• Korean Journal of Microbiology
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• v.36 no.4
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• pp.292-298
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• 2000

For scrutinizing the changes of aggregated bacteria in Lake Paldang, the FISH method was applied by using the rhodamine labeled probes, and total bacteria, chloropyll a concentrations and nutrients concentrations were measured. The aggregates were collected with sediment traps. The T-N, T-P, chlorophyll a concentrations of aggregates were higher 5-15 times, 81-140 and 49-66 times than water samples, respectively. Also, the bacterial numbers of aggregates were 200 times higher than those of water smaples. The ratios of each groups of water sample were 2.1-7.4% for $\alpha$-group, 4.5-8.3% for $\beta$-group, 2.1-7.4% for $\gamma$-group, 2.1-6.1% for Cytophaga-Flavobacterium group and 0.1-2.5% for 'other'group, respectively. While, in aggregates, the ratios of $\alpha$-, $\beta$-, $\gamma$- and Cytophaga-Flavobacterium groups were very small and most abundant group was 'other' bacteria. With these results, the aggregated bacteria in Lake Paldang had a particular group composition of bacteria.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.4
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• pp.593-601
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• 2012

Heavy metals and metalloids removal can be considered as one of the most important world challenges because of their toxicity and direct impact on human health. Many processes have been introduced but biological processes of remediation seem to offer the most suitable solution in terms of efficiency and low cost. Actinobacteria constitute one of the major microbial populations in soil, and this can be attributed to their adaptive morphological structure as well as their exceptional metabolic power. Among microbes, actinobacteria are morphologic intermediate between fungi and bacteria. Studies on microbial diversities in metal contaminated lands have shown that actinobacteria may constitute a dominantly active microbiota in addition to ${\alpha}$ Proteobacteria. Furthermore, isolation studies have shown metal removal mechanisms which are reminiscent of notable multiresistant strains, such as Cupriavidus metallidurans. Apart from members of genus Streptomyces, which produce more than 90% of commercialized antibiotics, and the nitrogen fixing Frankia, little attention has been given to other members of this phylum. This is because of difficult culture condition requirements and maintenance. In this review, we focused on specific isolation of actinobacteria and their potential applications in metal bioremediation and plant growth promotion.

• 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 Korean Society on Water Environment
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• v.22 no.6
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• pp.1014-1021
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• 2006

SMMIAR (Submerged Moving Media Intermittent Aeration Reactor) Process is a very efficient system which remove ammonia to nitrogen gas in one reactor. In this study, we determined the diversity of ammonia oxidizing bacteria and denitrifying bacteria using specific PCR amplification and the clone library construction. An ammonia monooxygenase gene(amoA) was analyzed to investigate the diversity of nitrifiers. Most of amoA gene fragments (27/29, 93%) were same types and they are very similar (>99%) to the sequences of Nitrosomonas europaea and other clones isolated from anoxic ammonia oxidizing reactors. ANAMMOX related bacteria have not determined by specific PCR amplification. A nitrite reductase gene(nirK) was analyzed to investigate the diversity of denitrifying bacteria. About half (9/20, 45%) of denitrifiers were clustered with Rhodobacter and most of others were clustered with Mesorhizobium (6/20, 30%) and Rhizobium (3/20, 15%). All of these nirK gene clones were clustered in alpha-Proteobacteria and this result is coincide with other system which also operate nitrification and denitrification in one reactor. The molecular monitoring of the population of nitrifiers and denitrifiers would be helpful for the system stabilization and scale-up.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.81-85
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• 2002

Oligotrophic bacteria isolated from forest soil showed a specific community consisting of various taxonomic groups compared with those in other soil or aquatic habitats. Based on the cell shape, the isolates were divided into four groups: regular rod, curved/spiral rod, irregular rod, and prosthecate bacteria. The cellular fatty acids 60 oligotrophic isolates were analyzed. At the dendrogram based on cellular fatty acid composition, four clusters(I-IV) were separated at a euclidian distance of about 50. Based on the 16S rDNA sequence analysis, the two representative strains(MH256 and MA828) of cluster 3 showed the close relation to genera, Xathomonas/Stenotrophomonas, but were not included in these genera. The isolates with Q-10 were also studied. They are corresponded to the two large groups in Proteobacteria alpha subdivision. One was incorporated in the genus Bradyrhizobium cluster, which also includes Agromonas, a genus for oligotrophic bacteria. The strains of the other group showed high similarity to the genus Agrobacterium. We attempted to screening of bioactive compounds from oligotrophs which was isolated from forest soil. The active compounds were analyzed by mass and NMR spectrum, one of them identified as crisamicin A. Another one designated as SAPH is a new compound. The results indicate that there were possibilities for finding new compounds from the rare microorganisms such as oligotrophs.

• Journal of Microbiology and Biotechnology
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• v.20 no.5
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• pp.853-861
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• 2010

High substrate costs decrease the profitability of polyhydroxyalkanoates (PHAs) production, and thus low-cost carbon substrates coming from agricultural and industrial residuals are tested for the production of these biopolymers. Among them, crude glycerol, formed as a by-product during biodiesel production, seems to be the most promising source of carbon. The object of this study was to characterize the mixed population responsible for the conversion of crude glycerol into PHAs by cultivation-dependent and -independent methods. Enrichment of the microbial community was monitored by applying the Ribosomal Intergenic Spacer Analysis (RISA), and the identification of community members was based on 16S rRNA gene sequencing of cultivable species. Molecular analysis revealed that mixed populations consisted of microorganisms affiliated with four bacterial lineages: ${\alpha}$, ${\gamma}$-Proteobacteria, Actinobacteria, and Bacteroides. Among these, three Pseudomonas strains and Rhodobacter sp. possessed genes coding for polyhydroxyalkanoates synthase. Comparative analysis revealed that most of the microorganisms detected by direct molecular analysis were obtained by the traditional culturing method.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.8_spc
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• pp.1321-1330
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• 2019

Recent development of novel techniques in systems biology have been used to improve and manipulate the rumen microbial ecosystem and gain a deeper understanding of its physiological and microbiological interactions and relationships. This provided a deeper insight and understanding of the relationship and interactions between the rumen microbiome and the host animal. New high-throughput techniques have revealed that the dominance of Proteobacteria in the neonatal gut might be derived from the maternal placenta through fetal swallowing of amniotic fluid in utero, which gradually decreases in the reticulum, omasum, and abomasum with increasing age after birth. Multi "omics" technologies have also enhanced rumen fermentation and production efficiency of dairy goats using dietary interventions through greater knowledge of the links between nutrition, metabolism, and the rumen microbiome and their effect in the environment. For example, supplementation of dietary lipid, such as linseed, affects rumen fermentation by favoring the accumulation of ${\alpha}$-linolenic acid biohydrogenation with a high correlation to the relative abundance of Fibrobacteriaceae. This provides greater resolution of the interlinkages among nutritional strategies, rumen microbes, and metabolism of the host animal that can set the foundation for new advancements in ruminant nutrition using multi 'omics' technologies.

• Journal of Microbiology and Biotechnology
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• v.29 no.1
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• pp.91-104
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• 2019

The taxonomic and functional characteristics of bacterial communities in the pre-chlorinated rapid filters and ozonated biological activated carbon (BAC) filters were compared using Illumina MiSeq sequencing of the 16S rRNA gene and community-level physiological profiling (CLPP) based on sole-carbon-source utilization patterns. Both the rapid filters and BAC filters were dominated by Rhizobiales within ${\alpha}-proteobacteria$, but other abundant orders and genera were significantly different in both types of filter. Firmicutes were abundant only in the intermediate chlorinated rapid filter, while Acidobacteria were abundant only in the BAC filters. Bacterial communities in the rapid filter showed high utilization of carbohydrates, while those in the BAC filters showed high utilization of polymers and carboxylic acids. These different characteristics of the bacterial communities could be related to the different substrates in the influents, filling materials, and residual disinfectants. Chlorination and ozonation inactivated the existing bacteria in the influent and formed different bacterial communities, which could be resistant to the oxidants and effectively utilize different substrates produced by the oxidant, including Phreatobacter in the rapid filters and Hyphomicrobium in the BAC filters. Bradyrhizobium and Leptothrix, which could utilize compounds adsorbed on the GAC, were abundant in the BAC filters. Ozonation increased taxonomic diversity but decreased functional diversity of the bacterial communities in the BAC filters. This study provides some new insights into the effects of oxidation processes and filling materials on the bacterial community structure in the biological filters of drinking water treatment plants.

• Journal of Life Science
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• v.13 no.6
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• pp.856-864
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• 2003

The 16S rRNA gene is the most common gene in the phylogenetic analysis of procaryotes. However very high conservative of 16S rRNA has limitation in the discrimination of highly related organisms, hence other molecule was applied in this study and the result was compared with that of 16S rRNA. Three COGs (Clusters of Orthologous of protein) were only detected in 42 procaryotes ; transcription elongation facto. (COG0195), bacterial DNA primase (COG0358) and uridylate kinase (COG0528). Uridylate kinase gene was selected because of the similarity and one single copy number in each genome. Bacteria, belong to same genus, and Archaebacteria were same position with high bootstrap value in phylogenetic tree like the tree of 16S rRNA. However, alpha and epsilon Proteobcteria showed different position and Spirochaetales of Eubarteria was grouped together with Archaebacteria unlike the result of 16S rRNA. Uridylate kinase may compensate the problem of very high conservative of 16S rRNA gene and it would help to access more accurate discrimination and phylogenetic analysis of bacteria.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.26 no.2
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• pp.99-115
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• 2023

Purpose: Exclusive breastfeeding promotes gut microbial compositions associated with lower rates of metabolic and autoimmune diseases. Its cessation is implicated in increased microbiome-metabolome discordance, suggesting a vulnerability to dietary changes. Formula supplementation is common within our low-income, ethnic-minority community. We studied exclusively breastfed (EBF) neonates' early microbiome-metabolome coupling in efforts to build foundational knowledge needed to target this inequality. Methods: Maternal surveys and stool samples from seven EBF neonates at first transitional stool (0-24 hours), discharge (30-48 hours), and at first appointment (days 3-5) were collected. Survey included demographics, feeding method, medications, medical history and tobacco and alcohol use. Stool samples were processed for 16S rRNA gene sequencing and lipid analysis by gas chromatography-mass spectrometry. Alpha and beta diversity analyses and Procrustes randomization for associations were carried out. Results: Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were the most abundant taxa. Variation in microbiome composition was greater between individuals than within (p=0.001). Palmitic, oleic, stearic, and linoleic acids were the most abundant lipids. Variation in lipid composition was greater between individuals than within (p=0.040). Multivariate composition of the metabolome, but not microbiome, correlated with time (p=0.030). Total lipids, saturated lipids, and unsaturated lipids concentrations increased over time (p=0.012, p=0.008, p=0.023). Alpha diversity did not correlate with time (p=0.403). Microbiome composition was not associated with each samples' metabolome (p=0.450). Conclusion: Neonate gut microbiomes were unique to each neonate; respective metabolome profiles demonstrated generalizable temporal developments. The overall variability suggests potential interplay between influences including maternal breastmilk composition, amount consumed and living environment.