• Asian-Australasian Journal of Animal Sciences
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• v.32 no.1
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• pp.82-91
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• 2019

Objective: This experiment was conducted to compare the structure and composition of ruminal microorganisms in goats with high and low neutral detergent fibre (NDF) digestibility. Methods: Nineteen crossbred goats were used as experimental animals and fed the same total mixed rations during the 30-day pre-treatment and 6-day digestion trialperiods. All faeces were collected during the digestion period for measuring the NDF digestibility. Then, high and the low NDF digestibility individuals were chosen for the high NDF digestibility group (HFD) and low NDF digestibility group (LFD), respectively. Rumen contents were collected for total microbial DNA extraction. The V4 region of the bacterial 16S rRNA gene was amplified using universal primers of bacteria and sequenced using high-throughput sequencer. The sequences were mainly analysed by QIIME 1.8.0. Results: A total of 18,694 operational taxonomic units were obtained, within 81.98% belonged to bacteria, 6.64% belonged to archaea and 11.38% was unassigned microorganisms. Bacteroidetes, Firmicutes, and Proteobacteria were the predominant microbial phyla in both groups. At the genus level, the relative abundance of fifteen microorganisms were significantly higher (p<0.05) and six microorganisms were extremely significantly higher (p<0.01) in LFD than HFD. Overall, 176 core shared genera were identified in the two groups. The relative abundance of 2 phyla, 5 classes, 10 orders, 13 families and 15 genera had a negative correlation with NDF digestibility, but only the relative abundance of Pyramidobacter had a positive correlation with NDF digestibility. Conclusion: There were substantial differences in NDF digestibility among the individual goats, and the NDF digestibility had significant correlation with the relative abundance of some ruminal microorganisms.

• Microbiology and Biotechnology Letters
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• v.47 no.3
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• pp.441-448
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• 2019

This study was aimed at identifying the lower airway microbiota in patients with lung cancer (LC) using protected brush sampling. We enrolled 37 patients undergoing diagnostic bronchoscopy for suspected LC, 26 with LC and 11 with benign diseases. Protected brush specimens were obtained from the contralateral lung and the side of the tumor; these specimens were analyzed by 16S rRNA-based-next-generation sequencing. The results indicated that the biodiversity was not different between groups, and there were no significant differences between the proportion of microorganisms in the tumor and in the contralateral side of patients with LC. In patients with LC, there was a higher abundance of several microorganisms including Capnocytophaga, Haemophilus, Enterococcus, and Streptococcus; whereas, in individuals without LC, Bacteroides, Lactobacillus, or Methylobacterium were more abundant. Malignancy could be determined with an accuracy of 70% by isolating Enterococcus, Capnocytophaga, or Actinomyces. Microbispora indicated benignity with a sensitivity of 55%, specificity of 88%, and accuracy of 78%. Lower airway microbiota in patients with LC is fairly similar in both the tumor and contralateral sites. Endobronchial microbiota is different in patients with and without LC, and these differences may have a potential clinical value as diagnostic or prognostic biomarkers.

• Microbiology and Biotechnology Letters
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• v.47 no.1
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• pp.105-115
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• 2019

Saline or alkaline condition in soil inhibits growth of most crop plants and limits crop yields in many parts of the world. Augmenting an alkaline soil with alkali-tolerant bacteria capable of promoting plant growth can be a promising approach in expanding fertile agricultural land. Near-shore environments of Dokdo Island, a remote island located in the middle of the East Sea, appear to have patches of seawater-influenced haloalkaline soil that is unsupportive for growth of conventional plants. To exploit metabolic capacities of alkali-tolerant bacteria for promoting plant growth in saline or alkaline soils, we isolated of alkali-tolerant bacteria from near-shore soil samples in Dokdo and investigated properties of the isolates. Alkali-tolerant bacteria were selectively cultivated by inoculating suspended and diluted soil samples on a plate medium adjusted to pH 10. Fifty colonies were identified based on their $GTG_5$-PCR genomic fingerprints and 16S rRNA gene sequences. Most isolates were affiliated to alkali-tolerant and/or halotolerant genera or species of the phyla Firmicutes (68%), Proteobacteria (30%) and Actinobacteria (2%). Unlike the typical soil bacterial flora in the island, alkali-tolerant isolates belonged to only certain taxa of terrestrial origin under the three phyla, which have traits of plant growth promoting activities including detoxification, phytohormone production, disease/pest control, nitrogen-fixation, phosphate solubilization or siderophore production. However, Firmicutes of marine origin generally dominated the alkali-tolerant community. Results of this study suggest that haloalkaline environments like Dokdo shore soils are important sources for plant growth promoting bacteria that can be employed in bio-augmentation of vegetation-poor alkaline soils.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.52 no.1
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• pp.67-73
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• 2019

We presented detailed morphological descriptions of the eggs, larvae and juvenile of Acanthaphritis unoorum based on specimens collected with bongo nets from Korean waters during the period May 2017-July 2018. We collected 18 individuals including eggs (n= 4, 0.77-0.85 mm in egg diameter), preflexion larvae (n= 6, 4.11-6.31 mm in standard length, SL), flexion larvae (n= 4, 6.60-7.82 mm SL), postflexion larvae (n= 3, 8.94-13.46 mm SL), and one juvenile (n= 1, 14.67 mm SL). The mitochondrial (mt) DNA 16S rRNA sequences of the eggs, and the cytochrome c oxidase subunit I (COI) sequences of the larvae were identical to those of A. unoorum adults (genetic distances <0.01). The A. unoorum larvae and the juvenile that we collected were morphologically similar to those of Dactylopsaron dimorphicum, but the A. unoorum specimens were readily distinguishable by the presence of lateral melanophores. This is the first record of A. unoorum in Korean waters. We propose a new Korean name for A. unoorum: "O-ri-bu-ri-nuntung-i".

• Journal of Microbiology and Biotechnology
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• v.29 no.1
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• pp.79-90
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• 2019

Lichens are generally known as self-sufficient, symbiotic life-forms between fungi and algae/cyanobacteria, and they also provide shelter for a wide range of beneficial bacteria. Currently, bacterial-derived biodegradable polyhydroxyalkanoate (PHA) is grabbing the attention of many researchers as a promising alternative to non-degradable plastics. This study was conducted to develop a new method of PHA production using unexplored lichen-associated bacteria, which can simultaneously degrade two ubiquitous industrial toxins, anthracene and naphthalene. Here, 49 lichen-associated bacteria were isolated and tested for PHA synthesis. During the GC-MS analysis, a potential strain of EL19 was found to be a 3-hydroxyhexanoate (3-HHx) accumulator and identified as Pseudomonas sp. based on the 16S rRNA sequencing. GC analysis revealed that EL19 was capable of accumulating 30.62% and 19.63% of 3-HHx from naphthalene and anthracene, respectively, resulting in significant degradation of 98% and 96% of naphthalene and anthracene, respectively, within seven days. Moreover, the highly expressed phaC gene verified the genetic basis of $PHA_{mcl}$ production under nitrogen starvation conditions. Thus, this study strongly supports the hypothesis that lichen-associated bacteria can detoxify naphthalene and anthracene, store energy for extreme conditions, and probably help the associated lichen to live in extreme conditions. So far, this is the first investigation of lichen-associated bacteria that might utilize harmful toxins as feasible supplements and convert anthracene and naphthalene into eco-friendly 3-HHx. Implementation of the developed method would reduce the production cost of $PHA_{mcl}$ while removing harmful waste products from the environment.

• Journal of Microbiology and Biotechnology
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• v.31 no.9
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• pp.1218-1230
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• 2021

Cold-adapted plant growth-promoting bacteria (PGPB) with multiple functions are an important resource for microbial fertilizers with low-temperature application. In this study, culturable cold-adapted PGPB strains with nitrogen fixation and phosphorus solubilization abilities were isolated. They were screened from root and rhizosphere of four dominant grass species in nondegraded alpine grasslands of the Qilian Mountains, China. Their other growth-promoting characteristics, including secretion of indole-3-acetic acid (IAA), production of siderophores and ACC deaminase, and antifungal activity, were further studied by qualitative and quantitative methods. In addition, whether the PGPB strains could still exert plant growth-promoting activity at 4℃ was verified. The results showed that 67 isolates could maintain one or more growth-promoting traits at 4℃, and these isolates were defined as cold-adapted PGPB. They were divided into 8 genera by 16S rRNA gene sequencing and phylogenetic analysis, of which Pseudomonas (64.2%) and Serratia (13.4%) were the common dominant genera, and a few specific genera varied among the plant species. A test-tube culture showed that inoculation of Elymus nutans seedlings with cold-adapted PGPB possessing different functional characteristics had a significant growth-promoting effect under controlled low-temperature conditions, including the development of the roots and aboveground parts. Pearson correlation analysis revealed that different growth-promoting characteristics made different contributions to the development of the roots and aboveground parts. These cold-adapted PGPB can be used as excellent strain resources suitable for the near-natural restoration of degraded alpine grasslands or agriculture stock production in cold areas.

• Journal of Microbiology and Biotechnology
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• v.31 no.10
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• pp.1420-1429
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• 2021

The safety of the probiotic strain Q180, which exerts postprandial lipid-lowering effects, was bioinformatically and phenotypically evaluated. The genome of strain Q180 was completely sequenced, and single circular chromosome of 3,197,263 bp without any plasmid was generated. Phylogenetic and related analyses using16S rRNA gene and whole-genome sequences revealed that strain Q180 is a member of Lactiplantibacillus (Lp., formerly Lactobacillus) plantarum. Antimicrobial resistance (AMR) genes were bioinformatically analyzed using all Lp. plantarum genomes available in GenBank, which showed that AMR genes are present differently depending on Lp. plantarum strains. Bioinformatic analysis demonstrated that some mobile genetic elements such as prophages and insertion sequences were identified in the genome of strain Q180, but because they did not contain harmful genes such as AMR genes and virulence factor (VF)- and toxin-related genes, it was suggested that there is no transferability of harmful genes. The minimum inhibition concentrations of seven tested antibiotics suggested by the European Food Safety Authority guidelines were slightly lower than or equal to the microbiological cut-off values for Lp. plantarum. Strain Q180 did not show hemolytic and gelatinase activities and biogenic amine-producing ability. Taken together, this study demonstrated the safety of strain Q180 in terms of absence of AMR genes and VF- and toxin-related genes as a probiotic strain.

• Journal of Korean Society on Water Environment
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• v.36 no.6
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• pp.581-591
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• 2020

In this study, two types of reactors were operated to examine the properties of methanol uptake under the high-rate denitrification process. In a sequencing batch reactor, the denitrifying activity was enriched up to 0.80 g-N/g-VSS-day for 72 days. Then, the enriched denitrifying sludge was transferred to a completely stirred tank reactor (CSTR). At the final phase on Day 46-50, the nitrogen removal efficiency was around 100% and the total nitrogen removal rate reached 0.097±0.003 kg-N/㎥-day. During the continuous process, the sludge settling index (SVI30) was stabilized as 118.3 mL/g with the biomass concentration of 1,607 mg/L. The continuous denitrifying process was accelerated by using a sequencing batch reactor (SBR) with a total nitrogen removal rate of 0.403±0.029 kg-N/㎥-day with a high biomass concentration of 8,433 mg-VSS/L. Because the reactor was open to ambient air with the dissolved oxygen range of 0.2-0.5 mg-O2/L, an increased organic carbon requirement of 5.58±0.70 COD/NO3--N was shown for the SBR in comparison to the value of 4.13±0.94 for the test of the same biomass in a completely anaerobic batch reactor. The molecular analysis based on the 16S rRNA gene showed that Methyloversatilis discipulorum and Hyphomicrobium zavarzinii were the responsible denitrifiers with the sole organic carbon source of methanol.

• Journal of Microbiology and Biotechnology
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• v.31 no.5
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• pp.747-755
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• 2021

The effects of the gut microbiome on both allergy and autoimmunity in dermatological diseases have been indicated in several recent studies. Chronic spontaneous urticaria (CSU) is a disease involving allergy and autoimmunity, and there is no report detailing the role of microbiota alterations in its development. This study was performed to identify the fecal microbial composition of CSU patients and investigate the different compositions and potential genetic functions on the fecal microbiota between CSU patients and normal controls. The gut microbiota of CSU patients and healthy individuals were obtained by 16s rRNA massive sequencing. Gut microbiota diversity and composition were compared, and bioinformatics analysis of the differences was performed. The gut microbiota composition results showed that Firmicutes, Bacteroidetes, Proteobacteria, and Verrucomicrobia were dominant microbiota in CSU patients. The differential analysis showed that relative abundance of the Proteobacteria (p = 0.03), Bacilli (p = 0.04), Enterobacterales (p = 0.03), Enterobacteriaceae (p = 0.03) was significantly increased in CSU patients. In contrast, the relative abundance of Megamonas, Megasphaera, and Dialister (all p < 0.05) in these patients significantly decreased compared with healthy controls. The different microbiological compositions impacted normal gastrointestinal functions based on function prediction, resulting in abnormal pathways, including transport and metabolism. We found CSU patients exhibited gut microbiota dysbiosis compared with healthy controls. Our results indicated CSU is associated with gut microbiota dysbiosis and pointed out that the bacterial taxa increased in CSU patients, which might be involved in the pathogenesis of CSU. These results provided clues for future microbial-based therapies on CSU.

• Journal of Applied Biological Chemistry
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• v.63 no.4
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• pp.429-437
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• 2020

This study aimed to investigate the change in physicochemical properties and lactic acid bacterial communities during kimchi fermentation at different temperatures (8, 15, and 25 ℃) using two molecular genetics approaches, multiplex polymerase chain reaction and 16S rRNA gene sequencing. The pH during fermentation at 8, 15, and 25 ℃ decreased from 6.17 on the initial fermentation day to 3.92, 3.79, and 3.48 after 54, 30, and 24 days of fermentation, respectively, while the acidity increased from 0.24% to 1.12, 1.35, and 1.54%, respectively. In particular, the levels of lactic acid increased from 3.74 g/L on the initial day (day 0) to 14.43, 20.60, and 27.69 g/L during the fermentation after 24, 18, and 12 days at 8, 15, and 25 ℃, respectively, after that the lactic acid concentrations decreased slowly. The predominance of lactic acid bacteria (LAB) in the fermented kimchi was dependent on fermentation stage and temperature: Lactobacillus sakei appeared during the initial stage and Leuconsotoc mesenteroides was observed during the optimum-ripening stage at 8, 15, and 25 ℃. Lac. sakei and Lactobacillus plantarum grew rapidly in kimchi produced at 8, 15, and 25 ℃. In addition, Weissella koreensis first appeared at days 12, 9, and 6 at 8, 15, and 25 ℃ of fermentation, respectively. This result suggests that LAB population dynamics are rather sensitive to environmental conditions, such as pH, acidity, salinity, temperature, and chemical factors including free sugar and organic acids.