• Journal of Periodontal and Implant Science
• /
• 제53권1호
• /
• pp.69-84
• /
• 2023

Purpose: The objective of this study was to analyze the microbial profile of individuals with peri-implantitis (PI) compared to those of periodontally healthy (PH) subjects and periodontitis (PT) subjects using Illumina sequencing. Methods: Buccal, supragingival, and subgingival plaque samples were collected from 109 subjects (PH: 30, PT: 49, and PI: 30). The V3-V4 region of 16S rRNA was sequenced and analyzed to profile the plaque microbiota. Results: Microbial community diversity in the PI group was higher than in the other groups, and the 3 groups showed significantly separated clusters in the buccal samples. The PI group showed different patterns of relative abundance from those in the PH and PT groups depending on the sampling site at both genus and phylum levels. In all samples, some bacterial species presented considerably higher relative abundances in the PI group than in the PH and PT groups, including Anaerotignum lactatifermentans, Bacteroides vulgatus, Faecalibacterium prausnitzii, Olsenella uli, Parasutterella excrementihominis, Prevotella buccae, Pseudoramibacter alactolyticus, Treponema parvum, and Slackia exigua. Network analysis identified that several well-known periodontal pathogens and newly recognized bacteria were closely correlated with each other. Conclusions: The composition of the microbiota was considerably different in PI subjects compared to PH and PT subjects, and these results could shed light on the mechanisms involved in the development of PI.

• Asian-Australasian Journal of Animal Sciences
• /
• 제30권7호
• /
• pp.1037-1047
• /
• 2017

Objective: Despite an increasing number of investigations into the pathophysiology of necrotic enteritis (NE) disease, etiology of NE-associated diseases, and gene expression profiling of NE-affected tissues, the microRNA (miRNA) profiles of NE-affected poultry have been poorly studied. The aim of this study was to induce NE disease in the genetically disparate Fayoumi chicken lines, and to perform non-coding RNA sequencing in the intestinal mucosal layer. Methods: NE disease was induced in the Fayoumi chicken lines (M5.1 and M15.2), and non-coding RNA sequencing was performed in the intestinal mucosal layer of both NE-affected and uninfected chickens to examine the differential expression of miRNAs. Next, quantitative real-time polymerase chain reaction (real-time qPCR) was performed to further examine four miRNAs that showed the highest fold differences. Finally, bioinformatics analyses were performed to examine the four miRNAs target genes involvement in the signaling pathways, and to examine their interaction. Results: According to non-coding RNA sequencing, total 50 upregulated miRNAs and 26 downregulated miRNAs were detected in the NE-induced M5.1 chickens. While 32 upregulated miRNAs and 11 downregulated miRNAs were detected in the NE-induced M15.2 chickens. Results of real-time qPCR analysis on the four miRNAs (gga-miR-9-5p, gga-miR-20b-5p, ggamiR-196-5p, and gga-let-7d) were mostly correlated with the results of RNAseq. Overall, ggamiR-20b-5p was significantly downregulated in the NE-induced M5.1 chickens and this was associated with the upregulation of its top-ranking target gene, mitogen-activated protein kinase, kinase 2. Further bioinformatics analyses revealed that 45 of the gene targets of gga-miR-20b-5p were involved in signal transduction and immune system-related pathways, and 35 of these targets were predicted to interact with each other. Conclusion: Our study is a novel report of miRNA expression in Fayoumi chickens, and could be very useful in understanding the role of differentially expressed miRNAs in a NE disease model.

• Journal of Microbiology
• /
• 제42권1호
• /
• pp.9-13
• /
• 2004

Culture-independent approaches, based on 16S rDNA sequences, are extensively used in modern microbial ecology. Sequencing of the clone library generated from environmental DNA has advantages over fingerprint-based methods, such as denaturing gradient gel electrophoresis, as it provides precise identification and quantification of the phylotypes present in samples. However, to date, no method exists for comparing multiple bacterial community structures using clone library sequences. In this study, an automated method to achieve this has been developed, by applying pair wise alignment, hierarchical clustering and principle component analysis. The method has been demonstrated to be successful in comparing samples from various environments. The program, named CommCluster, was written in JAVA, and is now freely available, at http://chunlab.snu.ac.kr/commcluster/.

• 한국해양생명과학회지
• /
• 제8권2호
• /
• pp.128-135
• /
• 2023

엽상자어(Leptocephalus)는 뱀장어목(Anguiliformes)에 속하는 어류의 자어로 5~6월에 우리나라 남해안 일대의 정치망에서 멸치와 함께 어획 후 방류하지만 대부분 폐사하는 실정이다. 따라서 본 연구의 목적은 멸치어업을 하는 정치망에서 무분별하게 포획되는 엽상자어의 종을 구명하여 수산자원보호 및 이들 자치어 생태 연구를 위한 기초 생물학적 자료를 제시하고자 수행하였다. 실험에 사용된 엽상자어는 5~6월에 남해의 정치망에서 채집하였으며, 외부형태와 유전학적 특성을 붕장어(Conger myriaster), 갯장어(Muraenesox cinereus) 및 뱀장어속(Anguilla) 4종의 성어와 비교하였다. 유전학적 분석은 추출한 DNA를 12s rRNA, 16s rRNA 부분단편을 PCR로 증폭하여 염기배열을 분석한 후 분자계통수를 작성하여 장어류 유생이 붕장어, 갯장어 및 뱀장어속 4종 중 어느 쪽의 성체와 클러스터 그룹화를 이루는지 계통학적 유연관계를 확인하였다. 엽상자어의 외부형태 계수 및 계측결과 엽상자어의 전장에 대한 머리길이의 백분비와 뒷지느러미 기점거리의 백분비는 붕장어와 가장 유사한 비율을 보였고, 척추골수 역시 붕장어와 가장 유사하였다. 또한 엽상자어의 유전자 분석결과는 모두 붕장어 성체와 클러스터 그룹화를 이루는 것을 확인함으로서 남해안에서 5~6월에 어획되는 엽상자어는 모두 붕장어의 자어임을 할 수 있었다.

• Journal of Veterinary Science
• /
• 제24권5호
• /
• pp.73.1-73.16
• /
• 2023

Background: Highly pathogenic avian influenza virus (HPAIV) is considered a global threat to both human health and the poultry industry. MicroRNAs (miRNA) can modulate the immune system by affecting gene expression patterns in HPAIV-infected chickens. Objectives: To gain further insights into the role of miRNAs in immune responses against H5N1 infection, as well as the development of strategies for breeding disease-resistant chickens, we characterized miRNA expression patterns in tracheal tissues from H5N1-infected Ri chickens. Methods: miRNAs expression was analyzed from two H5N1-infected Ri chicken lines using small RNA sequencing. The target genes of differentially expressed (DE) miRNAs were predicted using miRDB. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were then conducted. Furthermore, using quantitative real-time polymerase chain reaction, we validated the expression levels of DE miRNAs (miR-22-3p, miR-146b-3p, miR27b-3p, miR-128-3p, miR-2188-5p, miR-451, miR-205a, miR-203a, miR-21-3p, and miR-200a3p) from all comparisons and their immune-related target genes. Results: A total of 53 miRNAs were significantly expressed in the infection samples of the resistant compared to the susceptible line. Network analyses between the DE miRNAs and target genes revealed that DE miRNAs may regulate the expression of target genes involved in the transforming growth factor-beta, mitogen-activated protein kinase, and Toll-like receptor signaling pathways, all of which are related to influenza A virus progression. Conclusions: Collectively, our results provided novel insights into the miRNA expression patterns of tracheal tissues from H5N1-infected Ri chickens. More importantly, our findings offer insights into the relationship between miRNA and immune-related target genes and the role of miRNA in HPAIV infections in chickens.

• Pediatric Infection and Vaccine
• /
• 제26권3호
• /
• pp.129-139
• /
• 2019

사람의 호흡기계는 감염 질환을 일으키는 세균과 집락균이 복잡하게 공존하는 기관이다. 세균이 배양되지 않아도 분석이 가능한 16S 리보좀 RNA 유전자 서열분석 기법이 도입된 이래 사람의 미생물군 유전체에 대한 많은 연구 성과들이 보고되었다. 출생 후 영아기 호흡기 내의 미생물총 구조는 이후의 호흡기계 건강과 연관이 있음이 관찰되었다. 본 종설에서는 건강한 어린이의 호흡기 미생물총의 발달, 미생물 간 상호 작용, 숙주의 면역에 미치는 영향, 미생물군 유전체와 호흡기 건강의 연관성에 대하여 지금까지 알려진 내용들을 알아보고자 한다.

• Journal of Microbiology and Biotechnology
• /
• 제21권4호
• /
• pp.421-429
• /
• 2011

For precise identification of a Lactobacillus K1 isolate, LC-MS/MS analysis of the putative surface layer protein was performed. The results obtained from LTQ-FT-ICR mass spectrometry confirmed that the analyzed protein spot is the surface layer protein originating from Lb. helveticus species. Moreover, the identified protein has the highest similarity with the surface layer protein from Lb. helveticus R0052. To evaluate the proteomic study, multilocus sequence analysis of selected housekeeping gene sequences was performed. Combination of 16S rRNA sequencing with partial sequences for the genes encoding the RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), translational elongation factor Tu (tuf), and Hsp60 chaperonins (groEL) also allowed to classify the analyzed isolate as Lb. helveticus. Further classification at the strain level was achieved by sequencing of the slp gene. This gene showed 99.8% identity with the corresponding slp gene of Lb. helveticus R0052, which is in good agreement with data obtained by nano-HPLC coupled to an LTQ-FT-ICR mass spectrometer. Finally, LC-MS/MS analysis of surface layer proteins extracted from three other Lactobacillus strains proved that the proposed method is the appropriate molecular tool for the identification of S-layer-possessing lactobacilli at the species and even strain levels.

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

• Pediatric Infection and Vaccine
• /
• 제30권3호
• /
• pp.159-164
• /
• 2023

뇌농양은 생명을 위협할 수 있는 심각한 중추신경계 감염으로 특히 소아에서는 증상이 모호하여 시의적절한 진단이 이루어지지 않는 경우가 종종 발생한다. 저자들은 면역력이 정상인 소아에서 드문 병원체에 의한 중추신경계 감염을 진단 및 치료하여 보고하는 바이다. 7년 전 심방중격결손을 진단받았고, 1달 전부터 충치 치료를 받은 과거력이 있는 10세 여아가 10일 전 발생한 두통을 주소로 입원하였다. 뇌자기공명영상에서 4.2 cm 크기의 뇌농양이 오른쪽 두정엽에서 발견되어 두개골절개술과 농양 흡인을 시행하였다. 흡인된 농과 조직에서 Aggregatibacter aphrophilus가 배양되었고, 16S rRNA sequencing에서 Actinomyces georgiae가 확인되어 ampicillin-sulbactam을 8주간 투여하였다. 수술 및 항균요법으로 환자의 증상이 호전되었고, 추적한 뇌자기공명영상에서 농양과 부종도 호전되어 치료를 종료하였다.

• 미생물학회지
• /
• 제39권1호
• /
• pp.45-50
• /
• 2003

분자 생물학적 방법 인 DGGE를 이용하여 저온에서 김치가 발효되는 동안 관여하는 미생물의 다양성과 변화양상을 분석하였다. 김치를 저온 ($4^{\circ}C$)에서 발효시키는 60 일 동안 5 일 마다 시료를 채취하였으며, 채취한 김치 시료에서 genomic DNA를 추출하여 실험을 수행하였다. 김치 시료 genomic DNA로부터 16S rDNA의 V3영역을 증폭하여 DGGE를 수행한 결과에서 관찰된 amplicon들의 염기서열을 분석한 결과 저온에서 김치가 발효되는 동안 젖산균들이 주요 미생물 군집으로 나타났으며, 그 중에서도 Weissella koreensis가 발효 전 과정 동안, Lactobacillus sakei의 경우는 발효 10 일째부터, 그리고 Leuconostoc gelidurn은 발효30 일째부터 amplicon들의 농도가 진하게 나타나 이들이 저온에서 김치 발효 과정 동안의 우점종 균주들 임을 알 수 있었다.