• Asian-Australasian Journal of Animal Sciences
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• v.30 no.1
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• pp.100-110
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• 2017

Objective: The gastrointestinal tract of sheep contain complex microbial communities that influence numerous aspects of the sheep's health and development. The objective of this study was to analyze the composition and diversity of the microbiota in the gastrointestinal tract sections (rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum) of sheep. Methods: This analysis was performed by 454 pyrosequencing using the V3-V6 region of the 16S rRNA genes. Samples were collected from five healthy, small tailed Han sheep aged 10 months, obtained at market. The bacterial composition of sheep gastrointestinal microbiota was investigated at the phylum, class, order, family, genus, and species levels. Results: The dominant bacterial phyla in the entire gastrointestinal sections were Firmicutes, Bacteroidetes, and Proteobacteria. In the stomach, the three most dominant genera in the sheep were Prevotella, unclassified Lachnospiraceae, and Butyrivibrio. In the small intestine, the three most dominant genera in the sheep were Escherichia, unclassified Lachnospiraceae, and Ruminococcus. In the large intestine, the three most dominant genera in the sheep were Ruminococcus, unclassified Ruminococcaceae, and Prevotella. R. flavefaciens, B. fibrisolvens, and S. ruminantium were three most dominant species in the sheep gastrointestinal tract. Principal Coordinates Analysis showed that the microbial communities from each gastrointestinal section could be separated into three groups according to similarity of community composition: stomach (rumen, reticulum, omasum, and abomasum), small intestine (duodenum, jejunum, and ileum), and large intestine (cecum, colon, and rectum). Conclusion: This is the first study to characterize the entire gastrointestinal microbiota in sheep by use of 16S rRNA gene amplicon pyrosequencing, expanding our knowledge of the gastrointestinal bacterial community of sheep.

• Journal of Korean society of Dental Hygiene
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• v.18 no.5
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• pp.843-852
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• 2018

Objectives: The study aimed to isolate the abundant bacteria in dental caries in children and to investigate the bacterial species involved in addition to those that have been previously reported. Methods: The specimens were collected from the supragingival plaques of each dental caries area, pit and fissure caries, deep dentinal caries, smooth surface caries, and dental caries, and from healthy subjects in the control group. Bacteria were cultured from these specimens, DNA was extracted from the isolated bacteria, and the 16S rRNA gene sequences were analyzed and identified. Results: Based on the results of the 16S rRNA gene sequence analysis for the 90 strains of dominant bacteria from the 45 specimens, 5, 7, 8, 7, and 13 species were identified from the supragingival plaques from healthy teeth, pit and fissure caries, deep dentinal caries, smooth surface caries, and dental caries, respectively. In healthy teeth, Actinomyces naeslundii dominated. Corynebacterium durum, Ralstonia pickettii, and Streptococcus intermedius showed equal distribution. The dominant bacterial species in dental caries, S. sanguinis, showed the greatest difference in prevalence in pit and fissure caries. In deep dentinal caries, S. mutans and Lactobacillus rhamnosus were dominant; in smooth surface caries, S. mutans and S. sanguinis were dominant; and in the supragingival plaques of dental caries, S. sanguinis and S. mutans were dominant. Conclusions: The bacterial species isolated from dental caries encompassed four phyla, eight genera, and 22 species. In addition, the SS1-2 strain, belonging to the genus Neisseria, was identified as a new species from among the isolated strains.

• Journal of The Korean Astronomical Society
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• v.46 no.3
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• pp.125-131
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• 2013

We present the relation between the genus in cosmology and the Betti numbers for excursion sets of three- and two-dimensional smooth Gaussian random fields, and numerically investigate the Betti numbers as a function of threshold level. Betti numbers are topological invariants of figures that can be used to distinguish topological spaces. In the case of the excursion sets of a three-dimensional field there are three possibly non-zero Betti numbers; ${\beta}_0$ is the number of connected regions, ${\beta}_1$ is the number of circular holes (i.e., complement of solid tori), and ${\beta}_2$ is the number of three-dimensional voids (i.e., complement of three-dimensional excursion regions). Their sum with alternating signs is the genus of the surface of excursion regions. It is found that each Betti number has a dominant contribution to the genus in a specific threshold range. ${\beta}_0$ dominates the high-threshold part of the genus curve measuring the abundance of high density regions (clusters). ${\beta}_1$ dominates the genus near the median thresholds which measures the topology of negatively curved iso-density surfaces, and ${\beta}_2$ corresponds to the low-threshold part measuring the void abundance. We average the Betti number curves (the Betti numbers as a function of the threshold level) over many realizations of Gaussian fields and find that both the amplitude and shape of the Betti number curves depend on the slope of the power spectrum n in such a way that their shape becomes broader and their amplitude drops less steeply than the genus as n decreases. This behaviour contrasts with the fact that the shape of the genus curve is fixed for all Gaussian fields regardless of the power spectrum. Even though the Gaussian Betti number curves should be calculated for each given power spectrum, we propose to use the Betti numbers for better specification of the topology of large scale structures in the universe.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.9 no.3
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• pp.93-105
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• 2004

Spatio-temporal distribution patterns of the major dominant species were assessed from bimonthly monitoring of macrotidal flat in Cheokjeon, Incheon, Korea between September 1990 and July 1992. Overall, macrofauna comprised a total of 111 species, 25,491 inds.136 ㎡. The result of Le Bris index, dominance ranking of the lead-ing species showed that the top 15 species accounting for 74.8% (19,072 inds.) of total density. In Cheokjeon tidal flat, some species were especially habitat-restricted such as genus Nephtys (Annelids; Polychaetes) and Mac-rophthalmus (Crustaceans; Decapods). Based on the density data, the five dominant species were the polychaetes Het-eromastus filiformis, the bivalves Mactra veneriformis and Solen strictus, the brachyurans Macrophthalmus japonicus, the holothuriodeans Protankyra bidentata. The results of one-way ANOVA, mean value of H. filiformis and M. ven-eriformis did not show significant changes with tidal elevation and sediment composition (p>0.05). But, other species (S. strictus, M. japonicus and P. bidentata) showed significant variations (p<0.001). In conclusion, these indicate significant spatial fluctuation with tidal elevation and sediment characteristics in some species.

• Korean Journal of Agricultural Science
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• v.47 no.2
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• pp.219-227
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• 2020

Among insect species, black soldier fly larvae (BSFL) is a promising ingredient for animal feed as a dietary source. Moreover, BSFL contains a high content of lauric acid (C12:0), which has antimicrobial effects. Therefore, this study evaluated the effect of BSFL oil (BSFLO) as a partial or total replacement of soybean oil (SBO) on the cecal microbiota in broilers. A total of 210 male broiler chickens (Ross 308) at one-day of age were randomly allotted to 3 dietary treatments (10 replicates and 7 birds/group): a basal control diet (CON), the basal diet in which SBO was replaced by 50% (50 BSFLO) or 100% (100 BSFLO) BSFLO. At the end of the study (d 35), 18 birds (6 broilers/treatment) were randomly selected and slaughtered. Samples of cecal digesta were collected to verify their cecal microbiota. Overall, 235,978 gene sequences were generated, and a total of 4,398 operational taxonomic units were identified in the three groups. At the phylum level, Firmicutes was the dominant phyla in all three groups. At the genus level, Faecalibacterium was the dominant genera in all the treatments. There were no significant differences in the relative abundances of all the genera between the BSFLO groups and CON. However, the genus Erysipelatoclostridium was more abundant in the 50 BSFLO group than in the CON (p < 0.05). In conclusion, the substitution of SBO with BSFLO in broiler diets had no negative effect on the cecal microbiota of broilers.

• Journal of Microbiology and Biotechnology
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• v.30 no.9
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• pp.1355-1366
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• 2020

Sediment bacterial communities are critical to the biogeochemical cycle in river ecosystems, but our understanding of the relationship between sediment bacterial communities and their specific input streams in rivers remains insufficient. In this study, we analyzed the sediment bacterial community structure in a local river receiving discharge of urban domestic sewage by applying Illumina MiSeq high-throughput sequencing. The results showed that the bacterial communities of sediments samples of different pollution types had similar dominant phyla, mainly Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes, but their relative abundances were different. Moreover, there were great differences at the genus level. For example, the genus Bacillus showed statistically significant differences in the hotel site. The clustering of bacterial communities at various sites and the dominant families (i.e., Nocardioidaceae, and Sphingomonadaceae) observed in the residential quarter differed from other sites. This result suggested that environmentally induced species sorting greatly influenced the sediment bacterial community composition. The bacterial co-occurrence patterns showed that the river bacteria had a nonrandom modular structure. Microbial taxonomy from the same module had strong ecological links (such as the nitrogenium cycle and degradation of organic pollutants). Additionally, PICRUSt metabolic inference analysis showed the most important function of river bacterial communities under the influence of different types of domestic sewage was metabolism (e.g., genes related to xenobiotic degradation predominated in residential quarter samples). In general, our results emphasize that the adaptive changes and interactions in the bacterial community structure of river sediment represent responses to different exogenous pollution sources.

• Journal of Microbiology and Biotechnology
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• v.17 no.8
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• pp.1379-1384
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• 2007

Four Gram-negative, chemoheterotrophic, non-motile, yellow-colored strains were isolated from the East Sea or from deep-sea sediments of Nankai Trough by standard dilution plating. Characterization by polyphasic approaches indicated that the four strains are members of the same species. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains formed a coherent and novel genus-level lineage within the family Flavobacteriaceae. The dominant cellular fatty acids were i-C15:0, 3-OH i-C17:0, and 2-OH i-C15:0 and/or C16:1 ${\omega}7c$. Predominance of 2-OH i-C15:0 and/or C16:1 ${\omega}7c$ clearly differentiated the strains from closely related members. The DNA G+C contents ranged 35.1-36.2 mol%. It is proposed, from the polyphasic evidence, that the strains should be placed into a novel genus and species named Sufflavibacter maritimus gen. nov., sp. nov., with strain $IMCC1001^T(=KCCM\;42359^T=NBRC\;102039^T)$ as the type strain.

• Korean journal of applied entomology
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• v.42 no.3
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• pp.185-195
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• 2003

Phytoseiid mites are important predators of spider mites, rust mites and many of insect pests as well. From two-year (2001-2002) survey of apple orchards in Kyoungbuk and Suwon area, 13 species of phytoseiids, 12 species of the genus Amblyseius and one species of the genus Typhlodromus were found. Among them, Amblyseius womersleyi was the most dominant followed by A. rademacheri, A. orientalis, and A. makuwa. Amblyseius rademacheri and A. makuwa were mainly found from ground vegetation. Keys to genera and species were presented with some pictorial details and ecological notes of each species. Further discussion on systematics of the family Phytoseiidae and use in apple IPM were suggested.

• Korean Journal of Microbiology
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• v.28 no.4
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• pp.331-336
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• 1990

Annual distribution of hiterotrophic marine bacteria and seasonal characteristics were investigated in the intertidal waters and sediments in the vicinity of Kunsan of Yellow Sea, Korea. Annual distribution of heterotrophic marine bacteria ranged from $ 7.5*10^{2}$ to $1.1*10^{5}$ c.f.u./ml in water and from $1.6*10 ^{4}$ to $4.8*10^{6}$ c.f.u.per g dry sediments. As for the morphological distribution measured by epifluorescence microscopy, rod-form bacteria were distributed more than 74% of total observed bacteria during surveying periods. Average biovolume of sampled bacteria ranged from $3.19\;+-\;0.59*10^{-2}$ to $6.19\;+-\;0.76*10^{-2}$ $\mu$$m^{3}$ for coccus-form bacteria. Isolated bacteria showed various utilization of carbon sources such as glucose, maltose, lactose, xylose and arabinose, and showed tolerance at various range of salinity. It was isolated 82 genus in seawater and 114 genus in sediments. Dominant genera were Pseudomonas, Vibrio, Flavobacterium and Acinetobacter in seawater, and Pseudomonas, Acinetobacter, Vibrio, and Mycobacterium in sediments.

• Food Science of Animal Resources
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• v.44 no.2
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• pp.390-407
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• 2024

Kuflu cheese, a popular variety of traditional Turkish mold-ripened cheeses, is characterized by its semi-hard texture and blue-green color. It is important to elucidate the microbiota of Kuflu cheese produced from raw milk to standardize and sustain its sensory properties. This study aimed to examine the bacteria, yeasts, and filamentous mold communities in Kuflu cheese using high-throughput amplicon sequencing based on 16S and ITS2 regions. Lactococcus, Streptococcus, and Staphylococcus were the most dominant bacterial genera while Bifidobacterium genus was found to be remarkably high in some Kuflu cheese samples. Penicillium genus dominated the filamentous mold biota while the yeasts with the highest relative abundances were detected as Debaryomyces, Pichia, and Candida. The genera Virgibacillus and Paraliobacillus, which were not previously reported for mold-ripened cheeses, were detected at high relative abundances in some Kuflu cheese samples. None of the genera that include important food pathogens like Salmonella, Campylobacter, Listeria were detected in the samples. This is the first experiment in which the microbiota of Kuflu cheeses were evaluated with a metagenomic approach. This study provided an opportunity to evaluate Kuflu cheese, which was previously examined for fungal composition, in terms of both pathogenic and beneficial bacteria.