• Journal of Climate Change Research
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• v.5 no.3
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• pp.249-256
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• 2014

Permafrost is frozen soil below $0^{\circ}C$ for two or more years. Surface of permafrost is called as active layer that seasonally thaws during the summer. Although the thawing of permafrost may deepen the active layer and consequently increase the microbial activity, the microbial community structure in this habitat has not yet been well described. In this study, we presented bacterial and archaeal diversity in the active layer soil from Resolute, Canada using pyrosequencing analysis. The soil sample was collected from the surface of the marsh covered with moss and Carex. A total of 7,796 bacterial reads for 40 phyla and 245 archaeal reads for 4 phyla were collected, reflecting the high diversity of bacteria. Predominant bacterial groups were Proteobacteria (37.7%) and Bacteroidetes (30.0%) in this study. Major groups in Archaea were Euryarchaeota (51.4%) and Thaumarchaeota (46.1%). Both methane producing archaea and consuming bacteria were detected in this study. Although it might be difficult to characterize microbial community with only one sample, it could be used for the basis of assessing the relative importance of the specific groups with a high resolution on the bacterial and archaeal community in this habitat.

• Food Science and Industry
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• v.50 no.1
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• pp.2-10
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• 2017

Human have eaten various traditional fermented foods for a numbers of million years for health benefit as well as survival. The beneficial effects of fermented foods have been resulted from complex microbial communications within the fermented foods. Therefore, the holistic approaches for individual identification and complete microbial profiling involved in their communications have been of interest to food microbiology fields. Microbiome is the ecological community of microorganisms that literally share our environments including foods as well as human body. However, due to the limitation of culture-dependent methods such as simple isolations of just culturable microorganisms, the culture-independent methods have been consistently developed, resulting in new light on the diverse non-culturable and hitherto unknown microorganisms, and even microbial communities in the fermented foods. For the culture-independent approaches, the food microbiome has been deciphered by employing various molecular analysis tools such as fluorescence in situ hybridization, quantitative PCR, and denaturing gradient gel-electrophoresis. More recently, next-generation-sequencing (NGS) platform-based microbiome analysis has been of interest, because NGS is a powerful analytical tool capable of resolving the microbiome in respect to community structures, dynamics, and activities. In this overview, the development status of analysis tools for the fermented food microbiome is covered and research trend for NGS-based food microbiome analysis is also discussed.

• Journal of Microbiology and Biotechnology
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• v.27 no.1
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• pp.130-140
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• 2017

It is vital to understand the changing characteristics of interphase microbial communities and interspecies synergism during the fermentation of Chinese liquors. In this study, microbial communities in the three indispensable phases (pit mud, zaopei, and huangshui) of Luzhou-flavored liquor manufacturing pits and their shifts during cellars use were first investigated by polyphasic culture-independent approaches. The archaeal and eubacterial communities in the three phases were quantitatively assessed by combined phospholipid ether lipids/phospholipid fatty acid analysis and fluorescence in situ hybridization. In addition, qualitative information regarding the microbial community was analyzed by PCR-denaturing gradient gel electrophoresis. Results suggested that the interphase microbial community profiles were quite different, and the proportions of specific microbial groups evolved gradually. Anaerobic bacteria and gram-positive bacteria were dominant and their numbers were higher in pit mud ($10^9$ cells/g) than in huangshui ($10^7$ cells/ml) and zaopei ($10^7$ cells/g). Hydrogenotrophic methanogenic archaea were the dominant archaea, and their proportions were virtually unchanged in pit mud (around 65%), whereas they first increased and then decreased in zaopei (59%-82%-47%) and increased with pit age in huangshui (82%-92%). Interactions between microbial communities, especially between eubacteria and methanogens, played a key role in the formation of favorable niches for liquor fermentation. Furthermore, daqu (an essential saccharifying and fermentative agent) and metabolic regulation parameters greatly affected the microbial community.

• The Plant Pathology Journal
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• v.38 no.4
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• pp.372-382
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• 2022

Soybean is an important source of protein and for a wide range of agricultural, food, and industrial applications. Soybean is being affected by Xanthomonas citri pv. glycines, a causal pathogen of bacterial pustule disease, result in a reduction in yield and quality. Diverse microbial communities of plants are involved in various plant stresses is known. Therefore, we designed to investigate the microbial community differentiation depending on the infection of X. citri pv. glycines. The microbial community's abundance, diversity, and similarity showed a difference between infected and non-infected soybean. Microbiota community analysis, excluding X. citri pv. glycines, revealed that Pseudomonas spp. would increase the population of the infected soybean. Results of DESeq analyses suggested that energy metabolism, secondary metabolite, and TCA cycle metabolism were actively diverse in the non-infected soybeans. Additionally, Streptomyces bacillaris S8, an endophyte microbiota member, was nominated as a key microbe in the healthy soybeans. Genome analysis of S. bacillaris S8 presented that salinomycin may be the critical antibacterial metabolite. Our findings on the composition of soybean microbiota communities and the key strain information will contribute to developing biological control strategies against X. citri pv. glycines.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2004.09a
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• pp.164-167
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• 2004

To investigate the chemical and microbiological characteristics of groundwater and surface waters in contaminated sites, hydrochemical and microbial community analysis were executed. Different indigenous bacteria were observed at 4 contaminated sites and this is considered to decompose the contaminants of groundwater. The research results showed the close relationship between hydrochemistry and microbial characteristics and those are used for the information of natural attenuation and enhanced bioremediation.

• Journal of Microbiology and Biotechnology
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• v.12 no.3
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• pp.382-388
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• 2002

In order to assess the effects of organic fertilizer on soil microbial community structure and diversity in the greenhouse fields, fatty acid methyl ester (FAME) was analyzed by the MIDI (Microbial ID, Inc., Newark, DE, U.S.A.) system and enumerations were performed. In relation to bacterial division of each sample, low GC Gram-positive bacteria were predominant among bacteria cultured on aerobic bacteria media. On the other hand, alpha subdivision was predominant on proteobacteria of control and OM (organic matter) 1 treated plot, and Flavobacterium spp. existed in OM2 plot on crystal violet media of all samples. Shannon-weaver Index (H) of OM1 plot varied most by 1.9 and 5.0 among bacteria cultured on aerobic bacteria media and crystal violet media, respectively. Our results revealed that addition of the organic wastes to soil led to a highly diverse microbial community, but the excessive amounts of organic and mineral fertilizer applied in the greenhouse fields produced excess nutrients in soil and led to simplification on bacterial populations.

• Journal of Microbiology and Biotechnology
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• v.34 no.10
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• pp.2005-2011
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• 2024

This study aimed to analyze bacterial communities in breast milk obtained from five breastfeeding women. Culture-dependent and culture-independent methods were used to analyze microbial communities. Total bacterial count of breast milk determined using plate count agar ranged from 3.3×10⁴±3.5×10² colony forming unit (CFU)/g to 1.7×10⁵±3.5×10³ CFU/g, with a pH between 6.4 and 6.8. Only three species, Leuconostoc citreum (17 out of 160 strains; 10.63%), Staphylococcus epidermidis (118 strains; 73.75%), and Staphylococcus lugdunensis (25 strains; 15.63%), belong to the phylum Bacillota were detected by culture-dependent analysis. Microbial communities analyzed via pyrosequencing revealed greater diversity compared to the culture-dependent analysis. At the phylum level, Bacillota accounted for 60.9% of the microbial community. At the genus level, Staphylococcus (24.57%), Streptococcus (22.93%), and Methylobacterium (8.76%) were dominant genera. While pyrosequencing demonstrated greater microbial diversity than the agar plate culture method, identified microbes might lack information or include many unculturable microbes. Most of all, considering the low total bacterial count averaging 7.2×10⁴ CFU/g, further research is needed to determine the significance of microbial presence in breast milk.

• Journal of Microbiology
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• v.42 no.4
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• pp.267-277
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• 2004

Effects of elevated $CO_2$ on soil microorganisms are known to be mediated by various interactions with plants, for which such effects are relatively poorly documented. In this review, we summarize and syn­thesize results from studies assessing impacts of elevated $CO_2$ on soil ecosystems, focusing primarily on plants and a variety the of microbial processes. The processes considered include changes in microbial biomass of C and N, microbial number, respiration rates, organic matter decomposition, soil enzyme activities, microbial community composition, and functional groups of bacteria mediating trace gas emission such as methane and nitrous oxide. Elevated $CO_2$ in atmosphere may enhance certain micro­bial processes such as $CH_4$ emission from wetlands due to enhanced carbon supply from plants. How­ever, responses of extracellular enzyme activities and microbial community structure are still controversy, because interferences with other factors such as the types of plants, nutrient availabilitial in soil, soil types, analysis methods, and types of $CO_2$ fumigation systems are not fully understood.

• Journal of Microbiology and Biotechnology
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• v.33 no.6
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• pp.760-770
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• 2023

Continuous cropping obstacles have become a serious factor restricting sustainable development in modern agriculture, while companion planting is one of the most common and effective methods for solving this problem. Here, we monitored the effects of companion planting on soil fertility and the microbial community distribution pattern in pepper monoculture and companion plantings. Soil microbial communities were analyzed using high-throughput sequencing technology. Companion plants included garlic (T1), oat (T2), cabbage (T3), celery (T4), and white clover (T5). The results showed that compared with the monoculture system, companion planting significantly increased the activities of soil urease (except for T5) and sucrase, but decreased catalase activity. In addition, T2 significantly improved microbial diversity (Shannon index) while T1 resulted in a decrease of bacterial OTUs and an increase of fungal OTUs. Companion planting also significantly changed soil microbial community structures and compositions. Correlation analysis showed that soil enzyme activities were closely correlated with bacterial and fungal community structures. Moreover, the companion system weakened the complexity of microbial networks. These findings indicated that companion plants can provide nutrition to microbes and weaken the competition among them, which offers a theoretical basis and data for further research into methods for reducing continuous cropping obstacles in agriculture.

• Korean Journal of Microbiology
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• v.53 no.3
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• pp.170-179
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• 2017

Tea is the most popular beverage in the world. In fact, there are mainly three different kinds of tea (Green tea, black tea, and post-fermented tea). Post-fermented tea is produced by the microbial fermentation process using sun-dried green tea leaves (Camellia sinensis) as the raw material. Chungtaejeon was a traditional tea introduced in the age of the ancient three states and is the only "Ddeok-cha or Don-cha" culture in the world that survived on the southwestern shore of Republic of Korea. In this study, the structures of the bacterial community involved in the production of oriental traditional post-fermented tea (Chungtaejeon) were investigated using 16S rRNA gene analysis. The 16S rRNA gene analysis of dominant microbial bacteria in post-fermented tea confirmed the presence of Pantoea sp., and Klebsiella oxytoca. Phylogenetic analysis suggested that the taxonomic affiliation of the dominant species in the post-fermented tea was ${\gamma}$-proteobacteria. As a result of the microbial community size analysis, it was confirmed that the size of the microbial communities of Chungtaejeon was the largest compared to other teas