• Korean Journal of Microbiology
• /
• v.55 no.1
• /
• pp.1-8
• /
• 2019

Due to the major role played by several species of Streptococcus in the etiology of periodontitis, it is important to assess the pattern of Streptococcus pathogenic pathways within the infected subgingival pockets using a bacterial specific 16S rRNA fragment. From the total of 50 patients with periodontitis included in the study, only 23 Streptococcal isolates were considered for further analyses, in which their 16S rRNA fragments were amplified and sequenced. Then, a comprehensive phylogenetic tree was constructed and in silico prediction was performed for the observed Streptococcal species. The phylogenetic analysis of the subgingival Streptococcal species revealed a high discrimination power of the 16S rRNA fragment to accurately identify three groups of Streptococcus on the species level, including S. salivarius (14 isolates), S. anginosus (5 isolates), and S. gordonii (4 isolates). The employment of state-of-art in silico tools indicated that each Streptococcal species group was characterized with particular transcription factors that bound exclusively with a different 16S rRNA-based secondary structure. In conclusion, the observed data of the present study provided in-depth insights into the mechanism of each Streptococcal species in its pathogenesis, which differ in each observed group, according to the differences in the 16S rRNA secondary structure it takes, and the consequent binding with its corresponding transcription factors. This study paves the way for further interventions of the in silico prediction, with the main conventional in vitro microbiota identification to present an interesting insight in terms of the gene expression pattern and the signaling pathway that each pathogenic species follows in the infected subgingival site.

• Korean Journal of Environmental Agriculture
• /
• v.38 no.3
• /
• pp.185-196
• /
• 2019

BACKGROUND: This study investigated the effects of rice genetically modified to be resistant against rice blast and rice bacterial blight on the soil microbial community. A comparative analysis of the effects of rice genetically modified rice choline kinase (OsCK1) gene for disease resistance (GM rice) and the Nakdong parental cultivar (non-GM rice) on the soil microbial community at each stage was conducted using rhizosphere soil of the OsCK1 and Nakdong rice. METHODS AND RESULTS: The soil chemistry at each growth stage and the bacterial and fungal population densities were analyzed. Soil DNA was extracted from the samples, and the microbial community structures of the two soils were analyzed by pyrosequencing. No significant differences were observed in the soil chemistry and microbial population density between the two soils. The taxonomic analysis showed that Chloroflexi, Proteobacteria, Firmicutes, Actinobacteria, and Acidobacteria were present in all soils as the major phyla. Although the source tracking analysis per phylogenetic rank revealed that there were differences in the bacteria between the GM and non-GM soil as well as among the cultivation stages, the GM and non-GM soil were grouped according to the growth stages in the UPGMA dendrogram analysis. CONCLUSION: The difference in bacterial distributions between Nakdong and OsCK1 rice soils at each phylogenetic level detected in microbial community analysis by pyrosequencing may be due to the genetic modification done on GM rice or due to heterogeneity of the soil environment. In order to clarify this, it is necessary to analyze changes in root exudates along with the expression of transgene. A more detailed study involving additional multilateral soil analyses is required.

• The Korean Journal of Mycology
• /
• v.47 no.1
• /
• pp.89-94
• /
• 2019

A rust fungus on Iris domestica (syn. Belamcanda chinensis) from China was previously identified as Puccinia iridis. Accordingly, the identity of the rust fungus on the same host species in Korea needs to be reexamned. Morphological characteristics of the Korean materials matched with P. iridis. Molecular phylogenetic analyses based on internal transcribed spacer and large subunit rDNA sequences of two representative materials confirmed the identification by high sequence similarities of 100% and 99% with the reference sequences available in NCBI GenBank database. Phylogenetic tree inferred from neighbor-joining method proved them to be clustered in P. iridis group. Thus, the rust fungus on I. domestica in Korea was determined as P. iridis. On the other hand, a previous record that Puccinia belamcandae is another rust agent on I. domestica in Korea should be reconfirmed in future.

• Parasites, Hosts and Diseases
• /
• v.60 no.4
• /
• pp.289-293
• /
• 2022

Blastocystis is a genus of unicellular heterokont parasites belonging to a group of organisms known as Stramenopiles, which includes algae, diatoms, and water molds. Blastocystis includes several species that habitat in the gastrointestinal tracts of organisms as diverse as humans, farm animals, birds, rodents, reptiles, amphibians, fish, and cockroaches. It is important to public health and distributed globally, but its prevalence in dogs in Korea has not been reported to date. Here, we collected 787 canine fecal samples and assessed Blastocystis infection by age, sex, region, season, and diarrhea symptoms. We determined Blastocystis subtypes using phylogenetic analyses based on 18S rRNA gene sequences. We identified, 10 Blastocystis positive samples (1.3%). A higher proportion of infected dogs was asymptomatic; however, infection rates did not significantly differ according to region, age, sex, and season. Phylogenetic analysis showed that the Blastocystis sp. identified belonged to 4 subtypes (STs), ST1, ST5, ST10, and ST14, thus revealed the genetic diversity of Blastocystis sp. in dogs Korean. This is first report on the presence of Blastocystis sp. in dogs Korean. This study revealed a lower infection rate than expected and differed from previous studies in STs. Further studies are warranted to observe the national infection status of Blastocystis in dogs and the genetic characteristics of this genus.

• Genomics & Informatics
• /
• v.20 no.1
• /
• pp.12.1-12.7
• /
• 2022

The two complete mitochondrial genomes (mitogenomes) of Paedocypris progenetica, the smallest fish in the world which belonged to the Cyprinidae family, were sequenced and assembled. The circular DNA molecules of mitogenomes P1-P. progenetica and S3-P. progenetica were 16,827 and 16,616 bp in length, respectively, and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The gene arrangements of P. progenetica were identical to those of other Paedocypris species. BLAST and phylogenetic analyses revealed variations in the mitogenome sequences of two Paedocypris species from Perak and Selangor. The circular DNA molecule of P. progenetica yield a standard vertebrate gene arrangement and an overall nucleotide composition of A 33.0%, T 27.2%, C 23.5%, and G 15.5%. The overall AT content of this species was consistent with that of other species in other genera. The negative GC-skew and positive AT-skew of the control region in P. progenetica indicated rich genetic variability and AT nucleotide bias, respectively. The results of this study provide genomic variation information and enhance the understanding of the mitogenome of P. progenetica. They could later deliver highly valuable new insight into data for phylogenetic analysis and population genetics.

• ALGAE
• /
• v.37 no.1
• /
• pp.1-14
• /
• 2022

Cyanobacteria are distributed worldwide, and many new cyanobacterial species are discovered in tropical region. The Nostoc-like genus Amazonocrinis has been separated from the genus Nostoc based on polyphasic methods. However, species diversity within this genus remains poorly understood systematically because only one species (Amazonocrinis nigriterrae) has been described. In this study, two novel strains (NUACC02 and NUACC03) were isolated from moist rice field soil in Thailand. These two strains were characterized using a polyphasic approach, based on morphology, 16S rRNA phylogenetic analysis, internal transcribed spacer secondary structure and ecology. Phylogenetic analyses based on 16S rRNA gene sequences confirmed that the two novel strains formed a monophyletic clade related to the genus Amazonocrinis and were distant from the type species A. nigriterrae. The 16S rRNA gene sequence similarity (<98.1%) between novel strains and all other closely related taxa including the Amazonocrinis members exceeded the cutoff for species delimitation in bacteriology, reinforcing the presence of a new Amazonocrinis species. Furthermore, the novel strains possessed unique phenotypic characteristics such as the presence of the sheath, necridia-like cells, larger cell dimension and akinete cell arrangement in long-chains and the singularity of D1-D1', Box-B, V2, and V3 secondary structures that distinguished them from other Amazonocrinis members. Considering all the results, we described our two strains as Amazonocrinis thailandica sp. nov. in accordance with the International Code of Nomenclature for Algae, Fungi and Plants.

• Journal of Ecology and Environment
• /
• v.47 no.3
• /
• pp.118-133
• /
• 2023

Background: Free-living amoebae (FLA) are widely distributed in freshwater, seawater, soil, and extreme environments, and play a critical role as feeders on diverse preys in the ecosystem. Also, some FLA can become opportunistic pathogens in animals including humans. The taxa Amoebozoa and Heterolobosea are important amoeboid groups associated with human pathogens. However, the identification and habitat of amoebae belonging to Amoebozoa and Heterolobosea remain poorly reported in the Republic of Korea. This study highlights the first record for identification and source of four amoebae including putative pathogens in the Republic of Korea. Results: In the present study, four previously reported FLA were isolated from freshwaters in Sangju Gonggeomji Reservoir (strain GO001), one of the largest reservoirs during the Joseon Dynasty period, and along the Nakdong River, the largest river in the Republic of Korea (strains NR5-2, NR12-1, and NR14-1) for the first time. Microscopic observations and 18S rDNA phylogenetic trees revealed the four isolated strains to be Acanthamoeba polyphaga (strains NR5-2 and NR12-1), Tetramitus waccamawensis (strain GO001), and Naegleria australiensis (strain NR14-1). Strains NR5-2 and NR12-1 might be the same species and belonged to the morphological Group 2 and the T4 genotype of Acanthamoeba. Strain GO001 formed a clade with T. waccamawensis in 18S rDNA phylogeny, and showed morphological characteristics similar to previously recorded strains, although the species' flagellate form was not observed. Strain NR14-1 had the typical morphology of Naegleria and formed a strongly supported clade with previously recorded strains of N. australiensis in phylogenetic analysis of 18S rDNA sequences. Conclusions: On the bases of morphological and molecular analyses, four strains of FLA were newly observed and classified in the Republic of Korea. Three strains belonging to the two species (A. polyphaga and N. australiensis) isolated from the Nakdong River have the potential to act as opportunistic pathogens that can cause fatal diseases (i.e. granulomatous amoebic encephalitis, Acanthamoeba Keratitis, and meningoencephalitis) in animals including humans. The Nakdong River in the Republic of Korea may provide a habitat for potentially pathogenic amoebae, but additional research is required to confirm the true pathogenicity of these FLA now known in the Republic of Korea.

• ALGAE
• /
• v.38 no.4
• /
• pp.253-264
• /
• 2023

The Ceramiales is the most diverse and species-rich group (2,669 spp.) of red algae, and it is widely distributed from tropical to polar oceans. Mitochondrial genomes (mitogenomes) and other genes have contributed to our knowledge regarding the classification and phylogeny of this diverse red algal group; however, the mitogenome architecture remains understudied. Here, we compared 42 mitogenomes, including 19 newly generated in this study, to expand our knowledge. The number of genes in mitogenome varied from 43 to 68 due to gene duplication. The mitogenome architecture was also variable, categorized into four types (A-D): type A = ancestral type with a basic composition; type B = those with inverse transpositions; type C = those with inverted duplications; and type D = those with both inversion and duplication. The palindromic and inverted repeats were consistently found in flanking regions of the rearrangement, especially near the cob and nad6 genes. The three rearranged mitogenome architectures (types B, C, D) are the first report of these in red algae. Phylogenetic analyses of 23 protein-coding genes supported the current familial classification of the Ceramiales, implying that the diversity of mitogenome architecture preceded the phylogenetic relationships. Our study suggests that palindromic and inverted repeats may drive mitogenome architectural variation.

• Journal of Species Research
• /
• v.13 no.3
• /
• pp.318-325
• /
• 2024

Bacterial communities residing on islands have a significant impact on the functioning and establishment of a unique isolated ecosystem. Notwithstanding, systematic research on the indigenous microbial resources of domestic islands has been lacking. In order to understand the biodiversity and potential bioresources, we conducted sampling in 2023 from coastal waters from various islands off the west coast of the Korean Peninsula, including Baengnyeongdo, Daebudo, Deokjeokdo, Jangbongdo, Yeonpyeongdo Islands, along with Somaemuldo Island along the south coast. The coastal seawater samples were used to unearth microbial resources through the standard dilution plating. In total, approximately 1,600 bacterial strains were isolated from the samples as single colonies and identified using 16S rRNA gene sequence analyses. Eighteen strains, exhibiting ≥98.7% 16S rRNA gene sequence similarity to bacterial species with validly published names but not previously reported in Korea, were categorized as unrecorded bacterial species in Korea. These unrecorded bacterial strains displayed phylogenetic diversity, representing three phyla, four classes, 9 orders, 13 families, and 18 genera. The unrecorded species were assigned to the classes Alphaproteobacteria (Aliiroseovarius, Kiloniella, Maritalea, Palleronia, and Roseobacter), Gammaproteobacteria (Aliamphritea, Aliivibrio, Enterovibrio, Francisella, Leucothrix, Pseudoalteromonas, Psychrobium, Shewanella, and Vibrio), Flavobacteriia (Aquimarina, Pseudofulvibacter, and Tenacibaculum), and Verrucomicrobiae (Roseibacillus). This study presents comprehensive descriptions of the taxonomic attributes of these unrecorded species, covering morphology, biochemistry, and phylogenetic position.

• Journal of Life Science
• /
• v.21 no.3
• /
• pp.385-392
• /
• 2011

The otter (Lutra lutra) in Korea is classified as a first grade endangered species and is managed under state control. We performed a phylogenetic analysis of the otter that inhabits the Changnyeong, Jinju, and Geoje areas in Gyeongsangnamdo, Korea using mtDNA and microsatellite (MS) markers. As a result of the analysis using the 676-bp D-loop sequence of mtDNA, six haplotypes were estimated from five single nucleotide polymorphisms. The genetic distance between the Jinju and Geoje areas was greater than distances within the areas, and the distance between Jinju and Geoje was especially clear. From the phylogenetic tree estimated using the Bayesian Markov chain Monte Carlo analysis by the MrBays program, two subgroups, one containing samples from Jinju and the other containing samples from the Changnyeong and Geoje areas were clearly identified. The result of a parsimonious median-joining network analysis also showed two clear subgroups, supporting the result of the phylogenetic analysis. On the other hand, in the consensus tree estimated using the genetic distances estimated from the genotypes of 13 MS markers, there were clear two subgroups, one containing samples from the Jinju, Geoje and Changnyeong areas and the other containing samples from only the Jinju area. The samples were not identically classified into each subgroup defined by mtDNA and MS markers. It could be inferred that the differential classification of samples by the two different marker systems was because of the different characteristics of the marker systems used, that is, the mtDNA was for detecting maternal lineage and the MS markers were for estimating autosomal genetic distances. Nonetheless, the results from the two marker systems showed that there has been a progressive genetic fixation according to the habitats of the otters. Further analyses using not only newly developed MS markers that will possess more analytical power but also the whole mtDNA are needed. Expansion of the phylogenetic analysis using otter samples collected from the major habitats in Korea should be helpful in scientifically and efficiently maintaining and preserving them.