• Journal of Periodontal and Implant Science
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• 제52권5호
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• pp.394-410
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• 2022

Purpose: The purpose of this study was to compare the microbial composition of 3 types of oral samples through 16S metagenomic sequencing to determine how to resolve some sampling issues that occur during the collection of sub-gingival plaque samples. Methods: In total, 20 subjects were recruited. In both the healthy and periodontitis groups, samples of saliva and supra-gingival plaque were collected. Additionally, in the periodontitis group, sub-gingival plaque samples were collected from the deepest periodontal pocket. After DNA extraction from each sample, polymerase chain reaction amplification was performed on the V3-V4 hypervariable region on the 16S rRNA gene, followed by metagenomic sequencing and a bioinformatics analysis. Results: When comparing the healthy and periodontitis groups in terms of alpha-diversity, the saliva samples demonstrated much more substantial differences in bacterial diversity than the supra-gingival plaque samples. Moreover, in a comparison between the samples in the case group, the diversity score of the saliva samples was higher than that of the supra-gingival plaque samples, and it was similar to that of the sub-gingival plaque samples. In the beta-diversity analysis, the sub-gingival plaque samples exhibited a clustering pattern similar to that of the periodontitis group. Bacterial relative abundance analysis at the species level indicated lower relative frequencies of bacteria in the healthy group than in the periodontitis group. A statistically significant difference in frequency was observed in the saliva samples for specific pathogenic species (Porphyromonas gingivalis, Treponema denticola, and Prevotella intermedia). The saliva samples exhibited a similar relative richness of bacterial communities to that of sub-gingival plaque samples. Conclusions: In this 16S oral microbiome study, we confirmed that saliva samples had a microbial composition that was more similar to that of sub-gingival plaque samples than to that of supra-gingival plaque samples within the periodontitis group.

• Clinical and Experimental Pediatrics
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• 제61권6호
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• pp.200-204
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• 2018

Atopic dermatitis (AD) is a chronic inflammatory skin disease in children. Patients with AD experience a high rate of colonization of the skin surface by Staphylococcus aureus. Because of a skin barrier defect, there is a potential risk of staphylococcal invasive infection in patients with AD. Here, we present 2 cases of breast abscess caused by S. aureus in 2 adolescent girls with severe AD. Methicillin-sensitive S. aureus was identified from the breast abscess material. They were treated with appropriate antibiotics, however surgical drainage of the abscess was needed in case 1. Identical strains were found from the breast abscess material as well as the lesional and the nonlesional skin of the patients through matrix-assisted laser desorption/ionization time-of-flight analysis. We characterized the differential abundance of Firmicutes phylum in patients' skin in microbiota analysis. In particular, S. aureus, a member of Firmicutes, differed significantly between the lesional and the normal-appearing skin. Our cases demonstrate the potential severity of bacterial deep tissue infection in AD and the dysbiosis of skin microbiota may be involved in inflammation in AD.

• Journal of Animal Science and Technology
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• 제64권6호
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• pp.1144-1172
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• 2022

Salmonella enterica serovar Typhimurium isolate HJL777 is a virulent bacterial strain in pigs. The high rate of salmonella infection are at high risk of non-typhoidal salmonella gastroenteritis development. Salmonellosis is most common in young pigs. We investigated changes in gut microbiota and biological function in piglets infected with salmonella via analysis of rectal fecal metagenome and intestinal transcriptome using 16S rRNA and RNA sequencing. We identified a decrease in Bacteroides and increase in harmful bacteria such as Spirochaetes and Proteobacteria by microbial community analysis. We predicted that reduction of Bacteroides by salmonella infection causes proliferation of salmonella and harmful bacteria that can cause an intestinal inflammatory response. Functional profiling of microbial communities in piglets with salmonella infection showed increasing lipid metabolism associated with proliferation of harmful bacteria and inflammatory responses. Transcriptome analysis identified 31 differentially expressed genes. Using gene ontology and Innate Immune Database analysis, we identified that BGN, DCN, ZFPM2 and BPI genes were involved in extracellular and immune mechanisms, specifically salmonella adhesion to host cells and inflammatory responses during infection. We confirmed alterations in gut microbiota and biological function during salmonella infection in piglets. Our findings will help prevent disease and improve productivity in the swine industry.

• Animal Bioscience
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• 제35권10호
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• pp.1606-1615
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• 2022

Objective: The present study was conducted to investigate the potential effects of dietary supplemented propolis in two growing rabbit breeds on growth performance, immune response, blood parameters, carcass characteristics, and cecal microflora composition. Methods: A total of 90 growing rabbits aged 6 weeks from two breeds (V-line and Jabali) were randomly allocated to 3 dietary propolis experimental treatments. The experimental treatments consisted of a 2×3 factorial arrangement with two rabbit breeds and three levels of dietary propolis supplementation (0, 250 mg/kg, and 500 mg/kg). Each sub-treatment has 15 rabbits. The experimental period lasted six weeks. Results: There were no significant differences in growth performance and carcass characteristics due to propolis administration. Propolis supplementation at a high level significantly increased (linear; p<0.05) cellular-mediated immunity compared with the unsupplemented group. Furthermore, the rabbits receiving propolis exhibited a significant increase (linear and quadratic; p<0.03) in IgM immunoglobulins compared to the control. The current study provides further evidence that the dietary inclusion of propolis can significantly reduce pathogenic bacterial colonization in growing rabbits. The total count of microflora, E. coli, and Salmonella spp. was significantly lower (linear; p<0.01) in supplemented rabbit groups compared to the control group according to the microbiological analysis of cecal digesta. Based on breed effect, the results indicated that Jabali rabbits (local) performed better than V-line rabbits (foreign) in the majority of the studied traits. Conclusion: Dietary propolis is promising for further investigation into improving intestinal health and enhancing immunity in growing rabbits.

• 대한임상검사과학회지
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• 제52권3호
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• pp.202-213
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• 2020

미생물 연구에서 대량의 마이크로바이옴 데이터를 효율적으로 얻는 기술이 발전해왔지만, 마이크로바이옴 빅 데이터를 적절하게 분석하는 도구는 여전히 부족하다. 또한 빈약한 데이터베이스를 사용하여 미생물 군집을 분석하면 잘못된 결과를 초래할 수 있다. 따라서 본 연구는 대량의 미생물 데이터베이스 분석을 위한 적절한 방법을 설계하고자 하였다. 박테리아는 개인의 손끝과 개인 소지품(휴대 전화 및 랩탑 키보드)에서 수집되었다. 박테리아로부터 게놈 DNA를 추출하고 16S rRNA 유전자를 표적으로 하여 차세대 시퀀싱을 실시하였다. 손끝과 개인 소지품 간의 박테리아 매칭 비율의 정확성은 공식과 함께 환경 및 인간관련 데이터베이스를 사용하여 확인하였다. 적절한 분석을 설계하기 위해 다음 세가지 범주를 기준으로: 정성적 분석과 정량적 분석 비교, 성별에 관계없이 모든 참여자뿐만 아니라 동일 성별 참여자 내 비교, 환경(eDB) 및 인간 관련 데이터 베이스(hDB)를 이용하여 샘플간 비교하였다. 결과는 정성적 분석과 동일 성별 참가자 내에서의 비교 및 hDB의 사용이 비교적 정확한 결과를 제공하였다. 우리의 연구는 인간 유래 미생물을 사용하여 대량의 미생물학적 데이터를 포함하는 연구를 수행할 때 정확한 결과를 얻을 수 있는 분석 방법을 제공한다.

• 생명과학회지
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• 제23권3호
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• pp.406-414
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• 2013

강의 하류지역에서 미생물의 군집이 점진적인 염도의 증가에 따라 변한다는 것을 실험적으로 보기 위하여, 경북 형산강의 하류에서부터 연안해역으로 유입되는 곳까지 약 2.91 km 간격으로 0.02%, 1.48%, 2.63%, 3.62%의 염분을 포함하는 물 시료를 얻어 denaturing gradient gel electrophoresis (DGGE)를 수행하였다. 계통분석, 계통수 및 각 시료간의 연관성을 조사한 결과, 미생물 군집의 변화가 염분의 증가에 따라 점진적으로 변화하는 것을 확인하였으며, 이는 염분의 농도가 미생물 군집에 큰 영향을 미치는 요소임을 제시한다. 덧붙여 연안 지역이나 다른 수계환경에 비해 하류지역은 염분의 점진적인 변화로 인해 좁은 면적에 비하여 미생물 다양성이 크고, 이는 곧 특이하고 새로운 종을 찾기에 좋은 장소임을 시사하였다.

• Journal of Dairy Science and Biotechnology
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• 제38권2호
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• pp.70-88
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• 2020

대부분의 스타터 배양균은 유산균(LAB)군(group)에 속하며 미국 식품의약국(FDA)과 유럽식품안전청(EFSA)에 의해 안전하다고 인정받고 있다. 그러나, LAB는 항생제 내성(antibiotic resistance) 유전자를 위한 내적 또는 외적 저장소로 작용할 수 있다. 하지만 저항 유전자 전달이 수직이기 때문에 이 사실은 그 자체가 안전상의 문제가 아닐 수도 있다. 그럼에도 불구하고 외부 유전적 요소는 심각한 안전 문제를 나타내는 인체 장내 미생물뿐만 아니라 병원균의 저항성 수평 전달에 유리한 변화를 유도할 수 있다. 항생제 내성을 가진 유산균의 일부 속(genus)에는 발효육 및 유제품에서 분리된 Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, Streptococcus 등이 포함된다. 현재 WHO는 식품산업에서 사용되는 LAB는 저항이 없어야 한다고 권고하고 있다. 다행히도 한국의 식품의약품안전처가 인정한 프로바이오틱스 균주 중 Enterococcus에 해당되는 균주는 E. faecium과 E. faecalis인데, 2019년 4월 1일부터 E. faecium과 E. faecalis의 독성인자와 항생제 내성전달인자 모두 없다고 인정된 경우에면 사용이 허가된다. 따라서 LAB의 산업적 중요성을 고려할 때 앞으로 인체와 동물장관 유래의 LAB은 체계적인 탐색 및 동정, 병원성 및 항생제 내성 유전자의 확인, 식품 및 가축사료 첨가제로의 활용, 안전성 평가연구는 계속 필요하다고 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제30권11호
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• pp.1643-1650
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• 2017

Objective: The control of psychrotrophic bacteria causing milk spoilage and illness due to toxic compounds is an important issue in the dairy industry. In South Korea, Gangwon-do province is one of the coldest terrains in which eighty percent of the area is mountainous regions, and mainly plays an important role in the agriculture and dairy industries. The purposes of this study were to analyze the indigenous microbiota of raw milk in Gangwon-do and accurately investigate a putative microbial group causing deterioration in milk quality. Methods: We collected raw milk from the bulk tank of 18 dairy farms in the Hoengseong and Pyeongchang regions of Gangwon-do. Milk components were analyzed and the number of viable bacteria was confirmed. The V3 and V4 regions of 16S rRNA gene were amplified and sequenced on an Illumina Miseq platform. Sequences were then assigned to operational taxonomic units, followed by the selection of representative sequences using the QIIME software package. Results: The milk samples from Pyeongchang were higher in fat, protein, lactose, total solid, and solid non-fat, and bacterial cell counts were observed only for the Hoengseong samples. The phylum Proteobacteria was detected most frequently in both the Hoengseong and Pyeongchang samples, followed by the phyla Firmicutes and Actinobacteria. Notably, Corynebacterium, Pediococcus, Macrococcus, and Acinetobacter were significantly different from two regions. Conclusion: Although the predominant phylum in raw milk is same, the abundances of major genera in milk samples were different between Hoengseong and Pyeongchang. We assumed that these differences are caused by regional dissimilar farming environments such as soil, forage, and dairy farming equipment so that the quality of milk raw milk from Pyeongchang is higher than that of Hoengseong. These results could provide the crucial information for identifying the microbiota in raw milk of South Korea.

• Animal Bioscience
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• 제35권12호
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• pp.1967-1976
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• 2022

Objective: The aim of this study was to characterize the fecal microbiota of broiler chickens reared in the presence of different shades of light-emitting diode (LED) lights, correlating this information with biochemical and molecular evidence that allowed drawing conclusions on the state of health of the animals. Methods: Overall, the metagenomic approach on fecal samples was associated with evaluations on enzymes involved in the cellular response to oxidative stress: glutathione peroxidase (GPX), superoxide dismutase and catalase; while the inflammatory aspect was studied through the dosage of a proinflammatory cytokine, the interleukin 6 (IL-6), and the evaluation of the matrix metalloproteinases 2 (MMP-2) and 9 (MMP-9). Specifically, analysis was performed on distinct groups of chickens respectively raised in the presence of neutral (K = 3,300 to 3,700), cool (K = 5,500 to 6,000), and warm (K = 3,000 to 2,500) LED lightings, and a direct comparison was performed with animals reared with traditional neon lights. Results: The metagenomic analysis highlighted the presence of two most abundant bacterial phyla, the Firmicutes and the Bacteroidetes, with the latter characterized by a greater relative abundance (p<0.05) in the group of animals reared with Neutral LED light. The analysis on the enzymes involved in the antioxidant response showed an effect of the LED light, regardless of the applied shade, of reducing the expression of GPX (p<0.01), although this parameter is not correlated to an effective reduction in the tissue amount of the enzyme. Regarding the inflammatory state, no differences associated with IL-6 and MMP-9 were found; however, is noteworthy the significant reduction of MMP-2 activity in tissue samples obtained from animals subjected to illumination with neutral LED light. Conclusion: This evidence, combined with the metagenomic findings, supports a potential positive effect of neutral LED lighting on animal welfare, although these considerations must be reflected in more targeted biochemical evaluations.

• Journal of Animal Science and Technology
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• 제62권4호
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• pp.504-520
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• 2020

Proliferation of shrubs at the expense of native forage in pastures has been associated with large changes in dry-matter intake and dietary components for grazing ruminants. These changes can also affect the animals' physiology and metabolism. However, little information is available concerning the effect of pastoral-shrub grazing on the rumen bacterial community. To explore rumen bacteria composition in grazing yaks and the response of rumen bacteria to increasing shrub coverage in alpine meadows, 48 yak steers were randomly assigned to four pastures with shrub coverage of 0%, 5.4%, 11.3%, and 20.1% (referred as control, low, middle, and high, respectively), and ruminal fluid was collected from four yaks from each pasture group after 85 days. Rumen fermentation products were measured and microbiota composition determined using Ion S5™ XL sequencing of the 16S rRNA gene. Principal coordinates analysis (PCoA) and similarity analysis indicated that the degree of shrub coverage correlated with altered rumen bacterial composition of yaks grazing in alpine shrub meadows. At the phyla level, the relative abundance of Firmicutes in rumen increased with increasing shrub coverage, whereas the proportions of Bacteroidetes, Cyanobacteria and Verrucomicrobia decreased. Yaks grazing in the high shrub-coverage pasture had decreased species of the genus Prevotellaceae UCG-001, Lachnospiraceae XPB1014 group, Lachnospiraceae AC2044 group, Lachnospiraceae FCS020 group and Fretibacterium, but increased species of Christensenellaceae R-7 group, Ruminococcaceae NK4A214 group, Ruminococcus 1, Ruminococcaceae UCG-002, Ruminococcaceae UCG-005 and Lachnospiraceae UCG-008. These variations can enhance the animals' utilization efficiencies of cellulose and hemicellulose from native forage. Meanwhile, yaks grazed in the high shrub-coverage pasture had increased concentrations of ammonia nitrogen (NH₃-N) and branched-chain volatile fatty acids (isobutyrate and isovalerate) in rumen compared with yaks grazing in the pasture without shrubs. These results indicate that yaks grazing in a high shrub-coverage pasture may have improved dietary energy utilization and enhanced resistance to cold stress during the winter. Our findings provide evidence for the influence of shrub coverage on the rumen bacterial community of yaks grazing in alpine meadows as well as insights into the sustainable production of grazing yaks on lands with increasing shrub coverage on the Qinghai-Tibet Plateau.