• Journal of Microbiology and Biotechnology
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• v.31 no.7
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• pp.967-977
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• 2021

A total of 37 bacterial isolates were obtained from dye-contaminated soil samples at a textile processing factory in Nakhon Ratchasima Province, Thailand, and the potential of the isolates to decolorize and biotransform azo dye Reactive Red 141 (RR141) was investigated. The most potent bacterium was identified as Paenibacillus terrigena KKW2-005, which showed the ability to decolorize 96.45% of RR141 (50 mg/l) within 20 h under static conditions at pH 8.0 and a broad temperature range of 30-40℃. The biotransformation products were analyzed by using UV-Vis spectrophotometry and Fourier-transform infrared spectroscopy. Gas chromatography-mass spectroscopy analysis revealed four metabolites generated from the reductive biodegradation, namely sodium 3-diazenylnaphthalene-1,5-disulfonate (I), sodium naphthalene-2-sufonate (II), 4-chloro-1,3,5-triazin-2-amine (III) and N¹-(1,3,5-triazin-2-yl) benzene-1,4-diamine (IV). Decolorization intermediates reduced phytotoxicity as compared with the untreated dye. However, they had phytotoxicity when compared with control, probably due to naphthalene and triazine derivatives. Moreover, genotoxicity testing by high annealing temperature-random amplified polymorphic DNA technique exhibited different DNA polymorphism bands in seedlings exposed to the metabolites. They compared to the bands found in seedlings subjected to the untreated dye or distilled water. The data from this study provide evidence that the biodegradation of Reactive Red 141 by P. terrigena KKW2-005 was genotoxic to the DNA seedlings.

• Animal Bioscience
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• v.36 no.6
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• pp.879-890
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• 2023

Objective: This study was conducted to evaluate the use of Megasphaera elsdenii (M. elsdenii) as a probiotic on rumen fermentation, production performance, carcass traits and health of ruminants by integrating data from various related studies using meta-analysis. Methods: A total of 32 studies (consisted of 136 data points) were obtained and integrated into a database. The parameters integrated were fermentation products, rumen microbes, production performance, carcass quality, animal health, blood and urine metabolites. Statistical analysis of the compiled database used a mixed model methodology. Different studies were considered random effects, while M. elsdenii supplementation doses were considered fixed effects. p-values and the Akaike information criterion were employed as model statistics. The model was deemed significant at p<0.05 or had a tendency to be significant when p-value between 0.05<p<0.10. Results: Supplementation with M. elsdenii increased (p<0.05) some proportion of fermented rumen products such as propionate, butyrate, isobutyrate, and valerate, and significantly reduced (p<0.05) lactic acid concentration, acetate proportion, total bacterial population and methane emission. Furthermore, the probiotic supplementation enhanced (p<0.05) livestock production performance, especially in the average daily gain and body condition score. Regarding the carcass quality, hot carcass weight and carcass gain were elevated (p< 0.05) due to the M. elsdenii supplementation. Animal health also showed improvement as indicated by the lower (p<0.05) diarrhoea and bloat incidences as well as the liver abscess. However, M. elsdenii supplementation had negligible effects on blood and urine metabolites of ruminants. Conclusion: Supplementation of M. elsdenii is capable of decreasing ruminal lactic acid concentration, enhancing rumen health, elevating some favourable rumen fermentation products, and in turn, increasing production performance of ruminants.

• Journal of Microbiology and Biotechnology
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• v.33 no.6
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• pp.753-759
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• 2023

The genus Paenibacillus contains a variety of biologically active compounds that have potential applications in a range of fields, including medicine, agriculture, and livestock, playing an important role in the health and economy of society. Our study focused on the bacterium SS4^T (KCTC 43402^T = GDMCC 1.3498^T), which was characterized using a polyphasic taxonomic approach. This strain was analyzed using antiSMASH, BAGEL4, and PRISM to predict the secondary metabolites. Lassopeptide clusters were found using all three analysis methods, with the possibility of secretion. Additionally, PRISM found three biosynthetic gene clusters (BGC) and predicted the structure of the product. Genome analysis indicated that glucoamylase is present in SS4^T. 16S rRNA sequence analysis showed that strain SS4^T most closely resembled Paenibacillus marchantiophytorum DSM 29850^T (98.22%), Paenibacillus nebraskensis JJ-59^T (98.19%), and Paenibacillus aceris KCTC 13870^T (98.08%). Analysis of the 16S rRNA gene sequences and Type Strain Genome Server (TYGS) analysis revealed that SS4^T belongs to the genus Paenibacillus based on the results of the phylogenetic analysis. As a result of the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) results, SS4^T was determined to belong to the genus Paenibacillus. Comparing P. marchantiophytorum DSM 29850^T with average nucleotide identity (ANI 78.97%) and digital DNA-DNA hybridization (dDDH 23%) revealed values that were all less than the threshold for bacterial species differentiation. The results of this study suggest that strain SS4^T can be classified as a Paenibacillus andongensis species and is a novel member of the genus Paenibacillus.

• Journal of Microbiology and Biotechnology
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• v.34 no.6
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• pp.1214-1221
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• 2024

The accumulating evidence substantiates the indispensable role of gut microbiota in modulating the pathogenesis of type 2 diabetes. Uncovering the intricacies of the mechanism is imperative in aiding disease control efforts. Revealing key bacterial species, their metabolites and/or metabolic pathways from the vast array of gut microorganisms can significantly contribute to precise treatment of the disease. With a high prevalence of type 2 diabetes in Inner Mongolia, China, we recruited volunteers from among the Mongolian population to investigate the relationship between gut microbiota and the disease. Fecal samples were collected from the Volunteers of Mongolia with Type 2 Diabetes group and a Control group, and detected by metagenomic analysis and untargeted metabolomics analysis. The findings suggest that Firmicutes and Bacteroidetes phyla are the predominant gut microorganisms that exert significant influence on the pathogenesis of type 2 diabetes in the Mongolian population. In the disease group, despite an increase in the quantity of most gut microbial metabolic enzymes, there was a concomitant weakening of gut metabolic function, suggesting that the gut microbiota may be in a compensatory state during the disease stage. β-Tocotrienol may serve as a pivotal gut metabolite produced by gut microorganisms and a potential biomarker for type 2 diabetes. The metabolic biosynthesis pathways of ubiquinone and other terpenoid quinones could be the crucial mechanism through which the gut microbiota regulates type 2 diabetes. Additionally, certain Clostridium gut species may play a pivotal role in the progression of the disease.

• Microbiology and Biotechnology Letters
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• v.45 no.2
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• pp.124-132
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• 2017

Microbial secondary metabolites of marine organisms are regarded as major sources of structurally and biologically novel compounds with numerous potential uses. Sponge-microbe associations are among the most interesting sources for exploring bioactive compounds. In this study, the bacterial strain Microbulbifer sp. (127CP7-12) was isolated from the Asian marine sponge Hymeniacidon sinapium collected at an intertidal zone on the west coast of Korea. Cultured bacteria produced a violet pigment, and optimal culture conditions for violet pigment production were investigated. Maximum production of the violet pigment from the strain culture was observed under the conditions of $25^{\circ}C$, pH 6.0, and 3% NaCl. Acetone provided better extraction of the pigment from fermented broth compared with ethanol and methanol. The proposed structure of the major component in the extracted crude pigment was determined via high-performance liquid chromatography, nuclear magnetic resonance, mass spectrometry, and UV spectra analyses, which showed that the metabolite was the promising bioactive compound violacein. This study describes the examination of marine bioactive materials from microbe-engaged metabolites and the ecological implications of the sponge-microbe association in a changing ocean.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.67-67
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• 2018

Trichoderma species are a rich source of metabolites, but less known for biomedical potential. This work deals with antibacterial and antioxidant potentials of intracellular non-cytotoxic metabolites, extracted from Trichoderma atroviride (KNUP001). A total of 53 fractions was collected by column chromatography and tested for cytotoxicity by MTT assay. Only one fraction (F41) was found to be non-toxic to Vero cells with $95.4{\pm}0.61%$ of survival. The F41 was then subjected to chemical analysis, antibacterial and antioxidant assays. The F41 at $500{\mu}g.ml^{-1}$ showed the total antioxidant of $48.70{\pm}2.90%$, DPPH radical scavenging activity of $37.25{\pm}2.25$, nitric oxide (NO) radical scavenging activity of $54.55{\pm}1.95$ and $H_2O_2$ radical scavenging activity of $43.75{\pm}3.21$. The F41 at $25{\mu}g.ml^{-1}$ displayed antibacterial activity against E. coli ($14.25{\pm}0.2mm$), P. mirabilis ($10.4{\pm}0.6mm$), S. dysenteriae ($18.6{\pm}03mm$), S. paratyphi A ($14.1{\pm}1.1mm$), E. aerogenes ($5.6{\pm}0.4mm$) and S. marcescens ($14.25{\pm}0.2mm$). GC-MS analysis revealed the dominant presence of oleic acid C 18.1 (63.18%), n-hexadecanoic acid (6.17%), and ethyl oleate (4.93%) and potent molecules such as 8-[(2E)-2-(3-hydroxybenzylidene)hydrazinyl]-1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione, 2-(Dimethylamino)ethyl (1Z)-N-hydroxy-2-(4-morpholinyl)-2-oxoethanimidothioate, Fluorene in the F41, and virtual study revealed that these molecules are likely responsible for the antibacterial activities of F41. Hence, further investigation deserves on purification and characterization of the active metabolites from T. atroviride strain KNUP001 towards developing molecular leads to effective antibacterial drugs, and non-toxic to host cells.

• Food Science of Animal Resources
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• v.44 no.5
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• pp.1080-1095
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• 2024

In contemporary society, the increasing number of pet-owning households has significantly heightened interest in companion animal health, expanding the probiotics market aimed at enhancing pet well-being. Consequently, research into the gut microbiota of companion animals has gained momentum, however, ethical and societal challenges associated with experiments on intelligent and pain-sensitive animals necessitate alternative research methodologies to reduce reliance on live animal testing. To address this need, the Fermenter for Intestinal Microbiota Model (FIMM) is being investigated as an in vitro tool designed to replicate gastrointestinal conditions of living animals, offering a means to study gut microbiota while minimizing animal experimentation. The FIMM system explored interactions between intestinal microbiota and probiotics within a simulated gut environment. Two strains of commercial probiotic bacteria, Enterococcus faecium IDCC 2102 and Bifidobacterium lactis IDCC 4301, along with a newly isolated strain from domestic dogs, Lactobacillus acidophilus SLAM AK001, were introduced into the FIMM system with gut microbiota from a beagle model. Findings highlight the system's capacity to mirror and modulate the gut environment, evidenced by an increase in beneficial bacteria like Lactobacillus and Faecalibacterium and a decrease in the pathogen Clostridium. The study also verified the system's ability to facilitate accurate interactions between probiotics and commensal bacteria, demonstrated by the production of short-chain fatty acids and bacterial metabolites, including amino acids and gamma-aminobutyric acid precursors. Thus, the results advocate for FIMM as an in vitro system that authentically simulates the intestinal environment, presenting a viable alternative for examining gut microbiota and metabolites in companion animals.

• Korean Journal of Microbiology
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• v.47 no.3
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• pp.179-187
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• 2011

This review describes the characteristics of various unculturable soil bacteria, successfully-cultivating examples of those bacteria, and the diverse factors to be considered for successful cultivation. Most importantly, the selection of proper media is very important because unculturable bacteria demand different types of nutrients at various concentrations of substrates, nitrogens and phosphorus. To develop a new medium to successfully culture unculturable bacteria from soil, molecular ecological studies should be combined together. The inoculum size on a plate is also important: less than 50 bacterial cells are recommended to be plated on a single culture plate. The environmental factors such as pH and salt concentration of the medium need to be adjusted as similar as possible to mimic the original soil environments, and the trial of the various temperatures and extended period of cultivation are better. Since one cannot simply tell about which one was unculturable among a great number of colonies grown on a newly developed medium, some suitable detection methods and fast identification methods are required. Many soil bacteria live with cooperation one another in their communities, so that enrichment such as coculture of using other bacterial metabolites and subsequent pure cultures can also guarantee successful cultivation of the previously uncultured bacteria in soil. Here, this review will discuss for the future perspectives to culture the unculturable soil bacteria.

• Journal of Microbiology and Biotechnology
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• v.21 no.2
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• pp.204-211
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• 2011

To yield high concentrations of protein expressed by genetically modified Escherichia coli, it is important that the bacterial strains are cultivated to high cell density in industrial bioprocesses. Since the expressed target protein is mostly accumulated inside the E. coli cells, the cellular product formation can be directly correlated to the bacterial biomass concentration. The typical way to determine this concentration is to sample offline. Such manual sampling, however, wastes time and is not efficient for acquiring direct feedback to control a fedbatch fermentation. An E. coli K12-derived strain was cultivated to high cell density in a pressurized stirred bioreactor on a pilot scale, by detecting biomass concentration online using a capacitance probe. This E. coli strain was grown in pure minimal medium using two carbon sources (glucose and glycerol). By applying exponential feeding profiles corresponding to a constant specific growth rate, the E. coli culture grew under carbon-limited conditions to minimize overflow metabolites. A high linearity was found between capacitance and biomass concentration, whereby up to 85 g/L dry cell weight was measured. To validate the viability of the culture, the oxygen transfer rate (OTR) was determined online, yielding maximum values of 0.69 mol/l/h and 0.98mol/l/h by using glucose and glycerol as carbon sources, respectively. Consequently, online monitoring of biomass using a capacitance probe provides direct and fast information about the viable E. coli biomass generated under aerobic fermentation conditions at elevated headspace pressures.

• Journal of Microbiology and Biotechnology
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• v.17 no.6
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• pp.934-944
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• 2007

Paenibacillus polymyxa E681 is known to be able to suppress plant diseases by producing antimicrobial compounds and to promote plant growth by producing phytohormones, and secreting diverse degrading enzymes. In spite of these capabilities, little is known regarding the flow of information from the bacterial strain to the barley roots. In an attempt to determine the flow of information from the bacterial strain to barley roots, the strain was grown in the presence and absence of barley, and two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and MALDI-TOF mass spectrometry were used. 2D-PAGE detected approximately 1,000 spots in the cell and 1,100 spots in the supernatant at a pH 4-10 gradient. Interestingly, about 80 spots from each sample showed quantitative variations. Fifty-three spots from these were analyzed by MALDI-TOF mass spectrometry and 28 proteins were identified. Most of the cytosolic proteins expressed at higher levels were found in P. polymyxa E681 cells grown in the presence of barley rather than in the absence of barley. Proteins detected at a lower level in the surpernatant of P. polymyxa E68l cells grown in the presence of barley were lipoprotein, glucose-6-phosphate 1-dehydrogenase, heat-shock protein HtpG, spermidine synthase, OrfZ, ribonuclease PH, and coenzyme PQQ synthesis protein, and flagellar hook-associated protein 2 whereas proteins detected at a higher level in the surpernatant of P. polymyxa E681 cells grown in the presence of barley included D-alanyl-D-alanine ligase A, isopentenyl-diphosphate delta-isomerase, ABC transporter ATP-binding protein Uup, lipase. Many of the proteins belonging to plant-induced stimulons are associated with biosynthetic metabolism and metabolites of proteins and transport. Some of these proteins would be expected to be induced by environmental changes resulting from the accumulation of plant-secreted substances.