scholarly journals Correlation Between Salivary Microbiology and H2S Concentration of Oral Cavity

2021 ◽  
Author(s):  
Jiarui Jiang ◽  
Yufeng Huang ◽  
Na Luo ◽  
Qili Mi ◽  
Xuemei Li ◽  
...  
Keyword(s):  
Hydrogen Sulfide ◽  
Oral Cavity ◽  
Sulfur Metabolism ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Oral Diseases ◽  
Oral Malodor ◽  
High Group ◽  
Oral Microbes ◽  
Oral Microorganisms

Abstract Background: Halitosis is caused by metabolites produced by oral microorganisms. Hydrogen sulfide is the most important compound that leads to the oral malodor, and is thought to be closely correlated with the activity of oral microorganism. Therefore, it is important to clarify the correlation between oral microbes and metabolites. Methods: Based on the 16S rRNA gene amplicon and shotgun metagenomic sequencing of oral microorganism, and oral malodor test, this study attempted to explain the contribution of oral microorganisms to the hydrogen sulfide of oral malodor. Results: The data shows that microbial taxa consisted in the H2S low and high groups are different, and most of the enriched taxa in the H2S high group are genus that correlated with H2S concentration. The two species Fusobaeterium periodonticum and Prevotella nanceiensis are significant different in both coverage breadth and depth and LPS biosynthesis contributions in two groups. According to KEGG metabolism pathways detected by HUMAnN2, subjects of the H2S high group may have a high risk to bacterial infection, since the LPS biosynthesis is enrichment. The contribution of F. periodonticum to sulfur metabolism between two groups is significantly different, and the relative abundance of F. periodonticum is higher in the H2S high group as well. Conclusions: The H2S content, is significantly associated with the composition and abundance of microorganisms in the oral cavity. The increase of microbial abundance and metabolism of some sulfide products are the main causes of halitosis. The most of the enriched microorganisms enriched in people with high H2S are associated with oral diseases such as caries and periodontal diseases, indicating that the diseases associated with oral microbes are not independent of each other and have some associations between some oral diseases.

scholarly journals A computational protocol to characterize elusive Candidate Phyla Radiation bacteria in oral environments using metagenomic data

2018 ◽  
Author(s):  
Peiqi Meng ◽  
Chang Lu ◽  
Xinzhe Lou ◽  
Qian Zhang ◽  
Peizeng Jia ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Ribosomal Proteins ◽  
Morphological Changes ◽  
Metagenomic Data ◽  
Great Promise ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Human Oral Cavity ◽  
Candidate Phyla Radiation ◽  
Computational Protocol

AbstractSeveral studies have documented the diversity and potential pathogenic associations of organisms in the human oral cavity. Although much progress has been made in understanding the complex bacterial community inhabiting the human oral cavity, our understanding of some microorganisms is less resolved due to a variety of reasons. One such little-understood group is the candidate phyla radiation (CPR), which is a recently identified, but highly abundant group of ultrasmall bacteria with reduced genomes and unusual ribosomes. Here, we present a computational protocol for the detection of CPR organisms from metagenomic data. Our approach relies on a self-constructed dataset comprising published CPR genomic sequences as a filter to identify CPR sequences from metagenomic sequencing data. After assembly and functional prediction, the taxonomic affiliation of CPR contigs can be identified through phylogenetic analysis with publically available 16S rRNA gene and ribosomal proteins, in addition to sequence similarity analyses (e.g., average nucleotide identity calculations and contig mapping). Using this protocol, we reconstructed two draft genomes of organisms within the TM7 superphylum, that had genome sizes of 0.594 Mb and 0.678 Mb. Among the predicted functional genes of the constructed genomes, a high percentage were related to signal transduction, cell motility, and cell envelope biogenesis, which could contribute to cellular morphological changes in response to environmental cues.ImportanceCandidate phyla radiation (CPR) bacterial group is a recently identified, but highly diverse and abundant group of ultrasmall bacteria exhibiting reduced genomes and limited metabolic capacities. A number of studies have reported their potential pathogenic associations in multiple mucosal diseases including periodontitis, halitosis, and inflammatory bowel disease. However, CPR organisms are difficult to cultivate and are difficult to detect with PCR-based methods due to divergent genetic sequences. Thus, our understanding of CPR has lagged behind that of other bacterial component. Here, we used metagenomic approaches to overcome these previous barriers to CPR identification, and established a computational protocol for detection of CPR organisms from metagenomic samples. The protocol describe herein holds great promise for better understanding the potential biological functioning of CPR. Moreover, the pipeline could be applied to other organisms that are difficult to cultivate.

Essential oils and plant extracts with activity against oral microorganisms: prevention and treatment of oral diseases

2015 ◽  
Vol 62 (4) ◽  
pp. 250-257 ◽  
Author(s):  
Anna Herman ◽  
Andrzej Młynarczyk
Keyword(s):  
Oral Cavity ◽  
Essential Oils ◽  
Plant Extracts ◽  
Inhibitory Activity ◽  
Mentha Piperita ◽  
Diffusion Method ◽  
Thymus Vulgaris ◽  
Oral Diseases ◽  
Prevention And Treatment ◽  
Oral Microorganisms

The aim of this study was to compare the antimicrobial activity of essential oils and extracts of Salvia officinalis, Thymus vulgaris, Mentha piperita, Juniperus communis and Rosmarinus officinalis with antibiotics against physiological and pathological strains of microorganisms isolated from the oral cavity. The antibacterial and antifungal activities of essential oils, extracts and antibiotics were evaluated using the disc diffusion method. Essential oils exhibited higher inhibitory activity against physiological microflora and all tested pathogenic microorganism strains than those observed for antibiotics and plant extracts. Essential oils and ethanolic extracts of Thymus vulgaris were the most potent growth inhibitor of all microorganisms isolated from the oral cavity. Depending on the bacterial strain tested, Thymus vulgaris oil had 3–8 times higher inhibitory activity compared with all tested antibiotics and exhibited the same strength of antifungal activity as amfotericin and miconazol against Candida albicans. Essential oils and extracts may be useful in the prevention and treatment of oral diseases caused by oral microorganisms.

A new approach to treatment of stomatitis in experiments on white rats (experimental research)

2018 ◽  
pp. 168-173
Author(s):  
Е.Б. Ганина ◽  
Ю.В. Червинец ◽  
Н.В. Грудинин ◽  
В.Г. Шестакова ◽  
В.М. Червинец ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Oral Cavity ◽  
Experimental Research ◽  
Quantitative Composition ◽  
Oral Diseases ◽  
New Approach ◽  
Highly Active ◽  
White Rats ◽  
Before And After ◽  
Intact Rats

Цель исследования - охарактеризовать микробиологическую картину стоматита до и после его лечения высокоактивными культурами лактобацилл, дать оценку эффективности их применения при экспериментальном стоматите. Методика. Опыты проводились на 32 самках беспородных белых крыс массой 230 г. Моделирование стоматита включало 2 этапа: моделирование травматического стоматита и воспроизведение бактериального стоматита на базе травматического. У крыс контрольной и опытных серий на всех этапах эксперимента брали мазки с поверхности десен для характеристики микробиоценоза ротовой полости. Результаты. После обработки слизистой оболочки полости рта (СОПР) культурой патогенного штамма Staphylococcus aureus существенно снизились частота встречаемости и количество условно-патогенных микроорганизмов. Лечение стоматита у крыс культурами лактобацилл ( Lactobacillus 11 зв., Lactobacillus 2 п.рта, Lactobacillus 24 д.ст.) и их комбинацией приводило к снижению распространенности S. aureus вплоть до его исчезновения, а также к нормализации количества условно-патогенной микробиоты. Заключение. Исследования показали эффективность использования отдельных высокоактивных штаммов лактобацилл или их комбинации при лечении заболеваний СОПР, в частности бактериального стоматита. Aim. To characterize the microbiological picture of stomatitis in intact rats before and after the treatment with highly active cultured lactobacilli and to evaluate the effectiveness of this treatment in experiments on white rats. Methods. Experiments were carried out on 32 mongrel female white rats weighing 230 g. Smears were taken from the gum surface of control and experimental rats at all stages of the experiment to characterize the oral cavity microbiocenosis. Results. After treatment of the oral cavity with cultured Staphylococcus aureus , the occurrence and quantity of opportunistic microorganisms significantly decreased. The treatment of stomatitis in rats with cultured lactobacillus ( Lactobacillus 11 zv., Lactobacillus 2 p.r., Lactobacillus 24 d.st. and their combination) led to a decrease in S. aureus prevalence up to its extinction and to normalization of the quantitative composition of opportunistic microbiota. Conclusions. The study showed the effieacy of highly active lactobacillus strains individually or their combinations in the treatment of oral diseases, in particular, bacterial stomatitis.

scholarly journals Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Francesco Durazzi ◽  
Claudia Sala ◽  
Gastone Castellani ◽  
Gerardo Manfreda ◽  
Daniel Remondini ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Shotgun Sequencing ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Experimental Conditions ◽  
Rrna Gene Sequencing

AbstractIn this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.

scholarly journals Novel strain-level resolution of Crohn’s disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing

2021 ◽  
Author(s):  
J. J. Teh ◽  
E. M. Berendsen ◽  
E. C. Hoedt ◽  
S. Kang ◽  
J. Zhang ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Ex Vivo ◽  
Taxonomic Composition ◽  
Strain Level ◽  
Patient Specific ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Functional Characterisation ◽  
Bacterial Lineages

AbstractThe mucosa-associated microbiota is widely recognized as a potential trigger for Crohn’s disease pathophysiology but remains largely uncharacterised beyond its taxonomic composition. Unlike stool microbiota, the functional characterisation of these communities using current DNA/RNA sequencing approaches remains constrained by the relatively small microbial density on tissue, and the overwhelming amount of human DNA recovered during sample preparation. Here, we have used a novel ex vivo approach that combines microbe culture from anaerobically preserved tissue with metagenome sequencing (MC-MGS) to reveal patient-specific and strain-level differences among these communities in post-operative Crohn’s disease patients. The 16 S rRNA gene amplicon profiles showed these cultures provide a representative and holistic representation of the mucosa-associated microbiota, and MC-MGS produced both high quality metagenome-assembled genomes of recovered novel bacterial lineages. The MC-MGS approach also produced a strain-level resolution of key Enterobacteriacea and their associated virulence factors and revealed that urease activity underpins a key and diverse metabolic guild in these communities, which was confirmed by culture-based studies with axenic cultures. Collectively, these findings using MC-MGS show that the Crohn’s disease mucosa-associated microbiota possesses taxonomic and functional attributes that are highly individualistic, borne at least in part by novel bacterial lineages not readily isolated or characterised from stool samples using current sequencing approaches.

scholarly journals Characterization and Transcriptome Analysis of a Long-Chain n-Alkane-Degrading Strain Acinetobacter Pittii SW-1

2021 ◽  
Vol 18 (12) ◽  
pp. 6365
Author(s):  
Weina Kong ◽  
Cheng Zhao ◽  
Xingwang Gao ◽  
Liping Wang ◽  
Qianqian Tian ◽  
...  
Keyword(s):  
Unsaturated Fatty Acids ◽  
Sulfur Metabolism ◽  
Quantitative Polymerase Chain Reaction ◽  
Deep Ocean ◽  
Rrna Gene ◽  
Alkane Hydroxylase ◽  
Degradation Rates ◽  
Acinetobacter Pittii ◽  
Ocean Environment ◽  
Long Chain

Strain sw-1, isolated from 7619-m seawater of the Mariana Trench, was identified as Acinetobacter pittii by 16S rRNA gene and whole-genome sequencing. A. pittii sw-1 was able to efficiently utilize long-chain n-alkanes (C18–C36), but not short- and medium-chain n-alkanes (C8–C16). The degradation rate of C20 was 91.25%, followed by C18, C22, C24, C32, and C36 with the degradation rates of 89.30%, 84.03%, 80.29%, 30.29%, and 13.37%, respectively. To investigate the degradation mechanisms of n-alkanes for this strain, the genome and the transcriptome analyses were performed. Four key alkane hydroxylase genes (alkB, almA, ladA1, and ladA2) were identified in the genome. Transcriptomes of strain sw-1 grown in C20 or CH3COONa (NaAc) as the sole carbon source were compared. The transcriptional levels of alkB and almA, respectively, increased 78.28- and 3.51-fold in C20 compared with NaAc, while ladA1 and ladA2 did not show obvious change. The expression levels of other genes involved in the synthesis of unsaturated fatty acids, permeases, membrane proteins, and sulfur metabolism were also upregulated, and they might be involved in n-alkane uptake. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) confirmed that alkB expression was significantly induced by C20, C24, and C32, and almA induction extent by C24 and C32 was higher than that with C20. Furthermore, ladA2 expression was only induced by C32, and ladA1 expression was not induced by any of n-alkanes. In addition, A. pittii sw-1 could grow with 0%–3% NaCl or 8 out of 10 kinds of the tested heavy metals and degrade n-alkanes at 15 °C. Taken together, these results provide comprehensive insights into the degradation of long-chain n-alkanes by Acinetobacter isolated from the deep ocean environment.

scholarly journals Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yusuke Okazaki ◽  
Shohei Fujinaga ◽  
Michaela M. Salcher ◽  
Cristiana Callieri ◽  
Atsushi Tanaka ◽  
...  
Keyword(s):  
16S Rrna ◽  
Regional Scale ◽  
Scale Up ◽  
Amplicon Sequencing ◽  
Freshwater Ecosystems ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Long Read

Abstract Background Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. Results Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7–101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. Conclusions Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future.

scholarly journals The occurrence of Entamoeba gingivalis among patients with periodontal disease

2016 ◽  
Vol 29 (2) ◽  
pp. 86-89 ◽  
Author(s):  
Joanna Luszczak ◽  
Michal Bartosik ◽  
Jolanta Rzymowska ◽  
Agnieszka Sochaczewska-Dolecka ◽  
Ewa Tomaszek ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Periodontal Disease ◽  
Periodontal Diseases ◽  
Age Groups ◽  
Healthy People ◽  
Gingival Tissue ◽  
Pathological Changes ◽  
Oral Diseases

AbstractAccording to some studies, the Entamoeba gingivalis colonizing the gingival tissue is an important agent in bringing about periodontitis. Other studies, however, deem it an opportunist that is able to survive in the medium induced by periodontal disease. The aim of this study was to investigate the prevalence of Entamoeba gingivalis infection in patients from the Department of Periodontology, and compare this population with that of healthy people, so as to analyze the relationships between infection and patient sex and age. The result of this work is that in both groups, a correlation (p = 0,19) has been noted between the occurrence of amoebae and other diseases in the oral cavity. Indeed, 81,4% of all patients with some periodontal disease showed the presence of amoeba. Among those who are not afflicted with oral diseases, the presence of amoeba was indicated in 62,5% of the total. In addition, a correlation between the person's age and the presence of protozoa (p = 0,15) was strongly marked among women (p = 0,19). In the three age groups of women in this study (40-49, 60-69, and above 80 years), we observed a 100% presence of protozoa.Our study leads us to the conclusion that infections with Entamoeba gingivalis should be regarded as an factor that is associated with the pathological changes occurring in patients with periodontal diseases.

scholarly journals Diversity and Morphology of Members of the Phylum “Synergistetes” in Periodontal Health and Disease

2009 ◽  
Vol 75 (11) ◽  
pp. 3777-3786 ◽  
Author(s):  
S. R. Vartoukian ◽  
R. M. Palmer ◽  
W. G. Wade
Keyword(s):  
Oral Health ◽  
Oral Cavity ◽  
Positive Sample ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Subgingival Plaque ◽  
Pcr Cloning ◽  
Human Oral Cavity ◽  
Health And Disease

ABSTRACT Members of the phylum “Synergistetes” have frequently been detected in the human oral cavity at sites of dental disease, but they have rarely been detected in studies of oral health. Only two oral “Synergistetes” taxa are cultivable. The aims of this study were to investigate the diversity of “Synergistetes” in the oral cavity, to establish whether “Synergistetes” taxa are more strongly associated with periodontitis than with oral health, and to visualize unculturable “Synergistetes” in situ. Sixty samples (saliva, dental plaque, and mucosal swabs) were collected from five subjects with periodontitis and five periodontally healthy controls. Using phylum-specific 16S rRNA gene primers, “Synergistetes” were identified by PCR, cloning, and sequencing of 48 clones per PCR-positive sample. Subgingival plaque samples were labeled with probes targeting rRNA of unculturable oral “Synergistetes” using fluorescent in situ hybridization (FISH). Analysis of 1,664 clones revealed 12 “Synergistetes” operational taxonomic units (OTUs) at the 99% sequence identity level, 5 of which were novel. “Synergistetes” OTU 4.2 was found in significantly more subjects with periodontitis than controls (P = 0.048) and was more abundant in subgingival plaque at diseased sites than at healthy sites in subjects with periodontitis (P = 0.019) or controls (P = 0.019). FISH analysis revealed that unculturable oral “Synergistetes” cells were large curved bacilli. The human oral cavity harbors a diverse population of “Synergistetes.” “Synergistetes” OTU 4.2 is associated with periodontitis and may have a pathogenic role.

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