scholarly journals Historical and Contemporary Perspectives on the Microbiological Aspects of Endodontics

2018 ◽  
Vol 6 (4) ◽  
pp. 49 ◽  
Author(s):  
James Gutmann ◽  
Vivian Manjarrés
Keyword(s):  
Quorum Sensing ◽  
Oral Cavity ◽  
Microbial Growth ◽  
Bacterial Species ◽  
Vast Array ◽  
Wide Range ◽  
Oral Microbiology ◽  
Periapical Diseases ◽  
Investigative Techniques ◽  
Microbiological Aspects

The microbiota of the oral cavity plays a significant role in pulpal and periapical diseases. Historically, 100 years ago little was known on microbiota, but after a century of investigations, only now can many of the intimate secrets of microbial growth, expansion, persistence, communal activities, and virulence be revealed. However, with the capabilities of the microbiota for mutation, quorum sensing, and information transference, researchers are hard-pressed to keep up with both the changes and challenges that an amazingly wide range of bacterial species pose for both the scientist and clinician. Fortunately, the development and expansion of a vast array of molecular biological investigative techniques have enabled dentistry and its associated medical fields to attempt to keep pace with the wide and fascinating world of oral microbiology.

scholarly journals LuxS quorum sensing system, its protein modeling and active-binding sites and phylogenetic analysis from Aeromonas hydrophila

2017 ◽  
Author(s):  
Farman Ali ◽  
Zujie Yao ◽  
Wanxin Li ◽  
Sun Lina ◽  
Wenxiong Lin ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Binding Sites ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Three Dimensional ◽  
Alpha Helix ◽  
Zinc Ion ◽  
Dimensional Structure ◽  
Wide Range ◽  
Range Of Functions

LuxS is commonly found in various bacterial species, like A. hydrophila which causes infection in fish, shrimps, and prawns and is a great threat to aquaculture industry as well as public health. It is an essential enzyme and highly conserved in various bacterial species, and has a wide range of functions such as involved in quorum sensing (QS), sporulation, virulence and synthesis of biofilm. This study focused on the prediction of 3D-sturcture of LuxS by template similarity and its ligand binding sites analysis to define its structure-function relationship. Primary structure analysis of LuxS examined that about 42% of residues content are alpha-helix, which makes it stable for three-dimensional structure homology. For the con struction of homology modeling of LuxS, crystal structure (5e68.1.A) has been used as a template and Swiss model as a work space. The validation of model by ProSA, SAVES, PROCHECK, PROSAII and RMSD. All results analysis shows that refined model is reliable and it has78.11% amino acids sequence similarity with the template,0.4Åas RMSD, and Z-score is -6.21 and Ramachandran plot analysis shows that 83.4% of residues found in the most favored regions where only 0.4% falls into the disallowed regions. Zinc ion ligand was predicted with highest MAMMOTH score and its binding residues His-54, His-58 and Cys-128 were analyzed by COACH-Meta server. LuxS phylogeny was constructed by sequences and structures of the most similar sequences were analyzed. In silico, the information has been generated in this work expects to be the first step towards the structure determination of LuxS in A. hydrophila.

scholarly journals LuxS quorum sensing system, its protein modeling and active-binding sites and phylogenetic analysis from Aeromonas hydrophila

2017 ◽  
Author(s):  
Farman Ali ◽  
Zujie Yao ◽  
Wanxin Li ◽  
Sun Lina ◽  
Wenxiong Lin ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Binding Sites ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Three Dimensional ◽  
Alpha Helix ◽  
Zinc Ion ◽  
Dimensional Structure ◽  
Wide Range ◽  
Range Of Functions

LuxS is commonly found in various bacterial species, like A. hydrophila which causes infection in fish, shrimps, and prawns and is a great threat to aquaculture industry as well as public health. It is an essential enzyme and highly conserved in various bacterial species, and has a wide range of functions such as involved in quorum sensing (QS), sporulation, virulence and synthesis of biofilm. This study focused on the prediction of 3D-sturcture of LuxS by template similarity and its ligand binding sites analysis to define its structure-function relationship. Primary structure analysis of LuxS examined that about 42% of residues content are alpha-helix, which makes it stable for three-dimensional structure homology. For the con struction of homology modeling of LuxS, crystal structure (5e68.1.A) has been used as a template and Swiss model as a work space. The validation of model by ProSA, SAVES, PROCHECK, PROSAII and RMSD. All results analysis shows that refined model is reliable and it has78.11% amino acids sequence similarity with the template,0.4Åas RMSD, and Z-score is -6.21 and Ramachandran plot analysis shows that 83.4% of residues found in the most favored regions where only 0.4% falls into the disallowed regions. Zinc ion ligand was predicted with highest MAMMOTH score and its binding residues His-54, His-58 and Cys-128 were analyzed by COACH-Meta server. LuxS phylogeny was constructed by sequences and structures of the most similar sequences were analyzed. In silico, the information has been generated in this work expects to be the first step towards the structure determination of LuxS in A. hydrophila.

scholarly journals Quorum Sensing in Plaque Biofilms: Challenges and Future Prospects

2011 ◽  
Vol 12 (6) ◽  
pp. 479-485 ◽  
Author(s):  
Baswaraj Biradar ◽  
Prapulla Devi
Keyword(s):  
Dental Caries ◽  
Quorum Sensing ◽  
Periodontal Disease ◽  
Periodontal Diseases ◽  
Bacterial Species ◽  
Synthetic Methods ◽  
Future Prospects ◽  
Wide Range ◽  
Bacterial Quorum Sensing ◽  
Bacterial Quorum

ABSTRACT Aim This review intends to provide a brief overview regarding quorum sensing among bacteria in biofilms and also attempts to throw light on the new research focusing on interference with the quorum sensing. Background Dental plaque is an example of microbial biofilm leading to periodontal disease and dental caries. Quorum sensing is widely employed by a variety of gram-positive and gram-negative bacterial species to coordinate various activities in biofilms. Quorum-sensing-interfering compounds have either a positive or a negative effect on the expression of bacterial phenotypes regulated by quorum sensing. These studies of bacterial quorum sensing have also suggested several ideal targets for drug design which can be promising in preventive and therapeutic aspects of periodontal diseases and dental caries. Results Studies have shown that periodontal disease and dental caries is caused by plaque biofilm bacteria. Quorum sensing is the means of communication between these bacteria to regulate a wide range of behavior patterns among them. The in vitro studies reviewed here have a vital role in opening up this field, because they reveal the basic machinery of cell—cell signaling in microbial communities. The signal machinery bacteria use to coordinate a variety of their activities is identified by these studies. Further, this review aims to discuss several natural and synthetic methods which were used for manipulating bacterial quorum sensing. Conclusion The future challenge lies in the ability of the dental research to develop additional mechanisms for interfering with bacterial quorum sensing which can be used as preventive and therapeutic tools for combating oral polymicrobial diseases. Clinical significance This article aims at reviewing the literature and helping us to understand the ways of communication among bacteria in biofilms, which further open up the prospects in the treatment of diseases caused by biofilms. How to cite this article Biradar B, Devi P. Quorum Sensing in Plaque Biofilms: Challenges and Future Prospects. J Contemp Dent Pract 2011;12(6):479-485.

scholarly journals Chemical Inhibitors of DksA1, a Conserved Bacterial Transcriptional Regulator, Suppressed Quorum Sensing-Mediated Virulence in Pseudomonas aeruginosa

2020 ◽  
Author(s):  
Kyung Bae Min ◽  
Wontae Hwang ◽  
Kang-Mu Lee ◽  
Sang Sun Yoon
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Rna Polymerase ◽  
Bacterial Species ◽  
Stringent Response ◽  
Transcriptional Regulator ◽  
Nutrient Starvation ◽  
Transcriptional Level ◽  
Virulence Attenuation ◽  
Wide Range

AbstractPseudomonas aeruginosa is a Gram-negative bacterium of clinical importance. As an opportunistic pathogen, its virulence is dependent on quorum sensing (QS). Stringent response (SR), a conserved mechanism in the bacterial kingdom, is activated under diverse stress conditions including nutrient starvation. DksA1, an RNA polymerase-binding transcriptional regulator, plays a role in P. aeruginosa SR. Our recent study clearly demonstrated that, apart from SR, DksA1 regulates a wide range of phenotypes including QS-mediated virulence. This suggests that DksA1 is a potential target to be inhibited to control P. aeruginosa infections. Here, we screened a library of 6,970 chemical compounds and identified two compounds (termed Dkstatin-1 and Dkstatin-2) that specifically suppress DksA1 activity. Two Dkstatins substantially suppressed production of elastase and pyocyanin and protected a murine host against lethal infection with PAO1, a prototype strain of P. aeruginosa. Dkstatins also suppressed the production of homoserine lactone (HSL)-based autoinducers that activate P. aeruginosa QS. The level of 3-oxo-C12-HSL produced in Dkstatin-treated cells was almost identical to that in the ΔdksAI mutant of PAO1. Our RNASeq analysis showed that transcript levels of genes involved in QS and virulence were markedly reduced in Dkstatin-treated PAO1 cells, further demonstrating that Dkstatin-mediated suppression occurs at the transcriptional level. Importantly, Dkstatins increased antibiotic susceptibilities of PAO1, particularly to the antibiotics that inhibit protein synthesis. Our co-immunoprecipitation assay demonstrated that Dkstatins interfere with the binding of DksA1 to the β subunit of RNA polymerase, which potentially explains the mode of Dkstatin action. Collectively, our results suggest that the inhibition of P. aeruginosa QS, which has often been attempted, can be achieved by DksA1 inhibitors. Dkstatins will prove to be useful when establishing infection control strategies.Author summaryBacterial cells developed numerous systems to handle environmental stresses. Stringent response (SR) is one of those systems, and it is activated under the stress of nutrient starvation. Active SR requires DksA1, a protein conserved across bacterial species. Besides this well-recognized function, DksA1 in P. aeruginosa positively regulates its virulence by activating quorum sensing (QS). This finding led us to hypothesize that inhibiting DksA1 would result in virulence attenuation of the pathogenic P. aeruginosa. Herein, we identified two molecules that effectively suppressed DksA1 function through a large-scale compound library screen. These two compounds suppressed P. aeruginosa virulence and therefore protected a murine host from a deadly infection of P. aeruginosa. Moreover, the compounds also rendered P. aeruginosa more susceptible to antibiotics. Our results demonstrate that dangerous P. aeruginosa infections can be controlled by inhibiting DksA1.

Modulation of Gut Microbiota through Dietary Phytochemicals as a Novel Anti-infective Strategy

2020 ◽  
Vol 17 (4) ◽  
pp. 498-506 ◽  
Author(s):  
Pavan K. Mujawdiya ◽  
Suman Kapur
Keyword(s):  
Microbial Community ◽  
Quorum Sensing ◽  
Population Density ◽  
Gut Microbiota ◽  
Biofilm Formation ◽  
Chemical Interaction ◽  
Bacterial Species ◽  
Critical Role ◽  
Bacterial Cells ◽  
Gut Microbes

: Quorum Sensing (QS) is a phenomenon in which bacterial cells communicate with each other with the help of several low molecular weight compounds. QS is largely dependent on population density, and it triggers when the concentration of quorum sensing molecules accumulate in the environment and crosses a particular threshold. Once a certain population density is achieved and the concentration of molecules crosses a threshold, the bacterial cells show a collective behavior in response to various chemical stimuli referred to as “auto-inducers”. The QS signaling is crucial for several phenotypic characteristics responsible for bacterial survival such as motility, virulence, and biofilm formation. Biofilm formation is also responsible for making bacterial cells resistant to antibiotics. : The human gut is home to trillions of bacterial cells collectively called “gut microbiota” or “gut microbes”. Gut microbes are a consortium of more than 15,000 bacterial species and play a very crucial role in several body functions such as metabolism, development and maturation of the immune system, and the synthesis of several essential vitamins. Due to its critical role in shaping human survival and its modulating impact on body metabolisms, the gut microbial community has been referred to as “the forgotten organ” by O`Hara et al. (2006) [1]. Several studies have demonstrated that chemical interaction between the members of bacterial cells in the gut is responsible for shaping the overall microbial community. : Recent advances in phytochemical research have generated a lot of interest in finding new, effective, and safer alternatives to modern chemical-based medicines. In the context of antimicrobial research various plant extracts have been identified with Quorum Sensing Inhibitory (QSI) activities among bacterial cells. This review focuses on the mechanism of quorum sensing and quorum sensing inhibitors isolated from natural sources.

scholarly journals A Bacterial Tower of Babel: Quorum-Sensing Signaling Diversity and Its Evolution

2020 ◽  
Vol 74 (1) ◽  
pp. 587-606 ◽  
Author(s):  
Nitzan Aframian ◽  
Avigdor Eldar
Keyword(s):  
Quorum Sensing ◽  
Social Interactions ◽  
Signal Molecules ◽  
Allelic Polymorphism ◽  
Dependent Manner ◽  
Tower Of Babel ◽  
Cognate Receptor ◽  
Wide Range ◽  
Family Code ◽  
Bacterial Groups

Quorum sensing is a process in which bacteria secrete and sense a diffusible molecule, thereby enabling bacterial groups to coordinate their behavior in a density-dependent manner. Quorum sensing has evolved multiple times independently, utilizing different molecular pathways and signaling molecules. A common theme among many quorum-sensing families is their wide range of signaling diversity—different variants within a family code for different signal molecules with a cognate receptor specific to each variant. This pattern of vast allelic polymorphism raises several questions—How do different signaling variants interact with one another? How is this diversity maintained? And how did it come to exist in the first place? Here we argue that social interactions between signaling variants can explain the emergence and persistence of signaling diversity throughout evolution. Finally, we extend the discussion to include cases where multiple diverse systems work in concert in a single bacterium.

scholarly journals Pseudomonas aeruginosa PA80 is a cystic fibrosis isolate deficient in RhlRI quorum sensing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Syed A. K. Shifat Ahmed ◽  
Michelle Rudden ◽  
Sabrina M. Elias ◽  
Thomas J. Smyth ◽  
Roger Marchant ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Virulence Factors ◽  
Genomic Islands ◽  
Clinical Strain ◽  
Whole Genome ◽  
Synonymous Mutations ◽  
Wide Range

AbstractPseudomonas aeruginosa uses quorum sensing (QS) to modulate the expression of several virulence factors that enable it to establish severe infections. The QS system in P. aeruginosa is complex, intricate and is dominated by two main N-acyl-homoserine lactone circuits, LasRI and RhlRI. These two QS systems work in a hierarchical fashion with LasRI at the top, directly regulating RhlRI. Together these QS circuits regulate several virulence associated genes, metabolites, and enzymes in P. aeruginosa. Paradoxically, LasR mutants are frequently isolated from chronic P. aeruginosa infections, typically among cystic fibrosis (CF) patients. This suggests P. aeruginosa can undergo significant evolutionary pathoadaptation to persist in long term chronic infections. In contrast, mutations in the RhlRI system are less common. Here, we have isolated a clinical strain of P. aeruginosa from a CF patient that has deleted the transcriptional regulator RhlR entirely. Whole genome sequencing shows the rhlR locus is deleted in PA80 alongside a few non-synonymous mutations in virulence factors including protease lasA and rhamnolipid rhlA, rhlB, rhlC. Importantly we did not observe any mutations in the LasRI QS system. PA80 does not appear to have an accumulation of mutations typically associated with several hallmark pathoadaptive genes (i.e., mexT, mucA, algR, rpoN, exsS, ampR). Whole genome comparisons show that P. aeruginosa strain PA80 is closely related to the hypervirulent Liverpool epidemic strain (LES) LESB58. PA80 also contains several genomic islands (GI’s) encoding virulence and/or resistance determinants homologous to LESB58. To further understand the effect of these mutations in PA80 QS regulatory and virulence associated genes, we compared transcriptional expression of genes and phenotypic effects with isogenic mutants in the genetic reference strain PAO1. In PAO1, we show that deletion of rhlR has a much more significant impact on the expression of a wide range of virulence associated factors rather than deletion of lasR. In PA80, no QS regulatory genes were expressed, which we attribute to the inactivation of the RhlRI QS system by deletion of rhlR and mutation of rhlI. This study demonstrates that inactivation of the LasRI system does not impact RhlRI regulated virulence factors. PA80 has bypassed the common pathoadaptive mutations observed in LasR by targeting the RhlRI system. This suggests that RhlRI is a significant target for the long-term persistence of P. aeruginosa in chronic CF patients. This raises important questions in targeting QS systems for therapeutic interventions.

scholarly journals Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas

2021 ◽  
Vol 9 (4) ◽  
pp. 862
Author(s):  
Vittoria Catara ◽  
Jaime Cubero ◽  
Joël F. Pothier ◽  
Eran Bosis ◽  
Claude Bragard ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Bacterial Species ◽  
Management Strategies ◽  
Diagnostic Methods ◽  
Plant Diseases ◽  
Wild Plants ◽  
Future Climate Change ◽  
Climate Change Scenarios ◽  
Wide Range ◽  
Diversity Studies

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.

scholarly journals Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Hannes Petruschke ◽  
Christian Schori ◽  
Sebastian Canzler ◽  
Sarah Riesbeck ◽  
Anja Poehlein ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Intestinal Microbiota ◽  
De Novo ◽  
Bacterial Species ◽  
Intestinal Microbiome ◽  
Single Strain ◽  
Small Proteins ◽  
Human Intestinal Microbiota ◽  
Wide Range

Abstract Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. Results We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. Conclusions We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract.

scholarly journals SCAPP: an algorithm for improved plasmid assembly in metagenomes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

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