The Yeongsan River is a prominent inland waterway, alongside the Han River, Nakdong River, and Geum River in South Korea. Numerous bacterial strains were isolated from the Yeongsan River basin for a comprehensive investigation into indigenous prokaryotic species conducted between 2020 and 2023. These bacterial strains were identified using 16S rRNA gene sequencing, wherein 45 bacterial strains shared >98.7% sequence similarities with bacterial species not recorded in Korea thus far. Therefore, this study aimed to catalogue aforementioned unrecorded species and characterize them contingent upon their Gram nature, colony and cell morphologies, biochemical properties, and phylogenetic positions. These bacterial species were determined to be phylogenetically diverse. They were categorized into nine classes, 18 orders, and 25 families. These previously unrecorded species were classified into the following genera and classes: Chitinophaga (class Chitinophagia); Flavobacterium (class Flavobacteriia); Rhodopseudomonas, Gemmobacter, Paracoccus, Azospirillum, Sphingomonas, Novosphingobium, Sphingorhabdus, and Erythrobacter (class Alphaproteobacteria); Bordetella, Pararobbsia, Polynucleobacter, Rhodoferax, Aquabacterium, Malikia, Comamonas, Ideonella, Paucibacter, Undibacterium, Cupriavidus, and Thauera (class Betaproteobacteria); Pectobacterium, Arenimonas, Lysobacter, and Luteimonas (class Gammaproteobacteria); Luteolibacter (class Verrucomicrobiia); Mycolicibacterium, Angustibacter, Ornithinibacter, Janibacter, Schumannella, Aurantimicrobium, Luedemannella, Nocardioides, and Propionicimonas (class Actinomycetes); Geothrix (class Holophagae); and Lactococcus (class Bacilli).

As part of the research program “Freshwater Prokaryotic Organisms Research and Discovery,” freshwater samples were collected from the Nakdonggang River. After plating the samples on several culture media and incubating aerobically, approximately 900 bacterial strains were isolated and identified using 16S rRNA gene sequences. Among the bacterial isolates showing higher than 98.7% 16S rRNA gene sequence similarity with those of already confirmed bacterial species previously unreported in Korea, 29 strains were selected. These strains were phylogenetically diverse and belonged to 3 phyla, 6 classes, 13 orders, and 21 genera. At the genus level, these previously unreported species were found to be affiliated with Novosphingobium, Sphingomonas, Polymorphobacter, Croceibacterium, Devosia, Endobacterium, Agaricicola, Bradyrhizobium, Paracoccus, and Pseudotabrizicola of the class Alphaproteobacteria; Undibacterium, Azonexus, and Dechloromonas of the class Betaproteobacteria; Acinetobacter and Budvicia of the class Gammaproteobacteria; Streptomyces, Nocardioides, Mycobacterium, and Cellulomonas of the phylum Actinomycetota; Flavobacterium and Pedobacter of the phylum Bacteroidota. These species were further characterized by examining their Gram reaction, colony and cell morphologies, biochemical properties, and phylogenetic positions. Detailed descriptions of these 29 previously unreported species are provided.

Xenorhabdus와 Photorhabdus 속은 각각 곤충병원성 선충인 Steinernema와 Heterorhabditis에 공생하는 공생세 균이다. 감염성 선충의 유충은 공생세균을 표적 곤충의 혈강에 전달하고, 여기서 세균이 증식하여 숙주 선충의 발달을 돕는다. 이러한 선충과 세균 복합체의 성공적 공생관계는 세균의 이차대사산물을 통한 숙주의 면역억제 에 달려져 있다고 알려져 있다. 본 연구에서는 서로 다른 살충력을 보이는 6종의 Xenorhabdus를 확보하고 이러한 차이가 세균의 성장속도와 NRPS (Non ribosomal peptide synthease)에 의해 생성되는 세균의 이차대사산물 발현에 서 기원한다는 것을 확인하였다. 서로 다른 균주들은 콩명나방 (Tenebrio molitor)에 대한 살충력에 차이를 가지고 있었다. 이러한 세균들은 TSB 배지에서는 세균 성장 속도에 차이가 존재하지 않았지만 콩명나방 혈강 내에서는 세균의 성장 속도에 차이가 존재하는 것으로 나타났다. 또한 각 세균의 이차대사산물 추출물을 통한 곤충의 면역 억제 실험 결과 PLA2 활성 억제, 세포독성 능력들이 살충력과 상관관계가 있는 것으로 나타났다. 이러한 이차대 사산물의 경우 많은 물질이NRPS (Non ribosomal peptide synthease)에 의해 생성되므로 각 세균 별 NRPS의 유전자 발현을 보았을 때 흥미롭게도 살충력이 더 높은 스트레인의 세균이 일부 NRPS 유전자의 발현이 더 높은 것으로 나타났다. NRPS에 의해 합성되는 물질을 포함한 세균의 이차대사산물의 차이를 서로 비교하기 위하여 이차대사 산물 추출액을 GC-MS/MS를 이용하여 분석하였다. 본 연구를 통해 곤충병원세균에 살충력의 기원이 NRPS를 통해 합성되는 이차대사산물에 있다는 것을 확인하였으며 이를 이용한 다양한 NRPS 유래 물질 연구는 신규 살충 물질 개발에 들어가는 비용과 시간을 획기적으로 줄일 수 있을 것으로 기대된다.

This study investigated unrecorded freshwater bacterial species in Korea. Water and sediment samples were collected from the Nakdong River basin from 2020-2022. Bacterial isolates obtained through the conventional culture method with commercial media were subjected to 16S rRNA gene sequencing to identify unrecorded bacterial species. Results of 16S rRNA gene sequencing of the bacterial isolates revealed that a total of 44 bacterial isolates shared 16S rRNA gene sequence similarities of more than 98.65%, with validly published bacterial species not reported in Korea yet. These isolates were phylogenetically assigned to 4 phyla, 7 classes, 21 orders, 33 families, and 42 genera. A total of 2, 6, 12, and 24 species belonged to phyla Bacillota, Bacteroidota, Actinomycetota, and Pseudomonadota, respectively. Here, we provide details of these 44 unrecorded bacterial species, including Gram staining, colony and cellular morphologies, biochemical properties, and phylogenetic position.

In 2022, research for native prokaryotic species in Korea reported 10 unrecorded bacterial strains affiliated to phyla Actinomycetota, Bacillota, and Pseudomonadota. The strains formed monophyletic clades with the most closely related species (with ≥98.7% sequence similarity) in the 16S rRNA gene sequencing. Among them, four species of the phylum Actinomycetota, two species of the phylum Bacillota, and four species of the phylum Pseudomonadota have not been reported in Korea, suggesting unrecorded species in Korea. Information on strains such as Gram staining reaction, colony and cell morphology, biochemical characteristics, and isolation sources were provided in the species description.

A total of 31 bacterial strains were isolated from the Geum River basin in the Republic of Korea during our investigation of indigenous prokaryotic species. The isolated bacterial strains had high 16S rRNA gene sequence similarity (>98.7%) with those of validly published bacterial species, which have not been reported in Republic of Korea. The 31 bacterial strains were phylogenetically diverse and assigned to 4 phyla, 8 classes, 18 orders, 21 families, and 27 genera. At the genus level, the unreported species were affiliated with Kineococcus, Pedococcus, Rhodoluna, Salinibacterium, Rhodoluna, Arthrobacter, Williamsia, Nakamurella, Nocardioides of the class Actinobacteria, Patulibacter of the class Thermoleophilia, Pontibacter, Hymenobacter of the class Cytophagia, Flavobacterium of the class Flavobacteriia, Geomicrobium of the class Bacilli, Brevundimonas, Gellertiella, Rhizobium, Paracoccus, Taonella, Sphingomonas of the class Alphaproteobacteria, Burkholderia, Polaromonas, Hydrogenophaga, Chitinilyticum, Azospira, Zoogloea of the class Betaproteobacteria, and Pseudomonas of the class Gammaproteobacteria. The unreported bacterial species were further characterized by examining their morphological, cultural, physiological, and biochemical properties. The detailed descriptions of the 31 bacterial strains were provided.

Suncheon Bay Ecological Park, possessing abundant fisheries and biological diversity, was registered as a Ramsar wetland in Korea. Approximately 300 bacterial strains were isolated from the Suncheon Bay in a comprehensive study of indigenous prokaryotic species conducted during 2019-2020 in South Korea. A total of 12 bacterial strains were identified using 16S rRNA gene sequencing, demonstrating >98.7% sequence similarity with validly published species. These species were determined to be unrecorded bacterial species in Korea. A total of six strains were isolated from brackish water and Phragmites communis Trin (reed) species. These unrecorded species were phylogenetically diverse and belonged to three classes, six orders, and ten genera. Regarding the genus and class levels, the previously unrecorded species belonged to Jiella, Martelella, Rhizobium, Paracoccus, Rhodovulum, and Altererythrobacter of the class Alphaproteobacteria; Mycolicibacterium, Demequina, and Microbacterium of the class Actinobacteria; Confluentibacter of the class Flavobacteria. The twelve species were further characterized by gram staining, colony and cell morphology, biochemical properties, and phylogenetic position.

Nine fish and one clam species were collected from freshwater environments in Korea, including four lakes, two streams, and the Nakdong River, to investigate the host-associated bacteria. Hundreds of bacterial strains were isolated from the samples using a cell sorter and a dilution plating method. After identification of the bacterial strains using 16S rRNA gene sequences, 42 strains with greater than 98.7% sequence similarity with validly published species were determined to be unrecorded bacterial species in Korea. These strains were phylogenetically diverse and assigned to four phyla, six classes, 17 orders, 27 families, and 32 genera. At the genus level, the unrecorded species were classified as Corynebacterium, Mycobacterium, Mycolicibacterium, Gordonia, Williamsia, Modestobacter, Brachybacterium, Sanquibacter, Arthrobacter, and Mycolicibacterium of the class Actinobacteria; Empedobacter, and Flavobacterium of the class Flavobacteriia; Fictibacillus, Psychrobacillus, Cohnella, Paenibacillus, Rummeliibacillus, Enterococcus, and Vagococcus of the class Bacilli; Aquamicrobium, Paracoccus, and Sphingomonas of the class Alphaproteobacteria; Achromobacter, Delftia, and Deefgea of the class Betaproteobacteria; and Aeromonas, Providencia, Yersinia, Marinomonas, Acinetobacter, and Pseudomonas of the class Gammaproteobacteria. The 42 unrecorded species were subjected to further taxonomic characterization using gram staining, cellular and colony morphological determination, biochemical analyses, and phylogenetic analyses. This paper provides detailed descriptions of the 42 previously unrecorded bacterial species.

As part of the research program “2018 Rapid screening and identification of freshwater microorganisms using MALDI-TOF/MS library” freshwater samples were collected from a branch of the Nakdong River. Almost 300 antibiotic-resistant bacterial strains were isolated from freshwater samples and subsequently identified by 16S rRNA gene sequencing. Seventeen strains among the isolates shared high 16S rRNA gene sequence similarity (>99.0%) with known species that were not previously recorded in Korea, and each of the isolates also formed a robust phylogenetic clade with the closest species. These species were phylogenetically diverse, belonging to four phyla, seven classes, 10 orders, and 13 genera. At the genus and class level, the previously unrecorded species belonged to Rhodovarius, Xanthobacter, and Shinella of the class Alphaproteobacteria; Ottowia, Simplicispira, and Zoogloea of Betaproteobacteria; Pseudomonas, Acinetobacter, and Shewanella of Gammaproteobacteria; Arcobacter of Epsilonproteobacteria; Sphingobacterium of Sphingobacteriia; Trichococcus of Bacilli; and Leucobacter of Actinobacteria. The previously unrecorded species were further characterized by examining their gram-staining, colony and cell morphology, biochemical properties, and phylogenetic position.

Ostrea denselamellosa and Eriocheir japonica samples were collected from the Seomjin River in 2019 as part of the “Research of Host-Associated Bacteria” research program. Almost 200 bacterial strains were isolated from the O. denselamellosa and E. japonica samples and subsequently identified by 16S rRNA gene sequencing. Among the bacterial isolates, ten strains possessed greater than 98.7% sequence similarity with published bacterial species that had not previously been recorded in Korea. These species were phylogenetically diverse, belonging to three phyla, four classes, seven orders, and eight genera. At the genus and class level, the previously unrecorded species belonged to Pseudoalteromonas, Aliivibrio, Rheinheimera, Leucothrix, and Shewanella of the class Gamma-proteobacteria, Olleya of the class Flavobacteriia, Algoriphagus of the class Cytophagia, and Lactococcus of the class Bacilli. The previously unrecorded species were further characterized by examining their Gram staining, colony and cell morphology, biochemical properties, and phylogenetic positions.

The purpose of this study was to identify the oral bacterial species in sequestra from patients with bisphosphonate-related osteonecrosis of the jaw (BRONJ). Fifteen patients with BRONJ (2 males and 13 females) were evaluated. Clinical features, radiographic findings, and bisphosphonate intake history were investigated. All patients were treated with surgical methods (curettage or sequestrectomy). Infected bone samples were collected from the affected BRONJ site. Ten bacterial species were selected for polymerase chain reaction (PCR) detection. Two to nine bacterial species were detected by PCR. Gram-negative species were predominant and all identified bacteria were anaerobes. Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola were detected at high levels. These are major pathogenic species in periodontal disease. Orthopantomographic radiographs showed generalized alveolar bone loss in most patients. These radiographic findings may provide evidence of chronic periodontitis as a pre-existing inflammatory disease. Most patients had experienced a predisposing dental procedure, such as tooth extraction. Sequestra (necrotic bone) infected with oral bacterial species may be an important risk factor for BRONJ. As such, prevention and management of BRONJ may rely on effective control of bacteria in the oral cavity.

Pine trees are ecologically important in Korea. They are seriously imperiled by Pine wilt disease (PWD), by pine wood nematode (PWN, Bursaphelenchus xylophilus). Here, we isolated and characterized bacterial endophytes (BEs) from pine trees in Korea for biological control of PWN using BE metabolites. Using culture-dependent approach BE isolates were extracted from three tissues (needles, stems, and roots) of four pine species across 18 sampling sites in Korea. Bacterial isolates were characterized into 389 distinct isolates based on 16S rDNA sequencing. Ethyl acetate crude extracts (CEs) of bacterial liquid cultures were prepared using ethyl acetate and screened for nematicidal activity against PWN. BEs (1,622 isolates) were isolated; their taxonomic binning resulted in 215 operational taxonomic units (OTUs). Analysis of species richness and Shannon’s diversity of the three tissues revealed that BEs colonized the needles more than the stem and root tissues. Furthermore, based on nematicidal activity screening of 389 isolates, 44 BEs were identified, with two isolates exhibiting a significant inhibitory activity against PWN. Taken together, these data revealed numerous nematicidal BEs in pine trees, providing new insights that can serve as an effective and promising alternative approach to combat PWD.

Recurrent aphthous stomatitis (RAS) is a common oral mucosal disorder for which no curative treatment is available. We previously reported that decreased Streptococcus salivarius and increased Acinetobacter johnsonii on the oral mucosa are associated with RAS risk. The purpose of this study was to identify antibiotics that selectively inhibit A. johnsonii but minimally inhibit oral mucosal commensals. S. salivarius KCTC 5512, S. salivarius KCTC 3960, A. johnsonii KCTC 12405, Rothia mucilaginosa KCTC 19862, and Veillonella dispar KCOM 1864 were subjected to antibiotic susceptibility test using amoxicillin, cefotaxime, gentamicin, clindamycin, and metronidazole in liquid culture. The minimal inhibitory concentration (MIC) was defined as the concentration that inhibits 90% of growth. Only gentamicin presented a higher MIC for A. johnsonii than MICs for S. salivarius and several oral mucosal commensals. Interestingly, the growth of S. salivarius increased 10~200% in the presence of sub-MIC concentrations of gentamicin, which was independent of development of resistance to gentamicin. In conclusion, gentamicin may be useful to restore RAS associated imbalance in oral microbiota by selectively inhibiting the growth of A. johnsonii but enhancing the growth of S. salivarius.

Toothbrushes play an essential role in oral hygiene. However, they can be significant in microbial transmission and can increase the risk of infection, since they can serve as a reservoir for microorganisms in healthy, oral-diseased and medically ill adults. This study was conducted to evaluate toothbrush contamination in six toothbrushes donated from four people. Two participants each supplied two toothbrushes - one used in the bathroom and one used in the workplace. The other two people each donated two toothbrushes used in the workplace. Polymerase chain reaction was used to construct a 16S rRNA clone library. Sequences of cloned DNA were compared with those from the reference organisms provided by GenBank. A total 120 clones, representing 20 clones for each toothbrush, were analyzed. They are composed of six pylum, 46 genera and 79 species. The most dominant species were Streptococcus oralis, Streptococcus parasanguinis and Haemophilus parainfluenzae. Enterobacter and Escherichia were recovered from toothbrushes used domestically. Toothbrushes used in the workplace did not contain Enterobacteria.

This study was carried out to measure temperature, humidity, and bacterial concentration and species from the indoor air of a greenhouse used for shiitake cultivation. The highest level of humidity in the greenhouse was recorded at over 91.5% and the lowest humidity was recorded at 50% during 12 months. Temperature was between 5.1-30.5oC except for January. These results indicate that bacteria can survive in the indoor air of the greenhouse. Total bacterial concentration exceeded the Korean indoor air quality standard value (8.0 × 102 cfu/m3) in winter. A total of 13 genera and 17 species were isolated and identified from the indoor air of the greenhouse. Especially, 3 species (Kocuria rosea, Staphylococcus xylosus and Curtobacterium flaccumfaciens) have been reported to affect on human health. This is first report of airborne bacteria in a greenhouse used for shiitake cultivation.

LIVE/DEAD® BacLight™ and alamarBlue® are fluorescent materials used for the enumeration of live and dead bacteria. LIVE/DEAD® BacLight™ is generally used for confocal microscopy applications to differentiate live from dead bacteria in a biofilm or planktonic state. AlamarBlue® has also been used widely to assay live and dead bacteria in a planktonic state. Whilst these materials are successfully utilized in experiments to discriminate live from dead bacteria for several species of bacteria, the application of these techniques to oral bacteria is limited to the use of LIVE/DEAD® BacLight™ in biofilm studies. In our present study, we assessed whether these two methods could enumerate live and dead oral bacterial species in a planktonic state. We tested the reagents on Streptococcus mutans, Streptococcus sobrinus, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans and Enterococcus faecalis and found that only LIVE/DEAD® BacLight™ could differentiate live from dead cells for all five of these oral strains. AlamarBlue® was not effective in this regard for P. gingivalis or A. actinomycetemcomitans. In addition, the differentiation of live and dead bacterial cells by alamarBlue® could not be performed for concentrations lower than 2 × 106 cells/ml. Our data thus indicate that LIVE/DEAD® BacLight™ is a more effective reagent for this analysis.

The electron transport chain (ETC) delivers electrons from many substrates to reduce molecular oxygen to water. ETC accomplishes the stepwise transfer of electrons through series of protein complexes conferring oxidation‐reduction reactions with concomitant transport of p roton across membrane, g enerating a proton g radient which leads ATP s ynthesis b y F0F1ATPase. Bacterial ETC initiates with oxidation of NADH by NADH dehydrogenase complex (complex I). Therefore, damage of complex I leads to insufficient function of ETC and accumulation of NADH inside the cell. Contribution of ETC activity and its consequent changes of NADH levels to bacterial damage response against reactive oxygen and nitrogen species (ROS/RNS) has been poorly understood. In this study, by constructing ndh mutant Salmonella lacking complex I NADH dehydrogenase 2, we evaluated the effect of ETC deficiency to bacterial resistance against ROS and RNS. The growth of ndh mutant Salmonella is impaired in the culture media containing hydrogen peroxide, but rather accelerates in the media containing nitric oxide donors. Data suggest that redox potential of NADH accumulated inside the cell by ETC blockage may affect inversely to bacterial resistance against reactive oxygen species and reactive nitrogen species.

인위적으로 pH 구배가 조성된 회분배양 시스템 (batch culture system)내에서 산성화에 따른 종속영양 세균 군집의 종조성 변화를 분석하였다. 총세균의 개체수는 산성화에 영향을 받지 않았으며, 종속영양세균 군집의 크기는 pH가 낮아질수록 감소하였다. 전 pH구간에서 분리된 종속영양 세균들은 모두 12속 22종으로 나타났으며, 이중 그람음성 세균은 64%,그람양성 세균은 36%의 비율로 분포하였다. pH가 낮아짐에 따라 그람양성 세균의 분포

In this study, the amount of harmful fungi and bacteria contained in the drainage and culture medium from the paprika hydroponic facility is identified. In addition, by proposing the necessity of effective purification of discharged drainage, this study attempted to confirm the possibility of drainage reuse. Finally, this study provides basic data on the basis for calculating the need for purification facilities in the future, as well as improvements in horticulture facility for sustainable agriculture. As a result of the analysis, a total of 12 types of fungi were detected in paprika medium and 10 types of fungi were detected in the drainage, and their densities were 130 and 68, respectively. Among the fungi detected in the media and drainage of the paprika hydroponic facility, the fungi with the highest detection frequency are Fusarium, Phytophthora, and Pythium. In the case of bacteria, a total of 2 types of bacteria were detected in the paprika facilities, and the density was 28 and 23, respectively. Therefore, in order to reuse the drainage and settle the circulating hydroponic cultivation system, a water treatment process capable of appropriate treatment is required.