Identification of Dominant Bacteria Isolated From Periodontal Abscesses

2021 ◽  
pp. 232020682110507
Author(s):  
Kubra Karacam ◽  
Turgut Demir ◽  
Ozlem Baris
Keyword(s):  
Bacterial Species ◽  
The Body ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rdna Sequencing ◽  
Bacterial Content ◽  
Dominant Bacteria ◽  
Research Criteria ◽  
First Time ◽  
Culture Dependent

Aim: Various methods investigating the bacterial content causing periodontal abscesses have been applied in studies conducted until today. However, these studies have focused on periodontopathogens. Our study was carried out to research whether different pathogens other than the known periodontopathogens are present in periodontal abscess formation. Therefore, dominant bacterial samples obtained from the periodontal abscess content using the culture-dependent method were identified by 16S rDNA sequencing. Materials and Methods: Samples were obtained using a syringe or a periopaper from periodontal abscesses of 20 volunteers who met the research criteria. The three different bacterial colonies that were observed most intensely in each sample were selected and purified, and the isolates obtained were kept until the next characterization. Genomic DNA was isolated from each isolate; 16S rRNA genes were amplified by polymerase chain reaction and identified using DNA sequencing analyses. Results: As a result of culture-dependent methods, bacterial species belonging to Streptococcus, Staphylococcus, Neisseria, Actinomyces, Morococcus, Moraxella, and Enterococcus genera were isolated from a total of 60 bacterial isolates, three of which were the most densely growing colonies from each periodontal abscess sample. Conclusion: In our study, most of the bacterial species detected were identified for the first time in the bacterial content of periodontal abscesses. In some previously done studies, most of these bacteria species were shown to cause abscesses in different parts of the body. It was concluded that further studies are needed to determine the number and proportion of these bacteria species in total bacterial content to evaluate whether they cause periodontal abscesses.

scholarly journals Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Matthew R. Olm ◽  
Alexander Crits-Christoph ◽  
Spencer Diamond ◽  
Adi Lavy ◽  
Paula B. Matheus Carnevali ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Ribosomal Proteins ◽  
Large Scale ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Species Discrimination ◽  
Bacterial Genomes ◽  
Discrimination Power

ABSTRACT Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases, we compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of nonsynonymous and synonymous nucleotide differences (dN/dS) decrease until ANI values approach ∼98%, two methods for estimating homologous recombination approached zero at ∼95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full-length 16S rRNA genes were least useful, in part because they were underrecovered from metagenomes. However, many ribosomal proteins displayed both high metagenomic recoverability and species discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination. IMPORTANCE There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics.

scholarly journals Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses

Archaea ◽  
2005 ◽  
Vol 1 (6) ◽  
pp. 391-397 ◽  
Author(s):  
Atsuo Sugano ◽  
Hidetaka Tsuchimoto ◽  
Tun Cho Cho ◽  
Makoto Kimura ◽  
Susumu Asakawa
Keyword(s):  
Rice Straw ◽  
Rice Field ◽  
Previous History ◽  
Methanogenic Archaea ◽  
Leaf Sheath ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Crop Season ◽  
Rdna Sequencing ◽  
Archaeal Communities

The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related toMethanomicrobialesand Rice cluster I.Methanomicrobiales, Rice cluster I andMethanosarcinaleswere major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related toMethanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade) and the previous history of decomposition during the off-crop season.

scholarly journals Treatment nonresponse in children receiving silver diamine fluoride for caries: A pilot study

2020 ◽  
Author(s):  
Ryan Richard Ruff ◽  
Bidisha Paul ◽  
Maria A Sierra ◽  
Fangxi Xu ◽  
Yasmi Crystal ◽  
...  
Keyword(s):  
Pilot Study ◽  
Bacterial Species ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Lasso Regression ◽  
Silver Diamine Fluoride ◽  
Operational Taxonomic Units ◽  
Acid Tolerant ◽  
Nonsurgical Therapy

AbstractObjectives: Silver diamine fluoride (SDF) is a nonsurgical therapy for the arrest and prevention of dental caries with demonstrated clinical efficacy. Approximately 20% of children receiving SDF fail to respond to treatment. The objective of this study was to develop a predictive model of treatment nonresponse using machine learning. Methods: An observational pilot study (N=20) consisting of children with and without active decay and who did and did not respond to silver diamine fluoride provided salivary samples and plaque from infected and contralateral sites. 16S rRNA genes from samples were amplified and sequenced on an Illumina Miseq and analyzed using QIIME. The association between operational taxonomic units and treatment nonresponse was assessed using lasso regression and artificial neural networks. Results: Bivariate group comparisons of bacterial abundance indicate a number of genera were significantly different between nonresponders and those who responded to SDF therapy. No differences were found between nonresponders and caries-active subjects. Prevotella pallens and Veillonella denticariosi were retained in full lasso models and combined with clinical variables in a six-input multilayer perceptron. Discussion: The acidogenic and acid-tolerant nature of retained bacterial species may overcome the antimicrobial effects of SDF. Further research to validate the model in larger external samples is needed.

scholarly journals Comparative Analysis of the Fecal Bacterial Microbiota of Wintering Whooper Swans (Cygnus Cygnus)

2021 ◽  
Vol 8 ◽  
Author(s):  
Wenxia Wang ◽  
Songlin Huang ◽  
Liangliang Yang ◽  
Guogang Zhang
Keyword(s):  
Intestinal Microbiota ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
The Body ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Illumina Hiseq ◽  
Linear Discriminant ◽  
Bacterial Microbiota ◽  
And Control

There are many and diverse intestinal microbiota, and they are closely related to various physiological functions of the body. They directly participate in the host's food digestion, nutrient absorption, energy metabolism, immune response, and many other physiological activities and are also related to the occurrence of many diseases. The intestinal microbiota are extremely important for maintaining normal physical health. In order to explore the composition and differences of the intestinal microbiota of whooper swans in different wintering areas, we collected fecal samples of whooper swans in Sanmenxia, Henan, and Rongcheng, Shandong, and we used the Illumina HiSeq platform to perform high-throughput sequencing of bacterial 16S rRNA genes. Comparison between Sanmenxia and Rongcheng showed no significant differences in ACE, Chao 1, Simpson, and Shannon indices (p > 0.05). Beta diversity results showed significant differences in bacterial communities between two groups [analysis of similarity (ANOSIM): R = 0.80, p = 0.011]. Linear discriminant analysis effect size (LEfSe) analysis showed that at the phylum level, the relative abundance of Actinobacteria was significantly higher in Sanmenxia whooper swans than Rongcheng whooper swans. At the genus level, the amount of Psychrobacter and Carnobacterium in Sanmenxia was significantly higher in Rongcheng, while the relative abundance Catellicoccus and Lactobacillus was significantly higher in Rongcheng than in Sanmenxia. This study analyzed the composition, characteristics, and differences of the intestinal microbiota of the whooper swans in different wintering environments and provided theoretical support for further exploring the relationship between the intestinal microbiota of the whooper swans and the external environment. And it played an important role in the overwintering physiology and ecology, population management, and epidemic prevention and control of whooper swans.

scholarly journals Census of the Viral Metagenome within an Activated Sludge Microbial Assemblage

2010 ◽  
Vol 76 (8) ◽  
pp. 2673-2677 ◽  
Author(s):  
Larissa C. Parsley ◽  
Erin J. Consuegra ◽  
Stephen J. Thomas ◽  
Jaysheel Bhavsar ◽  
Andrew M. Land ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Activated Sludge ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Isolates ◽  
Microbial Assemblage ◽  
Culture Independent ◽  
Culture Dependent

ABSTRACT The viral metagenome within an activated sludge microbial assemblage was sampled using culture-dependent and culture-independent methods and compared to the diversity of activated sludge bacterial taxa. A total of 70 unique cultured bacterial isolates, 24 cultured bacteriophages, 829 bacterial metagenomic clones of 16S rRNA genes, and 1,161 viral metagenomic clones were subjected to a phylogenetic analysis.

scholarly journals Microbial contamination of a University dental clinic in Brazil

2017 ◽  
Vol 15 (4) ◽  
pp. 248
Author(s):  
Gisely Naura Venâncio ◽  
Victor Hugo Marques Coelho ◽  
Thiago Fontanella Cestari ◽  
Maxine Ennata Alves de Almeida ◽  
Carolinie Batista Nobre da Cruz
Keyword(s):  
Culture Media ◽  
Bacterial Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Dental Clinics ◽  
Dental Office ◽  
Dental Surface ◽  
The University ◽  
The Chairs ◽  
And Staphylococcus Aureus

Pathogens of the oral cavity of a patient can be transferred to the dental office surfaces by direct contact, aerosol instruments and blood or saliva. The objective of this study was to investigate the microbiological contamination presents in the stands, chairs and spittoons in the University Nilton Lins dental clinics, in Manaus, Amazonas. Samples were collected with sterile swabs and seeded in different microbiological culture media for the isolation of microorganisms collected from each room. Then, assays were carried out for identification of strains isolated from each environment, such as: Gram stain, DNA purification, Amplification of 16s rRNA genes and sequencing. All these experiments were performed in the LBS / ILMD / FIOCRUZ. It was found 40 CFU / mL in the stands, 43 on the chairs and 47 in the spittoons and it was also possible to identify microorganisms like Klebsiella pneumoniae, Shigella sonnei and Staphylococcus aureus. The greatest number of CFUs was found in Clinic 3 and it was observed that the spittoon was the dental surface with the highest number of CFUs. Some of the bacterial species isolated are opportunists, suggesting that more severe biosecurity measures must be taken in order to prevent cross-infection.Pathogens of the oral cavity of a patient can be transferred to the dental office surfaces by direct contact, aerosol instruments and blood or saliva. The objective of this study was to investigate the microbiological contamination presents in the stands, chairs and spittoons in the University Nilton Lins dental clinics, in Manaus, Amazonas. Samples were collected with sterile swabs and seeded in different microbiological culture media for the isolation of microorganisms collected from each room. Then, assays were carried out for identification of strains isolated from each environment, such as: Gram stain, DNA purification, Amplification of 16s rRNA genes and sequencing. All these experiments were performed in the LBS / ILMD / FIOCRUZ. It was found 40 CFU / mL in the stands, 43 on the chairs and 47 in the spittoons and it was also possible to identify microorganisms like Klebsiella pneumoniae, Shigella sonnei and Staphylococcus aureus. The greatest number of CFUs was found in Clinic 3 and it was observed that the spittoon was the dental surface with the highest number of CFUs. Some of the bacterial species isolated are opportunists, suggesting that more severe biosecurity measures must be taken in order to prevent cross-infection.

scholarly journals In-depth analysis of Bacillus anthracis 16S rRNA genes and transcripts reveals intra- and intergenomic diversity and facilitates anthrax detection

2021 ◽  
Author(s):  
Peter Braun ◽  
Fee Zimmermann ◽  
Mathias C Walter ◽  
Sonja Mantel ◽  
Karin Aistleitner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Close Relative ◽  
Rrna Gene ◽  
Copy Numbers ◽  
Depth Analysis

Analysis of 16S ribosomal RNA (rRNA) genes provides a central means of taxonomic classification of bacterial species. Based on presumed sequence identity among species of the Bacillus cereus sensu lato group, the 16S rRNA genes of B. anthracis have been considered unsuitable for diagnosis of the anthrax pathogen. With the recent identification of a single nucleotide polymorphism in some 16S rRNA gene copies, specific identification of B. anthracis becomes feasible. Here, we designed and evaluated a set of in situ-, in vitro- and in silico-assays to assess the yet unknown 16S-state of B. anthracis from different perspectives. Using a combination of digital PCR, fluorescence in situ hybridization, long-read genome sequencing and bioinformatics we were able to detect and quantify a unique 16S rRNA gene allele of B. anthracis (16S-BA-allele). This allele was found in all available B. anthracis genomes and may facilitate differentiation of the pathogen from any close relative. Bioinformatics analysis of 959 B. anthracis genome data-sets inferred that abundances and genomic arrangements of the 16S-BA-allele and the entire rRNA operon copy-numbers differ considerably between strains. Expression ratios of 16S-BA-alleles were proportional to the respective genomic allele copy-numbers. The findings and experimental tools presented here provide detailed insights into the intra- and intergenomic diversity of 16S rRNA genes and may pave the way for improved identification of B. anthracis and other pathogens with diverse rRNA operons.

scholarly journals Disturbance During Biofilm Community Succession Promotes Cooperation and Diversity

2018 ◽  
Author(s):  
James P. Stratford ◽  
Douglas M. Hodgson ◽  
Nelli J. Beecroft ◽  
Ann Smith ◽  
Julian R. Marchesi ◽  
...  
Keyword(s):  
Time Course ◽  
Explanatory Power ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Widespread Application ◽  
Operational Taxonomic Units ◽  
Microbial Biofilms ◽  
Macro Scale ◽  
First Time ◽  
High Diversity

AbstractDiversity-disturbance relationships have found widespread application in ecology, conservation and biodiversity management. In spite of their explanatory power, these conceptual frameworks have yet to be systematically applied to understanding succession in diverse microbial biofilms. Here we investigate community assembly in biofilms formed in replicate microbial bioelectrochemical systems using time-course sequencing of community 16S rRNA genes, corresponding to hundreds of operational taxonomic units (OTUs). For the first time we present a statistical model showing that a simple diversity-disturbance relationship can be used to explain dynamic changes in high diversity biofilm communities. This simple model reveals that succession in these systems is guided towards either a low diversity, generalist-dominated biofilm or a high diversity, cooperative-specialist biofilm, depending on the level of endogenous disturbance measured within the community. The pattern observed shows remarkable symmetry with findings from macro-scale communities such as grasslands, forests and coral reefs.

Stool bacteriomic profiling in patients with metastatic renal cell carcinoma suggests an etiology of VEGF TKI-related diarrhea.

2015 ◽  
Vol 33 (7_suppl) ◽  
pp. 421-421
Author(s):  
Sumanta Kumar Pal ◽  
Sierra Mi Li ◽  
Xiwei Wu ◽  
Manasvi Pinnamaneni ◽  
JoAnn Hsu ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
16S Rrna ◽  
Cell Carcinoma ◽  
Metastatic Renal Cell Carcinoma ◽  
Renal Cell ◽  
Clustering Algorithm ◽  
Bacterial Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
P Value

421 Background: Vascular endothelial growth factor-tyrosine kinase inhibitors (VEGF TKIs) remain a mainstay of therapy for patients with metastatic renal cell carcinoma (mRCC). Diarrhea represents a pervasive toxicity, with all grade diarrhea affecting roughly 50% of patients receiving VEGF TKIs. The underlying cause of diarrhea in these patients is poorly understood. Methods: Patients with mRCC receiving an FDA-approved VEGF TKI therapy for mRCC were consented. Stool was collected in a standardized fashion and total genomic DNA was isolated using the PowerSoil DNA isolation kit (Mo Bio, USA). A standard PCR protocol was used to amplify bacterial 16S rRNA genes from all samples. PCR primers were used to amplify the V4 and V5 regions of the 16S rRNA. Paired-end of sequencing 2X100bp was performed by Illumina HiSeq 2000, and sequences were clustered using the CD-HIT clustering algorithm. Taxonomy was then assigned using the RDP-II classifier. Non-clustered analyses were also performed, stratifying patients by the presence or absence of diarrhea at the time of stool collection. Results: Of 26 patients consented, 23 patients submitted stool specimens and 20 had sufficient data for the current analysis. Amongst these 20 patients, the median age was 63 and the majority of patients (60%) were intermediate risk by Heng criteria. Eight patients (40%) received VEGF TKI therapy in the first-line setting. Across all lines of therapy, the most commonly used VEGF TKI was sunitinib (44%). A total of 141 bacterial species were identified. With respect to differences in patients who did and did not have diarrhea, the Mann-Whitney U-test identified 7 species with a p value of <0.1. The largest difference was seen in two Bifidobacterium species, B. animalis and B. bifidum, with both bacteria more abundant in patients with no diarrhea. Conclusions: This is the first effort to use stool bacteriomic profiling to ascertain the etiology of VEGF TKI related diarrhea in patients with mRCC. Two Bifidobacterium spp identified in this analysis are commonly found in probiotics. Studies to use probiotics enriched with Bifidobacterium spp to prevent or ameliorate VEGF TKI-related diarrhea are currently in development.

Sign in / Sign up

Export Citation Format

Share Document