Recent advances in genomic technologies have enabled more in-depth study of the oral microbiome. In this study, we compared the amplicons generated by primers targeting different sites of the 16S rRNA gene found in the Human Oral Microbiome Database (HOMD). Six sets of primer targeting V1–V2, V1–V3, V3–V4, V4–V5, V5–V7 and V6–V8 regions of 16S rRNA were tested via in silico simulation. Primers targeting the V1–V2, V3–V4, and V4–V5 regions generated more than 90% of the original input sequences. Primers targeting the V1–V2 and V1–V3 regions exhibited a low number of mismatches and unclassified sequences at the taxonomic level, but there were notable discrepancies at the species level. Phylogenetic tree comparisons showed primers targeting the V1–V2 and V3–V4 regions showed performances similar to primers targeting the whole 16s RNA region in terms of separating total oral microbiomes and periodontopathogens. In an analysis of clinical oral samples, V1–V2 primers showed superior performance for identifying more taxa and had better resolution sensitivity for Streptococcus than V3–V4 primers. In conclusion, primers targeting the V1–V2 region of 16S rRNA showed the best performance for oral microbiome studies. In addition, the study demonstrates the need for careful PCR primer selections.

Several studies have demonstrated that nuclear magnetic resonance (NMR) metabolic profiles can differentiate patients with caries from healthy individuals; however, these studies only identified individual metabolites. The present study aimed to identify a salivary metabolite biomarker panel for the diagnosis of early childhood caries (ECC). Saliva samples from children with and without caries were analyzed using NMR spectroscopy. Multivariate and univariate analyses were performed to identify the discriminating metabolites. Selected metabolites were further evaluated and used to detect ECC. The saliva samples of children with ECC were characterized based on the increased levels of formate, glycerophosphocholine, and lactate and reduced levels of alanine, glycine, isoleucine, lysine, proline, and tyrosine. The levels of these metabolites were significantly different from those in the control in the ECC subgroup according to caries severity and correlated with the number of decayed and filled teeth or surfaces. Subsequently, an optimal salivary metabolite biomarker panel comprising formate, lactate, proline, and glycine was developed. This panel exhibited a better diagnostic performance for ECC than a single metabolite. These results demonstrate that salivary metabolic signatures can reflect oral conditions associated with dental caries, thereby emphasizing the importance of distinct salivary metabolic profiles as potential biomarkers of ECC.

Periodontitis is a chronic inflammatory disease driven by periodontal pathogens such as Porphyromonas gingivalis (P. gingivalis), and its prevalence increases with age. However, little is known about the effect of immunosenescence on inflammatory response to P. gingivalis infection. In the present study, 16S rDNA sequencing analysis showed the relative abundance of P. gingivalis was significantly higher in periodontitis patients than healthy group, but there was no difference between the young (20 to 40 years old) and old (65 to 86 years old) periodontitis groups. Furthermore, the cytotoxic effect of P. gingivalis was greater on old THP-1 macrophages and on bone mar-row-derived cells (BMDMs) from old mice, and levels of interleukin (IL)-1β, tumor necrosis factor (TNF)-α, and IL-12 were higher in old than in young THP-1 macrophages. Furthermore, the activations of inflammasome components for IL-1β production by P. gingivalis infection were greater in old THP-1 macrophages. Finally, bone loss was significantly greater in P. gingivalis-infected aged mice than in young mice. These findings indicate that aging aggravates P. gingivalis-induced inflammatory cytokine secretion and inflammasome activation. The study enhances understanding of the relationship between periodontal immunosenescence and inflammatory response in the elderly.

Intubated patients in intensive care units (ICUs) too frequently contract ventilator-associated pneumonia or Candida infections. Oropharyngeal microbes are believed to play an important etiologic role. This study was undertaken to determine whether next-generation sequencing (NGS) can be used to simultaneously analyze bacterial and fungal communities. Buccal samples were collected from intubated ICU patients. Primers targeting the V1-V2 region of bacterial 16S rRNA and the internal transcribed spacer 2 (ITS2) region of fungal 18S rRNA were used. V1-V2, ITS2, or mixed V1-V2/ITS2 primers were used to prepare an NGS library. Bacterial and fungal relative abundances were comparable for V1-V2, ITS2, or mixed V1-V2/ITS2 primers, respectively. A standard microbial community was used to adjust the relative abundances to theoretical abundance, and NGS and RT-PCR-adjusted relative abundances showed a high correlation. Using mixed V1-V2/ITS2 primers, bacterial and fungal abundances were simultaneously determined. The constructed microbiome network revealed novel interkingdom and intrakingdom interactions, and the simultaneous detection of bacterial and fungal communities using mixed V1-V2/ITS2 primers enabled analysis across two kingdoms. This study provides a novel approach to simultaneously determining bacterial and fungal communities using mixed V1-V2/ITS2 primers.

Periodontitis is caused by the inflammation of tooth-supporting tissue by pathogens such as Aggregatibacter actinomycetemcomitans. Interleukin-1β (IL-1β), a pro-inflammatory cytokine, triggers a series of inflammatory reactions and promotes bone resorption. The aim of this study was to examine the molecular mechanism and anti-inflammatory function of zingerone, a dietary phenolic found in Zingiber officinale, on periodontal inflammation induced by A. actinomycetemcomitans. Zingerone attenuated A. actinomycetemcomitans-induced nitric oxide (NO) production by inhibiting the expression of inducible nitric oxide synthase (iNOS) in THP-1 macrophages. Zingerone also inhibited the expression of tumor necrosis factor (TNF)-α, IL-1β, and their signal pathway molecules including the toll-like receptor (TLR)/mitogen-activated protein kinase (MAPKase). In particular, zingerone suppressed the expression of absent in melanoma 2 (AIM2) inflammasome components on IL-1β production. Moreover, zingerone enhanced autophagosome formation and the expressions of autophagy-associated molecules. Interestingly, zingerone reduced the intracellular survival of A. actinomycetemcomitans. This was blocked by an autophagy inhibitor, which reversed the decrease in IL-1β production by zingerone. Finally, zingerone alleviated alveolar bone absorption in an A. actnomycetemcomitans-induced periodontitis mice model. Our data suggested that zingerone has potential use as a treatment for periodontal inflammation induced by A. actinomycetemcomitans.

Healthy individuals often have different gut microbiota, and these differences can be influenced by their country of origin or their race. This study aimed to compare the gut microbiota compositions of healthy Germans and Koreans using 16S rRNA sequencing data extracted from public sources. Two cohorts, comprising 1592 samples (804 Germans and 788 Koreans), were analyzed for alpha and beta diversity, core microbiome, and abundances of specific taxa. The Prevotella enterotype was more prevalent in Koreans, and significant diversity differences were observed depending on cohorts and enterotypes. The core microbiomes across all enterotypes and cohorts included Bacteroides, Faecalibacterium, Parabacteroides, and Lachnospira. Several common core microbiomes were also found depending on enterotype. Koreans exhibited higher abundances of Faecalibacterium, Prevotella, and Bacteroides, while Germans had higher abundances of Blautia, Subdoligranulum, and Agathobacter. Distinctive microbiomes were identified by enterotype. The study enhances comprehension of gut microbiome variations linked to enterotype and geographical factors, and emphasizes the need for additional research to establish correlations between specific microbial properties and individual health status.