• 미생물학회지
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• 제36권4호
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• pp.292-298
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• 2000

팔당호에서 fluorescent in situ hybridization(FISH) 방법을 이용하여 aggregates에 부착한 세균군집의 변화를 조사하였다. 조사대상은 Eubacteria에 속하는 세균과 Class Proteobacteria에 속하는 세균중 $\alpha$-, $\beta$-, $\gamma$ -group과 Cytophaga-Flavobacterium group이었고, 환경요인의 변화를 파악하고자 영양염류와 엽록소 a를 측정하였다. Aggregate와 물시료의 조사항목을 비교하면, TN의 경우 5~15배, TP는 81~140배, 엽록소 a는 49~66배로 aggregate가 높게 나타났으며, 총 세균수 역시 물시료에서 전체적으로 1.0~$2.0{\times}10^6$cells.$ml^{-1}$이었고, aggregates 부착세균에서 0.2~~$3.6{\times}10^8$cells.$ml^{-1}$의 범위로 물시료보다는 aggregates에 부착한 세균의 밀도가 200배 높았다. 또 수심별로는 5m trap 보다 20m trap에서 더 많은 수가 측정되었다. 총 세균수에 대한 세균군집구조의 비율은 부유세균의 경우 $\alpha$-group이 4.5~8.3%, $\beta$-group이 2.2~8.0%, ${\gamma}$-group이 2.1~7.4%, Cytophaga-Flavobacterium group이 2.1~6.1% 'Other'group은 0.1~2.5로 매우 낮았으나 aggregate에 부착한 세균의 군집구조는 $\alpha$-, $\beta$-, $\gamma$-group과 Cytophaga-Flavobacterium group이 아닌 'Other'group이 약 10.2~32.1%로 우점하는 경향을 보였다. 이처럼 팔당호에서 aggregates에 부착한 세균의 군집구조는 부유세균과 비교해볼 때 독특한 군집구조를 나타내었다.

• 한국토양비료학회지
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• 제45권4호
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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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• 제12권3호
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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.

• 한국물환경학회지
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• 제22권6호
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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.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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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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• 제20권5호
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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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• 제32권8_spc호
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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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• 제29권1호
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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.

• 생명과학회지
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• 제13권6호
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• pp.856-864
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• 2003

원핵생물 (Procaryote)의 분류에 16S rRNA유전자가 많이 이용되어 있으나 제한된 해상력과 유전자의 수에 차이가 있는 등의 문제가 있어 이를 보완할 수 있는 새로운 생체분자를 찾고 그 분류 결과를 16S rRNA의 결과와 비교하였다. COG (Clusters of Orthologous of protein) 방법을 이용하여 43종의 미생물중에서 진핵생물을 제외한 42종의 원핵생물 (procaryote)에서만 발견되는 3종류의 COG인 Transcription elongation factor인 COG0195과 bacterial DNA primase인 COG0358 그리고 uridylate kinase인 COG0528를 구하였다. 이중 유사도와 유전자 수를 바탕으로 새로운 분류의 키로 uridylate kinase를 설정하여 분석한 결과, 같은 속 (genus)에 속하는 세균들은 아주 높은bootstrap value를 갖고 분류도에서 같은 위치에 분포하고 고세균 (Archaebacteria) 내부의 응집성이 높은 등의 유사성을 보였다. 한편 alpha와 epsilon 그룹의 Proteobacteria가 분류도에서 다르게 위치하고 진정세균 (Eubacteria)의 Spi-rochaetales에 속하는 Treponema pallidum (Tpa)와 Borrelia burgdorferi (Bbu)가 고세균과 유연관계가 높게 나타나는 등 차이점도 보였다. Uridylate kinase를 이용한 분류는, 아주 높은 보존성에 의해서 생기는 16S rRNA 유전자를 이용한 문제점을 보완하여 원핵생물의 정확한 분류에 기여할 수 있을 것으로 사료되었다.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제26권2호
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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.