• International Journal of Oral Biology
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• 제46권3호
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• pp.146-153
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• 2021

Accurate identification of microbes facilitates the prediction, prevention, and treatment of human diseases. To increase the accuracy of microbiome data analysis, a long region of the 16S rRNA is commonly sequenced via paired-end sequencing. In paired-end sequencing, a sufficient length of overlapping region is required for effective joining of the reads, and high-quality sequencing reads are needed at the overlapping region. Trimming sequences at the reads distal to a point where sequencing quality drops below a specific threshold enhance the joining process. In this study, we examined the effect of trimming conditions on the number of reads that remained after quality control and chimera removal in the Illumina paired-end reads of the V3-V4 hypervariable region. We also examined the alpha diversity and taxa assigned by each trimming condition. Optimum quality trimming increased the number of good reads and assigned more number of operational taxonomy units. The pre-analysis trimming step has a great influence on further microbiome analysis, and optimized trimming conditions should be applied for Divisive Amplicon Denoising Algorithm 2 analysis in QIIME2 platform.

• Restorative Dentistry and Endodontics
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• 제44권1호
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• pp.7.1-7.10
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• 2019

Apical periodontitis is a biofilm-mediated infection. The biofilm protects bacteria from host defenses and increase their resistance to intracanal disinfecting protocols. Understanding the virulence of these endodontic microbiota within biofilm is essential for the development of novel therapeutic procedures for intracanal disinfection. Both the disruption of biofilms and the killing of their bacteria are necessary to effectively treat apical periodontitis. Accordingly, a review of endodontic biofilm types, antimicrobial resistance mechanisms, and current and future therapeutic procedures for endodontic biofilm is provided.

• Journal of Periodontal and Implant Science
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• 제36권4호
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• pp.829-837
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• 2006

Halitosis, defined as an unpleasant oral odor, is a commonly experienced condition with a variety of etiological factors and may cause a significant social or psychological handicap to those suffering from it, In most cases, halitosis originates within the oral cavity itself and patients with periodontal disease often suffer from oral malodor, The most common cause of this disease is related to microbiota which reside on the tongue and in the periodontal pocket, This study was undertaken to examine the effect of full mouth disinfection including tongue scraping on oral malodor in a group of patients with chronic periodontitis, The relationship between halitosis and oral health status was also investigated, The volatile sulfur compounds (VSC) scores were significantly correlated with Plaque Index, Bleeding Index, pocket depth, and tongue coating score, The organoleptic ratings were significantly associated with Plaque Index, Bleeding Index. and tongue coating score, The VSC scores and organoleptic ratings correlated strongly with each other. Full mouth disinfection resulted in a significant reduction in the VSC scores. organoleptic ratings, and self-perception of malodor up to 12 weeks, This study indicates that in patients with chronic periodontitis. a full mouth disinfection including tongue scraping has a significant effect in the treatment of oral malodor.

• The Journal of Advanced Prosthodontics
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• 제14권5호
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• pp.273-284
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• 2022

PURPOSE. Computer-aided design and manufacturing (CAD-CAM) of implant abutments has been shown to result in surface contamination from site-specific milling and fabrication processes. If not removed, these contaminants can have a potentially adverse effect and may trigger inflammatory responses of the peri-implant tissues. The aim of the present study was to evaluate the bacterial disinfection and cleaning efficacy of ultrasonic reprocessing in approved disinfectants to reduce the microbial load of CAD-CAM abutments. MATERIALS AND METHODS. Four different types of custom implant abutments (total N = 32) with eight specimens in each test group (type I to IV) were CAD-CAM manufactured. In two separate contamination experiments, specimens were contaminated with heparinized sheep blood alone and with heparinized sheep blood and the test bacterium Enterococcus faecium. Abutments in the test group were processed according to a three-stage ultrasonic protocol and assessed qualitatively and quantitatively by determination of residual protein. Ultrasonicated specimens contaminated with sheep blood and E. faecium were additionally eluted and the dilutions were incubated on agar plates for seven days. The determined bacterial counts were expressed as colony-forming units (CFU). RESULTS. Ultrasonic reprocessing resulted in a substantial decrease in residual bacterial protein to less than 80 ㎍ and a reduction in microbiota of more than 7 log levels of CFU for all abutment types, exceeding the effect required for disinfection. CONCLUSION. A three-stage ultrasonic cleaning and disinfection protocol results in effective bacterial decontamination. The procedure is reproducible and complies with the standardized reprocessing and disinfection specifications for one- or two-piece CAD-CAM implant abutments.

• 식품과학과 산업
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• 제52권3호
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• pp.261-271
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• 2019

NGS 기술이 발전함에 따라 우리 몸의 생리와 면역조절에 있어서 장내미생물의 중요성이 알려지면서부터 장내미생물군집의 구조를 직접 조절할 수 있는 프로바이오틱스의 중요성 역시 재조명 받고 있다. 인류는 프로바이오틱스를 오랫동안 발효식품 등을 통하여 섭취하였는데, 프로바이오틱스는 식품의 보존성 및 영양성을 높일 뿐 아니라 인체의 건강에 이로운 역할을 한다. 특히 프로바이오틱스의 섭취는 생체 내에서 Treg의 기능을 활성화하여 장내 환경을 개선시켜 유익한 장내미생물의 생육을 도우며, 염증반응, 알러지질환, 자가면역질환 등을 완화시키는 효과가 있다. 특히 프로바이오틱스는 장내 유익균인 Bifidobacterium, Faecalibacterium, Akkermansia 및 Bacteroides 속 미생물의 빈도를 증가시키고, 이들은 단쇄지방산 및 신체에 이로운 대사체 등을 생산한다. 지금까지 프로바이오틱스는 대부분 건강기능식품으로 사용되어 왔으나, 최근 들어 장내 유익균에 대한 기능성이 알려지면서 기존 프로바이오틱스를 포함한 장내 미생물을 이용한 NGPs 개발이 활발히 진행되고 있다. 하지만 NGPs 개발에는 여전히 한계가 존재한다. 아직까지 장내 미생물의 분리, 동정은 일반 세균 배양에 비해 매우 까다롭고, 특별한 배양 기술이 필요하므로 현재까지 NGPs로 활용될 수 있는 장내 미생물은 매우 제한적이다. 또한 기존 프로바이오틱스와는 다르게 NGPs는 의약품처럼 전임상, 독성시험, 약물역학, 3단계의 임상시험을 거쳐야 한다. 하지만 기존 프로바이오틱스의 질병 개선 효과를 뛰어넘어 고형암, 대사질환 및 면역질환의 차세대 치료제로서의 활용 가능성이 매우 높기 때문에 앞으로 더 폭넓은 연구가 진행되어야 할 것이다.

• Journal of Ginseng Research
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• 제46권6호
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• pp.780-789
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• 2022

Background: Incretin impairment, characterized by insufficient secretion of L-cell-derived glucagon-like peptide-1 (GLP-1), is a defining step of type 2 diabetes mellitus (T2DM). Ginsenoside compound K (CK) can stimulate GLP-1 secretion; however, the potential mechanism underlying this effect has not been established. Methods: CK (40 mg/kg) was administered orally to male db/db mice for 4 weeks. The body weight, oral glucose tolerance, GLP-1 secretion, gut microbiota sequencing, bile acid (BA) profiles, and BA synthesis markers of each subject were then analyzed. Moreover, TGR5 expression was evaluated by immunoblotting and immunofluorescence, and L-cell lineage markers involved in L-cell abundance were analyzed. Results: CK ameliorated obesity and impaired glucose tolerance in db/db mice by altering the gut microbiota, especially Ruminococcaceae family, and this changed microbe was positively correlated with secondary BA synthesis. Additionally, CK treatment resulted in the up-regulation of CYP7B1 and CYP27A1 and the down-regulation of CYP8B1, thereby shifting BA biosynthesis from the classical pathway to the alternative pathway. CK altered the BA pool by mainly increasing LCA and DCA. Furthermore, CK induced L-cell number expansion leading to enhanced GLP-1 release through TGR5 activation. These increases were supported by the upregulation of genes governing GLP-1 secretion and L-cell differentiation. Conclusions: The results indicate that CK improves glucose homeostasis by increasing L-cell numbers, which enhances GLP-1 release through a mechanism partially mediated by the gut microbiota-BA-TGR5 pathway. Therefore, that therapeutic attempts with CK might be useful for patients with T2DM.

• 한방재활의학과학회지
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• 제33권3호
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• pp.1-15
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• 2023

Objectives We aimed to find out the improvement effect of Baekhogainsam-tang (Baihu Jia Renshen-tang, BIT) on metabolic syndrome and alteration of microbiota and gene expression. Methods We used male C57BI/6 mice and randomly assigned them into three groups. Normal control group was fed 10% kcal% fat diet, high-fat diet (HFD) group was fed 45% kcal% fat diet and 10% fructose water. BIT group was fed same diet as HFD group and treated by BIT for once daily, 6 days per week, total 8 weeks. We measured their body weight and food intake every week and performed oral glucose tolerance test 1 week before the end of the study. Then we collected the blood sample to measure triglyceride, total cholesterol, high-density lipoprotein cholesterol, insulin, and hemoglobin A1c. We harvested tissue of liver, muscle, fat, and large intestine for quantitative polymerase chain reaction (qPCR) and histopathological examination. Fresh fecal samples were collected from each animal to verify alterations of gut microbiota and we used RNA from liver tissue for microarray analysis. Results The body weight and fat weight of BIT group were reduced compared to HFD group. The qPCR markers usually up-regulated in metabolic syndrome were decreased in BIT group. Bacteroides were higher in BIT group than other groups. There were also differences in gene expressions between two groups such as Cyp3a11 and Scd1. Conclusions We could find out BIT can ameliorate metabolic syndrome and suggest its effect is related to gut microbiota composition and gene expression pattern.

• Journal of Periodontal and Implant Science
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• 제52권5호
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• pp.394-410
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• 2022

Purpose: The purpose of this study was to compare the microbial composition of 3 types of oral samples through 16S metagenomic sequencing to determine how to resolve some sampling issues that occur during the collection of sub-gingival plaque samples. Methods: In total, 20 subjects were recruited. In both the healthy and periodontitis groups, samples of saliva and supra-gingival plaque were collected. Additionally, in the periodontitis group, sub-gingival plaque samples were collected from the deepest periodontal pocket. After DNA extraction from each sample, polymerase chain reaction amplification was performed on the V3-V4 hypervariable region on the 16S rRNA gene, followed by metagenomic sequencing and a bioinformatics analysis. Results: When comparing the healthy and periodontitis groups in terms of alpha-diversity, the saliva samples demonstrated much more substantial differences in bacterial diversity than the supra-gingival plaque samples. Moreover, in a comparison between the samples in the case group, the diversity score of the saliva samples was higher than that of the supra-gingival plaque samples, and it was similar to that of the sub-gingival plaque samples. In the beta-diversity analysis, the sub-gingival plaque samples exhibited a clustering pattern similar to that of the periodontitis group. Bacterial relative abundance analysis at the species level indicated lower relative frequencies of bacteria in the healthy group than in the periodontitis group. A statistically significant difference in frequency was observed in the saliva samples for specific pathogenic species (Porphyromonas gingivalis, Treponema denticola, and Prevotella intermedia). The saliva samples exhibited a similar relative richness of bacterial communities to that of sub-gingival plaque samples. Conclusions: In this 16S oral microbiome study, we confirmed that saliva samples had a microbial composition that was more similar to that of sub-gingival plaque samples than to that of supra-gingival plaque samples within the periodontitis group.

• Journal of Microbiology and Biotechnology
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• 제33권8호
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• pp.1057-1065
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• 2023

Inflammatory bowel disease (IBD), a chronic inflammatory disease, results from dysregulation of the immune responses. Some lactic acid bacteria (LAB), including Lactobacillus, alleviate IBD through immunomodulation. In this study, the anti-colitis effect of LAB isolated from human breast milk was investigated in a mouse model induced acute colitis with 2,4,6-trinitrobenzene sulfonic acid (TNBS). TNBS remarkably increased weight loss, colon shortening, and colonic mucosal proliferation, as well as the expression levels of inflammatory cytokines, including tumor necrosis factor-alpha (TNF-α) and interleukin (IL)-1β. Oral administration of LAB isolated from human breast milk resulted in a reduction in TNBS-induced colon shortening, as well as induced cyclooxygenase (COX)-2, nitric oxide synthase (iNOS), nuclear factor-kappa B (NF-κB). In addition, LAB suppressed inflammatory cytokines such as TNF-α, IL-6, and IL-1β, and thus showed an effect of suppressing the level of inflammation induced by TNBS. Furthermore, LAB alleviated gut microbiota dysbiosis, and inhibited intestinal permeability by increasing the expression of intestinal tight junction protein including ZO-1. Collectively, these results suggest that LAB isolated from human breast milk can be used as a functional food for colitis treatment by regulating NF-κB signaling, gut microbiota and increasing expression of intestinal tight junction protein.

• Journal of Microbiology and Biotechnology
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• 제28권9호
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• pp.1443-1446
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• 2018

In the present study, we examined whether Lactobacillus johnsonii CJLJ103 (LJ) could alleviate cholinergic memory impairment in mice. Oral administration of LJ alleviated scopolamine-induced memory impairment in passive avoidance and Y-maze tasks. Furthermore, LJ treatment increased scopolamine-suppressed BDNF expression and CREB phosphorylation in the hippocampi of the brain, as well as suppressed $TNF-{\alpha}$ expression and $NF-{\kappa}B$ activation. LJ also increased BDNF expression in corticosterone-stimulated SH-SY5Y cells and inhibited $NF-{\kappa}B$ activation in LPS-stimulated microglial BV2 cells. However, LJ did not inhibit acetylcholinesterase activity. These findings suggest that LJ, a member of human gut microbiota, may mitigate cholinergic memory impairment by increasing BDNF expression and inhibiting $NF-{\kappa}B$ activation.