• Journal of Microbiology and Biotechnology
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• 제29권9호
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• pp.1391-1400
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• 2019

Canine parvoviral enteritis (PVE) is an important intestinal disease of the puppies; however, the potential impact of the canine parvovirus (CPV) on the gut microbiota has not been investigated. Therefore, the aim of this study was to evaluate the gut microbial shifts in puppies naturally infected with CPV. Fecal samples were collected from healthy dogs and those diagnosed with PVE at 4, 6, 8, and 12 weeks of age. The distal gut microbiota of dogs was characterized using Illumina MiSeq sequencing of the bacterial 16S rRNA genes. The sequence data were analyzed using QIIME with an Operational Taxonomic Unit definition at a similarity cutoff of 97%. Our results showed that the CPV was associated with significant microbial dysbiosis of the intestinal microbiota. Alpha diversity and species richness and evenness in dogs with PVE decreased compared to those of healthy dogs. At the phylum level, the proportion of Proteobacteria was significantly enriched in dogs with PVE while Bacteroidetes was significantly more abundant in healthy dogs (p < 0.05). In dogs with PVE, Enterobacteriaceae was the most abundant bacterial family accounting for 36.44% of the total bacterial population compared to only 0.21% in healthy puppies. The two most abundant genera in healthy dogs were Prevotella and Lactobacillus and their abundance was significantly higher compared to that of dogs with PVE (p < 0.05). These observations suggest that disturbances of gut microbial communities were associated with PVE in young dogs. Evaluation of the roles of these bacterial groups in the pathophysiology of PVE warrants further studies.

• 한국미생물·생명공학회지
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• 제47권3호
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• pp.401-411
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• 2019

All Idiomarina species are isolated from saline environments; microorganisms in such extreme habitats develop metabolic adaptations and can produce compounds such as proteases with an industrial potential. ARDRA and 16S rRNA gene sequencing are established methods for performing phylogenetic analysis and taxonomic identification. However, 16S-23S ITS is more variable than the 16S rRNA gene within a genus, and is therefore, used as a marker to achieve a more precise identification. In this study, ten protease producing Idiomarina strains isolated from the Peruvian salterns were characterized using biochemical and molecular methods to determine their bacterial diversity and industrial potential. In addition, comparison between the length and nucleotide sequences of a 16S-23S ITS region allowed us to assess the inter and intraspecies variability. Based on the 16S rRNA gene, two species of Idiomarina were identified (I. zobellii and I. fontislapidosi). However, biochemical tests revealed that there were differences between the strains of the same species. Moreover, it was found that the ITS contains two tRNA genes, $tRNA^{Ile(GAT)}$ and $tRNA^{Ala(TGC)}$, which are separated by an ISR of a variable size between strains of I. zobellii. In one strain of I. zobellii (PM21), we found nonconserved nucleotides that were previously not reported in the $tRNA^{Ala}$ gene sequences of Idiomarina spp. Thus, based on the biochemical and molecular characteristics, we can conclude that protease producing Idiomarina strains have industrial potential; only two I. zobellii strains (PM48 and PM72) exhibited the same properties. The differences between the other strains could be explained by the presence of subspecies.

• Journal of Microbiology and Biotechnology
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• 제29권3호
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• pp.441-453
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• 2019

Organic farming is considered an effective form of sustainable agricultural management. However, understanding of soil microbial diversity and composition under long-term organic and conventional farming is still limited and controversial. In this study, the Illumina MiSeq platform was applied to investigate the responses of soil bacterial and fungal diversity and compositions to organic farming (OF) and improved conventional farming (CF, applied straw retention) in the rice-wheat rotation system. The results highlighted that the alpha diversity of microbial communities did not differ significantly, except for higher bacterial diversity under OF. However, there were significant differences in the compositions of the soil bacterial and fungal communities between organic and conventional farming. Under our experimental conditions, through the ecological functional analysis of significant different or unique bacterial and fungal taxonomic members at the phyla and genus level, OF enhanced nitrogen, sulfur, phosphorus and carbon dynamic cycling in soil with the presence of Nodosilinea, Nitrospira, LCP-6, HB118, Lyngbya, GOUTA19, Mesorhizobium, Sandaracinobacter, Syntrophobacter and Sphingosinicella, and has the potential to strengthen soil metabolic ability with Novosphingobium. On the other hand, CF increased the intensity of nitrogen cycling with Ardenscatena, KD1-23, Iamia, Nitrosovibrio and Devosia, but enriched several pathogen fungal members, including Coniochaeta, Corallomycetella, Cyclaneusma, Cystostereum, Fistulina, Curvularia and Dissoconium.

• 한국물환경학회지
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• 제35권2호
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• pp.152-164
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• 2019

In this study, a Benthic Macroinvertebrates Family Index (BMFI) was developed using 100 indicator groups (99 families including Chironomidae with 2 phena). Families were assigned a score between 1 and 10 depending on their sensitivity to organic pollution. The BMFI was composed of the sensitivity and relative abundance of the indicator taxa. Sensitivity values of each group were generally similar to Biological Monitoring Working Party (BMWP) scores or Walley, Hawkes, Paisley, Trigg (WHPT) scores of UK, Japanese BMWP scores, and the FBI tolerance values of North America. However, sensitivity values of some taxa were significantly different from those of foreign countries, which seemed to have resulted from discrepancy in species composition, difference of taxonomic classification system, or methodological difference for estimation of sensitivity. As an annual average level, BMFI showed significant correlation with concentration of 5-day biochemical oxygen demand (BOD5) (correlation coefficient r = -0.80, n = 569 sites), total suspended solids (r = -0.68), and total phosphorus (r = -0.79). In addition, BMFI revealed strong correlation with Shannon-Weaver's species diversity (r = 0.85), Margalef's species richness (r = 0.85) and McNaughton's dominance (r = -0.84). Correlation between BMFI and water quality parameters or community indices such as species diversity did not show significant difference compared to that of species-level indices such as BMI (Benthic Macroinvertebrates Index). This means that BMFI is a more useful indicator in terms of easy identification of organisms. BMFI was used to assess the environmental status of 3,017 sites of Stream Ecosystem Survey conducted by the Korean Ministry of Environment between 2016 and 2018. As a result, about half of all sites appeared to be in good condition, and a quarter in poor condition.

• Mycobiology
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• 제49권4호
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• pp.385-395
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• 2021

Fungal endophytes have been recorded in various plant species with a richness of diversity, and their presence plays an essential role in host plant protection against biotic and abiotic stresses. This study applied the Illumina MiSeq sequencing platform based on the amplification of fungal ribosomal ITS2 region to analyze fungal endophytic communities of two oak species (Quercus mongolica and Q. serrata) with different oak wilt disease susceptibilities in Korea. The results showed a total of 230,768 sequencing reads were obtained and clustered at a 97% similarity threshold into 709 operational taxonomic units (OTUs). The OTUs of Q. serrata were higher than that of Q. mongolica with the number of 617 OTUs and 512 OTUs, respectively. Shannon index also showed that Q. serrata had a significantly higher level of fungal diversity than Q. mongolica. Total of OTUs were assigned into 5 fungal phyla, 17 classes, 60 orders, 133 families, 195 genera, and 280 species. Ascomycota was the dominant phylum with 75.11% relative abundance, followed by Basidiomycota with 5.28%. Leptosillia, Aureobasidium and Acanthostigma were the most abundant genera detected in Q. serrata with the average relative abundance of 2.85, 2.76, and 2.19%, respectively. On the other hand, Peltaster, Cladosporium and Monochaetia were the most common genera detected in Q. mongolica with the average relative abundance of 4.83, 3.03, and 2.87%, respectively. Our results indicated that fungal endophytic communities were significantly different between two oak species and these differences could influence responses of host trees to oak wilt disease caused by Raffaelea quercus-mongolicae.

• The Plant Pathology Journal
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• 제38권6호
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• pp.583-592
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• 2022

Root-knot nematode disease is a widespread and catastrophic disease of tobacco. However, little is known about the relationship between rhizosphere bacterial community and root-knot nematode disease. This study used 16S rRNA gene sequencing and PICRUSt to assess bacterial community structure and function changes in rhizosphere soil from Meloidogyne incognita-infected tobacco plants. We studied the rhizosphere bacterial community structure of M. incognita-infected and uninfected tobacco plants through a paired comparison design in two regions of tobacco planting area, Yuxi and Jiuxiang of Yunnan Province, southwest China. According to the findings, M. incognita infection can alter the bacterial population in the soil. Uninfested soil has more operational taxonomic unit numbers and richness than infested soil. Principal Coordinate Analysis revealed clear separations between bacterial communities from infested and uninfested soil, indicating that different infection conditions resulted in significantly different bacterial community structures in soils. Firmicutes was prevalent in infested soil, but Chloroflexi and Acidobacteria were prevalent in uninfested soil. Sphingomonas, Streptomyces, and Bradyrhizobium were the dominant bacteria genera, and their abundance were higher in infested soil. By PICRUSt analysis, some metabolism-related functions and signal transduction functions of the rhizosphere bacterial community in the M. incognita infection-tobacco plants had a higher relative abundance than those uninfected. As a result, rhizosphere soils from tobacco plants infected with M. incognita showed considerable bacterial community structure and function alterations.

• 대한본초학회지
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• 제34권4호
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• pp.1-8
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• 2019

Objectives : Rosae Multiflorae Fructus is a traditional medicine derived from the fruit of Rosa multiflora Thunb. a member of the Rosaceae family. Even though it has a single origin, the possibility of adulterants has always existed. In fact, we had discovered suspicious commercial samples of Rosae Multiflorae Fructus, imported from China. Methods : To define the taxonomic origin of Rosae Multiflorae Fructus and its adulterants, DNA barcode analysis of the internal transcribed spacer, trnL-F intergenic spacer, and psbA-trnH sequences was carried out. These DNA barcode sequences from the correct origin of Rosae Multiflorae Fructus were analyzed and compared with those of other samples from genus Rosa used as medicinal herbs. Results : The analyses of the three DNA barcode sequences efficiently distinguished Rosae Multiflorae Fructus from six other species in genus Rosa and also separated each species used in this study. According to the DNA barcoding results, none of the suspicious commercial samples were Rosae Multiflorae Fructus. RMF09 was identified as Rosa acicularis, whereas RMF10 and RMF11 were identified as Rosa davurica and Rosa rugosa, respectively. These results corroborated the existence of adulterants of Rosae Multiflorae Fructus. Conclusions : Our research provides useful information that could be used as a criterion for distinguishing between Rosae Multiflorae Fructus and its adulterants. These results will help in the prevention of adulteration and also suggest effective methods for verifying the origin of commercial herbal medicines derived from genus Rosa.

• Mass Spectrometry Letters
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• 제13권4호
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• pp.166-176
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• 2022

Banana peels are also widely used as bio-adsorbent in the removal of chemicals contaminants and heavy metals from water and soil. GC-MS plays an essential role in the phytochemical analysis and chemo taxonomic studies of medicinal plants containing biologically active components. Intrinsically, with the use of the flame ionization detector and the electron capture detector which have very high sensitivities, Gas chromatography can quantitatively determine materials present at very low concentrations and most important application is in pollution studies. In the present study banana peels were used as bio-adsorbent to remediate the heavy metal contaminated water taken from three different stations located around the industrial belts of Ranipet, Tamilnadu, India. The AAS analysis of the samples shows a decrement of chromium concentration of 98.93%, 96.16% and 96.5% in Station 1, 2 and 3 respectively which proves the efficiency of the powdered peels of Musa paradisiaca. The GC-MS analysis of the control and treated peels of Musa paradisiaca reveals the presence of phytochemicals like Acetic Acid, 1-Methylethyl Ester, DL-Glyceraldehyde Dimer, N-Hexadecanoic Acid, 3-Decyn-2-Ol, 26-Hydroxy, Cholesterol, Ergost-25-Ene-3,5,6,12-Tetrol, (3.Beta.,5.Alpha.,6.Beta.,12.Beta.)-, 1-Methylene-2b-Hydroxymethyl-3, and 3-Dimethyl-4b-(3-Methylbut-2-Enyl)-Cyclohexane in the control banana peels. The banana peels which were used for the treatment reveals the changes and alteration of the phytochemicals. It is concluded that the alteration in phytochemicals of the experimental banana peels were due to adsorption of chromium heavy metal from the sample.

• 한국미생물·생명공학회지
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• 제51권1호
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• pp.109-123
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• 2023

Preterm birth (PTB) is defined as giving birth prior to the 37th week of pregnancy and is a major cause of infant mortality. Studies have indicated that the vaginal microbiota's composition and its dysbiosis, particularly during pregnancy, may play a major role in PTB. While previous research work concentrated on well-studied microorganisms such as Lactobacillus, Prevotella, Gardnerella, various other microbes, and their significance in the vaginal microbiota's stability remain unknown. Moreover, current studies have focused primarily on the relative abundances of the microbes found, without considering their interactions with other members of the vaginal microbiota. In this work, we developed a novel computational approach and performed taxonomic classification of vaginal microbiota samples stratified longitudinally (Term/PTB) to observe compositional disparities and find underexamined microbes that may be contributing to PTB. Furthermore, we carried out a correlational analysis to build a microbial co-interaction network and investigated the functional implications of the genes present in both Term and PTB samples. The co-occurrence network revealed that Lactobacillus acts in solidarity to maintain the stability of the vaginal microbiota and did not have strong co-interactions with any of the other microbes. Similarly, microbes with strong interactions with Atopobium, a well-known marker microbe of PTB, were also observed. Additionally, several genes such as PTXA, FANCM, GPX, and DUSP were found to be playing an important role in the occurrence of PTB. This study provides a novel conceptual framework revealing distinct vaginal microbiota signatures that could be potential therapeutic targets for the prevention of PTB.

• Parasites, Hosts and Diseases
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• 제61권2호
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• pp.202-209
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• 2023

Lophomonas blattarum is an anaerobic protozoan living in the intestine of cockroaches and house dust mites, with ultramicroscopic characteristics such as the presence of a parabasal body, axial filament, and absence of mitochondria. More than 200 cases of Lophomonas infection of the respiratory tract have been reported worldwide. However, the current diagnosis of such infection depends only on light microscopic morphological findings from respiratory secretions. In this study, we attempted to provide more robust evidence of protozoal infection in an immunocompromised patient with atypical pneumonia, positive for Lophomonas-like protozoal cell forms. A direct search of bronchoalveolar lavage fluid via polymerase chain reaction (PCR), transmission electron microscopy (TEM), and metagenomic next-generation sequencing did not prove the presence of protozoal infection. PCR results were not validated with sufficient rigor, while de novo assembly and taxonomic classification results did not confirm the presence of an unidentified pathogen. The TEM results implied that such protozoal forms in light microscopy are actually non-detached ciliated epithelial cells. After ruling out infectious causes, the patient's final diagnosis was drug-induced pneumonitis. These findings underscore the lack of validation in the previously utilized diagnostic methods, and more evidence in the presence of L. blattarum is required to further prove its pathogenicity.