• Journal of the Korea Academia-Industrial cooperation Society
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• v.18 no.1
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• pp.141-147
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• 2017

In this study, a meta-analysis of fecal bacteria in dogs was conducted using 16S rRNA gene sequences that have been recovered from cloning and Sanger sequencing. For this meta-analysis, we retrieved all 16S rRNA gene sequences recovered from fecal bacteria in dogs in the RDP database (Release 11, Update 3). A total of 420 sequences were identified from the RDP database, 42 of which were also recovered from cultured isolates. The 420 sequences were assigned to five phyla, of which Firmicutes was the most predominant phylum, accounting for 55.2% of all 420 sequences. Bacteroidetes was the second most predominant phylum, accounting for 32.1% of the 420 sequences, followed by Actinobacteria (6.4%), Fusobacteria (3.8%), and Proteobacteria (2.4%). The genus Bacteroides within Bacteroidetes was the largest, representing 30.0% of all 420 sequences, while the putative genus Clostridium XI within Firmicutes was the second largest, representing 27.4% of all 420 sequences. A total of 82 operational taxonomic units (OTUs) that are putative species were identified from the retrieved sequences. The results of this study will improve understanding of the diversity of fecal bacteria in dogs and guide future studies on the health and well-being of dogs.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.18 no.12
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• pp.466-472
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• 2017

This study was designed to examine the diversity census of fungi in rumen microbiome via meta-analysis of fungal 28S rDNA sequences. Both terms, "rumen" and "ruminal," were searched to retrieve the sequences of rumen fungi. As of September 2016, these sequences (n=165) of ruminal origin were retrieved from the Ribosomal Database Project (RDP; http://rdp.cme.msu.edu), an archive of all 28S rDNA sequences and were assigned to the phyla Ascomycota, Neocallimastigomycota, and Basidiomycota, which accounted for 109, 48, and 8 of the 165 sequences, respectively. Ascomycota sequences were assigned to the genera Pseudonectria, Magnaporthe, Alternaria, Cochliobolus, Cladosporium, and Davidiella, including fungal plant pathogens or mycotoxigenic species. Moreover, Basidiomycota sequences were assigned to the genera Thanatephorus and Cryptococcus, including fungal plant pathogens. Furthermore, Neocallimastigomycota sequences were assigned to the genera Cyllamyces, Neocallimastix, Anaeromyces, Caecomyces, Orpinomyces, and Piromyces, which may degrade the major structural carbohydrates of the ingested plant material. This study provided a collective view of the rumen fungal diversity using a meta-analysis of 28S rDNA sequences. The present results will provide a direction for further studies on ruminal fungi and be applicable to the development of new analytic tools.

• Journal of Animal Reproduction and Biotechnology
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• v.34 no.3
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• pp.157-165
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• 2019

This study was conducted to analyze the diversity census of fecal microbiome in horses using meta-analysis of equine 16S rRNA gene sequences that are available in the Ribosomal Database Project (RDP; Release 11, Update 5). The search terms used were "horse feces (or faeces)" and "equine feces (or faeces)". A total of 842 sequences of equine feces origin were retrieved from the RDP database, where 744 sequences were assigned to 10 phyla placed within Domain Bacteria. Firmicutes (n = 391) and Bacteroidetes (n = 203) were the first and the second dominant phyla, respectively, followed by Verrucomicrobia (n = 58), Proteobacteria (n = 30) and Fibrobacteres (n = 24). Clostridia (n = 319) was the first dominant class placed within Bacteroidetes while Bacteroidia (n = 174) was the second dominant class placed within Bacteroidetes. The remaining 98 sequences were assigned to phylum Euryarchaeota placed within Domain Archaea, where 74 sequences were assigned to class Methanomicrobia. The current results will improve understanding of the diversity of fecal microbiome in horses and may be used to further analyze equine fecal microbiome in future studies.

• KSBB Journal
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• v.19 no.1
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• pp.72-77
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• 2004

The aim of this study was to isolate and identify the spoilage bacteria in the low salt cucumber brine. The PCR amplicons comprising a portion of the 16S rRNA gene of the isolated colonies were directly sequenced and the untrimmed whole sequencing results of the unknown strains were aligned with the type strains using BLAST of NCBI. Then Sequence Aligner and Sequence Match of RDP confirmed the outcome. The identified isolates were eight species and belong to three genuses: Clostridium, Lactobacillus, and Bacillus. The RFLP pattern of the 16S rRNA gene of isolates verified the identified species. From now on the complex spoiling process of law salt fermented cucumber could be analyzed using the isolated species individually or with certain combinations.

• Korean Journal of Microbiology
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• v.37 no.1
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• pp.72-79
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• 2001

The effect of phenol on the change of bacterial community in the effluent water from a wastewater treatment plant was analyzed by PCR and terminal restriction fragment length polymorphism (T-RFLP). The fragments of 16S rDNA were amplified by PCR with bacterial primers, where one of the primers was biotinylated at the 5'-end. After digestion with restriction enzymes, HaeIII and AluI, the biotinylated terminal restriction tragments (T-RFs) of the digested products were selectively isolated by using streptavidin paramagnetic particles. The single-stranded DNA of T-RFs was separated by electrophoresis on a polyacrylamide gel and detected by silver staining technique. When 10 standard strains were analyzed by our method, each strain had a unique T-RF which corresponded to the calculated size from the known sequences of RDP database. The T-RFLP fingerprint generated from the effluent water was very complex, and the predominant T-RFs corresponded to members of the genus Acinetobacter, Bacillus and Pseudomonas. In addition, the perturbation of bacterial community was observed when phenol was added to the sample at the final concentration of 250 $l^{-1}$. The number of T-RFs increased and the major bacterial population could be assigned to the genus Acinetobacter, Comamonas, Cytophaga and Pseudomonas. A intense band assigned to the putative genera of Acinetobacter and Cytophaga was eluted, amplified, and sequenced. The nucleotide sequence of the T-RF showed close relationship with the sequence of Acinetobacter junii.

• Environmental Engineering Research
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• v.14 no.1
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• pp.3-9
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• 2009

Microorganisms play an important role in the geochemical cycles, industry, environmental cleanup, and biotechnology among other fields. Given the high microbial diversity, identification of the microorganism is essential in understanding and managing the processes. One of the most popular and powerful method for microbial identification is comparative 16S rRNA gene analysis. Due to the highly conserved nature of this essential gene, sequencing and later comparison of it against known rRNA databases can provide assignment of the bacteria into the taxonomy, and the identity of its closest relatives. Isolation and sequencing of 16S rRNA genes directly from natural environments (either from DNA or RNA) can also be used to study the structure of the whole microbial community. Nowadays, novel sequencing technologies with massive outputs are giving researchers worldwide the chance to study the microbial world with a depth that was previously too expensive to achieve. In this article we describe commonly used research approaches for the study of individual microorganisms and microbial communities using the tools provided by Ribosomal Database Project website.

• Proceedings of the Microbiological Society of Korea Conference
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• 2003.05a
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• pp.118-121
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• 2003

A method for detection and quantification of aceticlastic methanogens using a real-time PCR with a TaqMan probe was developed. Two sets of primers and probes targeting the family Methanosarcinaceae and Methanosaetaceae were designed by using the Ribosormal Database Project (RDP) II, and softwares for phylogenetic probe design and sequence analysis. Target-group specificity of each set of primers and probe was verified by testing DNAs isolated from pure cultures of 28 archaeal strains purchased from DSMZ. Cell numbers in the 28 archaeal cultures and in the samples from anaerobic processes were quantified using a real-time PCR with the sets of primers and probe. In conclusion, the real-time PCR assay was very specific for the corresponding target methanogenic family and was proved to be a powerful method for quantification of aceticlastic methanogens in anaerobic processes.

• Microbiology and Biotechnology Letters
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• v.32 no.3
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• pp.218-223
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• 2004

Myxobacteria are Gram-negative soil bacteria known to be a rich source of potentially useful secondary metabolites. We have isolated 204 strains of bacteriolytic myxobacteria from soil samples collected in Korea and determined their 16S rRNA sequences. Sequence analysis of the partially determined 16S rRNA sequences has suggested that 132 isolates (65% of total isolates) belong to the genus Myxococcus and 59 isolates (29% of total isolates) belong to the genus Corallococcus. Meanwhile, 4 isolates appear to be Archangium spp. and the other 4 isolates appear to be Stigmatella spp. Genera of the remained 5 isolates have not been identified because their 16S rRNA sequences are distantly related to those of known myxobacteria.

• Journal of Animal Environmental Science
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• v.21 no.3
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• pp.93-98
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• 2015

The objective of this study was to review application of next-generation sequencing (NGS) to investigate microbiome in the livestock sector. Since the 16S rRNA gene is used as a phylogenetic marker, unculturable members of microbiome in nature or managed environments have been investigated using the NGS technique based on 16S rRNA genes. However, few NGS studies have been conducted to investigate microbiome in the livestock sector. The 16S rRNA gene sequences obtained from NGS are classified to microbial taxa against the 16S rRNA gene reference database such as RDP, Greengenes and Silva databases. The sequences also are clustered into species-level OTUs at 97% sequence similarity. Microbiome similarity among treatment groups is visualized using principal coordinates analysis, while microbiome shared among treatment groups is visualized using a venn diagram. The use of the NGS technique will contribute to elucidating roles of microbiome in the livestock sector.

• The Journal of Pediatrics of Korean Medicine
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• v.34 no.4
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• pp.43-58
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• 2020

Objectives The purpose of this study is to analyze the effect of various herbal medicin on gut microbiota. Methods Electronic searches were performed using NDSL, OASIS, KISS, KMBASE, K-portal, Pub med, Cochrane, CNKI. Results we analyzed 25 experimental studies on the effect of herbal medicine on microbiota. Diabetes, obesity, inflammatory bowel disease have been frequently studied in micobiota-related disease. The most common experimental animal model used in the studies C57BL/7 mouse. Among the studies wherein single herbal medication were used, Gynostemma pentaphyllum was most commonly studies, and different herbal medications were used in the studies wherein complex herbal medications were studied. Next generation sequencing was performed using Illumina MiSeq system, and gut microbiota analysis was performed using QIIME and Ribosomal Database Project (RDP). In most studies, the herbal medicines exerted regulatory effects on gut microbiota and improved the symptoms of the experimental groups. Conclusions This review provides basic data on the correlation between korean medicine and gut microbiota, as well as information for the development of korean medicine.