• Journal of Ginseng Research
• /
• v.40 no.2
• /
• pp.97-104
• /
• 2016

Background: Rhizobacteria play an important role in plant defense and could be promising sources of biocontrol agents. This study aimed to screen antagonistic bacteria and develop a biocontrol system for root rot complex of Panax notoginseng. Methods: Pure-culture methods were used to isolate bacteria from the rhizosphere soil of notoginseng plants. The identification of isolates was based on the analysis of 16S ribosomal RNA (rRNA) sequences. Results: A total of 279 bacteria were obtained from rhizosphere soils of healthy and root-rot notoginseng plants, and uncultivated soil. Among all the isolates, 88 showed antagonistic activity to at least one of three phytopathogenic fungi, Fusarium oxysporum, Fusarium solani, and Phoma herbarum mainly causing root rot disease of P. notoginseng. Based on the 16S rRNA sequencing, the antagonistic bacteria were characterized into four clusters, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetesi. The genus Bacillus was the most frequently isolated, and Bacillus siamensis (Hs02), Bacillus atrophaeus (Hs09) showed strong antagonistic activity to the three pathogens. The distribution pattern differed in soil types, genera Achromobacter, Acidovorax, Brevibacterium, Brevundimonas, Flavimonas, and Streptomyces were only found in rhizosphere of healthy plants, while Delftia, Leclercia, Brevibacillus, Microbacterium, Pantoea, Rhizobium, and Stenotrophomonas only exist in soil of diseased plant, and Acinetobacter only exist in uncultivated soil. Conclusion: The results suggest that diverse bacteria exist in the P. notoginseng rhizosphere soil, with differences in community in the same field, and antagonistic isolates may be good potential biological control agent for the notoginseng root-rot diseases caused by F. oxysporum, Fusarium solani, and Panax herbarum.

• Korean Journal of Microbiology
• /
• v.37 no.1
• /
• pp.1-8
• /
• 2001

Spiders are carnivores that prey upon insects and other small arthropods through digestion of food outside the body. Although spider poison may contain proteolytic enzymes, these are thought to play an insignificant role in actual digestion. The source of active proteolytic enzymes can be either the digestive tract cells of spider, or natural microbial flora in the digestive tract of spider. In this study, digestive tracts from the spider, Nephila clavata, were screened for bacteria that have protease or lipase activity. A total of $10^3-10^5$ CFU was recovered from a spider and more than 90% of them showed protease and lipase activity respectively. Of the microbial isolates, 63.3% showed protease or lipase activity, and 50% of these showed both protease and lipase activity. Some of the isolates were characterized using a battery of chemical, phenotypic and genotypic methods. Eleven Gram negative bacteriaa (Acinetobacter calcoaceticus, A. haemolyticus, Alcaligenes faecalis, Cedecea davisae, C. neteri, Klebsiella pneumoniae, Proteus vulgaris, Pseudomonas fluorescens, Serratia marcescens, Stenotrophomonas maltophilia, Suttonella indologenes) and 11 Gram positive bacteria (Bacillus cereus, B. coagulans, B. pasteurii, B. thuringiensis, Cellulomonas flavigena, Corynebacterium martruchotii, Enterococcus durans, E. faecalis, Micrococcus luteus, Staphylococcus hominis, S. sciuri) were identified.

• Journal of Microbiology and Biotechnology
• /
• v.31 no.10
• /
• pp.1409-1419
• /
• 2021

A growing number of healthy dietary ingredients in fruits and vegetables have been shown to exhibit diverse biological activities. Phloretin, a dihydrochalcone flavonoid that is abundant in apples and pears, has anti-inflammatory effects on ulcerative colitis (UC) mice. The gut microbiota and metabolism are closely related to each other due to the existence of the food-gut axis in the human colon. To investigate the interplay of faecal metabolites and the microbiota in UC mice after phloretin treatment, phloretin (60 mg/kg) was administered by gavage to ameliorate dextran sulfate sodium (DSS)-induced UC in mice. Gut microbes and faecal metabolite profiles were detected by high-throughput sequencing and liquid chromatography mass spectrometry (LC-MS) analysis, respectively. The correlations between gut microbes and their metabolites were evaluated by Spearman correlation coefficients. The results indicated that phloretin reshaped the disturbed faecal metabolite profile in UC mice and improved the metabolic pathways by balancing the composition of faecal metabolites such as norepinephrine, mesalazine, tyrosine, 5-acetyl-2,4-dimethyloxazole, and 6-acetyl-2,3-dihydro-2-(hydroxymethyl)-4(1H)-pyridinone. Correlation analysis identified the relations between the gut microbes and their metabolites. Proteus was negatively related to many faecal metabolites, such as norepinephrine, L-tyrosine, laccarin, dopamine glucuronide, and 5-acetyl-2,4-dimethyloxazole. The abundance of unidentified Bacteriodales_S24-7_group was positively related to ecgonine, 15-KETE and 6-acetyl-2,3-dihydro-2-(hydroxymethyl)-4(1H)-pyridinone. The abundance of Christensenellaceae_R-7_group was negatively related to the levels of 15-KETE and netilmicin. Stenotrophomonas and 15-KETE were negatively related, while Intestinimonas and alanyl-serine were positively related. In conclusion, phloretin treatment had positive impacts on faecal metabolites in UC mice, and the changes in faecal metabolites were closely related to the gut microbiota.

• Journal of Microbiology and Biotechnology
• /
• v.34 no.8
• /
• pp.1617-1626
• /
• 2024

Various antibiotic-resistant bacteria (ARB) are known to induce repeated pulmonary infections and increase morbidity and mortality. A thorough knowledge of antibiotic resistance is imperative for clinical practice to treat resistant pulmonary infections. In this study, we used a reads-based method and an assembly-based method according to the metagenomic next-generation sequencing (mNGS) data to reveal the spectra of ARB and corresponding antibiotic resistance genes (ARGs) in samples from patients with pulmonary infections. A total of 151 clinical samples from 144 patients with pulmonary infections were collected for retrospective analysis. The ARB and ARGs detection performance was compared by the reads-based method and assembly-based method with the culture method and antibiotic susceptibility testing (AST), respectively. In addition, ARGs and the attribution relationship of common ARB were analyzed by the two methods. The comparison results showed that the assembly-based method could assist in determining pathogens detected by the reads-based method as true ARB and improve the predictive capabilities (46% > 13%). ARG-ARB network analysis revealed that assembly-based method could promote determining clear ARG-bacteria attribution and 101 ARGs were detected both in two methods. 25 ARB were obtained by both methods, of which the most predominant ARB and its ARGs in the samples of pulmonary infections were Acinetobacter baumannii (ade), Pseudomonas aeruginosa (mex), Klebsiella pneumoniae (emr), and Stenotrophomonas maltophilia (sme). Collectively, our findings demonstrated that the assembly-based method could be a supplement to the reads-based method and uncovered pulmonary infection-associated ARB and ARGs as potential antibiotic treatment targets.

• Korean Journal of Soil Science and Fertilizer
• /
• v.35 no.2
• /
• pp.118-126
• /
• 2002

To evaluate the correlations of microbial populations with soil healthiness and crop production and establish the criteria for microbial population of soil types. We analyzed the microbial community structure of 13 soils which were different in physical and chemical properties and cultivation methods. According to the analysis of microbial population suing the dilution plate method, the large differences of the microbial population structures among soil types were shown: aerobic bacteria $2-27{\times}10^6$, fluorescent Pseudomonas $1-1,364{\times}10^5$, Gram negative bacteria $1-126{\times}10^4$, and mesophilic Bacillus $1-110{\times}10^5$. The density of Gram negative bacteria was highest on red pepper cultivating soils (sample no. 4 and 6) of Umsung and Gesan, Chungbuk, and the density of the fluorescent Pseudomonas was highest on greenhouse soil (sample no. 7) of Jinju, Kyungnam. The crop productivity of three soils was high as compared with those of other soils. It was supposed that the density of fluorescent Pseudomonas and mesophilic Bacillus were correlated with the incresed crop production. By MIDI analysis, 579 strains isolated from 13 soils composed of a variety of microbes including 102 isolates of Agrobacterium, 112 isolates of Bacillus, 32 isolates of Pseudomonas, 44 isolates of Kocuria, and 34 isolates of Pseudomonas. Among the 624 isolates of Gram negative bacteria, Pseudomonas including P. putida and p. fluorescens occupied the highest density (51%), and Stenotrophomonas maltophilia and Burkholderia cepacia also appeared at high density. From RAPD analysis, the fluorescent Pseudomonas strains isolated from 13 soil types showed a high level of strain diversities and were grouped into 2 - 14 patterns according to soil types. Many of unknown bacteria were recovered from the paddy soil, and needed to be further characterized on the molecular basis.

• Clinical and Experimental Pediatrics
• /
• v.46 no.8
• /
• pp.758-762
• /
• 2003

Purpose : Our examination was designed to determine the diagnostic properties of the cutoff point for the prediction of bacteremia in febrile children less than 3 years of age. Cutoff point is the value that simultaneously maximizes both sensitivity and specificity. Methods : We conducted a retrospective study of febrile children, less than 3 years of age, who clinically have no identifiable source of fever. Peripheral blood leukocyte count(WBC), absolute neutrophil count(ANC), erythrocyte sedimentation rate(ESR) and C-reactive protein(CRP) were measured at the same time. All patients received blood culture, urine culture and/or CSF culture. Bacterial infection was defined as single pathogen isolated from the CSF or blood or a urinary tract infection (UTI). Patients were dichotomized into two groups : those with bacterial infection and no bacterial infection. We analyzed the characteristics of the children in the two groups. Results : Seventy-one patients(44 males; 27 females) were enrolled in the study. Twenty patients (28%) had a serious bacterial infection(twelve urinary tract infection, five bacteremia, three meningitis) and fifty-one(72%) had no serious bacterial infection. WBC, ESR and CRP were significantly different between the two groups(P<0.05). The cutoff point of WBC, ESR and CRP were $20,000/mm^3$, 30 mm/hr and 3.0 mg/dL, respectively. The sensitivity and specificity of each cutoff point were WBC(75%, 75%), ESR(79%, 68%) and CRP(83%, 77%), respectively. Conclusion : These data show the ability of predictors to identify febrile children less than 3 years of age with bacterial infection. Febrile children who reach the cutoff point must be treated intensively and those who do not reach the cutoff point can be carefully managed without administering antimicrobial agents.

• Korean Journal of Food Science and Technology
• /
• v.42 no.4
• /
• pp.494-501
• /
• 2010

The purpose of this study was to examine the presence of Bacillus cereus, aerobic bacteria and coliforms in the raw material of infant formulas and investigate the manufacturing process in terms of microbial safety. Among ten kinds of raw infant formula material samples (n=20), Bacillus cereus appeared in two (n=4). Aerobic bacteria were not detected in raw infant formula material or maximum 4.15 log CFU/g. Eleven species of aerobic bacteria were isolated and 76% of them were Sphingomonas paucimobilis, Pseudomonas fluorescens, Rhizobium radiobactor, or Stenotrophomonas maltophilia. A Pearson's correlation analysis revealed that the most influential factors for detecting Bacillus cereus were aerobic bacteria and coliforms. In other words, when the measured values of aerobic bacteria and coliforms were higher, the possibility that Bacillus cereus would appear increased. In a regression model to predict Bacillus cereus, the rate of appearance was correlated with aerobic bacteria and coliforms, and its contribution rate for effectiveness was 86%. Improving microbial quality control by pasteurization, spray dry, popping and extrusion resulted in a decrease in the numbers of Bacillus cereus, aerobic bacteria and coliforms in the raw materials. The results suggest that a hazard analysis and critical control point system might be effective for reducing microbiological contamination.

• Food Science and Preservation
• /
• v.18 no.5
• /
• pp.786-794
• /
• 2011

To investigate the sanitary-quality level of commercial kimchi in South Korea, the pH, acidity, and microbial-flora changes in the kimchi were determined. Samples of kimchi produced by three different manufacturers (a small grocery store, a small/medium-sized enterprise, and a large food company) were collected. Freshly made kimchi was purchased and fermented at $10^{\circ}C$ for 10 days. The pH of the commercial kimchi on the purchased day was approximately pH 5.8, and that on the $10^{th}$ day of fermentation was ${\simeq}pH$ 4.1. The kimchi purchased from a large company showed a more rapid decline in pH level during fermentation. The saltiness of the kimchi purchased from a medium-sized company was slightly higher than those of the other commercial kimchi samples. The saccharinity index of the kimchi produced by a small grocery store was higher than those of the other samples, and its value deviation was also higher than those of the other commercial kimchi samples. A higher total viable-cell count and a higher lactic-acid bacteria (LAB) count were detected in the kimchi from the large food company at the beginning of fermentation compared to the samples of the two other kimchi manufacturers. The highest cell numbers of gram-positive bacteria (except LAB) and coliform bacteria were detected from the small-grocery-store kimchi, but the coliform bacteria count gradually decreased during fermentation although such bacteria were still detected until the $10^{th}$ day of fermentation. In contrast, coliform bacteria were not detected in the samples from the medium-sized and large food companies. Yeast, which is detected in over-ripened kimchi, was detected in the unfermented kimchi from the small grocery store, which had a below-0.36% acidity level. The gram-positive bacteria (except LAB) that were detected in all the tested commercial kimchi samples were determined to be Bacillus spp., and the gram-negative bacteria were determined to be Escherichia coli, Enterobacter spp., Sphingomonase spp., and Strenophomonas spp. The proportions of all the aforementioned bacteria in the kimchi samples, however, were different depending on the samples that were taken. These results indicate that a more sanitary kimchi production process and a more systematic kimchi production manual should be developed to industrialize and globalize kimchi.

• Journal of Life Science
• /
• v.25 no.2
• /
• pp.237-242
• /
• 2015

The use of calcite-forming bacteria (CFB) in crack remediation and durability improvements in construction materials creates a permanent and environmentally-friendly material. Therefore, research into this type of application is stimulating interdisciplinary studies between microbiology and architectural engineering. However, the mechanisms giving rise to these materials are dependent on calcite precipitation by the metabolism of the CFB, which raises concerns about possible hazards to cement-based construction due to microbial metabolic acid production. The aim of this study was to determine target microorganisms that possibly can have bio-corrosive effects on cement mortar and to assess multi-functional CFBs for their safe application to cement structures. The chalky test was first used to evaluate the $CaCO_3$ solubilization feature of construction sites by fungi, yeast, bacterial strains. Not all bacterial strains are able to solubilize $CaCO_3$, but C. sphaerospermum KNUC253 or P. prolifica KNUC263 showed $CaCO_3$ solubilization activity. Therefore, these two strains were identified as target microorganisms that require control in cement structures. The registered patented strains Bacillus aryabhatti KNUC205, Arthrobacter nicotianae KNUC2100, B. thuringiensis KNUC2103 and Stenotrophomonas maltophilia KNUC2106, reported as multifunctional CFB (fungal growth inhibition, crack remediation, and water permeability reduction of cement surfaces) and isolated from Dokdo or construction site were unable to solubilize $CaCO_3$. Notably, B. aryabhatti KNUC205 and A. nicotianae KNUC2100 could not hydrolyze cellulose or protein, which can be the major constituent macromolecules of internal materials for buildings. These results show that several reported multi-functional CFB can be applied to cement structures or diverse building environments without corrosive or bio-deteriorative risks.