• Journal of Microbiology and Biotechnology
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• 제25권6호
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• pp.765-770
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• 2015

Recent sequencing technology development has revolutionized fields of microbial ecology. MiSeq-based microbial community analysis allows us to sequence more than a few hundred samples at a time, which is far more cost-effective than pyrosequencing. The approach, however, has not been preferably used owing to computational difficulties of processing huge amounts of data as well as known Illumina-derived artefact problems with amplicon sequencing. The choice of assembly software to take advantage of paired-end sequencing and methods to remove Illumina artefacts sequences are discussed. The protocol we suggest not only removed erroneous reads, but also dramatically reduced computational workload, which allows even a typical desktop computer to process a huge amount of sequence data generated with Illumina sequencers. We also developed a Web interface (http://biotech.jejunu.ac.kr/ ~abl/16s/) that allows users to conduct fastq-merging and mothur batch creation. The study presented here should provide technical advantages and supports in applying MiSeq-based microbial community analysis.

• 미생물학회지
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• 제51권1호
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• pp.81-85
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• 2015

성장촉진제로 항생제 사용이 금지가 된 이후, 가축들의 사망률이 증가되어 항생제 대체제를 개발해야 하는 것이 시급하다. 그러한 대체제 개발에 새로운 접근 중 하나는 숙주의 신체적 기능에 영향을 준다고 알려진 장내미생물생태를 조절하는 것이다. 하지만 가축의 장내미생물에 대한 이해가 인간과 비교하여 볼 때 많이 부족한 실정이다. 본 연구에서는 돼지장내미생물생태가 지역적 차이가 있음에 대한 기본적인 정보를 제공한다. 돼지 분변샘플은 제주(n=40), 광주(n=28), 해남(n=30) 농가로부터 채취하였으며, MiSeq을 이용하여 16S rRNA V4 지역을 시퀀싱하였다. 또한 Mothur 파이프라인을 이용하여 MiSeq으로부터 얻은 데이터를 처리하였다. 총 5,642,125 reads를 얻었으며, 에러시퀀스들을 제거한 후 최종적으로 3,868,143 reads가 남았다. Phylum 수준의 taxonomic composition 분석에서는 제주 돼지들이 Firmicutes를 가장 많이 포함하고 있었으며, Operational Taxonomic Units 분포분석에서 또한 지역적 차이에 따라 돼지장내미생물생태가 다르다는 것을 확인하였다. Non-metric multidimensional scaling과 Phyla의 풍부함 사이의 상관관계분석에서는 Actinobacter, Verrucomicrobia, Firmicutes, Fibrobacteres이 세 개의 지역에 있는 돼지들의 장내미생물생태 차이를 나타나게 하는 장내 미생물 요소라는 것을 확인하였다. 그러한 가축의 장내미생물생태는 농장에서 사용하는 사료와 사양관리에 의해 많은 영향을 미치는 것으로 생각된다. 본 연구결과는 돼지장내미생물생태가 지역적으로 많은 차이가 있다는 것을 나타내며, 추후에 가축의 장내미생물생태에 관한 연구는 지역적 차이가 있다는 것을 고려하여 설계해야 될 것이다.

• 한국환경농학회지
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• 제40권3호
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• pp.194-202
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• 2021

BACKGROUND: Towards achievement of sustainable agriculture, using microbial inoculants may present promising alternatives without adverse environmental effects; however, there are challenging issues that should be addressed in terms of effectiveness and ecology. Viability and stability of the bacterial inoculants would be one of the major issues in effectiveness of microbial pesticide uses, and the changes within the indigenous microbial communities by the inoculants would be an important factor influencing soil ecology. Here we investigated the stability of the introduced bacterial strains in the soils planted with barley and its effect on the diversity shifts of the rhizosphere soil bacteria. METHODS AND RESULTS: Two different types of bacterial strains of Bacillus thuringiensis and Shewanella oneidensis MR-1 were inoculated to the soils planted with barley. To monitor the stability of the inoculated bacterial strains, genes specific to the strains (XRE and mtrA) were quantified by qPCR. In addition, bacterial community analyses were performed using v3-v4 regions of 16S rRNA gene sequences from the barley rhizosphere soils, which were analyzed using Illumina MiSeq system and Mothur. Alpha- and beta-diversity analyses indicated that the inoculated rhizosphere soils were grouped apart from the uninoculated soil, and plant growth also may have affected the soil bacterial diversity. CONCLUSION: Regardless of the survival of the introduced non-native microbes, non-indigenous bacteria may influence the soil microbial community and diversity.

• 한국환경보건학회지
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• 제43권6호
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• pp.491-498
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• 2017

Objective: Bacterial abundance and community compositions have been examined in Asian dust events, clarifying their impacts on public health. This study aims to determine the bacterial community compositions and viable bacteria in Asian dust particles in the Asian dust or non-Asian dust event of March 2016. Methods: The dust samples were collected using the high volume air sampler or high volume cascade impactor, and bacterial 16S rRNA genes were amplified using PCR, followed by pyrosequencing. Bacterial diversity index, richness estimate and community composition in the particles were analyzed from the sequencing data using Mothur software. Results: The results showed that the diversity and richness during Asian dust events were higher than them in non-Asian dust events. The total bacterial community analysis showed that at the phylum Proteobacteria, Actinobacteria and Firmicutes were the most dominant of Asian dust events and non-Asian dust events. In addition, the bacterial colony counts were higher during Asian dust event, comparing with non-Asian dust event. Conclusions: This study showed that bacterial community and richness of Asian dust samples was more complex and higher than non-Asian dust samples in Gyeonggi-do, Korea, which could affect public health and environment. Thus, the continuous monitoring of Asian dust could be an alternative for managing airborne bacteria.

• 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.