scholarly journals Structure and Function of Oral Microbial Community in Periodontitis Based on Integrated Data

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhengwen Cai ◽  
Shulan Lin ◽  
Shoushan Hu ◽  
Lei Zhao
Keyword(s):  
Microbial Community ◽  
Metabolic Pathways ◽  
Sequence Data ◽  
Periodontal Pocket ◽  
Integrated Analysis ◽  
Pocket Depth ◽  
Screening Criteria ◽  
Related Sequence ◽  
And Function ◽  
Potential Biomarkers

ObjectiveMicroorganisms play a key role in the initiation and progression of periodontal disease. Research studies have focused on seeking specific microorganisms for diagnosing and monitoring the outcome of periodontitis treatment. Large samples may help to discover novel potential biomarkers and capture the common characteristics among different periodontitis patients. This study examines how to screen and merge high-quality periodontitis-related sequence datasets from several similar projects to analyze and mine the potential information comprehensively.MethodsIn all, 943 subgingival samples from nine publications were included based on predetermined screening criteria. A uniform pipeline (QIIME2) was applied to clean the raw sequence datasets and merge them together. Microbial structure, biomarkers, and correlation network were explored between periodontitis and healthy individuals. The microbiota patterns at different periodontal pocket depths were described. Additionally, potential microbial functions and metabolic pathways were predicted using PICRUSt to assess the differences between health and periodontitis.ResultsThe subgingival microbial communities and functions in subjects with periodontitis were significantly different from those in healthy subjects. Treponema, TG5, Desulfobulbus, Catonella, Bacteroides, Aggregatibacter, Peptostreptococcus, and Eikenella were periodontitis biomarkers, while Veillonella, Corynebacterium, Neisseria, Rothia, Paludibacter, Capnocytophaga, and Kingella were signature of healthy periodontium. With the variation of pocket depth from shallow to deep pocket, the proportion of Spirochaetes, Bacteroidetes, TM7, and Fusobacteria increased, whereas that of Proteobacteria and Actinobacteria decreased. Synergistic relationships were observed among different pathobionts and negative relationships were noted between periodontal pathobionts and healthy microbiota.ConclusionThis study shows significant differences in the oral microbial community and potential metabolic pathways between the periodontitis and healthy groups. Our integrated analysis provides potential biomarkers and directions for in-depth research. Moreover, a new method for integrating similar sequence data is shown here that can be applied to other microbial-related areas.

scholarly journals TLR2 and TLR4 as Potential Biomarkers of Environmental Particulate Matter Exposed Human Myeloid Dendritic Cells

2007 ◽  
Vol 2 ◽  
pp. 117727190700200 ◽  
Author(s):  
Marc A. Williams ◽  
Chris Cheadle ◽  
Tonya Watkins ◽  
Anitaben Tailor ◽  
Smruti Killedar ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
Host Immunity ◽  
Tlr4 Expression ◽  
Myeloid Dendritic Cells ◽  
Critical Function ◽  
Danger Signals ◽  
Particulate Pollution ◽  
And Function ◽  
Biomarkers Of Effect ◽  
Potential Biomarkers

In many subjects who are genetically susceptible to asthma, exposure to environmental stimuli may exacerbate their condition. However, it is unknown how the expression and function of a family of pattern-recognition receptors called toll-like receptors (TLR) are affected by exposure to particulate pollution. TLRs serve a critical function in alerting the immune system of tissue damage or infection—the so-called “danger signals”. We are interested in the role that TLRs play in directing appropriate responses by innate immunity, particularly dendritic cells (DC), after exposing them to particulate pollution. Dendritic cells serve a pivotal role in directing host immunity. Thus, we hypothesized that alterations in TLR expression could be further explored as potential biomarkers of effect related to DC exposure to particulate pollution. We show some preliminary data that indicates that inhaled particulate pollution acts directly on DC by down-regulating TLR expression and altering the activation state of DC. While further studies are warranted, we suggest that alterations in TLR2 and TLR4 expression should be explored as potential biomarkers of DC exposure to environmental particulate pollution.

scholarly journals Microbiological Activity during Co-Composting of Food and Agricultural Waste for Soil Amendment

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 928
Author(s):  
Vladimir Mironov ◽  
Anna Vanteeva ◽  
Alexander Merkel
Keyword(s):  
Microbial Community ◽  
Agricultural Waste ◽  
Temperature Changes ◽  
Culture Independent ◽  
Mineralization Of Organic Matter ◽  
Microbial Number ◽  
Mature Compost ◽  
Stimulate Plant Growth ◽  
And Function ◽  
Favorable Conditions

This study aims to establish the relationship between ambient parameters and the diversity, composition, and function of microbial communities that predominate at each stage of the co-composting of food and agricultural waste. Culture-based and culture-independent methods were used to investigate the changes in the microbiota. The favorable conditions of high initial humidity and C/N ratio caused a decrease in the richness and biodiversity of the microbiota when such conditions existed. During the thermophilic stage, the total microbial number increased, and active mineralization of organic matter was carried out by members of the genera Bacillus, Caldibacillus, Aspergillus, and Penicillium. The fungal community was sensitive to drastic temperature changes. Byssochlamys dominated among fungi during the transition from the mesophilic to the thermophilic stage and during cooling. The biodiversity increased with time and was associated with the dynamics of germination and nitrification indices, so that the more diverse the microbial community, the higher the properties of compost that stimulate plant growth and development. The microbial community of the mature compost, together with mineral plant nutrients ready for consumption and humic compounds, make this compost a good soil additive.

Insights into the mechanism of the interference of sulfadiazine on soil microbial community and function

2021 ◽  
pp. 126388
Author(s):  
Linlin Qiu ◽  
Tim J. Daniell ◽  
Steven A. Banwart ◽  
Muhammad Nafees ◽  
Jingjing Wu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Microbial Community ◽  
Soil Microbial ◽  
And Function

scholarly journals How Changes in the Nutritional Landscape Shape Gut Immunometabolism

Nutrients ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 823
Author(s):  
Jian Tan ◽  
Duan Ni ◽  
Rosilene V. Ribeiro ◽  
Gabriela V. Pinget ◽  
Laurence Macia
Keyword(s):  
Immune Cells ◽  
Metabolic Pathways ◽  
Immune Cell ◽  
Food Additives ◽  
Cell Activity ◽  
Inflammatory Cells ◽  
Therapeutic Approaches ◽  
Food Antigens ◽  
And Function ◽  
Micro Organisms

Cell survival, proliferation and function are energy-demanding processes, fuelled by different metabolic pathways. Immune cells like any other cells will adapt their energy production to their function with specific metabolic pathways characteristic of resting, inflammatory or anti-inflammatory cells. This concept of immunometabolism is revolutionising the field of immunology, opening the gates for novel therapeutic approaches aimed at altering immune responses through immune metabolic manipulations. The first part of this review will give an extensive overview on the metabolic pathways used by immune cells. Diet is a major source of energy, providing substrates to fuel these different metabolic pathways. Protein, lipid and carbohydrate composition as well as food additives can thus shape the immune response particularly in the gut, the first immune point of contact with food antigens and gastrointestinal tract pathogens. How diet composition might affect gut immunometabolism and its impact on diseases will also be discussed. Finally, the food ingested by the host is also a source of energy for the micro-organisms inhabiting the gut lumen particularly in the colon. The by-products released through the processing of specific nutrients by gut bacteria also influence immune cell activity and differentiation. How bacterial metabolites influence gut immunometabolism will be covered in the third part of this review. This notion of immunometabolism and immune function is recent and a deeper understanding of how lifestyle might influence gut immunometabolism is key to prevent or treat diseases.

scholarly journals Characteristics, Treatment, and Prognosis of Cracked Teeth: A Comparison with Data from 10 Years Ago

2021 ◽  
Author(s):  
Tae Yeon Lee ◽  
Sung Eun Yang ◽  
Hye Min Kim ◽  
Min Joo Kye
Keyword(s):  
Root Canal ◽  
Statistical Significance ◽  
Treatment Method ◽  
Root Canal Treatment ◽  
Periodontal Pocket ◽  
P Value ◽  
Chi Square ◽  
Pocket Depth ◽  
Persistent Symptoms ◽  
Probing Depth

Abstract Objectives The purpose of this study was to analyze and to compare retrospectively the characteristics, the treatment process, and the prognosis of cracked teeth by comparing recent data with data from 10 years ago. Materials and Methods Sixty-eight cracked teeth from March 2009 to June 2010 (2009 data) and 185 cracked teeth from March 2019 to June 2020 (2019 data) were analyzed. The characteristics of cracked teeth and the treatment method depending on probing depth, caries, and symptoms, and prognosis depending on pocket depth and apical lesions were analyzed using R version 3.3.3 (R Foundation for Statistical Computing, Vienna, Austria) and T&F version 3.0 (YooJin BioSoft, Korea). To compare proportions, the two-sample proportion test was performed. The distribution of proportions within the samples from 2009 and 2019 data was analyzed using the Chi-square test or binomial test. A p-value <0.05 was considered to indicate statistical significance. Results Significantly fewer cracked teeth received root canal treatment before crown in 2019 than in 2009 (p = 0.032). In both 2009 and 2019, symptomatic cracked teeth and those with deep periodontal pockets (>6 mm) were significantly more likely to receive root canal treatment. In both years, cracked teeth with a probing depth less than 6 mm or without an apical lesion were significantly more likely to be asymptomatic at 3-month and 6-month follow-ups (p < 0.001). Conclusion Cracked teeth with a deep periodontal pocket or symptoms had a higher likelihood of endodontic treatment, and the presence of a deep periodontal pocket or apical lesion was associated with a higher risk of persistent symptoms. Therefore, clinicians should consider these factors when planning treatment and predicting patients’ prognosis.

scholarly journals Influence of Surgical Flap Design (Envelope and Szmyd) for Removal of Impacted Mandibular Third Molars on Clinical Periodontal Parameters: A Clinical Trial

2021 ◽  
Vol 18 (9) ◽  
pp. 4465
Author(s):  
Muhtada Ahmad ◽  
Zafar Ali Khan ◽  
Tahir Ullah Khan ◽  
Montaser N. Alqutub ◽  
Sameer A. Mokeem ◽  
...  
Keyword(s):  
Third Molar ◽  
Periodontal Pocket ◽  
Third Molars ◽  
Chi Square ◽  
Pocket Depth ◽  
Clinical Attachment Loss ◽  
Exact Test ◽  
Second Molar ◽  
Third Molar Extraction ◽  
Flap Design

The aim of the study was to assess the influence of flap designs (Envelope flap (EF) and Szmyd flap (SF)) for impacted mandibular third molar extraction, on periodontal pocket depth (PPD), clinical attachment loss (CAL) and bone levels (BL) of second molar. Sixty patients indicated for third molar extractions with healthy second molars were allocated into two groups: EF and SF (n = 30). Third molars were assessed for angulation, root patterns, depth of impactions and relation with ramus (Pell and Gregory classification). Extraction of third molars was performed and PPD, CAL and BL around second molars at 0, 3 and 6 month (mon) follow-ups (FU) were assessed clinically and radiographically. ANOVA, Chi-square and Fisher’s exact test were employed to compare periodontal factors between EF and SF groups, considering p ≤ 0.05 as significant. Sixty participants with a mean age of 23.22 ± 3.17 were included in the study. Based on angulation, the most common impaction in the EF and SF groups was mesio-angular (EF, 50%; SF, 36.7%). Buccal and distal PPD showed a significant increase (p < 0.001) in both EF and SF patients from baseline to 6 mon. EF patients showed significantly higher distal and buccal CAL (6.67 ± 0.18 mm; 6.91 ± 0.17 mm) and BL (7.64 ± 0.16 mm; 7.90 ± 0.15 mm) as compared to SF patients (CAL, 6.76 ± 0.26 mm; 6.91 ± 0.17 mm-BL, 7.42 ± 0.38 mm; 7.34 ± 0.34 mm) at 6 mon FU. SF showed better soft tissue attachment (PPD and CAL) and bone stability (less bone loss) around second molars compared to EF after third molar extractions regardless of the patient, tooth and operator factors.

Predicting Chromosome Flexibility from the Genomic Sequence Based on Deep Learning Neural Networks

2021 ◽  
Vol 16 ◽  
Author(s):  
Jinghao Peng ◽  
Jiajie Peng ◽  
Haiyin Piao ◽  
Zhang Luo ◽  
Kelin Xia ◽  
...  
Keyword(s):  
Deep Learning ◽  
High Performance ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Function Analysis ◽  
Double Helix ◽  
Gm12878 Cell ◽  
Genomic Sequence Analysis ◽  
And Function ◽  
Nuclear Processes

Background: The open and accessible regions of the chromosome are more likely to be bound by transcription factors which are important for nuclear processes and biological functions. Studying the change of chromosome flexibility can help to discover and analyze disease markers and improve the efficiency of clinical diagnosis. Current methods for predicting chromosome flexibility based on Hi-C data include the flexibility-rigidity index (FRI) and the Gaussian network model (GNM), which have been proposed to characterize chromosome flexibility. However, these methods require the chromosome structure data based on 3D biological experiments, which is time-consuming and expensive. Objective: Generally, the folding and curling of the double helix sequence of DNA have a great impact on chromosome flexibility and function. Motivated by the success of genomic sequence analysis in biomolecular function analysis, we hope to propose a method to predict chromosome flexibility only based on genomic sequence data. Method: We propose a new method (named "DeepCFP") using deep learning models to predict chromosome flexibility based on only genomic sequence features. The model has been tested in the GM12878 cell line. Results: The maximum accuracy of our model has reached 91%. The performance of DeepCFP is close to FRI and GNM. Conclusion: The DeepCFP can achieve high performance only based on genomic sequence.

scholarly journals Changes in Microbial Community Composition and Function during a Polyaromatic Hydrocarbon Phytoremediation Field Trial

2003 ◽  
Vol 69 (1) ◽  
pp. 483-489 ◽  
Author(s):  
Steven D. Siciliano ◽  
James J. Germida ◽  
Kathy Banks ◽  
Charles W. Greer
Keyword(s):  
Microbial Community ◽  
Festuca Arundinacea ◽  
Rhizosphere Soil ◽  
Microbial Community Composition ◽  
Hydrocarbon Degradation ◽  
Bulk Soil ◽  
Catabolic Gene ◽  
Soil Microbial ◽  
Catabolic Genes ◽  
And Function

ABSTRACT The purpose of this study was to investigate the mechanism by which phytoremediation systems promote hydrocarbon degradation in soil. The composition and degradation capacity of the bulk soil microbial community during the phytoremediation of soil contaminated with aged hydrocarbons was assessed. In the bulk soil, the level of catabolic genes involved in hydrocarbon degradation (ndoB, alkB, and xylE) as well as the mineralization of hexadecane and phenanthrene was higher in planted treatment cells than in treatment cells with no plants. There was no detectable shift in the 16S ribosomal DNA (rDNA) composition of the bulk soil community between treatments, but there were plant-specific and -selective effects on specific catabolic gene prevalence. Tall Fescue (Festuca arundinacea) increased the prevalence of ndoB, alkB, and xylE as well as naphthalene mineralization in rhizosphere soil compared to that in bulk soil. In contrast, Rose Clover (Trifolium hirtum) decreased catabolic gene prevalence and naphthalene mineralization in rhizosphere soil. The results demonstrated that phytoremediation systems increase the catabolic potential of rhizosphere soil by altering the functional composition of the microbial community. This change in composition was not detectable by 16S rDNA but was linked to specific functional genotypes with relevance to petroleum hydrocarbon degradation.

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