• Journal of Oral Medicine and Pain
• /
• v.47 no.1
• /
• pp.10-26
• /
• 2022

Purpose: The purpose of this study was to investigate whether various saliva collection methods affect the observed salivary microbiome and whether microbiomes of stimulated and unstimulated saliva and plaque differ in richness and diversity. Methods: Seven sampling methods for unstimulated saliva, stimulated saliva, and plaque samples were applied to six orally and systemically healthy participants. Bacterial 16S ribosomal RNA genes of 10 major oral bacterial species, namely, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum, Prevotella intermedia, Prevotella nigrescens, Streptococcus mitis, Streptococcus sobrinus, and Lactobacillus casei, were analyzed by real-time polymerase chain reaction. We comprehensively examined the dependence of the amount of bacterial ribosomal DNA (rDNA), bacterial-community composition, and relative abundance of each species on sample collection methods. Results: There were significant differences in the bacterial rDNA copy number depending on the collection method in three species: F. nucleatum, P. nigrescens, and S. mitis. The species with the highest richness was S. mitis, with the range from 89.31% to 100.00%, followed by F. nucleatum, P. nigrescens, T. denticola, T. forsythia, and P. intermedia, and the sum of the proportions of the remaining five species was less than 1%. The species with the lowest observed richness was P. gingivalis (<0.1%). The Shannon diversity index was the highest in unstimulated saliva collected with a funnel (4.449). The Shannon diversity index was higher in plaque samples (3.623) than in unstimulated (3.171) and stimulated (3.129) saliva and in mouthwash saliva samples (2.061). Conclusions: The oral microbial profile of saliva samples can be affected by sample collection methods, and saliva differs from plaque in the microbiome. An easy and rapid technique for saliva collection is desirable; however, observed microbial-community composition may more accurately reflect the actual microbiome when unstimulated saliva is assayed.

• Animal cells and systems
• /
• v.6 no.1
• /
• pp.13-18
• /
• 2002

Phylogenetic relationships of Korean Acidiella species were tested using mitochondrial 16S ribosomal RNA gene sequences. We used 16 published sequences as outgroup, and 10 new sequences for nine Korean Acidiella species as ingroup. The number of aligned sites was 1,281 bp, but 1,135 bp were used for the analysis after excluding sites with missing data or gaps. Among these 1,135 sites, 464 sites were variable and 340 were informative for parsimony analysis. Phylogenetic information was extracted from this data set using neighbor-joining, maximum likelihood and maximum parsimony methods and compared to a morphology-based phylogenetic hypothesis. Our molecular data suggest that: (1) the tribe Trypetini appears to be monophyletic even when the nine additional Acidiella species are added to our previous phylogenetic analysis; (2) all the Korean Acidiella species belong to the Trypeta group, but the genus Acidiella is not supported as monophyletic; (3) the close relationship of A. circumvaga, A. issikii, and A. sapporensis is supported; (4) the close relationship of A. pachypogon and two additional new Acidiella species is strongly supported; and (5) the possible presence of two or more cryptic species among the specimens previously identified as A. obscuripennis is suggested. Sequence data from the mitochondrial 16S rDNA allowed us to better understand the systematic status of Korean Acidiella species. They indicated that the current concept about the genus Acidiella is insufficient and needs to be refined further. This study also showed a few interesting relationships, that had not been recognized by morphological study alone. Based on this study, we were able to plan further experiments to analyze relationships within the Trypeta Group.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.26 no.2
• /
• pp.95-112
• /
• 2013

As a first step toward understanding the divergence and relationships of the Nymphalidae (Lepidoptera: Papilionoidea) occurring in South Korea, cytochrome oxidase subunit I (COI), 16S ribosomal RNA (16S rRNA), and elongation factor-$1{\alpha}$ (EF-$1{\alpha}$) that comprise 3,501-3,716 bp were either sequenced (55 species) or the sequences were obtained from GenBank (23 species). The concatenated sequence divergence of six nymphalid subfamilies ranked in the following order: Danainae (10.3%), Satyrinae (9.5%), Limenitidinae (8.0%), Apaturinae (7.0%), Nymphalinae (6.7%), and Heliconiinae (6.2%). As has been reported in previous large scale international studies, the subfamilial relationships of (((((Limenitidinae + Heliconiinae) + (Nymphalinae + Apaturinae)) + Satyrinae) + Libytheinae) + Danainae) were also confirmed, except for the switched positions between Danainae and Libytheinae, and supported all subfamilies and tribe monophylies. Unlikely consistent phylogenetic relationships among genera within the majority of tribes in Nymphalidae, a conflicting relationship within the subfamily Apaturinae was obvious, presenting Apatura as sister to either Mimathyma or (Mimathyma + (Sephisa + (Hestina + Sasakia))), and both of these relationships are unconventional. Within the subfamily Limenitidinae, the genus Neptis was consistently revealed as a paraphyletic with respect to the genus Aldania, requiring further taxonomic investigation of the genus. Although limited, current sequence information and phylogenetic relationships are expected to be helpful for further studies.

• Journal of Korean Society of Water and Wastewater
• /
• v.29 no.1
• /
• pp.47-55
• /
• 2015

Recently, the production of taste and odor (T&O) compounds is a common problem in water industry. Geosmin is one of the T&O components in drinking water. However, geosmin is hardly eliminated through the conventional water treatment systems. Among various advanced processes capable of removing geosmin, adsorption process using granular activated carbon (GAC) is the most commonly used process. As time passes, however GAC process changes into biological activated carbon (BAC) process. There is little information on the BAC process in the literature. In this study, we isolated and identified microorganisms existing within various BAC processes. The microbial concentrations of BAC processes examined were $3.5{\times}10^5$ colony forming units (CFU/g), $2.2{\times}10^6CFU/g$ and $7.0{\times}10^5CFU/g$ in the Seongnam plant, Goyang plant and Goryeong pilot plant, respectively. The dominant bacterial species were found to be Bradyrhizobium japonicum, Novosphingobium rosa and Afipia broomeae in each plants. Removal efficiencies of $3{\mu}g/L$ geosmin by the dominant species were 36.1%, 36.5% and 34.3% in mineral salts medium(MSM) where geosmin was a sole carbon source.

• Journal of Life Science
• /
• v.16 no.1
• /
• pp.71-75
• /
• 2006

We analyzed the phylogenic relationships of 23 partial 18S rDNA sequences of 22 species (1 species has 2 strains) belonging to Sarcorptiforms include 4 new sequences, using several tools. Although geographic distributions are quite far from, sequence similarity of two strains of Dermatophygoides pteronyssinus isolated from Japan and New Zealand were very high. This result suggests that mite migration by animals including human occurred in the two continents. We investigated the Endeostigmata taxonomic relationship between the Prostigmata and Oribatida subgroups using small fragments (340-400 bp) of their 185 rDNA sequences. But Endeostigmata was not grouped with Oribatida or Prostigmata. In conclusion, it is first reported phylogenic relationship for classified mites included in Sarcoptiformes using 185 rDNA sequence analysis and its system is a very powerful tool for classification of mites.

• Journal of Food Hygiene and Safety
• /
• v.35 no.3
• /
• pp.234-242
• /
• 2020

In this study, we monitored the raw materials in home-meal replacement (HMR) products, which have shown more than 63% growth in market size for two years. A total of 89 HMR products were purchased and the DNA barcodes of 112 raw materials in the product samples were analyzed. In order to identify the raw material species, a primer set specific for the 16S ribosomal RNA region of each raw material species was amplified. The amplicon was purified and sequenced, and then used to perform a BLAST search provided by the National Institutes of Health (NIH). The species of the raw material was determined by comparing the nucleotide sequences of the species registered in GenBank with identity and match score. Twenty-four species and three genera were identified from 112 raw materials. Three genera were identified at the genus level because a large number of species belonging to the same genus exist within 98% of the identity criteria. The results of the determination were compared with the available raw materials suggested in the Korea Food Code to determine the Korean name and availability of the foods. Six non-listed species were determined to be edible according to information provided by influential domestic and foreign organizations.

• Microbiology and Biotechnology Letters
• /
• v.40 no.4
• /
• pp.389-395
• /
• 2012

T-RFLP (terminal restriction fragment length polymorphism) analysis, one of the most highly adopted culture-independent microbial community analysis methods, was applied to evaluate the colonization of probiotics in experimental animal gut. Lactic acid bacteria that exhibited cinnamoyl esterase activity were isolated from Korean fermented vegetables and identified by 16S ribosomal RNA sequence analysis. Lactobacillus plantarum KK3, which demonstrated high chlorogenic acid hydrolysis by cinnamoyl esterase activity, and acid/bile salt resistances, was cultured, freeze-dried, and fed to mice and the microbiota in their feces were monitored by T-RFLP analysis. The T-RF of L. plantarum was detected in the feces of mice after the start of administration and lasted at least 31 days after the initial 7 day feeding. T-RFLP analysis was considered a useful tool to evaluate the gut colonization of probiotic L. plantarum. In order to prove that L. plantarum was from viable cells, we reisolated L. plantarum in the feces using cinnamoyl esterase activity media as the screening step. The colonization of L. plantarum KK3 in the mouse gut was confirmed by this research.

• Journal of Life Science
• /
• v.32 no.5
• /
• pp.391-410
• /
• 2022

Human microbiota is a community of microorganisms, including bacteria, fungi, and viruses, that inhabit various locations of the body, such as the gut, oral, and skin. Along with the development of metabolomic analysis and next-generation sequencing techniques for 16S ribosomal RNA, it has become possible to analyze the population for subtypes of microbiota, and with these techniques, it has been demonstrated that bacterial microbiota are involved in the metabolic and immunological processes of the hosts. While specific bacteria of microbiota, called commensal bacteria, positively affect hosts by producing essential nutrients and protecting hosts against other pathogenic microorganisms, dysbiosis, an abnormal microbiota composition, disrupts homeostasis and thereby has a detrimental effect on the development and progression of various types of diseases. Recently, several studies have reported that oral and gut bacteria of microbiota are involved in the carcinogenesis of gastrointestinal tumors and the therapeutic effects of anticancer therapy, such as radiation, chemotherapy, targeted therapy, and immunotherapy. Studying the complex relationships (bacterial microbiota-cancer-immunity) and microbiota-related carcinogenic mechanisms can provide important clues for understanding cancer and developing new cancer treatments. This review provides a summary of current studies focused on how bacterial microbiota affect gastrointestinal cancer and anticancer therapy and discusses compelling possibilities for using microbiota as a combinatorial therapy to improve the therapeutic effects of existing anticancer treatments.

• Korean Journal of Microbiology
• /
• v.42 no.1
• /
• pp.19-25
• /
• 2006

This study was undertaken to develop PCR primers for the identification and detection of Streptococcus mutans (by)using species-specific forward and universal reverse primers. These primers targeted the variable regions of the 16S ribosomal RNA coding gene (rDNA). The primer specificity was tested against 11S. mutans strains and 10 different species (22 strains) of oral bacteria. The primer sensitivity was determined by testing serial dilutions of the purified genomic DNA of S. mutans ATCC $25175^T$. The data showed that species-specific amplicons were obtained from all the S. mutans strains tested, which was not observed in the other species. The direct and nested PCR could detect as little as 2 pg and 2 fg of the chromosomal DNA from S. mutans ATCC $25175^T$, respectively. This shows that the PCR primers are highly sensitive and applicable to the detection and identification of S. mutans.

• Journal of Microbiology and Biotechnology
• /
• v.16 no.2
• /
• pp.193-199
• /
• 2006

Halotolerant spore-forming Gram-positive bacteria were isolated from the root, rhizosphere, and non-rhizosphere soil of Blutaparon portulacoides. The different isolates were characterized genetically using an amplified ribosomal DNA restriction analysis (ARDRA), and phenotypically based on their colonial morphology, physiology, and nutritional requirements. Three different 16S rRNA gene-based genotypes were observed at a 100% similarity using the enzymes HinfI, MspI, and RsaI, and the phenotypic results also followed the ARDRA groupings. Selected strains, representing the different ARDRA groups, were analyzed by 16S rDNA sequencing, and members of the genera Halobaeillus, Virgibacillus, and Oceanobacillus were found. Two isolates showed low 16S rDNA sequence similarities with the closest related species of Halobacillus, indicating the presence of new species among the isolates. The majority of the strains isolated in this study seemed to belong to the species O. iheyensis and were compared using an AP-PCR to determine whether they had a clonal origin or not. Different patterns allowed the grouping of the strains according to Pearson's coefficient, and the resulting dendrogram revealed the formation of two main clusters, denoted as A and B. All the strains isolated from the soil were grouped into cluster A, whereas cluster B was exclusively composed of the strains associated with the B. portulacoides roots. This is the first report on the isolation and characterization of halotolerant spore-forming Gram-positive bacteria that coexist with B. portulacoides. As such, these new strains may be a potential source for the discovery of bioactive compounds with industrial value.