• Journal of Microbiology and Biotechnology
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• 제20권3호
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• pp.602-608
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• 2010

An atrazine-degrading bacterium, strain KU001, was obtained from a sugarcane field at the Cane and Sugar Research and Development Center at the Kasetsart University, Kamphaeng Saen Campus, Thailand. Strain KU001 had a rod-to-coccus morphological cycle during growth. Biolog carbon source analysis indicated that the isolated bacterium was Arthrobacter histidinolovorans. Sequence analysis of the PCR product indicated that the 16S rRNA gene in strain KU001 was 99% identical to the same region in Arthrobacter sp. The atrazine degradation pathway in strain KU001 consisted of the catabolic genes trzN, atzB, and atzC. Strain KU001 was able to use atrazine as a sole nitrogen source for growth, and surprisingly, atrazine degradation was not inhibited in cells grown on ammonium, nitrate, or urea, as compared with cells cultivated on growth-limiting nitrogen sources. During the atrazine degradation process, the supplementation of nitrate completely inhibited atrazine degradation activity in strain KU001, whereas ammonium and urea had no effect on atrazine degradation activity. The addition of strain KU001 to sterile or nonsterile soils resulted in the disappearance of atrazine at a rate that was 4- to 5-fold more than that achieved by the indigenous microbial community. The addition of citrate to soils resulted in enhanced atrazine degradation, where 80% of atrazine disappeared within one day following nutrient supplementation.

• Journal of Microbiology and Biotechnology
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• 제25권4호
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• pp.431-438
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• 2015

Ever since the ban on antibiotic growth promoters (AGPs), the livestock death rate has increased owing to pathogenic bacterial infections. There is a need of developing AGP alternatives; however, the mechanisms by which AGP enhances livestock growth performance are not clearly understood. In this study, we fed 3-week-old swine for 9 weeks with and without AGPs containing chlortetracycline, sulfathiazole, and penicillin to investigate the effects of AGPs on swine gut microbiota. Microbial community analysis was done based on bacterial 16S rRNA genes using MiSeq. The use of AGP showed no growth promoting effect, but inhibited the growth of potential pathogens during the early growth stage. Our results showed the significant increase in species richness after the stabilization of gut microbiota during the post-weaning period (4-week-old). Moreover, the swine gut microbiota was divided into four clusters based on the distribution of operational taxonomic units, which was significantly correlated to the swine weight regardless of AGP treatments. Taxonomic abundance analysis indicated a negative correlation between host weight and the abundance of the family Prevotellaceae species, but showed positive correlation to the abundance of the family Spirochaetaceae, Clostridiaceae_1, and Peptostreptococcaeae species. Although no growth performance enhancement was observed, the use of AGP inhibited the potential pathogens in the early growth stage of swine. In addition, our results indicated the ecological succession of swine gut microbiota according to swine weight. Here, we present a characterization of swine gut microbiota with respect to the effects of AGPs on growth performance.

• 한국토양비료학회지
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• 제48권4호
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• pp.285-294
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• 2015

Ordination has been recognized useful method to analyze the effects of multiple environmental factors on dozens of species in vegetation ecology because of summarizing community data by producing a low-dimensional graphics. Main objective of this study was the application of ordination method, especially principal components analysis (PCA), to analyze the soil characterization on paddy treated by different green manure crops and tillage methods. Treatments included the three tillage treatments and two green manure crops as the following; (i) moldrotary + rotary tillage without green manure crop (Con), with (ii) hairy vetch (ConHv), and (iii) hairy vetch + green barely (ConHvGb), (iv) rotary tillage without green manure crop (Rot), with (v) hairy vetch (RotHv), and (vi) hairy vetch + green barly (RotHvGb), and (vii) no-tillage (Notill). Vectorial distance result from PCA of soil properties including physical, chemical, and microbial properties showed the two main difference. Firstly, soil properties among plots without green manure were strongly affected by tillage strength [Vectorial distance: Con-Notil (5.88) > Rot-Notill (4.58)] at PC1 (35.0%) axis. But it was difficult to find the fixed trend among plots when green manure crop was added in plot. Nevertheless, two groups were separated by adding green manure crop at PC2 (29.2%) axis. These results show that PCA ordination methods could be used the research for change of soil characterization.

• Tuberculosis and Respiratory Diseases
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• 제86권4호
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• pp.294-303
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• 2023

Background: The human lung serves as a niche for a unique and dynamic bacterial community related to the development and aggravation of multiple respiratory diseases. Therefore, identifying the microbiome status is crucial to maintaining the microecological balance and maximizing the therapeutic effect on lung diseases. Therefore, we investigated the histological type-based differences in the lung microbiomes of patients with lung cancer. Methods: We performed 16S rRNA sequencing to evaluate the respiratory tract microbiome present in bronchoalveolar lavage fluid. Patients with non-small cell lung cancer were stratified based on two main subtypes of lung cancer: adenocarcinoma and squamous cell carcinoma (SqCC). Results: Among the 84 patients analyzed, 64 (76.2%) had adenocarcinoma, and 20 (23.8%) had SqCC. The α- and β-diversities showed significant differences between the two groups (p=0.004 for Chao1, p=0.001 for Simpson index, and p=0.011 for PERMANOVA). Actinomyces graevenitzii was dominant in the SqCC group (linear discriminant analysis [LDA] score, 2.46); the populations of Haemophilus parainfluenza (LDA score, 4.08), Neisseria subflava (LDA score, 4.07), Porphyromonas endodontalis (LDA score, 3.88), and Fusobacterium nucleatum (LDA score, 3.72) were significantly higher in the adenocarcinoma group. Conclusion: Microbiome diversity is crucial for maintaining homeostasis in the lung environment, and dysbiosis may be related to the development and prognosis of lung cancer. The mortality rate was high, and the microbiome was not diverse in SqCC. Further large-scale studies are required to investigate the role of the microbiome in the development of different lung cancer types.

• Journal of Microbiology and Biotechnology
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• 제27권3호
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• pp.561-572
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• 2017

The global commercial cultivation of transgenic crops, including glyphosate-tolerant soybean, has increased widely in recent decades with potential impact on the environment. The bulk of previous studies showed different results on the effects of the release of transgenic plants on the soil microbial community, especially rhizosphere bacteria. In this study, comparative analyses of the bacterial communities in the rhizosphere soils and surrounding soils were performed between the glyphosate-tolerant soybean line NZL06-698 (or simply N698), containing a glyphosate-insensitive EPSPS gene, and its control cultivar Mengdou12 (or simply MD12), by a 16S ribosomal RNA gene (16S rDNA) amplicon sequencing-based Illumina MiSeq platform. No statistically significant difference was found in the overall alpha diversity of the rhizosphere bacterial communities, although the species richness and evenness of the bacteria increased in the rhizosphere of N698 compared with that of MD12. Some influence on phylogenetic diversity of the rhizosphere bacterial communities was found between N698 and MD12 by beta diversity analysis based on weighted UniFrac distance. Furthermore, the relative abundances of part rhizosphere bacterial phyla and genera, which included some nitrogen-fixing bacteria, were significantly different between N698 and MD12. Our present results indicate some impact of the glyphosate-tolerant soybean line N698 on the phylogenetic diversity of rhizosphere bacterial communities together with a significant difference in the relative abundances of part rhizosphere bacteria at different classification levels as compared with its control cultivar MD12, when a comparative analysis of surrounding soils between N698 and MD12 was used as a systematic contrast study.

• 대한환경공학회지
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• 제30권9호
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• pp.939-947
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• 2008

본 연구에서는 PCR-DGGE 기법을 이용하여 DO 농도에 따른 동시 질산화.탈질 반응조 내 미생물 군집 변화 양상을 규명하고자 하였다. DO 농도의 변화에 따른 eubacteria의 군집 변화 해석 실험에서, DO 농도를 2와 1 mg/L로 운전한 반응조 내의 band profile은 거의 유사하게 관찰되었으며 5종의 우점화 미생물(Uncultured Bacterium 3종, Bacillus sp. 1종, Uncultured Bacteroidetes sp. 1종)을 포함한 16종의 미생물을 동정할 수 있었다. 그리고 DO 농도 0.5 mg/L로 운전한 반응조 내의 DGGE 결과 7종의 우점화 미생물(Uncultured Bacterium 5종, Zoogloea sp. 2종)을 포함한 12종의 미생물을 동정할 수 있었으며, DO 농도 0.1 mg/L로 운전한 반응조의 경우 3종의 우점화 미생물(Uncultured Bacterium 1종, Zoogloea sp. 2종)을 포함한 11종의 미생물을 동정할 수 있었다. 반응조 내 DO 농도의 변화에 따른 $\beta$-AOB($\beta$-Ammonia Oxidizing Bacteria)의 군집 변화 해석 실험 결과, 하나의 band를 관찰할 수 있었다. 이 band는 Uncultured Nitrosomonas sp. done DNB Y20와 97%의 유사도를 갖는 것으로 나타났으며 2, 1, 그리고 0.5 mg/L의 DO 농도에서 추출한 sample에서는 선명하게 관측되었으나, 0.1 mg/L DO 농도에서 추출한 sample에서는 선명도가 현저히 감소하였다. 이는 NH$_4{^+}$-N의 질산화 양상과 상관관계가 있음을 보였다. 반응조 내 DO 농도에 따른 탈질 bacteria의 군집 변화 해석실험 결과, 다섯 개의 band(nirS를 함유하는 Uncultured organism 미생물 3종, nirK를 함유하는 Uncultured bacterium 미생물 2종)가 관측되었으며 관측된 band 중 한 band는 DO 농도가 낮아질수록 선명도가 현저히 증가하는 것을 확인할 수 있었다. 이 band에 해당하는 미생물은 86%의 유사도를 가진 Uncultured organism clone eS1 cd1 nirS gene, partial cds로, 본 연구의 탈질 반응에 직접적으로 관여 하는 미생물로 사료된다.

• 대한환경공학회지
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• 제36권4호
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• pp.277-285
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• 2014

본 연구에서는 구제역으로 인해 발생된 가축사체 매몰지의 조기 안정화를 위하여 유용 미생물 KEM을 사용하였고, 토질에 따른 효과를 알아보기 위하여 매몰지 모형의 반응기를 통해 연구하였다. 반응기는 랩 스케일로 제작하였고, 토질 특성에 다양성을 주기 위하여 일반 토양, 20%의 사토와 섞은 일반 토양, 20%의 점토와 섞은 일반 토양을 각각 준비하였다. 각각의 토양과 유용 미생물 KEM과 섞은 후 사체를 매몰하였다. 분석 대상 악취 성분은 총 8가지로 이산화탄소, 메탄, 암모니아, 트리메틸아민, 황화수소, 메칠메르캅탄, 황화메틸과 이황화메틸이었다. 악취 분석 결과 황화수소와 메틸메르캅탄은 사토를 적용한 반응기에서 저감 효과를 보였고(각각 배출 잔량 0.09, 0.35 mg), 암모니아와 트리메틸아민은 점토를 적용한 경우 저감 효율이 높았다(각각 배출잔량 0.31, 2.06 mg). 이에 근거하여 사토는 황 화합물 악취 저감에, 점토는 질소 화합물 악취 저감에 효과를 나타내는 것으로 보인다. 또한, 토질의 특성에 따라 우점화된 미생물의 군집과 분포도가 변화되는 것을 확인하였다.

• 미생물학회지
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• 제51권2호
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• pp.133-140
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• 2015

상수리림 산림토양 각 층위 내 물리 화학적, 미생물학적 환경변수간 상관관계를 확인한 결과, 낙엽 분해 층(F)과 부식층(H)은 각 환경변수와 높은 상관관계를 갖는 특징을 나타내었다. 특히, F층에서는 pH가 C 그리고 N과 높은 상관관계를 나타내었고, 부식층(H)에서는 각종 유기산이 토양 세균 밀도와 높은 상관관계를 나타내었다. 상수리림 산림토양의 층위별 세균군집 구조의 계통해석을 위해 각 층위의 계절별 시료로부터 DNA를 직접 추출하고 DGGE 분석한 결과 낙엽층(L)의 경우 43 bands, F층은 42 bands, H층은 43 bands 그리고 근권 토양층(A)은 47 bands로 총 175 bands가 상수리림 산림토양의 DGGE 주요 bands로 선발되었다. 확보된 총 175 DGGE 주요 bands의 16S rRNA 유전자 염기서열 정보를 바탕으로 세균군집의 계통 해석한 결과, 7개 phylum에 32개 order로 세 분류되었다. 각 order에 속하는 염기서열을 heat map 분석하고 상수리림 산림토양의 각 층위을 clustering 한 결과 F층과 H층이 L층 그리고 A층과 서로 다른 cluster를 형성하는 것이 확인되었다. 또한, 산림토양의 각 층위에 존재하는 세균군집 중 약 50%가 ${\alpha}$-proteobacteria로 우점계통군으로 나타났다. 특히, Rhizobiales, Burkholderiales, 그리고 Actinobacteriales 목은 모든 계절과 모든 층위에서 보여지는 세균군집으로 확인되어 상수리림 산림토양에서 대표적인 토착세균 군집임이 확인되었다.

• Asian-Australasian Journal of Animal Sciences
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• 제30권7호
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• pp.957-966
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• 2017

Objective: To understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages. Methods: The denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon contents of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analyze the DGGE fingerprint. The Illumina sequences were assembled, predicted to genes and functionally annotated, and then classified by querying protein sequences of the genes against the Kyoto encyclopedia of genes and genomes (KEGG) database. Results: Metagenomic sequencing showed that more than 85% of ribosomal RNA (rRNA) gene sequences belonged to the phylum Firmicutes and Bacteroidetes, indicating that the family Ruminococcaceae (46.5%), Rikenellaceae (11.3%), Lachnospiraceae (10.0%), and Bacteroidaceae (6.3%) were dominant gut microbes. Over 50% of non-rRNA gene sequences represented the metabolic pathways of amino acids (14.4%), proteins (12.3%), sugars (11.9%), nucleotides (6.8%), lipids (1.7%), xenobiotics (1.4%), coenzymes, and vitamins (3.6%). Gene functional classification showed that most of enzyme-coding genes were related to cellulose digestion and amino acids metabolic pathways. Conclusion: Yaks' age had a substantial effect on gut microbial composition. Comparative metagenomics of gut microbiota in 0.5-, 1.5-, and 2.5-year-old yaks revealed that the abundance of the class Clostridia, Bacteroidia, and Lentisphaeria, as well as the phylum Firmicutes, Bacteroidetes, Lentisphaerae, Tenericutes, and Cyanobacteria, varied more greatly during yaks' growth, especially in young animals (0.5 and 1.5 years old). Gut microbes, including Bacteroides, Clostridium, and Lentisphaeria, make a contribution to the energy metabolism and synthesis of amino acid, which are essential to the normal growth of yaks.

• 환경영향평가
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• 제28권6호
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• pp.604-615
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• 2019

본 연구에서는 폐기되는 조류 바이오매스를 재활용하여 퇴비화 과정을 통해 새로운 형태의 조류토양개량제(algae soil conditioner, ASC)로 제조하고 영양성분에 대한 특성을 평가하였다. ASCs는 응집부상공법을 통해 수집된 조류 바이오매스를 주원료로 하였으며 추가적으로 다양한 보조 원료(톱밥, 펄라이트, 깻묵 등)를 첨가하여 제조하였다. ASCs는 투입된 조류 바이오매스 질량 비율에 따라 각각 blank 0%, ASC1 11.7%, ASC2 21.6%, ASC3 37.6%, ASC4 59.5%로 구분하여 총 127일간 부숙하였다. ASCs는 호기성 미생물 반응에 의해 온도 증감이 뚜렷하게 나타났으며 6~7회의 크고 작은 온도 피크가 관찰되었다. 이화학 분석결과 유기물이 무기화(mineralization) 되면서 macronutrients (TN, P₂O₅, K₂O) 뿐만 아니라 secondary macronutrients (CaO, MgO)에서도 두드러진 증가를 보였다. 미생물 군집변화는 ASCs의 부숙과정에 따라 1단계(세균, 사상균)→2단계(방선균, 세균)→3단계(고초균)로 나타났으며 온도변화와 영양성분의 거동과 밀접한 관련이 있다고 판단되었다. 부숙 완성도에 따라 토양개량제의 품질이 결정될 수 있으며 본 연구결과에서는 조류 바이오매스를 59.5% 이내로 조절한다면 효과적인 미생물 활성을 유도할 수 있을 것으로 판단되었다. 결론적으로 조류 바이오매스를 재활용한 토양개량제의 제조 및 활용 가능성을 확인하였으며 추가적인 기술적 발전이 이루어진다면 향후 효과적인 토양개량제로 활용할 수 있을 것으로 판단된다.