• Journal of Ginseng Research
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• v.38 no.2
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• pp.106-115
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• 2014

Background: Gut microbiota is regarded as one of the major factors involved in the control of body weight. The antiobesity effects of ginseng and its main constituents have been demonstrated, but the effects on gut microbiota are still unknown. Methods: To investigate the effect of ginseng on gut microbiota, 10 obese middle-aged Korean women took Panax ginseng extracts for 8 wk and assessment of body composition parameters, metabolic biomarkers, and gut microbiota composition was performed using 16S rRNA gene-based pyrosequencing at baseline and at 8 wk. Significant changes were observed in body weight and body mass index; however, slight changes were observed in gut microbiota. We divided the participants into two groups, the effective and the ineffective weight loss groups, depending on weight loss effect, in order to determine whether the antiobesity effect was influenced by the composition of gut microbiota, and the composition of gut microbiota was compared between the two groups. Results: Prior to ginseng intake, significant differences of gut microbiota were observed between both at phyla and genera and the gut microbiota of the effective and ineffective weight loss groups was segregated on a principal coordinate analysis plot. Conclusion: Results of this study indicate that ginseng exerted a weight loss effect and slight effects on gut microbiota in all participants. In addition, its antiobesity effects differed depending on the composition of gut microbiota prior to ginseng intake.

• Korean Journal of Microbiology
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• v.52 no.1
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• pp.49-58
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• 2016

Compared to planktonic bacterial populations, biofilms have distinct bacterial community structures and play important ecological roles in various aquatic environments. Despite their ecological importance in nature, bacterial community structure and its succession during biofilm development in the Antarctic marine environment have not been elucidated. In this study, the succession of bacterial community, particularly during the early stage of biofilm development, in the Antarctic marine environment was investigated by pyrosequencing of the 16S rRNA gene. Overall bacterial distribution in biofilms differed considerably from surrounding seawater. Relative abundance of Gammaproteobacteria and Bacteroidetes which accounted for 78.9-88.3% of bacterial community changed drastically during biofilm succession. Gammaproteobacteria became more abundant with proceeding succession (75.7% on day 4) and decreased to 46.1% on day 7. The relative abundance of Bacteroidetes showed opposite trend to Gammaproteobacteria, decreasing from the early days to the intermediate days and becoming more abundant in the later days. There were striking differences in the composition of major OTUs (${\geq}1%$) among samples during the early stages of biofilm formation. Gammaproteobacterial species increased until day 4, while members of Bacteroidetes, the most dominant group on day 1, decreased until day 4 and then increased again. Interestingly, Pseudoalteromonas prydzensis was predominant, accounting for up to 67.4% of the biofilm bacterial community and indicating its important roles in the biofilm development.

• Journal of Life Science
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• v.25 no.3
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• pp.323-328
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• 2015

The study of microbial diversity and richness in soil samples from a volcanic island named Ulleungdo, located east of South Korea. The soil bacterial communities on the Ulleungdo were analyzed using pyrosequencing method based on 16S rRNA gene. There were 1,613 operational taxonomic units (OUT) form soil sample. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. Proteobacteria was the most dominant phylum with 48.28%, followed by acidobacteria (26.30%), actionbacteria (6.89%), Chloroflexi (4.58), Planctomycetes (4.56%), Nitrospirae (1.83%), Bacteroidetes (1.51%), Verrucomicrobia (1.48%), and Gemmatimonadetes (1.11%). α-proteobacteria was the most dominant class with 36.07% followed by Acidobacteria_c (10.65%), Solibacteres (10.64%), δ-proteobacteria (4.42%), γ-proteobacteria (4.29%), Planctomycetacia (4.16%), Actinobacteria_c (4.00%), Betaproteobacteria (3.50%), EU686603_c (2.97%), Ktedonobacteria (2.91%), Acidimicrobiia (1.32%), Verrucomicrobiae (1.27%), Gemmatimonadetes_c (1.11%), Sphingobacteria (1.09%), and GU444092_c (1.06%). Bradyrhizobiaceae was the most dominant family with 22.83% followed by Acidobacteriaceae (10.62%), EU445199_f (5.72%), Planctomycetaceae (4.03%), Solibacteraceae (3.63%), FM209092_f (3.58%), Steroidobacter_f (2.81%), EU686603_f (2.73%), Hyphomicrobiaceae (2.33%), Ktedonobacteraceae (1.75%), AF498716_f (1.46%), Rhizomicrobium_f (1.03%), and Mycobacteriaceae (1.01%). Differences in the diversity of bacterial communities have more to do with geography than the impact on environmental factors and also the type of vegetation seems to affect the diversity of bacterial communities.

• Journal of Life Science
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• v.29 no.9
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• pp.986-995
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• 2019

Intestinal microbiota play a key role in maintaining the host's health, and variety and richness of this microbiota is directly influenced and modulated by the host's diet. Kimchi is a fermented food rich in dietary fibers and lactic acid bacteria (LAB). To investigate the effect of fermented kimchi on the host's response and the composition of intestinal microbiota, 45 male Sprague-Dawley rats six weeks old were divided into three experimental groups that received either a basal diet (CON) or a basal diet supplemented with fermented kimchi (FK) or chitosan-added fermented kimchi (CFK) for four weeks. Body weights and feed intakes were measured weekly, and the intestinal contents were collected aseptically and were used for 16S rRNA gene profiling via pyrosequencing. As compared to the control, FK and CFK groups showed less body weight gain, feed efficiency, and blood triglyceride concentration. The diversity of intestinal microbiota was increased in both FK and CFK as compared to the control. At the phylum level, obesity-associated Firmicutes decreased, while leanness-associated Bacteroidetes increased. At the genus-level, the genera that consist of LAB, leanness-associated bacteria, and butyric acid-producing bacteria increased in FK and CFK as compared to the control. The overall results suggest that the consumption of fermented kimchi can reduce obesity and promote the host's health through mechanisms involving the modulation of intestinal microbiota.

• Journal of agriculture & life science
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• v.50 no.1
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• pp.117-124
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• 2016

Researches on soil microbial community are increasing to assess ecosystem responses to anthropogenic disturbances and to provide an indicator of ecosystem recovery. Microbial communities are able to respond more rapidly to environmental changes than plants and therefore they may provide an early indication of the ecosystem recovery trajectory. This study was conducted using 16S rRNA gene pyrosequencing of soil samples to compare soil bacterial community composition between artificially covered soils of the Baedudaegan ridgeline and their adjacent forest soils in two restoration project sites, Ihwaryeong and Yuksimnyeong, which were completed in 2012 and 2013, respectively. Richness of the Phylum level was 29.3 in Ihwaryeong and 32.3 in Yuksimnyeong. Significant difference in the richness between artificial restored soils and adjacent forest soils(p<0.01) was observed, however no significant difference was observed for site location and soil depth. Acidobacteria(37.3%) and Proteobacteria(31.1%) were more abundant than any other phylum in collected soil samples. Also, we found the significant difference in the relative abundance of the two abundant phyla between artificially restored soils and their adjacent forest soils (Proteobacteria, 38.1% in restored soils vs 24.2% in adjacent forest soils, p<0.01; Acidobacteria, 55.4% in restored soils vs 19.2% in adjacent forest soils, p<0.001). The results support the previous researches indicating that soil bacterial community composition is affected by nutritional status of soils and that Acidobacteria is also strongly influenced by pH, thus favoring soils with lower pH. This study could be utilized to monitor and evaluate restoration success of forest soil environment quantitatively.

• International Journal of Oral Biology
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• v.43 no.1
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• pp.13-21
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• 2018

Radiotherapy (RT) is a mainstay in the treatment of head and neck squamous cell carcinoma (HNSCC). For locally advanced HCSCC, concurrent chemoradiotherapy (CCRT) benefits HCSCC patients in terms of better survival and loco-regional control. In this study, we evaluated changes in oral microbiota in patients, who received CCRT for head and neck cancer. Oral rinsed samples were weekly collected before and during CCRT and at 4 weeks following treatment from HNSCC patients, who had received 70 Gy of radiation delivered to the primary sites for over 7 weeks and concurrent chemotherapy. Oral microbiota changes in three patients were analyzed by next-generation sequencing using 16S rRNA 454 pyrosequencing. On an average, 15,000 partial 16S rRNA gene sequences were obtained from each sample. All sequences fell into 11 different bacterial phyla. During early CCRT, the microbial diversity gradually decreased. In a patient, who did not receive any antibiotics during the CCRT, Firmicutes and Proteobacteria were the most abundant phylum. During the early CCRT, proteobacteria gradually decreased while Firmicutes increased. During the late CCRT, firmicutes gradually decreased while Bacteroides and Fusobacteria increased. In all the patients, yellow complex showed a gradual decrease, while orange and red complex showed a gradual increase during the CCRT. At 4 weeks after CCRT, the recovery of oral microbiota diversity was limited. During CCRT, there was a gradual increase in major periodontopathogens in association with the deterioration of the oral hygiene. Henceforth, it is proposed that understanding oral microbiota shift should provide better information for the development of effective oral care programs for patients receiving CCRT for HNSCC.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.12
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• pp.1726-1735
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• 2014

This study investigated the effects of acarbose addition on changes in ruminal fermentation characteristics and the composition of the ruminal bacterial community in vitro using batch cultures. Rumen fluid was collected from the rumens of three cannulated Holstein cattle fed forage ad libitum that was supplemented with 6 kg of concentrate. The batch cultures consisted of 8 mL of strained rumen fluid in 40 mL of an anaerobic buffer containing 0.49 g of corn grain, 0.21 g of soybean meal, 0.15 g of alfalfa and 0.15g of Leymus chinensis. Acarbose was added to incubation bottles to achieve final concentrations of 0.1, 0.2, and 0.4 mg/mL. After incubation for 24 h, the addition of acarbose linearly decreased (p<0.05) the total gas production and the concentrations of acetate, propionate, butyrate, total volatile fatty acids, lactate and lipopolysaccharide (LPS). It also linearly increased (p<0.05) the ratio of acetate to propionate, the concentrations of isovalerate, valerate and ammonia-nitrogen and the pH value compared with the control. Pyrosequencing of the 16S rRNA gene showed that the addition of acarbose decreased (p<0.05) the proportion of Firmicutes and Proteobacteria and increased (p<0.05) the percentage of Bacteroidetes, Fibrobacteres, and Synergistetes compared with the control. A principal coordinates analysis plot based on unweighted UniFrac values and molecular variance analysis revealed that the structure of the ruminal bacterial communities in the control was different to that of the ruminal microbiota in the acarbose group. In conclusion, acarbose addition can affect the composition of the ruminal microbial community and may be potentially useful for preventing the occurrence of ruminal acidosis and the accumulation of LPS in the rumen.

• BMB Reports
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• v.50 no.11
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• pp.578-583
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• 2017

Programmed cell death-1 (PD-1) is a coinhibitory molecule and plays a pivotal role in immune regulation. Here, we demonstrate a role for PD-1 in pathogenesis of inflammatory bowel disease (IBD). Wild-type (WT) mice had severe wasting disease during experimentally induced colitis, while mice deficient for PD-1 ($PD-1^{-/-}$) did not develop colon inflammation. Interestingly, $PD-1^{-/-}$ mice cohoused with WT mice became susceptible to colitis, suggesting that resistance of $PD-1^{-/-}$ mice to colitis is dependent on their gut microbiota. 16S rRNA gene-pyrosequencing analysis showed that $PD-1^{-/-}$ mice had altered composition of gut microbiota with significant reduction in Rikenellaceae family. These altered colon bacteria of $PD-1^{-/-}$ mice induced less amount of inflammatory mediators from colon epithelial cells, including interleukin (IL)-6, and inflammatory chemokines. Taken together, our study indicates that PD-1 expression is involved in the resistance to experimental colitis through altered bacterial communities of colon.

• Journal of Korean Society of Forest Science
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• v.106 no.2
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• pp.121-129
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• 2017

The soil microbiome plays important roles in material cycling and plant growth in forest ecosystem. Although a lot of researches on forest soil fungi in Korea have been performed, the studies on forest soil bacterial communities have been limited. In this study, we conducted next generation sequencing (NGS) targeting 16S rRNA gene to investigate the soil bacterial communities from natural red pine (Pinus densiflora) forest in Mt. Janggunbong, Bonghwa-gun, Gyeongbuk, Korea. Our results showed that the entire bacterial communities in the study sites include the phyla Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, which have been typically observed in forest soils. The composition ratio of Proteobacteria was the highest in the soil bacteria community. The results reflect that Proteobacteria is copiotroph, which generally favors relatively nutrient-rich conditions with abundant organic matter. Some rhizobia species such as Burkholderia, Bradyrhizobium, Rhizobium, which are known to contribute to soil nitrogen-fixation, exist in the study sites. As a result of correlation analysis between soil physicochemical characteristics and bacteria communities, the soil pH was significantly correlated with the soil bacteria compositions.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.4
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• pp.495-504
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• 2017

Objective: Manipulating the fermentation to improve the performance of the ruminant has attracted the attention of both farmers and animal scientists. Propionate salt supplementation in the diet could disturb the concentration of propionate and total volatile fatty acids in the rumen. This study was conducted to evaluate the effect of calcium propionate supplementation on the ruminal bacterial community composition in finishing bulls. Methods: Eight finishing bulls were randomly assigned to control group (CONT) and calcium propionate supplementation (PROP) feeding group, with four head per group. The control group was fed normal the total mixed ration (TMR) finishing diet, and PROP group was fed TMR supplemented with 200 g/d calcium propionate. At the end of the 51-day feeding trial, all bulls were slaughtered and rumen fluid was collected from each of the animals. Results: Propionate supplementation had no influence the rumen fermentation parameters (p>0.05). Ruminal bacterial community composition was analyzed by sequencing of hypervariable V3 regions of the 16S rRNA gene. The most abundant phyla were the Firmicutes (60.68%) and Bacteroidetes (23.67%), followed by Tenericutes (4.95%) and TM7 (3.39%). The predominant genera included Succiniclasticum (9.43%), Butyrivibrio (3.74%), Ruminococcus (3.46%) and Prevotella (2.86%). Bacterial community composition in the two groups were highly similar, except the abundance of Tenericutes declined along with the calcium propionate supplementation (p = 0.0078). Conclusion: These data suggest that the ruminal bacterial community composition is nearly unchanged by propionate supplementation in finishing bulls.