• Journal of Microbiology
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• 제44권2호
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• pp.155-161
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• 2006

Comparative analysis of microbial communities in a sequencing batch reactor which performed enhanced biological phosphorus removal (EBPR) was carried out using a cultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocol and a modified PCR protocol with low PCR cycle was applied to the two clone libraries of the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and the resulting 424 clones were analyzed using restriction fragment length polymorphisms (RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that the modified PCR protocol decreased the incidence of distinct fragment patterns from about 63 % (137 of 217) in the standard PCR method to about 34 % (70 of 207) under the modified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles) can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained using the modified PCR method revealed that the clones were affiliated with at least 11 phyla or classes of the domain Bacteria. However, the analyses of 327 colonies, which were grouped into just 41 distinct types by RFLP analysis, showed that they could be classified into five major bacterial lineages: ${\alpha},\;{\beta},\;{\gamma}-$ Proteobacteria, Actinobacteria, and the phylum Bacteroidetes, which indicated that the microbial community yielded from the cultivation-based method was still much simpler than that yielded from the PCR-based molecular method. In this study, the discrepancy observed between the communities obtained from PCR-based and cultivation-based methods seems to result from low culturabilities of bacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed to reduce this discrepancy.

• Fisheries and Aquatic Sciences
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• 제3권1호
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• pp.64-70
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• 2000

DNA probes for the l6S rRNA have been designed for the detection of Edwardsiella tarda. In order to accomplish this purpose, the l6S rRNA gene from E. tarda has been cloned and sequenced. Two highly feasible oligonucleotide probe sites have been determined by the database analysis programs presented by PCGENE and BLAST. These two probes have been evaluated by slot blot hybridization analysis. Hetero- and homo-trimeric templates have been synthesized using these two probe sites. The templates have been further multimerized by PCR to generate between 150 and 300 bp long DIG-11-dUTP labeled probes. Unlike 3' end labeled oligonucleotide probes or templates, multimerized probes showed no cross­hybridization in the given experimental condition. Furthermore, a significant increase in sensitivity has been observed with these probes. This method, we presented here, may be useful for the designing of probes for the detection of other fish pathogenic microorganisms also.

• Journal of Microbiology and Biotechnology
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• 제33권2호
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• pp.219-227
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• 2023

Lettuce is one of the most consumed vegetables worldwide. However, it has potential risks associated with pathogenic bacterial contamination because it is usually consumed raw. In this study, we investigated the changes in the bacterial community on lettuce (Lactuca sativa L.) in Chungcheong-do, South Korea, and the prevalence of foodborne pathogens on lettuce in different seasons using 16S rRNA gene-based sequencing. Our data revealed that the Shannon diversity index showed the same tendency in term of the number of OTUs, with the index being greatest for summer samples in comparison to other seasons. Moreover, the microbial communities were significantly different between the four seasons. The relative abundance of Actinobacteriota varied according to the season. Family Micrococcaceae was most dominant in all samples except summer, and Rhizobiaceae was predominant in the microbiome of the summer sample. At the genus level, the relative abundance of Bacillus was greatest in spring samples, whereas Pseudomonas was greatest in winter samples. Potential pathogens, such as Staphylococcus and Clostridium, were detected with low relative abundance in all lettuce samples. We also performed metagenome shotgun sequencing analysis on the selected summer and winter samples, which were expected to be contaminated with foodborne pathogens, to support 16S rRNA gene-based sequencing dataset. Moreover, we could detect seasonal biomarkers and microbial association networks of microbiota on lettuce samples. Our results suggest that seasonal characteristics of lettuce microbial communities, which include diverse potential pathogens, can be used as basic data for food safety management to predict and prevent future outbreaks.

• Animal Bioscience
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• 제37권7호
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• pp.1213-1224
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• 2024

Objective: Enterotypes (ETs) are the clustering of gut microbial community structures, which could serve as indicators of growth performance and carcass traits. However, ETs have been sparsely investigated in waterfowl. The objective of this study was to identify the ileal ETs and explore the correlation of the ETs with growth performance and carcass traits in Muscovy ducks. Methods: A total of 200 Muscovy ducks were randomly selected from a population of 5,000 ducks at 70-day old, weighed and slaughtered. The growth performance and carcass traits, including body weight, dressed weight and evidenced weight, dressed percentage, percentage of apparent yield, breast muscle weight, leg muscle weight, percentage of leg muscle and percentage of breast muscle, were determined. The contents of ileum were collected for the isolation of DNA and 16S rRNA gene sequencing. The ETs were identified based on the 16S rRNA gene sequencing data and the correlation of the ETs with growth performance and carcass traits was performed by Spearman correlation analysis. Results: Three ETs (ET1, ET2, and ET3) were observed in the ileal microbiota of Muscovy ducks with significant differences in number of features and α-diversity among these ETs (p<0.05). Streptococcus, Candida Arthritis, and Bacteroidetes were the presentative genus in ET1 to ET3, respectively. Correlation analysis revealed that Lactococcus and Bradyrhizobium were significantly correlated with percentage of eviscerated yield and leg muscle weight (p<0.05) while ETs were found to have a close association with percentage of eviscerated yield, leg muscle weight, and percentage of leg muscle in Muscovy ducks. However, the growth performance of ducks with different ETs did not show significant difference (p>0.05). Lactococcus were found to be significantly correlated with leg muscle weight, dressed weight, and percentage of eviscerated yield. Conclusion: Our findings revealed a substantial variation in carcass traits associated with ETs in Muscovy ducks. It is implied that ETs might have the potential to serve as a valuable biomarker for assessing duck carcass traits. It would provide novel insights into the interaction of gut microbiota with growth performance and carcass traits of ducks.

• 생명과학회지
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• 제19권6호
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• pp.711-719
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• 2009

본 연구는 2006년 8월부터 2007년 9월까지 여수, 남해, 진도, 무안, 거문도, 서산 및 중국의 산동에서 포획한 낙지 유전자 집단을 분석하기 위하여 미토콘드리아 16S rRNA 염기서열로 조사했다. 유전자 분석은 총 28 개체로부터 11개의 haplotype이 발견되었다. 유전자 분화율은 0.2-1.2% 범위로 나타났다. Haplotype에 대한 PHYLIP 및 network 조사에 따르면 낙지는 두개의 clade (clade AIclade B)로 나뉘어지며, clade 사이의 분화율은 0.4%로 나타났다. 지역적 거리에 따라 haplotype이 다음과 같이 분화되었다. 하나는 여수, 남해, 무안, 진도 haplotype과 다른 하나는 서산, 거문도, 산동 haplotype으로 나뉘어졌다. 계충구조 분석에서도 한국 낙지집단 및 중국과의 유전적 차이를 볼 수 있으나, 현저한 지역적 차이는 나타나지 않았다. 따라서 한국연안에 서식하고 있는 일부 낙지집단은 gene flow에 의해서 유전적 동질성을 나타낼 수 있지만, 한국집단 간 뿐만 아니라 중국집단과의 유전적 분화는 지역적 거리 및 장벽으로 인하여 제한적인 gene flow로 설명될 수 있다.

• 대한의생명과학회지
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• 제28권4호
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• pp.317-321
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• 2022

Due to COVID-19 pandemic, wearing face masks is obligatory to prevent respiratory virus transmissions in the community. However, there are few studies of the desirable number of wearing a face mask, and how to store them for reuse. Therefore, in this study, a survey was conducted among 208 healthy adults, and 27 kf-94 masks worn for 1, 2, and 3 days were collected. To estimate the risk of bacterial contamination, we analyzed the extent of bacterial contamination of the BHI medium and 16S rRNA gene sequencing. With an increase in the number of days of using the mask, the degree of bacterial contamination of the used mask gradually increased. As a result of 16S rRNA PCR performed for strain identification, Staphylococcus, known as a pathogenic bacterium, was identified the most. In conclusion, we found that wearing a cotton KF mask provides an optimal environment for microbes, which are related to the skin and respiratory system, to thrive. Therefore, it is also important to reduce the risk of bacterial infection of the face mask with appropriate sterilization methods.

• 한국동물생명공학회지
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• 제36권1호
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• pp.35-44
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• 2021

A pregnancy diagnosis is an important standard for control of livestock's reproduction in paricular dairy cattle. High reproductive performance in dairy animals is a essential condition to realize of high life-time production. Pregnancy diagnosis is crucial to shortening the calving interval by enabling the farmer to identify open animals so as to treat or re-breed them at the earliest opportunity. MicroRNAs are short RNA molecules which are critically involved in regulating gene expression during both health and disease. This study is sought to establish the feasible of circulating miRNAs as biomarkers of early pregnancy in cattle. We applied Illumina small-RNA sequencing to profile miRNAs in plasma samples collected from 12 non-pregnant cows ("open" cows: samples were collected before insemination (non-pregnant state) and after pregnancy check at the indicated time points) on weeks 0, 4, 8, 12 and 16. Using small RNA sequencing we identified a total of 115 miRNAs that were differentially expressed weeks 16 relative to non-pregnancy ("open" cows). Weeks 8, 12 and 16 of pregnancy commonly showed a distinct increase in circulating levels of miR-221 and miR-320a. Through genome-wide analyses we have successfully profiled plasma miRNA populations associated with pregnancy in cattle. Their application in the field of reproductive biology has opened up opportunities for research communities to look for pregnancy biomarker molecules in dairy cattle.

• Asian-Australasian Journal of Animal Sciences
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• 제29권9호
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• pp.1345-1352
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• 2016

The hindgut of horses is an anaerobic fermentative chamber for a complex and dynamic microbial population, which plays a critical role in health and energy requirements. Research on the gut microbiota of Mongolian horses has not been reported until now as far as we know. Mongolian horse is a major local breed in China. We performed high-throughput sequencing of the 16S rRNA genes V4 hypervariable regions from gut fecal material to characterize the gut microbiota of Mongolian horses and compare them to the microbiota in Thoroughbred horses. Fourteen Mongolian and 19 Thoroughbred horses were used in the study. A total of 593,678 sequence reads were obtained from 33 samples analyzed, which were found to belong to 16 phyla and 75 genera. The bacterial community compositions were similar for the two breeds. Firmicutes (56% in Mongolian horses and 53% in Thoroughbred horses) and Bacteroidetes (33% and 32% respectively) were the most abundant and predominant phyla followed by Spirochaete, Verrucomicrobia, Proteobacteria, and Fibrobacteres. Of these 16 phyla, five (Synergistetes, Planctomycetes, Proteobacteria, TM7, and Chloroflexi) were significantly different (p<0.05) between the two breeds. At the genus level, Treponema was the most abundant genus (43% in Mongolian horses vs 29% in Thoroughbred horses), followed by Ruminococcus, Roseburia, Pseudobutyrivibrio, and Anaeroplasma, which were detected in higher distribution proportion in Mongolian horses than in Thoroughbred horses. In contrast, Oscillibacter, Fibrobacter, Methanocorpusculum, and Succinivibrio levels were lower in Mongolian horses. Among 75 genera, 30 genera were significantly different (p<0.05) between the two breeds. We found that the environment was one of very important factors that influenced horse gut microbiota. These findings provide novel information about the gut microbiota of Mongolian horses and a foundation for future investigations of gut bacterial factors that may influence the development and progression of gastrointestinal disease in horses.

• 미생물학회지
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• 제34권4호
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• pp.194-199
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• 1998

한강의 본류와 만나는 탄천과 중랑천에서 16S rDAN를 증폭하고 부분적인 염기서열 분석을 통하여 한강의 세균 다양성을 결정하였다. 총 27개의 클론을 분리하였으며 RFLP를 이용하여 7개의 group으로 나누었다. 탄천의 15개 클론은 4개의 group으로 나뉘어졌으며 가장 많은 클론을 포함하는 group(HT-1 클론)은 class Proteobacteria의 ${\delta}$-subdivision에 속하는 Acrobacter cryaerophilius와 높은 유사도를 보였으며, 다른 두 group(HT-6과 HT-9 클론)은 모두 clas Cytophagales에 속하였다. 중랑천의 12개의 클론은 3개의 group으로 나뉘어졌으며 가장 많은 클론을 보이는 group(HJ-1 클론)은 class Proteobacteria의 ${\alpha}$-subdivision에 속하는 Sphingomonas sp. 와 높은 유사도를 나타내었다. 전체적으로는 Proteobateria(alpha, beta and delta subdivision), Cytophagales와 Actinomycetales가 검출되었다.

• 한국해양바이오학회지
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• 제7권2호
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• pp.42-51
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• 2015

The community structure of cultivable bacteria associated with the marine sponge, Petrosia corticata, collected from Jeju Island in summer (September) of 2012 and winter (January) of 2013, were compared by the PCR-ARDRA method. Bacterial strains were cultured for 4 days at $26^{\circ}C$ on Zobell medium and marine agar medium. After PCR amplification of 16S rRNA gene of individual strains, the restriction enzymes MspI and HaeIII were used to make restriction patterns. As a result, 24 ARDRA patterns from the summer sponge and 20 ARDRA patterns from the winter sponge were obtained. The sequencing result of 1-3 selected strains from each pattern showed over 98% similarities with the known sequences from the public database. At the phylum level, the bacterial community structures of both sponges (summer and winter) were identical qualitatively and composed of 4 phyla : Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Alphaproteobacteria accounted for 42.5% of total in summer sponge and 25.2% in winter, decreasing in the winter sample. Gammaproteobacteria accounted for 27.5% of total in summer sponge and 35.2% in winter, increasing in the winter sample. At the genus and species level, summer sponge had more diverse bacterial communities than winter sponge. Actinobacteria, Bacteroidetes, and Firmicutes increased in the winter sample.