• Journal of Microbiology and Biotechnology
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• v.25 no.6
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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.

• Korean Journal of Microbiology
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• v.51 no.1
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• pp.81-85
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• 2015

Since the banning of antibiotic growth promoters (AGPs), the death of livestock has been increased, thus there is a strong demand for AGP-alternatives. Modulation of gut microbiota has been reported to affect host physiological functions and suggested to be a novel approach for developing AGP-alternatives. However, little has been understood about livestock gut microbiota compared to that of humans. We conducted preliminary study provide fundamental information regarding to regional differences in swine gut microbiota. Swine fecal samples were obtained from farms in Jeju (n=40), Gwangju (n=28), and Haenam (n=30). MiSeq was used to sequence 16S rRNA V4 region, and Mothur pipeline (Schloss et al., 2009) was used for data processing. A total of 5,642,125 reads were obtained and 3,868,143 reads were remained after removing erroneous reads. Analysis of taxonomic composition at the phylum level indicated greater abundance of Firmicutes among Jeju swine, and cluster analysis of distribution of operational taxonomic units also showed regional differences among swine gut microbiota. In addition, correlation analysis between non-metric multidimensional scaling and abundance of phyla suggested that the phyla Actinobacter, Verrucomicrobia, Firmicutes, and Fibrobacteres were driving factors for the regional differences. Livestock gut microbiota may be affected by diet and practices in farms. Our results indicated significant regional differences in swine gut microbiota, suggesting that future livestock gut microbiota studies should be designed with the regional differences in mind.

• Korean Journal of Environmental Agriculture
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• v.40 no.3
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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.

• Journal of Environmental Health Sciences
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• v.43 no.6
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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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• v.25 no.4
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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.