• Journal of Microbiology
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• 제44권2호
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• pp.155-161
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• 2006

Comparative analysis of microbial communities in a sequencing batch reactor which performed enhanced biological phosphorus removal (EBPR) was carried out using a cultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocol and a modified PCR protocol with low PCR cycle was applied to the two clone libraries of the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and the resulting 424 clones were analyzed using restriction fragment length polymorphisms (RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that the modified PCR protocol decreased the incidence of distinct fragment patterns from about 63 % (137 of 217) in the standard PCR method to about 34 % (70 of 207) under the modified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles) can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained using the modified PCR method revealed that the clones were affiliated with at least 11 phyla or classes of the domain Bacteria. However, the analyses of 327 colonies, which were grouped into just 41 distinct types by RFLP analysis, showed that they could be classified into five major bacterial lineages: ${\alpha},\;{\beta},\;{\gamma}-$ Proteobacteria, Actinobacteria, and the phylum Bacteroidetes, which indicated that the microbial community yielded from the cultivation-based method was still much simpler than that yielded from the PCR-based molecular method. In this study, the discrepancy observed between the communities obtained from PCR-based and cultivation-based methods seems to result from low culturabilities of bacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed to reduce this discrepancy.

• Journal of Microbiology and Biotechnology
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• 제17권5호
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• pp.784-791
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• 2007

The present work aims to use a biofilter technology(aerated submerged filters) for the aerobic transformation at laboratory-scale of olive washing water(OWW) generated in the first steps of olive oil processing, as well as the genetic profiling and identification to the species level of the bacteria involved in the formation of the biofilm, by means of TGGE. Chemical parameters, such as biological oxygen demand at five days($BOD_5$) and chemical oxygen demand(COD), decreased markedly(up to 90 and 85%, respectively) by the biological treatment, and the efficiency of the process was significantly affected by aeration and inlet flow rates. The total polyphenol content of inlet OWW was only moderately reduced(around 50% decrease of the inlet content) after the biofilter treatment, under the conditions tested. Partial 16S rRNA genes were amplified using total DNA extracted from the biofilm and separated by TGGE. Sequences of isolated bands were mostly affiliated to the $\alpha-subclass$ of Proteobacteria, and often branched in the periphery of bacteria] genera commonly present in soil(Rhizobium, Reichenowia, Agrobacterium, and Sphingomonas). The data obtained by the experimentation at laboratory scale provided results that support the suitability of the submerged filter technology for the treatment of olive washing waters with the purpose of its reutilization.

• Journal of Microbiology and Biotechnology
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• 제30권9호
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• pp.1321-1334
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• 2020

Beef, pork, chicken and milk are considered representative protein sources in the human diet. Since the digestion of protein is important, the role of intestinal microflora is also important. Despite this, the pure effects of meat and milk intake on the microbiome are yet to be fully elucidated. To evaluate the effect of beef, pork, chicken and milk on intestinal microflora, we observed changes in the microbiome in response to different types of dietary animal proteins in vitro. Feces were collected from five 6-week-old pigs. The suspensions were pooled and inoculated into four different media containing beef, pork, chicken, or skim milk powder in distilled water. Changes in microbial communities were analyzed using 16S rRNA sequencing. The feces alone had the highest microbial alpha diversity. Among the treatment groups, beef showed the highest microbial diversity, followed by pork, chicken, and milk. The three dominant phyla were Proteobacteria, Firmicutes, and Bacteroidetes in all the groups. The most abundant genera in beef, pork, and chicken were Rummeliibacillus, Clostridium, and Phascolarctobacterium, whereas milk was enriched with Streptococcus, Lactobacillus, and Enterococcus. Aerobic bacteria decreased while anaerobic and facultative anaerobic bacteria increased in protein-rich nutrients. Functional gene groups were found to be over-represented in protein-rich nutrients. Our results provide baseline information for understanding the roles of dietary animal proteins in reshaping the gut microbiome. Furthermore, growth-promotion by specific species/genus may be used as a cultivation tool for uncultured gut microorganisms.

• Asian-Australasian Journal of Animal Sciences
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• 제32권11호
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• pp.1715-1724
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• 2019

Objective: As laying hens become aged, laying performance and egg quality are generally impaired. One of the practical methods to rejuvenate production and egg quality of aged laying hens with decreasing productivity is a forced molting. However, the changes in intestinal microbiota after forced molting of aged hens are not clearly known. The aim of the present study was to analyze the changes in excreta bacterial communities after forced molting of aged laying hens. Methods: A total of one hundred 66-wk-old Hy-Line Brown laying hens were induced to molt by a 2-d water removal and an 11-d fasting until egg production completely ceased. The excreta samples of 16 hens with similar body weight were collected before and immediately after molting. Excreta bacterial communities were analyzed by high-throughput sequencing of bacterial 16S rRNA genes. Results: Bacteroidetes, Firmicutes, and Proteobacteria were the three major bacterial phyla in pre-molting and immediate post-molting hens, accounting for more than 98.0%. Lactobacillus genus had relatively high abundance in both group, but decreased by molting (62.3% in premolting and 24.9% in post-molting hens). Moreover, pathogenic bacteria such as Enterococcus cecorum and Escherichia coli were more abundant in immediate post-molting hens than in pre-molting hens. Forced molting influenced the alpha diversity, with higher Chao1 (p = 0.012), phylogenetic diversity whole tree (p = 0.014), observed operational taxonomic unit indices (p = 0.006), and Simpson indices (p<0.001), which indicated that forced molting increased excreta bacterial richness of aged laying hens. Conclusion: This study improves the current knowledge of bacterial community alterations in the excreta by forced molting in aged laying hens, which can provide increasing opportunity to develop novel dietary and management skills for improving the gastrointestinal health of aged laying hens after molting.

• Journal of Animal Science and Technology
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• 제63권3호
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• pp.640-650
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• 2021

Particulate matter (PM) produced in pig houses may contain microbes which can spread by airborne transmission, and PM and microbes in PM adversely affect human and animal health. To investigate the microbiome in PM from pig houses, nine PM samples were collected in summer 2020 inside and outside of pig houses located in Jangseong-gun, Jeollanam-do Province, Korea, comprising three PM samples from within a nursery pig house (I-NPH), three samples from within a finishing pig house (I-FPH), and three samples from outside of the pig houses (O-PH). Microbiomes were analyzed using 16S rRNA gene amplicon sequencing. Firmicutes was the most dominant phylum and accounted for 64.8%-97.5% of total sequences in all the samples, followed by Proteobacteria (1.4%-21.8%) and Bacteroidetes (0.3%-13.7%). In total, 31 genera were represented by > 0.3% of all sequences, and only Lactobacillus, Turicibacter, and Aerococcus differed significantly among the three PM sample types. All three genera were more abundant in the I-FPH samples than in the O-PH samples. Alpha diversity indices did not differ significantly among the three PM types, and a principal coordinate analysis suggested that overall microbial communities were similar across PM types. The concentration of PM did not significantly differ among the three PM types, and no significant correlation of PM concentration with the abundance of any potential pathogen was observed. The present study demonstrates that microbial composition in PM inside and outside of pig houses is similar, indicating that most microbe-containing PM inside pig houses leaks to the outside from where it, along with microbe-containing PM on the outside, may re-enter the pig houses. Our results may provide useful insights regarding strategies to mitigate potential risk associated with pig farming PM and pathogens in PM.

• Journal of Microbiology and Biotechnology
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• 제29권9호
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• pp.1391-1400
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• 2019

Canine parvoviral enteritis (PVE) is an important intestinal disease of the puppies; however, the potential impact of the canine parvovirus (CPV) on the gut microbiota has not been investigated. Therefore, the aim of this study was to evaluate the gut microbial shifts in puppies naturally infected with CPV. Fecal samples were collected from healthy dogs and those diagnosed with PVE at 4, 6, 8, and 12 weeks of age. The distal gut microbiota of dogs was characterized using Illumina MiSeq sequencing of the bacterial 16S rRNA genes. The sequence data were analyzed using QIIME with an Operational Taxonomic Unit definition at a similarity cutoff of 97%. Our results showed that the CPV was associated with significant microbial dysbiosis of the intestinal microbiota. Alpha diversity and species richness and evenness in dogs with PVE decreased compared to those of healthy dogs. At the phylum level, the proportion of Proteobacteria was significantly enriched in dogs with PVE while Bacteroidetes was significantly more abundant in healthy dogs (p < 0.05). In dogs with PVE, Enterobacteriaceae was the most abundant bacterial family accounting for 36.44% of the total bacterial population compared to only 0.21% in healthy puppies. The two most abundant genera in healthy dogs were Prevotella and Lactobacillus and their abundance was significantly higher compared to that of dogs with PVE (p < 0.05). These observations suggest that disturbances of gut microbial communities were associated with PVE in young dogs. Evaluation of the roles of these bacterial groups in the pathophysiology of PVE warrants further studies.

• Journal of Animal Science and Technology
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• 제63권6호
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• pp.1301-1313
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• 2021

This study investigated the effects of applying cellulase and starch on the fermentation characteristics and microbial communities of Napier grass silage after ensiling for 30 d. Three groups were studied: No additives (control); added cellulase (Group 1); and added cellulase and starch (Group 2). The results showed that the addition of cellulase and starch decreased the crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF) and pH significantly (p < 0.05) and increased water-soluble carbohydrate (WSC) content (p < 0.05). The addition of additives in two treated groups exerted a positive effect on the lactic acid (LA) content, lactic acid bacteria (LAB) population, and lactic acid / acetic acid (LA/AA) ratio, even the changes were not significant (p > 0.05). Calculation of Flieg's scores indicated that cellulase application increased silage quality to some extent, while the application of cellulase and starch together significantly improved fermentation (p < 0.05). Compared with the control, both additive groups showed increased microbial diversity after ensiling with an abundance of favorable bacteria including Firmicutes and Weissella, and the bacteria including Proteobacteria, Bacteroidetes, Acinetobacter increased as well. For alpha diversity analysis, the combined application of cellulase and starch in Group 2 gave significant increases in all indices (p < 0.05). The study demonstrated that the application of cellulase and starch can increase the quality of Napier grass preserved as silage.

• 미생물학회지
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• 제53권2호
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• pp.83-96
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• 2017

부산시 영도구의 혁신지구의 인공해수천은 높아진 하상과 조류의 특성으로 인해 물이 순환되지 않고 더구나 주위의 오수가 유입되고 있어서 수질이 나빠지고 악취를 발생하고 있다. 이 문제를 해결하기 위한 방안으로 가장 오염되고 조류이동을 감안한 하천의 지점에 생물증강법을 적용하여 친환경적, 효율적으로 하천을 정화하고자 하였다. 현장에서 활성화된 복합미생물을 가장 오염된 지점(Site 2)에 7~10일 간격으로 투입하여, 수질의 pH, 온도, DO, ORP, SS, COD, T-N, 및 T-P를 측정하였고 또한 하상퇴적토의 COD 및 미생물군집을 분석하였다. 13개월 후 Site 2의 수질 SS, COD, T-N 및 COD (퇴적토)의 처리효율은 각각 51%, 58%, 27% 및 35%으로 나타났으나 T-P는 오히려 47% 증가를 보였다. 대부분의 측정지점에서 황산염환원세균(sulfate reducing bacteria)그룹 (Desulfobacteraceae_uc_s, Desulfobacterales_uc_s, Desulfuromonadaceae_uc_s, Desulfuromonas_g1_uc and Desulfobacter postgatei)과 Anaerolinaeles의 밀도는 대체적으로 생물증강에 의한 정화가 진행될수록 감소하였으며, 반면에 Gamma-proteobacteria (NOR5-6B_s and NOR5-6A_s), Bacteroidales_uc_s, 및 Flavobacteriales_uc_s의 밀도는 증가하는 경향이었다. 상대적으로 COD가 낮고 DO가 높은 청정지점인 St. 4에서는 호기성미생물인 Flavobacteriaceae_uc_s가 우점하였다. 이러한 미생물군은 하천의 정화과정을 추적할 수 있는 지표미생물로 활용될 수 있을 것으로 판단되었다. 생물증강 시행 후의 대표적 시점 퇴적토시료의 미생물군집 alpha diversity 지수(OTUs, Chao1 및 Shannon 지수)는 시행 전에 비해 감소하는 경향을 보였으며, 또한 beta diversity 분석기법(fast unifrac 분석)으로 분석한 결과 정화 전이나 초기에 비해서 정화가 진행될수록 전반적으로 시료에 무관하게 미생물군집의 유사성을 보여 생물증강이 현장 토착 미생물의 군집구조를 변화시키고 있음을 확인하였다. 이러한 사실로 보아 본 복합미생물에 의한 현장 생물증강법은 brine water 및 담수로 이루어진 오염된 하천을 환경친화적, 경제적으로 정화할 수 있는 대안으로 판단이 되었다.

• Journal of Microbiology
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• 제42권4호
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• pp.285-291
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• 2004

The soil bacterial community and some inoculated bacteria were monitored to assess the microbial responses to prescribed fire in their microcosm. An acridine orange direct count of the bacteria in the unburned control soil were maintained at a relatively stable level $(2.0\~2.7\times10^9\;cells/g^{-1}{\cdot}soil)$ during the 180 day study period. The number of bacteria in the surface soil was decreased by fire, but was restored after 3 months. Inoculation of some bacteria increased the number of inoculated bacteria sev­eral times and these elevated levels lasted several months. The ratios of eubacteria detected by a flu­orescent in situ hybridization (FISH) method to direct bacterial count were in the range of $60\~80\%$ during the study period, with the exception of some lower values at the beginning, but there were no definite differences between the burned and unburned soils or the inoculated and uninoculated soils. In the unburned control soil, the ratios of $\alpha-,\beta-\;and\;\gamma-subgroups$ of the proteobacteria, Cytophaga-Fla­vobacterium and other eubacteria groups to that of the entire eubacteria were 13.7, 31.7, 17.1, 16.8 and $20.8\%,$ respectively, at time 0. The overall change on the patterns of the ratios of the 5 subgroups of eubacteria in the uninoculated burned and inoculated soils were similar to those of the unburned con­trol soil, with the exception of some minor variations during the initial period. The proportions of each group of eubacteria became similar in the different microcosms after 6 months, which may indicate the recovery of the original soil microbial community structure after fire or the inoculation of some bac­teria. The populations of Azotobacter vinelandii, Bacillus megaterium and Pseudomonas fluorescens, which had been inoculated to enhance the microbial activities, and monitored by FISH method, showed similar changes in the microcosms, and maintained high levels for several months.

• 생명과학회지
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• 제19권5호
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• pp.659-663
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• 2009

장기간 경유로 오염된 지역의 토양으로부터 분리한 세균 3Y는 석유계 탄화수소를 구성하는 다양한 화합물을 유일 탄소원으로하여 성장하였다. Sphingomonas sp. 3Y는 지방족 화합물은 물론이고 방향족 화합물을 이용해서 성장할 수 있었다. 지방족 화합물로서는 hexane과 hexadecane을 이용하여 성장하였고, 한편 방향족 화합물로서는 BTEX는 물론이고 phenol, biphenyl, 또는 phenanthrene을 유일 탄소원으로 이용하여 성장하였다. 본 균주는 indole과 catechol을 이용한 실험결과 방향족 탄화수소의 생분해 과정에서 맨 첫 단계 반응에 관여하는 효소인 aromatic ring dioxygenase 활성과 benzene 환을 깨는 효소인 meta-cleavage dioxygenase 활성을 나타내었다. Sphingomonas sp. 3Y의 16S rRNA 유전자의 염기서열 분석과 계통수 작성 결과 본 균주는 ${\alpha}$-Proteobacteria인 Sphingomonas속에 해당하였으며 지금까지 잘 알려진 석유계 탄화수소를 분해하는 Sphingomonas sp. 균주들과는 다른 cluster를 형성하였다. 다양한 석유계 탄화수소 성분을 이용하여 성장하는 Sphingomonas sp. 3Y는 유류로 오염된 토양의 복원에 유용하게 사용될 것으로 여겨지며 이 균주의 최적 분해 조건을 조사한다면 그 결과는 이 균주가 분리된 오염지역의 생물학적 분해를 최적화하는데 기여할 것이다.