• Journal of Animal Science and Technology
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• v.64 no.6
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• pp.1144-1172
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• 2022

Salmonella enterica serovar Typhimurium isolate HJL777 is a virulent bacterial strain in pigs. The high rate of salmonella infection are at high risk of non-typhoidal salmonella gastroenteritis development. Salmonellosis is most common in young pigs. We investigated changes in gut microbiota and biological function in piglets infected with salmonella via analysis of rectal fecal metagenome and intestinal transcriptome using 16S rRNA and RNA sequencing. We identified a decrease in Bacteroides and increase in harmful bacteria such as Spirochaetes and Proteobacteria by microbial community analysis. We predicted that reduction of Bacteroides by salmonella infection causes proliferation of salmonella and harmful bacteria that can cause an intestinal inflammatory response. Functional profiling of microbial communities in piglets with salmonella infection showed increasing lipid metabolism associated with proliferation of harmful bacteria and inflammatory responses. Transcriptome analysis identified 31 differentially expressed genes. Using gene ontology and Innate Immune Database analysis, we identified that BGN, DCN, ZFPM2 and BPI genes were involved in extracellular and immune mechanisms, specifically salmonella adhesion to host cells and inflammatory responses during infection. We confirmed alterations in gut microbiota and biological function during salmonella infection in piglets. Our findings will help prevent disease and improve productivity in the swine industry.

• Korean Journal of Microbiology
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• v.47 no.3
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• pp.275-280
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• 2011

In order to evaluate the diversity and change of bacterial population during the manufacturing process of traditional soybean paste (doenjang), bacterial communities were analyzed using 16S rRNA gene-based pyrosequencing. In rice straw, the most important inoculum source for fermentation, the bacterial sequences with a relative abundance greater than 1% were assigned to four phyla, Proteobacteria (71%), Actinobacteria (20.6%), Bacteroidetes (4.2%), and Firmicutes (1.3%). Unlike bacterial community composition of rice straw, a different pattern of bacterial population in meju was observed with predominantly high abundance (99.1%) of Firmicutes. Phylum composition in young doenjang was almost same as that of meju. Major genera in young doenjang were Bacillus (81.3%), Clostridium (6.9%) and Enterococcus (6.3%) and the predominant species among bacterial population was B. amyloliquefaciens (63.6%). Abundance of the phylum Firmicutes in mature doenjang was 99.98%, which was even higher value than those in meju and young doenjang. Predominant species in mature doenjang were B. amyloliquefaciens (67.3%), B. atrophaeus (12.7%), B. methylotrophicus (6.5%), B. mojavensis (3.2%), and B. subtilis. (2.5%), which were also identified as major species of the microbial flora in meju. These results suggested that rice straw was a primary source for supplement of Bacillus species in manufacturing the traditional doenjang and that some species of Bacillus strains were mainly involved in the fermentation process of traditional doenjang.

• Journal of Life Science
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• v.22 no.1
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• pp.110-116
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• 2012

Nuruk plays a significant role in the flavor and quality of Takju and Yakju, which are produced through saccharification and alcohol fermentation by various microorganisms. In this study, we identified microbial strains isolated from a plate count and PCR-denaturing gradient gel electrophoresis (DGGE) analysis targeting the 16S and 28S rRNA genes, in order to characterize bacterial and fungal diversity in Sansung Nuruk. The numbers of bacteria and fungi in Nuruk were $1.5{\times}10^9$ CFU/g and $2.2{\tims}10^8$ CFU/g, respectively. The 16S rRNA gene sequence indicated that the predominant bacteria in the isolates and PCR-DGGE profile of Nuruk were Kocuria spp., Pantoea spp., Lactobacillus spp., Pediococcus spp., Weissella spp., Staphylococcus spp., endophytic bacterium, uncultured Gamma-proteobacteria, uncultured Cyanobacteria, and Actinobacteria. Dominant bacteria from the PCR-DGGE profile were Pediococcous pentosaceus and uncultured Cyanobacteria. The 28S rRNA gene sequence indicated the predominant fungi in the isolates and PCR-DGGE profile to be Trichomonascus spp. Pichia spp., Torulaspora spp., Wickerhamomyces spp., Sacharomycopsis spp., Lichtheimia spp., Mucor spp., Rhizopus spp. Aspergillus spp., and Cladosporium spp. Dominant fungi from the PCR-DGGE profile were Pichia kudriavzevii and Aspergillus oryzae. The PCR-DGGE technique was used for the first time in this study to assess a microbial community in Nuruk and proved to be an effective protocol for profiling microbial diversity.

• Korean Journal of Microbiology
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• v.53 no.1
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• pp.39-48
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• 2017

In order to evaluate the diversity of microbial population of Korean traditional Deonjang and Gochujang produced in Jeju, Jeonnam, and Jeonbuk province area, microbial communities were analyzed using next generation sequencing. In this result, the dominant bacteria of Deonjang in three area were Bacillus amyloliquefaciens, Tetragenococcus halophilus, and Bacillus was major dominant bacteria in Jeonnam (43.16%) and Jeonbuk (64.54%) area. But in Jeju area, Bacillus was 0.22%, which was significantly different from the other two. Equally, the dominant fungi of Deonjang in 3 area were Candida versatilis. Common fungus in Jeonnam and Jeonbuk area was Candida sp., respectively, 64.22% and 33.68% and Micor sp. was a common fungus in Jeonnam (15.66%) and Jeonbuk area (36.73%). But in Jeju area, Candida sp. and Zygosaccharomyces rouxii were dominant than mold. Bacillus subtilis, Bacillus licheniformis, and B. amyloliquenfaciens were the preminant bacteria in the traditional Gochujang in three regions. But there were no common dominant fungi in the 3 regions. Aspergillus sp. and Rhizopus sp. prevailed in Jeju and Jeonnam region, and Zygosaccharomycess rouxii predominanted in Jeonbuk area. These results suggested that the difference in the samples collected for the study were classified into similar groups according to the characteristics of each sample rather than regional characteristics.

• Journal of Life Science
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• v.30 no.7
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• pp.625-629
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• 2020

The Ocean is a rich source of diverse living organisms include viruses. In this study, we examined the microbial communities in the sea adjacent to Jeju Island in two seasons by metatranscriptomics. We collected and extracted total RNA, and, using the next-generation sequencing HiSeq 2000 and de novo transcriptome assembly, we identified 652,984 and 163,759 transcripts from the March and December samples, respectively. The most abundant organisms in March were bacteria, while eukaryotes were dominant in the December sample. The bacterial communities differed between the two samples, suggesting seasonal change. To identify the viruses, we searched the transcripts against a viral reference database using MegaBLAST with the most identified being bacteriophages infecting the marine bacteria. However, we also revealed an abundance of transcripts associated with diverse herpesviruses in the two transcriptomes, indicating the presence or possible threat of infection of fish in the sea around Jeju Island. This data is valuable for the study of marine microbial communities and for identifying possible viral pathogens.

• Journal of Microbiology and Biotechnology
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• v.22 no.3
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• pp.301-310
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• 2012

Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

• Korean Journal of Soil Science and Fertilizer
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• v.40 no.4
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• pp.234-241
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• 2007

Biological amendments consisting of suspensions of selected microorganisms are often used in conjunction with various organic materials for amending soils to improve soil quality and plant growth. The effects of the biological amendment on chemical and biological properties of soil were investigated for a biological amendmentalone and when combined with different organic materials includingmunicipal compost (MC), poultry litter (PL), and cover crops (red clover (RC) and spring oats). A liquid preparation of a biological amendment called Effective Microorganisms was sprayed on the tested plots three times over a two-year period. Effective Microorganisms alone did not influence pH, K, or organic matter content in soil. However, increases in P in PL-treated soils in fall of both years andCa in MC-treated soil in fall 2001, and decreases in Ca, Mg, and cation exchange capacity (CEC) in RC-planted soil were associated with EM. Increased dehydrogenase(DH) activitiesassociated with Effective Microorganismswere only detected in July (P=0.0222) and October (P=0.0834) for RC-planted soils in the first year. Fluorescein diacetate (FDA) hydrolysisappeared to be enhanced by Effective Microorganisms in soils untreated or treated with MC and oatsbut only sporadically during the sampling period. FDA hydrolysis in both PL- and RC-treated soils as well as DH activity in PL-treated soils decreased with Effective Microorganisms treatment. Effective Microorganisms did not influence substrate utilization patterns expressed by the BIOLOG assay. We conclude that Effective Microorganisms effects on soil chemical and biological properties varied depending on the added organic materials. Effective Microorganisms periodically increased soil DH activity and FDA hydrolysis with RC and with MC plus oats, respectively.

• Journal of Animal Science and Technology
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• v.64 no.5
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• pp.937-949
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• 2022

Health concern of dogs is the most important issue for pet owners. People who have companied the dogs long-term provide the utmost cares for their well-being and healthy life. Recently, it was revealed that the population and types of gut microbiota affect the metabolism and immunity of the host. However, there is little information on the gut microbiome of dogs. Hericium erinaceus (H. erinaceus; HE) is one of the well-known medicinal mushrooms and has multiple bioactive components including polyphenol, β-glucan, polysaccharides, ergothioneine, hericerin, erinacines, etc. Here we tested a pet food that contained H. erinaceus for improvement in the gut microbiota environment of aged dogs. A total of 18 dogs, each 11 years old, were utilized. For sixteen weeks, the dogs were fed with 0.4 g of H. erinaceus (HE-L), or 0.8 g (HE-H), or without H. erinaceus (CON) per body weight (kg) with daily diets (n = 6 per group). Taxonomic analysis was performed using metagenomics to investigate the difference in the gut microbiome. Resulting from principal coordinates analysis (PCoA) to confirm the distance difference between the groups, there was a significant difference between HE-H and CON due to weighted Unique fraction metric (Unifrac) distance (p = 0.047), but HE-L did not have a statistical difference compared to that of CON. Additionally, the result of Linear discriminate analysis of effect size (LEfSe) showed that phylum Bacteroidetes in HE-H and its order Bacteroidales increased, compared to that of CON, Additionally, phylum Firmicutes in HE-H, and its genera (Streptococcus, Tyzzerella) were reduced. Furthermore, at the family level, Campylobacteraceae and its genus Campylobacter in HE-H was decreased compared to that of CON. Summarily, our data demonstrated that the intake of H. erinaceus can regulate the gut microbial community in aged dogs, and an adequate supply of HE on pet diets would possibly improve immunity and anti-obesity on gut-microbiota in dogs.