• 생명과학회지
• /
• 제32권10호
• /
• pp.803-811
• /
• 2022

우리나라 전통 콩 발효식품은 탄수화물을 주식으로 하는 한국인의 식생활에 중요한 단백질 급원임에도 불구하고 콩 발효식품의 미생물 다양성과 군집 구조에 대해서는 거의 알려진 바가 없다. 본 연구는 16S rDNA 유전자 서열 분석 기반의 차세대 염기서열 분석법을 이용하여 한국 전통 발효식품인 된장과 간장의 미생물 군집 구조를 밝히고자 하였다. Alpha-diversity 분석 결과 미생물 다양성 지표인 Shannon과 Simpson에서 된장과 간장의 미생물 다양성에 통계학적인 차이가 있는 것으로 나타났으나, 종 풍부도 지표인 ACE, CHAO, Jackknife에서는 차이가 없는 것으로 나타났다. 된장과 간장의 미생물 분포 분석 결과 된장과 간장의 공통적인 우점균은 Firmicutes로 나타났으나, 속 수준에서의 미생물 분포를 분석한 결과 된장에서 Bacillus, Kroppenstedtia, Clostridium, Pseudomonas가 간장보다 높은 비율을 차지하고 있는 것으로 나타났으며, 간장에서는 Tetragenococcus, Chromhalobacter, Lentibacillus, Psychrobacter와 같은 호염성 또는 내염성 세균이 된장보다 높은 비율을 차지하는 것으로 나타났다. 된장과 간장의 미생물 군집구조에 통계학적인 차이가 있는지 확인하기 위해 paired-PERMANOVA 분석을 수행하였으며, 그 결과 통계학적으로 매우 유의한 수준의 차이가 있는 것으로 나타났다. 된장과 간장의 미생물 군집구조 차이에 큰 영향을 미치는 biomarker를 분석하기 위해 LEfSe 분석을 수행하였으며, 그 결과 Bacillus와 Tetragenococcus가 된장과 간장의 미생물 군집 구조에 차이를 나타내는 biomarker로 분석되었다.

• 생명과학회지
• /
• 제28권3호
• /
• pp.361-368
• /
• 2018

본 연구는 제주연안에서 채집한 옥돔(Branchiostegus japonicus)의 장내기관으로부터 장내미생물의 분리하여 다양성을 조사하였다. 1차로 1.5% BHIA, MA, TSA 및 R2A agar 배지상 순수분리한 결과, 1.5% BHIA에서 가장 많은 colony개수를 나타냈다. 호기성, 혐기배양은 평균 $1.7{\times}10^6CFU/g^{-1}$, $1.1{\times}10^5CFU/g^{-1}$로 나타났으며 총 147개의 순수 colony가 분리되었다. 16S rDNA염기서열 분석결과 58속 74종으로 나타났으며 기본균주와 95-100%의 유사도를 나타내었다. 크게 5문(Phylum)으로 나뉘었으며, 주요 계통군으로 Proteobacteria 문이 50%로 Moraxellaceae, Rhodobacteraceae, Shewanellae, Halomondaceae, Enterobacteriaceae, Vibrionaceae, Hahellaceae, Pseudomonadaceae, Erythrobacteraceae 총 9과 35속 35종으로 우점도가 제일 높게 나타났다. Actinobacteria문은 24%, Microbacteriaceae, Intrasporangiaceae, Dietziaceae, Dermabacteraceae, Dermacoccaceae, Nocardiodaceae, Brevibacteriaceae, Propionobacteriacea 총 8과 11속 17종, Frimicutes문은 16%, Bacillaceae, Staphylcoccaceae, Planococcaceae, Streptococcaceae, Paenibacillaceae, Clostridiaceae 총 6과 8속 17종, bacteroidetes문은 6%, Cyclobacteriaceae, Flavobacteriaceae 총 2과 3속 4종을, Deinococcus-thermus문은 4%로 Deinococcaceae 단일 1과 1속 1종으로 나타났다.

• Fisheries and Aquatic Sciences
• /
• 제22권8호
• /
• pp.18.1-18.5
• /
• 2019

The development of sex-specific genetic assays in a species provides both a method for identifying the system of sex determination and a valuable tool to address questions of conservation and management importance. In this study, we focused on the identification of single nucleotide polymorphisms (SNPs) that differentiate genetic sex in burbot Lota lota. Burbot are the only true freshwater representative of the cod family and a species of conservation and management importance throughout Eurasia and North America. To identify sex-specific SNPs, we utilized restriction site-associated DNA sequencing (RADseq) to interrogate thousands of SNPs in burbot samples of known phenotypic sex. We discovered 170,569 biallelic SNPs, none of which fit the pattern expected under female heterogamety. However, we identified 22 SNPs that fit the pattern expected under male heterogamety (males heterozygous XY, females fixed XX) and, from these, developed two genetic assays that robustly (~ 97% genotyping success) and accurately (> 99% correct) sexed burbot samples. These sex-specific genetic assays will benefit growing conservation aquaculture programs for this species and allow future assessments of sex-specific migration, growth, and mortality.

• 대한소아치과학회지
• /
• 제32권2호
• /
• pp.344-356
• /
• 2005

우리 인체에는 의학적으로 유용한 기능을 가진 세균들이 정상적으로 존재하며 구강내에도 독특한 기능을 나타내는 세균들이 상재한다. 본 연구에서는 치아우식증이 없는 소아의 타액에서 분리한 유산균 2주가 Streptococcus mutans에 의한 인공치태 형성과 혐기성 세균에 의한 휘발성 유황화합물 생성을 억제하는 것을 확인하고, API 50 CHL medium kit를 이용한 생화학적 검사와 16S rDNA sequencing으로 동정하여 다음과 같은 결과를 얻었다. 1. 분리균주는 2주 모두 그람양성 간균으로 과산화수소를 생성하였다. 2. 인공치태의 무게는 Streptococcus mutans의 단독 배양시 $124.4{\pm}30.4mg$이었으나, 분리균주와 병합 배양시에는 각각 $5.2{\pm}2.0mg,\;10.6{\pm}6.6mg$으로 현저하게 감소하였다(p<0.05). 3. Streptococcus mutans의 생균수는 단독 배양시 ml당 $3.4{\times}10^9$이었으나, 분리균주와 병합 배양시에는 각각 ml당 $4.6{\times}10^8$과 $2.4{\times}10^8$으로 감소하였다. 4. Fusobacterium nucleatum을 30분간 진탕한 후 측정한 상청액의 흡광도는 1.286이었으나, Fusobacterium nucleatum과 분리균주를 병합으로 30분간 진탕한 후 측정한 상청액의 흡광도는 각각 0.628과 0.497로 감소하였으며, 상호 결합 정도는 29.4%와 57.8%이었다. 5. Fusobacterium nucleatum의 단독 배양시 cysteine과 $FeSO_4$를 첨가한 배지를 가한 후 측정한 침전물의 배지 흡광도는 1.794이었으나, 분리균주와 병합 배양시 측정한 침전물의 배지 흡광도는 각각 1.144와 0.915로 감소하였으며, Porphyromonas gingivalis 단독 배양시 침전물의 배지 흡광도는 1.932이었으나 분리균주와 병합 배양시에는 침전물의 배지 흡광도가 각각 1.170과 1.266으로 감소하였다. 6. 분리균주를 API 50 CHL medium kit로 탄수화물 발효검사를 시행한 결과, 분리균주 1주는 Lactobacillus salivarius로, 다른 분리균주는 Lactobacillus delbrueckii subsp. lactis로 동정되었다. 7 분리균주를 16S rDNA partial sequencing으로 동정한 결과, 2주 모두 Lactobacillus salivarius subsp. salicinius와 유전자 유사치가 99.60%, 99.73%를 보여 Lactobacillus salivarius subsp. salicinius로 동정되었다. 이상의 결과를 종합하면 치아우식증이 없는 소아의 타액에서 분리된 유산균 중 과산화수소를 분비하여 인공치태 형성과 휘발성 유황화합물 생성을 억제하는 분리균주는 Lactobacillus salivarius subsp. salicinius로 동정되었다.

• 한국환경농학회지
• /
• 제37권2호
• /
• pp.135-140
• /
• 2018

한국에서 말벌은 양봉 산업에 큰 영향을 미치는 종이다. 특히 비교적 최근에 전국적으로 번식하는 말벌 종인 등검은말벌 (Vespa velutina nigrithorax)은 작은 체구에도 불구하고 높은 사냥 능력으로 꿀벌을 공격하여 양봉 업계에 큰 피해를 주고 있다. 그러나 이 새로운 침입 종에 대한 연구는 아직 시작단계에 있으며, 본 연구에서는 등검은말벌의 장내 박테리아 군집을 조사하고 이 결과를 꿀벌의 장내 박테리아 군집과 비교하여 등검은말벌의 방제를 위한 자료로 이용하고자 했다. 아시아 말벌과 꿀벌 장의 박테리아 게놈 DNA를 수집하여 16S rDNA를 증폭시켜 가변 부위인 V3, V4 염기서열을 판독 하였다. 계통별 분석결과 목 (order) 수준에서 Flavobacteriales는 등검은말벌에서 가장 우점인 박테리아였고, Aeromonadales와 Pseudomonadales가 그 뒤를 이었다. Flavobacteriaes는 꿀벌의 박테리아 군집과 비교했을 때 등검은말벌에서 증가하였으며, Aeromonadales와 Pseudomonadales는 우점종이지만 꿀벌에 비해 낮은 점유율을 보이는 등 두 개체 간의 차이를 확인할 수 있었다. 한편 이번 연구를 통해 이전에 동정되지 않은 등검은말벌 장 박테리아의 16S rDNA 염기 서열을 분석하였고, 이들 박테리아는 Thalassomonas, Caedobacter, Vampirovibrio, Alkaliphilus 및 Calothrix 속으로 분류되었다.

• Parasites, Hosts and Diseases
• /
• 제54권6호
• /
• pp.751-758
• /
• 2016

This study aimed at constructing a draft genome of the adult female worm Toxocara canis using next-generation sequencing (NGS) and de novo assembly, as well as to find new genes after annotation using functional genomics tools. Using an NGS machine, we produced DNA read data of T. canis. The de novo assembly of the read data was performed using SOAPdenovo. RNA read data were assembled using Trinity. Structural annotation, homology search, functional annotation, classification of protein domains, and KEGG pathway analysis were carried out. Besides them, recently developed tools such as MAKER, PASA, Evidence Modeler, and Blast2GO were used. The scaffold DNA was obtained, the N50 was 108,950 bp, and the overall length was 341,776,187 bp. The N50 of the transcriptome was 940 bp, and its length was 53,046,952 bp. The GC content of the entire genome was 39.3%. The total number of genes was 20,178, and the total number of protein sequences was 22,358. Of the 22,358 protein sequences, 4,992 were newly observed in T. canis. Following proteins previously unknown were found: E3 ubiquitin-protein ligase cbl-b and antigen T-cell receptor, zeta chain for T-cell and B-cell regulation; endoprotease bli-4 for cuticle metabolism; mucin 12Ea and polymorphic mucin variant C6/1/40r2.1 for mucin production; tropomodulin-family protein and ryanodine receptor calcium release channels for muscle movement. We were able to find new hypothetical polypeptides sequences unique to T. canis, and the findings of this study are capable of serving as a basis for extending our biological understanding of T. canis.

• BMB Reports
• /
• 제44권11호
• /
• pp.725-729
• /
• 2011

We report a novel mechanism of a CDH1 splicing mutation in a patient with signet ring cell carcinoma of the stomach. A 27-year-old man complaining of aggravated dyspepsia was diagnosed with signet ring cell carcinoma. Both his father and uncle had died of stomach cancer at a young age. DNA sequencing analysis of the CDH1 gene revealed a splice site mutation (c.833-2A>G). By RNA/cDNA sequencing analysis, CDH1 c.833-2A>G generated a new acceptor site within intron 6, causing the insertion of a 79-bp intronic sequence between exon 6 and 7 (r.833-79_833-1ins), and resulting in a frame shift. E-cadherin immunohistochemical staining revealed a loss of CDH1 expression. This study reveals the disease-causing mechanism of this splicing mutation, and emphasizes the need for functional studies using RNA samples for the accurate interpretation of detected splicing variant. This is the first reported case of a CDH1 mutation in a Korean patient.

• Parasites, Hosts and Diseases
• /
• 제57권2호
• /
• pp.207-211
• /
• 2019

Anisakiasis is a zoonotic disease induced by anisakid nematodes, and endoscopic inspection is used for a diagnosis or remedy for it. Anisakis simplex, Anisakis physeteris, and Pseudoterranova decipiens had been reported to be the major species causing human infections, particularly, in Japan. However, in Korea, recent studies strongly suggested that Anisakis pegreffii is the major species of human infections. To support this suggestion, we collected anisakid larvae (n=20) from 20 human patients who were undergone gastrointestinal endoscopy at a health check-up center in Korea, and molecular identification was performed on the larvae using PCR-RFLP analysis and gene sequencing of rDNA ITS regions and mtDNA cox2. In addition, anisakid larvae (n=53) collected from the sea eel (Astroconger myriaster) were also examined for comparison with those extracted from humans. The results showed that all human samples (100%) were identified as A. pegreffii, whereas 90.7% of the samples from the sea eel were A. pegreffii with the remaining 9.3% being Hysterothylacium aduncum. Our study confirmed that A. pegreffii is the predominant species causing human anisakiasis in Korea, and this seems to be due to the predominance of this larval type in the fish (sea eels) popularly consumed by the Korean people. The possibility of human infection with H. aduncum in Korea is also suggested.

• Journal of Veterinary Science
• /
• 제24권3호
• /
• pp.38.1-38.12
• /
• 2023

Background: Poor disease management and irregular vector control could predispose sheltered animals to disease such as feline Bartonella infection, a vector-borne zoonotic disease primarily caused by Bartonella henselae. Objectives: This study investigated the status of Bartonella infection in cats from eight (n = 8) shelters by molecular and serological approaches, profiling the CD4:CD8 ratio and the risk factors associated with Bartonella infection in shelter cats. Methods: Bartonella deoxyribonucleic acid (DNA) was detected through polymerase chain reaction (PCR) targeting 16S-23S rRNA internal transcribed spacer gene, followed by DNA sequencing. Bartonella IgM and IgG antibody titre, CD4 and CD8 profiles were detected using indirect immunofluorescence assay and flow cytometric analysis, respectively. Results: B. henselae was detected through PCR and sequencing in 1.0% (1/101) oral swab and 2.0% (1/50) cat fleas, while another 3/50 cat fleas carried B. clarridgeiae. Only 18/101 cats were seronegative against B. henselae, whereas 30.7% (31/101) cats were positive for both IgM and IgG, 8% (18/101) cats had IgM, and 33.7% (34/101) cats had IgG antibody only. None of the eight shelters sampled had Bartonella antibody-free cats. Although abnormal CD4:CD8 ratio was observed in 48/83 seropositive cats, flea infestation was the only significant risk factor observed in this study. Conclusions: The present study provides the first comparison on the Bartonella spp. antigen, antibody status and CD4:CD8 ratio among shelter cats. The high B. henselae seropositivity among shelter cats presumably due to significant flea infestation triggers an alarm of whether the infection could go undetectable and its potential transmission to humans.

• Journal of Microbiology and Biotechnology
• /
• 제31권11호
• /
• pp.1591-1600
• /
• 2021

Streptomyces coelicolor is a filamentous soil bacterium producing several kinds of antibiotics. S. coelicolor abs8752 is an abs (antibiotic synthesis deficient)-type mutation at the absR locus; it is characterized by an incapacity to produce any of the four antibiotics synthesized by its parental strain J1501. A chromosomal DNA fragment from S. coelicolor J1501, capable of complementing the abs- phenotype of the abs8752 mutant, was cloned and analyzed. DNA sequencing revealed that two complete ORFs (SCO6992 and SCO6993) were present in opposite directions in the clone. Introduction of SCO6992 in the mutant strain resulted in a remarkable increase in the production of two pigmented antibiotics, actinorhodin and undecylprodigiosin, in S. coelicolor J1501 and abs8752. However, introduction of SCO6993 did not show any significant difference compared to the control, suggesting that SCO6992 is primarily involved in stimulating the biosynthesis of antibiotics in S. coelicolor. In silico analysis of SCO6992 (359 aa, 39.5 kDa) revealed that sequences homologous to SCO6992 were all annotated as hypothetical proteins. Although a metalloprotease domain with a conserved metal-binding motif was found in SCO6992, the recombinant rSCO6992 did not show any protease activity. Instead, it showed very strong β-glucuronidase activity in an API ZYM assay and toward two artificial substrates, p-nitrophenyl-β-D-glucuronide and AS-BI-β-D-glucuronide. The binding between rSCO6992 and Zn²⁺ was confirmed by circular dichroism spectroscopy. We report for the first time that SCO6992 is a novel protein with β-glucuronidase activity, that has a distinct primary structure and physiological role from those of previously reported β-glucuronidases.