NDLI: Comparative analyses identified species-specific functional roles in oral microbial genomes

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Volume 11, 2019

Volume 10, 2018

Volume: 9 Issue: 2

Oral Microbiology – progress, myths and evidence

Comparative analyses identified species-specific functional roles in oral microbial genomes

The bacteriome and mycobiome associated with oral squamous cell carcinoma: metagenomic analysis of samples from Yemeni and Sri Lankan cohorts

Parvimonas micra enhance gingpain activity in multi-species consortia

Biofilm behavior of Tannerella forsythia strains and S-layer glycosylation mutants

Investigation of fitness cost, copy number variation and excision rate of Tn916/Tn916-like elements in oral streptococci and enterococci

OMICs in Cariology and Endodontology – what have we learned so far?

Defining saliva and tooth biofilm microbiota in adolescents in a low caries community and characterization by caries status

Bacterial metatranscriptome of dentin caries

The metatranscriptomes of root caries and sound root surface biofilms

The root canal system: a separate ecological niche?

The Endodontic Microbial Biofilms as An Extension of Dental Plaque, a general hypothesis

Dysbiosis and inflammation in periodontitis: synergism and implications for treatment

The role of periodontal niches in influencing the tongue microbiota: relationship with periodontitis and oral malodour

The role of Aggregatibacter actinomycetemcomitans and its leukotoxin in periodontitis

Role of outer membrane proteins in serum resistance of A. actinomycetemcomitans and A. aphrophilus

Structural characteristics of potential novel virulence factors, the host cytokine binding proteins of Aggregatibacter actinomycetemcomitans

Outer membrane channel protein of an oral pathogen binds human cytokine IL-8

Periodontal pathogen CaZymes: host-pathogen biology, biochemistry and biotechnological exploitation

Structural and functional studies of Porphyromonas gingivalis fimbrial proteins

In-depth sequence analysis of highly-conserved pyrH gene to study distributions of oral treponemes in periodontal disease versus health

Probiotic intervention improves gingival status and influences the salivary levels of Matrix Metalloproteinase (MMP)-9 and Tissue Inhibitor of metalloproteinases (TIMP)-1 in healthy adults

The subgingival microbiomes in periodontitis and health of individuals with rheumatoid arthritis and at risk of developing rheumatoid arthritis

Bacterial Communities within Gingival Tissues from Periodontal Lesions Compared with Subgingival Plaque

Microbiome associated with peri-implantitis versus periodontal health in individuals with a history of periodontal disease

Clinical oral microbiology and antimicrobial susceptibility – does it matter?

Prescription of antibiotics in dentistry - a report from the Swedish STRAMA work

Bacteriophages targeting Enterococcus faecalis strains - a potential new root canal therapy

Functional isoeugenol-modified nanogel coatings for implants

Antibacterial effects of bio-inspired nanostructured materials

Interactions of periodontal pathogens with megakaryocytic cells and platelets

Role of Porphyromonas gingivalis’s peptidylarginine deiminase in multispecies biofilm formation and bacterial adherence to host cells

Effects of statins on multispecies oral biofilm

Determination of MIC of amoxicillin among clinical strains of Aggregatibacter actinomycetemcomitans from various geographic regions endorse the continuous use of this drug for treatment of periodontitis

Shotgun proteomic analysis of Anaeroglobus geminatus

The microbiome of oral leukoplakia shows enrichment in Fusobacteria and Rothia species

The oral mucosal microbiome in children with Crohn’s disease exhibits reduced biodiversity compared to healthy children, revealed by 16s profiling

Site-specific plaque pH before and after short-term use of 1.5% Arginine dentifrice in caries-free and caries-active individuals

Herpes simplex virus type 1 and 2 in mucocutaneous infections

The cagE gene sequence as a diagnostic marker to identify JP2 and non-JP2 highly leukotoxic Aggregatibacter actinomycetemcomitans serotype b strains

Generation and characterisation of Porphyromonas gingivalis mutant lacking peptidylarginine deiminase activity

Modulation of neutrophil chemotaxis by Aggregatibacter actinomycetemcomitans leukotoxin

Comparison of paperpoint and curette sampling of subgingival microbiome composition as analyzed by 16S rRNA gene amplicon sequencing

Multilocus sequence typing (MLST) of JP2 genotype isolates of Aggregatibacter actinomycetemcomitans collected from carriers of African and non-African origin

Communication at the host-pathogen interface

The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on a periodontal biofilm model. An in vitro study.

Age related variations observed in the oral microbiome of wild wood mice, Apodemus sylvaticus

Investigation of the prevalence of Tn916/Tn916-like elements in oral streptococci

Modeling the development of proteolytic phenotypes in multi-species oral biofilms

Volume: 9 Issue: 1

Comparative analyses identified species-specific functional roles in oral microbial genomes

Content Provider	Taylor & Francis Online
Author	Chen, Tsute Gajare, Prasad Dewhirst, Floyd E. Olsen, Ingar
Abstract	The advent of next generation sequencing is producing more genomic sequences for various strains of many human oral microbial species and allows for insightful functional comparisons at both intra- and inter-species levels. This study performed in-silico functional comparisons for currently available genomic sequences of major species associated with periodontitis including Aggregatibacter actinomycetemcomitans (AA), Porphyromonas gingivalis (PG), Treponema denticola (TD), and Tannerella forsythia (TF), as well as several cariogenic and commensal streptococcal species. Complete or draft sequences were annotated with the RAST to infer structured functional subsystems for each genome. The subsystems profiles were clustered to groups of functions with similar patterns. Functional enrichment and depletion were evaluated based on hypergeometric distribution to identify subsystems that are unique or missing between two groups of genomes. Unique or missing metabolic pathways and biological functions were identified in different species. For example, components involved in flagellar motility were found only in the motile species TD, as expected, with few exceptions scattered in several streptococcal species, likely associated with chemotaxis. Transposable elements were only found in the two Bacteroidales species PG and TF, and half of the AA genomes. Genes involved in CRISPR were prevalent in most oral species. Furthermore, prophage related subsystems were also commonly found in most species except for PG and Streptococcus mutans, in which very few genomes contain prophage components. Comparisons between pathogenic (P) and nonpathogenic (NP) genomes also identified genes potentially important for virulence. Two such comparisons were performed between AA (P) and several A. aphrophilus (NP) strains, and between S. mutans + S. sobrinus (P) and other oral streptococcal species (NP). This comparative genomics approach can be readily used to identify functions unique to or prevalent in a group of genomes. It can work with annotation systems using structured functional terms, such as RAST, KEGG and Gene Ontology, and obtain comprehensive functional insights into microbial genomics.
File Format	PDF HTM / HTML
ISSN	20002297
DOI	10.1080/20002297.2017.1325185
Journal	Journal of Oral Microbiology
Volume Number	9
Issue Number	sup1
Language	English
Publisher	Taylor & Francis
Publisher Date	2017-06-23
Access Restriction	Open
Content Type	Text
Subject	Microbiology (medical) Dentistry Infectious Diseases 3500/3501

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