• 한국미생물·생명공학회지
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• 제47권3호
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• pp.423-433
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• 2019

Midgut microbiota is known to play a fundamental role in the biology and physiology of the agricultural pest, Spodoptera litura. This study reports the difference in the larval midgut microbiota of field-caught and laboratory-reared populations of S. litura by performing 16S rDNA amplicon pyrosequencing. Field populations for the study were collected from castor crops, whereas laboratory-reared larvae were fed on a regular chickpea based diet. In total, 23 bacterial phylotypes were observed from both laboratory-reared and field-caught caterpillars. Fisher's exact test with Storey's FDR multiple test correction demonstrated that bacterial genus, Clostridium was significantly abundant (p < 0.05) in field-caught larvae of S. litura as compared to that in the laboratory-reared larvae. Similarly, bacterial genera, such as Bradyrhizobium, Burkholderia, and Fibrisoma were identified (p < 0.05) predominantly in the laboratory-reared population. The Bray-Curtis dissimilarity matrix depicted a value of 0.986, which exhibited the maximum deviation between the midgut microbiota of the laboratory-reared and field-caught populations. No significant yeast diversity was seen in the laboratory-reared caterpillars. However, two yeast strains, namely Candida rugosa and Cyberlindnera fabianii were identified by PCR amplification and molecular cloning of the internal transcribed space region in the field-caught caterpillars. These results emphasize the differential colonization of gut residents based on environmental factors and diet.

• 생명과학회지
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• 제31권10호
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• pp.922-928
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• 2021

본 연구는 우리나라 전통 장류인 된장과 청국장의 미생물 분포와 시료간의 미생물학적 차이에 대해 차세대 염기서열 분석법(NGS)을 이용하여 분석하였다. α-diversity 분석 결과 된장에서 종 추정치와 풍부도가 통계학적으로 유의한 수준으로 높은 것으로 나타났다. 세균 분포를 분석한 결과 문 수준에서 Firmicutes가 된장에서 97.02%, 청국장에서 99.67%를 차지하여 공통적으로 가장 우점하는 것으로 나타났으며, 속 수준에서는 된장과 청국장에서 Bacillus가 각각 71.70%, 59.87%를 차지하여 가장 우점하는 것으로 확인되었다. 된장과 청국장의 미생물 분포에 차이가 있는지 분석하기 위해 PERMANOVA 분석을 수행한 결과 된장과 청국장의 미생물 분포에 통계학적으로 유의한 수준으로 차이가 나는 것으로 나타났다. 각 된장과 청국장 미생물 군집을 대표하는 biomarker를 분석하기 위해 LEfSe분석을 수행한 결과 된장에서 Bacillus subtilis, Tetragenococcus halophilus, Clostridium arbusti가 상대적으로 많이 분포하였으며, 청국장에서는 Bacillus thermoamylovorans, Enterococcus faecium, Lactobacillus sakei가 상대적으로 많이 분포하는 것으로 나타났다. 본 연구를 통해 콩을 주원료로 하는 우리나라 대표 전통장류인 된장과 청국장의 시료별 유사성과 차이점에 대한 미생물 분포를 정의하고 전통장류의 생화학적, 생리학적 특성과 미생물 분포의 상관관계를 규명하기 위한 기초 연구자료로 활용할 수 있을 것으로 기대된다.

• Animal Bioscience
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• 제34권7호
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• pp.1202-1209
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• 2021

Objective: The intestinal microbiota plays an important role in host physiology, metabolism, immunity, and behavior. And host genetics could influence the gut microbiota of hybrid animals. The three-way cross model is commonly utilized in commercial pig production; however, the use of this model to analyse the gut microbial composition is rarely reported. Methods: Two three-way hybrid pigs were selected, with Saba pigs as the starting maternal pig: Duroc× (Berkshire×Saba) (DBS) pig, Berkshire×(Duroc×Saba) (BDS) pig. One hundred pigs of each model were reared from 35 days (d) to 210 d. The body weight or feed consumption of all pigs were recorded and their feed/gain (F/G) ratio was calculated. On day 210, 10 pigs from each three-way cross were selected for slaughter, and cecal chyme samples were collected for 16S rRNA gene sequencing. Results: The final body weight (FBW) and average daily gain (ADG) of DBS pigs were significantly higher than those of BDS pigs (p<0.05), while the F/G ratios of DBS pigs were significantly lower than those of BDS pigs (p<0.05). The dominant phyla in DBS and BDS pigs were Bacteroidetes (55.23% vs 59%, respectively) and Firmicutes (36.65% vs 34.86%, respectively) (p>0.05). At the genus level, the abundance of Prevotella, Roseburia, and Anaerovibrio in DBS pigs was significantly lower than in BDS pigs (p<0.01). The abundance of Eubacterium, Clostridium XI, Bacteroides, Methanomassiliicoccus, and Parabacteroides in DBS pigs was significantly higher than in BDS pigs (p<0.05). The FBWs and ADGs were positively correlated with Bacteroides, ClostridiumXI, and Parabacteroides but negatively correlated with the Prevotella, Prevotella/Bacteroides (P/B) ratio, Roseburia, and Anaerovibrio. Conclusion: These results indicated that host genetics affect the cecal microbiota composition and the porcine gut microbiota is associated with growth performance, thereby suggesting that gut microbiota composition may be a useful biomarker in porcine genetics and breeding.

• Journal of Microbiology and Biotechnology
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• 제20권5호
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• pp.893-903
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• 2010

A cellulolytic and xylanolytic enzyme complex-producing alkalothermoanaerobacterium strain, Tepidimicrobium xylanilyticum BT14, is described. The cell was Grampositive, rod-shaped, and endospore-forming. Based on 16S rRNA gene analysis and various lines of biochemical and physiological properties, the strain BT14 is a new member of the genus Tepidimicrobium. The strain BT14 cells had the ability to bind to Avicel, xylan, and corn hull. The pH and temperature optima for growth were 9.0 and $60^{\circ}C$, respectively. The strain BT14 was able to use a variety of carbon sources. When the bacterium was grown on corn hulls under an anaerobic condition, a cellulolytic and xylanolytic enzyme complex was produced. Crude enzyme containing cellulase and xylanase of the strain BT14 was active in broad ranges of pH and temperature. The optimum conditions for cellulase and xylanase activities were pH 8.0 and 9.0 at $60^{\circ}C$, respectively. The crude enzyme had the ability to bind to Avicel and xylan. The analysis of native-PAGE and native-zymograms indicated the cellulosebinding protein showing both cellulase and xylanase activities, whereas SDS-PAGE zymograms showed 4 bands of cellulases and 5 bands of xylanases. Evidence of a cohesinlike amino acid sequence seemed to indicate that the protein complex shared a direct relationship with the cellulosome of Clostridium thermocellum. The crude enzyme from the strain BT14 showed effective degradation of plant biomass. When grown on corn hulls at pH 9.0 and $60^{\circ}C$ under anaerobic conditions, the strain BT14 produced ethanol and acetate as the main fermentation products.

• Journal of Microbiology and Biotechnology
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• 제30권9호
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• pp.1321-1334
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• 2020

Beef, pork, chicken and milk are considered representative protein sources in the human diet. Since the digestion of protein is important, the role of intestinal microflora is also important. Despite this, the pure effects of meat and milk intake on the microbiome are yet to be fully elucidated. To evaluate the effect of beef, pork, chicken and milk on intestinal microflora, we observed changes in the microbiome in response to different types of dietary animal proteins in vitro. Feces were collected from five 6-week-old pigs. The suspensions were pooled and inoculated into four different media containing beef, pork, chicken, or skim milk powder in distilled water. Changes in microbial communities were analyzed using 16S rRNA sequencing. The feces alone had the highest microbial alpha diversity. Among the treatment groups, beef showed the highest microbial diversity, followed by pork, chicken, and milk. The three dominant phyla were Proteobacteria, Firmicutes, and Bacteroidetes in all the groups. The most abundant genera in beef, pork, and chicken were Rummeliibacillus, Clostridium, and Phascolarctobacterium, whereas milk was enriched with Streptococcus, Lactobacillus, and Enterococcus. Aerobic bacteria decreased while anaerobic and facultative anaerobic bacteria increased in protein-rich nutrients. Functional gene groups were found to be over-represented in protein-rich nutrients. Our results provide baseline information for understanding the roles of dietary animal proteins in reshaping the gut microbiome. Furthermore, growth-promotion by specific species/genus may be used as a cultivation tool for uncultured gut microorganisms.

• Animal Bioscience
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• 제36권9호
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• pp.1453-1464
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• 2023

Objective: This study investigated the changes in bacterial communities within decomposing swine microcosms, comparing soil with or without intact microbial communities, and under aerobic and anaerobic conditions. Methods: The experimental microcosms consisted of four conditions: UA, unsterilized soil-aerobic condition; SA, sterilized soil-aerobic condition; UAn, unsterilized soil-anaerobic condition; and San, sterilized soil-anaerobic condition. The microcosms were prepared by mixing 112.5 g of soil and 37.5 g of ground carcass, which were then placed in sterile containers. The carcass-soil mixture was sampled at day 0, 5, 10, 30, and 60 of decomposition, and the bacterial communities that formed during carcass decomposition were assessed using Illumina MiSeq sequencing of the 16S rRNA gene. Results: A total of 1,687 amplicon sequence variants representing 22 phyla and 805 genera were identified in the microcosms. The Chao1 and Shannon diversity indices varied in between microcosms at each period (p<0.05). Metagenomic analysis showed variation in the taxa composition across the burial microcosms during decomposition, with Firmicutes being the dominant phylum, followed by Proteobacteria. At the genus level, Bacillus and Clostridium were the main genera within Firmicutes. Functional prediction revealed that the most abundant Kyoto encyclopedia of genes and genomes metabolic functions were carbohydrate and amino acid metabolisms. Conclusion: This study demonstrated a higher bacteria diversity in UA and UAn microcosms than in SA and SAn microcosms. In addition, the taxonomic composition of the microbial community also exhibited changes, highlighting the impact of soil sterilization and oxygen on carcass decomposition. Furthermore, this study provided insights into the microbial communities associated with decomposing swine carcasses in microcosm.

• 대한임상검사과학회지
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• 제49권4호
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• pp.407-412
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• 2017

본 연구에서는 계대배양과 세균 동정 시험에 소요되는 시간을 단축하고, 혈류감염의 새로운 검사 방법을 모색하여 간단하고 신속 정확한 동정 결과를 도출할 목적으로 질량분석기를 이용하여 다음과 같은 결과를 얻었다. 혈액배양에서 한 가지 세균만 배양된 검체는 총 254개였으며, Vitek 2에서 208주(81.8%)의 세균을 동정되었으며, 45주는 동정되지 않았다. 동정된 세균 중 그람양성 세균이 146개(57.5%), 그람음성 세균이 108개(42.5%)이었다. 전체적으로 233개는 종(species) 수준까지 동정 되었으며, 21개는 속(genus)수준까지 동정 되었다. 동정 오류는 Propionibacterium acnes를 Clostridium bifermentans로 동정 되었다. 균종별로는 enterobacteriaceae, glucose non-fermentative bacilli (GNFB), staphylococci의 정확도는 각각 81/83 (97.6%), 12/15 (80.0%), 72/85 (84.7%)로 나타났다. Vitek 2에 의한 표준법과 Vitek MS에 의한 직접법에 의한 동정의 일치율은 81.8%이었으며, 45주는 동정되지 않았다. 동정되지 않은 세균들의 대부분은 그람양성 세균(n=37)이었고, 그람양성 세균은 streptococci (14), coagulase-negative staphylococci (CNS) (11), enterococci (3), Staphylococcus aureus (2), Micrococcus spp. (2), Bacillus spp. (2) 그리고 Actinomyces odontolyticus, Finegoldia mag na, Peptostreptococcus spp.가 각각 1건씩 이었다. 결과 보고 시간은 기존의 검사 방법보다 24~72시간까지 단축되었다. 산소성 배양과 무산소성 배양 사이의 동정률의 차이는 없었으나 무산소성 배양을 사용하면 용해 과정이 필요 없어 검체 준비 시간을 단축할 수 있었다. 이상의 연구 결과로 혈액배양병에서 직접 동정하는 방법은 정확하고 결과 보고 시간이 신속하여 환자의 치료에 매우 유용할 것이라 생각된다. 향후 추가적인 연구에서는 본 연구에서 정확성이 부족했던 사슬알균(streptococci)과 혈장응고효소 음성 포도알균(CNS)을 동정하기 위한 방법을 더욱 개선할 필요가 있을 것으로 사료된다.

• 한국축산식품학회지
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• 제26권1호
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• pp.106-112
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• 2006

한우와 홀스타인의 분변으로부터 MRS 배지와 LAPT 배지를 이용하여 무작위 선발법으로 54균주의 유산균을 1차로 분리하였다. 1차로 분리된 54균주에 대해 내담즙성이 우수한 10균주를 분리한 다음 내산성을 조사한 결과 인공위액 pH 2.5에서 LS1, LS15 및 LL6 균주가 각각 66.5%, 82.6% 및 80.7%의 생존율을 나타내었다. Sal. typhimurium, Sta. aureus 및 Cl. perfringens의 병원균에 대해 가장 큰 항균력을 보인 균주는 LL6와 LL7이었다. API CHL kit로 동정한 결과 LS1, LS2 및 LMI 균주는 모두 L. fermentum, LL6와 LL7 균주는 L. acidophilus, LS3 균주는 L. plantarum으로 각각 동정되었고, 나머지 4균주는 Lactobacillus spp. 로 동정되어 분리된 10균주 모두 안전성 있는 유산간균임을 확인하였다. 10종류의 항생제에 대한 내성을 조사한 결과 ampicillin, amoxicillin과 erythromycin에 대해서는 감수성이 있으나 colistin과 ciprofloxacin에 대해 모두 내성을 나타내었다. LB1, LL6 및 LL7 균주는 gentamicin과 neomycin에 대해 내성을 보여 주었다. 분리 동정된 균주 중에 내산성, 내담즙성 및 병원성 균에 대한 특성을 기준으로 판단할 경우 probiotic 유산균으로 사용 가능성이 높은 것은 LL6인 L. acidophilus로 나타났다.

• 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.

• 한국초지조사료학회지
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• 제39권4호
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• pp.227-234
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• 2019

본 연구는 고온기 여름철 사육환경에서의 홀스타인종 젖소의 반추위내 미생물 균총 변화를 분석하고, 반추위내 미생물과 고온 스트레스간의 연관성을 규명하고자 수행하였다. 국립축산과학원 낙농과에서 사육 중인 홀스타인 젖소 10두의 반추위액을 채취하였으며, 채취한 시료 샘플은 PowerSoil® DNA Isolation Kit (Cat. No. 12888, MO BIO)를 이용하여 DNA를 추출한 후 Illumina HiSeq^TM platform (Illumina, CA, USA)을 이용하여 미생물 균총 분석을 실시하였다. 반추위액 내 미생물 균총을 분석한 결과, 사육환경 온습도에 따른 미생물 군집 구성에는 큰 차이는 없었으나, 미생물의 상대적 함량에는 차이가 있었다. LEfSe 분석을 통해 적온과 고온 환경에서 특정 미생물들의 상대적 조성이 유의적으로 증가함을 확인하였다. 이들 결과를 볼 때, 반추위내 미생물 균총은 고온과 같은 외부 환경변화에 영향을 받는 것으로 판단되어 젖소의 고온스트레스 반응에 있어 반추위 미생물 변화가 중요한 역할을 담당할 것으로 사료된다. 추후 연구는 이러한 차이를 나타내는 미생물들의 대사 경로나 대사 물질에 분석을 통해 환경변화와 미생물간의 연관성 및 이러한 미생물 균총 조절을 통한 고온기 젖소의 적응성 향상을 위한 미생물학적 전략 연구가가 필요할 것으로 생각된다.