With fast development and wide applications of next generation sequencing (NGS), genomic sequence information is within reach to various research fields. Three benchtop NGS instruments are now available. The 454 GS Junior (Roche), Ion PGM (Life Technologies) and MiSeq (Illumina) are laser-printer sized and offer modest set-up and running costs. By reviewing 2 studies that compared the performance of these instruments, the major characteristics of each benchtop platforms are compared to enable direct comparisons. The 454 GS Junior generated the longest reads and most contiguous assemblies but had the lowest throughput. The Ion Torrent PGM had the highest throughput and fastest run time. The MiSeq had the highest throughput per run and lowest error rates. The Ion Torrent PGM and 454 GS Junior both produced homopolymer-associated indel errors. Although all the platforms allow multiplexing of samples, details of experimental design, library preparation and data analysis may constrain the options. The features of the platforms provide opportunities both to conduct groundbreaking studies and to waste money. Thus, careful considerations should be made before purchasing or using any of them.
Research Design ; Running ; Statistics as Topic

Vast array of microbes colonize to each anatomical environment of human body. Culture based methods are important in investigating the microbial structure, but they are extremely biased in their evaluation of microbial diversity by selecting particular population of microbiota. Recent advance in molecular technology has allowed sophisticated analysis of complex human microbiota by culture-independent methods. Here, we will discuss features of tools for human microbiota studies including Roche-454 and Illumina platform. We will also briefly discuss features of some strategies that are commonly applied to these platforms including 16S rRNA targeting and shotgun sequencing. New platforms such as PacBio and Oxford Nanopore are also introduced.
Bias (Epidemiology) ; Colon ; Human Body ; Humans ; Metagenome ; Nanopores

In the gingival tissues of patients with periodontitis, inflammatory responses are mediated by a wide variety of genes. In this study, we screened for differentially expressed genes (DEGs) in periodontitis compared with normal tissue using an annealing control primer (ACP) system. By ACP RT-PCR analysis, we obtained about 160 amplicons, 8 of which were found to be differentially expressed. DEGs in patients with periodontitis were thus successfully and reliably identified by the ACP-based RT PCR technique. The DEGs identified in the screen may also enhance our understanding of the pathogenesis of periodontitis.
Humans ; Periodontitis ; Polymerase Chain Reaction

Diabetes mellitus (DM) is a complex disease with various systemic and oral complications including periodontitis. Periodontitis is a disease that leads to destruction of the soft and hard tissues of periodontium, which can result in periodontal bone loss and tooth loss. Although the etiology for periodontitis is bacterial plaque, the host immune response also mediates the destruction of periodontal tissues. DM is related to the development, progression and severity of periodontitis. There are several factors potentially contributing to the development of periodontitis in DM patients: 1) altered immune function, 2) hyperglycemia and advanced glycation end products, and 3) altered lipid metabolism. With limited number of studies, the potential mechanisms involved in the development of DM in periodontitis have also been suggested. DM clearly increases the risk of periodontitis and biological mechanisms have been illucidated. Less clear is the impact of periodontitis on the development of DM. It is possible that periodontitis may serve as initiators or propagators of insulin resistance in a way similar to obesity, thereby aggravating glycemic control.
Alveolar Bone Loss ; Diabetes Mellitus ; Glycosylation End Products, Advanced ; Humans ; Hyperglycemia ; Insulin Resistance ; Lipid Metabolism ; Obesity ; Periodontal Diseases* ; Periodontitis ; Periodontium ; Tooth Loss

Periodontitis is a disease that leads to destruction of the soft and hard tissues of periodontium, which can result in periodontal bone loss and tooth loss in severe cases. Atherosclerosis is a disease characterized by artery wall thickening as a result of invasion and accumulation of foam cells. Epidemiologic studies have suggested the association with periodontitis and atherosclerosis. Periodontopathogens are frequently found in atheroma plaque. The possible mechanisms for systemic dissemination of oral bacteria have been suggested: 1) direct translocation of bacteria from dental plaque to systemic circulation through transcellular mechanism or by physical perturbations of the gingiva, 2) indirect dissemination to distant sites via survival in immune cells including macrophages and dendritic cells. There are several mechanisms by which oral bacteria may contribute to atherosclerosis development: 1) activation of innate immune response, 2) mediators activated by oral bacteria and 3) involvement of cytokines and heat shock proteins from oral bacteria. Thus, better understanding the role of periodontitis in atherosclerosis may be the key to improve the prevention and treatment of atherosclerosis.
Alveolar Bone Loss ; Arteries ; Atherosclerosis* ; Bacteria ; Cytokines ; Dendritic Cells ; Dental Plaque ; Foam Cells ; Gingiva ; Heat-Shock Proteins ; Immunity, Innate ; Macrophages ; Periodontal Diseases* ; Periodontitis ; Periodontium ; Plaque, Atherosclerotic ; Tooth Loss

In the oral cavity, complex microbial community is shaped by various host and environmental factors. Extensive literature describing the oral microbiome in the context of oral health and disease is available. Advances in DNA sequencing technologies and data analysis have drastically improved the analysis of the oral microbiome. For microbiome study, bacterial 16S ribosomal RNA gene amplification and sequencing is often employed owing to the cost-effective and fast nature of the method. In this review, practical considerations for performing a microbiome study, including experimental design, molecular analysis technology, and general data analysis, will be discussed.

BACKGROUND: There have been several reports describing the capability of ginseng extracts as an adjuvant. In this study, we tested if ginsan, a polysaccharide extracted from Panax ginseng, was effective in enhancing antibody response to orally delivered Salmonella antigen. METHODS: Ginsan was treated before oral salmonella antigen administration. Salmonella specific antibody was determined by ELISA. mRNA expression was determined by RT-PCR. Cell migration was determined by confocal microscopy and flow cytometry. COX expression was detected by western blot. RESULTS: Ginsan treatment before oral Salmonella antigen delivery significantly increased both secretory and serum antibody production. Ginsan increased the expression of COX in the Peyer's patches. Various genes were screened and we found that CCL3 mRNA expression was increased in the Peyer's patch. Ginsan increased dendritic cells in the Peyer's patch and newly migrated dendritic cells were mostly found in the subepithelial dome region. When COX inhibitors were treated, the expression of CCL3 was reduced. COX inhibitor also antagonized both the migration of dendritic cells and the humoral immune response against oral Salmonella antigen. CONCLUSION: Ginsan effectively enhances the humoral immune response to orally delivered antigen, mediated by CCL3 via COX. Ginsan may serve as a potent vaccine suppliment for oral immunization.
Antibody Formation ; Blotting, Western ; Cell Movement ; Dendritic Cells ; Enzyme-Linked Immunosorbent Assay ; Flow Cytometry ; Immunity, Humoral ; Immunization ; Microscopy, Confocal ; Panax ; Peyer's Patches ; Polysaccharides ; Prostaglandin-Endoperoxide Synthases ; RNA, Messenger ; Salmonella

The presence of distinct bacterial species is found to be dependent on age, diet, and disease. We compared the detection rate of several oral bacterial strains in a cohort of 36 subjects including healthy volunteers, periodontal patients, and oral cancer patients. Gargling samples were obtained from these subjects from which DNA was then extracted. Specific primers for 29 bacterial species were used for PCR detection. In the oral cancer patients, Capnocytophaga ochracea, Gemella morbillorum, and Streptococcus salivarius were detected more frequently compared with the healthy volunteers and periodontitis patients. Fusobacterium nucleatum/polymorphym and Prevotella nigrescens were significantly less prevalent in oral cancer patients than the other groups. In periodontitis patients, Porphyromonas gingivalis and Treponema denticola were more frequently found compared with the healthy volunteers. In the healthy volunteer group, Peptostreptococcus anaerobius was more frequently found than the other groups. The detection rate of several oral bacterial species was thus found to differ between healthy volunteers, periodontitis patients and oral cancer patients.
Capnocytophaga ; Cohort Studies ; Diet ; DNA ; Fusobacterium ; Gemella ; Healthy Volunteers* ; Humans ; Microbiota* ; Mouth Neoplasms* ; Peptostreptococcus ; Periodontitis* ; Polymerase Chain Reaction ; Porphyromonas gingivalis ; Prevotella nigrescens ; Streptococcus ; Treponema denticola

BACKGROUND: Periodontitis is an inflammatory disease characterized by the breakdown of tooth-supporting tissues, leading to tooth loss. Aggregatibacter actinomycetemcomitans are major etiologic bacterium causing aggressive periodontitis. Ursodeoxycholic acid (UDCA), a hydrophilic gall bladder acid, has been used as an effective drug for various diseases related to immunity. The aim of this study was to investigate the effect of UDCA on the inflammatory response induced by A. actinomycetemcomitans. METHODS: A human acute monocytic leukemia cell line (THP-1) was differentiated to macrophage- like cells by treatment with phorbol 12-mystristate 13-acetate (PMA) and used for all experiments. The cytotoxic effect of UDCA was examined by MTT assay. THP-1 cells were pretreated with UDCA for 30 min before A. actinomycetemcomitans infection and the culture supernatant was analyzed for various cytokine production by ELISA. The effect of UDCA on bacterial growth was examined by measuring optical densities using a spectrophotometer. RESULTS: UDCA showed no cytotoxic effect on THP-1 cells, up to 80 µM Ed highlight: Please confirm technical meaning. UDCA pretreatment inhibited the A. actinomycetemcomitans-induced IL-1β, TNF-α, and IL-17A secretion in a dosedependent manner. UDCA also inhibited IL-21 production at 60 µM. The production of IL-12 and IL-4 was not influenced by A. actinomycetemcomitans infection. CONCLUSION: These findings indicate that UDCA inhibits the production of inflammatory cytokines involved in innate and Th17 immune responses in A. actinomycetemcomitans-infected THP-1-derived macrophages, which suggests its possible use for the control of aggressive periodontitis.
Aggregatibacter actinomycetemcomitans* ; Aggregatibacter* ; Aggressive Periodontitis ; Cell Line ; Cytokines ; Enzyme-Linked Immunosorbent Assay ; Humans ; Interleukin-12 ; Interleukin-17 ; Interleukin-4 ; Leukemia, Monocytic, Acute ; Macrophages ; Periodontitis ; Tooth Loss ; Urinary Bladder ; Ursodeoxycholic Acid*

BACKGROUND: Periodontitis is generally a chronic disorder characterized by the breakdown of tooth-supporting tissues. P. gingivalis, a Gram-negative anaerobic rod, is one of the major pathogens associated with periodontitis. Frequently, P. gingivalis infection leads to cell death. However, the correlation between P. gingivalis–induced cell death and periodontal inflammation remains to be elucidated. Among cell deaths, the death of immune cells appears to play a significant role in inflammatory response. Thus, the aim of this study was to examine P. gingivalis–induced cell death, focusing on autophagy and apoptosis in THP-1 cells. METHODS: Human acute monocytic leukemia cell line (THP-1) was used for all experiments. Autophagy induced by P. gingivalis in THP-1 cells was examined by Cyto ID staining. Intracellular autophagic vacuoles were observed by fluorescence microscopy using staining Acridine orange (AO); and 3-methyladenine (3-MA) was used to inhibit autophagy. Total cell death was measured by LDH assay. Cytokine production was measured by an ELISA method. RESULTS: P. gingivalis induced autophagy in an MOI-dependent manner in THP-1 cells, but 3-MA treatment decreased autophagy and increased the apoptotic blebs. P. gingivalis infection did not increase apoptosis compared to the control cells, whereas inhibition of autophagy by 3-MA significantly increased apoptosis in P. gingivalis-infected THP-1 cells. Inhibition of autophagy by 3-MA also increased total cell deaths and inflammatory cytokine production, including IL-1β and TNF-α. CONCLUSION: P. gingivalis induced autophagy in THP-1 cells, but the inhibition of autophagy by 3-MA stimulated apoptosis, leading to increased cell deaths and pro-inflammatory cytokines production. Hence, the modulation of cell deaths may provide a mechanism to fight against invading microorganisms in host cells and could be a promising way to control inflammation.
Acridine Orange ; Apoptosis ; Autophagy ; Blister ; Cell Death* ; Cell Line ; Cytokines ; Enzyme-Linked Immunosorbent Assay ; Humans ; Inflammation ; Leukemia, Monocytic, Acute ; Macrophages ; Methods ; Microscopy, Fluorescence ; Periodontitis ; Porphyromonas gingivalis* ; Porphyromonas* ; Vacuoles