Metagenomic Analysis of Subgingival Microbiota Following Non-Surgical Periodontal Therapy: a Pilot Study

This study tested the feasibility of a high throughput metagenomic approach to analyze the pre- and posttreatment of subgingival plaque in two subjects with aggressive periodontitis. DNA was extracted from subgingival samples and subjected to PCR amplification of the c2-c4 regions of the 16S rDNA using primers with bar codes to identify individual samples. The PCR products were pooled and sequenced for the v4 region of the 16S rDNA using the 454 FLX standard platform. The results were analyzed for species/phylotypes in the Human Oral Microbiome Database (HOMD) and Ribosomal Database Project (RDP) database. The sequencing of the amplicons resulted in 24,673 reads and identified 208 species/phylotypes. Of those, 129 species/phylotypes were identified in both patients but their proportions varied. While >120 species/phylotypes were identified in all samples, 28-42 species/phylotypes cumulatively represent 90% of all subgingival bacteria in each sample. The remaining species/phylotypes each constituted ≤0.2% of the total subgingival bacteria. In conclusion, the subgingival microbiota are characterized by high species richness dominated by a few species/ phylotypes. The microbiota changed after periodontal therapy. High throughput metagenomic analysis is applicable to assess the complexity and changes of the subgingival microbiota.

Download Full-text

Two Groups of Phytoplasmas from Japan Distinguished on the Basis of Amplification and Restriction Analysis of 16S rDNA

Plant Disease ◽

10.1094/pdis.1997.81.3.301 ◽

1997 ◽

Vol 81 (3) ◽

pp. 301-305 ◽

Cited By ~ 28

Author(s):

Seiichi Okuda ◽

James P. Prince ◽

Robert E. Davis ◽

Ellen L. Dally ◽

Ing-Ming Lee ◽

...

Keyword(s):

16S Rdna ◽

Restriction Analysis ◽

Pcr Amplification ◽

Enzyme Analysis ◽

Restriction Enzyme Analysis ◽

Rrna Gene ◽

Gene Group ◽

Beet Leafhopper ◽

Pcr Products ◽

Elm Yellows

Phytoplasmas (mycoplasmalike organisms, MLOs) associated with mitsuba (Japanese hone-wort) witches'-broom (JHW), garland chrysanthemum witches'-broom (GCW), eggplant dwarf (ED), tomato yellows (TY), marguerite yellows (MY), gentian witches'-broom (GW), and tsu-wabuki witches'-broom (TW) in Japan were investigated by polymerase chain reaction (PCR) amplification of DNA and restriction enzyme analysis of PCR products. The phytoplasmas could be separated into two groups, one containing strains JHW, GCW, ED, TY, and MY, and the other containing strains GW and TW, corresponding to two groups previously recognized on the basis of transmission by Macrosteles striifrons and Scleroracus flavopictus, respectively. The strains transmitted by M. striifrons were classified in 16S rRNA gene group 16SrI, which contains aster yellows and related phytoplasma strains. Strains GW and TW were classified in group 16SrIII, which contains phytoplasmas associated with peach X-disease, clover yellow edge, and related phytoplasmas. Digestion of amplified 16S rDNA with HpaII indicated that strains GW and TW were affiliated with subgroup 16SrIII-B, which contains clover yellow edge phytoplasma. All seven strains were distinguished from other phytoplasmas, including those associated with clover proliferation, ash yellows, elm yellows, and beet leafhopper-transmitted virescence in North America, and Malaysian periwinkle yellows and sweet potato witches'-broom in Asia.

Download Full-text

Automated High-Throughput Purification of PCR Products Using Wizard®MagneSil™ Paramagnetic Particles

JALA Journal of the Association for Laboratory Automation ◽

10.1016/s1535-5535(04)00232-1 ◽

2002 ◽

Vol 7 (6) ◽

pp. 120-124

Author(s):

P Otto

Keyword(s):

High Throughput ◽

Pcr Products

Download Full-text

01 / The oral microbiome in rheumatoid arthritis and the effect of periodontal therapy

10.26226/morressier.5ac3831a2afeeb00097a3f83 ◽

2018 ◽

Author(s):

Isabel Lopez-Oliva

Keyword(s):

Rheumatoid Arthritis ◽

Periodontal Therapy ◽

Oral Microbiome

Download Full-text

DETECTION OF ALFACORONAVIRUSES, BETACORONAVIRUSES AND ASTROVIRUSES IN BAT FECAL SAMPLES FROM MOSCOW REGION

Molecular Diagnostics and Biosafety – 2020. Russian national scientific and practical conference with international participation (October, 6–8, 2020): Conference Proceedings ◽

10.36233/978-5-9900432-9-9-42 ◽

2020 ◽

Author(s):

E.V. Korneenko ◽

◽

А.E. Samoilov ◽

I.V. Artyushin ◽

M.V. Safonova ◽

...

Keyword(s):

High Throughput ◽

Viral Genome ◽

High Throughput Sequencing ◽

Pcr Amplification ◽

Moscow Region ◽

Fecal Samples ◽

Genus Level ◽

Zoonotic Viruses ◽

Reservoir Hosts ◽

Blastn Search

In our study we analyzed viral RNA in bat fecal samples from Moscow region (Zvenigorod district) collected in 2015. To detect various virus families and genera in bat fecal samples we used PCR amplification of viral genome fragments, followed by high-throughput sequencing. Blastn search of unassembled reads revealed the presence of viruses from families Astroviridae, Coronaviridae and Herpesviridae. Assembly using SPAdes 3.14 yields contigs of length 460–530 b.p. which correspond to genome fragments of Coronaviridae and Astroviridae. The taxonomy of coronaviruses has been determined to the genus level. We also showed that one bat can be a reservoir of several virus genuses. Thus, the bats in the Moscow region were confirmed as reservoir hosts for potentially zoonotic viruses.

Download Full-text

Antibiotic Use in Periodontal Therapy among French Dentists and Factors Which Influence Prescribing Practices

Antibiotics ◽

10.3390/antibiotics10030303 ◽

2021 ◽

Vol 10 (3) ◽

pp. 303

Author(s):

Kevimy Agossa ◽

Kadiatou Sy ◽

Théo Mainville ◽

Marjolaine Gosset ◽

Sylvie Jeanne ◽

...

Keyword(s):

Antibiotic Use ◽

Aggressive Periodontitis ◽

Periodontal Therapy ◽

Research Network ◽

Prescribing Practices ◽

French Society ◽

Private Practitioners ◽

First Line Therapy ◽

Practice Based Research ◽

Systemic Antibiotics

The aim of the present survey is to investigate the use of antibiotics during periodontal therapy among French dentists with a focus on exploring potential differences between various groups of practitioners. A self-administered questionnaire was distributed to different groups of practitioners including members of (i) the French Society of Periodontology and Implantology; (ii) the College of University Teachers in Periodontology and, (iii) private practitioners participating in the French general dental practice-based research network. 272 questionnaires were included in the analysis. Prescription patterns were globally in line with the current recommendations. Systemic antibiotics are most frequently used as a first-line therapy in necrotizing periodontitis (92%) and aggressive periodontitis (53.3% to 66.1%). However, malpractice still exists, including in the management of periodontal abscesses. Antibiotics are prescribed (i) less frequently for periodontal abscesses and (ii) more frequently for generalized aggressive periodontitis by members of the periodontal society and University college (p < 0.05). Amoxicillin (59.9%) and the amoxicillin + metronidazole (59.6%) combination were the most frequently prescribed molecules. Providing a high number of periodontal treatments per week, being more recently graduated, having a post-graduate certificate in periodontology and holding or having held an academic position/hospital practice were all factors associated with a better knowledge of and/or more adequate antibiotic use.

Download Full-text

Presence of plasmid-mediated quinolone resistance (PMQR) genes in non-typhoidal Salmonella strains with reduced susceptibility to fluoroquinolones isolated from human salmonellosis in Gyeonggi-do, South Korea from 2016 to 2019

Gut Pathogens ◽

10.1186/s13099-021-00431-7 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Sohyun Lee ◽

Nanjoo Park ◽

Sujung Yun ◽

Eunseon Hur ◽

Jiwon Song ◽

...

Keyword(s):

South Korea ◽

Pcr Amplification ◽

Public Health Problem ◽

Test Method ◽

Quinolone Resistance ◽

Human Salmonellosis ◽

Pcr Products ◽

Antimicrobial Susceptibility Tests ◽

Susceptibility Tests ◽

Sequence Types

AbstractNon-typhoidal salmonellosis remains a pressing public health problem worldwide. Quinolones, particularly fluoroquinolones, are widely used to treat various infections, including non-typhoidal salmonellosis, which can be a serious illness. The emergence of fluoroquinolone-resistant Salmonella has resulted in treatment failure and high mortality rates. In this study, we estimated the presence of plasmid-mediated quinolone resistance (PMQR) genes in Salmonella enterica isolated from human salmonellosis patients in South Korea from 2016 to 2019. We evaluated the association of these genes with fluoroquinolone susceptibility. Antimicrobial susceptibility tests for Salmonella isolates were performed using the Vitek II system, and the minimum inhibitory concentrations (MIC) of ciprofloxacin and levofloxacin were determined using the E-test method. Plasmid-mediated quinolone resistance (PMQR) genes were detected by PCR amplification and quinolone resistance-determining regions (QRDRs) of the gyrA and parC genes were analyzed following Sanger sequencing of the PCR products. Thirty-four Salmonella strains with reduced susceptibility to fluoroquinolones (ciprofloxacin MIC ≥ 0.125 µg/mL and levofloxacin MIC ≥ 0.25 µg/mL) were selected from 208 human clinical Salmonella isolates. Among them, 22 Salmonella strains harbored one PMQR gene (qnrA, qnrB, or qnrS), and three Salmonella strains carried two PMQR genes (qnrS and aac(6′)-Ib-cr or qnrA and qnrB). qnrS was the most common PMQR gene. Serotyping revealed that Salmonella 4,[5]12:i:- (32.4%, 11/34) and Salmonella Typhimurium (29.4%, 10/34) were the two most predominant serovars, and Multi-locus sequence typing (MLST) showed that ST19 and ST34 were the most frequent sequence types. In conclusion, qnr gene-positive Salmonella 4,[5],12:i:- and Salmonella Typhimurium were the main serovars responsible for reduced susceptibility to fluoroquinolones. Therefore, our findings suggest that PMQR-positive Salmonella strains, which can be isolated from various samples including human, food, and the environment, should be carefully monitored.

Download Full-text

Two main clusters within Trypanosoma cruzi zymodeme 3 are defined by distinct regions of the ribosomal RNA cistron

Parasitology ◽

10.1017/s0031182001001172 ◽

2002 ◽

Vol 124 (2) ◽

pp. 177-184 ◽

Cited By ~ 28

Author(s):

M. B. A. MENDONÇA ◽

N. S. NEHME ◽

S. S. SANTOS ◽

E. CUPOLILLO ◽

N. VARGAS ◽

...

Keyword(s):

Trypanosoma Cruzi ◽

Ribosomal Rna ◽

Southern Blotting ◽

Pcr Amplification ◽

Rrna Gene ◽

Pcr Products ◽

Phylogenetic Lineages ◽

Definition Of ◽

Ribosomal Cistron ◽

Panstrongylus Geniculatus

Trypanosoma cruzi is currently classified into 2 major phylogenetic lineages, T. cruzi I and II, that correlate with the formerly described zymodeme 1 and 2, respectively. Another isoenzymic group (zymodeme 3–Z3) was also described. In this study, we analysed the genetic diversity among Z3 isolates of the Brazilian Amazon by restriction fragment length polymorphism of the intergenic transcribed spacers (ITSs) of the ribosomal RNA cistron and the size of the divergent domain D7 of the 24Sα rRNA gene. DNAs from 12 T. cruzi Z3 isolates obtained from humans (2), Panstrongylus geniculatus (1), and Rhodnius brethesi (9) were submitted to PCR amplification of the ITSs plus the 5·8S rDNA. The PCR products were digested with 4 distinct endonucleases and the profiles analysed by a numerical methodology. The phenetic dendrogram revealed a clear dichotomy in the Z3 group, defining 2 groups that were named Z3-A and Z3-B. Dimorphism was also found in the band sizes of the amplified D7 divergent domain of the 24Sα rDNA, which showed a perfect correlation with the ITSs clustering. The organization of the ribosomal cistron was investigated by Southern blotting and shown to be conserved in the genome of the 2 Z3 groups. This study shows that the rDNA cistron allows the definition of 2 distinct subclusters in Z3 isolates.

Download Full-text