Functional profile of oral plaque microbiome: Further insight into the bidirectional relationship between type 2 diabetes and periodontitis.

Increasing evidence support the association between the oral microbiome and human systemic diseases. This association may be attributed to the ability of many oral microbes to influence the inflammatory microenvironment. Herein, we focused our attention on the bidirectional relationship between periodontitis and type 2 diabetes using high-resolution whole metagenomic shotgun analysis to explore the composition and functional profile of the subgingival microbiome in diabetics and non-diabetics subjects with different periodontal conditions. In the present study, the abundance of metabolic pathways encoded by oral microbes was reconstructed from the metagenome, and we identified a set of dysregulated metabolic pathways significantly enriched in the periodontitis and/or diabetic patients. These pathways were mainly involved in branched and aromatic amino acids metabolism, fatty acid biosynthesis and adipocytokine signaling pathways, ferroptosis and iron homeostasis, nucleotide metabolism, and finally in the peptidoglycan and lipopolysaccharides synthesis. Overall, the results of the present study provide evidence in favor of the hypothesis that during the primary inflammatory challenge, regardless of whether it is induced by periodontitis or diabetes, endotoxemia and/or the release of inflammatory cytokines cause a change in precursor and/or in circulating innate immune cells. Dysbiosis and inflammation, also via oral-gut microbiome axis or adipose tissue, reduce the efficacy of the host immune response, while fueling inflammation and can induce that metabolic/epigenetic reprogramming of chromatin accessibility of genes related to the immune response. Moreover, the presence of an enhanced ferroptosis and an imbalance in purine/pyrimidine metabolism provides new insights into the role of ferroptotic death in this comorbidity.

Reconstruction of Acinetobacter johnsonii ICE_NC genome using hybrid de novo genome assemblies and identification of the 12α-hydroxysteroid dehydrogenase gene.

AIMS: The role of a Acinetobacter johnsonii strain, isolated from a soil sample, in the biotransformation of bile acids (BAs) was already described but the enzymes responsible for these transformations were only partially purified and molecularly characterized. METHODS AND RESULTS: This study describes the use of hybrid de novo assemblies, that combine long-read Oxford Nanopore and short-read Illumina sequencing strategies, to reconstruct the entire genome of A. johnsonii ICE_NC strain and to identify the coding region for a 12α-hydroxysteroid dehydrogenase (12α-HSDH), involved in BAs metabolism. The de novo assembly of the A. johnsonii ICE_NC genome was generated using Canu and Unicycler, both strategies yielded a circular chromosome of about 3.6 Mb and one 117 kb long plasmid. Gene annotation was performed on the final assemblies and the gene for 12α-HSDH was detected on the plasmid. CONCLUSIONS: Our findings illustrate the added value of long read sequencing in addressing the challenges of whole genome characterization and plasmid reconstruction in bacteria. These approaches also allowed the identification of the A. johnsonii ICE_NC gene for the 12α-HSDH enzyme, whose activity was confirmed at the biochemical level. SIGNIFICANCE AND IMPACT OR THE STUDY: At present, this is the first report on the characterization of a 12α-HSDH gene in an A. johnsonii strain able to biotransform cholic acid into ursodeoxycholic acid, a promising therapeutic agent for several diseases.

Tumor Necrosis Factor Receptor SF10A (TNFRSF10A) SNPs Correlate With Corticosteroid Response in Duchenne Muscular Dystrophy.

BACKGROUND: Duchenne muscular dystrophy (DMD) is a rare and severe X-linked muscular dystrophy in which the standard of care with variable outcome, also due to different drug response, is chronic off-label treatment with corticosteroids (CS). In order to search for SNP biomarkers for corticosteroid responsiveness, we genotyped variants across 205 DMD-related genes in patients with differential response to steroid treatment. METHODS AND FINDINGS: We enrolled a total of 228 DMD patients with identified dystrophin mutations, 78 of these patients have been under corticosteroid treatment for at least 5 years. DMD patients were defined as high responders (HR) if they had maintained the ability to walk after 15 years of age and low responders (LR) for those who had lost ambulation before the age of 10 despite corticosteroid therapy. Based on interactome mapping, we prioritized 205 genes and sequenced them in 21 DMD patients (discovery cohort or DiC = 21). We identified 43 SNPs that discriminate between HR and LR. Discriminant Analysis of Principal Components (DAPC) prioritized 2 response-associated SNPs in the TNFRSF10A gene. Validation of this genotype was done in two additional larger cohorts composed of 46 DMD patients on corticosteroid therapy (validation cohorts or VaC1), and 150 non ambulant DMD patients and never treated with corticosteroids (VaC2). SNP analysis in all validation cohorts (N = 207) showed that the CT haplotype is significantly associated with HR DMDs confirming the discovery results. CONCLUSION: We have shown that TNFRSF10A CT haplotype correlates with corticosteroid response in DMD patients and propose it as an exploratory CS response biomarker.

Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions.

OBJECTIVE: The aim of this study was to use high-resolution whole metagenomic shotgun sequencing to characterize the subgingival microbiome of patients with/without type 2 Diabetes Mellitus and with/without periodontitis. DESIGN: Twelve subjects, falling into one of the four study groups based on the presence/absence of poorly controlled type 2 Diabetes Mellitus and moderate-severe periodontitis, were selected. For each eligible subject, subgingival plaque samples were collected at 4 sites, all representative of the periodontal condition of the individual (i.e., non-bleeding sulci in subjects without a history of periodontitis, bleeding pockets in patients with moderate-severe periodontitis). The subgingival microbiome was evaluated using high-resolution whole metagenomic shotgun sequencing. RESULTS: The results showed that: (i) the presence of type 2 Diabetes Mellitus and/or periodontitis were associated with a tendency of the subgingival microbiome to decrease in richness and diversity; (ii) the presence of type 2 Diabetes Mellitus was not associated with significant differences in the relative abundance of one or more species in patients either with or without periodontitis; (iii) the presence of periodontitis was associated with a significantly higher relative abundance of Anaerolineaceae bacterium oral taxon 439 in type 2 Diabetes Mellitus patients. CONCLUSIONS: Whole metagenomic shotgun sequencing of the subgingival microbiome was extremely effective in the detection of low-abundant taxon. Our results point out a significantly higher relative abundance of Anaerolineaceae bacterium oral taxon 439 in patients with moderate to severe periodontitis vs patients without history of periodontitis, which was maintained when the comparison was restricted to type 2 diabetics.

VDR, RANKL and OPG polymorphisms as possible predisposing cofactors of postmenopausal osteoporosis: explorative study in Italian population.

Postmenopausal osteoporosis (PO) has a strong genetic component. Presently, the published evidence on the association between the main single-nucleotide polymorphisms (SNPs) of the receptor activator of nuclear factor-kb ligand (RANKL), osteoprotegerin (OPG) and vitamin D receptor (VDR) and bone mass density (BMD) are scarce, mostly considering Italian population. This study sought to determine whether OPG (rs2073618), RANKL (rs9525641) and the VDR (rs2228570) SNPs were associated with BMD in a sample of 139 North-Italian postmenopausal women. The allelic distribution of rs9525641 in women with PO or osteopenia (OP + OPE group) differed from controls (p < 0.05), suggesting that this allele might confer a greater susceptibility to bone resorption. Concerning rs2228570, CC genotype was associated with OP + OPE women, with a worst total hip BMD. Notably, the combined genotype RANK (CT)-VDR (TT) was significantly associated to spine BMD (p < 0.05). In conclusion, this pilot study showed that rs9525641 and rs2228570 polymorphisms might contribute, separately or in combination, in determining BMD phenotype in selected postmenopausal populations.

Surnames in Honduras: A study of the population of Honduras through isonymy.

In this work, we investigated surname distribution in 4,348,021 Honduran electors with the aim of detecting population structure through the study of isonymy in three administrative levels: the whole nation, the 18 departments, and the 298 municipalities. For each administrative level, we studied the surname effective number, α, the total inbreeding, FIT , the random inbreeding, FST , and the local inbreeding, FIS . Principal components analysis, multidimensional scaling, and cluster analysis were performed on Lasker's distance matrix to detect the direction of surname diffusion and for a graphic representation of the surname relationship between different locations. The values of FIT , FST , and FIS display a variation of random inbreeding between the administrative levels in the Honduras population, which is attributed to the "Prefecture effect." Multivariate analyses of department data identified two main clusters, one south-western and the second north-eastern, with the Bay Islands and the eastern Gracias a Dios out of the main clusters. The results suggest that currently the population structure of this country is the result of the joint action of short-range directional migration and drift, with drift dominating over migration, and that population diffusion may have taken place mainly in the NW-SE direction.

Surnames in Albania: a study of the population of Albania through isonymy.

In order to describe the isonymic structure of Albania, the distribution of 3,068,447 surnames was studied in the 12 prefectures and their administrative subdivisions: the 36 districts and 321 communes. The number of different surnames found was 37,184. Effective surname number for the entire country was 1327, the average for prefectures was 653.3 ± 84.3, for districts 365.9 ± 42.0 and for communes 122.6 ± 8.7. These values display a variation of inbreeding between administrative levels in the Albanian population, which can be attributed to the previously published "Prefecture effect". Matrices of isonymic distances between units within administrative levels were tested for correlation with geographic distances. The correlations were highest for prefectures (r = 0.71 ± 0.06 for Euclidean distance) and lowest for communes (r = 0.37 ± 0.011 for Nei's distance). The multivariate analyses (Principal component analysis and Multidimensional Scaling) of prefectures identify three main clusters, one toward the North, the second in Central Albania, and the third in the South. This pattern is consistent with important subclusters from districts and communes, which point out that the country may have been colonised by diffusion of groups in the North-South direction, and from Macedonia in the East, over a pre-existing Illiryan population.

A study of the population of Paraguay through isonymy.

In order to describe the isonymic structure of Paraguay, the distribution of 4,843,868 surnames of 2,882,163 persons was studied in the 18 departments and 237 districts of the nation. The correlations between isonymic and geographic distances for departments were r = 0.713 ± 0.052 for Euclidean distance, 0.597 ± 0.074 for Nei's and 0.582 ± 0.076 for Lasker's, and for districts r = 0.320 ± 0.007, 0.235 ± 0.009 and 0.422 ± 0.008, respectively. Average α was 151 for the entire country, 140.6 ± 6.5 for departments and 108.2 ± 2.7 for districts. The geographical distribution of districts'α is compatible with the settlement of subsequent groups of migrants moving from South towards the Centre and North of Paraguay. The geographical analysis of the first three components of Lasker's isonymy distance matrix is in agreement with such a process. The prevalence of Spanish-Amerindian ethnic groups and the relative absence of indigenous surnames (absence due mainly to the forced surname change of 1848) is in agreement with the diffusion of Spanish speaking males over a low-density area populated by indigenous groups. The present distribution of Y-markers and mt-markers in the available studies in most Latin American populations is compatible with this process.

Prevalence of bleeding on probing: a cohort study in a specialist periodontal clinic.

OBJECTIVES: to assess the prevalence and distribution of bleeding on probing (BoP) in a cohort of periodontally diseased patients, evaluate the influence of patient-related predictors on BoP variability, and characterize two subgroups of patients with a significantly different BoP score. METHOD AND MATERIALS: six hundred and one patients were retrospectively included. The percentage of BoP-positive sites was calculated for the entire dentition (%BoPtotal) and within different areas of the dentition. The influence of patient-related predictors on intersubject variability in %BoPtotal was evaluated. Two subgroups of patients, belonging to the lowest (LB, low bleeding) and highest (high bleeding, HB) quartile of patient distribution according to %BoPtotal, were identified. RESULTS: median %BoPtotal was 26.4%, with 99% of the population showing at least one BoP-positive site. %BoPtotal was positively correlated with patient age and number of sites with pocket probing depth (PPD) ⋝ 5 mm, and significantly more prevalent in mandibular vs maxillary sites, posterior vs anterior sites, interproximal vs oral/buccal sites, and sites with PPD ⋝ 5 mm vs PPD ⋜ 4 mm. LB and HB patients were significantly different for %BoPtotal, as well as in sites with PPD ⋜ 4 mm and PPD ⋝ 5 mm, but not for sex, age, smoking status, daily cigarette consumption, diabetic status, and number of sites with PPD ⋝ 5 mm. CONCLUSIONS: BoP was highly prevalent and variable in both patients and different areas of the dentition; patient-related factors and site-specific characteristics (such as age, number of periodontal pockets, probing depth, tooth type, and aspects) seem to be partly responsible for the individual variation in BoP; and HB and LB were not significantly different with respect to the investigated predictors.

Surnames in Bolivia: a study of the population of Bolivia through isonymy.

In Bolivia, the Hispanic dual surname system is used. To describe the isonymic structure of Bolivia, the surname distribution of 12,139,448 persons registered in the 2006 census data was studied in 9 districts and 112 provinces of the nation, for a total of 23,244,064 surnames. The number of different surnames found was 174,922. Matrices of isonymic distances between the administrative units (districts and provinces) were constructed and tested for correlation with geographic distance. In the 112 provinces, isonymic distances were correlated with geographic distance (r = 0.545 ± 0.011 for Euclidean, 0.501 ± 0.012 for Nei's, and 0.556 ± 0.010 for Lasker's distance). The multiple regression of the surname effective number (α), equivalent to the allele effective number in a genetic system, was nonsignificant on latitude and longitude; however, it was highly significant and negative on altitude (r = -0.72). Because the Andes extend from north to south in west-central Bolivia, random inbreeding was lowest in the eastern districts, and highest in mountainous western Bolivia. Average α for the provinces was 122 ± 2; for the districts, it was 216 ± 29, and for the whole of Bolivia it was 213. The geographical distribution of α in the provinces is compatible with the settlement of subsequent groups of migrants moving from east and north toward the center and south of Bolivia. The relative frequency of indigenous surnames is correlated positively with altitude. This suggests that the country was populated by recent low-density demic diffusion over a low-density indigenous population. This may have been a common phenomenon in the immigration to tropical South America.

Interleukin-1 beta levels in gingival crevicular fluid and serum under naturally occurring and experimentally induced gingivitis.

AIMS: To evaluate the interleukin-1 beta (IL-1 beta) levels in gingival crevicular fluid (GCF) and serum in either naturally occurring (N-O) or experimentally induced (E-I) plaque-associated gingivitis. MATERIAL AND METHODS: Thirty-seven periodontally healthy subjects were evaluated in real life conditions (N-O gingivitis) as well as after 21 days of experimental gingivitis trial (E-I gingivitis). During the experimental gingivitis trial, in one maxillary quadrant (test quadrant), gingival inflammation was induced by oral hygiene abstention, while in the contralateral (control) quadrant, oral hygiene was routinely continued. IL-1 beta concentrations in N-O and E-I gingivitis were investigated for IL-1B(+3954) and IL-1B(-511) gene polymorphisms. RESULTS: (i) GCF IL-1 beta concentrations in E-I gingivitis were significantly higher compared with N-O gingivitis; (ii) an intra-individual correlation between GCF concentrations of IL-1 beta detected in N-O and E-I gingivitis was observed in control quadrants, but not in test quadrants; (iii) IL-1 beta concentration in GCF was associated with IL-1B(+3954) genotype only at test quadrants; (iv) IL-1 beta was detectable in serum only at low levels in a limited number of subjects, without difference between gingivitis conditions. CONCLUSIONS: Aspects of the bacterial challenge to the gingival tissues, such as the amount of plaque deposits and plaque accumulation rate, appear to affect the IL-1 beta levels in GCF in subjects with a specific IL-1B genotype.

Age-related treatment response following non-surgical periodontal therapy.

BACKGROUND: To date, no studies have evaluated the effect of patient age on the treatment response following non-surgical periodontal therapy (NSPT). AIM: To evaluate the outcomes of NSPT in two cohorts of patients with a substantial age difference. MATERIALS AND METHODS: Two groups of periodontitis patients with a substantial age difference (younger group, Y, and older group, O) were retrospectively selected. The effectiveness of NSPT was assessed by evaluating the changes in the prevalence of sites with different pocket probing depths (PPD) as well as the changes in patient- and site-specific bleeding on probing (BoP) scores. RESULTS: Y group comprised 57 patients, mean age: 34.7 +/- 4.4 years, and O group comprised 60 patients, mean age: 58.9 +/- 5.3 years (p<0.0001). NSPT resulted in a significant improvement of PPD and BoP in both age groups. No statistically significant inter-group differences were observed in the investigated clinical parameters as well as their changes with respect to pre-treatment. However, multiple regression analysis showed a significantly higher risk of showing residual pockets following treatment in group O. CONCLUSIONS: The results of the present study seem to indicate that age has a limited effect on treatment response following NSPT in periodontitis patients.

Experimental gingivitis: reproducibility of plaque accumulation and gingival inflammation parameters in selected populations during a repeat trial.

OBJECTIVES: This study aimed to assess whether and to what extent the experimental gingivitis clinical parameters are reproducible within selected populations with different gingival inflammatory response (high or low) to plaque accumulation. In addition, the consistency in developing a high or low gingival inflammatory response within the selected populations was evaluated. MATERIAL AND METHODS: Thirty-seven subjects previously identified as high (HR, n=20) or low responders (LR, n=17) during an experimental gingivitis trial (first trial) were enrolled in a "repeat" experimental gingivitis trial. RESULTS: No significant differences in plaque accumulation parameters and bleeding index values were detected between first and repeat trial for the 37 participants. Gingival index was higher during the repeat trial but behaved consistently in terms of the temporal changes in the course of both trials in both populations. Of the 17 LR participants, 10 manifested low susceptibility to inflammation after repeat trial. Among the 20 HR, 10 manifested high susceptibility to inflammation after repeat trial. CONCLUSIONS: These results indicate that our experimental gingivitis model is reproducible to some extent in selected populations. The high reproducibility of plaque and, to a lesser extent, of inflammation parameters under the employed controlled conditions could be a valuable tool in gingivitis research.

Surnames in Western Europe: a comparison of the subcontinental populations through isonymy.

We studied the isonymic structure of Western Europe using the distributions of 26.2 million surnames in 8 countries, 125 regions and 2094 towns of the Subcontinent. We found that, for the whole of Western Europe, Nei's distance was correlated with geographic distance (r=0.610+/-0.009). It was observed that at long geographic distances the isonymyc distance stays below linearity and tends to become asymptotic, and this was attributed to long distance migration. A dendrogram of the125 regions was built and the clusters identified by the dendrogram are almost exactly coincident with the nations of the Subcontinent. Random inbreeding calculated from isonymy, F(ST), was highest in Spanish regions, and lowest in France. The geographical distribution of alpha in 2094 towns, high in the Center and East of the Subcontinent and lower in Spain, is compatible with the settlement of subsequent waves of migrants moving from the West and from the South toward the centre of the Continent. The present surname structure of Western Europe is strictly linked to local languages.