaction between AhR and the RANKL signaling axis in osteoclasts, as well as on how exogenous and endogenous ligands, including benzo[a]pyrene (B[a]P) and 6-formylindolo[3,2-b]carbazole (FICZ), modulate bone resorption and subchondral bone remodeling in temporomandibular joint osteoarthritis. Furthermore, the role of macrophages as osteoclast progenitors and immunomodulators has been highlighted, positioning AhR as a critical intermediary that links environmental exposure, inflammation, and skeletal metabolism.
Conclusion
In this review, we outlined the diverse functions of AhR signaling and its ligands in oral and temporomandibular joint osteoarthritis. AhR plays a central role in bone remodeling. The harmful exogenous ligand B[a]P generally promotes bone loss, whereas the endogenous ligand FICZ exerts protective actions. These insights highlight AhR as a key regulatory switch linking the skeletal and immune systems and as a promising therapeutic target for bone-destructive disorders.
{"title":"Roles of the aryl hydrocarbon receptor and its ligands in osteoclast differentiation and temporomandibular joint osteoarthritis","authors":"Takashi Izawa , Islamy Rahma Hutami , Yuri Yoshikawa , Gohji Kozaki , Yusaku Hamada , Yuki Namba , Misa Taguchi , Jiamin Chen , Janvier Habumugisha , Hiroshi Kamioka","doi":"10.1016/j.job.2025.100726","DOIUrl":"10.1016/j.job.2025.100726","url":null,"abstract":"<div><h3>Background</h3><div>The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that plays an essential role in skeletal homeostasis. Increasing evidence indicates that AhR critically regulates osteoclast differentiation and activity, thereby influencing bone mass, bone resorption, and susceptibility to skeletal diseases. Although AhR has also been implicated in osteoblast-lineage cells, its regulatory roles in osteoclasts and immune cells are less well understood but are increasingly recognized as central to bone remodeling. In particular, AhR signaling modulates immune cell subsets relevant to bone metabolism and governs the differentiation of bone marrow-derived macrophages into osteoclasts.</div></div><div><h3>Highlight</h3><div>This review summarizes the recent findings regarding the regulation of osteoclast differentiation by AhR and its ligands under both physiological and pathological conditions. Special emphasis is placed on the interaction between AhR and the RANKL signaling axis in osteoclasts, as well as on how exogenous and endogenous ligands, including benzo[<em>a</em>]pyrene (B[<em>a</em>]P) and 6-formylindolo[3,2-<em>b</em>]carbazole (FICZ), modulate bone resorption and subchondral bone remodeling in temporomandibular joint osteoarthritis. Furthermore, the role of macrophages as osteoclast progenitors and immunomodulators has been highlighted, positioning AhR as a critical intermediary that links environmental exposure, inflammation, and skeletal metabolism.</div></div><div><h3>Conclusion</h3><div>In this review, we outlined the diverse functions of AhR signaling and its ligands in oral and temporomandibular joint osteoarthritis. AhR plays a central role in bone remodeling. The harmful exogenous ligand B[<em>a</em>]P generally promotes bone loss, whereas the endogenous ligand FICZ exerts protective actions. These insights highlight AhR as a key regulatory switch linking the skeletal and immune systems and as a promising therapeutic target for bone-destructive disorders.</div></div>","PeriodicalId":45851,"journal":{"name":"Journal of Oral Biosciences","volume":"68 1","pages":"Article 100726"},"PeriodicalIF":2.3,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145839801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-20DOI: 10.1016/j.job.2025.100724
Mana Shintani , Wakana Sugimoto , Hiroshi Inoue , Nagako Sougawa , Seiji Goda , Aki Nishiura
Objectives
Muramyl dipeptide (MDP), a bacterial cell wall component, is recognized by NOD2 and vital in innate immune responses, including inflammatory cytokine production. MDP is transported into the cells via PEPT1/SLC15A1 and PEPT2/SLC15A2, which are members of the proton-coupled oligopeptide transporter family within the SLC15 solute carrier group. Although the effects of RANKL stimulation on certain transporters are known, its effects on the SLC15 family remain unclear. This study aimed to clarify the effects of RANKL stimulation on PEPT1/SLC15A1 and PEPT2/SLC15A2 in RAW264.7 cells and determine their role in osteoclast differentiation.
Methods
RAW264.7 cells were stimulated with RANKL and MDP. Expression levels of NOD2, PEPT1/SLC15A1, PEPT2/SLC15A2, cathepsin K, and NFATc1 were analyzed via Western blotting. Osteoclast differentiation was evaluated using a tartrate-resistant acid phosphatase (TRAP) activity assay.
Results
RANKL stimulation increased NOD2, PEPT1/SLC15A1, and PEPT2/SLC15A2 expression in RAW264.7 cells. Colistin and polymyxin B, which are PEPT1 and PEPT2 inhibitors, respectively, did not affect the stimulation of cells with RANKL alone. However, RANKL and MDP co-stimulation suppressed the RANKL/MDP-induced increase in TRAP activity and cathepsin K and NFATc1 expression.
Conclusions
RANKL stimulation increased PEPT1/SLC15A1 and PEPT2/SLC15A2 levels in RAW264.7 cells, suggesting an increase in the intracellular uptake of MDP. This may promote osteoclast differentiation, potentially through NOD2activation or NOD2-independent mechanisms.
{"title":"RANKL enhances the expression of PEPT1/SLC15A1 and PEPT2/SLC15A2 in RAW264.7 cells","authors":"Mana Shintani , Wakana Sugimoto , Hiroshi Inoue , Nagako Sougawa , Seiji Goda , Aki Nishiura","doi":"10.1016/j.job.2025.100724","DOIUrl":"10.1016/j.job.2025.100724","url":null,"abstract":"<div><h3>Objectives</h3><div>Muramyl dipeptide (MDP), a bacterial cell wall component, is recognized by NOD2 and vital in innate immune responses, including inflammatory cytokine production. MDP is transported into the cells via PEPT1/SLC15A1 and PEPT2/SLC15A2, which are members of the proton-coupled oligopeptide transporter family within the SLC15 solute carrier group. Although the effects of RANKL stimulation on certain transporters are known, its effects on the SLC15 family remain unclear. This study aimed to clarify the effects of RANKL stimulation on PEPT1/SLC15A1 and PEPT2/SLC15A2 in RAW264.7 cells and determine their role in osteoclast differentiation.</div></div><div><h3>Methods</h3><div>RAW264.7 cells were stimulated with RANKL and MDP. Expression levels of NOD2, PEPT1/SLC15A1, PEPT2/SLC15A2, cathepsin K, and NFATc1 were analyzed via Western blotting. Osteoclast differentiation was evaluated using a tartrate-resistant acid phosphatase (TRAP) activity assay.</div></div><div><h3>Results</h3><div>RANKL stimulation increased NOD2, PEPT1/SLC15A1, and PEPT2/SLC15A2 expression in RAW264.7 cells. Colistin and polymyxin B, which are PEPT1 and PEPT2 inhibitors, respectively, did not affect the stimulation of cells with RANKL alone. However, RANKL and MDP co-stimulation suppressed the RANKL/MDP-induced increase in TRAP activity and cathepsin K and NFATc1 expression.</div></div><div><h3>Conclusions</h3><div>RANKL stimulation increased PEPT1/SLC15A1 and PEPT2/SLC15A2 levels in RAW264.7 cells, suggesting an increase in the intracellular uptake of MDP. This may promote osteoclast differentiation, potentially through NOD2activation or NOD2-independent mechanisms.</div></div>","PeriodicalId":45851,"journal":{"name":"Journal of Oral Biosciences","volume":"68 1","pages":"Article 100724"},"PeriodicalIF":2.3,"publicationDate":"2025-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145796678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}