• Genomics & Informatics
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• v.21 no.3
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• pp.40.1-40.11
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• 2023

Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We present a streamlined pipeline that integrates FastP for read trimming, HmmUFOtu for operational taxonomic units (OTU) clustering, Vsearch for chimera checking, and Kraken2 for taxonomic assignment. To assess the pipeline's performance, we reprocessed two published stool datasets of normal Korean populations: one with 890 and the other with 1,462 independent samples. In the first dataset, HmmUFOtu retained 93.2% of over 104 million read pairs after quality trimming, discarding chimeric or unclassifiable reads, while DADA2, a commonly used ASV method, retained only 44.6% of the reads. Nonetheless, both methods yielded qualitatively similar β-diversity plots. For the second dataset, HmmUFOtu retained 89.2% of read pairs, while DADA2 retained a mere 18.4% of the reads. HmmUFOtu, being a closed-reference clustering method, facilitates merging separately processed datasets, with shared OTUs between the two datasets exhibiting a correlation coefficient of 0.92 in total abundance (log scale). While the first two dimensions of the β-diversity plot exhibited a cohesive mixture of the two datasets, the third dimension revealed the presence of a batch effect. Our comparative evaluation of ASV and OTU methods within this streamlined pipeline provides valuable insights into their performance when processing large-scale microbial 16S rRNA amplicon sequencing data. The strengths of HmmUFOtu and its potential for dataset merging are highlighted.

• Journal of Environmental Health Sciences
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• v.39 no.6
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• pp.513-521
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• 2013

Objectives: This study was performed in order to detect indicator bacteria in drinking spring water (DSW) samples in Seoul Metropolitan City, and to identify their genus through 16S rRNA sequencing and then assessing the genetic relation of their strains. Methods: For indicator bacteria detection and identification of total coliforms, we analyzed DSW between the spring and summer seasons. In particular, DSW samples were chosen from sites repeatedly found unsatisfactory in recent years. Results: Heterotrophic plate counts of DSW in the spring and summer season were investigated in the range of 0-550 and 0-800 CFU/mL, respectively. Total coliforms of these were 0-1,900 and 0-2,100 CFU/100mL, fecal coliforms were 0-600 and 0-550 CFU/100mL, and Escherichia coli were 0-7 and 0-326 MPN/100mL. The detection ratio of fecal pollution indicators and that of fecal coliforms increased to 58.6% in the summer from 12.5% in the spring and Escherichia coli increased to 51.4% from 4.7%. As a result of genetic analysis on the isolated bacteria, the genus of total coliforms was classified in the order of Enterobacter spp. 12.7%, Serratia spp. 7.3%, E. hermanii 6.4%, Rahnella spp. 5.5%, Hafnia spp. 4.5%, Escherichia coli 3.6%, Klebsiella spp. 3.6% in the spring season. In the summer season, it was classified in order of Klebsiella spp. 16.6%, Enterobacter spp. 13.0%, Escherichia coli 11.0%, Serratia spp. 8.6%, Raoultella spp. 7.0%, Kluyvera spp. 5.6% and Citrobacter spp. 3.0%. Conclusions: The increase of fecal pollution in summer indicates that special attention to drinking DSW is required.

• Journal of Korean Society of Environmental Engineers
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• v.35 no.7
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• pp.503-508
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• 2013

The aim of this study was to investigate the microbial communities in animal carcass disposal soils to examine the possible threat of pathogens from leachate. DNA extraction was performed for the soils in three carcass disposal sites located in Gyeonggi-do, Korea, and then 16S rRNA pyrosequencing was conducted to identify the microbial communities. Results indicate that, according to phylum classification, Proteobacteria (100%) was identified in soil A, Actinobacteria (66.4%) > Proteobacteria (31.1%) > Bacteriodetes (2.1%) > Acidobacteria (0.3%) in soil B, and Actinobacteria (63.1%) > Proteobacteria (36.9%) in soil C. According to genus classification, Pseudomonas was dominant in soil A (98%), Arthrobacter in soil B (68%) and C (61%). There were no detections of pathogens such as Salmonella, Campylobacter and Clostridium perfringens. However, high concentration of Ralstonia pickettii causing bacteremia was observed. Although carcass disposal soils examined in this study were not highly contaminated with pathogens, further monitoring is still needed to examine the potential threat of pathogens in leachate derived from carcass disposal sites.

• Microbiology and Biotechnology Letters
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• v.44 no.4
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• pp.512-521
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• 2016

A bacterial strain was isolated from a soil sample collected on Jeju Island, Korea. The strain, designated WJ-2, exhibited a high xylanase activity, whereas cellulase activity was not detected. The 16S rRNA gene sequence of WJ-2 was highly similar to type strains of the genus Streptomyces. A neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain WJ-2 is phylogenetically related to Streptomyces atrovirens. Furthermore, DNA-DNA hybridization analysis confirmed that strain WJ-2 is a novel subspecies of Streptomyces atrovirens. The genomic DNA G+C content was 73.98 mol% and the major fatty acid present was anteiso-C15:0 (36.19%). The growth and xylanase production of strain WJ-2 were significantly enhanced by using soytone and xylan as nitrogen and carbon sources, respectively. Crude enzyme preparations from the culture broth of strain WJ-2 exhibited maximal total xylanase activities at pH 7.0 and $55^{\circ}C$. Thin-layer chromatography analysis revealed that the crude enzyme degrades beechwood xylan to yield xylobiose and xylotriose as the principal hydrolyzed end products.

• Journal of Species Research
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• v.10 no.1
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• pp.63-71
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• 2021

Anteholosticha bergeri and Bakuella granulifera were isolated from soil samples collected from Muuidong and Songdo-dong, Incheon and confirmed new to South Korea. Including these two newly recorded species, 11 species of Anteholosticha and four species of Bakuella have been recorded in South Korea to date. Anteholosticha bergeri was discriminated from congeners by following characters: cortical granules, 12-16 macronuclei, 5-8 midventral pairs, 2-3 pretransverse cirri, 4-6 transverse cirri, and three dorsal kineties. Bakuella granulifera was identified by cortical granules, 5-11 buccal cirri, 2-5 frontoterminal cirri, 2-5 midventral cirri rows, and 8-12 transverse cirri. The Korean A. bergeri population corresponds to the Austrian population, except for the number of marginal and transverse cirri, and the Korean B. granulifera population corresponds to the Namibian population, except for body size. In addition, small subunit ribosomal RNA(18S rRNA) gene sequences from both species were determined.

• The Plant Pathology Journal
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• v.17 no.6
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• pp.361.4-361
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• 2001

• 대한치주과학회:학술대회논문집
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• 1998.11a
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• pp.94-94
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• 1998

• Proceedings of the Korean Society of Sericultural Science Conference
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• 2000.10a
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• pp.135-135
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• 2000

• Korean Journal of Microbiology
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• v.35 no.2
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• pp.121-127
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• 1999

An effective computer program for assembling fragments in DNA sequencing has been developed. The program, called SeqEditor (Sequence Editor), is usable on the pcrsonal computer systems of MS-Widows which is the mosl popular operating system in Korea. It c'm recd several sequence file formats such as GenBak, FASTA, and ASCII. In the SeqEditor program, a dynamic programming algorihm is applied to compute the maximalscoring overlapping alignment between each pjlr of fragments. A novel feature of the program is that SeqEdilor implemnents interaclive operation with a graphical user interface. The performance lests of the prograln 011 fragmen1 data from 16s and 18s rDNA sequencing pi-ojects produced saiisIactory results. This program may be useful to a person who has work of time with large-scale DNA sequencing projects.

• Journal of Microbiology and Biotechnology
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• v.24 no.11
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• pp.1473-1483
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• 2014

Reports of herbicide resistance events are proliferating worldwide, leading to new cultivation strategies using combinations of pre-emergence and post-emergence herbicides. We analyzed the impact during a one-year cultivation cycle of several herbicide combinations on the rhizobacterial community of glyphosate-tolerant Bt-maize and compared them to those of the untreated or glyphosate-treated soils. Samples were analyzed using pyrosequencing of the V6 hypervariable region of the 16S rRNA gene. The sequences obtained were subjected to taxonomic, taxonomy-independent, and phylogeny-based diversity studies, followed by a statistical analysis using principal components analysis and hierarchical clustering with jackknife statistical validation. The resilience of the microbial communities was analyzed by comparing their relative composition at the end of the cultivation cycle. The bacterial communites from soil subjected to a combined treatment with mesotrione plus s-metolachlor followed by glyphosate were not statistically different from those treated with glyphosate or the untreated ones. The use of acetochlor plus terbuthylazine followed by glyphosate, and the use of aclonifen plus isoxaflutole followed by mesotrione clearly affected the resilience of their corresponding bacterial communities. The treatment with pethoxamid followed by glyphosate resulted in an intermediate effect. The use of glyphosate alone seems to be the less aggressive one for bacterial communities. Should a combined treatment be needed, the combination of mesotrione and s-metolachlor shows the next best final resilience. Our results show the relevance of comparative rhizobacterial community studies when novel combined herbicide treatments are deemed necessary to control weed growth.