Draft genome sequences of 13 putatively novel Haemophilus species and strains assembled from human saliva.

We present the draft metagenome-assembled genomes (MAGs) of 13 Haemophilus representatives from human saliva. MAGs were reconstructed by a streamlined pre-assembly mapping approach performed against 9 clinically relevant reference genomes. Overall, genomes belonging to 2 potentially novel Haemophilus species and 11 strains were recovered, as determined by genome-wide ANI analysis.

Oral mucositis and microbial status in acute lymphoblastic leukemia subjects undergoing high-dose chemotherapy

Aim: To assess oral microbial status in patients with acute lymphoblastic leukemia (ALL) undergoing high-dose chemotherapy and to unravel possible associations between nosocomial pathogens and the establishment of chemotherapy-induced oral mucositis (CIOM). Methods: Oral mucosa, saliva, and peripheral blood samples were collected from 46 ALL subjects one day prior to chemotherapy (D0) and 2 weeks after treatment initiation (D14). Clinical intraoral inspection was performed by a single practitioner, with mucositis classification performed according to the WHO oral toxicity scale. Blood components were quantified by automatic flow cytometry, while oral Staphylococcus aureus and Pseudomonas aeruginosa were detected by Polymerase Chain Reaction with species-specific primers. Associations among bacteria and clinical findings were determined by Fisher's Exact test, longitudinal bacterial changes by paired Macnemar, and correlations among blood parameters and mucositis status or bacteria via Mann-Whitney. Results: S. aureus displayed higher detection rates at D14 (p < 0.05) and was positively associated with mucositis, adoption of a non-solid diet (all p < 0.001), nausea and fever (all p < 0.05). Conversely, P. aeruginosa did not correlate to CIOM clinical parameters. At the systemic standpoint, lower hemoglobin levels associated with CIOM and fever events (all p < 0.01). Conclusion: The study evidences S. aureus as a potential pathogen in ALL-CIOM, reaffirming microbial control as an important preventive measure during high-dose immunosuppressive therapy. The weight of non-white-blood-cell parameters should be validated as novel CIOM biomarkers in prospective research

Draft Genome Sequences of Five Putatively Novel Saccharibacteria Species Assembled from the Human Oral Metagenome.

We report the draft metagenome-assembled genomes (MAGs) of five putatively novel Saccharibacteria strains retrieved from the oral microbiome. MAGs were obtained from nonstimulated saliva samples from hosts with various clinical statuses and correspond to distinct species taxonomically placed within the Saccharimonadaceae family, as determined by genome-wide analysis against previously described TM7 genomes.

Avaliação in vitro da atividade de fosfolipase e proteinase de cepas de candida albicans isolada da cavidade bucal de pacientes diabéticos / In vitro evaluation of phospholipase and proteinase of candida albicans isolated from oral cavity of diabetic patients

Leveduras do gênero Candida são comuns na cavidade bucal e podem causar candidose na presença de fatores predisponentes, especialmente em paciente diabético, o qual é caracterizado por um aumento anormal da glicose no sangue. A manifestação da doença está relacionada a este conjunto de fatores locais, tais como a presença de próteses dentárias, pH salivar, fluxo salivar e tabaco. A redução da saliva é um dos principais fatores de risco para o aparecimento de infecção e o controle glicêmico inadequado causado por diabetes, em associação com todos estes fatores, pode aumentar a incidência de infecções. Os objetivos deste estudo foram: 1) isolar e identificar cepas de Candida albicans da mucosa bucal de pacientes diabéticos 2) avaliar os fatores de virulência: proteinase e fosfolipase. Amostras microbiológicas foram coletadas a partir de locais da mucosa bucal e semeadas em CHROMagar para posterior identificação de C. albicans por PCR. Foram realizados testes da atividade de proteinase e fosfolipase para todos os isolados de C. albicans. Neste estudo, 22 isolados foram identificados como C. albicans. Em relação às atividades de proteinases, todas as cepas de C. albicans foram capazes de produzir proteinase, enquanto que para fosfolipase, apenas 4,5% dos isolados não produziram esta exoenzima. Portanto, C. albicans presente na cavidade bucal de pacientes diabéticos tem potencial patogênico e pode participar de processos infecciosos e inflamatórios, causando lesões e invadindo os tecidos orais.

Candida yeasts are common in the oral cavity and can cause candidosis in the presence of predisposing factors, especially diabetes, which is characterized by an abnormal increasing in blood glucose concentration. The manifestation of the disease is related to a set of local factors such as the presence of dental prostheses, salivary pH, salivary flow and tobacco. The reduction in saliva is a major risk factor for the onset of infection and poor glycemic control caused by diabetes in association with all these factors further increases the incidence of candidosis. The objectives of this study were: 1) to isolate and identify Candida albicans strains from oral mucosa sites of diabetic patients 2) to evaluate the virulence factors: proteinase and phospholipase. Thus, microbial samples were collected from oral mucosa sites and seeded in CHROMagar for subsequent identification of C. albicans by PCR. For the phenotypic tests, all strains of C. albicans were evaluated for their proteinase and phospholipase productions. In this study, 22 isolates were identified as C. albicans. In regard to the proteinase activities, all strains of C. albicans were able to produce proteinase, while only 4.5% from those isolates were not able to produce phospholipase activity. In conclusion, C. albicans present in the oral cavity of diabetic patients is potentially pathogenic and can participate in infectious and inflammatory processes, causing injury and invading oral tissues.

Detection of Mogibacterium timidum in subgingival biofilm of aggressive and non-diabetic and diabetic chronic periodontitis patients

The aim of the present study was to evaluate the frequency of detection of Mogibacterium timidum in subgingival samples of subjects with generalized aggressive periodontitis (GAgP) and uncontrolled diabetic and non-diabetic subjects with generalized chronic periodontitis (GChP). 48 patients with GAgP, 50 non-diabetic and 39 uncontrolled (glycated hemoglobin >7%) type 2 diabetic subjects with GChP were enrolled in this study. Subgingival biofilm were collected from deep pockets (probing depth > 7 mm). After DNA extraction, M. timidum was detected by Nested Polymerase Chain Reaction and chi-square test was used to data analysis (p>0.05). There were no differences in the frequency of detection of M. timidum between subjects with GAgP (35%) and non-diabetic subjects with GChP (40%) (p>0.05). The frequency of detection of M. timidum was significantly higher in deep pockets of diabetic subjects with GChP (56%) when compared to GAgP (p<0.05), but similar to non-diabetic subjects with GChP (p>0.05). The frequency of detection of M. timidum was higher in subjects GChP presenting uncontrolled type 2 diabetes mellitus, when compared to GAgP subjects.

Detection of Mogibacterium timidum in subgingival biofilm of aggressive and non-diabetic and diabetic chronic periodontitis patients.

The aim of the present study was to evaluate the frequency of detection of Mogibacterium timidum in subgingival samples of subjects with generalized aggressive periodontitis (GAgP) and uncontrolled diabetic and non-diabetic subjects with generalized chronic periodontitis (GChP). 48 patients with GAgP, 50 non-diabetic and 39 uncontrolled (glycated hemoglobin >7%) type 2 diabetic subjects with GChP were enrolled in this study. Subgingival biofilm were collected from deep pockets (probing depth > 7 mm). After DNA extraction, M. timidum was detected by Nested Polymerase Chain Reaction and chi-square test was used to data analysis (p>0.05). There were no differences in the frequency of detection of M. timidum between subjects with GAgP (35%) and non-diabetic subjects with GChP (40%) (p>0.05). The frequency of detection of M. timidum was significantly higher in deep pockets of diabetic subjects with GChP (56%) when compared to GAgP (p<0.05), but similar to non-diabetic subjects with GChP (p>0.05). The frequency of detection of M. timidum was higher in subjects GChP presenting uncontrolled type 2 diabetes mellitus, when compared to GAgP subjects.

Real-time polymerase chain reaction quantification of Porphyromonas gingivalis and Tannerella forsythia in primary endodontic infections.

INTRODUCTION: Porphyromonas gingivalis and Tannerella forsythia are anaerobic bacteria commonly involved in root canal infections. Although previous investigations have assessed these species by strictly qualitative approaches, accurate determination of their cell levels by a sensitive quantitative technique may contribute with additional information regarding relevance in pain of endodontic origin. METHOD: The root canal levels of P. gingivalis, T. forsythia, and total bacteria were investigated by a quantitative polymerase chain reaction (PCR) assay based on unique copy molecular markers. A total of 32 symptomatic (n = 14) and asymptomatic (n = 18) cases of endodontic infections were analyzed. Root canal samples were collected; genomic DNA was extracted and submitted to SYBR Green I real-time PCR targeting the rgpB (P. gingivalis), bspA (T. forsythia), and rpoB (total bacteria) single copy genes. RESULTS: Overall, P. gingivalis, T. forsythia, and the coexistence of both species were encountered in 28%, 66%, and 22% of the subjects, respectively. P. gingivalis and T. forsythia levels ranged from 5.65 x 10(-6) to 1.20 x 10(-2) and from 5.76 x 10(-6) to 1.35 x 10(-1). T. forsythia was highly prevalent and numerous in the study groups, whereas P. gingivalis was moderately frequent and less abundant, displaying 19-fold lower average levels than the former. CONCLUSIONS: The endodontic levels of P. gingivalis and T. forsythia, individually or in conjunction, did not display significant associations with the manifestation of pain of endodontic origin.

Identification of citrus expressed sequence tags (ESTs) encoding pleiotropic drug resistance (PDR)-like proteins

Pleiotropic drug resistance (PDR) proteins, a subfamily of the ATP-binding cassette (ABC) transporters, have been recently shown to play a role in plant defense against biotic and abiotic stresses. However, nothing is known about their expression in citrus. To investigate the occurrence of PDR homologues in citrus species, we have surveyed EST sequences from different tissues and conditions of the Citrus Expressed Sequence Tags (CitEST) database, through sequence similarity search analyses and inspections for characteristic PDR domains. Multiple sequence alignments, prediction of transmembrane topology and phylogenetic analysis of PDR-like proteins were additionally performed. This study allowed the identification of nine putative proteins showing characteristic PDR features in citrus species under various conditions, which may indicate a potential correlation between PDRs and stress and metabolism of citrus plants. Moreover, a tissue-specific putative PDR-like protein was found in sweet orange fruits. To our knowledge, this is the first report regarding the identification of citrus ESTs encoding PDR-like proteins as well as the first to identify a putative full ABC transporter with specific expression in fruits.

Identification of bacteria in endodontic infections by sequence analysis of 16S rDNA clone libraries.

A significant proportion of oral bacteria are unable to undergo cultivation by existing techniques. In this regard, the microbiota from root canals still requires complementary characterization. The present study aimed at the identification of bacteria by sequence analysis of 16S rDNA clone libraries from seven endodontically infected teeth. Samples were collected from the root canals, subjected to the PCR with universal 16S rDNA primers, cloned and partially sequenced. Clones were clustered into groups of closely related sequences (phylotypes) and identification to the species level was performed by comparative analysis with the GenBank, EMBL and DDBJ databases, according to a 98% minimum identity. All samples were positive for bacteria and the number of phylotypes detected per subject varied from two to 14. The majority of taxa (65.2%) belonged to the phylum Firmicutes of the Gram-positive bacteria, followed by Proteobacteria (10.9%), Spirochaetes (4.3%), Bacteroidetes (6.5%), Actinobacteria (2.2%) and Deferribacteres (2.2%). A total of 46 distinct taxonomic units was identified. Four clones with low similarity to sequences previously deposited in the databases were sequenced to nearly full extent and were classified taxonomically as novel representatives of the order Clostridiales, including a putative novel species of Mogibacterium. The identification of novel phylotypes associated with endodontic infections suggests that the endodontium may still harbour a relevant proportion of uncharacterized taxa.

In silico characterization of microsatellites in Eucalyptus spp: abundance, length variation and transposon associations

This study assessed the abundance of microsatellites, or simple sequence repeats (SSR), in 19 Eucalyptus EST libraries from FORESTs, containing cDNA sequences from five species: E. grandis, E. globulus, E. saligna, E. urophylla and E. camaldulensis. Overall, a total of 11,534 SSRs and 8,447 SSR-containing sequences (25.5% of total ESTs) were identified, with an average of 1 SSR/2.5 kb when considering all motifs and 1 SSR/3.1 kb when mononucleotides were not included. Dimeric repeats were the most abundant (41.03%), followed by trimerics (36.11%) and monomerics (19.59%). The most frequent motifs were A/T (87.24%) for monomerics, AG/CT (94.44%) for dimerics, CCG/CGG (37.87%) for trimerics, AAGG/CCTT (18.75%) for tetramerics, AGAGG/CCTCT (14.04%) for pentamerics and ACGGCG/CGCCGT (6.30%) for hexamerics. According to sequence length, Class II or potentially variable markers were the most commonly found, followed by Class III. Two sequences presented high similarity to previously published Eucalyptus sequences from the NCBI database, EMBRA_72 and EMBRA_122. Local blastn search for transposons did not reveal the presence of any transposable elements with a cut-off value of 10-50. The large number of microsatellites identified will contribute to the refinement of marker-assisted mapping and to the discovery of novel markers for virtually all genes of economic interest

Microbiological changes with the use of locally delivered doxycycline in the periodontal treatment of smokers.

BACKGROUND: The aim of this study was to evaluate the effect of the association of locally delivered doxycycline 10% and scaling and root planing in the subgingival plaque of smokers. METHODS: Sixteen smokers with chronic periodontitis and a minimum of four pockets (> or = 5 mm) on anterior teeth that bled on probing were selected. Patients were randomly assigned to one of the following groups: scaling and root planing (SRP) or scaling and root planing followed by local application of doxycycline (SRP-D). Subgingival plaque samples were collected from initially moderate (5 to 6 mm) and deep (> or = 7 mm) pockets at baseline and 3 months. Polymerase chain reaction (PCR) analysis was used to detect the frequency of Actinobacillus actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), and Tannerella forsythensis (Tf). RESULTS: No statistically significant difference was found in the reduction of Aa in either the SRP-D or SRP group (P > 0.05). The reduction in Tf, Pg, and Tf + Pg was statistically significant for SRP-D only (P = 0.016, 0.027, and 0.027, respectively). The proportion of sites free of Tf at 3 months was 53% for SRP-D and 9% for SRP (P = 0.02). For Pg, this proportion was 82% and 40%, respectively (P = 0.05). CONCLUSION: The use of locally delivered doxycycline may promote the elimination of T. forsythensis and P. gingivalis in a greater proportion of sites compared to conventional scaling and root planing in smokers.