scholarly journals High-Resolution Taxonomic Profiling of the Subgingival Microbiome for Biomarker Discovery and Periodontitis Diagnosis

2014 ◽  
Vol 81 (3) ◽  
pp. 1047-1058 ◽  
Author(s):  
Szymon P. Szafranski ◽  
Melissa L. Wos-Oxley ◽  
Ramiro Vilchez-Vargas ◽  
Ruy Jáuregui ◽  
Iris Plumeier ◽  
...  
Keyword(s):  
High Resolution ◽  
Biomarker Discovery ◽  
Learning Algorithm ◽  
Individualized Medicine ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Periodontal Pathogens ◽  
Content Type ◽  
Linear Discriminant ◽  
Taxonomic Profiling

ABSTRACTThe oral microbiome plays a key role for caries, periodontitis, and systemic diseases. A method for rapid, high-resolution, robust taxonomic profiling of subgingival bacterial communities for early detection of periodontitis biomarkers would therefore be a useful tool for individualized medicine. Here, we used Illumina sequencing of the V1-V2 and V5-V6 hypervariable regions of the 16S rRNA gene. A sample stratification pipeline was developed in a pilot study of 19 individuals, 9 of whom had been diagnosed with chronic periodontitis. Five hundred twenty-three operational taxonomic units (OTUs) were obtained from the V1-V2 region and 432 from the V5-V6 region. Key periodontal pathogens likePorphyromonas gingivalis,Treponema denticola, andTannerella forsythiacould be identified at the species level with both primer sets. Principal coordinate analysis identified two outliers that were consistently independent of the hypervariable region and method of DNA extraction used. The linear discriminant analysis (LDA) effect size algorithm (LEfSe) identified 80 OTU-level biomarkers of periodontitis and 17 of health. Health- and periodontitis-related clusters of OTUs were identified using a connectivity analysis, and the results confirmed previous studies with several thousands of samples. A machine learning algorithm was developed which was trained on all but one sample and then predicted the diagnosis of the left-out sample (jackknife method). Using a combination of the 10 best biomarkers, 15 of 17 samples were correctly diagnosed. Training the algorithm on time-resolved community profiles might provide a highly sensitive tool to detect the onset of periodontitis.

scholarly journals Analysis of the Effects of Dietary Pattern on the Oral Microbiome of Elite Endurance Athletes

Nutrients ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 614 ◽  
Author(s):  
Nida Murtaza ◽  
Louise Burke ◽  
Nicole Vlahovich ◽  
Bronwen Charlesson ◽  
Hayley O’Neill ◽  
...  
Keyword(s):  
Discriminant Analysis ◽  
Relative Abundance ◽  
Distance Measure ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Unifrac Distance ◽  
Linear Discriminant ◽  
Principal Coordinates ◽  
Low Carbohydrate

Although the oral microbiota is known to play a crucial role in human health, there are few studies of diet x oral microbiota interactions, and none in elite athletes who may manipulate their intakes of macronutrients to achieve different metabolic adaptations in pursuit of optimal endurance performance. The aim of this study was to investigate the shifts in the oral microbiome of elite male endurance race walkers from Europe, Asia, the Americas and Australia, in response to one of three dietary patterns often used by athletes during a period of intensified training: a High Carbohydrate (HCHO; n = 9; with 60% energy intake from carbohydrates; ~8.5 g kg−1 day−1 carbohydrate, ~2.1 g kg−1 day−1 protein, 1.2 g kg−1 day−1 fat) diet, a Periodised Carbohydrate (PCHO; n = 10; same macronutrient composition as HCHO, but the intake of carbohydrates is different across the day and throughout the week to support training sessions with high or low carbohydrate availability) diet or a ketogenic Low Carbohydrate High Fat (LCHF; n = 10; 0.5 g kg−1 day−1 carbohydrate; 78% energy as fat; 2.1 g kg−1 day−1 protein) diet. Saliva samples were collected both before (Baseline; BL) and after the three-week period (Post treatment; PT) and the oral microbiota profiles for each athlete were produced by 16S rRNA gene amplicon sequencing. Principal coordinates analysis of the oral microbiota profiles based on the weighted UniFrac distance measure did not reveal any specific clustering with respect to diet or athlete ethnic origin, either at baseline (BL) or following the diet-training period. However, discriminant analyses of the oral microbiota profiles by Linear Discriminant Analysis (LDA) Effect Size (LEfSe) and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) did reveal changes in the relative abundance of specific bacterial taxa, and, particularly, when comparing the microbiota profiles following consumption of the carbohydrate-based diets with the LCHF diet. These analyses showed that following consumption of the LCHF diet the relative abundances of Haemophilus, Neisseria and Prevotella spp. were decreased, and the relative abundance of Streptococcus spp. was increased. Such findings suggest that diet, and, in particular, the LCHF diet can induce changes in the oral microbiota of elite endurance walkers.

scholarly journals Virulence of the Pathogen Porphyromonas gingivalis Is Controlled by the CRISPR-Cas Protein Cas3

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Jose Solbiati ◽  
Ana Duran-Pinedo ◽  
Fernanda Godoy Rocha ◽  
Frank C. Gibson ◽  
Jorge Frias-Lopez
Keyword(s):  
Chronic Inflammation ◽  
Porphyromonas Gingivalis ◽  
Clinical Findings ◽  
Bacterial Virulence ◽  
Oral Microbiome ◽  
Periodontal Pathogens ◽  
Content Type ◽  
Virulence Potential ◽  
Associated Proteins ◽  
Polymicrobial Disease

Porphyromonas gingivalis is a key pathogen of periodontitis, a polymicrobial disease characterized by a chronic inflammation that destroys the tissues supporting the teeth. Thus, understanding the virulence potential of P. gingivalis is essential to maintaining a healthy oral microbiome. In nonoral organisms, CRISPR-Cas systems have been shown to modulate a variety of microbial processes, including protection from exogenous nucleic acids, and, more recently, have been implicated in bacterial virulence. Previously, our clinical findings identified activation of the CRISPR-Cas system in patient samples at the transition to disease; however, the mechanism of contribution to disease remained unknown. The importance of the present study resides in that it is becoming increasingly clear that CRISPR-associated proteins have broader functions than initially thought and that those functions now include their role in the virulence of periodontal pathogens. Studying a P. gingivalis cas3 mutant, we demonstrate that at least one of the CRISPR-Cas systems is involved in the regulation of virulence during infection.

scholarly journals Adaptation of the Cecal Bacterial Microbiome of Growing Pigs in Response to Resistant Starch Type 4

2015 ◽  
Vol 81 (24) ◽  
pp. 8489-8499 ◽  
Author(s):  
Barbara U. Metzler-Zebeli ◽  
Stephan Schmitz-Esser ◽  
Evelyne Mann ◽  
Dietmar Grüll ◽  
Timea Molnar ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Resistant Starch ◽  
Control Diet ◽  
Short Chain Fatty Acids ◽  
Growing Pigs ◽  
Short Chain ◽  
Rrna Gene ◽  
Content Type ◽  
Linear Discriminant ◽  
The Impact

ABSTRACTResistant starch (RS) exacerbates health benefits on the host via modulation of the gut bacterial community. By far, these effects have been less well explored for RS of type 4. This study aimed at gaining a community-wide insight into the impact of enzymatically modified starch (EMS) on the cecal microbiota and hindgut fermentation in growing pigs. Castrated male pigs (n= 12/diet; 29-kg body weight) were fed diets with either 70% EMS or control starch for 10 days. The bacterial profile of each cecal sample was determined by sequencing of the V345 region of the 16S rRNA gene using the Illumina MiSeq platform. EMS diet reduced short-chain fatty acid concentrations in cecum and proximal colon compared to the control diet. Linear discriminant analyses andKmeans clustering indicated diet-specific cecal community profiles, whereby diversity and species richness were not different among diets. Pigs showed host-specific variation in their most abundant phyla,Firmicutes(55%),Proteobacteria(35%), andBacteroidetes(10%). The EMS diet decreased abundance ofRuminococcus,Parasutterella,Bilophila,Enterococcus, andLactobacillusoperational taxonomic units (OTU), whereasMeniscusandActinobacillusOTU were increased compared to those with the control diet (P< 0.05). Quantitative PCR confirmed results for host effect onEnterobacteriaceaeand diet effect on members of theLactobacillusgroup. The presence of less cecal short-chain fatty acids and the imputed metabolic functions of the cecal microbiome suggested that EMS was less degradable for cecal bacteria than the control starch. The present EMS effects on the bacterial community profiles were different than the previously reported RS effects and can be linked to the chemical structure of EMS.

scholarly journals Substantial Differences in the Subgingival Microbiome Measured by 16S Metagenomics According to Periodontitis Status in Older Women

2018 ◽  
Vol 6 (4) ◽  
pp. 58 ◽  
Author(s):  
Michael LaMonte ◽  
Robert Genco ◽  
Wei Zheng ◽  
Daniel McSkimming ◽  
Christopher Andrews ◽  
...  
Keyword(s):  
Postmenopausal Women ◽  
Krebs Cycle ◽  
Later Life ◽  
Oral Microbiome ◽  
Host Susceptibility ◽  
Rrna Gene ◽  
Periodontal Pathogens ◽  
Microbial Life ◽  
Severe Periodontitis ◽  
V3 Region

Aging invokes physiological changes, such as immunosenescence and inflammation, that could increase host susceptibility to oral microbiome shifts that enable periodontitis progression in later life. At present, there is a dearth of studies specifically evaluating the oral microbiome and periodontitis in older adults. We used high-throughput untargeted sequencing methods and functional metagenomic analyses to assess and compare the subgingival biofilm of postmenopausal women (mean age 71 years) according to periodontitis status. Subgingival plaque samples were obtained from 15 postmenopausal women with no periodontitis, and from 15 women with severe periodontitis, determined by probing measures. The 16S rRNA gene (V1–V3 region) was sequenced on the 454 FLX platform. The PICRUSt technique was used to provide information on what the potential functional characteristics of microbiota might be in healthy, compared with diseased, periodontium. The subgingival microbiome associated with periodontitis showed clear differences to that associated with health. Of the 464 species identified, 22.8% had elevated abundance in disease, while only 6.3% had elevated abundance in health. Among the 12 most prevalent organisms in periodontitis, one-half have previously been recognized as periodontal pathogens by other investigators. The subgingival microbiome in periodontitis contained genes that could code for specific activities, including microbial mobility, synthesis of endotoxin, and proteolytic degradation. The healthy microbiome included genes that could code for sustaining microbial life, including encoding for transporters, glycolysis, gluconeogenesis, the Krebs cycle, and protein kinases. In the present study on postmenopausal women, aged 60 and older, the subgingival microbiome differed in composition and potential function between those with and without periodontitis. Studies of functional gene expression, such as transcriptomics, are needed to definitively identify the molecules carrying out functions associated with pathogenic subgingival complexes. This, in turn, could lead to identification of targets for enhanced management of periodontitis and, possibly, other diseases, in later life.

An improved technique for face recognition applications

2018 ◽  
Vol 119 (9/10) ◽  
pp. 529-544 ◽  
Author(s):  
Ihab Zaqout ◽  
Mones Al-Hanjori
Keyword(s):  
Face Recognition ◽  
Computer Games ◽  
Recognition Accuracy ◽  
Learning Algorithm ◽  
Recognition Rate ◽  
Data Set ◽  
Content Type ◽  
Linear Discriminant ◽  
The Face ◽  
Feature Based

Purpose The face recognition problem has a long history and a significant practical perspective and one of the practical applications of the theory of pattern recognition, to automatically localize the face in the image and, if necessary, identify the person in the face. Interests in the procedures underlying the process of localization and individual’s recognition are quite significant in connection with the variety of their practical application in such areas as security systems, verification, forensic expertise, teleconferences, computer games, etc. This paper aims to recognize facial images efficiently. An averaged-feature based technique is proposed to reduce the dimensions of the multi-expression facial features. The classifier model is generated using a supervised learning algorithm called a back-propagation neural network (BPNN), implemented on a MatLab R2017. The recognition rate and accuracy of the proposed methodology is comparable with other methods such as the principle component analysis and linear discriminant analysis with the same data set. In total, 150 faces subjects are selected from the Olivetti Research Laboratory (ORL) data set, resulting 95.6 and 85 per cent recognition rate and accuracy, respectively, and 165 faces subjects from the Yale data set, resulting 95.5 and 84.4 per cent recognition rate and accuracy, respectively. Design/methodology/approach Averaged-feature based approach (dimension reduction) and BPNN (generate supervised classifier). Findings The recognition rate is 95.6 per cent and recognition accuracy is 85 per cent for the ORL data set, whereas the recognition rate is 95.5 per cent and recognition accuracy is 84.4 per cent for the Yale data set. Originality/value Averaged-feature based method.

scholarly journals Genomics of the Uncultivated, Periodontitis-Associated BacteriumTannerellasp. BU045 (Oral Taxon 808)

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Clifford J. Beall ◽  
Alisha G. Campbell ◽  
Ann L. Griffen ◽  
Mircea Podar ◽  
Eugene J. Leys
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Chronic Periodontitis ◽  
Bacterial Species ◽  
The United States ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Bacterial Cells ◽  
Data Set ◽  
Content Type

ABSTRACTDespite decades of research into the human oral microbiome, many species remain uncultivated. The technique of single-cell whole-genome amplification and sequencing provides a means of deriving genome sequences for species that can be informative on biological function and suggest pathways to cultivation.Tannerella forsythiahas long been known to be highly associated with chronic periodontitis and to cause periodontitis-like symptoms in experimental animals, andTannerellasp. BU045 (human oral taxon 808) is an uncultivated relative of this organism. In this work, we extend our previous sequencing of theTannerellasp. BU063 (human oral taxon 286) genome by sequencing amplified genomes from 11 cells ofTannerellasp. BU045, including 3 genomes that are at least 90% complete.Tannerellasp. BU045 is more closely related toTannerellasp. BU063 than toT. forsythiaby gene content and average nucleotide identity. However, two independent data sets of association with periodontitis, one based on 16S rRNA gene abundance and the other based on gene expression in a metatranscriptomic data set, show thatTannerellasp. BU045 is more highly associated with disease thanTannerellasp. BU063. Comparative genomics shows genes and functions that are shared or unique to the different species, which may direct further research of the pathogenesis of chronic periodontitis.IMPORTANCEPeriodontitis (gum disease) affects 47% of adults over 30 in the United States (P. I. Eke, B. A. Dye, L. Wei, G. O. Thornton-Evans, R. J. Genco, et al., J Dent Res 91:914–920, 2012), and it cost between $39 and $396 billion worldwide in 2015 (A. J. Righolt, M. Jevdjevic, W. Marcenes, and S. Listl, J Dent Res, 17 January 2018, https://doi.org/10.1177/0022034517750572). Many bacteria associated with the disease are known only by the DNA sequence of their 16S rRNA gene. In this publication, amplification and sequencing of DNA from single bacterial cells are used to obtain nearly complete genomes ofTannerellasp. BU045, a species of bacteria that is more prevalent in patients with periodontitis than in healthy patients. Comparing the complete genome of this bacterium to genomes of related bacterial species will help to better understand periodontitis and may help to grow this organism in pure culture, which would allow a better understanding of its role in the mouth.

Prevotella illustrans sp. nov., derived from human oropharyngeal abscess puncture fluid

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Michael E. J. Buhl ◽  
Jan P. Meier-Kolthoff ◽  
Matthias Marschal
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Routine Care ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Long Chain Fatty Acids ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type

An obligately anaerobic strain, designated as A2931T, was isolated from oropharyngeal abscess puncture fluid of a patient sampled during routine care at a hospital and further characterized both phenotypically, biochemically and genotypically. This Gram-negative rod-shaped bacterium was moderately saccharolytic and proteolytic. Phylogenetic analyses of full-length 16S rRNA gene and whole-genome sequences revealed it to be best placed in the genus Prevotella , but to be only comparatively distantly related to recognized species, with the closest relationship to Prevotella baroniae (average nucleotide identity and digital DNA–DNA hybridization values both well below the generally accepted thresholds). Strain A2931T had a genomic DNA G+C content of 47.7 mol%. Its most abundant cellular long-chain fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. Taken together, this polyphasic data suggests strain A2931T to represent a novel species within the genus Prevotella , for which the name Prevotella illustrans sp. nov. is proposed. The type strain is A2931T (=DSM 108028T=CCOS 1232T=CCUG 72806T). Interestingly, we found strain A2931T to correspond to the oral taxon Prevotella HMT-820 in the Human Oral Microbiome Database, as supported by overall genome relatedness index analyses >99 %. Thus, our work not only closes one of the gaps of knowledge about hitherto unnamed species isolated from humans, but also will facilitate identification of this taxon both in the clinical microbiology context and in research alike.

scholarly journals Gender Variations in the Oral Microbiomes of Elderly Patients with Initial Periodontitis

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Jie Zhao ◽  
Ying-Hui Zhou ◽  
Ya-Qiong Zhao ◽  
Yao Feng ◽  
Fei Yan ◽  
...  
Keyword(s):  
Immune System ◽  
Elderly Patients ◽  
16S Rrna Gene Sequencing ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Microbial Composition ◽  
Linear Discriminant ◽  
Immune System Diseases ◽  
Analytical Approaches

Periodontitis is a globally prevalent disease that imposes a functional and aesthetic burden on patients. The oral microbiome influences human health. The aim of this study was at assessing gender variation in the subgingival bacterial microbiome of elderly patients with initial periodontitis and to determine the causes of this variation. Twelve males and twenty females (range 50–68 years old) with initial periodontitis provided subgingival plaque samples. 16S rRNA gene sequencing, QIIME-based data processing, and statistical analyses were carried out using several different analytical approaches to detect differences in the oral microbiome between the two groups. Males had higher Chao1 index, observed species, and phylogenetic diversity whole tree values than females. Analysis of β-diversity indicated that the samples were reasonably divided by the gender. The linear discriminant analysis effect size showed that the most representative biomarkers were the genus Haemophilus in males, whereas the dominant bacteria in females were Campylobacter. Kyoto Encyclopedia of Genes and Genomes analysis showed that predicting changes in the female oral microbiota may be related to the immune system and immune system diseases are the main factor in males. These data suggest that gender may be a differentiating factor in the microbial composition of subgingival plaques in elderly patients with initial periodontitis. These results could deepen our understanding of the role of gender in the oral microbiota present during initial periodontitis.

scholarly journals Oral Microbiome Signatures in Hematological Cancers Reveal Predominance of Actinomyces and Rothia Species

2020 ◽  
Vol 9 (12) ◽  
pp. 4068
Author(s):  
Jean-Luc C. Mougeot ◽  
Micaela F. Beckman ◽  
Holden C. Langdon ◽  
Michael T. Brennan ◽  
Farah Bahrani Mougeot
Keyword(s):  
Bacterial Species ◽  
Alpha Diversity ◽  
In Silico Analysis ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Host Immune System ◽  
Linear Discriminant ◽  
Microbiome Composition ◽  
Hematological Cancers ◽  
Healthy Control

The endogenous microbiome of healthy individuals in oral cavities is diverse, representing over 700 bacterial species. Imbalance in oral and gut microbiome composition and associated gene expression has been linked to different forms of hematological (blood) cancers. Our objective is to compare oral microbiome profiles of patients with blood cancers (BC group: N = 39 patients, n = 124 oral samples) to those of healthy control subjects (HC group: N = 27 subjects, n = 100 oral samples). Saliva samples and swabs of buccal mucosa, supragingival plaque, and tongue were collected from blood cancer patients and healthy controls. Next-generation sequencing (16S-rRNA gene V3–V4 region) was used to determine the relative abundance of bacterial taxa present at the genus and species levels. Differences in oral microbiome beta-diversity were determined using multivariate permutational analysis of variance (PERMANOVA). Linear discriminant analysis (LDA) effect size (LEfSe) analysis was performed to identify differentiating bacterial taxa in pairwise comparisons. The PATRICv3.6.7 online tool was used to determine the predominance of potential pathogenicity in the BC group. The oral microbiome beta-diversities of the BC and HC groups differed and corresponded to a reduced alpha-diversity in the BC group. LEfSe analysis showed significant LDA scores for Actinomyces and Rothia spp., differentiating the BC group from the HC group. In silico analysis using PATRICv3.6.7 demonstrated that the groups of bacteria possessing traits of “antibiotic resistance”, “oral pathogen”, and “virulence” was enriched in the BC group. Although 56% of the BC patients received antibiotics within two weeks of the oral bacterial sampling, Actinomyces genus remained the top differentiating feature in the BC group regardless of the administration of antibiotics, while Rothia dentocariosa was detected as the top differentiating feature in the BC patients who did not receive antibiotics, but not in those who received antibiotics. Further investigation is needed to better understand the interactions of certain oral species with the host immune system to better characterize clinically relevant associations with hematological cancers.

scholarly journals Development of a Multilocus Sequence Typing Tool for High-Resolution Genotyping of Enterocytozoon bieneusi

2011 ◽  
Vol 77 (14) ◽  
pp. 4822-4828 ◽  
Author(s):  
Yaoyu Feng ◽  
Na Li ◽  
Theresa Dearen ◽  
Maria L. Lobo ◽  
Olga Matos ◽  
...  
Keyword(s):  
High Resolution ◽  
Multilocus Sequence Typing ◽  
Enterocytozoon Bieneusi ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Content Type ◽  
Health Significance ◽  
The One ◽  
Pcr Targeting ◽  
Typing Tool

ABSTRACTThus far, genotyping ofEnterocytozoon bieneusihas been based solely on DNA sequence analysis of the internal transcribed spacer (ITS) of the rRNA gene. Both host-adapted and zoonotic (human-pathogenic) genotypes ofE. bieneusihave been identified. In this study, we searched for microsatellite and minisatellite sequences in the whole-genome sequence database ofE. bieneusiisolate H348. Seven potential targets (MS1 to MS7) were identified. Testing of the seven targets by PCR using two human-pathogenicE. bieneusigenotypes (A and Peru10) led to the selection of four targets (MS1, MS3, MS4, and MS7). Further analysis of the four loci with an additional 24 specimens of both host-adapted and zoonoticE. bieneusigenotypes indicated that most host-adapted genotypes were not amplified by PCR targeting these loci. In contrast, 10 or 11 of the 13 specimens of the zoonotic genotypes were amplified by PCR at each locus. Altogether, 12, 8, 7, and 11 genotypes of were identified at MS1, MS3, MS4, and MS7, respectively. Phylogenetic analysis of the nucleotide sequences obtained produced a genetic relationship that was similar to the one at the ITS locus, with the formation of a large group of zoonotic genotypes that included mostE. bieneusigenotypes in humans. Thus, a multilocus sequence typing tool was developed for high-resolution genotyping ofE. bieneusi.Data obtained in the study should also have implications for understanding the taxonomy ofEnterocytozoonspp., the public health significance ofE. bieneusiin animals, and the sources of humanE. bieneusiinfections.

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