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Two novel bacterial species CJ51 T and CJ63 T belonging to the genus Chryseobacterium were isolated from the Upo wetland and the Han River, South Korea, respectively. Cells of these strains were Gram-stain-negative, aerobic, non-motile, rod-shaped, and catalase- and oxidase-positive. Both strains were shown to grow optimally at 30 °C and pH 7 in the absence of NaCl on tryptic soy agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ51 T and CJ63 T belonged to the genus Chryseobacterium and were most closely related to Chryseobacterium piperi CTM T and Chryseobacterium piscicola VQ-6316s T with 98.47% and 98.46% 16S rRNA sequence similarities, respectively. The average nucleotide identity values of strains CJ51 T and CJ63 T with its closely related type strains Chryseobacterium piperi CTM T and Chryseobacterium piscicola VQ-6316s T were 81.9% and 82.1%, respectively. The major fatty acids of strains CJ51 T and CJ63 T were iso-C 15:0 , iso-C 17:0 3-OH and summed feature 9 (C 16:0 10-methyl and/or iso-C 17:1 ω9c). Menaquinone 6 (MK-6) was identified as the primary respiratory quinone in both strains. The major polar lipids of strains CJ51 T and CJ63 T were phosphatidylethanolamine and several unidentified amino lipids and lipids. Based on polyphasic taxonomy data, strains CJ51 T and CJ63 T represent novel species of the genus Chryseobacterium, for which names Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. are proposed respectively. The type strains are CJ51 T (= KACC 22749 T  = JCM 35632 T ) and CJ63 T (= KACC 22750 T  = JCM 35633 T )., (© 2023. The Author(s), under exclusive licence to Microbiological Society of Korea.)

Background: There is an increasing interest in HER2-low breast cancer with promising data from clinical trials using novel anti-HER2 antibody-drug conjugates. We explored the differences in clinicopathological characteristics and survival outcomes between HER2-low and HER2-IHC 0 breast cancer., Methods: Using nationwide data from the Korean Breast Cancer Registry between 2006 and 2011, 30,491 patients with stages I to III breast cancer were included in the analysis: 9,506 (31.2%) in the HER2-low group and 20,985 (68.8%) in the HER2-IHC 0 group. Kaplan-Meier and Cox proportional hazards regression survival analysis were used to compare breast cancer-specific survival between the two groups., Results: HER2-low breast cancer was more frequent in patients with hormone receptor-positive breast cancer than in those with triple-negative breast cancer. In patients with hormone receptor-positive breast cancer, HER2-low breast cancer was associated with fewer T4 tumors, higher histological grade, and a negative lymphatic invasion. In patients with triple-negative breast cancer, HER2-low breast cancer was associated with a high lymph node ratio and positive lymphatic invasion. HER2-low breast cancer was significantly associated with a lower Ki-67 labeling index. No significant difference was observed in overall survival between the two groups. HER2-low breast cancer showed significantly better breast cancer-specific survival than HER2-IHC 0 breast cancer, regardless of the hormone receptor status. In multivariate analysis, the impact of low HER2 expression on breast cancer-specific survival was significant only in triple-negative breast cancer (HRs, 0.68; 95% CI, 0.49-0.93; P = 0.019)., Conclusions: These findings suggest that the biology and clinical impact of low HER2 expression can differ according to the hormone receptor status and support the need for further investigation on the understanding of the biology of HER2-low breast cancer., (© 2022. The Author(s).)

A Gram-stain-negative, aerobic, short rod-shaped, pale yellow-pigmented, non-motile and gentamycin-resistant bacterial strain designated CJ210 T was isolated from the Han River, Republic of Korea. Strain CJ210 T grew optimally at 30 °C and pH 7.0 in the absence of NaCl on tryptic soy agar. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain CJ210 T belonged to the genus Myroides within the family Flavobacteriaceae and was most closely related to Myroides odoratus KACC 14347 T (98.1 % similarity), followed by M. injenensis KCTC 23367 T (95.3 % similarity). The average nucleotide identity values between strain CJ210 T and two closely related type strains M. odoratus KACC 14347 T and M. injenensis KCTC 23367 T were 83.7 and 73.8 %, respectively. The digital DNA-DNA hybridization results between strain CJ210 T and the related type strains were 27.5 and 20.2 %, respectively. Strain CJ210 T contained menaquinone 6 (MK-6) as the predominant menaquinone. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. The major fatty acids of strain CJ210 T were iso-C 15 : 0 , iso-C 17 : 0 3-OH and summed feature 9 (comprising iso-C 17 : 1  ω 9 c and/or C 16 : 0 10-methyl). Whole genome sequencing revealed that strain CJ210 T had a genome of 3.8 Mbp with 36.5 % DNA G+C content. The genome contained several antimicrobial resistance genes including an aminoglycoside-resistant gene. On the basis of the polyphasic taxonomic study, strain CJ210 T represents a novel species in the genus Myroides , for which name Myrodies fluvii sp. nov. is proposed. The type strain is CJ210 T (=KACC 19954 T =JCM 33306 T ).

Purpose: The prognosis of patients with node-negative T1b tumors according to human epidermal growth factor receptor 2 (HER2) status is not known. This group of patients has not been studied in the available randomized trials. The objective of this study was to evaluate the survival of patients in a monoethnic group diagnosed with T1b lymph node-negative breast cancer depending on HER2 status., Methods: We analyzed 3110 patients with T1bN0M0 breast cancer whose data were deposited into the Korean Breast Cancer Society Registry database between 2000 and 2009. Overall survival (OS) and breast cancer-specific survival (BCSS) were compared according to HER2 status., Results: Among all patients, 494 (15.9%) had HER2-positive breast cancer. At a mean follow-up of 93 months, 108 deaths and 86 breast cancer-specific deaths were noted among all patients. There was no significant difference in OS between the HER2-negative and HER2-positive groups (p = 0.103). The same result was observed for BCSS. However, in the subgroup of estrogen receptor (ER)-positive women, HER2-negative patients had a better BCSS prognosis than HER2-positive patients (p = 0.025). Multivariate analysis also indicated a significant difference in BCSS in the ER-positive subgroup (HR 2.60; 95% CI 1.15-5.87; p = 0.021)., Conclusion: This study analyzed a large nationwide and monoethnic cohort and found a significant difference only in BCSS in the ER-positive subgroup according to HER2 status. Anti-HER2 therapy may be considered in HER2-positive and ER-positive patients with small, node-negative breast cancer.

To assess distribution of metal contamination and grain size in the sediments of Nakdong River (South Korea), surface sediments were collected from 21 sites and analyzed. Within the study area, sand was typically the dominant grain size. However, because of the reduced flow rate and flow velocity, sites adjacent to weirs were composed of relatively fine sediments. A comparison of sediment metal concentrations with sediment quality guidelines proposed by the USA, Canada, and South Korea revealed that sites adjacent to weirs had concentrations that exceeded the standard values. The enrichment factor, index of geo-accumulation, and pollution load index calculation results that the sites adjacent to weirs showed high contamination, with Cd accounting for the highest contamination levels. The metals in the study area varies due to the effect of fine sediments; therefore, high concentrations of metals accumulated adjacent to weirs where fine sediments were distributed in greater proportions. Furthermore, Cd exhibited the greatest contribution to metal contamination in the study area and the highest contamination levels were found at NS19 (adjacent to the Haman weir). Thus, the accumulation of fine sediment increased due to the influence of the weirs, thereby increasing the overall amount of metal contamination.

This study aimed to select rivers of priority management through the assessment of heavy metal pollution of sediments. We investigated the distribution characteristics of heavy metals in surface sediments of the Nakdong River in South Korea and used various pollution indices to assess pollution risk and identify factors influencing pollution. The kriging method was used to determine heavy metal distribution. The pollution load index, potential ecological risk index, mean PEL quotient, and the Canada Council of Ministers of the Environment sediment quality index were used as sediment pollution assessment methods. The toxicity evaluation was performed on sites that appeared to be contaminated, by applying existing methods for assessing sediment pollution level and the national standards for evaluating the pollution level. The toxicity test was performed on Hyalella azteca, and a methodology for assessing sediment pollution level was proposed. Ecotoxicity was assessed at seven sites that were found to have heavy metal contaminants. The results showed that sites N1, N8, T28, and T29 were not toxic, while T8, T19, and T21 were. Thus, this study shows that high heavy metal pollution does not necessarily lead to a toxic environment. To assess sediment pollution, an additional assessment of toxicity should be made, along with assessments of existing sediment pollution. Our results demonstrate that streams showing high sediment pollution levels should be granted priority in management. The efforts should particularly focus on Cu at T8, Cr at T19, and Hg at T21.

Background: The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthropogenically impacted environments is just a result of contamination by resistant fecal microbes or is mediated by indigenous environmental organisms. Here, to determine exactly how anthropogenic influences shape the environmental resistome, we resolved the microbiome, resistome, and mobilome of the planktonic microbial communities along a single river, the Han, which spans a gradient of human activities., Results: The bloom of antibiotic resistance genes (ARGs) was evident in the downstream regions and distinct successional dynamics of the river resistome occurred across the spatial continuum. We identified a number of widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile genetic elements rather than particular gut taxa and mainly responsible for anthropogenically driven bloom of the downstream river resistome. Furthermore, both sequence- and phenotype-based analyses revealed environmental relatives of clinically important proteobacteria as major carriers of these ARGs., Conclusions: Our results demonstrate a more nuanced view of the impact of anthropogenic activities on the river resistome: fecal contamination is present and allows the transmission of ARGs to the environmental resistome, but these mobile genes rather than resistant fecal bacteria proliferate in environmental relatives of their original hosts. Video abstract.

Purpose: The aim of this study was to investigate the therapeutic efficacy of adjuvant modalities for elderly Asian breast cancer patients using population-based data from the Korean Breast Cancer Registry database., Methods: We identified 53,582 patients who underwent curative surgery between January 2005 and December 2010. The primary end point was the comparison of overall survival between the administration or omission of adjuvant treatment modalities, including endocrine treatment, radiation therapy, and chemotherapy, in the elderly group (older than 75 years) compared with the control group (younger than 75 years)., Results: Of the 53,582 patients analyzed, the total number of elderly patients was 901 (1.7%), and the number of control patients was 52,681 (98.3%). Although elderly patients were found to have larger tumor sizes (p = 0.024) and higher pathological stages (p < 0.001) than the control group, elderly patients were less likely to undergo adjuvant treatment compared to the control group. However, use of endocrine treatment in elderly patients with HR-positive breast cancer is associated with improved overall survival (OS) (adjusted OR 0.417; 95% confidence interval [CI] 0.240-0.726; p = 0.002). Furthermore, chemotherapy was associated with a significant improvement in OS in patients with stage II and III breast cancer (adjusted OR 0.657; 95% CI 0.462-0.934; p = 0.019)., Conclusion: Endocrine treatment and chemotherapy for elderly patients are associated with improved OS. Therefore, personalized decision-making based on the potential survival benefit of adjuvant treatment modalities should be made with the careful counseling of all elderly patients with breast cancer.

This study aimed to develop methods for assessing and identifying nitrogen sources in the Cheongmi River, Korea, that has intensive livestock farming areas (ILFA) in its watershed. The assessment focused on the feasibility of the simultaneous use of stable isotopic compositions of ammonium (δ 15 N NH4 ) and nitrate (δ 15 N NO3 ) for identifying the main nitrogen pollution sources in the Cheongmi River watershed. Our results suggested that the organic nitrogen (Org-N) to total nitrogen (T-N) ratio could be used as an indicator for assessing the effect of livestock excreta on waterways in ILFA. We observed that the T-N concentration was much more strongly affected by livestock excreta than the T-P concentration in the mainstream of the Cheongmi River. The positive correlation was more significant between δ 15 N NH4 and NH 4 -N than that between δ 15 N NO3 and NO 3 -N for river water samples. Furthermore, the use of δ 15 N NH4 was more effective than that of δ 15 N NO3 in evaluating nitrogen variations between May and August in the Cheongmi River because the differences in δ 15 N NH4 between May and August were more remarkable compared to those in δ 15 N NO3 . Finally, the simultaneous use of δ 15 N NH4 and δ 15 N NO3 showed that the dominant nitrogen source at sites M3, M4, M5, and M6, specifically in May, was livestock excreta in the Cheongmi River. The results of this study could be used for sustainable water quality management in the Cheongmi River watershed.

A Gram-stain-variable, aerobic, rod-shaped, motile and spore-forming bacterial strain, designated CJ11 T , was isolated from a tidal flat sediment sample from Ganghwa-do, Republic of Korea. Strain CJ11 T grew optimally on R2A at 30 °C and pH 7.0. Sequencing results of the 16S rRNA gene revealed that strain CJ11 T possesses two copies of the 16S rRNA gene varying at five nucleotide positions. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CJ11 T belonged to the genus Paenibacillus within the family Paenibacillaceae and was most closely related to Paenibacillus lacus KCTC 33691 T (99.36-99.15 % similarity). DNA-DNA relatedness levels of strain CJ11 T was 41.7 % (reciprocal, 57.8 %) to P. lacus KCTC 33691 T . The G+C content of the genomic DNA was 51.0 mol%. Strain CJ11 T contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major isoprenoid quinone was menaquinone-7. The major cellular fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, an unidentified glycolipid and several unidentified lipids. On the basis of the polyphasic taxonomic study, strain CJ11 T represents a novel species in the genus Paenibacillus, for which the name Paenibacillustranslucens sp. nov. is proposed. The type strain is CJ11 T (=KACC 19304 T =JCM 32080 T ).

Background: Intestinal microbiota play an important role in maintaining the homeostasis of the host immune system. To analyze the alteration of the intestinal microbial community structure in Korean Crohn's disease (CD) patients, we performed a comparative metagenomic analysis between healthy people and CD patients using fecal samples and mucosal tissues of ileocecal valve., Methods: 16S rRNA genes from fecal samples or mucosal tissues of 35 CD patients and 15 healthy controls (HC) were amplified using a universal primer set and sequenced with GS FLX Titanium. The microbial composition and diversity of each sample were analyzed with the mothur pipeline, and the association between microbial community and clinical characteristics of the patients were investigated., Results: The contribution of bacterial groups to the intestinal microbial composition differed between CD and HC, especially in fecal samples. Global structure and individual bacterial abundance of intestinal microbial community were different between feces and ileocecal tissues in HC. In CD patients with active stage, relative abundances of Gammaproteobacteria and Fusobacteria were higher in both fecal and mucosal tissue samples. Moreover, the intestinal microbial community structure was altered by anti-tumor necrosis factor (anti-TNF) treatment., Conclusions: Our 16S rRNA sequence data demonstrate intestinal dysbiosis at the community level in Korean CD patients, which is similar to alterations of the intestinal microbial community seen in the western counterparts. Clinical disease activity and anti-TNF treatment might affect the intestinal microbial community structure in CD patients.

Background/aim: The natural course of hepatitis B virus (HBV) infection is likely related to host immune factors. Interleukin-18 (IL-18) plays a significant role in immune defense. This study was undertaken to determine the association between the presence of hepatocellular carcinoma (HCC) and single-nucleotide polymorphisms (SNPs) in the IL-18 gene in HBV-infected patients., Methods: Between March 2002 and December 2004, 730 Korean subjects were enrolled in two different groups: (1) chronic carrier without HCC (n=637) and (2) HCC (n=93). We analyzed SNPs at four polymorphic sites in the IL-18 gene at positions -667G>T, -148G>C, +8925C>G, and +13925A>C in the study subjects. To evaluate the functional significance of SNPs in the IL-18 gene promoter region, we performed a reporter gene assay in HepG2 and Hep3B cells transfected with different alleles., Results: The IL-18 -148C allele, +8925G allele, +13925C allele, and haplotype 3 (TCGC) were associated with the presence of HCC in codominant and dominant models. Furthermore, functional analyses using the reporter gene assay revealed that the -148C allele conferred significantly lower promoter activity., Conclusions: This study indicates that the -148C, +8925G, and +13925C alleles of the IL-18 gene are associated with the presence of HCC and the 148G>C SNP is functionally important in determining disease outcome., (© Springer Science+Business Media, LLC 2009)