scholarly journals Polymerase chain reaction in the identification of periodontopathogens: A reliable and satisfactory method?

2012 ◽  
Vol 64 (4) ◽  
pp. 1413-1423
Author(s):  
Natasa Nikolic-Jakoba ◽  
Sandra Vojnovic ◽  
A. Pavic ◽  
S. Jankovic ◽  
V. Lekovic ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
In Silico Analysis ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Conventional Pcr ◽  
Universal Primer ◽  
Health And Disease ◽  
Rrna Gene Sequencing ◽  
Species Specific

Aggregatibacter actinomycetemcomitans is considered one of the bacterial species of etiological importance in periodontitis. The aim of this study was to evaluate the serotype of A. actinomycetemcomitans in the subgingival biofilm in subjects with periodontal health and disease. Pooled samples of subgingival plaque were taken for culture-based identification of microorganisms. Colonies suspected to be A. actinomycetemcomitans were selected for molecular identification using either multiplex or conventional PCR in serotype-specific genotyping and 16S rRNA gene sequencing. In silico analysis showed that most selected colonies belong to the genus Campylobacter, although positive signals for serotypes of A. actinomycetemcomitans were obtained with these samples. Identification of A. actinomycetemcomitans by conventional PCR for 16S rRNA with one species-specific and one universal primer was inconclusive because an almost identical signal with Campylobacter gracilis was obtained. Although PCR-based methods for the identification of A. actinomycetemcomitans are more rapid, sequencing should not be omitted.

Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

2022 ◽  
Author(s):  
Chen Zheng-li ◽  
Peng Yu ◽  
Wu Guo-sheng ◽  
Hong Xu-Dong ◽  
Fan Hao ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sprague Dawley ◽  
Rrna Gene Sequencing

Abstract Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

scholarly journals Biotechnological Potential of Bacteria Isolated from the Sea Cucumber Holothuria leucospilota and Stichopus vastus from Lampung, Indonesia

Marine Drugs ◽  
2019 ◽  
Vol 17 (11) ◽  
pp. 635 ◽  
Author(s):  
Joko T. Wibowo ◽  
Matthias Y. Kellermann ◽  
Dennis Versluis ◽  
Masteria Y. Putra ◽  
Tutik Murniasih ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Cucumber ◽  
Bacterial Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sea Cucumbers ◽  
Biotechnological Potential ◽  
Rrna Gene Sequencing

In order to minimize re-discovery of already known anti-infective compounds, we focused our screening approach on understudied, almost untapped marine environments including marine invertebrates and their associated bacteria. Therefore, two sea cucumber species, Holothuria leucospilota and Stichopus vastus, were collected from Lampung (Indonesia), and 127 bacterial strains were identified by partial 16S rRNA-gene sequencing analysis and compared with the NCBI database. In addition, the overall bacterial diversity from tissue samples of the sea cucumbers H. leucospilota and S. vastus was analyzed using the cultivation-independent Illumina MiSEQ analysis. Selected bacterial isolates were grown to high densities and the extracted biomass was tested against a selection of bacteria and fungi as well as the hepatitis C virus (HCV). Identification of putative bioactive bacterial-derived compounds were performed by analyzing the accurate mass of the precursor/parent ions (MS1) as well as product/daughter ions (MS2) using high resolution mass spectrometry (HRMS) analysis of all active fractions. With this attempt we were able to identify 23 putatively known and two previously unidentified precursor ions. Moreover, through 16S rRNA-gene sequencing we were able to identify putatively novel bacterial species from the phyla Actinobacteria, Proteobacteria and also Firmicutes. Our findings suggest that sea cucumbers like H. leucospilota and S. vastus are promising sources for the isolation of novel bacterial species that produce compounds with potentially high biotechnological potential.

scholarly journals Long-Term Recovery of the Fecal Microbiome and Metabolome of Dogs with Steroid-Responsive Enteropathy

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2498
Author(s):  
Rachel Pilla ◽  
Blake C Guard ◽  
Amanda B Blake ◽  
Mark Ackermann ◽  
Craig Webb ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Elimination Diet ◽  
Rrna Gene ◽  
Fecal Microbiome ◽  
Rrna Gene Sequencing ◽  
One Year ◽  
Long Term Impact

The long-term impact of treatment of dogs with steroid-responsive enteropathy (SRE) on the fecal microbiome and metabolome has not been investigated. Therefore, this study aimed to evaluate the fecal microbiome and metabolome of dogs with SRE before, during, and following treatment with standard immunosuppressive therapy and an elimination diet. We retrospectively selected samples from 9 dogs with SRE enrolled in a previous clinical trial, which received treatment for 8 weeks, and had achieved remission as indicated by the post-treatment clinical scores. Long-term (1 year) samples were obtained from a subset (5/9) of dogs. Samples from 13 healthy dogs were included as controls (HC). We evaluated the microbiome using 16S rRNA sequencing and qPCR. To evaluate the recovery of gut function, we measured fecal metabolites using an untargeted approach. While improvement was observed for some bacterial taxa after 8 weeks of treatment, several bacterial taxa remained significantly different from HC. Seventy-five metabolites were altered in dogs with SRE, including increased fecal amino acids and vitamins, suggesting malabsorption as a component of SRE. One year after treatment, however, all bacterial species were evaluated by qPCR and 16S rRNA gene sequencing, and all but thirteen metabolites were no longer different from healthy controls.

scholarly journals Long-term recovery of the fecal microbiome and metabolome of dogs with steroid-responsive enteropathy

2021 ◽  
Author(s):  
Rachel Pilla ◽  
Blake Guard ◽  
Amanda B Blake ◽  
Mark Ackermann ◽  
Craig Webb ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Elimination Diet ◽  
Rrna Gene ◽  
Fecal Microbiome ◽  
Rrna Gene Sequencing ◽  
One Year ◽  
Long Term Impact

The long-term impact of treatment of dogs with steroid-responsive enteropathy (SRE) on the fe-cal microbiome and metabolome has not been investigated. Therefore, this study aimed to evaluate the fecal microbiome and metabolome of dogs with SRE before, during, and following treatment with standard immunosuppressive therapy and an elimination diet. We retrospec-tively selected samples from 9 dogs with SRE enrolled in a previous clinical trial, which received treatment for 8 weeks, and had achieved remission as indicated by the post-treatment clinical scores. Long-term (1 year) samples were obtained from a subset (5/9) of dogs. Samples from 13 healthy dogs were included as controls (HC). We evaluated the microbiome using 16S rRNA sequencing and qPCR. To evaluate the recovery of gut function, we measured fecal metabolites using an untargeted approach. While improvement was observed for some bacterial taxa after 8 weeks of treatment, several bacterial taxa remained significantly different from HC. Seven-ty-five metabolites were altered in dogs with SRE, including increased fecal amino acids and vitamins, suggesting malabsorption as a component of SRE. One year after treatment, however, all bacterial species evaluated by qPCR and 16S rRNA gene sequencing, and all but thirteen me-tabolites were no longer different from healthy controls.

scholarly journals Species-Specific Identification of Campylobacters by Partial 16S rRNA Gene Sequencing

2003 ◽  
Vol 41 (6) ◽  
pp. 2537-2546 ◽  
Author(s):  
G. Gorkiewicz ◽  
G. Feierl ◽  
C. Schober ◽  
F. Dieber ◽  
J. Kofer ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Specific Identification ◽  
Rrna Gene Sequencing ◽  
Species Specific

scholarly journals Novel high-resolution targeted sequencing of the cervicovaginal microbiome

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Karolina M. Andralojc ◽  
Mariano A. Molina ◽  
Mengjie Qiu ◽  
Bram Spruijtenburg ◽  
Menno Rasing ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Species Level ◽  
Rrna Gene ◽  
High Grade ◽  
Cervical Lesions ◽  
Health And Disease ◽  
Rrna Gene Sequencing

Abstract Background The cervicovaginal microbiome (CVM) plays a significant role in women’s cervical health and disease. Microbial alterations at the species level and characteristic community state types (CST) have been associated with acquisition and persistence of high-risk human papillomavirus (hrHPV) infections that may result in progression of cervical lesions to malignancy. Current sequencing methods, especially most commonly used multiplex 16S rRNA gene sequencing, struggle to fully clarify these changes because they generally fail to provide sufficient taxonomic resolution to adequately perform species-level associative studies. To improve CVM species designation, we designed a novel sequencing tool targeting microbes at the species taxonomic rank and examined its potential for profiling the CVM. Results We introduce an accessible and practical circular probe-based RNA sequencing (CiRNAseq) technology with the potential to profile and quantify the CVM. In vitro and in silico validations demonstrate that CiRNAseq can distinctively detect species in a mock mixed microbial environment, with the output data reflecting its ability to estimate microbes’ abundance. Moreover, compared to 16S rRNA gene sequencing, CiRNAseq provides equivalent results but with improved sequencing sensitivity. Analyses of a cohort of cervical smears from hrHPV-negative women versus hrHPV-positive women with high-grade cervical intraepithelial neoplasia confirmed known differences in CST occurring in the CVM of women with hrHPV-induced lesions. The technique also revealed variations in microbial diversity and abundance in the CVM of hrHPV-positive women when compared to hrHPV-negative women. Conclusions CiRNAseq is a promising tool for studying the interplay between the CVM and hrHPV in cervical carcinogenesis. This technology could provide a better understanding of cervicovaginal CST and microbial species during health and disease, prompting the discovery of biomarkers, additional to hrHPV, that can help detect high-grade cervical lesions.

scholarly journals Species-Specific Identification of Leptospiraceae by 16S rRNA Gene Sequencing

2006 ◽  
Vol 44 (10) ◽  
pp. 3510-3516 ◽  
Author(s):  
R. E. Morey ◽  
R. L. Galloway ◽  
S. L. Bragg ◽  
A. G. Steigerwalt ◽  
L. W. Mayer ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Specific Identification ◽  
Rrna Gene Sequencing ◽  
Species Specific

scholarly journals In silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria

2011 ◽  
Vol 60 (9) ◽  
pp. 1281-1286 ◽  
Author(s):  
Jade L. L. Teng ◽  
Ming-Yiu Yeung ◽  
Geoffrey Yue ◽  
Rex K. H. Au-Yeung ◽  
Eugene Y. H. Yeung ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
In Silico Analysis ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Rrna Gene Sequencing ◽  
Silico Analysis

scholarly journals Female lower urinary tract microbiota do not correspond to IC/PBS symptoms: a case-controlled study

2019 ◽  
Author(s):  
L. Bresler ◽  
T.K. Price ◽  
M. Tulke ◽  
E.E. Hilt ◽  
C. Joyce ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Species ◽  
Gene Sequencing ◽  
Preliminary Finding ◽  
16S Rrna Gene Sequencing ◽  
Controlled Study ◽  
Rrna Gene ◽  
Bladder Pain ◽  
Rrna Gene Sequencing

ABSTRACTOBJECTIVECurrent etiology of interstitial cystitis/painful bladder syndrome (IC/PBS) is poorly understood and multifactorial. Recent studies suggest the female urinary microbiota (FUM) contribute to IC/PBS symptoms. This study was designed to determine if the FUM, analyzed using mid-stream voided urine samples, differs between IC/PBS patients and controls.MATERIALS AND METHODSThis prospective case-controlled study compared the voided FUM of women with symptoms of urinary frequency, urgency, and bladder pain for greater than 6 months to the voided FUM of healthy female controls without pain. Bacterial identification was performed using 16S rRNA gene sequencing and EQUC, a validated enhanced urine culture approach. Urotype was defined by a genus present at >50% relative abundance. If no genus was present above this threshold, the urotype was classified as ‘mixe’. Chi-square and Fisher’s exact tests were performed. P-values <0.05 were considered significant.RESULTSA mid-stream voided specimen was collected from 21 IC/PBS patients and 20 asymptomatic controls. Both groups had similar demographics. Urotypes did not differ between cohorts as assessed by either EQUC or 16S rRNA gene sequencing. We detected no significant differences between cohorts in terms of alpha-diversity. Cohorts also were not distinct using Principle Component Analysis or hierarchical clustering. Detection by EQUC of bacterial species considered uropathogenic was high in both cohorts, but detection of these uropathogenic species did not differ between groups (p=0.10).CONCLUSIONSEnhanced culture and modern DNA sequencing methods provide evidence that IC/PBS symptoms may not be related to differences in the FUM, at least not its bacterial components. Future larger studies are needed to confirm this preliminary finding.

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