• Journal of Microbiology and Biotechnology
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• 제27권12호
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• pp.2241-2244
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• 2017

The structure of concanavalin A (ConA) has been studied intensively owing to its specific interactions with carbohydrates and its heterometal ($Ca^{2+}$ and $Mn^{2+}$) coordination. Most structures from X-ray crystallography have shown ConA as a dimer or tetramer, because the complex formation requires specific crystallization conditions. Here, we reported the monomeric structure of ConA with a resolution of $1.6{\AA}$, which revealed that metal coordination could trigger sugar-binding ability. The calcium coordination residue, Asn14, changed the orientation of carbohydrate-binding residues and biophysical details, including structural information, providing valuable clues for the development and application of detection kits using ConA.

• 한국환경과학회지
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• 제17권1호
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• pp.7-17
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• 2008

Simultaneous removal of $NH_3,\;H_2S$ and toluene in a contaminated air stream was investigated over 185 days in a biofilter packed with Zeocarbon granule as microbial support. In this study, multi-microorganisms including Nitrosomonas and Nitrobacter for nitrogen removal, Thiobacillus thioparus (ATCC 23645) for $H_2S$ removal, and Pseudomonas aeruginosa (ATCC 15692), Pseudomonas putida (ATCC 17484) and Pseudomonas putida (ATCC 23973) for toluene removal were used simultaneously. The empty bed residence time (EBRT) was 40-120 seconds and the feed (inlet) concentrations of $NH_3,\;H_2S$ and toluene were 0.02-0.11, 0.05-0.23 and 0.15-0.21 ppmv, respectively. The observed removal efficiency was 85%-99% for $NH_3$, 100% for $H_2S$, and 20-90% for toluene, respectively. The maximum elimination capacities were 9.3, 20.6 and $17g/m^3/hr\;for\;NH_3,\;H_2S$ and toluene, respectively. The results of kinetic model analysis showed that there were no particular evidences of interactions or inhibitions among the microorganisms, and that the three bio degradation reactions took place independently within a finite area of biofilm developed on the surface of the Zeocarbon carrier.

• Ecology and Resilient Infrastructure
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• 제4권2호
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• pp.93-96
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• 2017

Spatial variations of physicochemical and microbiological variables were examined to understand spatial heterogeneity of those variables in intertidal flat. Variograms were constructed for understanding spatial autocorrelations of variables by a geostatistical analysis and spatial correlations between two variables were evaluated by applications of a Cross-Mantel test with a Monte Carlo procedure (with 999 permutations). Water content, organic matter content, pH, nitrate, sulfate, chloride, dissolved organic carbon (DOC), four extracellular enzyme activities (${\beta}-glucosidase$, N-acetyl-glucosaminidase, phosphatase, arylsulfatase), and bacterial diversity in soil were measured along a transect perpendicular to shore line. Most variables showed strong spatial autocorrelation or no spatial structure except for DOC. It was suggested that complex interactions between physicochemical and microbiological properties in sediment might controls DOC. Intertidal flat sediment appeared to be spatially heterogeneous. Bacterial diversity was found to be spatially correlated with enzyme activities. Chloride and sulfate were spatially correlated with microbial properties indicating that salinity in coastal environment would influence spatial distributions of decomposition capacities mediated by microorganisms. Overall, it was suggested that considerations on the spatial distributions of physicochemical and microbiological properties in intertidal flat sediment should be included when sampling scheme is designed for decomposition processes in intertidal flat sediment.

• Journal of Microbiology and Biotechnology
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• 제23권10호
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• pp.1472-1477
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• 2013

Microalgae have been regarded as a natural resource for sustainable materials and fuels, as well as for removal of nutrients and micropollutants from wastewater, and their interaction with bacteria in wastewater is a critical factor to consider because of the microbial diversity and complexity in a variety of wastewater conditions. Despite their importance, very little is known about the ecological interactions between algae and bacteria in a wastewater environment. In this study, we characterized the wastewater bacterial community in response to the growth of a Selenastrum gracile UTEX 325 population in a real municipal wastewater environment. The Roche 454 GS-FLX Titanium pyrosequencing technique was used for indepth analysis of amplicons of 16S rRNA genes from different conditions in each reactor, with and without the algal population. The algal growth reduced the bacterial diversity and affected the bacterial community structure in the wastewater. The following in-depth analysis of the deep-sequenced amplicons showed that the algal growth selectively stimulated Sphingobacteria class members, especially the Sediminibacterium genus population, in the municipal wastewater environment.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• Journal of Microbiology and Biotechnology
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• 제28권10호
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• pp.1706-1715
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• 2018

Several non-methylotrophic bacteria have been reported to improve the growth and activity of methanotrophs; however, their interactions remain to be elucidated. We investigated the interaction between Methylocystis sp. M6 and Microbacterium sp. NM2. A batch co-culture experiment showed that NM2 markedly increased the biomass and methane removal of M6. qPCR analysis revealed that NM2 enhanced both the growth and methane-monooxygenase gene expression of M6. A fed-batch experiment showed that co-culture was more efficient in removing methane than M6 alone (28.4 vs. $18.8{\mu}mol{\cdot}l^{-1}{\cdot}d^{-1}$), although the biomass levels were similar. A starvation experiment for 21 days showed that M6 population remained stable while NM2 population decreased by 66% in co-culture, but the results were opposite in pure cultures, indicating that M6 may cross-feed growth substrates from NM2. These results indicate that M6 apparently had no negative effect on NM2 when M6 actively proliferated with methane. Interestingly, a batch experiment involving a dialysis membrane indicates that physical proximity between NM2 and M6 is required for such biomass and methane removal enhancement. Collectively, the observed interaction is beneficial to the methanotroph but adversely affects the non-methylotroph; moreover, it requires physical proximity, suggesting a tight association between methanotrophs and non-methylotrophs in natural environments.

• The Plant Pathology Journal
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• 제36권2호
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• pp.185-191
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• 2020

Streptomyces griseus S4-7, a well-characterized keystone taxon among strawberry microbial communities, shows exceptional disease-preventing ability. The whole-genome sequence, functional genes, and bioactive secondary metabolites of the strain have been described in previous studies. However, proteomics studies of not only the S4-7 strain, but also the Streptomyces genus as a whole, remain limited to date. Therefore, in the present study, we created a proteomics reference map for S. griseus S4-7. Additionally, analysis of differentially expressed proteins was performed against a wblE2 mutant, which was deficient in spore chain development and did not express an antifungal activity-regulatory transcription factor. We believe that our data provide a foundation for further in-depth studies of functional keystone taxa of the phytobiome and elucidation of the mechanisms underlying plant-microbe interactions, especially those involving the Streptomyces genus.

• 한국식품영양학회지
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• 제31권3호
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• pp.319-327
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• 2018

This paper defines the common features of synbiotics based on the definition of probiotics and prebiotics, and reviews the effectiveness of synbiotic food. The concept of synbiotics is defined as 'a mixture of prebiotics and probiotics that have a beneficial effect on the host, as a dietary supplement that alters living organisms in the gastrointestinal tract and improves their survival.' Synbiotic food contains ingredients with beneficial microbes that are expected to improve interactions between microbial and useful substances. Synbiotic foods may have anti-cancer and immune system-boosting effects. Improved digestion, healthier bowel movements, and overall increased intestinal health has been reported were reported after increasing the healthy microorganisms within the intestinal tract. In addition, depending on the type of food containing the symbiotic ingredients, more consistent weight control, improvement of cardiovascular health, and lower blood glucose levels may also be expected. Unlike previous studies, this review of synbiotics has shown that it is necessary for synergistic effects to take place among microorganisms and components to be further studied. Further research is needed on the safety and ingestion of microorganisms contained in synbiotics.

• Environmental Engineering Research
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• 제25권3호
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• pp.274-280
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• 2020

The marine sediment sustains from the anoxic condition due to increased nutrients of external sources. The nutrients are liberated from the sediment, which acts as an internal source. In hypoxic environments, anaerobic respiration results in the formation of several reduced matters, such as N₂ and NH₄⁺, N₂O, Fe²⁺, H₂S, etc. The experimental results have shown that nitrogen and sulfur played an influential, notable role in this biogeochemical cycle with expected chemical reductions and a 'diffusive' release of present nutrient components trapped in pore water inside sediment toward the bulk water. Nitate/ammonium, sulfate/sulfides, and ferrous/ferric irons are found to be the key players in these sediment-waters mutual interactions. Organonitrogen and nitrate in the sediment were likely to be converted to a form of ammonium. Reductive nitrogen is called dissimilatory nitrate reduction to ammonium and denitrification. The steady accumulation in the sediment and surplus increases in the overlying waters of ammonium strongly support this hypothesis as well as a diffusive action of the involved chemical species. Sulfate would serve as an essential electron acceptor so as to form acid volatile sulfides in present of Fe³⁺, which ended up as the Fe²⁺ positively with an aid of the residential microbial community.

• 치위생과학회지
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• 제19권2호
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• pp.77-85
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• 2019

In the past gut microbiome has been the main focus of microbiome research. Studies about the microbiome inside oral cavities and other organs are underway. Studies about the relationship between noninfectious diseases and periodontal diseases, and the negative effects of harmful oral microbes on systemic health have been published in the recent past. A lot of attention is being paid towards fostering a healthy oral microbial ecosystem. This study aimed to understand the roles and effects of the microbiome inside the human body can potentially help cure various diseases including inflammatory bowel diseases with no known cure such as Crohn's disease, atopic dermatitis, obesity, cancer, diabetes, brain diseases and oral diseases. The present study examined technological trends in the correlation between the human microbiome and diseases in the human body, interactions between the human body's immunity, the metabolic system, and the microbiome, and research trends in other countries. While it has been proven that human microbiome is closely correlated with human diseases, most studies are still in the early stage of trying to compare the composition of microbiomes between health and patient groups. Since the oral environment is a dynamic environment that changes due to not only food intake but also other external factors such as lifestyle, hygiene, and drug intake, it is necessary to continue in-depth research on the microbiome composition characteristics to understand the complex functions of oral microorganisms. Analyzing the oral microbiome using computational technology may aid in disease diagnosis and prevention.