• Biomolecules & Therapeutics
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• v.32 no.4
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• pp.403-423
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• 2024

The human gastrointestinal (GI) tract houses a diverse microbial community, known as the gut microbiome comprising bacteria, viruses, fungi, and protozoa. The gut microbiome plays a crucial role in maintaining the body's equilibrium and has recently been discovered to influence the functioning of the central nervous system (CNS). The communication between the nervous system and the GI tract occurs through a two-way network called the gut-brain axis. The nervous system and the GI tract can modulate each other through activated neuronal cells, the immune system, and metabolites produced by the gut microbiome. Extensive research both in preclinical and clinical realms, has highlighted the complex relationship between the gut and diseases associated with the CNS, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. This review aims to delineate receptor and target enzymes linked with gut microbiota metabolites and explore their specific roles within the brain, particularly their impact on CNS-related diseases.

• Journal of The Korean Society of Grassland and Forage Science
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• v.38 no.2
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• pp.106-111
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• 2018

This study was conducted to investigate the relationship between changes of rumen microflora and bloat in Jersey cow. Jersey cows (control age: 42 months, control weight: 558kg; treatment age: 29 months, treatment weight 507kg) were fed on the basis of dairy feeding management at dairy science division in National Institute of Animal Science. The change of microbial population in rumen was analyzed by using next generation sequencing (NGS) technologies due to metabolic disease. The diversity of Ruminococcus bromii, Bifidobacterium pseudolongum, Bifidobacterium merycicum and Butyrivibrio fibrisolvens known as major starch fermenting bacteria was increased more than 36-fold in bloated Jersey, while cellulolytic bacteria community such as Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens was increased more than 12-fold in non-bloated Jersey. The proportion of bacteroidetes and firmicutes was 33.4% and 39.6% in non-bloated Jersey's rumen, while bacteroidetes and firmicutes were 24.9% and 55.1% in bloated Jersey's. In conclusion, the change of rumen microbial community, in particular the increase in starch fermenting bacteria, might have an effect to occur the bloat in Jersey cow.

• Journal of Food Hygiene and Safety
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• v.29 no.1
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• pp.1-5
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• 2014

Many community gardens in large cities worldwide grow vegetables; however, no information regarding the levels of sanitary indicator bacteria and prevalence of foodborne pathogens in vegetables grown in urban community gardens is available. To evaluate the microbiological quality of vegetables from urban community gardens in Korea, 530 samples (nine types of vegetable, including Chinese cabbage, lettuce, radish leaves, spinach, mustard leaves, crown daisy, leek, Korean cabbage, and chicory) were collected at 11 urban community gardens in Seoul, Korea from September through October 2012. The levels of total aerobic bacteria, Escherichia coli, total coliforms, Salmonella spp. Listeria monocytogenes, and E. coli O157:H7 were evaluated quantitatively and/or qualitatively. The mean numbers of total aerobic bacteria and coliforms were 6.3 log CFU/g (range 3.8-8.1 log CFU/g) and 4.3 log CFU/g (range 2.1-6.4 log CFU/g), respectively. Total coliforms were detected on 67% of whole vegetables. Chicory showed the highest number of total aerobic bacteria and coliforms, whereas the lowest number of coliforms was detected on leeks. E. coli was detected on 2.3% of whole vegetables, including lettuce, radish leaves, mustard leaves, and chicory; however, foodborne pathogenic bacteria were not detected on any of the vegetable samples using this highly sensitive and validated procedure. Based on these findings, the presence of coliforms and E. coli demonstrates that opportunity for improvement of microbiological safety exists throughout the produce production chain, although no major foodborne pathogens were present in vegetables grown in urban community gardens.

• Korean Journal of Soil Science and Fertilizer
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• v.33 no.4
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• pp.266-274
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• 2000

Understanding of microbial community structure in soil-root system is necessary to use beneficial soil and rhizosphere microbes for improvement of crop production and biocontrol. The knowledge of behavior and function of microbes in soil-root system plays a key role for the application of beneficial inocula. Because the majority of the intact bacteria in soil are unable to grow on nutrient media, both culturable and nonculturable bacteria have to be studied together. In our study, culture-independent survey of bacterial community in the soil-root system of red pepper fields was conducted by the sequence analysis of three universal clone libraries of genes which code for small-subunit rRNA (rDNA). Universal small subunit rRNA primers were used to amplify DNA extracted from each sample and PCR products were cloned into pGEM-T. Out of 27 clones sequenced, 25 clones were from domain bacteria. Two of the rDNA sequences were derived from eukaryotic organelles. Within the domain bacteria, several kingdoms were represented : the Proteobacteria (16 clones). Cytophyga-Flexibacter-Bacteroides group (2 clones). the high G+C content gram-positive group(1 clone) and 4 unknown clones.

• Korean Journal of Microbiology
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• v.40 no.3
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• pp.189-198
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• 2004

T-RFLP analysis and clone sequencing analysis based on bacterial 16S rDNA were conducted to assess bacterial community structure and diversity in two layers (0-1cm, 6-7cm depth) of the sediment from Janghwari intertidal flat in Ganghwa Island. The results of T-RFLP (terminal-restriction fragment length polymorphism) analysis using restriction enzyme HhaI showed that the T-RFs of various size ($60{\pm}2$) bp-($667{\pm}2$) bp) appeared evenly at the surface sediments but two T-RFs with 60(${\pm}2$)bp and 93 (${\pm}2$)bp predominated at 6-7cm depth. Analysis of partial sequences for 172 clones revealed that 98% of the clones were not matched with the sequences of cultured bacteria strains in the GenBank (${\geq}similarity$ 98%), and approximately 86% of them were classified as different phylotypes. Most clones belonged to $\alpha$-, $\gamma$-, and $\delta$-Proteobacteria, Acidobacteria/Holophaga and green nonsulfur bacteria group. Proteobacteria group occupied the highest proportion in both layers (69% at 0-1cm depth and 46% at 6-7cm depth). $\gamma$-Proteobacteria and $\delta$-Proteobacteria that are associated with oxidation and reduction of sulfur compounds were appeared to be dominant, and comprised 21.5% and 15.7% of total clones, respectively. Overall results indicated that extremely diverse bacterial groups were inhabiting in the sediment of Ganghwa intertidal flat, and bacterial communities associated with the behaviour of sulfur seemed to playa significant role in the biogeochemical environment in this anoxic sediment.

• Journal of Korean Society of Environmental Engineers
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• v.28 no.7
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• pp.752-756
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• 2006

The independent anoxic reactor was introduced in biological aerated filters as the regulation of water quality requirement, especially total nitrogen, had been strengthened. The process studied in this work was upflow $Biobead^{(R)}$ process which was used commercial invented for removal of organic materials and nitrification. For the purpose of evaluating the independent anoxic reactor, PCR-DGGE, of the molecular biological methods, was performed. Two types of nitrite reductase genes were selected. One is nirS represented cytocrome $cd_1$ nitrite reductase gene and the other is nirK represented Cu-containing nitrite reductase gene. Denitrifier community in the independent anoxic reactor was analyzed with PCR-DGGE using these two denitrifying functional genes. As the result of the PCR, only nirS gene was detected between nirS and nirK. With the result of the DGGE, specific bands became strong, as the operating days were longer, nitrate loading rate was increased. otherwise those of the initial activated sludge showed various bands. In the consequence of the sequence of DGGE bands, various denitrifiers were sequenced in the initial activated sludge, while specific denitrifiers like alcaligenes faecalis were predominant in the anoxic reactor. Consequently, introduction of the independent anoxic reactor made it possible to achieve 96% denitrification efficiency, and was proper for the modification of BAF process.

• Korean Journal of Ecology and Environment
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• v.52 no.1
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• pp.40-49
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• 2019

Seasonal succession of zooplankton community and species composition was studied from 2003 to 2014 in a deep reservoir, Lake Soyang, in monsoon climate region, Korea. Annual precipitation was concentrated more than 70% between June and September and it showed remarkably that seasonal variation in water quality. Seasonal variation of water quality in Lake Soyang appeared to be more significant than annual variations, and the inflow of turbid water during the summer rainfall was the most important environmental factor. Zooplankton sepecies composition in Lake Soyang showed obvious tendency through two periods (May to June and August to October) every year. Small zooplankton (rotifer; Keratella cochlearis, Polyarthra vulgaris) dominated in spring and mesozooplankton such as copepods and crustaceans were dominant in summer and fall. Zooplankton biomass showed the maximum in September after monsoon rainfall, and chlorophyll showed a similar seasonal variation and it showed a high correlation (r=0.45). The increase of zooplankton biomass is considered to be a bottom-up effect due to the increase of primary producers and inflow of nutrients and organic matter from rainfall. In this study, we found that the variation of zooplankton community was affected by rainfall in monsoon climate region and inflow of turbid water was an important environmental factor, which influenced the water quality, zooplankton seasonal succession in Lake Soyang. It was also considered to be influenced by hydrological characteristics of lake and environment of watershed. In conclusion, seasonal succession of zooplankton species composition was the same as the PEG model. But seasonal succession of zooplankton biomass differed not only in the temperate lake but also in the monsoon region.

• Journal of Wetlands Research
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• v.24 no.2
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• pp.69-82
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• 2022

In this study, we investigated the bacterial community structure in organic rice-fish mixed farming paddy soil by using high-throughput sequencing technology. The results showed that compared with the organic rice cultivated soil, the content of AP (available phosphorus) increased by 310.23 % and the content of OM (organic matter) increased by 168.83%. The most abundant phyla in paddy soils were Proteobacteria, Bacteriodetes, and Chloroflexi, whose relative abundance was above 47.83%. Among the dominant genera, the relative abundance of Limisphaera in paddy soils was observed. Alpha diversity indicated that the bacterial diversity of paddy soils was similar among each other. The bacterial community structure was affected by the relative abundance of bacteria, not the species of bacteria. Principal Coordinated Analysis (PCoA) results showed that the bacterial communities in organic rice-fish mixed farming soil and organic paddy soil were correlated to each other; the bacterial community structure was distinctively grouped by four different systems (paddy soil under organic rice-fish mixed farming system, organic rice cultivation, and conventional rice cultivation), where the first two are closely related to each other than the third one. The results provide basal support for organic agri-cultivation while improving an ecological value at the same time.

• Journal of Korean Society of Environmental Engineers
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• v.30 no.9
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• pp.939-947
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• 2008

PCR-DGGE method was applied to analyze changes of microbial community in simultaneous nitrification and denitrification (SND) bioreactor with various DO concentrations. In the analysis of eubacterial community, band profiles of DGGE were similar with 2 or 1 mg/L DO concentrations in the reactor. Experimental results led to 16 different bacteria being identified, including 5 dominant strains(3 strains of Uncultured Bacterium, 1 strains of Bacillus, 1 strains of Uncultured Bacteroidetes). DGGE results at 0.5 mg/L DO concentration led to 12 strains being identified, including 7 dominant strains(5 strains of Uncultured Bacterium, 2 strains of Zoogloea sp.). DGGE results at 0.1 mg/L DO concentration led to 11 strains being identified, including 3 dominant strains(1 strains of Uncultured Bacterium, 2 strains of Zoogloea sp.). In DGGE band profiles of $\beta$-AOB($\beta$-Ammonia Oxidizing Bacteria), only one band was observed. This band had 97% similarity with Nitrosomonas sp. done DNB Y20. This band was clearly observed at the 2, 1 and 0.5 mg/L DO concentrations, while the brightness of the band at 0.1 mg/L DO concentration was mostly dimmed. In DGGE band profiles of denitrification process, 5 bands(3 strains of Uncultured organism containing nirS, 2 strains of Uncultured organism containing nirK) were observed. Among those bands, the brightness of one band was gradually increased at the lower DO concentrations. This band has 86% identity with Uncultured organism clone eS1 cd1 nirS gene, partial cds. Based on this result, it could be concluded that Uncultured organism clone eS1 cd1 nirS gene, partial cds is a predominant microorganism in the denitrification process.

• Horticultural Science & Technology
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• v.32 no.3
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• pp.400-407
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• 2014

Urban farming supplies emotional stability and fresh vegetables to participating persons, however, no information regarding the biosafety of agricultural products from urban farming is available. Here, we collected 260 samples of Chinese cabbages and lettuce from 4 urban community gardens and 6 roof gardens in Seoul from September through October 2012, and monitored the microbiological and parasitological contamination quantitatively and/or qualitatively. The mean counts of total aerobic bacteria and coliforms were $6.1{\pm}0.8\;log\;CFU{\cdot}g^{-1}$ ( range, $5.4{\pm}0.6{\sim}7.1{\pm}0.8\;log\;CFU{\cdot}g^{-1}$) and $4.0{\pm}0.7\;log\;CFU{\cdot}g^{-1}$ (range, $2.3{\pm}0.6{\sim}6.1{\pm}0.9\;log\;CFU{\cdot}g^{-1}$), respectively. Coliforms were detected on 59.6% among 260 vegetable samples. There were no significant differences in the contamination levels of total aerobic bacteria and coliforms between the Chinese cabbages and lettuce, whereas both levels of vegetables from urban community gardens were higher than those of roof gardens (p > 0.05). Escherichia coli was isolated at 3.1% among whole vegetables, and contamination level was $1.5{\pm}0.2\;log\;CFU{\cdot}g^{-1}$. Among foodborne pathogens, Staphylococcus aureus was detected in 1.5%, however, Salmonella spp., Listeria monocytogenes and E. coli O157:H7 were not detected on any of the vegetable samples. We also found undefined parasite eggs from two samples of Chinese cabbages (0.8% of total vegetables we tested). From these study, we found the presence of microbial contamination of agricultural products from urban farming, thus we need further concern to improve the biosafety during production of agricultural products.