• Journal of Microbiology and Biotechnology
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• v.22 no.3
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• pp.360-370
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• 2012

Current ecological knowledge of methanotrophic biofilms is incomplete, although they have been broadly studied in biotechnological processes. Four individual DNA samples were prepared from a methanotrophic biofilm, and a multiplex 16S rDNA pyrosequencing was performed. A complete library (before being de-multiplexed) contained 33,639 sequences (average length, 415 nt). Interestingly, methanotrophs were not dominant, only making up 23% of the community. Methylosinus, Methylomonas, and Methylosarcina were the dominant methanotrophs. Type II methanotrophs were more abundant than type I (56 vs. 44%), but less richer and diverse. Dominant non-methanotrophic genera included Hydrogenophaga, Flavobacterium, and Hyphomicrobium. The library was de-multiplexed into four libraries, with different sequencing efforts (3,915 - 20,133 sequences). Sorrenson abundance similarity results showed that the four libraries were almost identical (indices > 0.97), and phylogenetic comparisons using UniFrac test and P-test revealed the same results. It was demonstrated that the pyrosequencing was highly reproducible. These survey results can provide an insight into the management and/or manipulation of methanotrophic biofilms.

• Korean Journal of Environmental Biology
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• v.36 no.3
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• pp.424-437
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• 2018

The incidence of freshwater algal bloom has been increasing globally in recent years and poses a major threat to environmental health. Cyanobacteria are the major component of the bloom forming community that must be monitored frequently. Their morphological identities, however, have remained elusive, due to their small size in cells and morphological resemblances among species. We have analyzed molecular diversity and seasonal changes of cyanobacteria in Paldang Reservoir, Korea, using morphological and 16S rRNA pyrosequencing methods. Samples were collected at monthly intervals from the reservoir March-December 2012. In total, 40 phylotypes of cyanobacteria were identified after comparing 49,131 pyrosequence reads. Cyanobacterial genera such as Anabaena, Aphanizomenon, Microcystis and Synechocystis were predominantly present in samples. However, the majority of cyanobacterial sequences (65.9%) identified in this study were of uncultured origins, not detected morphologically. Relative abundance of cyanobacterial sequences was observed as high in August, with no occurrence in March and December. These results suggested that pyrosequencing approach may reveal cyanobacterial diversity undetected morphologically, and may be used as reference for studying and monitoring cyanobacterial communities in aquatic environments.

• Microbiology and Biotechnology Letters
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• v.47 no.3
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• pp.354-358
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• 2019

In order to evaluate the migration of fungi into doenjang from its materials, meju and solar salt, microbial communities were analyzed using pyrosequencing. Dominant fungi of meju were Botrytis spp. (57.94%) and Dothiorella samentorum (24.08%). Unidentified fungal species (37.53%), unassigned species (32.60%) and several fungal species of small portion were identified in solar salt. In doenjang, Candida versatilis were predominantly detected (92.62%). Non-halophilic mold were dominantly identified from meju (low-salt fermented soybean), while halophilic bacteria and archaea for solar salt and salt-tolerance fungi such as C. versatilis for doenjang (high-salt fermented soybean) were frequently detected. These results implied that most predominant fungal species might not be migrated from meju and/or solar salt into doenjang.

• Restorative Dentistry and Endodontics
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• v.36 no.6
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• pp.498-505
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• 2011

Objectives: The purpose of this in vivo study was to investigate the microbial diversity in symptomatic and asymptomatic canals with primary endodontic infections by using GS FLX Titanium pyrosequencing. Materials and Methods: Sequencing was performed on 6 teeth (symptomatic, n = 3; asymptomatic, n = 3) with primary endodontic infections. Amplicons from hypervariable region of the small-subunit ribosomal RNA gene were generated by polymerized chain reaction (PCR), and sequenced by means of the GS FLX Titanium pyrosequencing. Results: On average, 10,639 and 45,455 16S rRNA sequences for asymptomatic and symptomatic teeth were obtained, respectively. Based on Ribosomal Database Project Classifier analysis, pyrosequencing identified the 141 bacterial genera in 13 phyla. The vast majority of sequences belonged to one of the seven phyla: Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, Spirochetes, and Synergistetes. In genus level, Pyramidobacter, Streptococcus, and Leptotrichia constituted about 50% of microbial profile in asymptomatic teeth, whereas Neisseria, Propionibacterium, and Tessaracoccus were frequently found in symptomatic teeth (69%). Grouping the sequences in operational taxonomic units (3%) yielded 450 and 1,997 species level phylotypes in asymptomatic and symptomatic teeth, respectively. The total bacteria counts were significantly higher in symptomatic teeth than that of asymptomatic teeth (p < 0.05). Conclusions: GS FLX Titanium pyrosequencing could reveal a previously unidentified high bacterial diversity in primary endodontic infections.

• Journal of Microbiology and Biotechnology
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• v.23 no.10
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• pp.1428-1433
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• 2013

Jeotgal fermentation is dependent upon a diverse microbial community, although a detailed understanding of its microbial composition is limited to a relatively small number of jeotgal. Pyrosequencing-based bacterial community analysis was performed in fermented squid, ojingeo jeotgal. Leuconostoc was identified as the predominant bacterial genus, with Bacillus and Staphylococcus also accounting for a large proportion of the bacterial community. Phylogenetic analysis with 16S rRNA genes of Leuconostoc type species indicated that L. citreum- and L. holzapfelii-like strains could be the major Leuconostoc strains in jeotgal. High concentrations of NaCl were thought to be an important factor determining the makeup of the bacterial community in the fermented squid; however, a genomic survey with osmotic stress-related genes suggests the existence of more complex factors selecting the dominant bacterial species in fermented squid.

• Journal of Dairy Science and Biotechnology
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• v.36 no.2
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• pp.125-131
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• 2018

The present study aimed to investigate the microbial diversity in Gouda cheese within the four months of ripening, via next-generation sequencing (NGS). Lactococcus (96.03%), and Leuconostoc (3.83%), used as starter cultures, constituted the majority of bacteria upon 454 pyrosequencing based on 16S rDNA sequences. However, no drastic differences were observed among other populations between the center and the surface portions of Gouda cheese during ripening. Although the proportion of subdominant species was <1%, slight differences in bacterial populations were observed in both the center and the surface portions. Taken together, our results suggest that environmental and processing variables of cheese manufacturing including pasteurization, starter, ripening conditions are important factors influencing the bacterial diversity in cheese and they can be used to alter nutrient profiles and metabolism and the flavor during ripening.

• Korean Journal of Microbiology
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• v.47 no.3
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• pp.209-217
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• 2011

Archaeal communities were investigated using 454 pyrosequencing technology based on 16S rRNA gene in 11 samples collected from six different full-scale anaerobic digesters. Observed operational taxonomic units (OTUs) estimated from the archaeal 16S rRNA gene sequences were 13-55 OTUs (3% cutoff) which was corresponded to 29-89% of Chao1 richness estimates. In the anaerobic digesters there were archaeal sequences within the orders Thermoproteales, Thermoplasmatales, Desulfurococcales as well as within the orders Methanomicrobiales, Methanobacteriales, Methanococcales, Methanosarcinales, and Methanocellales, which are known to produce methane. Among these orders, Methanococcales known to produce methane using hydrogen was the predominant taxon and constituted 51.8-99.7% of total sequences. All samples showed a very similar community structure (Pearson correlation coefficient=0.99) except for one sample based on a heat map analysis. In addition, canonical correspondence analysis correlating archaeal communities to the environmental variables demonstrated that digester temperature and total solids removal rate were the two important explanatory variables. Overall results suggested that environmental and operational variables of anaerobic digester are important factors determining archaeal diversity and community structure.

• 한국약용작물학회:학술대회논문집
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• 2012.05a
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• pp.151-152
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• 2012

• KOGO NEWS
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• v.7 no.4
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• pp.10-11
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• 2007

• Korean Journal of Microbiology
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• v.49 no.3
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• pp.237-244
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• 2013

Bacterial diversities in the guts of sea cucumbers (Apostichopus japonicus) and shrimps (Litopenaeus vannamei) were investigated using barcoded or tag-encoded 454 pyrosequencing of 16S rRNA genes. In sea cucumbers, most of sequences were related to two genera, the genus Propionigenium in the phylum Fusobacteria and an unclassified genus in the family Flavobacteriaceae of phylum Bacteroidetes. Shrimps showed various kinds of genera including Lactococcus, Leuconostoc, Prochlorococcus, and Vibrio as well as the unclassified genera in the families, Flavobacteriaceae, Rhodobacteraceae, Desulfobulbaceae, and Helicobacteraceae and in the order Mycoplasmatales. Unclassified genera containing environmental sequences only are more than half of genera from sea cucumbers and shrimps. Sea cucumbers and shrimps could be unexplored sources of novel microbes and the bacterial diversity of them was revealed by high throughput 454 pyrosequencing.