• Journal of Microbiology and Biotechnology
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• v.17 no.5
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• pp.784-791
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• 2007

The present work aims to use a biofilter technology(aerated submerged filters) for the aerobic transformation at laboratory-scale of olive washing water(OWW) generated in the first steps of olive oil processing, as well as the genetic profiling and identification to the species level of the bacteria involved in the formation of the biofilm, by means of TGGE. Chemical parameters, such as biological oxygen demand at five days($BOD_5$) and chemical oxygen demand(COD), decreased markedly(up to 90 and 85%, respectively) by the biological treatment, and the efficiency of the process was significantly affected by aeration and inlet flow rates. The total polyphenol content of inlet OWW was only moderately reduced(around 50% decrease of the inlet content) after the biofilter treatment, under the conditions tested. Partial 16S rRNA genes were amplified using total DNA extracted from the biofilm and separated by TGGE. Sequences of isolated bands were mostly affiliated to the $\alpha-subclass$ of Proteobacteria, and often branched in the periphery of bacteria] genera commonly present in soil(Rhizobium, Reichenowia, Agrobacterium, and Sphingomonas). The data obtained by the experimentation at laboratory scale provided results that support the suitability of the submerged filter technology for the treatment of olive washing waters with the purpose of its reutilization.

• Journal of Soil and Groundwater Environment
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• v.27 no.2
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• pp.61-75
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• 2022

This study evaluated the potential threat of agricultural and human activities to groundwater in the Noseong stream watershed, a typical agricultural area, through hydrogeochemical characteristics and microbial community analyses. The groundwater in the study area was Ca-SO₄ and Ca-HCO₃ types alluvial aquifer mainly used for agricultural and living purposes, and contained high levels of NO₃^- and Cl^- ions generated from anthropogenic sources such as fertilizer, livestock wastewater, and domestic sewage. Proteobacteria was most abundant in all samples with an average of 46.1% while Actinobacteria, Bacteroidetes, and Cyanobacteria were dominant on an occasional basis. The prevalence of aerobic bacteria such as the genus Mycobacterium, Flavobacterium, and Sphingomonas suggests that groundwater was well connected with the surface layer. The potential pathogen Mycobacterium was detected in most samples, and other pathogenic bacteria were also widely distributed, indicating the vulnerability to contamination. Therefore, an integrated management system is required to secure the sustainable use of groundwater in agricultural areas with high groundwater dependence.

• The Plant Pathology Journal
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• v.38 no.6
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• pp.583-592
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• 2022

Root-knot nematode disease is a widespread and catastrophic disease of tobacco. However, little is known about the relationship between rhizosphere bacterial community and root-knot nematode disease. This study used 16S rRNA gene sequencing and PICRUSt to assess bacterial community structure and function changes in rhizosphere soil from Meloidogyne incognita-infected tobacco plants. We studied the rhizosphere bacterial community structure of M. incognita-infected and uninfected tobacco plants through a paired comparison design in two regions of tobacco planting area, Yuxi and Jiuxiang of Yunnan Province, southwest China. According to the findings, M. incognita infection can alter the bacterial population in the soil. Uninfested soil has more operational taxonomic unit numbers and richness than infested soil. Principal Coordinate Analysis revealed clear separations between bacterial communities from infested and uninfested soil, indicating that different infection conditions resulted in significantly different bacterial community structures in soils. Firmicutes was prevalent in infested soil, but Chloroflexi and Acidobacteria were prevalent in uninfested soil. Sphingomonas, Streptomyces, and Bradyrhizobium were the dominant bacteria genera, and their abundance were higher in infested soil. By PICRUSt analysis, some metabolism-related functions and signal transduction functions of the rhizosphere bacterial community in the M. incognita infection-tobacco plants had a higher relative abundance than those uninfected. As a result, rhizosphere soils from tobacco plants infected with M. incognita showed considerable bacterial community structure and function alterations.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.25 no.3
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• pp.194-210
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• 2022

Human milk contains a number of nutritional and bioactive molecules including microorganisms that constitute the so-called "Human Milk Microbiota (HMM)". Recent studies have shown that not only bacterial but also viral, fungal, and archaeal components are present in the HMM. Previous research has established, a "core" microbiome, consisting of Firmicutes (i.e., Streptococcus, Staphylococcus), Proteobacteria (i.e., Serratia, Pseudomonas, Ralstonia, Sphingomonas, Bradyrhizobium), and Actinobacteria (i.e., Propionibacterium, Corynebacterium). This review aims to summarize the main characteristics of HMM and the role it plays in shaping a child's health. We reviewed the most recent literature on the topic (2019-2021), using the PubMed database. The main sources of HMM origin were identified as the retrograde flow and the entero-mammary pathway. Several factors can influence its composition, such as maternal body mass index and diet, use of antibiotics, time and type of delivery, and mode of breastfeeding. The COVID-19 pandemic, by altering the mother-infant dyad and modifying many of our previous habits, has emerged as a new risk factor for the modification of HMM. HMM is an important contributor to gastrointestinal colonization in children and therefore, it is fundamental to avoid any form of perturbation in the HMM that can alter the microbial equilibrium, especially in the first 100 days of life. Microbial dysbiosis can be a trigger point for the development of necrotizing enterocolitis, especially in preterm infants, and for onset of chronic diseases, such as asthma and obesity, later in life.

• Food Science of Animal Resources
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• v.42 no.6
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• pp.1061-1073
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• 2022

Receptor activator of NF-kB ligand (RANKL) is known to play a major role in bone metabolism and the immune system, and its recombinant form has been expressed in bacterial systems for research since the last two decades. However, most of these recombinant forms are used after purification or directly using living cells. Here, there were cell extracts of recombinant Lactococcus lactis expressing mouse RANKL (mRANKL) used to evaluate its biological activity in mice. Mice were divided into three groups that were fed phosphate-buffered saline (PBS), wild-type L. lactis IL1403 (WT_CE), and recombinant L. lactis expressing mRANKL (mRANKL_CE). The small intestinal transcriptome and fecal microbiome were then profiled. The biological activity of mRANKL_CE was confirmed by studying RANK-RANKL signaling in vitro and in vivo. For small intestinal transcriptome, differentially expressed genes (DEGs) were identified in the mRANKL_CE group, and no DEGs were found in the WT_CE group. In the PBS vs. mRANKL_CE gene enrichment analysis, upregulated genes were enriched for heat shock protein binding, regulation of bone resorption, and calcium ion binding. In the gut microbiome analysis, there were no critical changes among the three groups. However, Lactobacillus and Sphingomonas were more abundant in the mRANKL_CE group than in the other two groups. Our results indicate that cell extracts of mRANKL_CE can play an effective role without a significant impact on the intestine. This strategy may be useful for the development of protein drugs.

• Journal of Microbiology and Biotechnology
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• v.32 no.12
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• pp.1561-1572
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• 2022

Plastic pollution has been recognized as a serious environmental problem, and microbial degradation of plastics is a potential, environmentally friendly solution to this. Here, we analyzed and compared microbial communities on waste plastic films (WPFs) buried for long periods at four landfill sites with those in nearby soils to identify microbes with the potential to degrade plastics. Fourier-transform infrared spectroscopy spectra of these WPFs showed that most were polyethylene and had signs of oxidation, such as carbon-carbon double bonds, carbon-oxygen single bonds, or hydrogen-oxygen single bonds, but the presence of carbonyl groups was rare. The species richness and diversity of the bacterial and fungal communities on the films were generally lower than those in nearby soils. Principal coordinate analysis of the bacterial and fungal communities showed that their overall structures were determined by their geographical locations; however, the microbial communities on the films were generally different from those in the soils. For the pulled data from the four landfill sites, the relative abundances of Bradyrhizobiaceae, Pseudarthrobacter, Myxococcales, Sphingomonas, and Spartobacteria were higher on films than in soils at the bacterial genus level. At the species level, operational taxonomic units classified as Bradyrhizobiaceae and Pseudarthrobacter in bacteria and Mortierella in fungi were enriched on the films. PICRUSt analysis showed that the predicted functions related to amino acid and carbohydrate metabolism and xenobiotic degradation were more abundant on films than in soils. These results suggest that specific microbial groups were enriched on the WPFs and may be involved in plastic degradation.

• The Plant Pathology Journal
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• v.39 no.1
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• pp.123-135
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• 2023

Previously, Pseudomonas plecoglossicida YJR13 and Pseudomonas putida YJR92 from a sequential screening procedure were proven to effectively control Phytophthora blight caused by Phytophthora capsici. In this study, we further investigated the anti-oomycete activities of these strains against mycelial growth, zoospore germination, and germ tube elongation of P. capsici. We also investigated root colonization ability of the bacterial strains in square dishes, including cell motility (swimming and swarming motilities) and biofilm formation. Both strains significantly inhibited mycelial growth in liquid and solid V8 juice media and M9 minimal media, zoospore germination, and germ tube elongation compared with Bacillus vallismortis EXTN-1 (positive biocontrol strain), Sphingomonas aquatilis KU408 (negative biocontrol strain), and MgSO₄ solution (untreated control). In diluted (nutrient-deficient) V₈ juice broth, the tested strain populations were maintained at >10⁸ cells/ml, simultaneously providing mycelial inhibitory activity. Additionally, these strains colonized pepper roots at a 10⁶ cells/ml concentration for 7 days. The root colonization of the strains was supported by strong swimming and swarming activities, biofilm formation, and chemotactic activity towards exudate components (amino acids, organic acids, and sugars) of pepper roots. Collectively, these results suggest that strains YJR13 and YJR92 can effectively suppress Phytophthora blight of pepper through direct anti-oomycete activities against mycelial growth, zoospore germination and germ tube elongation. Bacterial colonization of pepper roots may be mediated by cell motility and biofilm formation together with chemotaxis to root exudates.

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.313-320
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• 2013

Biofilm formed on stainless and copper in water treatment plant was investigated for sixteen weeks. Biofilm reactor was specially designed for this study. It was similar to that of a real distribution pipe. Raw water, coagulated, settled, filtered and treated water were used in this study. The average number of heterotrophic bacteria counts was $1.6{\times}10^4CFU/ml$, $5.8{\times}10^3CFU/ml$, $1.8{\times}10^3CFU/ml$, $1.3{\times}10^2CFU/ml$, 1 CFU/ml, respectively. Density of biofilm bacteria formed on stainless and copper pipes in raw, coagulated and settled water increased above $2.9{\times}10^3CFU/cm^2$ within second weeks while more biofilm bacteria counts were found on the stainless pipe than on the copper pipe. In case of filtered water (free residue chlorine 0.44 mg/L), there was no significant difference in the number of biofilm bacteria on both pipes and biofilm bacteria below $18CFU/cm^2$ were detected on both pipe materials after fifth weeks. Biofilm bacteria were not detected on both pipe materials in treated water (free residue chlorine 0.88 mg/L). According to the results of DGGE analysis, Sphingomonadacae was a dominant species of biofilm bacteria formed on the stainless pipe while the copper pipe had Bradyrhizobiaceae and Sphingomonadaceae as dominant bands. In case of filtered water, a few bands (similar to Propionibacterium sp., Sphingomonas sp., Escherichia sp., and etc.) that have 16S rRNA sequences were detected in biofilm bacteria formed on both pipes after fifth weeks. Stainless pipe had higher species richness and diversity than the copper pipe.

• The korean journal of orthodontics
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• v.36 no.4
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• pp.251-262
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• 2006

Objective: The purpose of this study was to compare the bacterial flora at the peri-implant sulcus of the orthodontic mini-implant placed in the alveolar mucosa with the bacterial flora at the adjacent healthy gingival sulcus. Methods: Two plaque samples from 7 patients were collected by inserting paper points into the sulcus between the mini-implant and ligature wire connected to the mini-implant head and inflamed alveolar mucosa, and from the gingival sulcus of a healthy tooth adjacent to the mini-implant. Results: Using 16S rDNA clone library, the 24 kinds of bacteria including Haemophilus aphrophilus, Sphingomonas species, Capnocytophaga species, Prevotella melaninogenica, Lachnospiraceae species, Porphyromonas species, Neisseria flava were identified only from the sulcus around the mini-implant. These bacteria constituted only 9.2% of total clones, and the bacteria identified from both the sulcus around mini-implants and the gingival sulcus constituted 80.4% of total clones. Of these bacteria, clones of Prevotella species, Atopobium rimae, Veillonella species, Streptococcus intermedius/constellatus, Streptococcus salivarius were more frequently isolated from the peri-implant sulcus. Conclusion: This study suggests that a broad epidemiological study is needed to find causative bacteria which induce inflammation from the peri-implant sulcus.

• Korean Journal of Microbiology
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• v.44 no.3
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• pp.244-250
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• 2008

To evaluate bacteriological water quality, samples were taken from drinking water dispensers placed at S company (S-C) and U highschool (U-H) in Ulsan. The medians of heterotrophic plate counts (HPCs) were 53 CFU/ml for the 74 water samples of S-C and 80 CFU/ml for the 36 cold water samples of U-H, and 38% of the S-C and 42% of the U-H samples showed HPC bacterial concentrations higher than 100 CFU/ml. Coliform bacteria were detected from one sample of S-C. To determine the major source of bacterial contamination, water samples were taken daily for $6\sim8$ days from the bottled water containers as well as the faucets of an experimental water dispenser. While the average HPCs in the bottled water containers were 33 CFU/ml for the first and 132 CFU/ml for the 2nd analysis, the HPC concentration in the cold water samples was 1,022 CFU/ml for the 2nd analysis. These results suggest that the majority of bacteria detected in the cold water samples were originated from the biofilms on the surface of water passages within the water dispensers. There was no significant increase in HPC bacterial concentrations within the bottled water container after installation on the water dispenser. We could isolate and tentatively identify 3 genera 6 species of Gram-positive and 7 genera 7 species of Gram-negative bacteria from the plate count agar plates of U-H samples. Among the isolates, 72% were observed as Gram-positive, and Micrococcus spp. was the most abundant with 54% of the total, followed by Sphingomonas paucimobilis with 16%. It appears that most of the HPC bacteria detected in water dispensers originate from indoor airborne bacteria, which may play important roles in the formation of biofilms on the surface of water passages within the water dispensers.